ecology/cb_dissim: cb_dissimilarity.r annotate

annotate cb_dissimilarity.r @ 1:f941081e03f0 draft default tip

planemo upload for repository https://github.com/Marie59/champ_blocs commit 075fd90d1a39ae7912b48549e5537971635b9620

author	ecology
date	Sat, 18 Mar 2023 16:48:52 +0000
parents	42b51a52e308
children

rev	line source
0 42b51a52e308 planemo upload for repository https://github.com/Marie59/champ_blocs commit 0d86db7d42b608c386a54500064f5f9c9d7019a4 ecology parents: diff changeset	1 # author: "Jonathan Richir"
42b51a52e308 planemo upload for repository https://github.com/Marie59/champ_blocs commit 0d86db7d42b608c386a54500064f5f9c9d7019a4 ecology parents: diff changeset	2 # date: "01 October 2022"
42b51a52e308 planemo upload for repository https://github.com/Marie59/champ_blocs commit 0d86db7d42b608c386a54500064f5f9c9d7019a4 ecology parents: diff changeset	3
42b51a52e308 planemo upload for repository https://github.com/Marie59/champ_blocs commit 0d86db7d42b608c386a54500064f5f9c9d7019a4 ecology parents: diff changeset	4
42b51a52e308 planemo upload for repository https://github.com/Marie59/champ_blocs commit 0d86db7d42b608c386a54500064f5f9c9d7019a4 ecology parents: diff changeset	5 #Rscript
42b51a52e308 planemo upload for repository https://github.com/Marie59/champ_blocs commit 0d86db7d42b608c386a54500064f5f9c9d7019a4 ecology parents: diff changeset	6
42b51a52e308 planemo upload for repository https://github.com/Marie59/champ_blocs commit 0d86db7d42b608c386a54500064f5f9c9d7019a4 ecology parents: diff changeset	7 ###############################
42b51a52e308 planemo upload for repository https://github.com/Marie59/champ_blocs commit 0d86db7d42b608c386a54500064f5f9c9d7019a4 ecology parents: diff changeset	8 ## ##
42b51a52e308 planemo upload for repository https://github.com/Marie59/champ_blocs commit 0d86db7d42b608c386a54500064f5f9c9d7019a4 ecology parents: diff changeset	9 ###############################
42b51a52e308 planemo upload for repository https://github.com/Marie59/champ_blocs commit 0d86db7d42b608c386a54500064f5f9c9d7019a4 ecology parents: diff changeset	10
42b51a52e308 planemo upload for repository https://github.com/Marie59/champ_blocs commit 0d86db7d42b608c386a54500064f5f9c9d7019a4 ecology parents: diff changeset	11 #####Packages : dplyr
42b51a52e308 planemo upload for repository https://github.com/Marie59/champ_blocs commit 0d86db7d42b608c386a54500064f5f9c9d7019a4 ecology parents: diff changeset	12 # tidyr
42b51a52e308 planemo upload for repository https://github.com/Marie59/champ_blocs commit 0d86db7d42b608c386a54500064f5f9c9d7019a4 ecology parents: diff changeset	13 # readr
42b51a52e308 planemo upload for repository https://github.com/Marie59/champ_blocs commit 0d86db7d42b608c386a54500064f5f9c9d7019a4 ecology parents: diff changeset	14 # writexl
42b51a52e308 planemo upload for repository https://github.com/Marie59/champ_blocs commit 0d86db7d42b608c386a54500064f5f9c9d7019a4 ecology parents: diff changeset	15 # stringr
42b51a52e308 planemo upload for repository https://github.com/Marie59/champ_blocs commit 0d86db7d42b608c386a54500064f5f9c9d7019a4 ecology parents: diff changeset	16 # readxl
42b51a52e308 planemo upload for repository https://github.com/Marie59/champ_blocs commit 0d86db7d42b608c386a54500064f5f9c9d7019a4 ecology parents: diff changeset	17 # tibble
42b51a52e308 planemo upload for repository https://github.com/Marie59/champ_blocs commit 0d86db7d42b608c386a54500064f5f9c9d7019a4 ecology parents: diff changeset	18 # lubridate
42b51a52e308 planemo upload for repository https://github.com/Marie59/champ_blocs commit 0d86db7d42b608c386a54500064f5f9c9d7019a4 ecology parents: diff changeset	19 # cowplot
42b51a52e308 planemo upload for repository https://github.com/Marie59/champ_blocs commit 0d86db7d42b608c386a54500064f5f9c9d7019a4 ecology parents: diff changeset	20 # magrittr
42b51a52e308 planemo upload for repository https://github.com/Marie59/champ_blocs commit 0d86db7d42b608c386a54500064f5f9c9d7019a4 ecology parents: diff changeset	21 # rmarkdown
42b51a52e308 planemo upload for repository https://github.com/Marie59/champ_blocs commit 0d86db7d42b608c386a54500064f5f9c9d7019a4 ecology parents: diff changeset	22 library(magrittr)
1 f941081e03f0 planemo upload for repository https://github.com/Marie59/champ_blocs commit 075fd90d1a39ae7912b48549e5537971635b9620 ecology parents: 0 diff changeset	23
0 42b51a52e308 planemo upload for repository https://github.com/Marie59/champ_blocs commit 0d86db7d42b608c386a54500064f5f9c9d7019a4 ecology parents: diff changeset	24 #####Load arguments
42b51a52e308 planemo upload for repository https://github.com/Marie59/champ_blocs commit 0d86db7d42b608c386a54500064f5f9c9d7019a4 ecology parents: diff changeset	25
42b51a52e308 planemo upload for repository https://github.com/Marie59/champ_blocs commit 0d86db7d42b608c386a54500064f5f9c9d7019a4 ecology parents: diff changeset	26 args <- commandArgs(trailingOnly = TRUE)
42b51a52e308 planemo upload for repository https://github.com/Marie59/champ_blocs commit 0d86db7d42b608c386a54500064f5f9c9d7019a4 ecology parents: diff changeset	27
42b51a52e308 planemo upload for repository https://github.com/Marie59/champ_blocs commit 0d86db7d42b608c386a54500064f5f9c9d7019a4 ecology parents: diff changeset	28 #####Import data
42b51a52e308 planemo upload for repository https://github.com/Marie59/champ_blocs commit 0d86db7d42b608c386a54500064f5f9c9d7019a4 ecology parents: diff changeset	29
42b51a52e308 planemo upload for repository https://github.com/Marie59/champ_blocs commit 0d86db7d42b608c386a54500064f5f9c9d7019a4 ecology parents: diff changeset	30 if (length(args) < 1) {
42b51a52e308 planemo upload for repository https://github.com/Marie59/champ_blocs commit 0d86db7d42b608c386a54500064f5f9c9d7019a4 ecology parents: diff changeset	31 stop("This tool needs at least 1 argument")
42b51a52e308 planemo upload for repository https://github.com/Marie59/champ_blocs commit 0d86db7d42b608c386a54500064f5f9c9d7019a4 ecology parents: diff changeset	32 }else {
42b51a52e308 planemo upload for repository https://github.com/Marie59/champ_blocs commit 0d86db7d42b608c386a54500064f5f9c9d7019a4 ecology parents: diff changeset	33 fiche_val <- args[1]
42b51a52e308 planemo upload for repository https://github.com/Marie59/champ_blocs commit 0d86db7d42b608c386a54500064f5f9c9d7019a4 ecology parents: diff changeset	34 input_data <- args[2]
42b51a52e308 planemo upload for repository https://github.com/Marie59/champ_blocs commit 0d86db7d42b608c386a54500064f5f9c9d7019a4 ecology parents: diff changeset	35 choice <- args[3]
42b51a52e308 planemo upload for repository https://github.com/Marie59/champ_blocs commit 0d86db7d42b608c386a54500064f5f9c9d7019a4 ecology parents: diff changeset	36 choice_date <- as.numeric(args[4])
42b51a52e308 planemo upload for repository https://github.com/Marie59/champ_blocs commit 0d86db7d42b608c386a54500064f5f9c9d7019a4 ecology parents: diff changeset	37 }
42b51a52e308 planemo upload for repository https://github.com/Marie59/champ_blocs commit 0d86db7d42b608c386a54500064f5f9c9d7019a4 ecology parents: diff changeset	38
42b51a52e308 planemo upload for repository https://github.com/Marie59/champ_blocs commit 0d86db7d42b608c386a54500064f5f9c9d7019a4 ecology parents: diff changeset	39 #############################################################
42b51a52e308 planemo upload for repository https://github.com/Marie59/champ_blocs commit 0d86db7d42b608c386a54500064f5f9c9d7019a4 ecology parents: diff changeset	40 # #
42b51a52e308 planemo upload for repository https://github.com/Marie59/champ_blocs commit 0d86db7d42b608c386a54500064f5f9c9d7019a4 ecology parents: diff changeset	41 # Loading and cleaning data #
42b51a52e308 planemo upload for repository https://github.com/Marie59/champ_blocs commit 0d86db7d42b608c386a54500064f5f9c9d7019a4 ecology parents: diff changeset	42 # #
42b51a52e308 planemo upload for repository https://github.com/Marie59/champ_blocs commit 0d86db7d42b608c386a54500064f5f9c9d7019a4 ecology parents: diff changeset	43 #############################################################
42b51a52e308 planemo upload for repository https://github.com/Marie59/champ_blocs commit 0d86db7d42b608c386a54500064f5f9c9d7019a4 ecology parents: diff changeset	44 # load qecb data
42b51a52e308 planemo upload for repository https://github.com/Marie59/champ_blocs commit 0d86db7d42b608c386a54500064f5f9c9d7019a4 ecology parents: diff changeset	45
42b51a52e308 planemo upload for repository https://github.com/Marie59/champ_blocs commit 0d86db7d42b608c386a54500064f5f9c9d7019a4 ecology parents: diff changeset	46 qecb <- read.csv2(input_data, header = TRUE, fileEncoding = "Latin1") # fileEncoding = "Latin1", cfr é in variable names
42b51a52e308 planemo upload for repository https://github.com/Marie59/champ_blocs commit 0d86db7d42b608c386a54500064f5f9c9d7019a4 ecology parents: diff changeset	47
42b51a52e308 planemo upload for repository https://github.com/Marie59/champ_blocs commit 0d86db7d42b608c386a54500064f5f9c9d7019a4 ecology parents: diff changeset	48 # import csv files ficheterrain
42b51a52e308 planemo upload for repository https://github.com/Marie59/champ_blocs commit 0d86db7d42b608c386a54500064f5f9c9d7019a4 ecology parents: diff changeset	49
42b51a52e308 planemo upload for repository https://github.com/Marie59/champ_blocs commit 0d86db7d42b608c386a54500064f5f9c9d7019a4 ecology parents: diff changeset	50 fiche <- read.csv2(fiche_val, header = TRUE, fileEncoding = "Latin1") # fileEncoding = "Latin1", cfr é in variable names
42b51a52e308 planemo upload for repository https://github.com/Marie59/champ_blocs commit 0d86db7d42b608c386a54500064f5f9c9d7019a4 ecology parents: diff changeset	51
42b51a52e308 planemo upload for repository https://github.com/Marie59/champ_blocs commit 0d86db7d42b608c386a54500064f5f9c9d7019a4 ecology parents: diff changeset	52 ## work on "Fiche terrain"
42b51a52e308 planemo upload for repository https://github.com/Marie59/champ_blocs commit 0d86db7d42b608c386a54500064f5f9c9d7019a4 ecology parents: diff changeset	53
42b51a52e308 planemo upload for repository https://github.com/Marie59/champ_blocs commit 0d86db7d42b608c386a54500064f5f9c9d7019a4 ecology parents: diff changeset	54 date_fiche <- as.Date(stringr::str_sub(fiche$date.sortie, end = 10), origin = "1970-01-01")
42b51a52e308 planemo upload for repository https://github.com/Marie59/champ_blocs commit 0d86db7d42b608c386a54500064f5f9c9d7019a4 ecology parents: diff changeset	55 fiche <- tibble::add_column(fiche, date_fiche, .after = "date.sortie")
42b51a52e308 planemo upload for repository https://github.com/Marie59/champ_blocs commit 0d86db7d42b608c386a54500064f5f9c9d7019a4 ecology parents: diff changeset	56 rm(date_fiche)
42b51a52e308 planemo upload for repository https://github.com/Marie59/champ_blocs commit 0d86db7d42b608c386a54500064f5f9c9d7019a4 ecology parents: diff changeset	57
42b51a52e308 planemo upload for repository https://github.com/Marie59/champ_blocs commit 0d86db7d42b608c386a54500064f5f9c9d7019a4 ecology parents: diff changeset	58 ## qecb vs fiche terrain
42b51a52e308 planemo upload for repository https://github.com/Marie59/champ_blocs commit 0d86db7d42b608c386a54500064f5f9c9d7019a4 ecology parents: diff changeset	59
42b51a52e308 planemo upload for repository https://github.com/Marie59/champ_blocs commit 0d86db7d42b608c386a54500064f5f9c9d7019a4 ecology parents: diff changeset	60 fiche_red <- dplyr::filter(fiche, fiche$ID.Fiche %in% unique(qecb[, c("id")]))
42b51a52e308 planemo upload for repository https://github.com/Marie59/champ_blocs commit 0d86db7d42b608c386a54500064f5f9c9d7019a4 ecology parents: diff changeset	61
42b51a52e308 planemo upload for repository https://github.com/Marie59/champ_blocs commit 0d86db7d42b608c386a54500064f5f9c9d7019a4 ecology parents: diff changeset	62 id_count <- qecb %>% dplyr::group_by(id) %>% dplyr::count()
42b51a52e308 planemo upload for repository https://github.com/Marie59/champ_blocs commit 0d86db7d42b608c386a54500064f5f9c9d7019a4 ecology parents: diff changeset	63 id_count <- dplyr::rename(id_count, "ID.Fiche" = "id")
42b51a52e308 planemo upload for repository https://github.com/Marie59/champ_blocs commit 0d86db7d42b608c386a54500064f5f9c9d7019a4 ecology parents: diff changeset	64 id_count <- data.frame(id_count)
42b51a52e308 planemo upload for repository https://github.com/Marie59/champ_blocs commit 0d86db7d42b608c386a54500064f5f9c9d7019a4 ecology parents: diff changeset	65 fiche_red <- dplyr::left_join(fiche_red, id_count)
42b51a52e308 planemo upload for repository https://github.com/Marie59/champ_blocs commit 0d86db7d42b608c386a54500064f5f9c9d7019a4 ecology parents: diff changeset	66
42b51a52e308 planemo upload for repository https://github.com/Marie59/champ_blocs commit 0d86db7d42b608c386a54500064f5f9c9d7019a4 ecology parents: diff changeset	67 # rep fiche terrain information
42b51a52e308 planemo upload for repository https://github.com/Marie59/champ_blocs commit 0d86db7d42b608c386a54500064f5f9c9d7019a4 ecology parents: diff changeset	68 fiche_expanded <- fiche_red[rep(row.names(fiche_red), fiche_red$n), 1:ncol(fiche_red)]
42b51a52e308 planemo upload for repository https://github.com/Marie59/champ_blocs commit 0d86db7d42b608c386a54500064f5f9c9d7019a4 ecology parents: diff changeset	69 fiche_expanded <- dplyr::rename(fiche_expanded, "id" = "ID.Fiche")
42b51a52e308 planemo upload for repository https://github.com/Marie59/champ_blocs commit 0d86db7d42b608c386a54500064f5f9c9d7019a4 ecology parents: diff changeset	70
42b51a52e308 planemo upload for repository https://github.com/Marie59/champ_blocs commit 0d86db7d42b608c386a54500064f5f9c9d7019a4 ecology parents: diff changeset	71 ## merge qecb data and ficheterrain information
42b51a52e308 planemo upload for repository https://github.com/Marie59/champ_blocs commit 0d86db7d42b608c386a54500064f5f9c9d7019a4 ecology parents: diff changeset	72
42b51a52e308 planemo upload for repository https://github.com/Marie59/champ_blocs commit 0d86db7d42b608c386a54500064f5f9c9d7019a4 ecology parents: diff changeset	73 qecb <- dplyr::bind_cols(qecb, fiche_expanded)
42b51a52e308 planemo upload for repository https://github.com/Marie59/champ_blocs commit 0d86db7d42b608c386a54500064f5f9c9d7019a4 ecology parents: diff changeset	74 qecb <- dplyr::rename(qecb, "id_qecb" = "id...1")
42b51a52e308 planemo upload for repository https://github.com/Marie59/champ_blocs commit 0d86db7d42b608c386a54500064f5f9c9d7019a4 ecology parents: diff changeset	75 qecb <- dplyr::rename(qecb, "id_fiche" = "id...68")
42b51a52e308 planemo upload for repository https://github.com/Marie59/champ_blocs commit 0d86db7d42b608c386a54500064f5f9c9d7019a4 ecology parents: diff changeset	76
42b51a52e308 planemo upload for repository https://github.com/Marie59/champ_blocs commit 0d86db7d42b608c386a54500064f5f9c9d7019a4 ecology parents: diff changeset	77 rm(fiche_expanded, fiche_red, id_count)
42b51a52e308 planemo upload for repository https://github.com/Marie59/champ_blocs commit 0d86db7d42b608c386a54500064f5f9c9d7019a4 ecology parents: diff changeset	78
42b51a52e308 planemo upload for repository https://github.com/Marie59/champ_blocs commit 0d86db7d42b608c386a54500064f5f9c9d7019a4 ecology parents: diff changeset	79 qecb <- qecb %>% tidyr::separate(date_fiche, c("Year", "Month", "Day"), sep = "-", remove = FALSE)
42b51a52e308 planemo upload for repository https://github.com/Marie59/champ_blocs commit 0d86db7d42b608c386a54500064f5f9c9d7019a4 ecology parents: diff changeset	80
42b51a52e308 planemo upload for repository https://github.com/Marie59/champ_blocs commit 0d86db7d42b608c386a54500064f5f9c9d7019a4 ecology parents: diff changeset	81
42b51a52e308 planemo upload for repository https://github.com/Marie59/champ_blocs commit 0d86db7d42b608c386a54500064f5f9c9d7019a4 ecology parents: diff changeset	82 ## quadrat nb : in contrast to ivr df, quadrat number is missing for many observations in qecb df ; but from the Numero.Photo variable (boulder photo associated to field data collection), I could get back most missing quadrat numbers
42b51a52e308 planemo upload for repository https://github.com/Marie59/champ_blocs commit 0d86db7d42b608c386a54500064f5f9c9d7019a4 ecology parents: diff changeset	83
42b51a52e308 planemo upload for repository https://github.com/Marie59/champ_blocs commit 0d86db7d42b608c386a54500064f5f9c9d7019a4 ecology parents: diff changeset	84 quadrat <- stringr::str_extract(qecb$Numero.Photo, "Q[12345]")
42b51a52e308 planemo upload for repository https://github.com/Marie59/champ_blocs commit 0d86db7d42b608c386a54500064f5f9c9d7019a4 ecology parents: diff changeset	85 qecb <- tibble::add_column(qecb, quadrat, .after = "Numero.Photo")
42b51a52e308 planemo upload for repository https://github.com/Marie59/champ_blocs commit 0d86db7d42b608c386a54500064f5f9c9d7019a4 ecology parents: diff changeset	86 rm(quadrat)
42b51a52e308 planemo upload for repository https://github.com/Marie59/champ_blocs commit 0d86db7d42b608c386a54500064f5f9c9d7019a4 ecology parents: diff changeset	87
42b51a52e308 planemo upload for repository https://github.com/Marie59/champ_blocs commit 0d86db7d42b608c386a54500064f5f9c9d7019a4 ecology parents: diff changeset	88 # check
42b51a52e308 planemo upload for repository https://github.com/Marie59/champ_blocs commit 0d86db7d42b608c386a54500064f5f9c9d7019a4 ecology parents: diff changeset	89 quadrat_bis <- rep(NA, length = nrow(qecb))
42b51a52e308 planemo upload for repository https://github.com/Marie59/champ_blocs commit 0d86db7d42b608c386a54500064f5f9c9d7019a4 ecology parents: diff changeset	90 qecb <- tibble::add_column(qecb, quadrat_bis, .after = "quadrat")
42b51a52e308 planemo upload for repository https://github.com/Marie59/champ_blocs commit 0d86db7d42b608c386a54500064f5f9c9d7019a4 ecology parents: diff changeset	91 rm(quadrat_bis)
42b51a52e308 planemo upload for repository https://github.com/Marie59/champ_blocs commit 0d86db7d42b608c386a54500064f5f9c9d7019a4 ecology parents: diff changeset	92
42b51a52e308 planemo upload for repository https://github.com/Marie59/champ_blocs commit 0d86db7d42b608c386a54500064f5f9c9d7019a4 ecology parents: diff changeset	93 qecb$quadrat_bis <- ifelse(qecb$Numéro.Bloc.échantillon %in% c(1, 2) & qecb$Type.Bloc == "Bloc mobile", "Q1", qecb$quadrat_bis)
42b51a52e308 planemo upload for repository https://github.com/Marie59/champ_blocs commit 0d86db7d42b608c386a54500064f5f9c9d7019a4 ecology parents: diff changeset	94 qecb$quadrat_bis <- ifelse(qecb$Numéro.Bloc.échantillon %in% c(3, 4) & qecb$Type.Bloc == "Bloc mobile", "Q2", qecb$quadrat_bis)
42b51a52e308 planemo upload for repository https://github.com/Marie59/champ_blocs commit 0d86db7d42b608c386a54500064f5f9c9d7019a4 ecology parents: diff changeset	95 qecb$quadrat_bis <- ifelse(qecb$Numéro.Bloc.échantillon %in% c(5, 6) & qecb$Type.Bloc == "Bloc mobile", "Q3", qecb$quadrat_bis)
42b51a52e308 planemo upload for repository https://github.com/Marie59/champ_blocs commit 0d86db7d42b608c386a54500064f5f9c9d7019a4 ecology parents: diff changeset	96 qecb$quadrat_bis <- ifelse(qecb$Numéro.Bloc.échantillon %in% c(7, 8) & qecb$Type.Bloc == "Bloc mobile", "Q4", qecb$quadrat_bis)
42b51a52e308 planemo upload for repository https://github.com/Marie59/champ_blocs commit 0d86db7d42b608c386a54500064f5f9c9d7019a4 ecology parents: diff changeset	97 qecb$quadrat_bis <- ifelse(qecb$Numéro.Bloc.échantillon %in% c(9, 10) & qecb$Type.Bloc == "Bloc mobile", "Q5", qecb$quadrat_bis)
42b51a52e308 planemo upload for repository https://github.com/Marie59/champ_blocs commit 0d86db7d42b608c386a54500064f5f9c9d7019a4 ecology parents: diff changeset	98
42b51a52e308 planemo upload for repository https://github.com/Marie59/champ_blocs commit 0d86db7d42b608c386a54500064f5f9c9d7019a4 ecology parents: diff changeset	99
42b51a52e308 planemo upload for repository https://github.com/Marie59/champ_blocs commit 0d86db7d42b608c386a54500064f5f9c9d7019a4 ecology parents: diff changeset	100 qecb$quadrat_bis <- ifelse(qecb$Numéro.Bloc.échantillon == 1 & qecb$Type.Bloc %in% c("Bloc fixé", "Roche en place"), "Q1", qecb$quadrat_bis)
42b51a52e308 planemo upload for repository https://github.com/Marie59/champ_blocs commit 0d86db7d42b608c386a54500064f5f9c9d7019a4 ecology parents: diff changeset	101 qecb$quadrat_bis <- ifelse(qecb$Numéro.Bloc.échantillon == 2 & qecb$Type.Bloc %in% c("Bloc fixé", "Roche en place"), "Q2", qecb$quadrat_bis)
42b51a52e308 planemo upload for repository https://github.com/Marie59/champ_blocs commit 0d86db7d42b608c386a54500064f5f9c9d7019a4 ecology parents: diff changeset	102 qecb$quadrat_bis <- ifelse(qecb$Numéro.Bloc.échantillon == 3 & qecb$Type.Bloc %in% c("Bloc fixé", "Roche en place"), "Q3", qecb$quadrat_bis)
42b51a52e308 planemo upload for repository https://github.com/Marie59/champ_blocs commit 0d86db7d42b608c386a54500064f5f9c9d7019a4 ecology parents: diff changeset	103 qecb$quadrat_bis <- ifelse(qecb$Numéro.Bloc.échantillon == 4 & qecb$Type.Bloc %in% c("Bloc fixé", "Roche en place"), "Q4", qecb$quadrat_bis)
42b51a52e308 planemo upload for repository https://github.com/Marie59/champ_blocs commit 0d86db7d42b608c386a54500064f5f9c9d7019a4 ecology parents: diff changeset	104 qecb$quadrat_bis <- ifelse(qecb$Numéro.Bloc.échantillon == 5 & qecb$Type.Bloc %in% c("Bloc fixé", "Roche en place"), "Q5", qecb$quadrat_bis)
42b51a52e308 planemo upload for repository https://github.com/Marie59/champ_blocs commit 0d86db7d42b608c386a54500064f5f9c9d7019a4 ecology parents: diff changeset	105
42b51a52e308 planemo upload for repository https://github.com/Marie59/champ_blocs commit 0d86db7d42b608c386a54500064f5f9c9d7019a4 ecology parents: diff changeset	106 ## I create two new variables for Site names, one for data analysis and one for data reporting. Only works for actual ivr df with 22 sites !
42b51a52e308 planemo upload for repository https://github.com/Marie59/champ_blocs commit 0d86db7d42b608c386a54500064f5f9c9d7019a4 ecology parents: diff changeset	107
42b51a52e308 planemo upload for repository https://github.com/Marie59/champ_blocs commit 0d86db7d42b608c386a54500064f5f9c9d7019a4 ecology parents: diff changeset	108 # Name for data analysis
42b51a52e308 planemo upload for repository https://github.com/Marie59/champ_blocs commit 0d86db7d42b608c386a54500064f5f9c9d7019a4 ecology parents: diff changeset	109
42b51a52e308 planemo upload for repository https://github.com/Marie59/champ_blocs commit 0d86db7d42b608c386a54500064f5f9c9d7019a4 ecology parents: diff changeset	110 qecb <- tibble::add_column(qecb, Site = qecb$zone.habitat, .after = "ID.Fiche")
42b51a52e308 planemo upload for repository https://github.com/Marie59/champ_blocs commit 0d86db7d42b608c386a54500064f5f9c9d7019a4 ecology parents: diff changeset	111
42b51a52e308 planemo upload for repository https://github.com/Marie59/champ_blocs commit 0d86db7d42b608c386a54500064f5f9c9d7019a4 ecology parents: diff changeset	112 for (x in seq_along(qecb$Site)) {
42b51a52e308 planemo upload for repository https://github.com/Marie59/champ_blocs commit 0d86db7d42b608c386a54500064f5f9c9d7019a4 ecology parents: diff changeset	113 if (grepl(pattern = "Locmariaquer", qecb$Site[x]) == TRUE) {
42b51a52e308 planemo upload for repository https://github.com/Marie59/champ_blocs commit 0d86db7d42b608c386a54500064f5f9c9d7019a4 ecology parents: diff changeset	114 qecb$Site[x] <- "GDMO_Locmariaquer"
42b51a52e308 planemo upload for repository https://github.com/Marie59/champ_blocs commit 0d86db7d42b608c386a54500064f5f9c9d7019a4 ecology parents: diff changeset	115 } else if (grepl(pattern = "Beg Lann", qecb$Site[x]) == TRUE) {
42b51a52e308 planemo upload for repository https://github.com/Marie59/champ_blocs commit 0d86db7d42b608c386a54500064f5f9c9d7019a4 ecology parents: diff changeset	116 qecb$Site[x] <- "GDMO_BegLann"
42b51a52e308 planemo upload for repository https://github.com/Marie59/champ_blocs commit 0d86db7d42b608c386a54500064f5f9c9d7019a4 ecology parents: diff changeset	117 } else if (grepl(pattern = "Plateau du Four", qecb$Site[x]) == TRUE) {
42b51a52e308 planemo upload for repository https://github.com/Marie59/champ_blocs commit 0d86db7d42b608c386a54500064f5f9c9d7019a4 ecology parents: diff changeset	118 qecb$Site[x] <- "FOUR_PlateauFour"
42b51a52e308 planemo upload for repository https://github.com/Marie59/champ_blocs commit 0d86db7d42b608c386a54500064f5f9c9d7019a4 ecology parents: diff changeset	119 } else if (grepl(pattern = "Grouin", qecb$Site[x]) == TRUE) {
42b51a52e308 planemo upload for repository https://github.com/Marie59/champ_blocs commit 0d86db7d42b608c386a54500064f5f9c9d7019a4 ecology parents: diff changeset	120 qecb$Site[x] <- "EGMP_GroinCou"
42b51a52e308 planemo upload for repository https://github.com/Marie59/champ_blocs commit 0d86db7d42b608c386a54500064f5f9c9d7019a4 ecology parents: diff changeset	121 } else if (grepl(pattern = "Ensembert", qecb$Site[x]) == TRUE) {
42b51a52e308 planemo upload for repository https://github.com/Marie59/champ_blocs commit 0d86db7d42b608c386a54500064f5f9c9d7019a4 ecology parents: diff changeset	122 qecb$Site[x] <- "EGMP_PasEmsembert"
42b51a52e308 planemo upload for repository https://github.com/Marie59/champ_blocs commit 0d86db7d42b608c386a54500064f5f9c9d7019a4 ecology parents: diff changeset	123 } else if (grepl(pattern = "Brée-les-Bains", qecb$Site[x]) == TRUE) {
42b51a52e308 planemo upload for repository https://github.com/Marie59/champ_blocs commit 0d86db7d42b608c386a54500064f5f9c9d7019a4 ecology parents: diff changeset	124 qecb$Site[x] <- "EGMP_BreeBains"
42b51a52e308 planemo upload for repository https://github.com/Marie59/champ_blocs commit 0d86db7d42b608c386a54500064f5f9c9d7019a4 ecology parents: diff changeset	125 } else if (grepl(pattern = "Antiochat", qecb$Site[x]) == TRUE) {
42b51a52e308 planemo upload for repository https://github.com/Marie59/champ_blocs commit 0d86db7d42b608c386a54500064f5f9c9d7019a4 ecology parents: diff changeset	126 qecb$Site[x] <- "EGMP_PerreAntiochat"
42b51a52e308 planemo upload for repository https://github.com/Marie59/champ_blocs commit 0d86db7d42b608c386a54500064f5f9c9d7019a4 ecology parents: diff changeset	127 } else if (grepl(pattern = "Chassiron", qecb$Site[x]) == TRUE) {
42b51a52e308 planemo upload for repository https://github.com/Marie59/champ_blocs commit 0d86db7d42b608c386a54500064f5f9c9d7019a4 ecology parents: diff changeset	128 qecb$Site[x] <- "EGMP_Chassiron"
42b51a52e308 planemo upload for repository https://github.com/Marie59/champ_blocs commit 0d86db7d42b608c386a54500064f5f9c9d7019a4 ecology parents: diff changeset	129 } else if (grepl(pattern = "zone p", qecb$Site[x]) == TRUE) {
42b51a52e308 planemo upload for repository https://github.com/Marie59/champ_blocs commit 0d86db7d42b608c386a54500064f5f9c9d7019a4 ecology parents: diff changeset	130 qecb$Site[x] <- "BASQ_FlotsBleusZP"
42b51a52e308 planemo upload for repository https://github.com/Marie59/champ_blocs commit 0d86db7d42b608c386a54500064f5f9c9d7019a4 ecology parents: diff changeset	131 } else if (grepl(pattern = "zone f", qecb$Site[x]) == TRUE) {
42b51a52e308 planemo upload for repository https://github.com/Marie59/champ_blocs commit 0d86db7d42b608c386a54500064f5f9c9d7019a4 ecology parents: diff changeset	132 qecb$Site[x] <- "BASQ_FlotsBleusZF"
42b51a52e308 planemo upload for repository https://github.com/Marie59/champ_blocs commit 0d86db7d42b608c386a54500064f5f9c9d7019a4 ecology parents: diff changeset	133 } else if (grepl(pattern = "Saint-Michel", qecb$Site[x]) == TRUE) {
42b51a52e308 planemo upload for repository https://github.com/Marie59/champ_blocs commit 0d86db7d42b608c386a54500064f5f9c9d7019a4 ecology parents: diff changeset	134 qecb$Site[x] <- "GONB_IlotStMichel"
42b51a52e308 planemo upload for repository https://github.com/Marie59/champ_blocs commit 0d86db7d42b608c386a54500064f5f9c9d7019a4 ecology parents: diff changeset	135 } else if (grepl(pattern = "Quéménès", qecb$Site[x]) == TRUE) {
42b51a52e308 planemo upload for repository https://github.com/Marie59/champ_blocs commit 0d86db7d42b608c386a54500064f5f9c9d7019a4 ecology parents: diff changeset	136 qecb$Site[x] <- "FINS_Quemenes"
42b51a52e308 planemo upload for repository https://github.com/Marie59/champ_blocs commit 0d86db7d42b608c386a54500064f5f9c9d7019a4 ecology parents: diff changeset	137 } else if (grepl(pattern = "Goulenez", qecb$Site[x]) == TRUE) {
42b51a52e308 planemo upload for repository https://github.com/Marie59/champ_blocs commit 0d86db7d42b608c386a54500064f5f9c9d7019a4 ecology parents: diff changeset	138 qecb$Site[x] <- "FINS_SeinGoulenez"
42b51a52e308 planemo upload for repository https://github.com/Marie59/champ_blocs commit 0d86db7d42b608c386a54500064f5f9c9d7019a4 ecology parents: diff changeset	139 } else if (grepl(pattern = "Kilaourou", qecb$Site[x]) == TRUE) {
42b51a52e308 planemo upload for repository https://github.com/Marie59/champ_blocs commit 0d86db7d42b608c386a54500064f5f9c9d7019a4 ecology parents: diff changeset	140 qecb$Site[x] <- "FINS_SeinKilaourou"
42b51a52e308 planemo upload for repository https://github.com/Marie59/champ_blocs commit 0d86db7d42b608c386a54500064f5f9c9d7019a4 ecology parents: diff changeset	141 } else if (grepl(pattern = "Verdelet", qecb$Site[x]) == TRUE) {
42b51a52e308 planemo upload for repository https://github.com/Marie59/champ_blocs commit 0d86db7d42b608c386a54500064f5f9c9d7019a4 ecology parents: diff changeset	142 qecb$Site[x] <- "ARMO_Verdelet"
42b51a52e308 planemo upload for repository https://github.com/Marie59/champ_blocs commit 0d86db7d42b608c386a54500064f5f9c9d7019a4 ecology parents: diff changeset	143 } else if (grepl(pattern = "Piégu", qecb$Site[x]) == TRUE) {
42b51a52e308 planemo upload for repository https://github.com/Marie59/champ_blocs commit 0d86db7d42b608c386a54500064f5f9c9d7019a4 ecology parents: diff changeset	144 qecb$Site[x] <- "ARMO_Piegu"
42b51a52e308 planemo upload for repository https://github.com/Marie59/champ_blocs commit 0d86db7d42b608c386a54500064f5f9c9d7019a4 ecology parents: diff changeset	145 } else if (grepl(pattern = "Bilfot", qecb$Site[x]) == TRUE) {
42b51a52e308 planemo upload for repository https://github.com/Marie59/champ_blocs commit 0d86db7d42b608c386a54500064f5f9c9d7019a4 ecology parents: diff changeset	146 qecb$Site[x] <- "ARMO_Bilfot"
42b51a52e308 planemo upload for repository https://github.com/Marie59/champ_blocs commit 0d86db7d42b608c386a54500064f5f9c9d7019a4 ecology parents: diff changeset	147 } else if (grepl(pattern = "Plate", qecb$Site[x]) == TRUE) {
42b51a52e308 planemo upload for repository https://github.com/Marie59/champ_blocs commit 0d86db7d42b608c386a54500064f5f9c9d7019a4 ecology parents: diff changeset	148 qecb$Site[x] <- "ARMO_IlePlate"
42b51a52e308 planemo upload for repository https://github.com/Marie59/champ_blocs commit 0d86db7d42b608c386a54500064f5f9c9d7019a4 ecology parents: diff changeset	149 } else if (grepl(pattern = "Perharidy", qecb$Site[x]) == TRUE) {
42b51a52e308 planemo upload for repository https://github.com/Marie59/champ_blocs commit 0d86db7d42b608c386a54500064f5f9c9d7019a4 ecology parents: diff changeset	150 qecb$Site[x] <- "PDMO_Perharidy"
42b51a52e308 planemo upload for repository https://github.com/Marie59/champ_blocs commit 0d86db7d42b608c386a54500064f5f9c9d7019a4 ecology parents: diff changeset	151 } else if (grepl(pattern = "Keraliou", qecb$Site[x]) == TRUE) {
42b51a52e308 planemo upload for repository https://github.com/Marie59/champ_blocs commit 0d86db7d42b608c386a54500064f5f9c9d7019a4 ecology parents: diff changeset	152 qecb$Site[x] <- "BRES_Keraliou"
42b51a52e308 planemo upload for repository https://github.com/Marie59/champ_blocs commit 0d86db7d42b608c386a54500064f5f9c9d7019a4 ecology parents: diff changeset	153 } else if (grepl(pattern = "Mousterlin", qecb$Site[x]) == TRUE) {
42b51a52e308 planemo upload for repository https://github.com/Marie59/champ_blocs commit 0d86db7d42b608c386a54500064f5f9c9d7019a4 ecology parents: diff changeset	154 qecb$Site[x] <- "FINS_Mousterlin"
42b51a52e308 planemo upload for repository https://github.com/Marie59/champ_blocs commit 0d86db7d42b608c386a54500064f5f9c9d7019a4 ecology parents: diff changeset	155 } else if (grepl(pattern = "Nicolas", qecb$Site[x]) == TRUE) {
42b51a52e308 planemo upload for repository https://github.com/Marie59/champ_blocs commit 0d86db7d42b608c386a54500064f5f9c9d7019a4 ecology parents: diff changeset	156 qecb$Site[x] <- "FINS_StNicolasGlenan"
42b51a52e308 planemo upload for repository https://github.com/Marie59/champ_blocs commit 0d86db7d42b608c386a54500064f5f9c9d7019a4 ecology parents: diff changeset	157 }
42b51a52e308 planemo upload for repository https://github.com/Marie59/champ_blocs commit 0d86db7d42b608c386a54500064f5f9c9d7019a4 ecology parents: diff changeset	158 if (grepl(pattern = "Roz", qecb$site[x]) == TRUE) {
42b51a52e308 planemo upload for repository https://github.com/Marie59/champ_blocs commit 0d86db7d42b608c386a54500064f5f9c9d7019a4 ecology parents: diff changeset	159 qecb$Site[x] <- "FINS_AnseRoz"
42b51a52e308 planemo upload for repository https://github.com/Marie59/champ_blocs commit 0d86db7d42b608c386a54500064f5f9c9d7019a4 ecology parents: diff changeset	160 }
42b51a52e308 planemo upload for repository https://github.com/Marie59/champ_blocs commit 0d86db7d42b608c386a54500064f5f9c9d7019a4 ecology parents: diff changeset	161 }
42b51a52e308 planemo upload for repository https://github.com/Marie59/champ_blocs commit 0d86db7d42b608c386a54500064f5f9c9d7019a4 ecology parents: diff changeset	162
42b51a52e308 planemo upload for repository https://github.com/Marie59/champ_blocs commit 0d86db7d42b608c386a54500064f5f9c9d7019a4 ecology parents: diff changeset	163 # Name for report/plot
42b51a52e308 planemo upload for repository https://github.com/Marie59/champ_blocs commit 0d86db7d42b608c386a54500064f5f9c9d7019a4 ecology parents: diff changeset	164
42b51a52e308 planemo upload for repository https://github.com/Marie59/champ_blocs commit 0d86db7d42b608c386a54500064f5f9c9d7019a4 ecology parents: diff changeset	165 qecb <- tibble::add_column(qecb, Site_bis = qecb$Site, .after = "Site")
42b51a52e308 planemo upload for repository https://github.com/Marie59/champ_blocs commit 0d86db7d42b608c386a54500064f5f9c9d7019a4 ecology parents: diff changeset	166
42b51a52e308 planemo upload for repository https://github.com/Marie59/champ_blocs commit 0d86db7d42b608c386a54500064f5f9c9d7019a4 ecology parents: diff changeset	167 qecb$Site_bis <- ifelse(qecb$Site == "GDMO_Locmariaquer", "Locmariaquer", qecb$Site_bis)
42b51a52e308 planemo upload for repository https://github.com/Marie59/champ_blocs commit 0d86db7d42b608c386a54500064f5f9c9d7019a4 ecology parents: diff changeset	168 qecb$Site_bis <- ifelse(qecb$Site == "GDMO_BegLann", "Beg Lann", qecb$Site_bis)
42b51a52e308 planemo upload for repository https://github.com/Marie59/champ_blocs commit 0d86db7d42b608c386a54500064f5f9c9d7019a4 ecology parents: diff changeset	169 qecb$Site_bis <- ifelse(qecb$Site == "FOUR_PlateauFour", "Plateau du Four", qecb$Site_bis)
42b51a52e308 planemo upload for repository https://github.com/Marie59/champ_blocs commit 0d86db7d42b608c386a54500064f5f9c9d7019a4 ecology parents: diff changeset	170 qecb$Site_bis <- ifelse(qecb$Site == "EGMP_GroinCou", "Groin du Cou", qecb$Site_bis)
42b51a52e308 planemo upload for repository https://github.com/Marie59/champ_blocs commit 0d86db7d42b608c386a54500064f5f9c9d7019a4 ecology parents: diff changeset	171 qecb$Site_bis <- ifelse(qecb$Site == "EGMP_PasEmsembert", "Le Pas d'Emsembert", qecb$Site_bis)
42b51a52e308 planemo upload for repository https://github.com/Marie59/champ_blocs commit 0d86db7d42b608c386a54500064f5f9c9d7019a4 ecology parents: diff changeset	172 qecb$Site_bis <- ifelse(qecb$Site == "EGMP_BreeBains", "La Brée-les-Bains", qecb$Site_bis)
42b51a52e308 planemo upload for repository https://github.com/Marie59/champ_blocs commit 0d86db7d42b608c386a54500064f5f9c9d7019a4 ecology parents: diff changeset	173 qecb$Site_bis <- ifelse(qecb$Site == "EGMP_PerreAntiochat", "Le Perré d'Antiochat", qecb$Site_bis)
42b51a52e308 planemo upload for repository https://github.com/Marie59/champ_blocs commit 0d86db7d42b608c386a54500064f5f9c9d7019a4 ecology parents: diff changeset	174 qecb$Site_bis <- ifelse(qecb$Site == "EGMP_Chassiron", "Chassiron", qecb$Site_bis)
42b51a52e308 planemo upload for repository https://github.com/Marie59/champ_blocs commit 0d86db7d42b608c386a54500064f5f9c9d7019a4 ecology parents: diff changeset	175 qecb$Site_bis <- ifelse(qecb$Site == "BASQ_FlotsBleusZP", "Les Flots Bleus / zone pêcheurs", qecb$Site_bis)
42b51a52e308 planemo upload for repository https://github.com/Marie59/champ_blocs commit 0d86db7d42b608c386a54500064f5f9c9d7019a4 ecology parents: diff changeset	176 qecb$Site_bis <- ifelse(qecb$Site == "BASQ_FlotsBleusZF", "Les Flots Bleus / zone familles", qecb$Site_bis)
42b51a52e308 planemo upload for repository https://github.com/Marie59/champ_blocs commit 0d86db7d42b608c386a54500064f5f9c9d7019a4 ecology parents: diff changeset	177 qecb$Site_bis <- ifelse(qecb$Site == "GONB_IlotStMichel", "Îlot Saint-Michel", qecb$Site_bis)
42b51a52e308 planemo upload for repository https://github.com/Marie59/champ_blocs commit 0d86db7d42b608c386a54500064f5f9c9d7019a4 ecology parents: diff changeset	178 qecb$Site_bis <- ifelse(qecb$Site == "FINS_Quemenes", "Quéménès", qecb$Site_bis)
42b51a52e308 planemo upload for repository https://github.com/Marie59/champ_blocs commit 0d86db7d42b608c386a54500064f5f9c9d7019a4 ecology parents: diff changeset	179 qecb$Site_bis <- ifelse(qecb$Site == "FINS_SeinGoulenez", "Île de Sein - Goulenez", qecb$Site_bis)
42b51a52e308 planemo upload for repository https://github.com/Marie59/champ_blocs commit 0d86db7d42b608c386a54500064f5f9c9d7019a4 ecology parents: diff changeset	180 qecb$Site_bis <- ifelse(qecb$Site == "FINS_SeinKilaourou", "Île de Sein - Kilaourou", qecb$Site_bis)
42b51a52e308 planemo upload for repository https://github.com/Marie59/champ_blocs commit 0d86db7d42b608c386a54500064f5f9c9d7019a4 ecology parents: diff changeset	181 qecb$Site_bis <- ifelse(qecb$Site == "ARMO_Verdelet", "Îlot du Verdelet", qecb$Site_bis)
42b51a52e308 planemo upload for repository https://github.com/Marie59/champ_blocs commit 0d86db7d42b608c386a54500064f5f9c9d7019a4 ecology parents: diff changeset	182 qecb$Site_bis <- ifelse(qecb$Site == "ARMO_Piegu", "Piégu", qecb$Site_bis)
42b51a52e308 planemo upload for repository https://github.com/Marie59/champ_blocs commit 0d86db7d42b608c386a54500064f5f9c9d7019a4 ecology parents: diff changeset	183 qecb$Site_bis <- ifelse(qecb$Site == "ARMO_Bilfot", "Pointe de Bilfot", qecb$Site_bis)
42b51a52e308 planemo upload for repository https://github.com/Marie59/champ_blocs commit 0d86db7d42b608c386a54500064f5f9c9d7019a4 ecology parents: diff changeset	184 qecb$Site_bis <- ifelse(qecb$Site == "ARMO_IlePlate", "Île Plate", qecb$Site_bis)
42b51a52e308 planemo upload for repository https://github.com/Marie59/champ_blocs commit 0d86db7d42b608c386a54500064f5f9c9d7019a4 ecology parents: diff changeset	185 qecb$Site_bis <- ifelse(qecb$Site == "PDMO_Perharidy", "Perharidy", qecb$Site_bis)
42b51a52e308 planemo upload for repository https://github.com/Marie59/champ_blocs commit 0d86db7d42b608c386a54500064f5f9c9d7019a4 ecology parents: diff changeset	186 qecb$Site_bis <- ifelse(qecb$Site == "BRES_Keraliou", "Keraliou", qecb$Site_bis)
42b51a52e308 planemo upload for repository https://github.com/Marie59/champ_blocs commit 0d86db7d42b608c386a54500064f5f9c9d7019a4 ecology parents: diff changeset	187 qecb$Site_bis <- ifelse(qecb$Site == "FINS_Mousterlin", "Pointe de Mousterlin", qecb$Site_bis)
42b51a52e308 planemo upload for repository https://github.com/Marie59/champ_blocs commit 0d86db7d42b608c386a54500064f5f9c9d7019a4 ecology parents: diff changeset	188 qecb$Site_bis <- ifelse(qecb$Site == "FINS_StNicolasGlenan", "Saint-Nicolas des Glénan", qecb$Site_bis)
42b51a52e308 planemo upload for repository https://github.com/Marie59/champ_blocs commit 0d86db7d42b608c386a54500064f5f9c9d7019a4 ecology parents: diff changeset	189 qecb$Site_bis <- ifelse(qecb$Site == "FINS_AnseRoz", "Pointe de l'Anse du Roz", qecb$Site_bis)
42b51a52e308 planemo upload for repository https://github.com/Marie59/champ_blocs commit 0d86db7d42b608c386a54500064f5f9c9d7019a4 ecology parents: diff changeset	190
42b51a52e308 planemo upload for repository https://github.com/Marie59/champ_blocs commit 0d86db7d42b608c386a54500064f5f9c9d7019a4 ecology parents: diff changeset	191 ## change some variables to factor
42b51a52e308 planemo upload for repository https://github.com/Marie59/champ_blocs commit 0d86db7d42b608c386a54500064f5f9c9d7019a4 ecology parents: diff changeset	192
42b51a52e308 planemo upload for repository https://github.com/Marie59/champ_blocs commit 0d86db7d42b608c386a54500064f5f9c9d7019a4 ecology parents: diff changeset	193 # change 'X..' variables that are indeed % to numeric; https://stackoverflow.com/questions/59410939/apply-function-to-all-variables-with-string-in-name
42b51a52e308 planemo upload for repository https://github.com/Marie59/champ_blocs commit 0d86db7d42b608c386a54500064f5f9c9d7019a4 ecology parents: diff changeset	194 ix <- grep("^X..", names(qecb))
42b51a52e308 planemo upload for repository https://github.com/Marie59/champ_blocs commit 0d86db7d42b608c386a54500064f5f9c9d7019a4 ecology parents: diff changeset	195 qecb[ix] <- lapply(qecb[ix], as.numeric)
42b51a52e308 planemo upload for repository https://github.com/Marie59/champ_blocs commit 0d86db7d42b608c386a54500064f5f9c9d7019a4 ecology parents: diff changeset	196 rm(ix)
42b51a52e308 planemo upload for repository https://github.com/Marie59/champ_blocs commit 0d86db7d42b608c386a54500064f5f9c9d7019a4 ecology parents: diff changeset	197
42b51a52e308 planemo upload for repository https://github.com/Marie59/champ_blocs commit 0d86db7d42b608c386a54500064f5f9c9d7019a4 ecology parents: diff changeset	198
42b51a52e308 planemo upload for repository https://github.com/Marie59/champ_blocs commit 0d86db7d42b608c386a54500064f5f9c9d7019a4 ecology parents: diff changeset	199 ## save the final, complete qecb df_
42b51a52e308 planemo upload for repository https://github.com/Marie59/champ_blocs commit 0d86db7d42b608c386a54500064f5f9c9d7019a4 ecology parents: diff changeset	200
42b51a52e308 planemo upload for repository https://github.com/Marie59/champ_blocs commit 0d86db7d42b608c386a54500064f5f9c9d7019a4 ecology parents: diff changeset	201 qecb <- qecb[, c(72:107, 1:71)]
42b51a52e308 planemo upload for repository https://github.com/Marie59/champ_blocs commit 0d86db7d42b608c386a54500064f5f9c9d7019a4 ecology parents: diff changeset	202
42b51a52e308 planemo upload for repository https://github.com/Marie59/champ_blocs commit 0d86db7d42b608c386a54500064f5f9c9d7019a4 ecology parents: diff changeset	203 ## qecb df preparation prior qecb calculation
42b51a52e308 planemo upload for repository https://github.com/Marie59/champ_blocs commit 0d86db7d42b608c386a54500064f5f9c9d7019a4 ecology parents: diff changeset	204
42b51a52e308 planemo upload for repository https://github.com/Marie59/champ_blocs commit 0d86db7d42b608c386a54500064f5f9c9d7019a4 ecology parents: diff changeset	205 # Several issues to solve in the df first
42b51a52e308 planemo upload for repository https://github.com/Marie59/champ_blocs commit 0d86db7d42b608c386a54500064f5f9c9d7019a4 ecology parents: diff changeset	206
42b51a52e308 planemo upload for repository https://github.com/Marie59/champ_blocs commit 0d86db7d42b608c386a54500064f5f9c9d7019a4 ecology parents: diff changeset	207
42b51a52e308 planemo upload for repository https://github.com/Marie59/champ_blocs commit 0d86db7d42b608c386a54500064f5f9c9d7019a4 ecology parents: diff changeset	208 qecb$Type.Bloc <- factor(qecb$Type.Bloc, levels = c("Bloc mobile", "Bloc fixé", "Roche en place"))
42b51a52e308 planemo upload for repository https://github.com/Marie59/champ_blocs commit 0d86db7d42b608c386a54500064f5f9c9d7019a4 ecology parents: diff changeset	209
42b51a52e308 planemo upload for repository https://github.com/Marie59/champ_blocs commit 0d86db7d42b608c386a54500064f5f9c9d7019a4 ecology parents: diff changeset	210 qecb$Face <- factor(qecb$Face, levels = c("face supérieure", "face inférieure"))
42b51a52e308 planemo upload for repository https://github.com/Marie59/champ_blocs commit 0d86db7d42b608c386a54500064f5f9c9d7019a4 ecology parents: diff changeset	211
42b51a52e308 planemo upload for repository https://github.com/Marie59/champ_blocs commit 0d86db7d42b608c386a54500064f5f9c9d7019a4 ecology parents: diff changeset	212 qecb <- dplyr::arrange(qecb, Type.Bloc, Face, Numéro.Bloc.échantillon)
42b51a52e308 planemo upload for repository https://github.com/Marie59/champ_blocs commit 0d86db7d42b608c386a54500064f5f9c9d7019a4 ecology parents: diff changeset	213
42b51a52e308 planemo upload for repository https://github.com/Marie59/champ_blocs commit 0d86db7d42b608c386a54500064f5f9c9d7019a4 ecology parents: diff changeset	214 qecb <- tibble::add_column(qecb, site_year_month_day = paste0(qecb$Site, ".", qecb$Year, ".", qecb$Month, ".", qecb$Day), .after = "Site_bis")
42b51a52e308 planemo upload for repository https://github.com/Marie59/champ_blocs commit 0d86db7d42b608c386a54500064f5f9c9d7019a4 ecology parents: diff changeset	215
42b51a52e308 planemo upload for repository https://github.com/Marie59/champ_blocs commit 0d86db7d42b608c386a54500064f5f9c9d7019a4 ecology parents: diff changeset	216 # save qecb as a new df_ for analysis purpose => several changes to operate to run the code and functions
42b51a52e308 planemo upload for repository https://github.com/Marie59/champ_blocs commit 0d86db7d42b608c386a54500064f5f9c9d7019a4 ecology parents: diff changeset	217
42b51a52e308 planemo upload for repository https://github.com/Marie59/champ_blocs commit 0d86db7d42b608c386a54500064f5f9c9d7019a4 ecology parents: diff changeset	218 qecbnew <- qecb
42b51a52e308 planemo upload for repository https://github.com/Marie59/champ_blocs commit 0d86db7d42b608c386a54500064f5f9c9d7019a4 ecology parents: diff changeset	219
42b51a52e308 planemo upload for repository https://github.com/Marie59/champ_blocs commit 0d86db7d42b608c386a54500064f5f9c9d7019a4 ecology parents: diff changeset	220 # df with list object nb and corresponding site_year_month_day value to solve for loop issues
42b51a52e308 planemo upload for repository https://github.com/Marie59/champ_blocs commit 0d86db7d42b608c386a54500064f5f9c9d7019a4 ecology parents: diff changeset	221
42b51a52e308 planemo upload for repository https://github.com/Marie59/champ_blocs commit 0d86db7d42b608c386a54500064f5f9c9d7019a4 ecology parents: diff changeset	222 df_list_loop <- data.frame("site_year_month_day" = unique(qecbnew$site_year_month_day),
42b51a52e308 planemo upload for repository https://github.com/Marie59/champ_blocs commit 0d86db7d42b608c386a54500064f5f9c9d7019a4 ecology parents: diff changeset	223 "loop nb" = c(1:seq_along(unique(qecbnew$site_year_month_day))))
42b51a52e308 planemo upload for repository https://github.com/Marie59/champ_blocs commit 0d86db7d42b608c386a54500064f5f9c9d7019a4 ecology parents: diff changeset	224
42b51a52e308 planemo upload for repository https://github.com/Marie59/champ_blocs commit 0d86db7d42b608c386a54500064f5f9c9d7019a4 ecology parents: diff changeset	225 # dplyr::filter for df that makes problem, then eventually correct in the dataframe for wrong coding; brackets (xx) for nb because will change when qecb df_ enlarged.
42b51a52e308 planemo upload for repository https://github.com/Marie59/champ_blocs commit 0d86db7d42b608c386a54500064f5f9c9d7019a4 ecology parents: diff changeset	226 # these listed boulder field survey error when highlighted when running the loop, that ran into an error ; it was a step by step procedure with solving one listed observation after another when issues appeared. Surely not the best way to proceed, maybe better just to skip these surveys (site + date), but in the present case I wanted to keep most of the observations, therefore I corrected them manually whenever needed.
42b51a52e308 planemo upload for repository https://github.com/Marie59/champ_blocs commit 0d86db7d42b608c386a54500064f5f9c9d7019a4 ecology parents: diff changeset	227
42b51a52e308 planemo upload for repository https://github.com/Marie59/champ_blocs commit 0d86db7d42b608c386a54500064f5f9c9d7019a4 ecology parents: diff changeset	228 # list nb (28) - EGMP_BreeBains.2016.04.06
42b51a52e308 planemo upload for repository https://github.com/Marie59/champ_blocs commit 0d86db7d42b608c386a54500064f5f9c9d7019a4 ecology parents: diff changeset	229 qecbnew$Face <- as.character(qecbnew$Face)
42b51a52e308 planemo upload for repository https://github.com/Marie59/champ_blocs commit 0d86db7d42b608c386a54500064f5f9c9d7019a4 ecology parents: diff changeset	230 qecbnew$Face <- ifelse(qecbnew$ID.Fiche == "BDD_IVR&QECB_La Bree_20160406_VImport.xlsx" & qecbnew$Référence.bloc == "avr16-LaBreeB9sup", "face supérieure", qecbnew$Face)
42b51a52e308 planemo upload for repository https://github.com/Marie59/champ_blocs commit 0d86db7d42b608c386a54500064f5f9c9d7019a4 ecology parents: diff changeset	231 qecbnew$Face <- ifelse(qecbnew$ID.Fiche == "BDD_IVR&QECB_La Bree_20160406_VImport.xlsx" & qecbnew$Référence.bloc == "avr16-LaBreeB10sup", "face supérieure", qecbnew$Face)
42b51a52e308 planemo upload for repository https://github.com/Marie59/champ_blocs commit 0d86db7d42b608c386a54500064f5f9c9d7019a4 ecology parents: diff changeset	232 qecbnew$Face <- as.factor(qecbnew$Face)
42b51a52e308 planemo upload for repository https://github.com/Marie59/champ_blocs commit 0d86db7d42b608c386a54500064f5f9c9d7019a4 ecology parents: diff changeset	233
42b51a52e308 planemo upload for repository https://github.com/Marie59/champ_blocs commit 0d86db7d42b608c386a54500064f5f9c9d7019a4 ecology parents: diff changeset	234 # list nb 33 - EGMP_PerreAntiochat.2016.04.07
42b51a52e308 planemo upload for repository https://github.com/Marie59/champ_blocs commit 0d86db7d42b608c386a54500064f5f9c9d7019a4 ecology parents: diff changeset	235 qecbnew$Face <- as.character(qecbnew$Face)
42b51a52e308 planemo upload for repository https://github.com/Marie59/champ_blocs commit 0d86db7d42b608c386a54500064f5f9c9d7019a4 ecology parents: diff changeset	236 qecbnew$Face <- ifelse(qecbnew$ID.Fiche == "BDD_IVR&QECB_PerAnt_20160407_VImport.xlsx" & qecbnew$Référence.bloc == "avr16-PerAntB9sup", "face supérieure", qecbnew$Face)
42b51a52e308 planemo upload for repository https://github.com/Marie59/champ_blocs commit 0d86db7d42b608c386a54500064f5f9c9d7019a4 ecology parents: diff changeset	237 qecbnew$Face <- ifelse(qecbnew$ID.Fiche == "BDD_IVR&QECB_PerAnt_20160407_VImport.xlsx" & qecbnew$Référence.bloc == "avr16-PerAntB10sup", "face supérieure", qecbnew$Face)
42b51a52e308 planemo upload for repository https://github.com/Marie59/champ_blocs commit 0d86db7d42b608c386a54500064f5f9c9d7019a4 ecology parents: diff changeset	238 qecbnew$Face <- as.factor(qecbnew$Face)
42b51a52e308 planemo upload for repository https://github.com/Marie59/champ_blocs commit 0d86db7d42b608c386a54500064f5f9c9d7019a4 ecology parents: diff changeset	239
42b51a52e308 planemo upload for repository https://github.com/Marie59/champ_blocs commit 0d86db7d42b608c386a54500064f5f9c9d7019a4 ecology parents: diff changeset	240 # list nb 37 - EGMP_Chassiron.2016.03.09
42b51a52e308 planemo upload for repository https://github.com/Marie59/champ_blocs commit 0d86db7d42b608c386a54500064f5f9c9d7019a4 ecology parents: diff changeset	241 qecbnew$Face <- as.character(qecbnew$Face)
42b51a52e308 planemo upload for repository https://github.com/Marie59/champ_blocs commit 0d86db7d42b608c386a54500064f5f9c9d7019a4 ecology parents: diff changeset	242 qecbnew$Face <- ifelse(qecbnew$ID.Fiche == "BDD_IVR&QECB_Chassiron_20160309&10_VImport.xlsx" & qecbnew$Référence.bloc == "mars16-ChassB9sup", "face supérieure", qecbnew$Face)
42b51a52e308 planemo upload for repository https://github.com/Marie59/champ_blocs commit 0d86db7d42b608c386a54500064f5f9c9d7019a4 ecology parents: diff changeset	243 qecbnew$Face <- ifelse(qecbnew$ID.Fiche == "BDD_IVR&QECB_Chassiron_20160309&10_VImport.xlsx" & qecbnew$Référence.bloc == "mars16-ChasB10sup", "face supérieure", qecbnew$Face)
42b51a52e308 planemo upload for repository https://github.com/Marie59/champ_blocs commit 0d86db7d42b608c386a54500064f5f9c9d7019a4 ecology parents: diff changeset	244 qecbnew$Face <- as.factor(qecbnew$Face)
42b51a52e308 planemo upload for repository https://github.com/Marie59/champ_blocs commit 0d86db7d42b608c386a54500064f5f9c9d7019a4 ecology parents: diff changeset	245
42b51a52e308 planemo upload for repository https://github.com/Marie59/champ_blocs commit 0d86db7d42b608c386a54500064f5f9c9d7019a4 ecology parents: diff changeset	246 # list nb 76 - ARMO_Verdelet.2015.03.23
42b51a52e308 planemo upload for repository https://github.com/Marie59/champ_blocs commit 0d86db7d42b608c386a54500064f5f9c9d7019a4 ecology parents: diff changeset	247 qecbnew$Face <- as.character(qecbnew$Face)
42b51a52e308 planemo upload for repository https://github.com/Marie59/champ_blocs commit 0d86db7d42b608c386a54500064f5f9c9d7019a4 ecology parents: diff changeset	248 qecbnew$Face <- ifelse(qecbnew$ID.Fiche == "BDD_IVR&QECB_Verdelet_20150323_VImport.xlsx" & qecbnew$Référence.bloc == "mar15-VerB10inf", "face inférieure", qecbnew$Face)
42b51a52e308 planemo upload for repository https://github.com/Marie59/champ_blocs commit 0d86db7d42b608c386a54500064f5f9c9d7019a4 ecology parents: diff changeset	249 qecbnew$Face <- as.factor(qecbnew$Face)
42b51a52e308 planemo upload for repository https://github.com/Marie59/champ_blocs commit 0d86db7d42b608c386a54500064f5f9c9d7019a4 ecology parents: diff changeset	250
42b51a52e308 planemo upload for repository https://github.com/Marie59/champ_blocs commit 0d86db7d42b608c386a54500064f5f9c9d7019a4 ecology parents: diff changeset	251 # list nb 116 - "GDMO_Locmariaquer.2018.09.10"
42b51a52e308 planemo upload for repository https://github.com/Marie59/champ_blocs commit 0d86db7d42b608c386a54500064f5f9c9d7019a4 ecology parents: diff changeset	252 qecbnew$Type.Bloc <- as.character(qecbnew$Type.Bloc)
42b51a52e308 planemo upload for repository https://github.com/Marie59/champ_blocs commit 0d86db7d42b608c386a54500064f5f9c9d7019a4 ecology parents: diff changeset	253 qecbnew$Type.Bloc <- ifelse(qecbnew$ID.Fiche == "2018-09-10-GDMO-CDB-001" & qecbnew$Numero.Photo == "2018-09-10_GDMO_01_CDB-5_sup_392578.jpg", "Roche en place", qecbnew$Type.Bloc)
42b51a52e308 planemo upload for repository https://github.com/Marie59/champ_blocs commit 0d86db7d42b608c386a54500064f5f9c9d7019a4 ecology parents: diff changeset	254 qecbnew$Type.Bloc <- as.factor(qecbnew$Type.Bloc)
42b51a52e308 planemo upload for repository https://github.com/Marie59/champ_blocs commit 0d86db7d42b608c386a54500064f5f9c9d7019a4 ecology parents: diff changeset	255 qecbnew$quadrat_bis <- ifelse(qecbnew$ID.Fiche == "2018-09-10-GDMO-CDB-001" & qecbnew$Numero.Photo == "2018-09-10_GDMO_01_CDB-5_sup_392578.jpg", "Q5", qecbnew$quadrat_bis)
42b51a52e308 planemo upload for repository https://github.com/Marie59/champ_blocs commit 0d86db7d42b608c386a54500064f5f9c9d7019a4 ecology parents: diff changeset	256 qecbnew <- qecbnew %>% dplyr::filter(!(ID.Fiche == "2018-09-10-GDMO-CDB-001" & Numero.Photo == ""))
42b51a52e308 planemo upload for repository https://github.com/Marie59/champ_blocs commit 0d86db7d42b608c386a54500064f5f9c9d7019a4 ecology parents: diff changeset	257
42b51a52e308 planemo upload for repository https://github.com/Marie59/champ_blocs commit 0d86db7d42b608c386a54500064f5f9c9d7019a4 ecology parents: diff changeset	258 # Few sites to remove prior running the for loop because it was not just a encoding mistake for one data, but a globally wroing coding for the site + date survey.
42b51a52e308 planemo upload for repository https://github.com/Marie59/champ_blocs commit 0d86db7d42b608c386a54500064f5f9c9d7019a4 ecology parents: diff changeset	259
42b51a52e308 planemo upload for repository https://github.com/Marie59/champ_blocs commit 0d86db7d42b608c386a54500064f5f9c9d7019a4 ecology parents: diff changeset	260 qecb_i <- qecbnew %>% dplyr::filter(site_year_month_day == "FINS_StNicolasGlenan.2016.04.08") # no bloc fixe !
42b51a52e308 planemo upload for repository https://github.com/Marie59/champ_blocs commit 0d86db7d42b608c386a54500064f5f9c9d7019a4 ecology parents: diff changeset	261 qecbnew <- qecbnew %>% dplyr::filter(site_year_month_day != "FINS_StNicolasGlenan.2016.04.08")
42b51a52e308 planemo upload for repository https://github.com/Marie59/champ_blocs commit 0d86db7d42b608c386a54500064f5f9c9d7019a4 ecology parents: diff changeset	262 qecb_i <- qecbnew %>% dplyr::filter(site_year_month_day == "GDMO_Locmariaquer.2019.09.30") # most faces of blocs mobiles do not correspond to each other; only 3 over 10 boulder have data for both face supérieure and face inférieure
42b51a52e308 planemo upload for repository https://github.com/Marie59/champ_blocs commit 0d86db7d42b608c386a54500064f5f9c9d7019a4 ecology parents: diff changeset	263 qecbnew <- qecbnew %>% dplyr::filter(site_year_month_day != "GDMO_Locmariaquer.2019.09.30")
42b51a52e308 planemo upload for repository https://github.com/Marie59/champ_blocs commit 0d86db7d42b608c386a54500064f5f9c9d7019a4 ecology parents: diff changeset	264 rm(df_list_loop, qecb_i)
42b51a52e308 planemo upload for repository https://github.com/Marie59/champ_blocs commit 0d86db7d42b608c386a54500064f5f9c9d7019a4 ecology parents: diff changeset	265
42b51a52e308 planemo upload for repository https://github.com/Marie59/champ_blocs commit 0d86db7d42b608c386a54500064f5f9c9d7019a4 ecology parents: diff changeset	266
42b51a52e308 planemo upload for repository https://github.com/Marie59/champ_blocs commit 0d86db7d42b608c386a54500064f5f9c9d7019a4 ecology parents: diff changeset	267 # check for species with count within sub-0.1m^2-quadrat (i.e. reduced size quadrat compare to most organisms on boulder to count them, because abundant ; then some extrapolation)
42b51a52e308 planemo upload for repository https://github.com/Marie59/champ_blocs commit 0d86db7d42b608c386a54500064f5f9c9d7019a4 ecology parents: diff changeset	268
42b51a52e308 planemo upload for repository https://github.com/Marie59/champ_blocs commit 0d86db7d42b608c386a54500064f5f9c9d7019a4 ecology parents: diff changeset	269 # first for Spirobranchus
42b51a52e308 planemo upload for repository https://github.com/Marie59/champ_blocs commit 0d86db7d42b608c386a54500064f5f9c9d7019a4 ecology parents: diff changeset	270
42b51a52e308 planemo upload for repository https://github.com/Marie59/champ_blocs commit 0d86db7d42b608c386a54500064f5f9c9d7019a4 ecology parents: diff changeset	271 qecbnew$Nb.Spirobranchus.lamarckii.total.ini <- qecbnew$Nb.Spirobranchus.lamarckii.total
42b51a52e308 planemo upload for repository https://github.com/Marie59/champ_blocs commit 0d86db7d42b608c386a54500064f5f9c9d7019a4 ecology parents: diff changeset	272 qecbnew$Nb.Spirobranchus.lamarckii.total <- as.character(qecbnew$Nb.Spirobranchus.lamarckii.total)
42b51a52e308 planemo upload for repository https://github.com/Marie59/champ_blocs commit 0d86db7d42b608c386a54500064f5f9c9d7019a4 ecology parents: diff changeset	273
42b51a52e308 planemo upload for repository https://github.com/Marie59/champ_blocs commit 0d86db7d42b608c386a54500064f5f9c9d7019a4 ecology parents: diff changeset	274
42b51a52e308 planemo upload for repository https://github.com/Marie59/champ_blocs commit 0d86db7d42b608c386a54500064f5f9c9d7019a4 ecology parents: diff changeset	275 qecbnew_spirobranchus <- (dplyr::filter(qecbnew, Nb.Spirobranchus.lamarckii.total %in% c(NA, "NaN", "Inf", "-Inf")))
42b51a52e308 planemo upload for repository https://github.com/Marie59/champ_blocs commit 0d86db7d42b608c386a54500064f5f9c9d7019a4 ecology parents: diff changeset	276 qecbnew_spirobranchus[, c("Nb.Spirobranchus.lamarckii.1B", "Nb.Spirobranchus.lamarckii.2B", "Nb.Spirobranchus.lamarckii.3B", "Nb.Spirobranchus.lamarckii.4B", "Nb.Spirobranchus.lamarckii.5B")] <- sapply(qecbnew_spirobranchus[, c("Nb.Spirobranchus.lamarckii.1B", "Nb.Spirobranchus.lamarckii.2B", "Nb.Spirobranchus.lamarckii.3B", "Nb.Spirobranchus.lamarckii.4B", "Nb.Spirobranchus.lamarckii.5B")], as.character)
42b51a52e308 planemo upload for repository https://github.com/Marie59/champ_blocs commit 0d86db7d42b608c386a54500064f5f9c9d7019a4 ecology parents: diff changeset	277 (spirobranchus_data <- subset(qecbnew_spirobranchus, !is.na(qecbnew_spirobranchus$Nb.Spirobranchus.lamarckii.1B) \|\| !is.na(qecbnew_spirobranchus$Nb.Spirobranchus.lamarckii.2B) \|\| !is.na(qecbnew_spirobranchus$Nb.Spirobranchus.lamarckii.3B) \|\| !is.na(qecbnew_spirobranchus$Nb.Spirobranchus.lamarckii.4B) \|\| !is.na(qecbnew_spirobranchus$Nb.Spirobranchus.lamarckii.5B))[, c("site_year_month_day", "Nb.Spirobranchus.lamarckii.1B", "Nb.Spirobranchus.lamarckii.2B", "Nb.Spirobranchus.lamarckii.3B", "Nb.Spirobranchus.lamarckii.4B", "Nb.Spirobranchus.lamarckii.5B", "Nb.Spirobranchus.lamarckii.total")])
42b51a52e308 planemo upload for repository https://github.com/Marie59/champ_blocs commit 0d86db7d42b608c386a54500064f5f9c9d7019a4 ecology parents: diff changeset	278
42b51a52e308 planemo upload for repository https://github.com/Marie59/champ_blocs commit 0d86db7d42b608c386a54500064f5f9c9d7019a4 ecology parents: diff changeset	279 quemenes <- dplyr::filter(qecbnew, Site == "FINS_Quemenes")
42b51a52e308 planemo upload for repository https://github.com/Marie59/champ_blocs commit 0d86db7d42b608c386a54500064f5f9c9d7019a4 ecology parents: diff changeset	280 quemenes <- dplyr::arrange(quemenes, date_fiche)
42b51a52e308 planemo upload for repository https://github.com/Marie59/champ_blocs commit 0d86db7d42b608c386a54500064f5f9c9d7019a4 ecology parents: diff changeset	281 # for Quemenes, issue because for sampling date "FINS_Quemenes.2015.09.30" the 5 counts of Spirobranchus were encoded in 1B instead of total !!! I noticed this issue when mining data (see below), therefore I corrected before running below script for Spirobranchus.
42b51a52e308 planemo upload for repository https://github.com/Marie59/champ_blocs commit 0d86db7d42b608c386a54500064f5f9c9d7019a4 ecology parents: diff changeset	282 qecbnew$Nb.Spirobranchus.lamarckii.total <- ifelse(qecbnew$site_year_month_day == "FINS_Quemenes.2015.09.30" & is.na(qecbnew$Nb.Spirobranchus.lamarckii.total), qecbnew$Nb.Spirobranchus.lamarckii.1B, qecbnew$Nb.Spirobranchus.lamarckii.total)
42b51a52e308 planemo upload for repository https://github.com/Marie59/champ_blocs commit 0d86db7d42b608c386a54500064f5f9c9d7019a4 ecology parents: diff changeset	283
42b51a52e308 planemo upload for repository https://github.com/Marie59/champ_blocs commit 0d86db7d42b608c386a54500064f5f9c9d7019a4 ecology parents: diff changeset	284 (quemenes <- dplyr::filter(qecbnew, site_year_month_day == "FINS_Quemenes.2015.09.30")[, c("site_year_month_day", "Nb.Spirobranchus.lamarckii.1B", "Nb.Spirobranchus.lamarckii.2B", "Nb.Spirobranchus.lamarckii.3B", "Nb.Spirobranchus.lamarckii.4B", "Nb.Spirobranchus.lamarckii.5B", "Nb.Spirobranchus.lamarckii.total")])
42b51a52e308 planemo upload for repository https://github.com/Marie59/champ_blocs commit 0d86db7d42b608c386a54500064f5f9c9d7019a4 ecology parents: diff changeset	285 rm(quemenes)
42b51a52e308 planemo upload for repository https://github.com/Marie59/champ_blocs commit 0d86db7d42b608c386a54500064f5f9c9d7019a4 ecology parents: diff changeset	286
42b51a52e308 planemo upload for repository https://github.com/Marie59/champ_blocs commit 0d86db7d42b608c386a54500064f5f9c9d7019a4 ecology parents: diff changeset	287 seinkilaourou <- dplyr::filter(qecbnew, Site == "FINS_SeinKilaourou")
42b51a52e308 planemo upload for repository https://github.com/Marie59/champ_blocs commit 0d86db7d42b608c386a54500064f5f9c9d7019a4 ecology parents: diff changeset	288 seinkilaourou <- dplyr::arrange(seinkilaourou, date_fiche)
42b51a52e308 planemo upload for repository https://github.com/Marie59/champ_blocs commit 0d86db7d42b608c386a54500064f5f9c9d7019a4 ecology parents: diff changeset	289 # same issue with SeinKilaourou
42b51a52e308 planemo upload for repository https://github.com/Marie59/champ_blocs commit 0d86db7d42b608c386a54500064f5f9c9d7019a4 ecology parents: diff changeset	290 qecbnew$Nb.Spirobranchus.lamarckii.total <- ifelse(qecbnew$site_year_month_day == "FINS_SeinKilaourou.2015.04.21" & is.na(qecbnew$Nb.Spirobranchus.lamarckii.total), qecbnew$Nb.Spirobranchus.lamarckii.1B, qecbnew$Nb.Spirobranchus.lamarckii.total)
42b51a52e308 planemo upload for repository https://github.com/Marie59/champ_blocs commit 0d86db7d42b608c386a54500064f5f9c9d7019a4 ecology parents: diff changeset	291 (seinkilaourou <- dplyr::filter(qecbnew, site_year_month_day == "FINS_SeinKilaourou.2015.04.21")[, c("site_year_month_day", "Nb.Spirobranchus.lamarckii.1B", "Nb.Spirobranchus.lamarckii.2B", "Nb.Spirobranchus.lamarckii.3B", "Nb.Spirobranchus.lamarckii.4B", "Nb.Spirobranchus.lamarckii.5B", "Nb.Spirobranchus.lamarckii.total")])
42b51a52e308 planemo upload for repository https://github.com/Marie59/champ_blocs commit 0d86db7d42b608c386a54500064f5f9c9d7019a4 ecology parents: diff changeset	292 rm(seinkilaourou)
42b51a52e308 planemo upload for repository https://github.com/Marie59/champ_blocs commit 0d86db7d42b608c386a54500064f5f9c9d7019a4 ecology parents: diff changeset	293
42b51a52e308 planemo upload for repository https://github.com/Marie59/champ_blocs commit 0d86db7d42b608c386a54500064f5f9c9d7019a4 ecology parents: diff changeset	294 # some more issues however with "x100"count data
42b51a52e308 planemo upload for repository https://github.com/Marie59/champ_blocs commit 0d86db7d42b608c386a54500064f5f9c9d7019a4 ecology parents: diff changeset	295 spirobranchus <- subset(qecbnew, !is.na(qecbnew$Nb.Spirobranchus.lamarckii.1B) & !is.na(qecbnew$Nb.Spirobranchus.lamarckii.2B) & !is.na(qecbnew$Nb.Spirobranchus.lamarckii.3B) & !is.na(qecbnew$Nb.Spirobranchus.lamarckii.4B) & !is.na(qecbnew$Nb.Spirobranchus.lamarckii.5B) & !is.na(qecbnew$Nb.Spirobranchus.lamarckii.total))[, c("site_year_month_day", "Nb.Spirobranchus.lamarckii.1B", "Nb.Spirobranchus.lamarckii.2B", "Nb.Spirobranchus.lamarckii.3B", "Nb.Spirobranchus.lamarckii.4B", "Nb.Spirobranchus.lamarckii.5B", "Nb.Spirobranchus.lamarckii.total")]
42b51a52e308 planemo upload for repository https://github.com/Marie59/champ_blocs commit 0d86db7d42b608c386a54500064f5f9c9d7019a4 ecology parents: diff changeset	296
42b51a52e308 planemo upload for repository https://github.com/Marie59/champ_blocs commit 0d86db7d42b608c386a54500064f5f9c9d7019a4 ecology parents: diff changeset	297 for (i in c(1:nrow(spirobranchus))) {
42b51a52e308 planemo upload for repository https://github.com/Marie59/champ_blocs commit 0d86db7d42b608c386a54500064f5f9c9d7019a4 ecology parents: diff changeset	298 spirobranchus$mean.x.100[[i]] <- sum(spirobranchus[i, c(2:6)], na.rm = TRUE) / sum(!is.na(spirobranchus[i, c(2:6)])) * 100
42b51a52e308 planemo upload for repository https://github.com/Marie59/champ_blocs commit 0d86db7d42b608c386a54500064f5f9c9d7019a4 ecology parents: diff changeset	299 }
42b51a52e308 planemo upload for repository https://github.com/Marie59/champ_blocs commit 0d86db7d42b608c386a54500064f5f9c9d7019a4 ecology parents: diff changeset	300
42b51a52e308 planemo upload for repository https://github.com/Marie59/champ_blocs commit 0d86db7d42b608c386a54500064f5f9c9d7019a4 ecology parents: diff changeset	301 spirobranchus$mean.x.100 <- unlist(spirobranchus$mean.x.100)
42b51a52e308 planemo upload for repository https://github.com/Marie59/champ_blocs commit 0d86db7d42b608c386a54500064f5f9c9d7019a4 ecology parents: diff changeset	302 spirobranchus$Nb.Spirobranchus.lamarckii.total <- as.numeric(spirobranchus$Nb.Spirobranchus.lamarckii.total)
42b51a52e308 planemo upload for repository https://github.com/Marie59/champ_blocs commit 0d86db7d42b608c386a54500064f5f9c9d7019a4 ecology parents: diff changeset	303 for (i in c(1:nrow(spirobranchus))) {
42b51a52e308 planemo upload for repository https://github.com/Marie59/champ_blocs commit 0d86db7d42b608c386a54500064f5f9c9d7019a4 ecology parents: diff changeset	304 spirobranchus$diff[[i]] <- spirobranchus[i, "Nb.Spirobranchus.lamarckii.total"] - spirobranchus[i, "mean.x.100"]
42b51a52e308 planemo upload for repository https://github.com/Marie59/champ_blocs commit 0d86db7d42b608c386a54500064f5f9c9d7019a4 ecology parents: diff changeset	305 }
42b51a52e308 planemo upload for repository https://github.com/Marie59/champ_blocs commit 0d86db7d42b608c386a54500064f5f9c9d7019a4 ecology parents: diff changeset	306
42b51a52e308 planemo upload for repository https://github.com/Marie59/champ_blocs commit 0d86db7d42b608c386a54500064f5f9c9d7019a4 ecology parents: diff changeset	307 spirobranchus$diff <- abs(as.integer(spirobranchus$diff))
42b51a52e308 planemo upload for repository https://github.com/Marie59/champ_blocs commit 0d86db7d42b608c386a54500064f5f9c9d7019a4 ecology parents: diff changeset	308 spirobranchus <- dplyr::arrange(spirobranchus, desc(diff), mean.x.100)
42b51a52e308 planemo upload for repository https://github.com/Marie59/champ_blocs commit 0d86db7d42b608c386a54500064f5f9c9d7019a4 ecology parents: diff changeset	309 spirobranchus <- dplyr::arrange(dplyr::filter(spirobranchus, diff != 0 & mean.x.100 != 0), desc(diff))
42b51a52e308 planemo upload for repository https://github.com/Marie59/champ_blocs commit 0d86db7d42b608c386a54500064f5f9c9d7019a4 ecology parents: diff changeset	310
42b51a52e308 planemo upload for repository https://github.com/Marie59/champ_blocs commit 0d86db7d42b608c386a54500064f5f9c9d7019a4 ecology parents: diff changeset	311 # check it all in the qecbnew df
42b51a52e308 planemo upload for repository https://github.com/Marie59/champ_blocs commit 0d86db7d42b608c386a54500064f5f9c9d7019a4 ecology parents: diff changeset	312
42b51a52e308 planemo upload for repository https://github.com/Marie59/champ_blocs commit 0d86db7d42b608c386a54500064f5f9c9d7019a4 ecology parents: diff changeset	313 for (i in c(1:nrow(qecbnew))) {
42b51a52e308 planemo upload for repository https://github.com/Marie59/champ_blocs commit 0d86db7d42b608c386a54500064f5f9c9d7019a4 ecology parents: diff changeset	314 qecbnew$mean.x.100[[i]] <-
42b51a52e308 planemo upload for repository https://github.com/Marie59/champ_blocs commit 0d86db7d42b608c386a54500064f5f9c9d7019a4 ecology parents: diff changeset	315 sum(qecbnew[i, c("Nb.Spirobranchus.lamarckii.1B", "Nb.Spirobranchus.lamarckii.2B", "Nb.Spirobranchus.lamarckii.3B", "Nb.Spirobranchus.lamarckii.4B", "Nb.Spirobranchus.lamarckii.5B")], na.rm = TRUE) / sum(!is.na(qecbnew[i, c("Nb.Spirobranchus.lamarckii.1B", "Nb.Spirobranchus.lamarckii.2B", "Nb.Spirobranchus.lamarckii.3B", "Nb.Spirobranchus.lamarckii.4B", "Nb.Spirobranchus.lamarckii.5B")])) * 100
42b51a52e308 planemo upload for repository https://github.com/Marie59/champ_blocs commit 0d86db7d42b608c386a54500064f5f9c9d7019a4 ecology parents: diff changeset	316 } # sum of only NAs/0 = NaN; so replace NaN by Na
42b51a52e308 planemo upload for repository https://github.com/Marie59/champ_blocs commit 0d86db7d42b608c386a54500064f5f9c9d7019a4 ecology parents: diff changeset	317 qecbnew$mean.x.100 <- as.character(qecbnew$mean.x.100)
42b51a52e308 planemo upload for repository https://github.com/Marie59/champ_blocs commit 0d86db7d42b608c386a54500064f5f9c9d7019a4 ecology parents: diff changeset	318
42b51a52e308 planemo upload for repository https://github.com/Marie59/champ_blocs commit 0d86db7d42b608c386a54500064f5f9c9d7019a4 ecology parents: diff changeset	319
42b51a52e308 planemo upload for repository https://github.com/Marie59/champ_blocs commit 0d86db7d42b608c386a54500064f5f9c9d7019a4 ecology parents: diff changeset	320 for (i in c(1:nrow(qecbnew))) {
42b51a52e308 planemo upload for repository https://github.com/Marie59/champ_blocs commit 0d86db7d42b608c386a54500064f5f9c9d7019a4 ecology parents: diff changeset	321 qecbnew$mean.x.100[[i]] <- ifelse(qecbnew$mean.x.100[[i]] == "NaN", NA, qecbnew$mean.x.100[[i]])
42b51a52e308 planemo upload for repository https://github.com/Marie59/champ_blocs commit 0d86db7d42b608c386a54500064f5f9c9d7019a4 ecology parents: diff changeset	322 }
42b51a52e308 planemo upload for repository https://github.com/Marie59/champ_blocs commit 0d86db7d42b608c386a54500064f5f9c9d7019a4 ecology parents: diff changeset	323 qecbnew$mean.x.100 <- as.integer(qecbnew$mean.x.100)
42b51a52e308 planemo upload for repository https://github.com/Marie59/champ_blocs commit 0d86db7d42b608c386a54500064f5f9c9d7019a4 ecology parents: diff changeset	324
42b51a52e308 planemo upload for repository https://github.com/Marie59/champ_blocs commit 0d86db7d42b608c386a54500064f5f9c9d7019a4 ecology parents: diff changeset	325 qecbnew$Nb.Spirobranchus.lamarckii.total <- as.integer(qecbnew$Nb.Spirobranchus.lamarckii.total)
42b51a52e308 planemo upload for repository https://github.com/Marie59/champ_blocs commit 0d86db7d42b608c386a54500064f5f9c9d7019a4 ecology parents: diff changeset	326 qecbnew$Nb.Spirobranchus.lamarckii.total.diff <- abs((qecbnew$Nb.Spirobranchus.lamarckii.total - qecbnew$mean.x.100))
42b51a52e308 planemo upload for repository https://github.com/Marie59/champ_blocs commit 0d86db7d42b608c386a54500064f5f9c9d7019a4 ecology parents: diff changeset	327 spirobranchus_diff <- qecbnew[, c("Nb.Spirobranchus.lamarckii.1B", "Nb.Spirobranchus.lamarckii.2B", "Nb.Spirobranchus.lamarckii.3B", "Nb.Spirobranchus.lamarckii.4B", "Nb.Spirobranchus.lamarckii.5B", "Nb.Spirobranchus.lamarckii.total", "Nb.Spirobranchus.lamarckii.total.ini", "mean.x.100", "Nb.Spirobranchus.lamarckii.total.diff")]
42b51a52e308 planemo upload for repository https://github.com/Marie59/champ_blocs commit 0d86db7d42b608c386a54500064f5f9c9d7019a4 ecology parents: diff changeset	328 spirobranchus_diff <- dplyr::arrange(spirobranchus_diff, desc(Nb.Spirobranchus.lamarckii.total.diff), mean.x.100)
42b51a52e308 planemo upload for repository https://github.com/Marie59/champ_blocs commit 0d86db7d42b608c386a54500064f5f9c9d7019a4 ecology parents: diff changeset	329 spirobranchus_diff <- dplyr::arrange(dplyr::filter(spirobranchus_diff, Nb.Spirobranchus.lamarckii.total.diff != 0 & mean.x.100 != 0), desc(Nb.Spirobranchus.lamarckii.total.diff))
42b51a52e308 planemo upload for repository https://github.com/Marie59/champ_blocs commit 0d86db7d42b608c386a54500064f5f9c9d7019a4 ecology parents: diff changeset	330
42b51a52e308 planemo upload for repository https://github.com/Marie59/champ_blocs commit 0d86db7d42b608c386a54500064f5f9c9d7019a4 ecology parents: diff changeset	331 qecbnew$Nb.Spirobranchus.lamarckii.total <- ifelse(qecbnew$Nb.Spirobranchus.lamarckii.total.diff != 0 & qecbnew$mean.x.100 != 0, qecbnew$mean.x.100, qecbnew$Nb.Spirobranchus.lamarckii.total)
42b51a52e308 planemo upload for repository https://github.com/Marie59/champ_blocs commit 0d86db7d42b608c386a54500064f5f9c9d7019a4 ecology parents: diff changeset	332 spirobranchus_diff <- qecbnew[, c("Nb.Spirobranchus.lamarckii.1B", "Nb.Spirobranchus.lamarckii.2B", "Nb.Spirobranchus.lamarckii.3B", "Nb.Spirobranchus.lamarckii.4B", "Nb.Spirobranchus.lamarckii.5B", "Nb.Spirobranchus.lamarckii.total", "Nb.Spirobranchus.lamarckii.total.ini", "mean.x.100", "Nb.Spirobranchus.lamarckii.total.diff")]
42b51a52e308 planemo upload for repository https://github.com/Marie59/champ_blocs commit 0d86db7d42b608c386a54500064f5f9c9d7019a4 ecology parents: diff changeset	333 spirobranchus_diff$Nb.Spirobranchus.lamarckii.total.diff <- abs(as.integer(spirobranchus_diff$Nb.Spirobranchus.lamarckii.total.diff))
42b51a52e308 planemo upload for repository https://github.com/Marie59/champ_blocs commit 0d86db7d42b608c386a54500064f5f9c9d7019a4 ecology parents: diff changeset	334 spirobranchus_diff <- dplyr::arrange(spirobranchus_diff, desc(Nb.Spirobranchus.lamarckii.total.diff), mean.x.100)
42b51a52e308 planemo upload for repository https://github.com/Marie59/champ_blocs commit 0d86db7d42b608c386a54500064f5f9c9d7019a4 ecology parents: diff changeset	335 spirobranchus_diff <- dplyr::arrange(dplyr::filter(spirobranchus_diff, Nb.Spirobranchus.lamarckii.total.diff != 0 & mean.x.100 != 0), desc(Nb.Spirobranchus.lamarckii.total.diff))
42b51a52e308 planemo upload for repository https://github.com/Marie59/champ_blocs commit 0d86db7d42b608c386a54500064f5f9c9d7019a4 ecology parents: diff changeset	336 # ok, change made when data x 100 was not correct.
42b51a52e308 planemo upload for repository https://github.com/Marie59/champ_blocs commit 0d86db7d42b608c386a54500064f5f9c9d7019a4 ecology parents: diff changeset	337
42b51a52e308 planemo upload for repository https://github.com/Marie59/champ_blocs commit 0d86db7d42b608c386a54500064f5f9c9d7019a4 ecology parents: diff changeset	338 # finally, change NA by mean.x100 for Spirobranchus total
42b51a52e308 planemo upload for repository https://github.com/Marie59/champ_blocs commit 0d86db7d42b608c386a54500064f5f9c9d7019a4 ecology parents: diff changeset	339 qecbnew$Nb.Spirobranchus.lamarckii.total <- as.character(qecbnew$Nb.Spirobranchus.lamarckii.total)
42b51a52e308 planemo upload for repository https://github.com/Marie59/champ_blocs commit 0d86db7d42b608c386a54500064f5f9c9d7019a4 ecology parents: diff changeset	340 for (i in c(1:nrow(qecbnew))) {
42b51a52e308 planemo upload for repository https://github.com/Marie59/champ_blocs commit 0d86db7d42b608c386a54500064f5f9c9d7019a4 ecology parents: diff changeset	341 qecbnew$Nb.Spirobranchus.lamarckii.total[[i]] <- ifelse(qecbnew$Nb.Spirobranchus.lamarckii.total[[i]] %in% c(NA, "NaN", "Inf", "-Inf"), sum(qecbnew[i, c("Nb.Spirobranchus.lamarckii.1B", "Nb.Spirobranchus.lamarckii.2B", "Nb.Spirobranchus.lamarckii.3B", "Nb.Spirobranchus.lamarckii.4B", "Nb.Spirobranchus.lamarckii.5B")], na.rm = TRUE) / sum(!is.na(qecbnew[i, c("Nb.Spirobranchus.lamarckii.1B", "Nb.Spirobranchus.lamarckii.2B", "Nb.Spirobranchus.lamarckii.3B", "Nb.Spirobranchus.lamarckii.4B", "Nb.Spirobranchus.lamarckii.5B")])) * 100, qecbnew$Nb.Spirobranchus.lamarckii.total[[i]])
42b51a52e308 planemo upload for repository https://github.com/Marie59/champ_blocs commit 0d86db7d42b608c386a54500064f5f9c9d7019a4 ecology parents: diff changeset	342 } # sum of only NAs/0 = NaN; so replace NaN by Na
42b51a52e308 planemo upload for repository https://github.com/Marie59/champ_blocs commit 0d86db7d42b608c386a54500064f5f9c9d7019a4 ecology parents: diff changeset	343
42b51a52e308 planemo upload for repository https://github.com/Marie59/champ_blocs commit 0d86db7d42b608c386a54500064f5f9c9d7019a4 ecology parents: diff changeset	344
42b51a52e308 planemo upload for repository https://github.com/Marie59/champ_blocs commit 0d86db7d42b608c386a54500064f5f9c9d7019a4 ecology parents: diff changeset	345 for (i in c(1:nrow(qecbnew))) {
42b51a52e308 planemo upload for repository https://github.com/Marie59/champ_blocs commit 0d86db7d42b608c386a54500064f5f9c9d7019a4 ecology parents: diff changeset	346 qecbnew$Nb.Spirobranchus.lamarckii.total[[i]] <- ifelse(qecbnew$Nb.Spirobranchus.lamarckii.total[[i]] == "NaN", NA, qecbnew$Nb.Spirobranchus.lamarckii.total[[i]])
42b51a52e308 planemo upload for repository https://github.com/Marie59/champ_blocs commit 0d86db7d42b608c386a54500064f5f9c9d7019a4 ecology parents: diff changeset	347 }
42b51a52e308 planemo upload for repository https://github.com/Marie59/champ_blocs commit 0d86db7d42b608c386a54500064f5f9c9d7019a4 ecology parents: diff changeset	348
42b51a52e308 planemo upload for repository https://github.com/Marie59/champ_blocs commit 0d86db7d42b608c386a54500064f5f9c9d7019a4 ecology parents: diff changeset	349 qecbnew$Nb.Spirobranchus.lamarckii.total <- as.integer(qecbnew$Nb.Spirobranchus.lamarckii.total)
42b51a52e308 planemo upload for repository https://github.com/Marie59/champ_blocs commit 0d86db7d42b608c386a54500064f5f9c9d7019a4 ecology parents: diff changeset	350
42b51a52e308 planemo upload for repository https://github.com/Marie59/champ_blocs commit 0d86db7d42b608c386a54500064f5f9c9d7019a4 ecology parents: diff changeset	351 qecbnew$Nb.Spirobranchus.lamarckii.total.diff <- abs(qecbnew$Nb.Spirobranchus.lamarckii.total - qecbnew$Nb.Spirobranchus.lamarckii.total.ini)
42b51a52e308 planemo upload for repository https://github.com/Marie59/champ_blocs commit 0d86db7d42b608c386a54500064f5f9c9d7019a4 ecology parents: diff changeset	352 spirobranchus_diff <- qecbnew[, c("Nb.Spirobranchus.lamarckii.1B", "Nb.Spirobranchus.lamarckii.2B", "Nb.Spirobranchus.lamarckii.3B", "Nb.Spirobranchus.lamarckii.4B", "Nb.Spirobranchus.lamarckii.5B", "Nb.Spirobranchus.lamarckii.total", "Nb.Spirobranchus.lamarckii.total.ini", "mean.x.100", "Nb.Spirobranchus.lamarckii.total.diff")]
42b51a52e308 planemo upload for repository https://github.com/Marie59/champ_blocs commit 0d86db7d42b608c386a54500064f5f9c9d7019a4 ecology parents: diff changeset	353 spirobranchus_diff <- dplyr::arrange(spirobranchus_diff, desc(Nb.Spirobranchus.lamarckii.total.diff), mean.x.100)
42b51a52e308 planemo upload for repository https://github.com/Marie59/champ_blocs commit 0d86db7d42b608c386a54500064f5f9c9d7019a4 ecology parents: diff changeset	354 spirobranchus_diff <- dplyr::arrange(dplyr::filter(spirobranchus_diff, Nb.Spirobranchus.lamarckii.total.diff != 0 & mean.x.100 != 0), desc(Nb.Spirobranchus.lamarckii.total.diff))
42b51a52e308 planemo upload for repository https://github.com/Marie59/champ_blocs commit 0d86db7d42b608c386a54500064f5f9c9d7019a4 ecology parents: diff changeset	355
42b51a52e308 planemo upload for repository https://github.com/Marie59/champ_blocs commit 0d86db7d42b608c386a54500064f5f9c9d7019a4 ecology parents: diff changeset	356 qecbnew <- subset(qecbnew, select = -c(Nb.Spirobranchus.lamarckii.total.ini, mean.x.100, Nb.Spirobranchus.lamarckii.total.diff))
42b51a52e308 planemo upload for repository https://github.com/Marie59/champ_blocs commit 0d86db7d42b608c386a54500064f5f9c9d7019a4 ecology parents: diff changeset	357
42b51a52e308 planemo upload for repository https://github.com/Marie59/champ_blocs commit 0d86db7d42b608c386a54500064f5f9c9d7019a4 ecology parents: diff changeset	358 rm(qecbnew_spirobranchus, spirobranchus, spirobranchus_data, spirobranchus_diff)
42b51a52e308 planemo upload for repository https://github.com/Marie59/champ_blocs commit 0d86db7d42b608c386a54500064f5f9c9d7019a4 ecology parents: diff changeset	359
42b51a52e308 planemo upload for repository https://github.com/Marie59/champ_blocs commit 0d86db7d42b608c386a54500064f5f9c9d7019a4 ecology parents: diff changeset	360 # do the same for spirorbis
42b51a52e308 planemo upload for repository https://github.com/Marie59/champ_blocs commit 0d86db7d42b608c386a54500064f5f9c9d7019a4 ecology parents: diff changeset	361
42b51a52e308 planemo upload for repository https://github.com/Marie59/champ_blocs commit 0d86db7d42b608c386a54500064f5f9c9d7019a4 ecology parents: diff changeset	362 qecbnew$Nb.spirorbis.total.ini <- qecbnew$Nb.spirorbis.total
42b51a52e308 planemo upload for repository https://github.com/Marie59/champ_blocs commit 0d86db7d42b608c386a54500064f5f9c9d7019a4 ecology parents: diff changeset	363 qecbnew$Nb.spirorbis.total <- as.character(qecbnew$Nb.spirorbis.total)
42b51a52e308 planemo upload for repository https://github.com/Marie59/champ_blocs commit 0d86db7d42b608c386a54500064f5f9c9d7019a4 ecology parents: diff changeset	364
42b51a52e308 planemo upload for repository https://github.com/Marie59/champ_blocs commit 0d86db7d42b608c386a54500064f5f9c9d7019a4 ecology parents: diff changeset	365 qecbnew_spirorbis <- (dplyr::filter(qecbnew, Nb.spirorbis.total %in% c(NA, "NaN", "Inf", "-Inf")))
42b51a52e308 planemo upload for repository https://github.com/Marie59/champ_blocs commit 0d86db7d42b608c386a54500064f5f9c9d7019a4 ecology parents: diff changeset	366 qecbnew_spirorbis[, c("Nb.spirorbis.1A", "Nb.spirorbis.2A", "Nb.spirorbis.3A", "Nb.spirorbis.4A", "Nb.spirorbis.5A")] <- sapply(qecbnew_spirorbis[, c("Nb.spirorbis.1A", "Nb.spirorbis.2A", "Nb.spirorbis.3A", "Nb.spirorbis.4A", "Nb.spirorbis.5A")], as.character)
42b51a52e308 planemo upload for repository https://github.com/Marie59/champ_blocs commit 0d86db7d42b608c386a54500064f5f9c9d7019a4 ecology parents: diff changeset	367 (spirobranchus_data <- subset(qecbnew_spirorbis, !is.na(qecbnew_spirorbis$Nb.spirorbis.1A) \|\| !is.na(qecbnew_spirorbis$Nb.spirorbis.2A) \|\| !is.na(qecbnew_spirorbis$Nb.spirorbis.3A) \|\| !is.na(qecbnew_spirorbis$Nb.spirorbis.4A) \|\| !is.na(qecbnew_spirorbis$Nb.spirorbis.5A))[, c("site_year_month_day", "Nb.spirorbis.1A", "Nb.spirorbis.2A", "Nb.spirorbis.3A", "Nb.spirorbis.4A", "Nb.spirorbis.5A", "Nb.spirorbis.total")])
42b51a52e308 planemo upload for repository https://github.com/Marie59/champ_blocs commit 0d86db7d42b608c386a54500064f5f9c9d7019a4 ecology parents: diff changeset	368
42b51a52e308 planemo upload for repository https://github.com/Marie59/champ_blocs commit 0d86db7d42b608c386a54500064f5f9c9d7019a4 ecology parents: diff changeset	369 # In contrast to Spirobranchus data, no encoding issues for spirorbis data, cfr when sub-quadrat 1A-5A are ALL encoded, NA for total.
42b51a52e308 planemo upload for repository https://github.com/Marie59/champ_blocs commit 0d86db7d42b608c386a54500064f5f9c9d7019a4 ecology parents: diff changeset	370
42b51a52e308 planemo upload for repository https://github.com/Marie59/champ_blocs commit 0d86db7d42b608c386a54500064f5f9c9d7019a4 ecology parents: diff changeset	371 # some more issues however with "x200"count data
42b51a52e308 planemo upload for repository https://github.com/Marie59/champ_blocs commit 0d86db7d42b608c386a54500064f5f9c9d7019a4 ecology parents: diff changeset	372
42b51a52e308 planemo upload for repository https://github.com/Marie59/champ_blocs commit 0d86db7d42b608c386a54500064f5f9c9d7019a4 ecology parents: diff changeset	373 spirorbis <- subset(qecbnew, !is.na(qecbnew$Nb.spirorbis.1A) & !is.na(qecbnew$Nb.spirorbis.2A) & !is.na(qecbnew$Nb.spirorbis.3A) & !is.na(qecbnew$Nb.spirorbis.4A) & !is.na(qecbnew$Nb.spirorbis.5A) & !is.na(qecbnew$Nb.spirorbis.total))[, c("site_year_month_day", "Nb.spirorbis.1A", "Nb.spirorbis.2A", "Nb.spirorbis.3A", "Nb.spirorbis.4A", "Nb.spirorbis.5A", "Nb.spirorbis.total")]
42b51a52e308 planemo upload for repository https://github.com/Marie59/champ_blocs commit 0d86db7d42b608c386a54500064f5f9c9d7019a4 ecology parents: diff changeset	374 for (i in c(1:nrow(spirorbis))) {
42b51a52e308 planemo upload for repository https://github.com/Marie59/champ_blocs commit 0d86db7d42b608c386a54500064f5f9c9d7019a4 ecology parents: diff changeset	375 spirorbis$mean.x.200[[i]] <- sum(spirorbis[i, c(2:6)], na.rm = TRUE) / sum(!is.na(spirorbis[i, c(2:6)])) * 200
42b51a52e308 planemo upload for repository https://github.com/Marie59/champ_blocs commit 0d86db7d42b608c386a54500064f5f9c9d7019a4 ecology parents: diff changeset	376 }
42b51a52e308 planemo upload for repository https://github.com/Marie59/champ_blocs commit 0d86db7d42b608c386a54500064f5f9c9d7019a4 ecology parents: diff changeset	377 spirorbis$mean.x.200 <- unlist(spirorbis$mean.x.200)
42b51a52e308 planemo upload for repository https://github.com/Marie59/champ_blocs commit 0d86db7d42b608c386a54500064f5f9c9d7019a4 ecology parents: diff changeset	378 spirorbis$Nb.spirorbis.total <- as.numeric(spirorbis$Nb.spirorbis.total)
42b51a52e308 planemo upload for repository https://github.com/Marie59/champ_blocs commit 0d86db7d42b608c386a54500064f5f9c9d7019a4 ecology parents: diff changeset	379 for (i in c(1:nrow(spirorbis))) {
42b51a52e308 planemo upload for repository https://github.com/Marie59/champ_blocs commit 0d86db7d42b608c386a54500064f5f9c9d7019a4 ecology parents: diff changeset	380 spirorbis$diff[[i]] <- spirorbis[i, "Nb.spirorbis.total"] - spirorbis[i, "mean.x.200"]
42b51a52e308 planemo upload for repository https://github.com/Marie59/champ_blocs commit 0d86db7d42b608c386a54500064f5f9c9d7019a4 ecology parents: diff changeset	381 }
42b51a52e308 planemo upload for repository https://github.com/Marie59/champ_blocs commit 0d86db7d42b608c386a54500064f5f9c9d7019a4 ecology parents: diff changeset	382 spirorbis$diff <- abs(as.integer(spirorbis$diff))
42b51a52e308 planemo upload for repository https://github.com/Marie59/champ_blocs commit 0d86db7d42b608c386a54500064f5f9c9d7019a4 ecology parents: diff changeset	383 spirorbis <- dplyr::arrange(spirorbis, desc(diff), mean.x.200)
42b51a52e308 planemo upload for repository https://github.com/Marie59/champ_blocs commit 0d86db7d42b608c386a54500064f5f9c9d7019a4 ecology parents: diff changeset	384 (gonb_ilotstmichel_2015_04_18 <- dplyr::filter(spirorbis, site_year_month_day == "GONB_IlotStMichel.2015.04.18"))
42b51a52e308 planemo upload for repository https://github.com/Marie59/champ_blocs commit 0d86db7d42b608c386a54500064f5f9c9d7019a4 ecology parents: diff changeset	385 rm(gonb_ilotstmichel_2015_04_18)
42b51a52e308 planemo upload for repository https://github.com/Marie59/champ_blocs commit 0d86db7d42b608c386a54500064f5f9c9d7019a4 ecology parents: diff changeset	386 spirorbis <- dplyr::arrange(dplyr::filter(spirorbis, diff != 0 & mean.x.200 != 0), desc(diff))
42b51a52e308 planemo upload for repository https://github.com/Marie59/champ_blocs commit 0d86db7d42b608c386a54500064f5f9c9d7019a4 ecology parents: diff changeset	387
42b51a52e308 planemo upload for repository https://github.com/Marie59/champ_blocs commit 0d86db7d42b608c386a54500064f5f9c9d7019a4 ecology parents: diff changeset	388 # check it all in the qecbnew df
42b51a52e308 planemo upload for repository https://github.com/Marie59/champ_blocs commit 0d86db7d42b608c386a54500064f5f9c9d7019a4 ecology parents: diff changeset	389
42b51a52e308 planemo upload for repository https://github.com/Marie59/champ_blocs commit 0d86db7d42b608c386a54500064f5f9c9d7019a4 ecology parents: diff changeset	390 for (i in c(1:nrow(qecbnew))) {
42b51a52e308 planemo upload for repository https://github.com/Marie59/champ_blocs commit 0d86db7d42b608c386a54500064f5f9c9d7019a4 ecology parents: diff changeset	391 qecbnew$mean.x.200[[i]] <- sum(qecbnew[i, c("Nb.spirorbis.1A", "Nb.spirorbis.2A", "Nb.spirorbis.3A", "Nb.spirorbis.4A", "Nb.spirorbis.5A")], na.rm = TRUE) / sum(!is.na(qecbnew[i, c("Nb.spirorbis.1A", "Nb.spirorbis.2A", "Nb.spirorbis.3A", "Nb.spirorbis.4A", "Nb.spirorbis.5A")])) * 200
42b51a52e308 planemo upload for repository https://github.com/Marie59/champ_blocs commit 0d86db7d42b608c386a54500064f5f9c9d7019a4 ecology parents: diff changeset	392 } # sum of only NAs/0 = NaN; so replace NaN by Na
42b51a52e308 planemo upload for repository https://github.com/Marie59/champ_blocs commit 0d86db7d42b608c386a54500064f5f9c9d7019a4 ecology parents: diff changeset	393 qecbnew$mean.x.200 <- as.character(qecbnew$mean.x.200)
42b51a52e308 planemo upload for repository https://github.com/Marie59/champ_blocs commit 0d86db7d42b608c386a54500064f5f9c9d7019a4 ecology parents: diff changeset	394
42b51a52e308 planemo upload for repository https://github.com/Marie59/champ_blocs commit 0d86db7d42b608c386a54500064f5f9c9d7019a4 ecology parents: diff changeset	395 for (i in c(1:nrow(qecbnew))) {
42b51a52e308 planemo upload for repository https://github.com/Marie59/champ_blocs commit 0d86db7d42b608c386a54500064f5f9c9d7019a4 ecology parents: diff changeset	396 qecbnew$mean.x.200[[i]] <- ifelse(qecbnew$mean.x.200[[i]] == "NaN", NA, qecbnew$mean.x.200[[i]])
42b51a52e308 planemo upload for repository https://github.com/Marie59/champ_blocs commit 0d86db7d42b608c386a54500064f5f9c9d7019a4 ecology parents: diff changeset	397 }
42b51a52e308 planemo upload for repository https://github.com/Marie59/champ_blocs commit 0d86db7d42b608c386a54500064f5f9c9d7019a4 ecology parents: diff changeset	398
42b51a52e308 planemo upload for repository https://github.com/Marie59/champ_blocs commit 0d86db7d42b608c386a54500064f5f9c9d7019a4 ecology parents: diff changeset	399 qecbnew$mean.x.200 <- as.integer(qecbnew$mean.x.200)
42b51a52e308 planemo upload for repository https://github.com/Marie59/champ_blocs commit 0d86db7d42b608c386a54500064f5f9c9d7019a4 ecology parents: diff changeset	400
42b51a52e308 planemo upload for repository https://github.com/Marie59/champ_blocs commit 0d86db7d42b608c386a54500064f5f9c9d7019a4 ecology parents: diff changeset	401 qecbnew$Nb.spirorbis.total <- as.integer(qecbnew$Nb.spirorbis.total)
42b51a52e308 planemo upload for repository https://github.com/Marie59/champ_blocs commit 0d86db7d42b608c386a54500064f5f9c9d7019a4 ecology parents: diff changeset	402 qecbnew$Nb.spirorbis.total.diff <- abs((qecbnew$Nb.spirorbis.total - qecbnew$mean.x.200))
42b51a52e308 planemo upload for repository https://github.com/Marie59/champ_blocs commit 0d86db7d42b608c386a54500064f5f9c9d7019a4 ecology parents: diff changeset	403 spirorbis_diff <- qecbnew[, c("Nb.spirorbis.1A", "Nb.spirorbis.2A", "Nb.spirorbis.3A", "Nb.spirorbis.4A", "Nb.spirorbis.5A", "Nb.spirorbis.total", "Nb.spirorbis.total.ini", "mean.x.200", "Nb.spirorbis.total.diff")]
42b51a52e308 planemo upload for repository https://github.com/Marie59/champ_blocs commit 0d86db7d42b608c386a54500064f5f9c9d7019a4 ecology parents: diff changeset	404 spirorbis_diff <- dplyr::arrange(spirorbis_diff, desc(Nb.spirorbis.total.diff), mean.x.200)
42b51a52e308 planemo upload for repository https://github.com/Marie59/champ_blocs commit 0d86db7d42b608c386a54500064f5f9c9d7019a4 ecology parents: diff changeset	405 spirorbis_diff <- dplyr::arrange(dplyr::filter(spirorbis_diff, Nb.spirorbis.total.diff != 0 & mean.x.200 != 0), desc(Nb.spirorbis.total.diff))
42b51a52e308 planemo upload for repository https://github.com/Marie59/champ_blocs commit 0d86db7d42b608c386a54500064f5f9c9d7019a4 ecology parents: diff changeset	406
42b51a52e308 planemo upload for repository https://github.com/Marie59/champ_blocs commit 0d86db7d42b608c386a54500064f5f9c9d7019a4 ecology parents: diff changeset	407 qecbnew$Nb.spirorbis.total <- ifelse(qecbnew$Nb.spirorbis.total.diff != 0 & qecbnew$mean.x.200 != 0, qecbnew$mean.x.200, qecbnew$Nb.spirorbis.total)
42b51a52e308 planemo upload for repository https://github.com/Marie59/champ_blocs commit 0d86db7d42b608c386a54500064f5f9c9d7019a4 ecology parents: diff changeset	408 spirorbis_diff <- qecbnew[, c("Nb.spirorbis.1A", "Nb.spirorbis.2A", "Nb.spirorbis.3A", "Nb.spirorbis.4A", "Nb.spirorbis.5A", "Nb.spirorbis.total", "Nb.spirorbis.total.ini", "mean.x.200", "Nb.spirorbis.total.diff")]
42b51a52e308 planemo upload for repository https://github.com/Marie59/champ_blocs commit 0d86db7d42b608c386a54500064f5f9c9d7019a4 ecology parents: diff changeset	409 spirorbis_diff$Nb.spirorbis.total.diff <- abs(as.integer(spirorbis_diff$Nb.spirorbis.total.diff))
42b51a52e308 planemo upload for repository https://github.com/Marie59/champ_blocs commit 0d86db7d42b608c386a54500064f5f9c9d7019a4 ecology parents: diff changeset	410 spirorbis_diff <- dplyr::arrange(spirorbis_diff, desc(Nb.spirorbis.total.diff), mean.x.200)
42b51a52e308 planemo upload for repository https://github.com/Marie59/champ_blocs commit 0d86db7d42b608c386a54500064f5f9c9d7019a4 ecology parents: diff changeset	411 spirorbis_diff <- dplyr::arrange(dplyr::filter(spirorbis_diff, Nb.spirorbis.total.diff != 0 & mean.x.200 != 0), desc(Nb.spirorbis.total.diff))
42b51a52e308 planemo upload for repository https://github.com/Marie59/champ_blocs commit 0d86db7d42b608c386a54500064f5f9c9d7019a4 ecology parents: diff changeset	412 # ok, change made when data x 200 was not correct.
42b51a52e308 planemo upload for repository https://github.com/Marie59/champ_blocs commit 0d86db7d42b608c386a54500064f5f9c9d7019a4 ecology parents: diff changeset	413
42b51a52e308 planemo upload for repository https://github.com/Marie59/champ_blocs commit 0d86db7d42b608c386a54500064f5f9c9d7019a4 ecology parents: diff changeset	414 # finally, change NA by mean.x200 for spirorbis total
42b51a52e308 planemo upload for repository https://github.com/Marie59/champ_blocs commit 0d86db7d42b608c386a54500064f5f9c9d7019a4 ecology parents: diff changeset	415 qecbnew$Nb.spirorbis.total <- as.character(qecbnew$Nb.spirorbis.total)
42b51a52e308 planemo upload for repository https://github.com/Marie59/champ_blocs commit 0d86db7d42b608c386a54500064f5f9c9d7019a4 ecology parents: diff changeset	416 for (i in c(1:nrow(qecbnew))) {
42b51a52e308 planemo upload for repository https://github.com/Marie59/champ_blocs commit 0d86db7d42b608c386a54500064f5f9c9d7019a4 ecology parents: diff changeset	417 qecbnew$Nb.spirorbis.total[[i]] <- ifelse(qecbnew$Nb.spirorbis.total[[i]] %in% c(NA, "NaN", "Inf", "-Inf"), sum(qecbnew[i, c("Nb.spirorbis.1A", "Nb.spirorbis.2A", "Nb.spirorbis.3A", "Nb.spirorbis.4A", "Nb.spirorbis.5A")], na.rm = TRUE) / sum(!is.na(qecbnew[i, c("Nb.spirorbis.1A", "Nb.spirorbis.2A", "Nb.spirorbis.3A", "Nb.spirorbis.4A", "Nb.spirorbis.5A")])) * 200, qecbnew$Nb.spirorbis.total[[i]])
42b51a52e308 planemo upload for repository https://github.com/Marie59/champ_blocs commit 0d86db7d42b608c386a54500064f5f9c9d7019a4 ecology parents: diff changeset	418 } # sum of only NAs/0 = NaN; so replace NaN by Na
42b51a52e308 planemo upload for repository https://github.com/Marie59/champ_blocs commit 0d86db7d42b608c386a54500064f5f9c9d7019a4 ecology parents: diff changeset	419
42b51a52e308 planemo upload for repository https://github.com/Marie59/champ_blocs commit 0d86db7d42b608c386a54500064f5f9c9d7019a4 ecology parents: diff changeset	420 for (i in c(1:nrow(qecbnew))) {
42b51a52e308 planemo upload for repository https://github.com/Marie59/champ_blocs commit 0d86db7d42b608c386a54500064f5f9c9d7019a4 ecology parents: diff changeset	421 qecbnew$Nb.spirorbis.total[[i]] <- ifelse(qecbnew$Nb.spirorbis.total[[i]] == "NaN", NA, qecbnew$Nb.spirorbis.total[[i]])
42b51a52e308 planemo upload for repository https://github.com/Marie59/champ_blocs commit 0d86db7d42b608c386a54500064f5f9c9d7019a4 ecology parents: diff changeset	422 }
42b51a52e308 planemo upload for repository https://github.com/Marie59/champ_blocs commit 0d86db7d42b608c386a54500064f5f9c9d7019a4 ecology parents: diff changeset	423
42b51a52e308 planemo upload for repository https://github.com/Marie59/champ_blocs commit 0d86db7d42b608c386a54500064f5f9c9d7019a4 ecology parents: diff changeset	424 qecbnew$Nb.spirorbis.total <- as.integer(qecbnew$Nb.spirorbis.total)
42b51a52e308 planemo upload for repository https://github.com/Marie59/champ_blocs commit 0d86db7d42b608c386a54500064f5f9c9d7019a4 ecology parents: diff changeset	425
42b51a52e308 planemo upload for repository https://github.com/Marie59/champ_blocs commit 0d86db7d42b608c386a54500064f5f9c9d7019a4 ecology parents: diff changeset	426 qecbnew$Nb.spirorbis.total.diff <- abs(qecbnew$Nb.spirorbis.total - qecbnew$Nb.spirorbis.total.ini)
42b51a52e308 planemo upload for repository https://github.com/Marie59/champ_blocs commit 0d86db7d42b608c386a54500064f5f9c9d7019a4 ecology parents: diff changeset	427 spirorbis_diff <- qecbnew[, c("Nb.spirorbis.1A", "Nb.spirorbis.2A", "Nb.spirorbis.3A", "Nb.spirorbis.4A", "Nb.spirorbis.5A", "Nb.spirorbis.total", "Nb.spirorbis.total.ini", "mean.x.200", "Nb.spirorbis.total.diff")]
42b51a52e308 planemo upload for repository https://github.com/Marie59/champ_blocs commit 0d86db7d42b608c386a54500064f5f9c9d7019a4 ecology parents: diff changeset	428 spirorbis_diff <- dplyr::arrange(spirorbis_diff, desc(Nb.spirorbis.total.diff), mean.x.200)
42b51a52e308 planemo upload for repository https://github.com/Marie59/champ_blocs commit 0d86db7d42b608c386a54500064f5f9c9d7019a4 ecology parents: diff changeset	429 spirorbis_diff <- dplyr::arrange(dplyr::filter(spirorbis_diff, Nb.spirorbis.total.diff != 0 & mean.x.200 != 0), desc(Nb.spirorbis.total.diff))
42b51a52e308 planemo upload for repository https://github.com/Marie59/champ_blocs commit 0d86db7d42b608c386a54500064f5f9c9d7019a4 ecology parents: diff changeset	430
42b51a52e308 planemo upload for repository https://github.com/Marie59/champ_blocs commit 0d86db7d42b608c386a54500064f5f9c9d7019a4 ecology parents: diff changeset	431 qecbnew <- subset(qecbnew, select = -c(Nb.spirorbis.total.ini, mean.x.200, Nb.spirorbis.total.diff))
42b51a52e308 planemo upload for repository https://github.com/Marie59/champ_blocs commit 0d86db7d42b608c386a54500064f5f9c9d7019a4 ecology parents: diff changeset	432
42b51a52e308 planemo upload for repository https://github.com/Marie59/champ_blocs commit 0d86db7d42b608c386a54500064f5f9c9d7019a4 ecology parents: diff changeset	433 rm(qecbnew_spirorbis, spirorbis, spirobranchus_data, spirorbis_diff, i)
42b51a52e308 planemo upload for repository https://github.com/Marie59/champ_blocs commit 0d86db7d42b608c386a54500064f5f9c9d7019a4 ecology parents: diff changeset	434
42b51a52e308 planemo upload for repository https://github.com/Marie59/champ_blocs commit 0d86db7d42b608c386a54500064f5f9c9d7019a4 ecology parents: diff changeset	435
42b51a52e308 planemo upload for repository https://github.com/Marie59/champ_blocs commit 0d86db7d42b608c386a54500064f5f9c9d7019a4 ecology parents: diff changeset	436 # dplyr::filter for abnormal data, based on histogram distribution of data
42b51a52e308 planemo upload for repository https://github.com/Marie59/champ_blocs commit 0d86db7d42b608c386a54500064f5f9c9d7019a4 ecology parents: diff changeset	437
42b51a52e308 planemo upload for repository https://github.com/Marie59/champ_blocs commit 0d86db7d42b608c386a54500064f5f9c9d7019a4 ecology parents: diff changeset	438 dplyr::filter(qecbnew, X..algues.brunes > 100)[, c("Site", "date_fiche", "Type.Bloc", "Numéro.Bloc.échantillon", "Face", "X..algues.brunes")]
42b51a52e308 planemo upload for repository https://github.com/Marie59/champ_blocs commit 0d86db7d42b608c386a54500064f5f9c9d7019a4 ecology parents: diff changeset	439 qecbnew$X..algues.brunes <- ifelse(qecbnew$X..algues.brunes > 100, 100, qecbnew$X..algues.brunes)
42b51a52e308 planemo upload for repository https://github.com/Marie59/champ_blocs commit 0d86db7d42b608c386a54500064f5f9c9d7019a4 ecology parents: diff changeset	440 dplyr::filter(qecbnew, X..algues.rouges > 100)[, c("Site", "date_fiche", "Type.Bloc", "Numéro.Bloc.échantillon", "Face", "X..algues.rouges")]
42b51a52e308 planemo upload for repository https://github.com/Marie59/champ_blocs commit 0d86db7d42b608c386a54500064f5f9c9d7019a4 ecology parents: diff changeset	441 qecbnew$X..algues.rouges <- ifelse(qecbnew$X..algues.rouges > 100, 100, qecbnew$X..algues.rouges)
42b51a52e308 planemo upload for repository https://github.com/Marie59/champ_blocs commit 0d86db7d42b608c386a54500064f5f9c9d7019a4 ecology parents: diff changeset	442
42b51a52e308 planemo upload for repository https://github.com/Marie59/champ_blocs commit 0d86db7d42b608c386a54500064f5f9c9d7019a4 ecology parents: diff changeset	443
42b51a52e308 planemo upload for repository https://github.com/Marie59/champ_blocs commit 0d86db7d42b608c386a54500064f5f9c9d7019a4 ecology parents: diff changeset	444 ## SCRIPT I - NAs <- 0 ; cfr previous comment makes no sense to have NA encoded when the presence of an organism is in reality = 0
42b51a52e308 planemo upload for repository https://github.com/Marie59/champ_blocs commit 0d86db7d42b608c386a54500064f5f9c9d7019a4 ecology parents: diff changeset	445
42b51a52e308 planemo upload for repository https://github.com/Marie59/champ_blocs commit 0d86db7d42b608c386a54500064f5f9c9d7019a4 ecology parents: diff changeset	446 # We are facing an issues with NA observations, because either they were not measured/counted, then they are effectively NAs; or these NAs = indeed "0"; but I cannot have NAs for variables that are included in the index determination, cfr if 5+0 = 5, 5+NA = NA; see for example site_year_month_day == "ARMO_Bilfot.2014.04.28", Nb.Spirobranchus.lamarckii.total is NA ...
42b51a52e308 planemo upload for repository https://github.com/Marie59/champ_blocs commit 0d86db7d42b608c386a54500064f5f9c9d7019a4 ecology parents: diff changeset	447 # I theregore change these NAs by 0
42b51a52e308 planemo upload for repository https://github.com/Marie59/champ_blocs commit 0d86db7d42b608c386a54500064f5f9c9d7019a4 ecology parents: diff changeset	448
42b51a52e308 planemo upload for repository https://github.com/Marie59/champ_blocs commit 0d86db7d42b608c386a54500064f5f9c9d7019a4 ecology parents: diff changeset	449 # replace NAs by "0" for variables used in qecb determination
42b51a52e308 planemo upload for repository https://github.com/Marie59/champ_blocs commit 0d86db7d42b608c386a54500064f5f9c9d7019a4 ecology parents: diff changeset	450 qecbnew[, c("X..algues.brunes",
42b51a52e308 planemo upload for repository https://github.com/Marie59/champ_blocs commit 0d86db7d42b608c386a54500064f5f9c9d7019a4 ecology parents: diff changeset	451 "X..algues.rouges",
42b51a52e308 planemo upload for repository https://github.com/Marie59/champ_blocs commit 0d86db7d42b608c386a54500064f5f9c9d7019a4 ecology parents: diff changeset	452 "X..Lithophyllum",
42b51a52e308 planemo upload for repository https://github.com/Marie59/champ_blocs commit 0d86db7d42b608c386a54500064f5f9c9d7019a4 ecology parents: diff changeset	453 "X..Cladophora",
42b51a52e308 planemo upload for repository https://github.com/Marie59/champ_blocs commit 0d86db7d42b608c386a54500064f5f9c9d7019a4 ecology parents: diff changeset	454 "Nb.Littorina.obtusata",
42b51a52e308 planemo upload for repository https://github.com/Marie59/champ_blocs commit 0d86db7d42b608c386a54500064f5f9c9d7019a4 ecology parents: diff changeset	455 "Nb.Gibbula.cineraria",
42b51a52e308 planemo upload for repository https://github.com/Marie59/champ_blocs commit 0d86db7d42b608c386a54500064f5f9c9d7019a4 ecology parents: diff changeset	456 "Nb.Gibbula.pennanti",
42b51a52e308 planemo upload for repository https://github.com/Marie59/champ_blocs commit 0d86db7d42b608c386a54500064f5f9c9d7019a4 ecology parents: diff changeset	457 "Nb.Gibbula.umbilicalis",
42b51a52e308 planemo upload for repository https://github.com/Marie59/champ_blocs commit 0d86db7d42b608c386a54500064f5f9c9d7019a4 ecology parents: diff changeset	458 "X..Eponges",
42b51a52e308 planemo upload for repository https://github.com/Marie59/champ_blocs commit 0d86db7d42b608c386a54500064f5f9c9d7019a4 ecology parents: diff changeset	459 "X..Ascidies.Coloniales",
42b51a52e308 planemo upload for repository https://github.com/Marie59/champ_blocs commit 0d86db7d42b608c386a54500064f5f9c9d7019a4 ecology parents: diff changeset	460 "X..Ascidies.Solitaires",
42b51a52e308 planemo upload for repository https://github.com/Marie59/champ_blocs commit 0d86db7d42b608c386a54500064f5f9c9d7019a4 ecology parents: diff changeset	461 "X..Bryozoaires.Dresses",
42b51a52e308 planemo upload for repository https://github.com/Marie59/champ_blocs commit 0d86db7d42b608c386a54500064f5f9c9d7019a4 ecology parents: diff changeset	462 "X..algues.vertes",
42b51a52e308 planemo upload for repository https://github.com/Marie59/champ_blocs commit 0d86db7d42b608c386a54500064f5f9c9d7019a4 ecology parents: diff changeset	463 "X..Roche.Nue",
42b51a52e308 planemo upload for repository https://github.com/Marie59/champ_blocs commit 0d86db7d42b608c386a54500064f5f9c9d7019a4 ecology parents: diff changeset	464 "Nb.spirorbis.total",
42b51a52e308 planemo upload for repository https://github.com/Marie59/champ_blocs commit 0d86db7d42b608c386a54500064f5f9c9d7019a4 ecology parents: diff changeset	465 "X..Balanes.Vivantes",
42b51a52e308 planemo upload for repository https://github.com/Marie59/champ_blocs commit 0d86db7d42b608c386a54500064f5f9c9d7019a4 ecology parents: diff changeset	466 "Nb.Spirobranchus.lamarckii.total",
42b51a52e308 planemo upload for repository https://github.com/Marie59/champ_blocs commit 0d86db7d42b608c386a54500064f5f9c9d7019a4 ecology parents: diff changeset	467 "X..Surface.Accolement")] <- lapply(qecbnew[,
42b51a52e308 planemo upload for repository https://github.com/Marie59/champ_blocs commit 0d86db7d42b608c386a54500064f5f9c9d7019a4 ecology parents: diff changeset	468 c("X..algues.brunes",
42b51a52e308 planemo upload for repository https://github.com/Marie59/champ_blocs commit 0d86db7d42b608c386a54500064f5f9c9d7019a4 ecology parents: diff changeset	469 "X..algues.rouges",
42b51a52e308 planemo upload for repository https://github.com/Marie59/champ_blocs commit 0d86db7d42b608c386a54500064f5f9c9d7019a4 ecology parents: diff changeset	470 "X..Lithophyllum",
42b51a52e308 planemo upload for repository https://github.com/Marie59/champ_blocs commit 0d86db7d42b608c386a54500064f5f9c9d7019a4 ecology parents: diff changeset	471 "X..Cladophora",
42b51a52e308 planemo upload for repository https://github.com/Marie59/champ_blocs commit 0d86db7d42b608c386a54500064f5f9c9d7019a4 ecology parents: diff changeset	472 "Nb.Littorina.obtusata",
42b51a52e308 planemo upload for repository https://github.com/Marie59/champ_blocs commit 0d86db7d42b608c386a54500064f5f9c9d7019a4 ecology parents: diff changeset	473 "Nb.Gibbula.cineraria",
42b51a52e308 planemo upload for repository https://github.com/Marie59/champ_blocs commit 0d86db7d42b608c386a54500064f5f9c9d7019a4 ecology parents: diff changeset	474 "Nb.Gibbula.pennanti",
42b51a52e308 planemo upload for repository https://github.com/Marie59/champ_blocs commit 0d86db7d42b608c386a54500064f5f9c9d7019a4 ecology parents: diff changeset	475 "Nb.Gibbula.umbilicalis",
42b51a52e308 planemo upload for repository https://github.com/Marie59/champ_blocs commit 0d86db7d42b608c386a54500064f5f9c9d7019a4 ecology parents: diff changeset	476 "X..Eponges",
42b51a52e308 planemo upload for repository https://github.com/Marie59/champ_blocs commit 0d86db7d42b608c386a54500064f5f9c9d7019a4 ecology parents: diff changeset	477 "X..Ascidies.Coloniales",
42b51a52e308 planemo upload for repository https://github.com/Marie59/champ_blocs commit 0d86db7d42b608c386a54500064f5f9c9d7019a4 ecology parents: diff changeset	478 "X..Ascidies.Solitaires",
42b51a52e308 planemo upload for repository https://github.com/Marie59/champ_blocs commit 0d86db7d42b608c386a54500064f5f9c9d7019a4 ecology parents: diff changeset	479 "X..Bryozoaires.Dresses",
42b51a52e308 planemo upload for repository https://github.com/Marie59/champ_blocs commit 0d86db7d42b608c386a54500064f5f9c9d7019a4 ecology parents: diff changeset	480 "X..algues.vertes",
42b51a52e308 planemo upload for repository https://github.com/Marie59/champ_blocs commit 0d86db7d42b608c386a54500064f5f9c9d7019a4 ecology parents: diff changeset	481 "X..Roche.Nue",
42b51a52e308 planemo upload for repository https://github.com/Marie59/champ_blocs commit 0d86db7d42b608c386a54500064f5f9c9d7019a4 ecology parents: diff changeset	482 "Nb.spirorbis.total",
42b51a52e308 planemo upload for repository https://github.com/Marie59/champ_blocs commit 0d86db7d42b608c386a54500064f5f9c9d7019a4 ecology parents: diff changeset	483 "X..Balanes.Vivantes",
42b51a52e308 planemo upload for repository https://github.com/Marie59/champ_blocs commit 0d86db7d42b608c386a54500064f5f9c9d7019a4 ecology parents: diff changeset	484 "Nb.Spirobranchus.lamarckii.total",
42b51a52e308 planemo upload for repository https://github.com/Marie59/champ_blocs commit 0d86db7d42b608c386a54500064f5f9c9d7019a4 ecology parents: diff changeset	485 "X..Surface.Accolement")],
42b51a52e308 planemo upload for repository https://github.com/Marie59/champ_blocs commit 0d86db7d42b608c386a54500064f5f9c9d7019a4 ecology parents: diff changeset	486 function(x) replace(x, is.na(x), 0))
42b51a52e308 planemo upload for repository https://github.com/Marie59/champ_blocs commit 0d86db7d42b608c386a54500064f5f9c9d7019a4 ecology parents: diff changeset	487
42b51a52e308 planemo upload for repository https://github.com/Marie59/champ_blocs commit 0d86db7d42b608c386a54500064f5f9c9d7019a4 ecology parents: diff changeset	488 # and also replace NA for bivalve by 0 for EGMP and BASQ surveys cfr for accollement correction later on.
42b51a52e308 planemo upload for repository https://github.com/Marie59/champ_blocs commit 0d86db7d42b608c386a54500064f5f9c9d7019a4 ecology parents: diff changeset	489
42b51a52e308 planemo upload for repository https://github.com/Marie59/champ_blocs commit 0d86db7d42b608c386a54500064f5f9c9d7019a4 ecology parents: diff changeset	490 qecbnew$X..Mytilus.sp. <- ifelse((substr(qecbnew$Site, 1, 4) %in% c("EGMP", "BASQ")) & is.na(qecbnew$X..Mytilus.sp.), 0, qecbnew$X..Mytilus.sp.)
42b51a52e308 planemo upload for repository https://github.com/Marie59/champ_blocs commit 0d86db7d42b608c386a54500064f5f9c9d7019a4 ecology parents: diff changeset	491 qecbnew$Nb.Crassostrea.gigas <- ifelse((substr(qecbnew$Site, 1, 4) %in% c("EGMP", "BASQ")) & is.na(qecbnew$Nb.Crassostrea.gigas), 0, qecbnew$Nb.Crassostrea.gigas)
42b51a52e308 planemo upload for repository https://github.com/Marie59/champ_blocs commit 0d86db7d42b608c386a54500064f5f9c9d7019a4 ecology parents: diff changeset	492 qecbnew$Nb.Ostrea.edulis <- ifelse((substr(qecbnew$Site, 1, 4) %in% c("EGMP", "BASQ")) & is.na(qecbnew$Nb.Ostrea.edulis), 0, qecbnew$Nb.Ostrea.edulis)
42b51a52e308 planemo upload for repository https://github.com/Marie59/champ_blocs commit 0d86db7d42b608c386a54500064f5f9c9d7019a4 ecology parents: diff changeset	493
42b51a52e308 planemo upload for repository https://github.com/Marie59/champ_blocs commit 0d86db7d42b608c386a54500064f5f9c9d7019a4 ecology parents: diff changeset	494
42b51a52e308 planemo upload for repository https://github.com/Marie59/champ_blocs commit 0d86db7d42b608c386a54500064f5f9c9d7019a4 ecology parents: diff changeset	495 # add a region variable
42b51a52e308 planemo upload for repository https://github.com/Marie59/champ_blocs commit 0d86db7d42b608c386a54500064f5f9c9d7019a4 ecology parents: diff changeset	496 region <- rep(NA, nrow(qecbnew))
42b51a52e308 planemo upload for repository https://github.com/Marie59/champ_blocs commit 0d86db7d42b608c386a54500064f5f9c9d7019a4 ecology parents: diff changeset	497 qecbnew <- tibble::add_column(qecbnew, region, .after = "Site_bis")
42b51a52e308 planemo upload for repository https://github.com/Marie59/champ_blocs commit 0d86db7d42b608c386a54500064f5f9c9d7019a4 ecology parents: diff changeset	498 qecbnew$region <- ifelse(qecbnew$Site %in% c("EGMP_GroinCou", "EGMP_PasEmsembert", "EGMP_BreeBains", "EGMP_PerreAntiochat", "EGMP_Chassiron", "BASQ_FlotsBleusZP", "BASQ_FlotsBleusZF"), "EGMP.BASQ", "Bretagne")
42b51a52e308 planemo upload for repository https://github.com/Marie59/champ_blocs commit 0d86db7d42b608c386a54500064f5f9c9d7019a4 ecology parents: diff changeset	499 rm(region)
42b51a52e308 planemo upload for repository https://github.com/Marie59/champ_blocs commit 0d86db7d42b608c386a54500064f5f9c9d7019a4 ecology parents: diff changeset	500 qecbnew <- dplyr::arrange(qecbnew, region, site_year_month_day, Type.Bloc, Numéro.Bloc.échantillon, Face)
42b51a52e308 planemo upload for repository https://github.com/Marie59/champ_blocs commit 0d86db7d42b608c386a54500064f5f9c9d7019a4 ecology parents: diff changeset	501
42b51a52e308 planemo upload for repository https://github.com/Marie59/champ_blocs commit 0d86db7d42b608c386a54500064f5f9c9d7019a4 ecology parents: diff changeset	502 # accolement function according to recent 'retournement'
42b51a52e308 planemo upload for repository https://github.com/Marie59/champ_blocs commit 0d86db7d42b608c386a54500064f5f9c9d7019a4 ecology parents: diff changeset	503
42b51a52e308 planemo upload for repository https://github.com/Marie59/champ_blocs commit 0d86db7d42b608c386a54500064f5f9c9d7019a4 ecology parents: diff changeset	504 ## before I go further ahead, I have to correct for surface d'accollement for several variable for BM.FI !!
42b51a52e308 planemo upload for repository https://github.com/Marie59/champ_blocs commit 0d86db7d42b608c386a54500064f5f9c9d7019a4 ecology parents: diff changeset	505
42b51a52e308 planemo upload for repository https://github.com/Marie59/champ_blocs commit 0d86db7d42b608c386a54500064f5f9c9d7019a4 ecology parents: diff changeset	506 # not the same file name between script qecb script (qecbNew) and this script (qecbNew); doesn't matter, only appears here in the first dplyr::filter lines.
42b51a52e308 planemo upload for repository https://github.com/Marie59/champ_blocs commit 0d86db7d42b608c386a54500064f5f9c9d7019a4 ecology parents: diff changeset	507
42b51a52e308 planemo upload for repository https://github.com/Marie59/champ_blocs commit 0d86db7d42b608c386a54500064f5f9c9d7019a4 ecology parents: diff changeset	508 qecbnew <- tibble::add_column(qecbnew, terri_ = substr(qecbnew$Site, 1, 4), .after = "Site_bis")
42b51a52e308 planemo upload for repository https://github.com/Marie59/champ_blocs commit 0d86db7d42b608c386a54500064f5f9c9d7019a4 ecology parents: diff changeset	509
42b51a52e308 planemo upload for repository https://github.com/Marie59/champ_blocs commit 0d86db7d42b608c386a54500064f5f9c9d7019a4 ecology parents: diff changeset	510 qecbnew$X..Eponges_ini <- qecbnew$X..Eponges
42b51a52e308 planemo upload for repository https://github.com/Marie59/champ_blocs commit 0d86db7d42b608c386a54500064f5f9c9d7019a4 ecology parents: diff changeset	511 qecbnew$X..Ascidies.Coloniales_ini <- qecbnew$X..Ascidies.Coloniales
42b51a52e308 planemo upload for repository https://github.com/Marie59/champ_blocs commit 0d86db7d42b608c386a54500064f5f9c9d7019a4 ecology parents: diff changeset	512 qecbnew$X..Ascidies.Solitaires_ini <- qecbnew$X..Ascidies.Solitaires
42b51a52e308 planemo upload for repository https://github.com/Marie59/champ_blocs commit 0d86db7d42b608c386a54500064f5f9c9d7019a4 ecology parents: diff changeset	513 qecbnew$X..Bryozoaires.Dresses_ini <- qecbnew$X..Bryozoaires.Dresses
42b51a52e308 planemo upload for repository https://github.com/Marie59/champ_blocs commit 0d86db7d42b608c386a54500064f5f9c9d7019a4 ecology parents: diff changeset	514 qecbnew$X..Lithophyllum_ini <- qecbnew$X..Lithophyllum
42b51a52e308 planemo upload for repository https://github.com/Marie59/champ_blocs commit 0d86db7d42b608c386a54500064f5f9c9d7019a4 ecology parents: diff changeset	515 qecbnew$X..Balanes.Vivantes_ini <- qecbnew$X..Balanes.Vivantes
42b51a52e308 planemo upload for repository https://github.com/Marie59/champ_blocs commit 0d86db7d42b608c386a54500064f5f9c9d7019a4 ecology parents: diff changeset	516
42b51a52e308 planemo upload for repository https://github.com/Marie59/champ_blocs commit 0d86db7d42b608c386a54500064f5f9c9d7019a4 ecology parents: diff changeset	517 df_bm_fs <- qecbnew %>% dplyr::filter(Type.Bloc == "Bloc mobile" & Face == "face supérieure")
42b51a52e308 planemo upload for repository https://github.com/Marie59/champ_blocs commit 0d86db7d42b608c386a54500064f5f9c9d7019a4 ecology parents: diff changeset	518 df_bm_fi <- qecbnew %>% dplyr::filter(Type.Bloc == "Bloc mobile" & Face == "face inférieure")
42b51a52e308 planemo upload for repository https://github.com/Marie59/champ_blocs commit 0d86db7d42b608c386a54500064f5f9c9d7019a4 ecology parents: diff changeset	519 df_bf <- qecbnew %>% dplyr::filter(Type.Bloc != "Bloc mobile")
42b51a52e308 planemo upload for repository https://github.com/Marie59/champ_blocs commit 0d86db7d42b608c386a54500064f5f9c9d7019a4 ecology parents: diff changeset	520
42b51a52e308 planemo upload for repository https://github.com/Marie59/champ_blocs commit 0d86db7d42b608c386a54500064f5f9c9d7019a4 ecology parents: diff changeset	521 `%notin%` <- Negate(`%in%`)
42b51a52e308 planemo upload for repository https://github.com/Marie59/champ_blocs commit 0d86db7d42b608c386a54500064f5f9c9d7019a4 ecology parents: diff changeset	522
42b51a52e308 planemo upload for repository https://github.com/Marie59/champ_blocs commit 0d86db7d42b608c386a54500064f5f9c9d7019a4 ecology parents: diff changeset	523 acco_fct <- function(var_) {
42b51a52e308 planemo upload for repository https://github.com/Marie59/champ_blocs commit 0d86db7d42b608c386a54500064f5f9c9d7019a4 ecology parents: diff changeset	524
42b51a52e308 planemo upload for repository https://github.com/Marie59/champ_blocs commit 0d86db7d42b608c386a54500064f5f9c9d7019a4 ecology parents: diff changeset	525 df_bm_fi$var_cor.acco. <<- NA
42b51a52e308 planemo upload for repository https://github.com/Marie59/champ_blocs commit 0d86db7d42b608c386a54500064f5f9c9d7019a4 ecology parents: diff changeset	526
42b51a52e308 planemo upload for repository https://github.com/Marie59/champ_blocs commit 0d86db7d42b608c386a54500064f5f9c9d7019a4 ecology parents: diff changeset	527 for (i in c(1:nrow(df_bm_fi))) {
42b51a52e308 planemo upload for repository https://github.com/Marie59/champ_blocs commit 0d86db7d42b608c386a54500064f5f9c9d7019a4 ecology parents: diff changeset	528
42b51a52e308 planemo upload for repository https://github.com/Marie59/champ_blocs commit 0d86db7d42b608c386a54500064f5f9c9d7019a4 ecology parents: diff changeset	529 df_bm_fi$var_cor.acco.[[i]] <<- if (df_bm_fi$terri_[[i]] %notin% c("EGMP", "BASQ")) {
42b51a52e308 planemo upload for repository https://github.com/Marie59/champ_blocs commit 0d86db7d42b608c386a54500064f5f9c9d7019a4 ecology parents: diff changeset	530 ifelse(#df_$Couleur.dominante %in% c("Rouge", "Brune", "Brune-Rouge") \|\|
42b51a52e308 planemo upload for repository https://github.com/Marie59/champ_blocs commit 0d86db7d42b608c386a54500064f5f9c9d7019a4 ecology parents: diff changeset	531 df_bm_fs$Couleur.dominante[[i]] %in% c("Blanche", "Verte", "Blanche-Verte", "Colorée"), df_bm_fi[i, var_] / (100 - df_bm_fi$X..Surface.Accolement[[i]]) * 100, df_bm_fi[i, var_])
42b51a52e308 planemo upload for repository https://github.com/Marie59/champ_blocs commit 0d86db7d42b608c386a54500064f5f9c9d7019a4 ecology parents: diff changeset	532 } else {
42b51a52e308 planemo upload for repository https://github.com/Marie59/champ_blocs commit 0d86db7d42b608c386a54500064f5f9c9d7019a4 ecology parents: diff changeset	533 ifelse(df_bm_fs$Couleur.dominante[[i]] %in% c("Blanche", "Verte", "Blanche-Verte", "Colorée")
42b51a52e308 planemo upload for repository https://github.com/Marie59/champ_blocs commit 0d86db7d42b608c386a54500064f5f9c9d7019a4 ecology parents: diff changeset	534 & df_bm_fi$X..Surface.Accolement[[i]] != 0 # I have to use it in dplyr::filter this time as well for EGMP- BASQ (but not for Bretagne, although could be added, same result); identical/repeated measure for BM.FI and BM.FS
42b51a52e308 planemo upload for repository https://github.com/Marie59/champ_blocs commit 0d86db7d42b608c386a54500064f5f9c9d7019a4 ecology parents: diff changeset	535 & df_bm_fs$X..Mytilus.sp.[[i]] == 0, df_bm_fi[i, var_] / (100 - df_bm_fi$X..Surface.Accolement[[i]]) * 100, df_bm_fi[i, var_])
42b51a52e308 planemo upload for repository https://github.com/Marie59/champ_blocs commit 0d86db7d42b608c386a54500064f5f9c9d7019a4 ecology parents: diff changeset	536 }
42b51a52e308 planemo upload for repository https://github.com/Marie59/champ_blocs commit 0d86db7d42b608c386a54500064f5f9c9d7019a4 ecology parents: diff changeset	537
42b51a52e308 planemo upload for repository https://github.com/Marie59/champ_blocs commit 0d86db7d42b608c386a54500064f5f9c9d7019a4 ecology parents: diff changeset	538 }
42b51a52e308 planemo upload for repository https://github.com/Marie59/champ_blocs commit 0d86db7d42b608c386a54500064f5f9c9d7019a4 ecology parents: diff changeset	539
42b51a52e308 planemo upload for repository https://github.com/Marie59/champ_blocs commit 0d86db7d42b608c386a54500064f5f9c9d7019a4 ecology parents: diff changeset	540 }
42b51a52e308 planemo upload for repository https://github.com/Marie59/champ_blocs commit 0d86db7d42b608c386a54500064f5f9c9d7019a4 ecology parents: diff changeset	541
42b51a52e308 planemo upload for repository https://github.com/Marie59/champ_blocs commit 0d86db7d42b608c386a54500064f5f9c9d7019a4 ecology parents: diff changeset	542 # I would only consider colors in c("Rouge", "Brune", "Brune-Rouge") for BM.FI correction [ and not the series c("Blanche-Brune", "Rouge", "Brune", "Blanche-Rouge", "Brune-Rouge", "Rouge-Verte", "Brune-Verte") ] ; and for BM.FS, the list c("Blanche", "Verte", "Colorée") => we do the correction for BM.FI accollement based on BM.FS color !!!
42b51a52e308 planemo upload for repository https://github.com/Marie59/champ_blocs commit 0d86db7d42b608c386a54500064f5f9c9d7019a4 ecology parents: diff changeset	543
42b51a52e308 planemo upload for repository https://github.com/Marie59/champ_blocs commit 0d86db7d42b608c386a54500064f5f9c9d7019a4 ecology parents: diff changeset	544
42b51a52e308 planemo upload for repository https://github.com/Marie59/champ_blocs commit 0d86db7d42b608c386a54500064f5f9c9d7019a4 ecology parents: diff changeset	545 # apply acco_fct to BM.FI variables
42b51a52e308 planemo upload for repository https://github.com/Marie59/champ_blocs commit 0d86db7d42b608c386a54500064f5f9c9d7019a4 ecology parents: diff changeset	546
42b51a52e308 planemo upload for repository https://github.com/Marie59/champ_blocs commit 0d86db7d42b608c386a54500064f5f9c9d7019a4 ecology parents: diff changeset	547 apply_acco_fct <- function(var_) {
42b51a52e308 planemo upload for repository https://github.com/Marie59/champ_blocs commit 0d86db7d42b608c386a54500064f5f9c9d7019a4 ecology parents: diff changeset	548
42b51a52e308 planemo upload for repository https://github.com/Marie59/champ_blocs commit 0d86db7d42b608c386a54500064f5f9c9d7019a4 ecology parents: diff changeset	549 show(sort(df_bm_fi[, var_], decreasing = TRUE, index.return = FALSE)[1:50])
42b51a52e308 planemo upload for repository https://github.com/Marie59/champ_blocs commit 0d86db7d42b608c386a54500064f5f9c9d7019a4 ecology parents: diff changeset	550 pre_ <- as.vector(df_bm_fi[, var_])
42b51a52e308 planemo upload for repository https://github.com/Marie59/champ_blocs commit 0d86db7d42b608c386a54500064f5f9c9d7019a4 ecology parents: diff changeset	551 acco_fct(var_)
42b51a52e308 planemo upload for repository https://github.com/Marie59/champ_blocs commit 0d86db7d42b608c386a54500064f5f9c9d7019a4 ecology parents: diff changeset	552 df_bm_fi <<- tibble::add_column(df_bm_fi, var_cor. = df_bm_fi$var_cor.acco., .after = var_)
42b51a52e308 planemo upload for repository https://github.com/Marie59/champ_blocs commit 0d86db7d42b608c386a54500064f5f9c9d7019a4 ecology parents: diff changeset	553 show(sort(df_bm_fi$var_cor., decreasing = TRUE, index.return = FALSE)[1:50])
42b51a52e308 planemo upload for repository https://github.com/Marie59/champ_blocs commit 0d86db7d42b608c386a54500064f5f9c9d7019a4 ecology parents: diff changeset	554 df_bm_fi$var_cor. <<- as.numeric(ifelse(as.character(df_bm_fi$var_cor.) %in% c(NA, "NaN", "-Inf", "Inf"), "0", as.character(df_bm_fi$var_cor.)))
42b51a52e308 planemo upload for repository https://github.com/Marie59/champ_blocs commit 0d86db7d42b608c386a54500064f5f9c9d7019a4 ecology parents: diff changeset	555 df_bm_fi$var_cor. <<- ifelse(df_bm_fi$var_cor. > 100, 100, df_bm_fi$var_cor.)
42b51a52e308 planemo upload for repository https://github.com/Marie59/champ_blocs commit 0d86db7d42b608c386a54500064f5f9c9d7019a4 ecology parents: diff changeset	556 show(sort(df_bm_fi$var_cor., decreasing = TRUE, index.return = FALSE)[1:50])
42b51a52e308 planemo upload for repository https://github.com/Marie59/champ_blocs commit 0d86db7d42b608c386a54500064f5f9c9d7019a4 ecology parents: diff changeset	557 show(length(na.omit(which(abs(as.vector(df_bm_fi$var_cor.) - pre_) != 0))) / na.omit(length(df_bm_fi$var_cor.)) * 100)
42b51a52e308 planemo upload for repository https://github.com/Marie59/champ_blocs commit 0d86db7d42b608c386a54500064f5f9c9d7019a4 ecology parents: diff changeset	558 par(mfrow = c(1, 3))
42b51a52e308 planemo upload for repository https://github.com/Marie59/champ_blocs commit 0d86db7d42b608c386a54500064f5f9c9d7019a4 ecology parents: diff changeset	559 hist(pre_, main = var_, xlab = "pre-corection")
42b51a52e308 planemo upload for repository https://github.com/Marie59/champ_blocs commit 0d86db7d42b608c386a54500064f5f9c9d7019a4 ecology parents: diff changeset	560 hist(df_bm_fi$var_cor., main = var_, xlab = "post-corection")
42b51a52e308 planemo upload for repository https://github.com/Marie59/champ_blocs commit 0d86db7d42b608c386a54500064f5f9c9d7019a4 ecology parents: diff changeset	561 hist(df_bm_fi[as.vector(which(abs(as.vector(df_bm_fi$var_cor.) - pre_) != 0)), var_], main = var_, xlab = "diff. post-pre != 0")
42b51a52e308 planemo upload for repository https://github.com/Marie59/champ_blocs commit 0d86db7d42b608c386a54500064f5f9c9d7019a4 ecology parents: diff changeset	562 par(mfrow = c(1, 1))
42b51a52e308 planemo upload for repository https://github.com/Marie59/champ_blocs commit 0d86db7d42b608c386a54500064f5f9c9d7019a4 ecology parents: diff changeset	563 df_bm_fi <<- df_bm_fi[, -which(names(df_bm_fi) %in% c(var_, "var_cor.acco."))]
42b51a52e308 planemo upload for repository https://github.com/Marie59/champ_blocs commit 0d86db7d42b608c386a54500064f5f9c9d7019a4 ecology parents: diff changeset	564 colnames(df_bm_fi)[colnames(df_bm_fi) == "var_cor."] <<- var_
42b51a52e308 planemo upload for repository https://github.com/Marie59/champ_blocs commit 0d86db7d42b608c386a54500064f5f9c9d7019a4 ecology parents: diff changeset	565
42b51a52e308 planemo upload for repository https://github.com/Marie59/champ_blocs commit 0d86db7d42b608c386a54500064f5f9c9d7019a4 ecology parents: diff changeset	566 rm(pre_)
42b51a52e308 planemo upload for repository https://github.com/Marie59/champ_blocs commit 0d86db7d42b608c386a54500064f5f9c9d7019a4 ecology parents: diff changeset	567
42b51a52e308 planemo upload for repository https://github.com/Marie59/champ_blocs commit 0d86db7d42b608c386a54500064f5f9c9d7019a4 ecology parents: diff changeset	568 }
42b51a52e308 planemo upload for repository https://github.com/Marie59/champ_blocs commit 0d86db7d42b608c386a54500064f5f9c9d7019a4 ecology parents: diff changeset	569
42b51a52e308 planemo upload for repository https://github.com/Marie59/champ_blocs commit 0d86db7d42b608c386a54500064f5f9c9d7019a4 ecology parents: diff changeset	570 apply_acco_fct("X..Eponges")
42b51a52e308 planemo upload for repository https://github.com/Marie59/champ_blocs commit 0d86db7d42b608c386a54500064f5f9c9d7019a4 ecology parents: diff changeset	571 apply_acco_fct("X..Ascidies.Coloniales")
42b51a52e308 planemo upload for repository https://github.com/Marie59/champ_blocs commit 0d86db7d42b608c386a54500064f5f9c9d7019a4 ecology parents: diff changeset	572 apply_acco_fct("X..Ascidies.Solitaires")
42b51a52e308 planemo upload for repository https://github.com/Marie59/champ_blocs commit 0d86db7d42b608c386a54500064f5f9c9d7019a4 ecology parents: diff changeset	573 apply_acco_fct("X..Bryozoaires.Dresses")
42b51a52e308 planemo upload for repository https://github.com/Marie59/champ_blocs commit 0d86db7d42b608c386a54500064f5f9c9d7019a4 ecology parents: diff changeset	574 apply_acco_fct("X..Lithophyllum")
42b51a52e308 planemo upload for repository https://github.com/Marie59/champ_blocs commit 0d86db7d42b608c386a54500064f5f9c9d7019a4 ecology parents: diff changeset	575 apply_acco_fct("X..Balanes.Vivantes")
42b51a52e308 planemo upload for repository https://github.com/Marie59/champ_blocs commit 0d86db7d42b608c386a54500064f5f9c9d7019a4 ecology parents: diff changeset	576
42b51a52e308 planemo upload for repository https://github.com/Marie59/champ_blocs commit 0d86db7d42b608c386a54500064f5f9c9d7019a4 ecology parents: diff changeset	577 qecbnew <- dplyr::bind_rows(df_bm_fs, df_bm_fi)
42b51a52e308 planemo upload for repository https://github.com/Marie59/champ_blocs commit 0d86db7d42b608c386a54500064f5f9c9d7019a4 ecology parents: diff changeset	578 qecbnew <- dplyr::bind_rows(qecbnew, df_bf)
42b51a52e308 planemo upload for repository https://github.com/Marie59/champ_blocs commit 0d86db7d42b608c386a54500064f5f9c9d7019a4 ecology parents: diff changeset	579
42b51a52e308 planemo upload for repository https://github.com/Marie59/champ_blocs commit 0d86db7d42b608c386a54500064f5f9c9d7019a4 ecology parents: diff changeset	580 qecbnew <- dplyr::arrange(qecbnew, region, site_year_month_day, Type.Bloc, Numéro.Bloc.échantillon, Face)
42b51a52e308 planemo upload for repository https://github.com/Marie59/champ_blocs commit 0d86db7d42b608c386a54500064f5f9c9d7019a4 ecology parents: diff changeset	581
42b51a52e308 planemo upload for repository https://github.com/Marie59/champ_blocs commit 0d86db7d42b608c386a54500064f5f9c9d7019a4 ecology parents: diff changeset	582 # do remove some more data ...
42b51a52e308 planemo upload for repository https://github.com/Marie59/champ_blocs commit 0d86db7d42b608c386a54500064f5f9c9d7019a4 ecology parents: diff changeset	583 # "FINS_Quemenes.2020.10.16", bad encoding, I let know Anna Capietto to make changes => was corrected normally, so unactivate next time I download ESTAMP data
42b51a52e308 planemo upload for repository https://github.com/Marie59/champ_blocs commit 0d86db7d42b608c386a54500064f5f9c9d7019a4 ecology parents: diff changeset	584 qecbnew <- dplyr::filter(qecbnew, site_year_month_day != "FINS_Quemenes.2020.10.16")
42b51a52e308 planemo upload for repository https://github.com/Marie59/champ_blocs commit 0d86db7d42b608c386a54500064f5f9c9d7019a4 ecology parents: diff changeset	585
42b51a52e308 planemo upload for repository https://github.com/Marie59/champ_blocs commit 0d86db7d42b608c386a54500064f5f9c9d7019a4 ecology parents: diff changeset	586 # save the final qecbnew df_
42b51a52e308 planemo upload for repository https://github.com/Marie59/champ_blocs commit 0d86db7d42b608c386a54500064f5f9c9d7019a4 ecology parents: diff changeset	587
42b51a52e308 planemo upload for repository https://github.com/Marie59/champ_blocs commit 0d86db7d42b608c386a54500064f5f9c9d7019a4 ecology parents: diff changeset	588 qecb <- qecbnew
42b51a52e308 planemo upload for repository https://github.com/Marie59/champ_blocs commit 0d86db7d42b608c386a54500064f5f9c9d7019a4 ecology parents: diff changeset	589
42b51a52e308 planemo upload for repository https://github.com/Marie59/champ_blocs commit 0d86db7d42b608c386a54500064f5f9c9d7019a4 ecology parents: diff changeset	590
42b51a52e308 planemo upload for repository https://github.com/Marie59/champ_blocs commit 0d86db7d42b608c386a54500064f5f9c9d7019a4 ecology parents: diff changeset	591 `%notin%` <- Negate(`%in%`)
42b51a52e308 planemo upload for repository https://github.com/Marie59/champ_blocs commit 0d86db7d42b608c386a54500064f5f9c9d7019a4 ecology parents: diff changeset	592
42b51a52e308 planemo upload for repository https://github.com/Marie59/champ_blocs commit 0d86db7d42b608c386a54500064f5f9c9d7019a4 ecology parents: diff changeset	593 ## reorder and/or create new variables
42b51a52e308 planemo upload for repository https://github.com/Marie59/champ_blocs commit 0d86db7d42b608c386a54500064f5f9c9d7019a4 ecology parents: diff changeset	594
42b51a52e308 planemo upload for repository https://github.com/Marie59/champ_blocs commit 0d86db7d42b608c386a54500064f5f9c9d7019a4 ecology parents: diff changeset	595 # variable site_year_month_day moved for clarity purpose, not needed necessarily
42b51a52e308 planemo upload for repository https://github.com/Marie59/champ_blocs commit 0d86db7d42b608c386a54500064f5f9c9d7019a4 ecology parents: diff changeset	596 qecb <- tibble::add_column(qecb, qecb$site_year_month_day, .after = "Site_bis")
42b51a52e308 planemo upload for repository https://github.com/Marie59/champ_blocs commit 0d86db7d42b608c386a54500064f5f9c9d7019a4 ecology parents: diff changeset	597 qecb <- qecb[, -which(names(qecb) %in% c("site_year_month_day"))]
42b51a52e308 planemo upload for repository https://github.com/Marie59/champ_blocs commit 0d86db7d42b608c386a54500064f5f9c9d7019a4 ecology parents: diff changeset	598 qecb <- dplyr::rename(qecb, site_year_month_day = `qecb$site_year_month_day`)
42b51a52e308 planemo upload for repository https://github.com/Marie59/champ_blocs commit 0d86db7d42b608c386a54500064f5f9c9d7019a4 ecology parents: diff changeset	599
42b51a52e308 planemo upload for repository https://github.com/Marie59/champ_blocs commit 0d86db7d42b608c386a54500064f5f9c9d7019a4 ecology parents: diff changeset	600 # new variable period (nothing to see with the existing périod variable)
42b51a52e308 planemo upload for repository https://github.com/Marie59/champ_blocs commit 0d86db7d42b608c386a54500064f5f9c9d7019a4 ecology parents: diff changeset	601 period <- rep(NA, nrow(qecb))
42b51a52e308 planemo upload for repository https://github.com/Marie59/champ_blocs commit 0d86db7d42b608c386a54500064f5f9c9d7019a4 ecology parents: diff changeset	602 qecb <- tibble::add_column(qecb, period, .after = "Day")
42b51a52e308 planemo upload for repository https://github.com/Marie59/champ_blocs commit 0d86db7d42b608c386a54500064f5f9c9d7019a4 ecology parents: diff changeset	603 qecb$period <- ifelse(as.numeric(qecb$Month) < 7, "p1", "p2")
42b51a52e308 planemo upload for repository https://github.com/Marie59/champ_blocs commit 0d86db7d42b608c386a54500064f5f9c9d7019a4 ecology parents: diff changeset	604 qecb$period <- as.factor(qecb$period)
42b51a52e308 planemo upload for repository https://github.com/Marie59/champ_blocs commit 0d86db7d42b608c386a54500064f5f9c9d7019a4 ecology parents: diff changeset	605 rm(period)
42b51a52e308 planemo upload for repository https://github.com/Marie59/champ_blocs commit 0d86db7d42b608c386a54500064f5f9c9d7019a4 ecology parents: diff changeset	606
42b51a52e308 planemo upload for repository https://github.com/Marie59/champ_blocs commit 0d86db7d42b608c386a54500064f5f9c9d7019a4 ecology parents: diff changeset	607 qecb <- dplyr::arrange(qecb, region, site_year_month_day, Type.Bloc, Numéro.Bloc.échantillon, Face)
42b51a52e308 planemo upload for repository https://github.com/Marie59/champ_blocs commit 0d86db7d42b608c386a54500064f5f9c9d7019a4 ecology parents: diff changeset	608
42b51a52e308 planemo upload for repository https://github.com/Marie59/champ_blocs commit 0d86db7d42b608c386a54500064f5f9c9d7019a4 ecology parents: diff changeset	609 # NB: les infos surface d'accolement sont dupliquées de la face inf vers la face sup de blocs mobiles (même si peu de sens d'avoir cette info pour les face sup ...)
42b51a52e308 planemo upload for repository https://github.com/Marie59/champ_blocs commit 0d86db7d42b608c386a54500064f5f9c9d7019a4 ecology parents: diff changeset	610 # NB: les data "Abondance ressources ciblées par pêcheurs à pied" présentes uniquement pour les blocs mobiles sont dupliquées entre face inf et face sup.
42b51a52e308 planemo upload for repository https://github.com/Marie59/champ_blocs commit 0d86db7d42b608c386a54500064f5f9c9d7019a4 ecology parents: diff changeset	611
42b51a52e308 planemo upload for repository https://github.com/Marie59/champ_blocs commit 0d86db7d42b608c386a54500064f5f9c9d7019a4 ecology parents: diff changeset	612 ## SCRIPT I - NAs <- 0
42b51a52e308 planemo upload for repository https://github.com/Marie59/champ_blocs commit 0d86db7d42b608c386a54500064f5f9c9d7019a4 ecology parents: diff changeset	613
42b51a52e308 planemo upload for repository https://github.com/Marie59/champ_blocs commit 0d86db7d42b608c386a54500064f5f9c9d7019a4 ecology parents: diff changeset	614 # already performed for part in the CB_qecb script ; but here I also consider mobile organisms, logical observation (or not) according to boulders, faces etc ... so more complete. Could be some kind of script fusion to only keep Na to 0 correction in one script, i.e. moving this script to the CB_qecb script ...
42b51a52e308 planemo upload for repository https://github.com/Marie59/champ_blocs commit 0d86db7d42b608c386a54500064f5f9c9d7019a4 ecology parents: diff changeset	615
42b51a52e308 planemo upload for repository https://github.com/Marie59/champ_blocs commit 0d86db7d42b608c386a54500064f5f9c9d7019a4 ecology parents: diff changeset	616 bretagne_bm <- dplyr::filter(qecb, region == "Bretagne" & Type.Bloc == "Bloc mobile")
42b51a52e308 planemo upload for repository https://github.com/Marie59/champ_blocs commit 0d86db7d42b608c386a54500064f5f9c9d7019a4 ecology parents: diff changeset	617 bretagne_bf <- dplyr::filter(qecb, region == "Bretagne" & Type.Bloc %in% c("Bloc fixé", "Roche en place"))
42b51a52e308 planemo upload for repository https://github.com/Marie59/champ_blocs commit 0d86db7d42b608c386a54500064f5f9c9d7019a4 ecology parents: diff changeset	618 egmp_basq_bm <- dplyr::filter(qecb, region == "EGMP.BASQ" & Type.Bloc == "Bloc mobile")
42b51a52e308 planemo upload for repository https://github.com/Marie59/champ_blocs commit 0d86db7d42b608c386a54500064f5f9c9d7019a4 ecology parents: diff changeset	619 egmp_basq_bf <- dplyr::filter(qecb, region == "EGMP.BASQ" & Type.Bloc %in% c("Bloc fixé", "Roche en place"))
42b51a52e308 planemo upload for repository https://github.com/Marie59/champ_blocs commit 0d86db7d42b608c386a54500064f5f9c9d7019a4 ecology parents: diff changeset	620
42b51a52e308 planemo upload for repository https://github.com/Marie59/champ_blocs commit 0d86db7d42b608c386a54500064f5f9c9d7019a4 ecology parents: diff changeset	621 # replace NAs by "0" for variables used in qecb determination
42b51a52e308 planemo upload for repository https://github.com/Marie59/champ_blocs commit 0d86db7d42b608c386a54500064f5f9c9d7019a4 ecology parents: diff changeset	622
42b51a52e308 planemo upload for repository https://github.com/Marie59/champ_blocs commit 0d86db7d42b608c386a54500064f5f9c9d7019a4 ecology parents: diff changeset	623 bretagne_bm[, c(
42b51a52e308 planemo upload for repository https://github.com/Marie59/champ_blocs commit 0d86db7d42b608c386a54500064f5f9c9d7019a4 ecology parents: diff changeset	624 "X..algues.brunes",
42b51a52e308 planemo upload for repository https://github.com/Marie59/champ_blocs commit 0d86db7d42b608c386a54500064f5f9c9d7019a4 ecology parents: diff changeset	625 "Strate.algues.brunes",
42b51a52e308 planemo upload for repository https://github.com/Marie59/champ_blocs commit 0d86db7d42b608c386a54500064f5f9c9d7019a4 ecology parents: diff changeset	626 "X..algues.rouges",
42b51a52e308 planemo upload for repository https://github.com/Marie59/champ_blocs commit 0d86db7d42b608c386a54500064f5f9c9d7019a4 ecology parents: diff changeset	627 "Strate.algues.rouges",
42b51a52e308 planemo upload for repository https://github.com/Marie59/champ_blocs commit 0d86db7d42b608c386a54500064f5f9c9d7019a4 ecology parents: diff changeset	628 "X..algues.vertes",
42b51a52e308 planemo upload for repository https://github.com/Marie59/champ_blocs commit 0d86db7d42b608c386a54500064f5f9c9d7019a4 ecology parents: diff changeset	629 "Strate.algues.vertes",
42b51a52e308 planemo upload for repository https://github.com/Marie59/champ_blocs commit 0d86db7d42b608c386a54500064f5f9c9d7019a4 ecology parents: diff changeset	630 "X..Cladophora",
42b51a52e308 planemo upload for repository https://github.com/Marie59/champ_blocs commit 0d86db7d42b608c386a54500064f5f9c9d7019a4 ecology parents: diff changeset	631 "X..Lithophyllum",
42b51a52e308 planemo upload for repository https://github.com/Marie59/champ_blocs commit 0d86db7d42b608c386a54500064f5f9c9d7019a4 ecology parents: diff changeset	632 "X..Recouvrement.Sediment", # is NA, then replace by 0 as well because no sense to have a NA value for "% recouvrement sédiment" as well.
42b51a52e308 planemo upload for repository https://github.com/Marie59/champ_blocs commit 0d86db7d42b608c386a54500064f5f9c9d7019a4 ecology parents: diff changeset	633 #"Type.Sediment",
42b51a52e308 planemo upload for repository https://github.com/Marie59/champ_blocs commit 0d86db7d42b608c386a54500064f5f9c9d7019a4 ecology parents: diff changeset	634 "X..Roche.Nue", # is NA, then replace by 0 as well because no sense to have a NA value for "% roche nue" as well.
42b51a52e308 planemo upload for repository https://github.com/Marie59/champ_blocs commit 0d86db7d42b608c386a54500064f5f9c9d7019a4 ecology parents: diff changeset	635 "Nb.Littorina.obtusata",
42b51a52e308 planemo upload for repository https://github.com/Marie59/champ_blocs commit 0d86db7d42b608c386a54500064f5f9c9d7019a4 ecology parents: diff changeset	636 "Nb.Gibbula.cineraria",
42b51a52e308 planemo upload for repository https://github.com/Marie59/champ_blocs commit 0d86db7d42b608c386a54500064f5f9c9d7019a4 ecology parents: diff changeset	637 "Nb.Gibbula.pennanti",
42b51a52e308 planemo upload for repository https://github.com/Marie59/champ_blocs commit 0d86db7d42b608c386a54500064f5f9c9d7019a4 ecology parents: diff changeset	638 "Nb.Gibbula.umbilicalis",
42b51a52e308 planemo upload for repository https://github.com/Marie59/champ_blocs commit 0d86db7d42b608c386a54500064f5f9c9d7019a4 ecology parents: diff changeset	639 "Nb.Phallusia.mamillata",
42b51a52e308 planemo upload for repository https://github.com/Marie59/champ_blocs commit 0d86db7d42b608c386a54500064f5f9c9d7019a4 ecology parents: diff changeset	640 "Nb.Tethya.aurantium",
42b51a52e308 planemo upload for repository https://github.com/Marie59/champ_blocs commit 0d86db7d42b608c386a54500064f5f9c9d7019a4 ecology parents: diff changeset	641 #"Nb.Spirobranchus.lamarckii.1B",
42b51a52e308 planemo upload for repository https://github.com/Marie59/champ_blocs commit 0d86db7d42b608c386a54500064f5f9c9d7019a4 ecology parents: diff changeset	642 #"Nb.Spirobranchus.lamarckii.2B",
42b51a52e308 planemo upload for repository https://github.com/Marie59/champ_blocs commit 0d86db7d42b608c386a54500064f5f9c9d7019a4 ecology parents: diff changeset	643 #"Nb.Spirobranchus.lamarckii.3B",
42b51a52e308 planemo upload for repository https://github.com/Marie59/champ_blocs commit 0d86db7d42b608c386a54500064f5f9c9d7019a4 ecology parents: diff changeset	644 #"Nb.Spirobranchus.lamarckii.4B",
42b51a52e308 planemo upload for repository https://github.com/Marie59/champ_blocs commit 0d86db7d42b608c386a54500064f5f9c9d7019a4 ecology parents: diff changeset	645 #"Nb.Spirobranchus.lamarckii.5B",
42b51a52e308 planemo upload for repository https://github.com/Marie59/champ_blocs commit 0d86db7d42b608c386a54500064f5f9c9d7019a4 ecology parents: diff changeset	646 "Nb.Spirobranchus.lamarckii.total",
42b51a52e308 planemo upload for repository https://github.com/Marie59/champ_blocs commit 0d86db7d42b608c386a54500064f5f9c9d7019a4 ecology parents: diff changeset	647 #"Nb.spirorbis.1A",
42b51a52e308 planemo upload for repository https://github.com/Marie59/champ_blocs commit 0d86db7d42b608c386a54500064f5f9c9d7019a4 ecology parents: diff changeset	648 #"Nb.spirorbis.2A",
42b51a52e308 planemo upload for repository https://github.com/Marie59/champ_blocs commit 0d86db7d42b608c386a54500064f5f9c9d7019a4 ecology parents: diff changeset	649 #"Nb.spirorbis.3A",
42b51a52e308 planemo upload for repository https://github.com/Marie59/champ_blocs commit 0d86db7d42b608c386a54500064f5f9c9d7019a4 ecology parents: diff changeset	650 #"Nb.spirorbis.4A",
42b51a52e308 planemo upload for repository https://github.com/Marie59/champ_blocs commit 0d86db7d42b608c386a54500064f5f9c9d7019a4 ecology parents: diff changeset	651 #"Nb.spirorbis.5A",
42b51a52e308 planemo upload for repository https://github.com/Marie59/champ_blocs commit 0d86db7d42b608c386a54500064f5f9c9d7019a4 ecology parents: diff changeset	652 "Nb.spirorbis.total",
42b51a52e308 planemo upload for repository https://github.com/Marie59/champ_blocs commit 0d86db7d42b608c386a54500064f5f9c9d7019a4 ecology parents: diff changeset	653 #.."Nb.Crassostrea.gigas",
42b51a52e308 planemo upload for repository https://github.com/Marie59/champ_blocs commit 0d86db7d42b608c386a54500064f5f9c9d7019a4 ecology parents: diff changeset	654 #.."Nb.Ostrea.edulis",
42b51a52e308 planemo upload for repository https://github.com/Marie59/champ_blocs commit 0d86db7d42b608c386a54500064f5f9c9d7019a4 ecology parents: diff changeset	655 #.."X..Mytilus.sp.",
42b51a52e308 planemo upload for repository https://github.com/Marie59/champ_blocs commit 0d86db7d42b608c386a54500064f5f9c9d7019a4 ecology parents: diff changeset	656 #.."X..Hermelles",
42b51a52e308 planemo upload for repository https://github.com/Marie59/champ_blocs commit 0d86db7d42b608c386a54500064f5f9c9d7019a4 ecology parents: diff changeset	657 #.."X..Hydraires",
42b51a52e308 planemo upload for repository https://github.com/Marie59/champ_blocs commit 0d86db7d42b608c386a54500064f5f9c9d7019a4 ecology parents: diff changeset	658 "X..Eponges",
42b51a52e308 planemo upload for repository https://github.com/Marie59/champ_blocs commit 0d86db7d42b608c386a54500064f5f9c9d7019a4 ecology parents: diff changeset	659 "X..Ascidies.Coloniales",
42b51a52e308 planemo upload for repository https://github.com/Marie59/champ_blocs commit 0d86db7d42b608c386a54500064f5f9c9d7019a4 ecology parents: diff changeset	660 "X..Ascidies.Solitaires",
42b51a52e308 planemo upload for repository https://github.com/Marie59/champ_blocs commit 0d86db7d42b608c386a54500064f5f9c9d7019a4 ecology parents: diff changeset	661 "X..Bryozoaires.Dresses",
42b51a52e308 planemo upload for repository https://github.com/Marie59/champ_blocs commit 0d86db7d42b608c386a54500064f5f9c9d7019a4 ecology parents: diff changeset	662 "X..Balanes.Vivantes",
42b51a52e308 planemo upload for repository https://github.com/Marie59/champ_blocs commit 0d86db7d42b608c386a54500064f5f9c9d7019a4 ecology parents: diff changeset	663 #"Commentaires.Avant",
42b51a52e308 planemo upload for repository https://github.com/Marie59/champ_blocs commit 0d86db7d42b608c386a54500064f5f9c9d7019a4 ecology parents: diff changeset	664 "X..Surface.Accolement", # is NA, then replace by 0 as well because no sense to have a NA value for "% surface accolement" as well.
42b51a52e308 planemo upload for repository https://github.com/Marie59/champ_blocs commit 0d86db7d42b608c386a54500064f5f9c9d7019a4 ecology parents: diff changeset	665 #"Type.sustrat.observé",
42b51a52e308 planemo upload for repository https://github.com/Marie59/champ_blocs commit 0d86db7d42b608c386a54500064f5f9c9d7019a4 ecology parents: diff changeset	666 #"Commentaires",
42b51a52e308 planemo upload for repository https://github.com/Marie59/champ_blocs commit 0d86db7d42b608c386a54500064f5f9c9d7019a4 ecology parents: diff changeset	667 "Nb.Cancer.pagurus..Tourteau.",
42b51a52e308 planemo upload for repository https://github.com/Marie59/champ_blocs commit 0d86db7d42b608c386a54500064f5f9c9d7019a4 ecology parents: diff changeset	668 "Nb.Necora.puber..Etrille.",
42b51a52e308 planemo upload for repository https://github.com/Marie59/champ_blocs commit 0d86db7d42b608c386a54500064f5f9c9d7019a4 ecology parents: diff changeset	669 "Nb.Carcinus.maenas..Crabe.vert.",
42b51a52e308 planemo upload for repository https://github.com/Marie59/champ_blocs commit 0d86db7d42b608c386a54500064f5f9c9d7019a4 ecology parents: diff changeset	670 "Nb.Nucella.lapilus..Pourpre.",
42b51a52e308 planemo upload for repository https://github.com/Marie59/champ_blocs commit 0d86db7d42b608c386a54500064f5f9c9d7019a4 ecology parents: diff changeset	671 #.."Nb.Eriphia.verrucosa..Crabe.verruqueux.",
42b51a52e308 planemo upload for repository https://github.com/Marie59/champ_blocs commit 0d86db7d42b608c386a54500064f5f9c9d7019a4 ecology parents: diff changeset	672 #.."Nb.Octopus.vulgaris..Poulpe.",
42b51a52e308 planemo upload for repository https://github.com/Marie59/champ_blocs commit 0d86db7d42b608c386a54500064f5f9c9d7019a4 ecology parents: diff changeset	673 "Nb.Galathea..Galathées.",
42b51a52e308 planemo upload for repository https://github.com/Marie59/champ_blocs commit 0d86db7d42b608c386a54500064f5f9c9d7019a4 ecology parents: diff changeset	674 #.."Nb.Paracentrotus.lividus..Oursin.",
42b51a52e308 planemo upload for repository https://github.com/Marie59/champ_blocs commit 0d86db7d42b608c386a54500064f5f9c9d7019a4 ecology parents: diff changeset	675 "Nb.Lophozozymus.incisus..ancien.Xantho.incisus.",
42b51a52e308 planemo upload for repository https://github.com/Marie59/champ_blocs commit 0d86db7d42b608c386a54500064f5f9c9d7019a4 ecology parents: diff changeset	676 "Nb.Palaemon.sp..Crevette.bouquet.ou.crevette.rose.",
42b51a52e308 planemo upload for repository https://github.com/Marie59/champ_blocs commit 0d86db7d42b608c386a54500064f5f9c9d7019a4 ecology parents: diff changeset	677 "Nb.Haliotis.tuberculata..Ormeau.",
42b51a52e308 planemo upload for repository https://github.com/Marie59/champ_blocs commit 0d86db7d42b608c386a54500064f5f9c9d7019a4 ecology parents: diff changeset	678 #"Nb.Stramonita.haemastoma..Pourpre.bouche.de.sang.",
42b51a52e308 planemo upload for repository https://github.com/Marie59/champ_blocs commit 0d86db7d42b608c386a54500064f5f9c9d7019a4 ecology parents: diff changeset	679 "Nb.Littorina.littorea..Bigorneau.",
42b51a52e308 planemo upload for repository https://github.com/Marie59/champ_blocs commit 0d86db7d42b608c386a54500064f5f9c9d7019a4 ecology parents: diff changeset	680 "Nb.Xantho.pilipes..Xanthe.poilu.",
42b51a52e308 planemo upload for repository https://github.com/Marie59/champ_blocs commit 0d86db7d42b608c386a54500064f5f9c9d7019a4 ecology parents: diff changeset	681 "Nb.Mimachlamys.varia..Pétoncle.noir."
42b51a52e308 planemo upload for repository https://github.com/Marie59/champ_blocs commit 0d86db7d42b608c386a54500064f5f9c9d7019a4 ecology parents: diff changeset	682 )
42b51a52e308 planemo upload for repository https://github.com/Marie59/champ_blocs commit 0d86db7d42b608c386a54500064f5f9c9d7019a4 ecology parents: diff changeset	683 ] <- lapply(bretagne_bm[, c(
42b51a52e308 planemo upload for repository https://github.com/Marie59/champ_blocs commit 0d86db7d42b608c386a54500064f5f9c9d7019a4 ecology parents: diff changeset	684 "X..algues.brunes",
42b51a52e308 planemo upload for repository https://github.com/Marie59/champ_blocs commit 0d86db7d42b608c386a54500064f5f9c9d7019a4 ecology parents: diff changeset	685 "Strate.algues.brunes",
42b51a52e308 planemo upload for repository https://github.com/Marie59/champ_blocs commit 0d86db7d42b608c386a54500064f5f9c9d7019a4 ecology parents: diff changeset	686 "X..algues.rouges",
42b51a52e308 planemo upload for repository https://github.com/Marie59/champ_blocs commit 0d86db7d42b608c386a54500064f5f9c9d7019a4 ecology parents: diff changeset	687 "Strate.algues.rouges",
42b51a52e308 planemo upload for repository https://github.com/Marie59/champ_blocs commit 0d86db7d42b608c386a54500064f5f9c9d7019a4 ecology parents: diff changeset	688 "X..algues.vertes",
42b51a52e308 planemo upload for repository https://github.com/Marie59/champ_blocs commit 0d86db7d42b608c386a54500064f5f9c9d7019a4 ecology parents: diff changeset	689 "Strate.algues.vertes",
42b51a52e308 planemo upload for repository https://github.com/Marie59/champ_blocs commit 0d86db7d42b608c386a54500064f5f9c9d7019a4 ecology parents: diff changeset	690 "X..Cladophora",
42b51a52e308 planemo upload for repository https://github.com/Marie59/champ_blocs commit 0d86db7d42b608c386a54500064f5f9c9d7019a4 ecology parents: diff changeset	691 "X..Lithophyllum",
42b51a52e308 planemo upload for repository https://github.com/Marie59/champ_blocs commit 0d86db7d42b608c386a54500064f5f9c9d7019a4 ecology parents: diff changeset	692 "X..Recouvrement.Sediment", # is NA, then replace by 0 as well because no sense to have a NA value for "% recouvrement sédiment" as well.
42b51a52e308 planemo upload for repository https://github.com/Marie59/champ_blocs commit 0d86db7d42b608c386a54500064f5f9c9d7019a4 ecology parents: diff changeset	693 #"Type.Sediment",
42b51a52e308 planemo upload for repository https://github.com/Marie59/champ_blocs commit 0d86db7d42b608c386a54500064f5f9c9d7019a4 ecology parents: diff changeset	694 "X..Roche.Nue", # is NA, then replace by 0 as well because no sense to have a NA value for "% roche nue" as well.
42b51a52e308 planemo upload for repository https://github.com/Marie59/champ_blocs commit 0d86db7d42b608c386a54500064f5f9c9d7019a4 ecology parents: diff changeset	695 "Nb.Littorina.obtusata",
42b51a52e308 planemo upload for repository https://github.com/Marie59/champ_blocs commit 0d86db7d42b608c386a54500064f5f9c9d7019a4 ecology parents: diff changeset	696 "Nb.Gibbula.cineraria",
42b51a52e308 planemo upload for repository https://github.com/Marie59/champ_blocs commit 0d86db7d42b608c386a54500064f5f9c9d7019a4 ecology parents: diff changeset	697 "Nb.Gibbula.pennanti",
42b51a52e308 planemo upload for repository https://github.com/Marie59/champ_blocs commit 0d86db7d42b608c386a54500064f5f9c9d7019a4 ecology parents: diff changeset	698 "Nb.Gibbula.umbilicalis",
42b51a52e308 planemo upload for repository https://github.com/Marie59/champ_blocs commit 0d86db7d42b608c386a54500064f5f9c9d7019a4 ecology parents: diff changeset	699 "Nb.Phallusia.mamillata",
42b51a52e308 planemo upload for repository https://github.com/Marie59/champ_blocs commit 0d86db7d42b608c386a54500064f5f9c9d7019a4 ecology parents: diff changeset	700 "Nb.Tethya.aurantium",
42b51a52e308 planemo upload for repository https://github.com/Marie59/champ_blocs commit 0d86db7d42b608c386a54500064f5f9c9d7019a4 ecology parents: diff changeset	701 #"Nb.Spirobranchus.lamarckii.1B",
42b51a52e308 planemo upload for repository https://github.com/Marie59/champ_blocs commit 0d86db7d42b608c386a54500064f5f9c9d7019a4 ecology parents: diff changeset	702 #"Nb.Spirobranchus.lamarckii.2B",
42b51a52e308 planemo upload for repository https://github.com/Marie59/champ_blocs commit 0d86db7d42b608c386a54500064f5f9c9d7019a4 ecology parents: diff changeset	703 #"Nb.Spirobranchus.lamarckii.3B",
42b51a52e308 planemo upload for repository https://github.com/Marie59/champ_blocs commit 0d86db7d42b608c386a54500064f5f9c9d7019a4 ecology parents: diff changeset	704 #"Nb.Spirobranchus.lamarckii.4B",
42b51a52e308 planemo upload for repository https://github.com/Marie59/champ_blocs commit 0d86db7d42b608c386a54500064f5f9c9d7019a4 ecology parents: diff changeset	705 #"Nb.Spirobranchus.lamarckii.5B",
42b51a52e308 planemo upload for repository https://github.com/Marie59/champ_blocs commit 0d86db7d42b608c386a54500064f5f9c9d7019a4 ecology parents: diff changeset	706 "Nb.Spirobranchus.lamarckii.total",
42b51a52e308 planemo upload for repository https://github.com/Marie59/champ_blocs commit 0d86db7d42b608c386a54500064f5f9c9d7019a4 ecology parents: diff changeset	707 #"Nb.spirorbis.1A",
42b51a52e308 planemo upload for repository https://github.com/Marie59/champ_blocs commit 0d86db7d42b608c386a54500064f5f9c9d7019a4 ecology parents: diff changeset	708 #"Nb.spirorbis.2A",
42b51a52e308 planemo upload for repository https://github.com/Marie59/champ_blocs commit 0d86db7d42b608c386a54500064f5f9c9d7019a4 ecology parents: diff changeset	709 #"Nb.spirorbis.3A",
42b51a52e308 planemo upload for repository https://github.com/Marie59/champ_blocs commit 0d86db7d42b608c386a54500064f5f9c9d7019a4 ecology parents: diff changeset	710 #"Nb.spirorbis.4A",
42b51a52e308 planemo upload for repository https://github.com/Marie59/champ_blocs commit 0d86db7d42b608c386a54500064f5f9c9d7019a4 ecology parents: diff changeset	711 #"Nb.spirorbis.5A",
42b51a52e308 planemo upload for repository https://github.com/Marie59/champ_blocs commit 0d86db7d42b608c386a54500064f5f9c9d7019a4 ecology parents: diff changeset	712 "Nb.spirorbis.total",
42b51a52e308 planemo upload for repository https://github.com/Marie59/champ_blocs commit 0d86db7d42b608c386a54500064f5f9c9d7019a4 ecology parents: diff changeset	713 #.."Nb.Crassostrea.gigas",
42b51a52e308 planemo upload for repository https://github.com/Marie59/champ_blocs commit 0d86db7d42b608c386a54500064f5f9c9d7019a4 ecology parents: diff changeset	714 #.."Nb.Ostrea.edulis",
42b51a52e308 planemo upload for repository https://github.com/Marie59/champ_blocs commit 0d86db7d42b608c386a54500064f5f9c9d7019a4 ecology parents: diff changeset	715 #.."X..Mytilus.sp.",
42b51a52e308 planemo upload for repository https://github.com/Marie59/champ_blocs commit 0d86db7d42b608c386a54500064f5f9c9d7019a4 ecology parents: diff changeset	716 #.."X..Hermelles",
42b51a52e308 planemo upload for repository https://github.com/Marie59/champ_blocs commit 0d86db7d42b608c386a54500064f5f9c9d7019a4 ecology parents: diff changeset	717 #.."X..Hydraires",
42b51a52e308 planemo upload for repository https://github.com/Marie59/champ_blocs commit 0d86db7d42b608c386a54500064f5f9c9d7019a4 ecology parents: diff changeset	718 "X..Eponges",
42b51a52e308 planemo upload for repository https://github.com/Marie59/champ_blocs commit 0d86db7d42b608c386a54500064f5f9c9d7019a4 ecology parents: diff changeset	719 "X..Ascidies.Coloniales",
42b51a52e308 planemo upload for repository https://github.com/Marie59/champ_blocs commit 0d86db7d42b608c386a54500064f5f9c9d7019a4 ecology parents: diff changeset	720 "X..Ascidies.Solitaires",
42b51a52e308 planemo upload for repository https://github.com/Marie59/champ_blocs commit 0d86db7d42b608c386a54500064f5f9c9d7019a4 ecology parents: diff changeset	721 "X..Bryozoaires.Dresses",
42b51a52e308 planemo upload for repository https://github.com/Marie59/champ_blocs commit 0d86db7d42b608c386a54500064f5f9c9d7019a4 ecology parents: diff changeset	722 "X..Balanes.Vivantes",
42b51a52e308 planemo upload for repository https://github.com/Marie59/champ_blocs commit 0d86db7d42b608c386a54500064f5f9c9d7019a4 ecology parents: diff changeset	723 #"Commentaires.Avant",
42b51a52e308 planemo upload for repository https://github.com/Marie59/champ_blocs commit 0d86db7d42b608c386a54500064f5f9c9d7019a4 ecology parents: diff changeset	724 "X..Surface.Accolement", # is NA, then replace by 0 as well because no sense to have a NA value for "% surface accolement" as well.
42b51a52e308 planemo upload for repository https://github.com/Marie59/champ_blocs commit 0d86db7d42b608c386a54500064f5f9c9d7019a4 ecology parents: diff changeset	725 #"Type.sustrat.observé",
42b51a52e308 planemo upload for repository https://github.com/Marie59/champ_blocs commit 0d86db7d42b608c386a54500064f5f9c9d7019a4 ecology parents: diff changeset	726 #"Commentaires",
42b51a52e308 planemo upload for repository https://github.com/Marie59/champ_blocs commit 0d86db7d42b608c386a54500064f5f9c9d7019a4 ecology parents: diff changeset	727 "Nb.Cancer.pagurus..Tourteau.",
42b51a52e308 planemo upload for repository https://github.com/Marie59/champ_blocs commit 0d86db7d42b608c386a54500064f5f9c9d7019a4 ecology parents: diff changeset	728 "Nb.Necora.puber..Etrille.",
42b51a52e308 planemo upload for repository https://github.com/Marie59/champ_blocs commit 0d86db7d42b608c386a54500064f5f9c9d7019a4 ecology parents: diff changeset	729 "Nb.Carcinus.maenas..Crabe.vert.",
42b51a52e308 planemo upload for repository https://github.com/Marie59/champ_blocs commit 0d86db7d42b608c386a54500064f5f9c9d7019a4 ecology parents: diff changeset	730 "Nb.Nucella.lapilus..Pourpre.",
42b51a52e308 planemo upload for repository https://github.com/Marie59/champ_blocs commit 0d86db7d42b608c386a54500064f5f9c9d7019a4 ecology parents: diff changeset	731 #.."Nb.Eriphia.verrucosa..Crabe.verruqueux.",
42b51a52e308 planemo upload for repository https://github.com/Marie59/champ_blocs commit 0d86db7d42b608c386a54500064f5f9c9d7019a4 ecology parents: diff changeset	732 #.."Nb.Octopus.vulgaris..Poulpe.",
42b51a52e308 planemo upload for repository https://github.com/Marie59/champ_blocs commit 0d86db7d42b608c386a54500064f5f9c9d7019a4 ecology parents: diff changeset	733 "Nb.Galathea..Galathées.",
42b51a52e308 planemo upload for repository https://github.com/Marie59/champ_blocs commit 0d86db7d42b608c386a54500064f5f9c9d7019a4 ecology parents: diff changeset	734 #.."Nb.Paracentrotus.lividus..Oursin.",
42b51a52e308 planemo upload for repository https://github.com/Marie59/champ_blocs commit 0d86db7d42b608c386a54500064f5f9c9d7019a4 ecology parents: diff changeset	735 "Nb.Lophozozymus.incisus..ancien.Xantho.incisus.",
42b51a52e308 planemo upload for repository https://github.com/Marie59/champ_blocs commit 0d86db7d42b608c386a54500064f5f9c9d7019a4 ecology parents: diff changeset	736 "Nb.Palaemon.sp..Crevette.bouquet.ou.crevette.rose.",
42b51a52e308 planemo upload for repository https://github.com/Marie59/champ_blocs commit 0d86db7d42b608c386a54500064f5f9c9d7019a4 ecology parents: diff changeset	737 "Nb.Haliotis.tuberculata..Ormeau.",
42b51a52e308 planemo upload for repository https://github.com/Marie59/champ_blocs commit 0d86db7d42b608c386a54500064f5f9c9d7019a4 ecology parents: diff changeset	738 #"Nb.Stramonita.haemastoma..Pourpre.bouche.de.sang.",
42b51a52e308 planemo upload for repository https://github.com/Marie59/champ_blocs commit 0d86db7d42b608c386a54500064f5f9c9d7019a4 ecology parents: diff changeset	739 "Nb.Littorina.littorea..Bigorneau.",
42b51a52e308 planemo upload for repository https://github.com/Marie59/champ_blocs commit 0d86db7d42b608c386a54500064f5f9c9d7019a4 ecology parents: diff changeset	740 "Nb.Xantho.pilipes..Xanthe.poilu.",
42b51a52e308 planemo upload for repository https://github.com/Marie59/champ_blocs commit 0d86db7d42b608c386a54500064f5f9c9d7019a4 ecology parents: diff changeset	741 "Nb.Mimachlamys.varia..Pétoncle.noir."
42b51a52e308 planemo upload for repository https://github.com/Marie59/champ_blocs commit 0d86db7d42b608c386a54500064f5f9c9d7019a4 ecology parents: diff changeset	742 )
42b51a52e308 planemo upload for repository https://github.com/Marie59/champ_blocs commit 0d86db7d42b608c386a54500064f5f9c9d7019a4 ecology parents: diff changeset	743 ], function(x) replace(x, is.na(x), 0))
42b51a52e308 planemo upload for repository https://github.com/Marie59/champ_blocs commit 0d86db7d42b608c386a54500064f5f9c9d7019a4 ecology parents: diff changeset	744
42b51a52e308 planemo upload for repository https://github.com/Marie59/champ_blocs commit 0d86db7d42b608c386a54500064f5f9c9d7019a4 ecology parents: diff changeset	745
42b51a52e308 planemo upload for repository https://github.com/Marie59/champ_blocs commit 0d86db7d42b608c386a54500064f5f9c9d7019a4 ecology parents: diff changeset	746 # bretagne_bf
42b51a52e308 planemo upload for repository https://github.com/Marie59/champ_blocs commit 0d86db7d42b608c386a54500064f5f9c9d7019a4 ecology parents: diff changeset	747 bretagne_bf[, c(
42b51a52e308 planemo upload for repository https://github.com/Marie59/champ_blocs commit 0d86db7d42b608c386a54500064f5f9c9d7019a4 ecology parents: diff changeset	748 "X..algues.brunes",
42b51a52e308 planemo upload for repository https://github.com/Marie59/champ_blocs commit 0d86db7d42b608c386a54500064f5f9c9d7019a4 ecology parents: diff changeset	749 "Strate.algues.brunes",
42b51a52e308 planemo upload for repository https://github.com/Marie59/champ_blocs commit 0d86db7d42b608c386a54500064f5f9c9d7019a4 ecology parents: diff changeset	750 "X..algues.rouges",
42b51a52e308 planemo upload for repository https://github.com/Marie59/champ_blocs commit 0d86db7d42b608c386a54500064f5f9c9d7019a4 ecology parents: diff changeset	751 "Strate.algues.rouges",
42b51a52e308 planemo upload for repository https://github.com/Marie59/champ_blocs commit 0d86db7d42b608c386a54500064f5f9c9d7019a4 ecology parents: diff changeset	752 "X..algues.vertes",
42b51a52e308 planemo upload for repository https://github.com/Marie59/champ_blocs commit 0d86db7d42b608c386a54500064f5f9c9d7019a4 ecology parents: diff changeset	753 "Strate.algues.vertes",
42b51a52e308 planemo upload for repository https://github.com/Marie59/champ_blocs commit 0d86db7d42b608c386a54500064f5f9c9d7019a4 ecology parents: diff changeset	754 "X..Cladophora",
42b51a52e308 planemo upload for repository https://github.com/Marie59/champ_blocs commit 0d86db7d42b608c386a54500064f5f9c9d7019a4 ecology parents: diff changeset	755 "X..Lithophyllum",
42b51a52e308 planemo upload for repository https://github.com/Marie59/champ_blocs commit 0d86db7d42b608c386a54500064f5f9c9d7019a4 ecology parents: diff changeset	756 "X..Recouvrement.Sediment", # is NA, then replace by 0 as well because no sense to have a NA value for "% recouvrement sédiment" as well.
42b51a52e308 planemo upload for repository https://github.com/Marie59/champ_blocs commit 0d86db7d42b608c386a54500064f5f9c9d7019a4 ecology parents: diff changeset	757 #"Type.Sediment",
42b51a52e308 planemo upload for repository https://github.com/Marie59/champ_blocs commit 0d86db7d42b608c386a54500064f5f9c9d7019a4 ecology parents: diff changeset	758 "X..Roche.Nue", # is NA, then replace by 0 as well because no sense to have a NA value for "% roche nue" as well.
42b51a52e308 planemo upload for repository https://github.com/Marie59/champ_blocs commit 0d86db7d42b608c386a54500064f5f9c9d7019a4 ecology parents: diff changeset	759 "Nb.Littorina.obtusata",
42b51a52e308 planemo upload for repository https://github.com/Marie59/champ_blocs commit 0d86db7d42b608c386a54500064f5f9c9d7019a4 ecology parents: diff changeset	760 "Nb.Gibbula.cineraria",
42b51a52e308 planemo upload for repository https://github.com/Marie59/champ_blocs commit 0d86db7d42b608c386a54500064f5f9c9d7019a4 ecology parents: diff changeset	761 "Nb.Gibbula.pennanti",
42b51a52e308 planemo upload for repository https://github.com/Marie59/champ_blocs commit 0d86db7d42b608c386a54500064f5f9c9d7019a4 ecology parents: diff changeset	762 "Nb.Gibbula.umbilicalis",
42b51a52e308 planemo upload for repository https://github.com/Marie59/champ_blocs commit 0d86db7d42b608c386a54500064f5f9c9d7019a4 ecology parents: diff changeset	763 "Nb.Phallusia.mamillata",
42b51a52e308 planemo upload for repository https://github.com/Marie59/champ_blocs commit 0d86db7d42b608c386a54500064f5f9c9d7019a4 ecology parents: diff changeset	764 "Nb.Tethya.aurantium",
42b51a52e308 planemo upload for repository https://github.com/Marie59/champ_blocs commit 0d86db7d42b608c386a54500064f5f9c9d7019a4 ecology parents: diff changeset	765 #"Nb.Spirobranchus.lamarckii.1B",
42b51a52e308 planemo upload for repository https://github.com/Marie59/champ_blocs commit 0d86db7d42b608c386a54500064f5f9c9d7019a4 ecology parents: diff changeset	766 #"Nb.Spirobranchus.lamarckii.2B",
42b51a52e308 planemo upload for repository https://github.com/Marie59/champ_blocs commit 0d86db7d42b608c386a54500064f5f9c9d7019a4 ecology parents: diff changeset	767 #"Nb.Spirobranchus.lamarckii.3B",
42b51a52e308 planemo upload for repository https://github.com/Marie59/champ_blocs commit 0d86db7d42b608c386a54500064f5f9c9d7019a4 ecology parents: diff changeset	768 #"Nb.Spirobranchus.lamarckii.4B",
42b51a52e308 planemo upload for repository https://github.com/Marie59/champ_blocs commit 0d86db7d42b608c386a54500064f5f9c9d7019a4 ecology parents: diff changeset	769 #"Nb.Spirobranchus.lamarckii.5B",
42b51a52e308 planemo upload for repository https://github.com/Marie59/champ_blocs commit 0d86db7d42b608c386a54500064f5f9c9d7019a4 ecology parents: diff changeset	770 "Nb.Spirobranchus.lamarckii.total",
42b51a52e308 planemo upload for repository https://github.com/Marie59/champ_blocs commit 0d86db7d42b608c386a54500064f5f9c9d7019a4 ecology parents: diff changeset	771 #"Nb.spirorbis.1A",
42b51a52e308 planemo upload for repository https://github.com/Marie59/champ_blocs commit 0d86db7d42b608c386a54500064f5f9c9d7019a4 ecology parents: diff changeset	772 #"Nb.spirorbis.2A",
42b51a52e308 planemo upload for repository https://github.com/Marie59/champ_blocs commit 0d86db7d42b608c386a54500064f5f9c9d7019a4 ecology parents: diff changeset	773 #"Nb.spirorbis.3A",
42b51a52e308 planemo upload for repository https://github.com/Marie59/champ_blocs commit 0d86db7d42b608c386a54500064f5f9c9d7019a4 ecology parents: diff changeset	774 #"Nb.spirorbis.4A",
42b51a52e308 planemo upload for repository https://github.com/Marie59/champ_blocs commit 0d86db7d42b608c386a54500064f5f9c9d7019a4 ecology parents: diff changeset	775 #"Nb.spirorbis.5A",
42b51a52e308 planemo upload for repository https://github.com/Marie59/champ_blocs commit 0d86db7d42b608c386a54500064f5f9c9d7019a4 ecology parents: diff changeset	776 "Nb.spirorbis.total",
42b51a52e308 planemo upload for repository https://github.com/Marie59/champ_blocs commit 0d86db7d42b608c386a54500064f5f9c9d7019a4 ecology parents: diff changeset	777 #.."Nb.Crassostrea.gigas",
42b51a52e308 planemo upload for repository https://github.com/Marie59/champ_blocs commit 0d86db7d42b608c386a54500064f5f9c9d7019a4 ecology parents: diff changeset	778 #.."Nb.Ostrea.edulis",
42b51a52e308 planemo upload for repository https://github.com/Marie59/champ_blocs commit 0d86db7d42b608c386a54500064f5f9c9d7019a4 ecology parents: diff changeset	779 #.."X..Mytilus.sp.",
42b51a52e308 planemo upload for repository https://github.com/Marie59/champ_blocs commit 0d86db7d42b608c386a54500064f5f9c9d7019a4 ecology parents: diff changeset	780 #.."X..Hermelles",
42b51a52e308 planemo upload for repository https://github.com/Marie59/champ_blocs commit 0d86db7d42b608c386a54500064f5f9c9d7019a4 ecology parents: diff changeset	781 #.."X..Hydraires",
42b51a52e308 planemo upload for repository https://github.com/Marie59/champ_blocs commit 0d86db7d42b608c386a54500064f5f9c9d7019a4 ecology parents: diff changeset	782 "X..Eponges",
42b51a52e308 planemo upload for repository https://github.com/Marie59/champ_blocs commit 0d86db7d42b608c386a54500064f5f9c9d7019a4 ecology parents: diff changeset	783 "X..Ascidies.Coloniales",
42b51a52e308 planemo upload for repository https://github.com/Marie59/champ_blocs commit 0d86db7d42b608c386a54500064f5f9c9d7019a4 ecology parents: diff changeset	784 "X..Ascidies.Solitaires",
42b51a52e308 planemo upload for repository https://github.com/Marie59/champ_blocs commit 0d86db7d42b608c386a54500064f5f9c9d7019a4 ecology parents: diff changeset	785 "X..Bryozoaires.Dresses",
42b51a52e308 planemo upload for repository https://github.com/Marie59/champ_blocs commit 0d86db7d42b608c386a54500064f5f9c9d7019a4 ecology parents: diff changeset	786 "X..Balanes.Vivantes",
42b51a52e308 planemo upload for repository https://github.com/Marie59/champ_blocs commit 0d86db7d42b608c386a54500064f5f9c9d7019a4 ecology parents: diff changeset	787 #"Commentaires.Avant",
42b51a52e308 planemo upload for repository https://github.com/Marie59/champ_blocs commit 0d86db7d42b608c386a54500064f5f9c9d7019a4 ecology parents: diff changeset	788 "X..Surface.Accolement"#, # is NA, then replace by 0 as well because no sense to have a NA value for "% surface accolement" as well.
42b51a52e308 planemo upload for repository https://github.com/Marie59/champ_blocs commit 0d86db7d42b608c386a54500064f5f9c9d7019a4 ecology parents: diff changeset	789 #"Type.sustrat.observé",
42b51a52e308 planemo upload for repository https://github.com/Marie59/champ_blocs commit 0d86db7d42b608c386a54500064f5f9c9d7019a4 ecology parents: diff changeset	790 #"Commentaires",
42b51a52e308 planemo upload for repository https://github.com/Marie59/champ_blocs commit 0d86db7d42b608c386a54500064f5f9c9d7019a4 ecology parents: diff changeset	791 #."Nb.Cancer.pagurus..Tourteau.",
42b51a52e308 planemo upload for repository https://github.com/Marie59/champ_blocs commit 0d86db7d42b608c386a54500064f5f9c9d7019a4 ecology parents: diff changeset	792 #.."Nb.Necora.puber..Etrille.",
42b51a52e308 planemo upload for repository https://github.com/Marie59/champ_blocs commit 0d86db7d42b608c386a54500064f5f9c9d7019a4 ecology parents: diff changeset	793 #."Nb.Carcinus.maenas..Crabe.vert.",
42b51a52e308 planemo upload for repository https://github.com/Marie59/champ_blocs commit 0d86db7d42b608c386a54500064f5f9c9d7019a4 ecology parents: diff changeset	794 #."Nb.Nucella.lapilus..Pourpre.",
42b51a52e308 planemo upload for repository https://github.com/Marie59/champ_blocs commit 0d86db7d42b608c386a54500064f5f9c9d7019a4 ecology parents: diff changeset	795 #.."Nb.Eriphia.verrucosa..Crabe.verruqueux.",
42b51a52e308 planemo upload for repository https://github.com/Marie59/champ_blocs commit 0d86db7d42b608c386a54500064f5f9c9d7019a4 ecology parents: diff changeset	796 #.."Nb.Octopus.vulgaris..Poulpe.",
42b51a52e308 planemo upload for repository https://github.com/Marie59/champ_blocs commit 0d86db7d42b608c386a54500064f5f9c9d7019a4 ecology parents: diff changeset	797 #."Nb.Galathea..Galathées.",
42b51a52e308 planemo upload for repository https://github.com/Marie59/champ_blocs commit 0d86db7d42b608c386a54500064f5f9c9d7019a4 ecology parents: diff changeset	798 #.."Nb.Paracentrotus.lividus..Oursin.",
42b51a52e308 planemo upload for repository https://github.com/Marie59/champ_blocs commit 0d86db7d42b608c386a54500064f5f9c9d7019a4 ecology parents: diff changeset	799 #."Nb.Lophozozymus.incisus..ancien.Xantho.incisus.",
42b51a52e308 planemo upload for repository https://github.com/Marie59/champ_blocs commit 0d86db7d42b608c386a54500064f5f9c9d7019a4 ecology parents: diff changeset	800 #."Nb.Palaemon.sp..Crevette.bouquet.ou.crevette.rose.",
42b51a52e308 planemo upload for repository https://github.com/Marie59/champ_blocs commit 0d86db7d42b608c386a54500064f5f9c9d7019a4 ecology parents: diff changeset	801 #."Nb.Haliotis.tuberculata..Ormeau.",
42b51a52e308 planemo upload for repository https://github.com/Marie59/champ_blocs commit 0d86db7d42b608c386a54500064f5f9c9d7019a4 ecology parents: diff changeset	802 #."Nb.Stramonita.haemastoma..Pourpre.bouche.de.sang.",
42b51a52e308 planemo upload for repository https://github.com/Marie59/champ_blocs commit 0d86db7d42b608c386a54500064f5f9c9d7019a4 ecology parents: diff changeset	803 #."Nb.Littorina.littorea..Bigorneau.",
42b51a52e308 planemo upload for repository https://github.com/Marie59/champ_blocs commit 0d86db7d42b608c386a54500064f5f9c9d7019a4 ecology parents: diff changeset	804 #."Nb.Xantho.pilipes..Xanthe.poilu.",
42b51a52e308 planemo upload for repository https://github.com/Marie59/champ_blocs commit 0d86db7d42b608c386a54500064f5f9c9d7019a4 ecology parents: diff changeset	805 #."Nb.Mimachlamys.varia..Pétoncle.noir."
42b51a52e308 planemo upload for repository https://github.com/Marie59/champ_blocs commit 0d86db7d42b608c386a54500064f5f9c9d7019a4 ecology parents: diff changeset	806 )
42b51a52e308 planemo upload for repository https://github.com/Marie59/champ_blocs commit 0d86db7d42b608c386a54500064f5f9c9d7019a4 ecology parents: diff changeset	807 ] <- lapply(bretagne_bf[, c(
42b51a52e308 planemo upload for repository https://github.com/Marie59/champ_blocs commit 0d86db7d42b608c386a54500064f5f9c9d7019a4 ecology parents: diff changeset	808 "X..algues.brunes",
42b51a52e308 planemo upload for repository https://github.com/Marie59/champ_blocs commit 0d86db7d42b608c386a54500064f5f9c9d7019a4 ecology parents: diff changeset	809 "Strate.algues.brunes",
42b51a52e308 planemo upload for repository https://github.com/Marie59/champ_blocs commit 0d86db7d42b608c386a54500064f5f9c9d7019a4 ecology parents: diff changeset	810 "X..algues.rouges",
42b51a52e308 planemo upload for repository https://github.com/Marie59/champ_blocs commit 0d86db7d42b608c386a54500064f5f9c9d7019a4 ecology parents: diff changeset	811 "Strate.algues.rouges",
42b51a52e308 planemo upload for repository https://github.com/Marie59/champ_blocs commit 0d86db7d42b608c386a54500064f5f9c9d7019a4 ecology parents: diff changeset	812 "X..algues.vertes",
42b51a52e308 planemo upload for repository https://github.com/Marie59/champ_blocs commit 0d86db7d42b608c386a54500064f5f9c9d7019a4 ecology parents: diff changeset	813 "Strate.algues.vertes",
42b51a52e308 planemo upload for repository https://github.com/Marie59/champ_blocs commit 0d86db7d42b608c386a54500064f5f9c9d7019a4 ecology parents: diff changeset	814 "X..Cladophora",
42b51a52e308 planemo upload for repository https://github.com/Marie59/champ_blocs commit 0d86db7d42b608c386a54500064f5f9c9d7019a4 ecology parents: diff changeset	815 "X..Lithophyllum",
42b51a52e308 planemo upload for repository https://github.com/Marie59/champ_blocs commit 0d86db7d42b608c386a54500064f5f9c9d7019a4 ecology parents: diff changeset	816 "X..Recouvrement.Sediment", # is NA, then replace by 0 as well because no sense to have a NA value for "% recouvrement sédiment" as well.
42b51a52e308 planemo upload for repository https://github.com/Marie59/champ_blocs commit 0d86db7d42b608c386a54500064f5f9c9d7019a4 ecology parents: diff changeset	817 #"Type.Sediment",
42b51a52e308 planemo upload for repository https://github.com/Marie59/champ_blocs commit 0d86db7d42b608c386a54500064f5f9c9d7019a4 ecology parents: diff changeset	818 "X..Roche.Nue", # is NA, then replace by 0 as well because no sense to have a NA value for "% roche nue" as well.
42b51a52e308 planemo upload for repository https://github.com/Marie59/champ_blocs commit 0d86db7d42b608c386a54500064f5f9c9d7019a4 ecology parents: diff changeset	819 "Nb.Littorina.obtusata",
42b51a52e308 planemo upload for repository https://github.com/Marie59/champ_blocs commit 0d86db7d42b608c386a54500064f5f9c9d7019a4 ecology parents: diff changeset	820 "Nb.Gibbula.cineraria",
42b51a52e308 planemo upload for repository https://github.com/Marie59/champ_blocs commit 0d86db7d42b608c386a54500064f5f9c9d7019a4 ecology parents: diff changeset	821 "Nb.Gibbula.pennanti",
42b51a52e308 planemo upload for repository https://github.com/Marie59/champ_blocs commit 0d86db7d42b608c386a54500064f5f9c9d7019a4 ecology parents: diff changeset	822 "Nb.Gibbula.umbilicalis",
42b51a52e308 planemo upload for repository https://github.com/Marie59/champ_blocs commit 0d86db7d42b608c386a54500064f5f9c9d7019a4 ecology parents: diff changeset	823 "Nb.Phallusia.mamillata",
42b51a52e308 planemo upload for repository https://github.com/Marie59/champ_blocs commit 0d86db7d42b608c386a54500064f5f9c9d7019a4 ecology parents: diff changeset	824 "Nb.Tethya.aurantium",
42b51a52e308 planemo upload for repository https://github.com/Marie59/champ_blocs commit 0d86db7d42b608c386a54500064f5f9c9d7019a4 ecology parents: diff changeset	825 #"Nb.Spirobranchus.lamarckii.1B",
42b51a52e308 planemo upload for repository https://github.com/Marie59/champ_blocs commit 0d86db7d42b608c386a54500064f5f9c9d7019a4 ecology parents: diff changeset	826 #"Nb.Spirobranchus.lamarckii.2B",
42b51a52e308 planemo upload for repository https://github.com/Marie59/champ_blocs commit 0d86db7d42b608c386a54500064f5f9c9d7019a4 ecology parents: diff changeset	827 #"Nb.Spirobranchus.lamarckii.3B",
42b51a52e308 planemo upload for repository https://github.com/Marie59/champ_blocs commit 0d86db7d42b608c386a54500064f5f9c9d7019a4 ecology parents: diff changeset	828 #"Nb.Spirobranchus.lamarckii.4B",
42b51a52e308 planemo upload for repository https://github.com/Marie59/champ_blocs commit 0d86db7d42b608c386a54500064f5f9c9d7019a4 ecology parents: diff changeset	829 #"Nb.Spirobranchus.lamarckii.5B",
42b51a52e308 planemo upload for repository https://github.com/Marie59/champ_blocs commit 0d86db7d42b608c386a54500064f5f9c9d7019a4 ecology parents: diff changeset	830 "Nb.Spirobranchus.lamarckii.total",
42b51a52e308 planemo upload for repository https://github.com/Marie59/champ_blocs commit 0d86db7d42b608c386a54500064f5f9c9d7019a4 ecology parents: diff changeset	831 #"Nb.spirorbis.1A",
42b51a52e308 planemo upload for repository https://github.com/Marie59/champ_blocs commit 0d86db7d42b608c386a54500064f5f9c9d7019a4 ecology parents: diff changeset	832 #"Nb.spirorbis.2A",
42b51a52e308 planemo upload for repository https://github.com/Marie59/champ_blocs commit 0d86db7d42b608c386a54500064f5f9c9d7019a4 ecology parents: diff changeset	833 #"Nb.spirorbis.3A",
42b51a52e308 planemo upload for repository https://github.com/Marie59/champ_blocs commit 0d86db7d42b608c386a54500064f5f9c9d7019a4 ecology parents: diff changeset	834 #"Nb.spirorbis.4A",
42b51a52e308 planemo upload for repository https://github.com/Marie59/champ_blocs commit 0d86db7d42b608c386a54500064f5f9c9d7019a4 ecology parents: diff changeset	835 #"Nb.spirorbis.5A",
42b51a52e308 planemo upload for repository https://github.com/Marie59/champ_blocs commit 0d86db7d42b608c386a54500064f5f9c9d7019a4 ecology parents: diff changeset	836 "Nb.spirorbis.total",
42b51a52e308 planemo upload for repository https://github.com/Marie59/champ_blocs commit 0d86db7d42b608c386a54500064f5f9c9d7019a4 ecology parents: diff changeset	837 #.."Nb.Crassostrea.gigas",
42b51a52e308 planemo upload for repository https://github.com/Marie59/champ_blocs commit 0d86db7d42b608c386a54500064f5f9c9d7019a4 ecology parents: diff changeset	838 #.."Nb.Ostrea.edulis",
42b51a52e308 planemo upload for repository https://github.com/Marie59/champ_blocs commit 0d86db7d42b608c386a54500064f5f9c9d7019a4 ecology parents: diff changeset	839 #.."X..Mytilus.sp.",
42b51a52e308 planemo upload for repository https://github.com/Marie59/champ_blocs commit 0d86db7d42b608c386a54500064f5f9c9d7019a4 ecology parents: diff changeset	840 #.."X..Hermelles",
42b51a52e308 planemo upload for repository https://github.com/Marie59/champ_blocs commit 0d86db7d42b608c386a54500064f5f9c9d7019a4 ecology parents: diff changeset	841 #.."X..Hydraires",
42b51a52e308 planemo upload for repository https://github.com/Marie59/champ_blocs commit 0d86db7d42b608c386a54500064f5f9c9d7019a4 ecology parents: diff changeset	842 "X..Eponges",
42b51a52e308 planemo upload for repository https://github.com/Marie59/champ_blocs commit 0d86db7d42b608c386a54500064f5f9c9d7019a4 ecology parents: diff changeset	843 "X..Ascidies.Coloniales",
42b51a52e308 planemo upload for repository https://github.com/Marie59/champ_blocs commit 0d86db7d42b608c386a54500064f5f9c9d7019a4 ecology parents: diff changeset	844 "X..Ascidies.Solitaires",
42b51a52e308 planemo upload for repository https://github.com/Marie59/champ_blocs commit 0d86db7d42b608c386a54500064f5f9c9d7019a4 ecology parents: diff changeset	845 "X..Bryozoaires.Dresses",
42b51a52e308 planemo upload for repository https://github.com/Marie59/champ_blocs commit 0d86db7d42b608c386a54500064f5f9c9d7019a4 ecology parents: diff changeset	846 "X..Balanes.Vivantes",
42b51a52e308 planemo upload for repository https://github.com/Marie59/champ_blocs commit 0d86db7d42b608c386a54500064f5f9c9d7019a4 ecology parents: diff changeset	847 #"Commentaires.Avant",
42b51a52e308 planemo upload for repository https://github.com/Marie59/champ_blocs commit 0d86db7d42b608c386a54500064f5f9c9d7019a4 ecology parents: diff changeset	848 "X..Surface.Accolement"#, # is NA, then replace by 0 as well because no sense to have a NA value for "% surface accolement" as well.
42b51a52e308 planemo upload for repository https://github.com/Marie59/champ_blocs commit 0d86db7d42b608c386a54500064f5f9c9d7019a4 ecology parents: diff changeset	849 #"Type.sustrat.observé",
42b51a52e308 planemo upload for repository https://github.com/Marie59/champ_blocs commit 0d86db7d42b608c386a54500064f5f9c9d7019a4 ecology parents: diff changeset	850 #"Commentaires",
42b51a52e308 planemo upload for repository https://github.com/Marie59/champ_blocs commit 0d86db7d42b608c386a54500064f5f9c9d7019a4 ecology parents: diff changeset	851 #."Nb.Cancer.pagurus..Tourteau.",
42b51a52e308 planemo upload for repository https://github.com/Marie59/champ_blocs commit 0d86db7d42b608c386a54500064f5f9c9d7019a4 ecology parents: diff changeset	852 #.."Nb.Necora.puber..Etrille.",
42b51a52e308 planemo upload for repository https://github.com/Marie59/champ_blocs commit 0d86db7d42b608c386a54500064f5f9c9d7019a4 ecology parents: diff changeset	853 #."Nb.Carcinus.maenas..Crabe.vert.",
42b51a52e308 planemo upload for repository https://github.com/Marie59/champ_blocs commit 0d86db7d42b608c386a54500064f5f9c9d7019a4 ecology parents: diff changeset	854 #."Nb.Nucella.lapilus..Pourpre.",
42b51a52e308 planemo upload for repository https://github.com/Marie59/champ_blocs commit 0d86db7d42b608c386a54500064f5f9c9d7019a4 ecology parents: diff changeset	855 #.."Nb.Eriphia.verrucosa..Crabe.verruqueux.",
42b51a52e308 planemo upload for repository https://github.com/Marie59/champ_blocs commit 0d86db7d42b608c386a54500064f5f9c9d7019a4 ecology parents: diff changeset	856 #.."Nb.Octopus.vulgaris..Poulpe.",
42b51a52e308 planemo upload for repository https://github.com/Marie59/champ_blocs commit 0d86db7d42b608c386a54500064f5f9c9d7019a4 ecology parents: diff changeset	857 #."Nb.Galathea..Galathées.",
42b51a52e308 planemo upload for repository https://github.com/Marie59/champ_blocs commit 0d86db7d42b608c386a54500064f5f9c9d7019a4 ecology parents: diff changeset	858 #.."Nb.Paracentrotus.lividus..Oursin.",
42b51a52e308 planemo upload for repository https://github.com/Marie59/champ_blocs commit 0d86db7d42b608c386a54500064f5f9c9d7019a4 ecology parents: diff changeset	859 #."Nb.Lophozozymus.incisus..ancien.Xantho.incisus.",
42b51a52e308 planemo upload for repository https://github.com/Marie59/champ_blocs commit 0d86db7d42b608c386a54500064f5f9c9d7019a4 ecology parents: diff changeset	860 #."Nb.Palaemon.sp..Crevette.bouquet.ou.crevette.rose.",
42b51a52e308 planemo upload for repository https://github.com/Marie59/champ_blocs commit 0d86db7d42b608c386a54500064f5f9c9d7019a4 ecology parents: diff changeset	861 #."Nb.Haliotis.tuberculata..Ormeau.",
42b51a52e308 planemo upload for repository https://github.com/Marie59/champ_blocs commit 0d86db7d42b608c386a54500064f5f9c9d7019a4 ecology parents: diff changeset	862 #."Nb.Stramonita.haemastoma..Pourpre.bouche.de.sang.",
42b51a52e308 planemo upload for repository https://github.com/Marie59/champ_blocs commit 0d86db7d42b608c386a54500064f5f9c9d7019a4 ecology parents: diff changeset	863 #."Nb.Littorina.littorea..Bigorneau.",
42b51a52e308 planemo upload for repository https://github.com/Marie59/champ_blocs commit 0d86db7d42b608c386a54500064f5f9c9d7019a4 ecology parents: diff changeset	864 #."Nb.Xantho.pilipes..Xanthe.poilu.",
42b51a52e308 planemo upload for repository https://github.com/Marie59/champ_blocs commit 0d86db7d42b608c386a54500064f5f9c9d7019a4 ecology parents: diff changeset	865 #."Nb.Mimachlamys.varia..Pétoncle.noir."
42b51a52e308 planemo upload for repository https://github.com/Marie59/champ_blocs commit 0d86db7d42b608c386a54500064f5f9c9d7019a4 ecology parents: diff changeset	866 )
42b51a52e308 planemo upload for repository https://github.com/Marie59/champ_blocs commit 0d86db7d42b608c386a54500064f5f9c9d7019a4 ecology parents: diff changeset	867 ], function(x) replace(x, is.na(x), 0))
42b51a52e308 planemo upload for repository https://github.com/Marie59/champ_blocs commit 0d86db7d42b608c386a54500064f5f9c9d7019a4 ecology parents: diff changeset	868
42b51a52e308 planemo upload for repository https://github.com/Marie59/champ_blocs commit 0d86db7d42b608c386a54500064f5f9c9d7019a4 ecology parents: diff changeset	869
42b51a52e308 planemo upload for repository https://github.com/Marie59/champ_blocs commit 0d86db7d42b608c386a54500064f5f9c9d7019a4 ecology parents: diff changeset	870 # egmp_basq_bm
42b51a52e308 planemo upload for repository https://github.com/Marie59/champ_blocs commit 0d86db7d42b608c386a54500064f5f9c9d7019a4 ecology parents: diff changeset	871 egmp_basq_bm[, c(
42b51a52e308 planemo upload for repository https://github.com/Marie59/champ_blocs commit 0d86db7d42b608c386a54500064f5f9c9d7019a4 ecology parents: diff changeset	872 "X..algues.brunes",
42b51a52e308 planemo upload for repository https://github.com/Marie59/champ_blocs commit 0d86db7d42b608c386a54500064f5f9c9d7019a4 ecology parents: diff changeset	873 "Strate.algues.brunes",
42b51a52e308 planemo upload for repository https://github.com/Marie59/champ_blocs commit 0d86db7d42b608c386a54500064f5f9c9d7019a4 ecology parents: diff changeset	874 "X..algues.rouges",
42b51a52e308 planemo upload for repository https://github.com/Marie59/champ_blocs commit 0d86db7d42b608c386a54500064f5f9c9d7019a4 ecology parents: diff changeset	875 "Strate.algues.rouges",
42b51a52e308 planemo upload for repository https://github.com/Marie59/champ_blocs commit 0d86db7d42b608c386a54500064f5f9c9d7019a4 ecology parents: diff changeset	876 "X..algues.vertes",
42b51a52e308 planemo upload for repository https://github.com/Marie59/champ_blocs commit 0d86db7d42b608c386a54500064f5f9c9d7019a4 ecology parents: diff changeset	877 "Strate.algues.vertes",
42b51a52e308 planemo upload for repository https://github.com/Marie59/champ_blocs commit 0d86db7d42b608c386a54500064f5f9c9d7019a4 ecology parents: diff changeset	878 "X..Cladophora",
42b51a52e308 planemo upload for repository https://github.com/Marie59/champ_blocs commit 0d86db7d42b608c386a54500064f5f9c9d7019a4 ecology parents: diff changeset	879 "X..Lithophyllum",
42b51a52e308 planemo upload for repository https://github.com/Marie59/champ_blocs commit 0d86db7d42b608c386a54500064f5f9c9d7019a4 ecology parents: diff changeset	880 "X..Recouvrement.Sediment", # is NA, then replace by 0 as well because no sense to have a NA value for "% recouvrement sédiment" as well.
42b51a52e308 planemo upload for repository https://github.com/Marie59/champ_blocs commit 0d86db7d42b608c386a54500064f5f9c9d7019a4 ecology parents: diff changeset	881 #"Type.Sediment",
42b51a52e308 planemo upload for repository https://github.com/Marie59/champ_blocs commit 0d86db7d42b608c386a54500064f5f9c9d7019a4 ecology parents: diff changeset	882 "X..Roche.Nue", # is NA, then replace by 0 as well because no sense to have a NA value for "% roche nue" as well.
42b51a52e308 planemo upload for repository https://github.com/Marie59/champ_blocs commit 0d86db7d42b608c386a54500064f5f9c9d7019a4 ecology parents: diff changeset	883 "Nb.Littorina.obtusata",
42b51a52e308 planemo upload for repository https://github.com/Marie59/champ_blocs commit 0d86db7d42b608c386a54500064f5f9c9d7019a4 ecology parents: diff changeset	884 "Nb.Gibbula.cineraria",
42b51a52e308 planemo upload for repository https://github.com/Marie59/champ_blocs commit 0d86db7d42b608c386a54500064f5f9c9d7019a4 ecology parents: diff changeset	885 "Nb.Gibbula.pennanti",
42b51a52e308 planemo upload for repository https://github.com/Marie59/champ_blocs commit 0d86db7d42b608c386a54500064f5f9c9d7019a4 ecology parents: diff changeset	886 "Nb.Gibbula.umbilicalis",
42b51a52e308 planemo upload for repository https://github.com/Marie59/champ_blocs commit 0d86db7d42b608c386a54500064f5f9c9d7019a4 ecology parents: diff changeset	887 "Nb.Phallusia.mamillata",
42b51a52e308 planemo upload for repository https://github.com/Marie59/champ_blocs commit 0d86db7d42b608c386a54500064f5f9c9d7019a4 ecology parents: diff changeset	888 "Nb.Tethya.aurantium",
42b51a52e308 planemo upload for repository https://github.com/Marie59/champ_blocs commit 0d86db7d42b608c386a54500064f5f9c9d7019a4 ecology parents: diff changeset	889 #"Nb.Spirobranchus.lamarckii.1B",
42b51a52e308 planemo upload for repository https://github.com/Marie59/champ_blocs commit 0d86db7d42b608c386a54500064f5f9c9d7019a4 ecology parents: diff changeset	890 #"Nb.Spirobranchus.lamarckii.2B",
42b51a52e308 planemo upload for repository https://github.com/Marie59/champ_blocs commit 0d86db7d42b608c386a54500064f5f9c9d7019a4 ecology parents: diff changeset	891 #"Nb.Spirobranchus.lamarckii.3B",
42b51a52e308 planemo upload for repository https://github.com/Marie59/champ_blocs commit 0d86db7d42b608c386a54500064f5f9c9d7019a4 ecology parents: diff changeset	892 #"Nb.Spirobranchus.lamarckii.4B",
42b51a52e308 planemo upload for repository https://github.com/Marie59/champ_blocs commit 0d86db7d42b608c386a54500064f5f9c9d7019a4 ecology parents: diff changeset	893 #"Nb.Spirobranchus.lamarckii.5B",
42b51a52e308 planemo upload for repository https://github.com/Marie59/champ_blocs commit 0d86db7d42b608c386a54500064f5f9c9d7019a4 ecology parents: diff changeset	894 "Nb.Spirobranchus.lamarckii.total",
42b51a52e308 planemo upload for repository https://github.com/Marie59/champ_blocs commit 0d86db7d42b608c386a54500064f5f9c9d7019a4 ecology parents: diff changeset	895 #"Nb.spirorbis.1A",
42b51a52e308 planemo upload for repository https://github.com/Marie59/champ_blocs commit 0d86db7d42b608c386a54500064f5f9c9d7019a4 ecology parents: diff changeset	896 #"Nb.spirorbis.2A",
42b51a52e308 planemo upload for repository https://github.com/Marie59/champ_blocs commit 0d86db7d42b608c386a54500064f5f9c9d7019a4 ecology parents: diff changeset	897 #"Nb.spirorbis.3A",
42b51a52e308 planemo upload for repository https://github.com/Marie59/champ_blocs commit 0d86db7d42b608c386a54500064f5f9c9d7019a4 ecology parents: diff changeset	898 #"Nb.spirorbis.4A",
42b51a52e308 planemo upload for repository https://github.com/Marie59/champ_blocs commit 0d86db7d42b608c386a54500064f5f9c9d7019a4 ecology parents: diff changeset	899 #"Nb.spirorbis.5A",
42b51a52e308 planemo upload for repository https://github.com/Marie59/champ_blocs commit 0d86db7d42b608c386a54500064f5f9c9d7019a4 ecology parents: diff changeset	900 "Nb.spirorbis.total",
42b51a52e308 planemo upload for repository https://github.com/Marie59/champ_blocs commit 0d86db7d42b608c386a54500064f5f9c9d7019a4 ecology parents: diff changeset	901 "Nb.Crassostrea.gigas",
42b51a52e308 planemo upload for repository https://github.com/Marie59/champ_blocs commit 0d86db7d42b608c386a54500064f5f9c9d7019a4 ecology parents: diff changeset	902 "Nb.Ostrea.edulis",
42b51a52e308 planemo upload for repository https://github.com/Marie59/champ_blocs commit 0d86db7d42b608c386a54500064f5f9c9d7019a4 ecology parents: diff changeset	903 "X..Mytilus.sp.",
42b51a52e308 planemo upload for repository https://github.com/Marie59/champ_blocs commit 0d86db7d42b608c386a54500064f5f9c9d7019a4 ecology parents: diff changeset	904 "X..Hermelles",
42b51a52e308 planemo upload for repository https://github.com/Marie59/champ_blocs commit 0d86db7d42b608c386a54500064f5f9c9d7019a4 ecology parents: diff changeset	905 "X..Hydraires",
42b51a52e308 planemo upload for repository https://github.com/Marie59/champ_blocs commit 0d86db7d42b608c386a54500064f5f9c9d7019a4 ecology parents: diff changeset	906 "X..Eponges",
42b51a52e308 planemo upload for repository https://github.com/Marie59/champ_blocs commit 0d86db7d42b608c386a54500064f5f9c9d7019a4 ecology parents: diff changeset	907 "X..Ascidies.Coloniales",
42b51a52e308 planemo upload for repository https://github.com/Marie59/champ_blocs commit 0d86db7d42b608c386a54500064f5f9c9d7019a4 ecology parents: diff changeset	908 "X..Ascidies.Solitaires",
42b51a52e308 planemo upload for repository https://github.com/Marie59/champ_blocs commit 0d86db7d42b608c386a54500064f5f9c9d7019a4 ecology parents: diff changeset	909 "X..Bryozoaires.Dresses",
42b51a52e308 planemo upload for repository https://github.com/Marie59/champ_blocs commit 0d86db7d42b608c386a54500064f5f9c9d7019a4 ecology parents: diff changeset	910 "X..Balanes.Vivantes",
42b51a52e308 planemo upload for repository https://github.com/Marie59/champ_blocs commit 0d86db7d42b608c386a54500064f5f9c9d7019a4 ecology parents: diff changeset	911 #"Commentaires.Avant",
42b51a52e308 planemo upload for repository https://github.com/Marie59/champ_blocs commit 0d86db7d42b608c386a54500064f5f9c9d7019a4 ecology parents: diff changeset	912 "X..Surface.Accolement", # is NA, then replace by 0 as well because no sense to have a NA value for "% surface accolement" as well.
42b51a52e308 planemo upload for repository https://github.com/Marie59/champ_blocs commit 0d86db7d42b608c386a54500064f5f9c9d7019a4 ecology parents: diff changeset	913 #"Type.sustrat.observé",
42b51a52e308 planemo upload for repository https://github.com/Marie59/champ_blocs commit 0d86db7d42b608c386a54500064f5f9c9d7019a4 ecology parents: diff changeset	914 #"Commentaires",
42b51a52e308 planemo upload for repository https://github.com/Marie59/champ_blocs commit 0d86db7d42b608c386a54500064f5f9c9d7019a4 ecology parents: diff changeset	915 "Nb.Cancer.pagurus..Tourteau.",
42b51a52e308 planemo upload for repository https://github.com/Marie59/champ_blocs commit 0d86db7d42b608c386a54500064f5f9c9d7019a4 ecology parents: diff changeset	916 "Nb.Necora.puber..Etrille.",
42b51a52e308 planemo upload for repository https://github.com/Marie59/champ_blocs commit 0d86db7d42b608c386a54500064f5f9c9d7019a4 ecology parents: diff changeset	917 "Nb.Carcinus.maenas..Crabe.vert.",
42b51a52e308 planemo upload for repository https://github.com/Marie59/champ_blocs commit 0d86db7d42b608c386a54500064f5f9c9d7019a4 ecology parents: diff changeset	918 "Nb.Nucella.lapilus..Pourpre.",
42b51a52e308 planemo upload for repository https://github.com/Marie59/champ_blocs commit 0d86db7d42b608c386a54500064f5f9c9d7019a4 ecology parents: diff changeset	919 "Nb.Eriphia.verrucosa..Crabe.verruqueux.",
42b51a52e308 planemo upload for repository https://github.com/Marie59/champ_blocs commit 0d86db7d42b608c386a54500064f5f9c9d7019a4 ecology parents: diff changeset	920 "Nb.Octopus.vulgaris..Poulpe.",
42b51a52e308 planemo upload for repository https://github.com/Marie59/champ_blocs commit 0d86db7d42b608c386a54500064f5f9c9d7019a4 ecology parents: diff changeset	921 "Nb.Galathea..Galathées.",
42b51a52e308 planemo upload for repository https://github.com/Marie59/champ_blocs commit 0d86db7d42b608c386a54500064f5f9c9d7019a4 ecology parents: diff changeset	922 "Nb.Paracentrotus.lividus..Oursin.",
42b51a52e308 planemo upload for repository https://github.com/Marie59/champ_blocs commit 0d86db7d42b608c386a54500064f5f9c9d7019a4 ecology parents: diff changeset	923 "Nb.Lophozozymus.incisus..ancien.Xantho.incisus.",
42b51a52e308 planemo upload for repository https://github.com/Marie59/champ_blocs commit 0d86db7d42b608c386a54500064f5f9c9d7019a4 ecology parents: diff changeset	924 "Nb.Palaemon.sp..Crevette.bouquet.ou.crevette.rose.",
42b51a52e308 planemo upload for repository https://github.com/Marie59/champ_blocs commit 0d86db7d42b608c386a54500064f5f9c9d7019a4 ecology parents: diff changeset	925 "Nb.Haliotis.tuberculata..Ormeau.",
42b51a52e308 planemo upload for repository https://github.com/Marie59/champ_blocs commit 0d86db7d42b608c386a54500064f5f9c9d7019a4 ecology parents: diff changeset	926 "Nb.Stramonita.haemastoma..Pourpre.bouche.de.sang.",
42b51a52e308 planemo upload for repository https://github.com/Marie59/champ_blocs commit 0d86db7d42b608c386a54500064f5f9c9d7019a4 ecology parents: diff changeset	927 "Nb.Littorina.littorea..Bigorneau.",
42b51a52e308 planemo upload for repository https://github.com/Marie59/champ_blocs commit 0d86db7d42b608c386a54500064f5f9c9d7019a4 ecology parents: diff changeset	928 "Nb.Xantho.pilipes..Xanthe.poilu.",
42b51a52e308 planemo upload for repository https://github.com/Marie59/champ_blocs commit 0d86db7d42b608c386a54500064f5f9c9d7019a4 ecology parents: diff changeset	929 "Nb.Mimachlamys.varia..Pétoncle.noir."
42b51a52e308 planemo upload for repository https://github.com/Marie59/champ_blocs commit 0d86db7d42b608c386a54500064f5f9c9d7019a4 ecology parents: diff changeset	930 )
42b51a52e308 planemo upload for repository https://github.com/Marie59/champ_blocs commit 0d86db7d42b608c386a54500064f5f9c9d7019a4 ecology parents: diff changeset	931 ] <- lapply(egmp_basq_bm[, c(
42b51a52e308 planemo upload for repository https://github.com/Marie59/champ_blocs commit 0d86db7d42b608c386a54500064f5f9c9d7019a4 ecology parents: diff changeset	932 "X..algues.brunes",
42b51a52e308 planemo upload for repository https://github.com/Marie59/champ_blocs commit 0d86db7d42b608c386a54500064f5f9c9d7019a4 ecology parents: diff changeset	933 "Strate.algues.brunes",
42b51a52e308 planemo upload for repository https://github.com/Marie59/champ_blocs commit 0d86db7d42b608c386a54500064f5f9c9d7019a4 ecology parents: diff changeset	934 "X..algues.rouges",
42b51a52e308 planemo upload for repository https://github.com/Marie59/champ_blocs commit 0d86db7d42b608c386a54500064f5f9c9d7019a4 ecology parents: diff changeset	935 "Strate.algues.rouges",
42b51a52e308 planemo upload for repository https://github.com/Marie59/champ_blocs commit 0d86db7d42b608c386a54500064f5f9c9d7019a4 ecology parents: diff changeset	936 "X..algues.vertes",
42b51a52e308 planemo upload for repository https://github.com/Marie59/champ_blocs commit 0d86db7d42b608c386a54500064f5f9c9d7019a4 ecology parents: diff changeset	937 "Strate.algues.vertes",
42b51a52e308 planemo upload for repository https://github.com/Marie59/champ_blocs commit 0d86db7d42b608c386a54500064f5f9c9d7019a4 ecology parents: diff changeset	938 "X..Cladophora",
42b51a52e308 planemo upload for repository https://github.com/Marie59/champ_blocs commit 0d86db7d42b608c386a54500064f5f9c9d7019a4 ecology parents: diff changeset	939 "X..Lithophyllum",
42b51a52e308 planemo upload for repository https://github.com/Marie59/champ_blocs commit 0d86db7d42b608c386a54500064f5f9c9d7019a4 ecology parents: diff changeset	940 "X..Recouvrement.Sediment", # is NA, then replace by 0 as well because no sense to have a NA value for "% recouvrement sédiment" as well.
42b51a52e308 planemo upload for repository https://github.com/Marie59/champ_blocs commit 0d86db7d42b608c386a54500064f5f9c9d7019a4 ecology parents: diff changeset	941 #"Type.Sediment",
42b51a52e308 planemo upload for repository https://github.com/Marie59/champ_blocs commit 0d86db7d42b608c386a54500064f5f9c9d7019a4 ecology parents: diff changeset	942 "X..Roche.Nue", # is NA, then replace by 0 as well because no sense to have a NA value for "% roche nue" as well.
42b51a52e308 planemo upload for repository https://github.com/Marie59/champ_blocs commit 0d86db7d42b608c386a54500064f5f9c9d7019a4 ecology parents: diff changeset	943 "Nb.Littorina.obtusata",
42b51a52e308 planemo upload for repository https://github.com/Marie59/champ_blocs commit 0d86db7d42b608c386a54500064f5f9c9d7019a4 ecology parents: diff changeset	944 "Nb.Gibbula.cineraria",
42b51a52e308 planemo upload for repository https://github.com/Marie59/champ_blocs commit 0d86db7d42b608c386a54500064f5f9c9d7019a4 ecology parents: diff changeset	945 "Nb.Gibbula.pennanti",
42b51a52e308 planemo upload for repository https://github.com/Marie59/champ_blocs commit 0d86db7d42b608c386a54500064f5f9c9d7019a4 ecology parents: diff changeset	946 "Nb.Gibbula.umbilicalis",
42b51a52e308 planemo upload for repository https://github.com/Marie59/champ_blocs commit 0d86db7d42b608c386a54500064f5f9c9d7019a4 ecology parents: diff changeset	947 "Nb.Phallusia.mamillata",
42b51a52e308 planemo upload for repository https://github.com/Marie59/champ_blocs commit 0d86db7d42b608c386a54500064f5f9c9d7019a4 ecology parents: diff changeset	948 "Nb.Tethya.aurantium",
42b51a52e308 planemo upload for repository https://github.com/Marie59/champ_blocs commit 0d86db7d42b608c386a54500064f5f9c9d7019a4 ecology parents: diff changeset	949 #"Nb.Spirobranchus.lamarckii.1B",
42b51a52e308 planemo upload for repository https://github.com/Marie59/champ_blocs commit 0d86db7d42b608c386a54500064f5f9c9d7019a4 ecology parents: diff changeset	950 #"Nb.Spirobranchus.lamarckii.2B",
42b51a52e308 planemo upload for repository https://github.com/Marie59/champ_blocs commit 0d86db7d42b608c386a54500064f5f9c9d7019a4 ecology parents: diff changeset	951 #"Nb.Spirobranchus.lamarckii.3B",
42b51a52e308 planemo upload for repository https://github.com/Marie59/champ_blocs commit 0d86db7d42b608c386a54500064f5f9c9d7019a4 ecology parents: diff changeset	952 #"Nb.Spirobranchus.lamarckii.4B",
42b51a52e308 planemo upload for repository https://github.com/Marie59/champ_blocs commit 0d86db7d42b608c386a54500064f5f9c9d7019a4 ecology parents: diff changeset	953 #"Nb.Spirobranchus.lamarckii.5B",
42b51a52e308 planemo upload for repository https://github.com/Marie59/champ_blocs commit 0d86db7d42b608c386a54500064f5f9c9d7019a4 ecology parents: diff changeset	954 "Nb.Spirobranchus.lamarckii.total",
42b51a52e308 planemo upload for repository https://github.com/Marie59/champ_blocs commit 0d86db7d42b608c386a54500064f5f9c9d7019a4 ecology parents: diff changeset	955 #"Nb.spirorbis.1A",
42b51a52e308 planemo upload for repository https://github.com/Marie59/champ_blocs commit 0d86db7d42b608c386a54500064f5f9c9d7019a4 ecology parents: diff changeset	956 #"Nb.spirorbis.2A",
42b51a52e308 planemo upload for repository https://github.com/Marie59/champ_blocs commit 0d86db7d42b608c386a54500064f5f9c9d7019a4 ecology parents: diff changeset	957 #"Nb.spirorbis.3A",
42b51a52e308 planemo upload for repository https://github.com/Marie59/champ_blocs commit 0d86db7d42b608c386a54500064f5f9c9d7019a4 ecology parents: diff changeset	958 #"Nb.spirorbis.4A",
42b51a52e308 planemo upload for repository https://github.com/Marie59/champ_blocs commit 0d86db7d42b608c386a54500064f5f9c9d7019a4 ecology parents: diff changeset	959 #"Nb.spirorbis.5A",
42b51a52e308 planemo upload for repository https://github.com/Marie59/champ_blocs commit 0d86db7d42b608c386a54500064f5f9c9d7019a4 ecology parents: diff changeset	960 "Nb.spirorbis.total",
42b51a52e308 planemo upload for repository https://github.com/Marie59/champ_blocs commit 0d86db7d42b608c386a54500064f5f9c9d7019a4 ecology parents: diff changeset	961 "Nb.Crassostrea.gigas",
42b51a52e308 planemo upload for repository https://github.com/Marie59/champ_blocs commit 0d86db7d42b608c386a54500064f5f9c9d7019a4 ecology parents: diff changeset	962 "Nb.Ostrea.edulis",
42b51a52e308 planemo upload for repository https://github.com/Marie59/champ_blocs commit 0d86db7d42b608c386a54500064f5f9c9d7019a4 ecology parents: diff changeset	963 "X..Mytilus.sp.",
42b51a52e308 planemo upload for repository https://github.com/Marie59/champ_blocs commit 0d86db7d42b608c386a54500064f5f9c9d7019a4 ecology parents: diff changeset	964 "X..Hermelles",
42b51a52e308 planemo upload for repository https://github.com/Marie59/champ_blocs commit 0d86db7d42b608c386a54500064f5f9c9d7019a4 ecology parents: diff changeset	965 "X..Hydraires",
42b51a52e308 planemo upload for repository https://github.com/Marie59/champ_blocs commit 0d86db7d42b608c386a54500064f5f9c9d7019a4 ecology parents: diff changeset	966 "X..Eponges",
42b51a52e308 planemo upload for repository https://github.com/Marie59/champ_blocs commit 0d86db7d42b608c386a54500064f5f9c9d7019a4 ecology parents: diff changeset	967 "X..Ascidies.Coloniales",
42b51a52e308 planemo upload for repository https://github.com/Marie59/champ_blocs commit 0d86db7d42b608c386a54500064f5f9c9d7019a4 ecology parents: diff changeset	968 "X..Ascidies.Solitaires",
42b51a52e308 planemo upload for repository https://github.com/Marie59/champ_blocs commit 0d86db7d42b608c386a54500064f5f9c9d7019a4 ecology parents: diff changeset	969 "X..Bryozoaires.Dresses",
42b51a52e308 planemo upload for repository https://github.com/Marie59/champ_blocs commit 0d86db7d42b608c386a54500064f5f9c9d7019a4 ecology parents: diff changeset	970 "X..Balanes.Vivantes",
42b51a52e308 planemo upload for repository https://github.com/Marie59/champ_blocs commit 0d86db7d42b608c386a54500064f5f9c9d7019a4 ecology parents: diff changeset	971 #"Commentaires.Avant",
42b51a52e308 planemo upload for repository https://github.com/Marie59/champ_blocs commit 0d86db7d42b608c386a54500064f5f9c9d7019a4 ecology parents: diff changeset	972 "X..Surface.Accolement", # is NA, then replace by 0 as well because no sense to have a NA value for "% surface accolement" as well.
42b51a52e308 planemo upload for repository https://github.com/Marie59/champ_blocs commit 0d86db7d42b608c386a54500064f5f9c9d7019a4 ecology parents: diff changeset	973 #"Type.sustrat.observé",
42b51a52e308 planemo upload for repository https://github.com/Marie59/champ_blocs commit 0d86db7d42b608c386a54500064f5f9c9d7019a4 ecology parents: diff changeset	974 #"Commentaires",
42b51a52e308 planemo upload for repository https://github.com/Marie59/champ_blocs commit 0d86db7d42b608c386a54500064f5f9c9d7019a4 ecology parents: diff changeset	975 "Nb.Cancer.pagurus..Tourteau.",
42b51a52e308 planemo upload for repository https://github.com/Marie59/champ_blocs commit 0d86db7d42b608c386a54500064f5f9c9d7019a4 ecology parents: diff changeset	976 "Nb.Necora.puber..Etrille.",
42b51a52e308 planemo upload for repository https://github.com/Marie59/champ_blocs commit 0d86db7d42b608c386a54500064f5f9c9d7019a4 ecology parents: diff changeset	977 "Nb.Carcinus.maenas..Crabe.vert.",
42b51a52e308 planemo upload for repository https://github.com/Marie59/champ_blocs commit 0d86db7d42b608c386a54500064f5f9c9d7019a4 ecology parents: diff changeset	978 "Nb.Nucella.lapilus..Pourpre.",
42b51a52e308 planemo upload for repository https://github.com/Marie59/champ_blocs commit 0d86db7d42b608c386a54500064f5f9c9d7019a4 ecology parents: diff changeset	979 "Nb.Eriphia.verrucosa..Crabe.verruqueux.",
42b51a52e308 planemo upload for repository https://github.com/Marie59/champ_blocs commit 0d86db7d42b608c386a54500064f5f9c9d7019a4 ecology parents: diff changeset	980 "Nb.Octopus.vulgaris..Poulpe.",
42b51a52e308 planemo upload for repository https://github.com/Marie59/champ_blocs commit 0d86db7d42b608c386a54500064f5f9c9d7019a4 ecology parents: diff changeset	981 "Nb.Galathea..Galathées.",
42b51a52e308 planemo upload for repository https://github.com/Marie59/champ_blocs commit 0d86db7d42b608c386a54500064f5f9c9d7019a4 ecology parents: diff changeset	982 "Nb.Paracentrotus.lividus..Oursin.",
42b51a52e308 planemo upload for repository https://github.com/Marie59/champ_blocs commit 0d86db7d42b608c386a54500064f5f9c9d7019a4 ecology parents: diff changeset	983 "Nb.Lophozozymus.incisus..ancien.Xantho.incisus.",
42b51a52e308 planemo upload for repository https://github.com/Marie59/champ_blocs commit 0d86db7d42b608c386a54500064f5f9c9d7019a4 ecology parents: diff changeset	984 "Nb.Palaemon.sp..Crevette.bouquet.ou.crevette.rose.",
42b51a52e308 planemo upload for repository https://github.com/Marie59/champ_blocs commit 0d86db7d42b608c386a54500064f5f9c9d7019a4 ecology parents: diff changeset	985 "Nb.Haliotis.tuberculata..Ormeau.",
42b51a52e308 planemo upload for repository https://github.com/Marie59/champ_blocs commit 0d86db7d42b608c386a54500064f5f9c9d7019a4 ecology parents: diff changeset	986 "Nb.Stramonita.haemastoma..Pourpre.bouche.de.sang.",
42b51a52e308 planemo upload for repository https://github.com/Marie59/champ_blocs commit 0d86db7d42b608c386a54500064f5f9c9d7019a4 ecology parents: diff changeset	987 "Nb.Littorina.littorea..Bigorneau.",
42b51a52e308 planemo upload for repository https://github.com/Marie59/champ_blocs commit 0d86db7d42b608c386a54500064f5f9c9d7019a4 ecology parents: diff changeset	988 "Nb.Xantho.pilipes..Xanthe.poilu.",
42b51a52e308 planemo upload for repository https://github.com/Marie59/champ_blocs commit 0d86db7d42b608c386a54500064f5f9c9d7019a4 ecology parents: diff changeset	989 "Nb.Mimachlamys.varia..Pétoncle.noir."
42b51a52e308 planemo upload for repository https://github.com/Marie59/champ_blocs commit 0d86db7d42b608c386a54500064f5f9c9d7019a4 ecology parents: diff changeset	990 )
42b51a52e308 planemo upload for repository https://github.com/Marie59/champ_blocs commit 0d86db7d42b608c386a54500064f5f9c9d7019a4 ecology parents: diff changeset	991 ], function(x) replace(x, is.na(x), 0))
42b51a52e308 planemo upload for repository https://github.com/Marie59/champ_blocs commit 0d86db7d42b608c386a54500064f5f9c9d7019a4 ecology parents: diff changeset	992
42b51a52e308 planemo upload for repository https://github.com/Marie59/champ_blocs commit 0d86db7d42b608c386a54500064f5f9c9d7019a4 ecology parents: diff changeset	993
42b51a52e308 planemo upload for repository https://github.com/Marie59/champ_blocs commit 0d86db7d42b608c386a54500064f5f9c9d7019a4 ecology parents: diff changeset	994 # egmp_basq_bf
42b51a52e308 planemo upload for repository https://github.com/Marie59/champ_blocs commit 0d86db7d42b608c386a54500064f5f9c9d7019a4 ecology parents: diff changeset	995 egmp_basq_bf[, c(
42b51a52e308 planemo upload for repository https://github.com/Marie59/champ_blocs commit 0d86db7d42b608c386a54500064f5f9c9d7019a4 ecology parents: diff changeset	996 "X..algues.brunes",
42b51a52e308 planemo upload for repository https://github.com/Marie59/champ_blocs commit 0d86db7d42b608c386a54500064f5f9c9d7019a4 ecology parents: diff changeset	997 "Strate.algues.brunes",
42b51a52e308 planemo upload for repository https://github.com/Marie59/champ_blocs commit 0d86db7d42b608c386a54500064f5f9c9d7019a4 ecology parents: diff changeset	998 "X..algues.rouges",
42b51a52e308 planemo upload for repository https://github.com/Marie59/champ_blocs commit 0d86db7d42b608c386a54500064f5f9c9d7019a4 ecology parents: diff changeset	999 "Strate.algues.rouges",
42b51a52e308 planemo upload for repository https://github.com/Marie59/champ_blocs commit 0d86db7d42b608c386a54500064f5f9c9d7019a4 ecology parents: diff changeset	1000 "X..algues.vertes",
42b51a52e308 planemo upload for repository https://github.com/Marie59/champ_blocs commit 0d86db7d42b608c386a54500064f5f9c9d7019a4 ecology parents: diff changeset	1001 "Strate.algues.vertes",
42b51a52e308 planemo upload for repository https://github.com/Marie59/champ_blocs commit 0d86db7d42b608c386a54500064f5f9c9d7019a4 ecology parents: diff changeset	1002 "X..Cladophora",
42b51a52e308 planemo upload for repository https://github.com/Marie59/champ_blocs commit 0d86db7d42b608c386a54500064f5f9c9d7019a4 ecology parents: diff changeset	1003 "X..Lithophyllum",
42b51a52e308 planemo upload for repository https://github.com/Marie59/champ_blocs commit 0d86db7d42b608c386a54500064f5f9c9d7019a4 ecology parents: diff changeset	1004 "X..Recouvrement.Sediment", # is NA, then replace by 0 as well because no sense to have a NA value for "% recouvrement sédiment" as well.
42b51a52e308 planemo upload for repository https://github.com/Marie59/champ_blocs commit 0d86db7d42b608c386a54500064f5f9c9d7019a4 ecology parents: diff changeset	1005 #"Type.Sediment",
42b51a52e308 planemo upload for repository https://github.com/Marie59/champ_blocs commit 0d86db7d42b608c386a54500064f5f9c9d7019a4 ecology parents: diff changeset	1006 "X..Roche.Nue", # is NA, then replace by 0 as well because no sense to have a NA value for "% roche nue" as well.
42b51a52e308 planemo upload for repository https://github.com/Marie59/champ_blocs commit 0d86db7d42b608c386a54500064f5f9c9d7019a4 ecology parents: diff changeset	1007 "Nb.Littorina.obtusata",
42b51a52e308 planemo upload for repository https://github.com/Marie59/champ_blocs commit 0d86db7d42b608c386a54500064f5f9c9d7019a4 ecology parents: diff changeset	1008 "Nb.Gibbula.cineraria",
42b51a52e308 planemo upload for repository https://github.com/Marie59/champ_blocs commit 0d86db7d42b608c386a54500064f5f9c9d7019a4 ecology parents: diff changeset	1009 "Nb.Gibbula.pennanti",
42b51a52e308 planemo upload for repository https://github.com/Marie59/champ_blocs commit 0d86db7d42b608c386a54500064f5f9c9d7019a4 ecology parents: diff changeset	1010 "Nb.Gibbula.umbilicalis",
42b51a52e308 planemo upload for repository https://github.com/Marie59/champ_blocs commit 0d86db7d42b608c386a54500064f5f9c9d7019a4 ecology parents: diff changeset	1011 "Nb.Phallusia.mamillata",
42b51a52e308 planemo upload for repository https://github.com/Marie59/champ_blocs commit 0d86db7d42b608c386a54500064f5f9c9d7019a4 ecology parents: diff changeset	1012 "Nb.Tethya.aurantium",
42b51a52e308 planemo upload for repository https://github.com/Marie59/champ_blocs commit 0d86db7d42b608c386a54500064f5f9c9d7019a4 ecology parents: diff changeset	1013 #"Nb.Spirobranchus.lamarckii.1B",
42b51a52e308 planemo upload for repository https://github.com/Marie59/champ_blocs commit 0d86db7d42b608c386a54500064f5f9c9d7019a4 ecology parents: diff changeset	1014 #"Nb.Spirobranchus.lamarckii.2B",
42b51a52e308 planemo upload for repository https://github.com/Marie59/champ_blocs commit 0d86db7d42b608c386a54500064f5f9c9d7019a4 ecology parents: diff changeset	1015 #"Nb.Spirobranchus.lamarckii.3B",
42b51a52e308 planemo upload for repository https://github.com/Marie59/champ_blocs commit 0d86db7d42b608c386a54500064f5f9c9d7019a4 ecology parents: diff changeset	1016 #"Nb.Spirobranchus.lamarckii.4B",
42b51a52e308 planemo upload for repository https://github.com/Marie59/champ_blocs commit 0d86db7d42b608c386a54500064f5f9c9d7019a4 ecology parents: diff changeset	1017 #"Nb.Spirobranchus.lamarckii.5B",
42b51a52e308 planemo upload for repository https://github.com/Marie59/champ_blocs commit 0d86db7d42b608c386a54500064f5f9c9d7019a4 ecology parents: diff changeset	1018 "Nb.Spirobranchus.lamarckii.total",
42b51a52e308 planemo upload for repository https://github.com/Marie59/champ_blocs commit 0d86db7d42b608c386a54500064f5f9c9d7019a4 ecology parents: diff changeset	1019 #"Nb.spirorbis.1A",
42b51a52e308 planemo upload for repository https://github.com/Marie59/champ_blocs commit 0d86db7d42b608c386a54500064f5f9c9d7019a4 ecology parents: diff changeset	1020 #"Nb.spirorbis.2A",
42b51a52e308 planemo upload for repository https://github.com/Marie59/champ_blocs commit 0d86db7d42b608c386a54500064f5f9c9d7019a4 ecology parents: diff changeset	1021 #"Nb.spirorbis.3A",
42b51a52e308 planemo upload for repository https://github.com/Marie59/champ_blocs commit 0d86db7d42b608c386a54500064f5f9c9d7019a4 ecology parents: diff changeset	1022 #"Nb.spirorbis.4A",
42b51a52e308 planemo upload for repository https://github.com/Marie59/champ_blocs commit 0d86db7d42b608c386a54500064f5f9c9d7019a4 ecology parents: diff changeset	1023 #"Nb.spirorbis.5A",
42b51a52e308 planemo upload for repository https://github.com/Marie59/champ_blocs commit 0d86db7d42b608c386a54500064f5f9c9d7019a4 ecology parents: diff changeset	1024 "Nb.spirorbis.total",
42b51a52e308 planemo upload for repository https://github.com/Marie59/champ_blocs commit 0d86db7d42b608c386a54500064f5f9c9d7019a4 ecology parents: diff changeset	1025 "Nb.Crassostrea.gigas",
42b51a52e308 planemo upload for repository https://github.com/Marie59/champ_blocs commit 0d86db7d42b608c386a54500064f5f9c9d7019a4 ecology parents: diff changeset	1026 "Nb.Ostrea.edulis",
42b51a52e308 planemo upload for repository https://github.com/Marie59/champ_blocs commit 0d86db7d42b608c386a54500064f5f9c9d7019a4 ecology parents: diff changeset	1027 "X..Mytilus.sp.",
42b51a52e308 planemo upload for repository https://github.com/Marie59/champ_blocs commit 0d86db7d42b608c386a54500064f5f9c9d7019a4 ecology parents: diff changeset	1028 "X..Hermelles",
42b51a52e308 planemo upload for repository https://github.com/Marie59/champ_blocs commit 0d86db7d42b608c386a54500064f5f9c9d7019a4 ecology parents: diff changeset	1029 "X..Hydraires",
42b51a52e308 planemo upload for repository https://github.com/Marie59/champ_blocs commit 0d86db7d42b608c386a54500064f5f9c9d7019a4 ecology parents: diff changeset	1030 "X..Eponges",
42b51a52e308 planemo upload for repository https://github.com/Marie59/champ_blocs commit 0d86db7d42b608c386a54500064f5f9c9d7019a4 ecology parents: diff changeset	1031 "X..Ascidies.Coloniales",
42b51a52e308 planemo upload for repository https://github.com/Marie59/champ_blocs commit 0d86db7d42b608c386a54500064f5f9c9d7019a4 ecology parents: diff changeset	1032 "X..Ascidies.Solitaires",
42b51a52e308 planemo upload for repository https://github.com/Marie59/champ_blocs commit 0d86db7d42b608c386a54500064f5f9c9d7019a4 ecology parents: diff changeset	1033 "X..Bryozoaires.Dresses",
42b51a52e308 planemo upload for repository https://github.com/Marie59/champ_blocs commit 0d86db7d42b608c386a54500064f5f9c9d7019a4 ecology parents: diff changeset	1034 "X..Balanes.Vivantes",
42b51a52e308 planemo upload for repository https://github.com/Marie59/champ_blocs commit 0d86db7d42b608c386a54500064f5f9c9d7019a4 ecology parents: diff changeset	1035 #"Commentaires.Avant",
42b51a52e308 planemo upload for repository https://github.com/Marie59/champ_blocs commit 0d86db7d42b608c386a54500064f5f9c9d7019a4 ecology parents: diff changeset	1036 "X..Surface.Accolement"#, # is NA, then replace by 0 as well because no sense to have a NA value for "% surface accolement" as well.
42b51a52e308 planemo upload for repository https://github.com/Marie59/champ_blocs commit 0d86db7d42b608c386a54500064f5f9c9d7019a4 ecology parents: diff changeset	1037 #"Type.sustrat.observé",
42b51a52e308 planemo upload for repository https://github.com/Marie59/champ_blocs commit 0d86db7d42b608c386a54500064f5f9c9d7019a4 ecology parents: diff changeset	1038 #"Commentaires",
42b51a52e308 planemo upload for repository https://github.com/Marie59/champ_blocs commit 0d86db7d42b608c386a54500064f5f9c9d7019a4 ecology parents: diff changeset	1039 #."Nb.Cancer.pagurus..Tourteau.",
42b51a52e308 planemo upload for repository https://github.com/Marie59/champ_blocs commit 0d86db7d42b608c386a54500064f5f9c9d7019a4 ecology parents: diff changeset	1040 #.."Nb.Necora.puber..Etrille.",
42b51a52e308 planemo upload for repository https://github.com/Marie59/champ_blocs commit 0d86db7d42b608c386a54500064f5f9c9d7019a4 ecology parents: diff changeset	1041 #."Nb.Carcinus.maenas..Crabe.vert.",
42b51a52e308 planemo upload for repository https://github.com/Marie59/champ_blocs commit 0d86db7d42b608c386a54500064f5f9c9d7019a4 ecology parents: diff changeset	1042 #."Nb.Nucella.lapilus..Pourpre.",
42b51a52e308 planemo upload for repository https://github.com/Marie59/champ_blocs commit 0d86db7d42b608c386a54500064f5f9c9d7019a4 ecology parents: diff changeset	1043 #.."Nb.Eriphia.verrucosa..Crabe.verruqueux.",
42b51a52e308 planemo upload for repository https://github.com/Marie59/champ_blocs commit 0d86db7d42b608c386a54500064f5f9c9d7019a4 ecology parents: diff changeset	1044 #.."Nb.Octopus.vulgaris..Poulpe.",
42b51a52e308 planemo upload for repository https://github.com/Marie59/champ_blocs commit 0d86db7d42b608c386a54500064f5f9c9d7019a4 ecology parents: diff changeset	1045 #."Nb.Galathea..Galathées.",
42b51a52e308 planemo upload for repository https://github.com/Marie59/champ_blocs commit 0d86db7d42b608c386a54500064f5f9c9d7019a4 ecology parents: diff changeset	1046 #.."Nb.Paracentrotus.lividus..Oursin.",
42b51a52e308 planemo upload for repository https://github.com/Marie59/champ_blocs commit 0d86db7d42b608c386a54500064f5f9c9d7019a4 ecology parents: diff changeset	1047 #."Nb.Lophozozymus.incisus..ancien.Xantho.incisus.",
42b51a52e308 planemo upload for repository https://github.com/Marie59/champ_blocs commit 0d86db7d42b608c386a54500064f5f9c9d7019a4 ecology parents: diff changeset	1048 #."Nb.Palaemon.sp..Crevette.bouquet.ou.crevette.rose.",
42b51a52e308 planemo upload for repository https://github.com/Marie59/champ_blocs commit 0d86db7d42b608c386a54500064f5f9c9d7019a4 ecology parents: diff changeset	1049 #."Nb.Haliotis.tuberculata..Ormeau.",
42b51a52e308 planemo upload for repository https://github.com/Marie59/champ_blocs commit 0d86db7d42b608c386a54500064f5f9c9d7019a4 ecology parents: diff changeset	1050 #."Nb.Stramonita.haemastoma..Pourpre.bouche.de.sang.",
42b51a52e308 planemo upload for repository https://github.com/Marie59/champ_blocs commit 0d86db7d42b608c386a54500064f5f9c9d7019a4 ecology parents: diff changeset	1051 #."Nb.Littorina.littorea..Bigorneau.",
42b51a52e308 planemo upload for repository https://github.com/Marie59/champ_blocs commit 0d86db7d42b608c386a54500064f5f9c9d7019a4 ecology parents: diff changeset	1052 #."Nb.Xantho.pilipes..Xanthe.poilu.",
42b51a52e308 planemo upload for repository https://github.com/Marie59/champ_blocs commit 0d86db7d42b608c386a54500064f5f9c9d7019a4 ecology parents: diff changeset	1053 #."Nb.Mimachlamys.varia..Pétoncle.noir."
42b51a52e308 planemo upload for repository https://github.com/Marie59/champ_blocs commit 0d86db7d42b608c386a54500064f5f9c9d7019a4 ecology parents: diff changeset	1054 )
42b51a52e308 planemo upload for repository https://github.com/Marie59/champ_blocs commit 0d86db7d42b608c386a54500064f5f9c9d7019a4 ecology parents: diff changeset	1055 ] <- lapply(egmp_basq_bf[, c(
42b51a52e308 planemo upload for repository https://github.com/Marie59/champ_blocs commit 0d86db7d42b608c386a54500064f5f9c9d7019a4 ecology parents: diff changeset	1056 "X..algues.brunes",
42b51a52e308 planemo upload for repository https://github.com/Marie59/champ_blocs commit 0d86db7d42b608c386a54500064f5f9c9d7019a4 ecology parents: diff changeset	1057 "Strate.algues.brunes",
42b51a52e308 planemo upload for repository https://github.com/Marie59/champ_blocs commit 0d86db7d42b608c386a54500064f5f9c9d7019a4 ecology parents: diff changeset	1058 "X..algues.rouges",
42b51a52e308 planemo upload for repository https://github.com/Marie59/champ_blocs commit 0d86db7d42b608c386a54500064f5f9c9d7019a4 ecology parents: diff changeset	1059 "Strate.algues.rouges",
42b51a52e308 planemo upload for repository https://github.com/Marie59/champ_blocs commit 0d86db7d42b608c386a54500064f5f9c9d7019a4 ecology parents: diff changeset	1060 "X..algues.vertes",
42b51a52e308 planemo upload for repository https://github.com/Marie59/champ_blocs commit 0d86db7d42b608c386a54500064f5f9c9d7019a4 ecology parents: diff changeset	1061 "Strate.algues.vertes",
42b51a52e308 planemo upload for repository https://github.com/Marie59/champ_blocs commit 0d86db7d42b608c386a54500064f5f9c9d7019a4 ecology parents: diff changeset	1062 "X..Cladophora",
42b51a52e308 planemo upload for repository https://github.com/Marie59/champ_blocs commit 0d86db7d42b608c386a54500064f5f9c9d7019a4 ecology parents: diff changeset	1063 "X..Lithophyllum",
42b51a52e308 planemo upload for repository https://github.com/Marie59/champ_blocs commit 0d86db7d42b608c386a54500064f5f9c9d7019a4 ecology parents: diff changeset	1064 "X..Recouvrement.Sediment", # is NA, then replace by 0 as well because no sense to have a NA value for "% recouvrement sédiment" as well.
42b51a52e308 planemo upload for repository https://github.com/Marie59/champ_blocs commit 0d86db7d42b608c386a54500064f5f9c9d7019a4 ecology parents: diff changeset	1065 #"Type.Sediment",
42b51a52e308 planemo upload for repository https://github.com/Marie59/champ_blocs commit 0d86db7d42b608c386a54500064f5f9c9d7019a4 ecology parents: diff changeset	1066 "X..Roche.Nue", # is NA, then replace by 0 as well because no sense to have a NA value for "% roche nue" as well.
42b51a52e308 planemo upload for repository https://github.com/Marie59/champ_blocs commit 0d86db7d42b608c386a54500064f5f9c9d7019a4 ecology parents: diff changeset	1067 "Nb.Littorina.obtusata",
42b51a52e308 planemo upload for repository https://github.com/Marie59/champ_blocs commit 0d86db7d42b608c386a54500064f5f9c9d7019a4 ecology parents: diff changeset	1068 "Nb.Gibbula.cineraria",
42b51a52e308 planemo upload for repository https://github.com/Marie59/champ_blocs commit 0d86db7d42b608c386a54500064f5f9c9d7019a4 ecology parents: diff changeset	1069 "Nb.Gibbula.pennanti",
42b51a52e308 planemo upload for repository https://github.com/Marie59/champ_blocs commit 0d86db7d42b608c386a54500064f5f9c9d7019a4 ecology parents: diff changeset	1070 "Nb.Gibbula.umbilicalis",
42b51a52e308 planemo upload for repository https://github.com/Marie59/champ_blocs commit 0d86db7d42b608c386a54500064f5f9c9d7019a4 ecology parents: diff changeset	1071 "Nb.Phallusia.mamillata",
42b51a52e308 planemo upload for repository https://github.com/Marie59/champ_blocs commit 0d86db7d42b608c386a54500064f5f9c9d7019a4 ecology parents: diff changeset	1072 "Nb.Tethya.aurantium",
42b51a52e308 planemo upload for repository https://github.com/Marie59/champ_blocs commit 0d86db7d42b608c386a54500064f5f9c9d7019a4 ecology parents: diff changeset	1073 #"Nb.Spirobranchus.lamarckii.1B",
42b51a52e308 planemo upload for repository https://github.com/Marie59/champ_blocs commit 0d86db7d42b608c386a54500064f5f9c9d7019a4 ecology parents: diff changeset	1074 #"Nb.Spirobranchus.lamarckii.2B",
42b51a52e308 planemo upload for repository https://github.com/Marie59/champ_blocs commit 0d86db7d42b608c386a54500064f5f9c9d7019a4 ecology parents: diff changeset	1075 #"Nb.Spirobranchus.lamarckii.3B",
42b51a52e308 planemo upload for repository https://github.com/Marie59/champ_blocs commit 0d86db7d42b608c386a54500064f5f9c9d7019a4 ecology parents: diff changeset	1076 #"Nb.Spirobranchus.lamarckii.4B",
42b51a52e308 planemo upload for repository https://github.com/Marie59/champ_blocs commit 0d86db7d42b608c386a54500064f5f9c9d7019a4 ecology parents: diff changeset	1077 #"Nb.Spirobranchus.lamarckii.5B",
42b51a52e308 planemo upload for repository https://github.com/Marie59/champ_blocs commit 0d86db7d42b608c386a54500064f5f9c9d7019a4 ecology parents: diff changeset	1078 "Nb.Spirobranchus.lamarckii.total",
42b51a52e308 planemo upload for repository https://github.com/Marie59/champ_blocs commit 0d86db7d42b608c386a54500064f5f9c9d7019a4 ecology parents: diff changeset	1079 #"Nb.spirorbis.1A",
42b51a52e308 planemo upload for repository https://github.com/Marie59/champ_blocs commit 0d86db7d42b608c386a54500064f5f9c9d7019a4 ecology parents: diff changeset	1080 #"Nb.spirorbis.2A",
42b51a52e308 planemo upload for repository https://github.com/Marie59/champ_blocs commit 0d86db7d42b608c386a54500064f5f9c9d7019a4 ecology parents: diff changeset	1081 #"Nb.spirorbis.3A",
42b51a52e308 planemo upload for repository https://github.com/Marie59/champ_blocs commit 0d86db7d42b608c386a54500064f5f9c9d7019a4 ecology parents: diff changeset	1082 #"Nb.spirorbis.4A",
42b51a52e308 planemo upload for repository https://github.com/Marie59/champ_blocs commit 0d86db7d42b608c386a54500064f5f9c9d7019a4 ecology parents: diff changeset	1083 #"Nb.spirorbis.5A",
42b51a52e308 planemo upload for repository https://github.com/Marie59/champ_blocs commit 0d86db7d42b608c386a54500064f5f9c9d7019a4 ecology parents: diff changeset	1084 "Nb.spirorbis.total",
42b51a52e308 planemo upload for repository https://github.com/Marie59/champ_blocs commit 0d86db7d42b608c386a54500064f5f9c9d7019a4 ecology parents: diff changeset	1085 "Nb.Crassostrea.gigas",
42b51a52e308 planemo upload for repository https://github.com/Marie59/champ_blocs commit 0d86db7d42b608c386a54500064f5f9c9d7019a4 ecology parents: diff changeset	1086 "Nb.Ostrea.edulis",
42b51a52e308 planemo upload for repository https://github.com/Marie59/champ_blocs commit 0d86db7d42b608c386a54500064f5f9c9d7019a4 ecology parents: diff changeset	1087 "X..Mytilus.sp.",
42b51a52e308 planemo upload for repository https://github.com/Marie59/champ_blocs commit 0d86db7d42b608c386a54500064f5f9c9d7019a4 ecology parents: diff changeset	1088 "X..Hermelles",
42b51a52e308 planemo upload for repository https://github.com/Marie59/champ_blocs commit 0d86db7d42b608c386a54500064f5f9c9d7019a4 ecology parents: diff changeset	1089 "X..Hydraires",
42b51a52e308 planemo upload for repository https://github.com/Marie59/champ_blocs commit 0d86db7d42b608c386a54500064f5f9c9d7019a4 ecology parents: diff changeset	1090 "X..Eponges",
42b51a52e308 planemo upload for repository https://github.com/Marie59/champ_blocs commit 0d86db7d42b608c386a54500064f5f9c9d7019a4 ecology parents: diff changeset	1091 "X..Ascidies.Coloniales",
42b51a52e308 planemo upload for repository https://github.com/Marie59/champ_blocs commit 0d86db7d42b608c386a54500064f5f9c9d7019a4 ecology parents: diff changeset	1092 "X..Ascidies.Solitaires",
42b51a52e308 planemo upload for repository https://github.com/Marie59/champ_blocs commit 0d86db7d42b608c386a54500064f5f9c9d7019a4 ecology parents: diff changeset	1093 "X..Bryozoaires.Dresses",
42b51a52e308 planemo upload for repository https://github.com/Marie59/champ_blocs commit 0d86db7d42b608c386a54500064f5f9c9d7019a4 ecology parents: diff changeset	1094 "X..Balanes.Vivantes",
42b51a52e308 planemo upload for repository https://github.com/Marie59/champ_blocs commit 0d86db7d42b608c386a54500064f5f9c9d7019a4 ecology parents: diff changeset	1095 #"Commentaires.Avant",
42b51a52e308 planemo upload for repository https://github.com/Marie59/champ_blocs commit 0d86db7d42b608c386a54500064f5f9c9d7019a4 ecology parents: diff changeset	1096 "X..Surface.Accolement"#, # is NA, then replace by 0 as well because no sense to have a NA value for "% surface accolement" as well.
42b51a52e308 planemo upload for repository https://github.com/Marie59/champ_blocs commit 0d86db7d42b608c386a54500064f5f9c9d7019a4 ecology parents: diff changeset	1097 #"Type.sustrat.observé",
42b51a52e308 planemo upload for repository https://github.com/Marie59/champ_blocs commit 0d86db7d42b608c386a54500064f5f9c9d7019a4 ecology parents: diff changeset	1098 #"Commentaires",
42b51a52e308 planemo upload for repository https://github.com/Marie59/champ_blocs commit 0d86db7d42b608c386a54500064f5f9c9d7019a4 ecology parents: diff changeset	1099 #."Nb.Cancer.pagurus..Tourteau.",
42b51a52e308 planemo upload for repository https://github.com/Marie59/champ_blocs commit 0d86db7d42b608c386a54500064f5f9c9d7019a4 ecology parents: diff changeset	1100 #.."Nb.Necora.puber..Etrille.",
42b51a52e308 planemo upload for repository https://github.com/Marie59/champ_blocs commit 0d86db7d42b608c386a54500064f5f9c9d7019a4 ecology parents: diff changeset	1101 #."Nb.Carcinus.maenas..Crabe.vert.",
42b51a52e308 planemo upload for repository https://github.com/Marie59/champ_blocs commit 0d86db7d42b608c386a54500064f5f9c9d7019a4 ecology parents: diff changeset	1102 #."Nb.Nucella.lapilus..Pourpre.",
42b51a52e308 planemo upload for repository https://github.com/Marie59/champ_blocs commit 0d86db7d42b608c386a54500064f5f9c9d7019a4 ecology parents: diff changeset	1103 #.."Nb.Eriphia.verrucosa..Crabe.verruqueux.",
42b51a52e308 planemo upload for repository https://github.com/Marie59/champ_blocs commit 0d86db7d42b608c386a54500064f5f9c9d7019a4 ecology parents: diff changeset	1104 #.."Nb.Octopus.vulgaris..Poulpe.",
42b51a52e308 planemo upload for repository https://github.com/Marie59/champ_blocs commit 0d86db7d42b608c386a54500064f5f9c9d7019a4 ecology parents: diff changeset	1105 #."Nb.Galathea..Galathées.",
42b51a52e308 planemo upload for repository https://github.com/Marie59/champ_blocs commit 0d86db7d42b608c386a54500064f5f9c9d7019a4 ecology parents: diff changeset	1106 #.."Nb.Paracentrotus.lividus..Oursin.",
42b51a52e308 planemo upload for repository https://github.com/Marie59/champ_blocs commit 0d86db7d42b608c386a54500064f5f9c9d7019a4 ecology parents: diff changeset	1107 #."Nb.Lophozozymus.incisus..ancien.Xantho.incisus.",
42b51a52e308 planemo upload for repository https://github.com/Marie59/champ_blocs commit 0d86db7d42b608c386a54500064f5f9c9d7019a4 ecology parents: diff changeset	1108 #."Nb.Palaemon.sp..Crevette.bouquet.ou.crevette.rose.",
42b51a52e308 planemo upload for repository https://github.com/Marie59/champ_blocs commit 0d86db7d42b608c386a54500064f5f9c9d7019a4 ecology parents: diff changeset	1109 #."Nb.Haliotis.tuberculata..Ormeau.",
42b51a52e308 planemo upload for repository https://github.com/Marie59/champ_blocs commit 0d86db7d42b608c386a54500064f5f9c9d7019a4 ecology parents: diff changeset	1110 #."Nb.Stramonita.haemastoma..Pourpre.bouche.de.sang.",
42b51a52e308 planemo upload for repository https://github.com/Marie59/champ_blocs commit 0d86db7d42b608c386a54500064f5f9c9d7019a4 ecology parents: diff changeset	1111 #."Nb.Littorina.littorea..Bigorneau.",
42b51a52e308 planemo upload for repository https://github.com/Marie59/champ_blocs commit 0d86db7d42b608c386a54500064f5f9c9d7019a4 ecology parents: diff changeset	1112 #."Nb.Xantho.pilipes..Xanthe.poilu.",
42b51a52e308 planemo upload for repository https://github.com/Marie59/champ_blocs commit 0d86db7d42b608c386a54500064f5f9c9d7019a4 ecology parents: diff changeset	1113 #."Nb.Mimachlamys.varia..Pétoncle.noir."
42b51a52e308 planemo upload for repository https://github.com/Marie59/champ_blocs commit 0d86db7d42b608c386a54500064f5f9c9d7019a4 ecology parents: diff changeset	1114 )
42b51a52e308 planemo upload for repository https://github.com/Marie59/champ_blocs commit 0d86db7d42b608c386a54500064f5f9c9d7019a4 ecology parents: diff changeset	1115 ], function(x) replace(x, is.na(x), 0))
42b51a52e308 planemo upload for repository https://github.com/Marie59/champ_blocs commit 0d86db7d42b608c386a54500064f5f9c9d7019a4 ecology parents: diff changeset	1116
42b51a52e308 planemo upload for repository https://github.com/Marie59/champ_blocs commit 0d86db7d42b608c386a54500064f5f9c9d7019a4 ecology parents: diff changeset	1117
42b51a52e308 planemo upload for repository https://github.com/Marie59/champ_blocs commit 0d86db7d42b608c386a54500064f5f9c9d7019a4 ecology parents: diff changeset	1118 # merge dfs.
42b51a52e308 planemo upload for repository https://github.com/Marie59/champ_blocs commit 0d86db7d42b608c386a54500064f5f9c9d7019a4 ecology parents: diff changeset	1119 qecbnato0 <- dplyr::bind_rows(bretagne_bm, bretagne_bf)
42b51a52e308 planemo upload for repository https://github.com/Marie59/champ_blocs commit 0d86db7d42b608c386a54500064f5f9c9d7019a4 ecology parents: diff changeset	1120 qecbnato0 <- dplyr::bind_rows(qecbnato0, egmp_basq_bm)
42b51a52e308 planemo upload for repository https://github.com/Marie59/champ_blocs commit 0d86db7d42b608c386a54500064f5f9c9d7019a4 ecology parents: diff changeset	1121 qecbnato0 <- dplyr::bind_rows(qecbnato0, egmp_basq_bf)
42b51a52e308 planemo upload for repository https://github.com/Marie59/champ_blocs commit 0d86db7d42b608c386a54500064f5f9c9d7019a4 ecology parents: diff changeset	1122
42b51a52e308 planemo upload for repository https://github.com/Marie59/champ_blocs commit 0d86db7d42b608c386a54500064f5f9c9d7019a4 ecology parents: diff changeset	1123 qecbnato0 <- dplyr::arrange(qecbnato0, region, site_year_month_day, Type.Bloc, Numéro.Bloc.échantillon, Face)
42b51a52e308 planemo upload for repository https://github.com/Marie59/champ_blocs commit 0d86db7d42b608c386a54500064f5f9c9d7019a4 ecology parents: diff changeset	1124
42b51a52e308 planemo upload for repository https://github.com/Marie59/champ_blocs commit 0d86db7d42b608c386a54500064f5f9c9d7019a4 ecology parents: diff changeset	1125 rm(bretagne_bm, bretagne_bf, egmp_basq_bm, egmp_basq_bf)
42b51a52e308 planemo upload for repository https://github.com/Marie59/champ_blocs commit 0d86db7d42b608c386a54500064f5f9c9d7019a4 ecology parents: diff changeset	1126
42b51a52e308 planemo upload for repository https://github.com/Marie59/champ_blocs commit 0d86db7d42b608c386a54500064f5f9c9d7019a4 ecology parents: diff changeset	1127
42b51a52e308 planemo upload for repository https://github.com/Marie59/champ_blocs commit 0d86db7d42b608c386a54500064f5f9c9d7019a4 ecology parents: diff changeset	1128 ## analyse matricielle
42b51a52e308 planemo upload for repository https://github.com/Marie59/champ_blocs commit 0d86db7d42b608c386a54500064f5f9c9d7019a4 ecology parents: diff changeset	1129
42b51a52e308 planemo upload for repository https://github.com/Marie59/champ_blocs commit 0d86db7d42b608c386a54500064f5f9c9d7019a4 ecology parents: diff changeset	1130 # NB some variables were dplyr::renamed or created, cfr I originally merged qecb and ivr data in below script to do some correlation analysis. This is not the case anymore, so no more merging anymore.
42b51a52e308 planemo upload for repository https://github.com/Marie59/champ_blocs commit 0d86db7d42b608c386a54500064f5f9c9d7019a4 ecology parents: diff changeset	1131
42b51a52e308 planemo upload for repository https://github.com/Marie59/champ_blocs commit 0d86db7d42b608c386a54500064f5f9c9d7019a4 ecology parents: diff changeset	1132 qecbnato0 <- tibble::add_column(qecbnato0, region.site_year_month_day = paste0(qecbnato0$region, qecbnato0$site_year_month_day), .before = "region")
42b51a52e308 planemo upload for repository https://github.com/Marie59/champ_blocs commit 0d86db7d42b608c386a54500064f5f9c9d7019a4 ecology parents: diff changeset	1133
42b51a52e308 planemo upload for repository https://github.com/Marie59/champ_blocs commit 0d86db7d42b608c386a54500064f5f9c9d7019a4 ecology parents: diff changeset	1134
42b51a52e308 planemo upload for repository https://github.com/Marie59/champ_blocs commit 0d86db7d42b608c386a54500064f5f9c9d7019a4 ecology parents: diff changeset	1135 numero_quadrat <- stringr::str_sub(qecbnato0$quadrat_bis, start = -1)
42b51a52e308 planemo upload for repository https://github.com/Marie59/champ_blocs commit 0d86db7d42b608c386a54500064f5f9c9d7019a4 ecology parents: diff changeset	1136 qecbnato0 <- tibble::add_column(qecbnato0, numero_quadrat, .after = "quadrat_bis")
42b51a52e308 planemo upload for repository https://github.com/Marie59/champ_blocs commit 0d86db7d42b608c386a54500064f5f9c9d7019a4 ecology parents: diff changeset	1137 rm(numero_quadrat)
42b51a52e308 planemo upload for repository https://github.com/Marie59/champ_blocs commit 0d86db7d42b608c386a54500064f5f9c9d7019a4 ecology parents: diff changeset	1138 qecbnato0$numero_quadrat <- as.integer(qecbnato0$numero_quadrat)
42b51a52e308 planemo upload for repository https://github.com/Marie59/champ_blocs commit 0d86db7d42b608c386a54500064f5f9c9d7019a4 ecology parents: diff changeset	1139
42b51a52e308 planemo upload for repository https://github.com/Marie59/champ_blocs commit 0d86db7d42b608c386a54500064f5f9c9d7019a4 ecology parents: diff changeset	1140
42b51a52e308 planemo upload for repository https://github.com/Marie59/champ_blocs commit 0d86db7d42b608c386a54500064f5f9c9d7019a4 ecology parents: diff changeset	1141 qecbnato0$Year <- as.integer(qecbnato0$Year)
42b51a52e308 planemo upload for repository https://github.com/Marie59/champ_blocs commit 0d86db7d42b608c386a54500064f5f9c9d7019a4 ecology parents: diff changeset	1142 qecbnato0$Month <- as.integer(qecbnato0$Month)
42b51a52e308 planemo upload for repository https://github.com/Marie59/champ_blocs commit 0d86db7d42b608c386a54500064f5f9c9d7019a4 ecology parents: diff changeset	1143 qecbnato0$Day <- as.integer(qecbnato0$Day)
42b51a52e308 planemo upload for repository https://github.com/Marie59/champ_blocs commit 0d86db7d42b608c386a54500064f5f9c9d7019a4 ecology parents: diff changeset	1144
42b51a52e308 planemo upload for repository https://github.com/Marie59/champ_blocs commit 0d86db7d42b608c386a54500064f5f9c9d7019a4 ecology parents: diff changeset	1145 ############################################################
42b51a52e308 planemo upload for repository https://github.com/Marie59/champ_blocs commit 0d86db7d42b608c386a54500064f5f9c9d7019a4 ecology parents: diff changeset	1146 #!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!
42b51a52e308 planemo upload for repository https://github.com/Marie59/champ_blocs commit 0d86db7d42b608c386a54500064f5f9c9d7019a4 ecology parents: diff changeset	1147 # Anna still hasn't corrected for boulder nb in FINS_Quemenes.2020.10.16 data encoding ! removed from the df_
42b51a52e308 planemo upload for repository https://github.com/Marie59/champ_blocs commit 0d86db7d42b608c386a54500064f5f9c9d7019a4 ecology parents: diff changeset	1148 qecbnato0 <- qecbnato0 %>% dplyr::filter(site_year_month_day != "FINS_Quemenes.2020.10.16")
42b51a52e308 planemo upload for repository https://github.com/Marie59/champ_blocs commit 0d86db7d42b608c386a54500064f5f9c9d7019a4 ecology parents: diff changeset	1149 ############################################################
42b51a52e308 planemo upload for repository https://github.com/Marie59/champ_blocs commit 0d86db7d42b608c386a54500064f5f9c9d7019a4 ecology parents: diff changeset	1150
42b51a52e308 planemo upload for repository https://github.com/Marie59/champ_blocs commit 0d86db7d42b608c386a54500064f5f9c9d7019a4 ecology parents: diff changeset	1151 # what to do with spirorbes & Nb.Spirobranchus.lamarckii.total? log10 transformation
42b51a52e308 planemo upload for repository https://github.com/Marie59/champ_blocs commit 0d86db7d42b608c386a54500064f5f9c9d7019a4 ecology parents: diff changeset	1152
42b51a52e308 planemo upload for repository https://github.com/Marie59/champ_blocs commit 0d86db7d42b608c386a54500064f5f9c9d7019a4 ecology parents: diff changeset	1153 qecbnato0 <- tibble::add_column(qecbnato0, log10.Nb.spirorbis.total = log10(qecbnato0$Nb.spirorbis.total + 1), .after = "Nb.spirorbis.total")
42b51a52e308 planemo upload for repository https://github.com/Marie59/champ_blocs commit 0d86db7d42b608c386a54500064f5f9c9d7019a4 ecology parents: diff changeset	1154 qecbnato0 <- tibble::add_column(qecbnato0, log10.Nb.Spirobranchus.lamarckii.total = log10(qecbnato0$Nb.Spirobranchus.lamarckii.total + 1), .after = "Nb.Spirobranchus.lamarckii.total")
42b51a52e308 planemo upload for repository https://github.com/Marie59/champ_blocs commit 0d86db7d42b608c386a54500064f5f9c9d7019a4 ecology parents: diff changeset	1155
42b51a52e308 planemo upload for repository https://github.com/Marie59/champ_blocs commit 0d86db7d42b608c386a54500064f5f9c9d7019a4 ecology parents: diff changeset	1156 saveRDS(qecbnato0, "qecbnato0.RDS")
42b51a52e308 planemo upload for repository https://github.com/Marie59/champ_blocs commit 0d86db7d42b608c386a54500064f5f9c9d7019a4 ecology parents: diff changeset	1157
42b51a52e308 planemo upload for repository https://github.com/Marie59/champ_blocs commit 0d86db7d42b608c386a54500064f5f9c9d7019a4 ecology parents: diff changeset	1158
42b51a52e308 planemo upload for repository https://github.com/Marie59/champ_blocs commit 0d86db7d42b608c386a54500064f5f9c9d7019a4 ecology parents: diff changeset	1159 ###############################################################
42b51a52e308 planemo upload for repository https://github.com/Marie59/champ_blocs commit 0d86db7d42b608c386a54500064f5f9c9d7019a4 ecology parents: diff changeset	1160 # #
42b51a52e308 planemo upload for repository https://github.com/Marie59/champ_blocs commit 0d86db7d42b608c386a54500064f5f9c9d7019a4 ecology parents: diff changeset	1161 # Start dissimilarity calculation with some data handling #
42b51a52e308 planemo upload for repository https://github.com/Marie59/champ_blocs commit 0d86db7d42b608c386a54500064f5f9c9d7019a4 ecology parents: diff changeset	1162 # #
42b51a52e308 planemo upload for repository https://github.com/Marie59/champ_blocs commit 0d86db7d42b608c386a54500064f5f9c9d7019a4 ecology parents: diff changeset	1163 ###############################################################
42b51a52e308 planemo upload for repository https://github.com/Marie59/champ_blocs commit 0d86db7d42b608c386a54500064f5f9c9d7019a4 ecology parents: diff changeset	1164
42b51a52e308 planemo upload for repository https://github.com/Marie59/champ_blocs commit 0d86db7d42b608c386a54500064f5f9c9d7019a4 ecology parents: diff changeset	1165 # first, create vector (4) for qecb and fishing by region (same as above)
42b51a52e308 planemo upload for repository https://github.com/Marie59/champ_blocs commit 0d86db7d42b608c386a54500064f5f9c9d7019a4 ecology parents: diff changeset	1166
42b51a52e308 planemo upload for repository https://github.com/Marie59/champ_blocs commit 0d86db7d42b608c386a54500064f5f9c9d7019a4 ecology parents: diff changeset	1167 bret_egmp_basq_qecb <- c(
42b51a52e308 planemo upload for repository https://github.com/Marie59/champ_blocs commit 0d86db7d42b608c386a54500064f5f9c9d7019a4 ecology parents: diff changeset	1168 "X..algues.brunes",
42b51a52e308 planemo upload for repository https://github.com/Marie59/champ_blocs commit 0d86db7d42b608c386a54500064f5f9c9d7019a4 ecology parents: diff changeset	1169 "X..algues.rouges",
42b51a52e308 planemo upload for repository https://github.com/Marie59/champ_blocs commit 0d86db7d42b608c386a54500064f5f9c9d7019a4 ecology parents: diff changeset	1170 "X..algues.vertes",
42b51a52e308 planemo upload for repository https://github.com/Marie59/champ_blocs commit 0d86db7d42b608c386a54500064f5f9c9d7019a4 ecology parents: diff changeset	1171 "X..Cladophora",
42b51a52e308 planemo upload for repository https://github.com/Marie59/champ_blocs commit 0d86db7d42b608c386a54500064f5f9c9d7019a4 ecology parents: diff changeset	1172 "X..Lithophyllum",
42b51a52e308 planemo upload for repository https://github.com/Marie59/champ_blocs commit 0d86db7d42b608c386a54500064f5f9c9d7019a4 ecology parents: diff changeset	1173 "Nb.Littorina.obtusata",
42b51a52e308 planemo upload for repository https://github.com/Marie59/champ_blocs commit 0d86db7d42b608c386a54500064f5f9c9d7019a4 ecology parents: diff changeset	1174 "Nb.Gibbula.cineraria",
42b51a52e308 planemo upload for repository https://github.com/Marie59/champ_blocs commit 0d86db7d42b608c386a54500064f5f9c9d7019a4 ecology parents: diff changeset	1175 "Nb.Gibbula.pennanti",
42b51a52e308 planemo upload for repository https://github.com/Marie59/champ_blocs commit 0d86db7d42b608c386a54500064f5f9c9d7019a4 ecology parents: diff changeset	1176 "Nb.Gibbula.umbilicalis",
42b51a52e308 planemo upload for repository https://github.com/Marie59/champ_blocs commit 0d86db7d42b608c386a54500064f5f9c9d7019a4 ecology parents: diff changeset	1177 "Nb.Phallusia.mamillata",
42b51a52e308 planemo upload for repository https://github.com/Marie59/champ_blocs commit 0d86db7d42b608c386a54500064f5f9c9d7019a4 ecology parents: diff changeset	1178 "Nb.Tethya.aurantium",
42b51a52e308 planemo upload for repository https://github.com/Marie59/champ_blocs commit 0d86db7d42b608c386a54500064f5f9c9d7019a4 ecology parents: diff changeset	1179 "Nb.Spirobranchus.lamarckii.total",
42b51a52e308 planemo upload for repository https://github.com/Marie59/champ_blocs commit 0d86db7d42b608c386a54500064f5f9c9d7019a4 ecology parents: diff changeset	1180 "Nb.spirorbis.total",
42b51a52e308 planemo upload for repository https://github.com/Marie59/champ_blocs commit 0d86db7d42b608c386a54500064f5f9c9d7019a4 ecology parents: diff changeset	1181 "X..Eponges",
42b51a52e308 planemo upload for repository https://github.com/Marie59/champ_blocs commit 0d86db7d42b608c386a54500064f5f9c9d7019a4 ecology parents: diff changeset	1182 "X..Ascidies.Coloniales",
42b51a52e308 planemo upload for repository https://github.com/Marie59/champ_blocs commit 0d86db7d42b608c386a54500064f5f9c9d7019a4 ecology parents: diff changeset	1183 "X..Ascidies.Solitaires",
42b51a52e308 planemo upload for repository https://github.com/Marie59/champ_blocs commit 0d86db7d42b608c386a54500064f5f9c9d7019a4 ecology parents: diff changeset	1184 "X..Bryozoaires.Dresses",
42b51a52e308 planemo upload for repository https://github.com/Marie59/champ_blocs commit 0d86db7d42b608c386a54500064f5f9c9d7019a4 ecology parents: diff changeset	1185 "X..Balanes.Vivantes"
42b51a52e308 planemo upload for repository https://github.com/Marie59/champ_blocs commit 0d86db7d42b608c386a54500064f5f9c9d7019a4 ecology parents: diff changeset	1186 #, "X..Recouvrement.Sediment"
42b51a52e308 planemo upload for repository https://github.com/Marie59/champ_blocs commit 0d86db7d42b608c386a54500064f5f9c9d7019a4 ecology parents: diff changeset	1187 #, "X..Roche.Nue"
42b51a52e308 planemo upload for repository https://github.com/Marie59/champ_blocs commit 0d86db7d42b608c386a54500064f5f9c9d7019a4 ecology parents: diff changeset	1188 #, "X..Surface.Accolement"
42b51a52e308 planemo upload for repository https://github.com/Marie59/champ_blocs commit 0d86db7d42b608c386a54500064f5f9c9d7019a4 ecology parents: diff changeset	1189 )
42b51a52e308 planemo upload for repository https://github.com/Marie59/champ_blocs commit 0d86db7d42b608c386a54500064f5f9c9d7019a4 ecology parents: diff changeset	1190
42b51a52e308 planemo upload for repository https://github.com/Marie59/champ_blocs commit 0d86db7d42b608c386a54500064f5f9c9d7019a4 ecology parents: diff changeset	1191 egmp_basq_qecb <- c("Nb.Crassostrea.gigas", "Nb.Ostrea.edulis", "X..Mytilus.sp.", "X..Hermelles", "X..Hydraires")
42b51a52e308 planemo upload for repository https://github.com/Marie59/champ_blocs commit 0d86db7d42b608c386a54500064f5f9c9d7019a4 ecology parents: diff changeset	1192
42b51a52e308 planemo upload for repository https://github.com/Marie59/champ_blocs commit 0d86db7d42b608c386a54500064f5f9c9d7019a4 ecology parents: diff changeset	1193 bret_egmp_basq_fishing <- c("Nb.Cancer.pagurus..Tourteau.",
42b51a52e308 planemo upload for repository https://github.com/Marie59/champ_blocs commit 0d86db7d42b608c386a54500064f5f9c9d7019a4 ecology parents: diff changeset	1194 "Nb.Necora.puber..Etrille.",
42b51a52e308 planemo upload for repository https://github.com/Marie59/champ_blocs commit 0d86db7d42b608c386a54500064f5f9c9d7019a4 ecology parents: diff changeset	1195 "Nb.Carcinus.maenas..Crabe.vert.",
42b51a52e308 planemo upload for repository https://github.com/Marie59/champ_blocs commit 0d86db7d42b608c386a54500064f5f9c9d7019a4 ecology parents: diff changeset	1196 "Nb.Nucella.lapilus..Pourpre.",
42b51a52e308 planemo upload for repository https://github.com/Marie59/champ_blocs commit 0d86db7d42b608c386a54500064f5f9c9d7019a4 ecology parents: diff changeset	1197 "Nb.Galathea..Galathées.",
42b51a52e308 planemo upload for repository https://github.com/Marie59/champ_blocs commit 0d86db7d42b608c386a54500064f5f9c9d7019a4 ecology parents: diff changeset	1198 "Nb.Lophozozymus.incisus..ancien.Xantho.incisus.",
42b51a52e308 planemo upload for repository https://github.com/Marie59/champ_blocs commit 0d86db7d42b608c386a54500064f5f9c9d7019a4 ecology parents: diff changeset	1199 "Nb.Palaemon.sp..Crevette.bouquet.ou.crevette.rose.",
42b51a52e308 planemo upload for repository https://github.com/Marie59/champ_blocs commit 0d86db7d42b608c386a54500064f5f9c9d7019a4 ecology parents: diff changeset	1200 "Nb.Haliotis.tuberculata..Ormeau.",
42b51a52e308 planemo upload for repository https://github.com/Marie59/champ_blocs commit 0d86db7d42b608c386a54500064f5f9c9d7019a4 ecology parents: diff changeset	1201 "Nb.Littorina.littorea..Bigorneau.",
42b51a52e308 planemo upload for repository https://github.com/Marie59/champ_blocs commit 0d86db7d42b608c386a54500064f5f9c9d7019a4 ecology parents: diff changeset	1202 "Nb.Xantho.pilipes..Xanthe.poilu.",
42b51a52e308 planemo upload for repository https://github.com/Marie59/champ_blocs commit 0d86db7d42b608c386a54500064f5f9c9d7019a4 ecology parents: diff changeset	1203 "Nb.Mimachlamys.varia..Pétoncle.noir.")
42b51a52e308 planemo upload for repository https://github.com/Marie59/champ_blocs commit 0d86db7d42b608c386a54500064f5f9c9d7019a4 ecology parents: diff changeset	1204
42b51a52e308 planemo upload for repository https://github.com/Marie59/champ_blocs commit 0d86db7d42b608c386a54500064f5f9c9d7019a4 ecology parents: diff changeset	1205 egmp_basq_fishing <- c("Nb.Eriphia.verrucosa..Crabe.verruqueux.", "Nb.Octopus.vulgaris..Poulpe.", "Nb.Paracentrotus.lividus..Oursin.", "Nb.Stramonita.haemastoma..Pourpre.bouche.de.sang.")
42b51a52e308 planemo upload for repository https://github.com/Marie59/champ_blocs commit 0d86db7d42b608c386a54500064f5f9c9d7019a4 ecology parents: diff changeset	1206
42b51a52e308 planemo upload for repository https://github.com/Marie59/champ_blocs commit 0d86db7d42b608c386a54500064f5f9c9d7019a4 ecology parents: diff changeset	1207 # here I can choose to either replace spirorbis and/or spirobranchus by their log10 transformation in bret_egmp_basq_qecb vector
42b51a52e308 planemo upload for repository https://github.com/Marie59/champ_blocs commit 0d86db7d42b608c386a54500064f5f9c9d7019a4 ecology parents: diff changeset	1208 bret_egmp_basq_qecb <- replace(bret_egmp_basq_qecb, bret_egmp_basq_qecb == "Nb.spirorbis.total", "log10.Nb.spirorbis.total")
42b51a52e308 planemo upload for repository https://github.com/Marie59/champ_blocs commit 0d86db7d42b608c386a54500064f5f9c9d7019a4 ecology parents: diff changeset	1209 saveRDS(bret_egmp_basq_qecb, "bret_egmp_basq_qecb.RDS")
42b51a52e308 planemo upload for repository https://github.com/Marie59/champ_blocs commit 0d86db7d42b608c386a54500064f5f9c9d7019a4 ecology parents: diff changeset	1210
42b51a52e308 planemo upload for repository https://github.com/Marie59/champ_blocs commit 0d86db7d42b608c386a54500064f5f9c9d7019a4 ecology parents: diff changeset	1211
42b51a52e308 planemo upload for repository https://github.com/Marie59/champ_blocs commit 0d86db7d42b608c386a54500064f5f9c9d7019a4 ecology parents: diff changeset	1212 #############################################################
42b51a52e308 planemo upload for repository https://github.com/Marie59/champ_blocs commit 0d86db7d42b608c386a54500064f5f9c9d7019a4 ecology parents: diff changeset	1213 # #
42b51a52e308 planemo upload for repository https://github.com/Marie59/champ_blocs commit 0d86db7d42b608c386a54500064f5f9c9d7019a4 ecology parents: diff changeset	1214 # Compute dissimilarity #
42b51a52e308 planemo upload for repository https://github.com/Marie59/champ_blocs commit 0d86db7d42b608c386a54500064f5f9c9d7019a4 ecology parents: diff changeset	1215 # #
42b51a52e308 planemo upload for repository https://github.com/Marie59/champ_blocs commit 0d86db7d42b608c386a54500064f5f9c9d7019a4 ecology parents: diff changeset	1216 #############################################################
42b51a52e308 planemo upload for repository https://github.com/Marie59/champ_blocs commit 0d86db7d42b608c386a54500064f5f9c9d7019a4 ecology parents: diff changeset	1217 ### determination of coefficient of dissimilarity face sup mobile bloc vs fixed bloc
42b51a52e308 planemo upload for repository https://github.com/Marie59/champ_blocs commit 0d86db7d42b608c386a54500064f5f9c9d7019a4 ecology parents: diff changeset	1218
42b51a52e308 planemo upload for repository https://github.com/Marie59/champ_blocs commit 0d86db7d42b608c386a54500064f5f9c9d7019a4 ecology parents: diff changeset	1219 # loop in a fct
42b51a52e308 planemo upload for repository https://github.com/Marie59/champ_blocs commit 0d86db7d42b608c386a54500064f5f9c9d7019a4 ecology parents: diff changeset	1220
42b51a52e308 planemo upload for repository https://github.com/Marie59/champ_blocs commit 0d86db7d42b608c386a54500064f5f9c9d7019a4 ecology parents: diff changeset	1221 matri_fct_bmf <- function(data, conca) {
42b51a52e308 planemo upload for repository https://github.com/Marie59/champ_blocs commit 0d86db7d42b608c386a54500064f5f9c9d7019a4 ecology parents: diff changeset	1222
42b51a52e308 planemo upload for repository https://github.com/Marie59/champ_blocs commit 0d86db7d42b608c386a54500064f5f9c9d7019a4 ecology parents: diff changeset	1223 matri_df <- data
42b51a52e308 planemo upload for repository https://github.com/Marie59/champ_blocs commit 0d86db7d42b608c386a54500064f5f9c9d7019a4 ecology parents: diff changeset	1224
42b51a52e308 planemo upload for repository https://github.com/Marie59/champ_blocs commit 0d86db7d42b608c386a54500064f5f9c9d7019a4 ecology parents: diff changeset	1225 for (x in c(1:length(unique(matri_df$site_year_month_day)))) {
42b51a52e308 planemo upload for repository https://github.com/Marie59/champ_blocs commit 0d86db7d42b608c386a54500064f5f9c9d7019a4 ecology parents: diff changeset	1226
42b51a52e308 planemo upload for repository https://github.com/Marie59/champ_blocs commit 0d86db7d42b608c386a54500064f5f9c9d7019a4 ecology parents: diff changeset	1227 qecbnato0_x <- matri_df %>% dplyr::filter(site_year_month_day == unique(matri_df$site_year_month_day)[[x]])
42b51a52e308 planemo upload for repository https://github.com/Marie59/champ_blocs commit 0d86db7d42b608c386a54500064f5f9c9d7019a4 ecology parents: diff changeset	1228
42b51a52e308 planemo upload for repository https://github.com/Marie59/champ_blocs commit 0d86db7d42b608c386a54500064f5f9c9d7019a4 ecology parents: diff changeset	1229 rownames(qecbnato0_x) <- paste0(qecbnato0_x$Type.Bloc, "_", qecbnato0_x$Face, "_", qecbnato0_x$Numéro.Bloc.échantillon, "_", qecbnato0_x$quadrat_bis)
42b51a52e308 planemo upload for repository https://github.com/Marie59/champ_blocs commit 0d86db7d42b608c386a54500064f5f9c9d7019a4 ecology parents: diff changeset	1230
42b51a52e308 planemo upload for repository https://github.com/Marie59/champ_blocs commit 0d86db7d42b608c386a54500064f5f9c9d7019a4 ecology parents: diff changeset	1231
42b51a52e308 planemo upload for repository https://github.com/Marie59/champ_blocs commit 0d86db7d42b608c386a54500064f5f9c9d7019a4 ecology parents: diff changeset	1232 mtxdis <- vegan::vegdist(
42b51a52e308 planemo upload for repository https://github.com/Marie59/champ_blocs commit 0d86db7d42b608c386a54500064f5f9c9d7019a4 ecology parents: diff changeset	1233 sqrt(qecbnato0_x[, conca]), #Transform your species abundance data_ Typically, raw abundances are transformed prior to analysis. Usually you will use square root, fourth-root, log(X+1), or presence-absence (square root being least extreme, P/A being most). I would start with square root. (https://stats.stackexchange.com/questions/234495/double-zeroes-problem-with-euclidean-distance-and-abundance-data-is-the-proble)
42b51a52e308 planemo upload for repository https://github.com/Marie59/champ_blocs commit 0d86db7d42b608c386a54500064f5f9c9d7019a4 ecology parents: diff changeset	1234
42b51a52e308 planemo upload for repository https://github.com/Marie59/champ_blocs commit 0d86db7d42b608c386a54500064f5f9c9d7019a4 ecology parents: diff changeset	1235 na.rm = TRUE,
42b51a52e308 planemo upload for repository https://github.com/Marie59/champ_blocs commit 0d86db7d42b608c386a54500064f5f9c9d7019a4 ecology parents: diff changeset	1236 method = "bray" #Construct species abundance dissimilarity matrices with Bray-Curtis. If your data contains samples that are all-zero you will run into the double zero problem. This can be overcome by using a zero-adjusted Bray-Curtis coefficient, which is sometimes referred to as a 'dummy variable' which damps down the similarity fluctuations between samples that are both zero (undefined). => see below for zero-adjusted Bray-Curtis coefficient ; #another possibility, sqrt + 1 ??
42b51a52e308 planemo upload for repository https://github.com/Marie59/champ_blocs commit 0d86db7d42b608c386a54500064f5f9c9d7019a4 ecology parents: diff changeset	1237 )
42b51a52e308 planemo upload for repository https://github.com/Marie59/champ_blocs commit 0d86db7d42b608c386a54500064f5f9c9d7019a4 ecology parents: diff changeset	1238
42b51a52e308 planemo upload for repository https://github.com/Marie59/champ_blocs commit 0d86db7d42b608c386a54500064f5f9c9d7019a4 ecology parents: diff changeset	1239
42b51a52e308 planemo upload for repository https://github.com/Marie59/champ_blocs commit 0d86db7d42b608c386a54500064f5f9c9d7019a4 ecology parents: diff changeset	1240 #https://rdrr.io/github/phytomosaic/ecole/man/bray0.html
42b51a52e308 planemo upload for repository https://github.com/Marie59/champ_blocs commit 0d86db7d42b608c386a54500064f5f9c9d7019a4 ecology parents: diff changeset	1241 # mtxdis <- ecole::bray0(
42b51a52e308 planemo upload for repository https://github.com/Marie59/champ_blocs commit 0d86db7d42b608c386a54500064f5f9c9d7019a4 ecology parents: diff changeset	1242 # sqrt
42b51a52e308 planemo upload for repository https://github.com/Marie59/champ_blocs commit 0d86db7d42b608c386a54500064f5f9c9d7019a4 ecology parents: diff changeset	1243 # (qecbnato0_x[,conca]), na.rm = TRUE)
42b51a52e308 planemo upload for repository https://github.com/Marie59/champ_blocs commit 0d86db7d42b608c386a54500064f5f9c9d7019a4 ecology parents: diff changeset	1244
42b51a52e308 planemo upload for repository https://github.com/Marie59/champ_blocs commit 0d86db7d42b608c386a54500064f5f9c9d7019a4 ecology parents: diff changeset	1245 expand.grid(mtxdis)
42b51a52e308 planemo upload for repository https://github.com/Marie59/champ_blocs commit 0d86db7d42b608c386a54500064f5f9c9d7019a4 ecology parents: diff changeset	1246
42b51a52e308 planemo upload for repository https://github.com/Marie59/champ_blocs commit 0d86db7d42b608c386a54500064f5f9c9d7019a4 ecology parents: diff changeset	1247 mtxdisdf_ <- as.data.frame(as.matrix(mtxdis))
42b51a52e308 planemo upload for repository https://github.com/Marie59/champ_blocs commit 0d86db7d42b608c386a54500064f5f9c9d7019a4 ecology parents: diff changeset	1248
42b51a52e308 planemo upload for repository https://github.com/Marie59/champ_blocs commit 0d86db7d42b608c386a54500064f5f9c9d7019a4 ecology parents: diff changeset	1249 a_ <- NA
42b51a52e308 planemo upload for repository https://github.com/Marie59/champ_blocs commit 0d86db7d42b608c386a54500064f5f9c9d7019a4 ecology parents: diff changeset	1250 b_ <- NA
42b51a52e308 planemo upload for repository https://github.com/Marie59/champ_blocs commit 0d86db7d42b608c386a54500064f5f9c9d7019a4 ecology parents: diff changeset	1251 c_ <- NA
42b51a52e308 planemo upload for repository https://github.com/Marie59/champ_blocs commit 0d86db7d42b608c386a54500064f5f9c9d7019a4 ecology parents: diff changeset	1252 d_ <- NA
42b51a52e308 planemo upload for repository https://github.com/Marie59/champ_blocs commit 0d86db7d42b608c386a54500064f5f9c9d7019a4 ecology parents: diff changeset	1253 e_ <- NA
42b51a52e308 planemo upload for repository https://github.com/Marie59/champ_blocs commit 0d86db7d42b608c386a54500064f5f9c9d7019a4 ecology parents: diff changeset	1254 f_ <- NA
42b51a52e308 planemo upload for repository https://github.com/Marie59/champ_blocs commit 0d86db7d42b608c386a54500064f5f9c9d7019a4 ecology parents: diff changeset	1255 g_ <- NA
42b51a52e308 planemo upload for repository https://github.com/Marie59/champ_blocs commit 0d86db7d42b608c386a54500064f5f9c9d7019a4 ecology parents: diff changeset	1256 h_ <- NA
42b51a52e308 planemo upload for repository https://github.com/Marie59/champ_blocs commit 0d86db7d42b608c386a54500064f5f9c9d7019a4 ecology parents: diff changeset	1257 i_ <- NA
42b51a52e308 planemo upload for repository https://github.com/Marie59/champ_blocs commit 0d86db7d42b608c386a54500064f5f9c9d7019a4 ecology parents: diff changeset	1258 j_ <- NA
42b51a52e308 planemo upload for repository https://github.com/Marie59/champ_blocs commit 0d86db7d42b608c386a54500064f5f9c9d7019a4 ecology parents: diff changeset	1259 k_ <- NA
42b51a52e308 planemo upload for repository https://github.com/Marie59/champ_blocs commit 0d86db7d42b608c386a54500064f5f9c9d7019a4 ecology parents: diff changeset	1260 l_ <- NA
42b51a52e308 planemo upload for repository https://github.com/Marie59/champ_blocs commit 0d86db7d42b608c386a54500064f5f9c9d7019a4 ecology parents: diff changeset	1261 m_ <- NA
42b51a52e308 planemo upload for repository https://github.com/Marie59/champ_blocs commit 0d86db7d42b608c386a54500064f5f9c9d7019a4 ecology parents: diff changeset	1262 n_ <- NA
42b51a52e308 planemo upload for repository https://github.com/Marie59/champ_blocs commit 0d86db7d42b608c386a54500064f5f9c9d7019a4 ecology parents: diff changeset	1263
42b51a52e308 planemo upload for repository https://github.com/Marie59/champ_blocs commit 0d86db7d42b608c386a54500064f5f9c9d7019a4 ecology parents: diff changeset	1264 for (z in c(1:nrow(mtxdisdf_))) {
42b51a52e308 planemo upload for repository https://github.com/Marie59/champ_blocs commit 0d86db7d42b608c386a54500064f5f9c9d7019a4 ecology parents: diff changeset	1265
42b51a52e308 planemo upload for repository https://github.com/Marie59/champ_blocs commit 0d86db7d42b608c386a54500064f5f9c9d7019a4 ecology parents: diff changeset	1266 a_[[z]] <- (paste0(rownames(mtxdisdf_[z + 1, ]), " & ", ifelse(nrow(mtxdisdf_) >= 1, colnames(mtxdisdf_[1]), NA)))
42b51a52e308 planemo upload for repository https://github.com/Marie59/champ_blocs commit 0d86db7d42b608c386a54500064f5f9c9d7019a4 ecology parents: diff changeset	1267 b_[[z]] <- (paste0(rownames(mtxdisdf_[z + 2, ]), " & ", ifelse(nrow(mtxdisdf_) >= 2, colnames(mtxdisdf_[2]), NA)))
42b51a52e308 planemo upload for repository https://github.com/Marie59/champ_blocs commit 0d86db7d42b608c386a54500064f5f9c9d7019a4 ecology parents: diff changeset	1268 c_[[z]] <- (paste0(rownames(mtxdisdf_[z + 3, ]), " & ", ifelse(nrow(mtxdisdf_) >= 3, colnames(mtxdisdf_[3]), NA)))
42b51a52e308 planemo upload for repository https://github.com/Marie59/champ_blocs commit 0d86db7d42b608c386a54500064f5f9c9d7019a4 ecology parents: diff changeset	1269 d_[[z]] <- (paste0(rownames(mtxdisdf_[z + 4, ]), " & ", ifelse(nrow(mtxdisdf_) >= 4, colnames(mtxdisdf_[4]), NA)))
42b51a52e308 planemo upload for repository https://github.com/Marie59/champ_blocs commit 0d86db7d42b608c386a54500064f5f9c9d7019a4 ecology parents: diff changeset	1270 e_[[z]] <- (paste0(rownames(mtxdisdf_[z + 5, ]), " & ", ifelse(nrow(mtxdisdf_) >= 5, colnames(mtxdisdf_[5]), NA)))
42b51a52e308 planemo upload for repository https://github.com/Marie59/champ_blocs commit 0d86db7d42b608c386a54500064f5f9c9d7019a4 ecology parents: diff changeset	1271 f_[[z]] <- (paste0(rownames(mtxdisdf_[z + 6, ]), " & ", ifelse(nrow(mtxdisdf_) >= 6, colnames(mtxdisdf_[6]), NA)))
42b51a52e308 planemo upload for repository https://github.com/Marie59/champ_blocs commit 0d86db7d42b608c386a54500064f5f9c9d7019a4 ecology parents: diff changeset	1272 g_[[z]] <- (paste0(rownames(mtxdisdf_[z + 7, ]), " & ", ifelse(nrow(mtxdisdf_) >= 7, colnames(mtxdisdf_[7]), NA)))
42b51a52e308 planemo upload for repository https://github.com/Marie59/champ_blocs commit 0d86db7d42b608c386a54500064f5f9c9d7019a4 ecology parents: diff changeset	1273 h_[[z]] <- (paste0(rownames(mtxdisdf_[z + 8, ]), " & ", ifelse(nrow(mtxdisdf_) >= 8, colnames(mtxdisdf_[8]), NA)))
42b51a52e308 planemo upload for repository https://github.com/Marie59/champ_blocs commit 0d86db7d42b608c386a54500064f5f9c9d7019a4 ecology parents: diff changeset	1274 i_[[z]] <- (paste0(rownames(mtxdisdf_[z + 9, ]), " & ", ifelse(nrow(mtxdisdf_) >= 9, colnames(mtxdisdf_[9]), NA)))
42b51a52e308 planemo upload for repository https://github.com/Marie59/champ_blocs commit 0d86db7d42b608c386a54500064f5f9c9d7019a4 ecology parents: diff changeset	1275 j_[[z]] <- (paste0(rownames(mtxdisdf_[z + 10, ]), " & ", ifelse(nrow(mtxdisdf_) >= 10, colnames(mtxdisdf_[10]), NA)))
42b51a52e308 planemo upload for repository https://github.com/Marie59/champ_blocs commit 0d86db7d42b608c386a54500064f5f9c9d7019a4 ecology parents: diff changeset	1276 k_[[z]] <- (paste0(rownames(mtxdisdf_[z + 11, ]), " & ", ifelse(nrow(mtxdisdf_) >= 11, colnames(mtxdisdf_[11]), NA)))
42b51a52e308 planemo upload for repository https://github.com/Marie59/champ_blocs commit 0d86db7d42b608c386a54500064f5f9c9d7019a4 ecology parents: diff changeset	1277 l_[[z]] <- (paste0(rownames(mtxdisdf_[z + 12, ]), " & ", ifelse(nrow(mtxdisdf_) >= 12, colnames(mtxdisdf_[12]), NA)))
42b51a52e308 planemo upload for repository https://github.com/Marie59/champ_blocs commit 0d86db7d42b608c386a54500064f5f9c9d7019a4 ecology parents: diff changeset	1278 m_[[z]] <- (paste0(rownames(mtxdisdf_[z + 13, ]), " & ", ifelse(nrow(mtxdisdf_) >= 13, colnames(mtxdisdf_[13]), NA)))
42b51a52e308 planemo upload for repository https://github.com/Marie59/champ_blocs commit 0d86db7d42b608c386a54500064f5f9c9d7019a4 ecology parents: diff changeset	1279 n_[[z]] <- (paste0(rownames(mtxdisdf_[z + 14, ]), " & ", ifelse(nrow(mtxdisdf_) >= 14, colnames(mtxdisdf_[14]), NA)))
42b51a52e308 planemo upload for repository https://github.com/Marie59/champ_blocs commit 0d86db7d42b608c386a54500064f5f9c9d7019a4 ecology parents: diff changeset	1280
42b51a52e308 planemo upload for repository https://github.com/Marie59/champ_blocs commit 0d86db7d42b608c386a54500064f5f9c9d7019a4 ecology parents: diff changeset	1281 }
42b51a52e308 planemo upload for repository https://github.com/Marie59/champ_blocs commit 0d86db7d42b608c386a54500064f5f9c9d7019a4 ecology parents: diff changeset	1282
42b51a52e308 planemo upload for repository https://github.com/Marie59/champ_blocs commit 0d86db7d42b608c386a54500064f5f9c9d7019a4 ecology parents: diff changeset	1283 rm(z)
42b51a52e308 planemo upload for repository https://github.com/Marie59/champ_blocs commit 0d86db7d42b608c386a54500064f5f9c9d7019a4 ecology parents: diff changeset	1284
42b51a52e308 planemo upload for repository https://github.com/Marie59/champ_blocs commit 0d86db7d42b608c386a54500064f5f9c9d7019a4 ecology parents: diff changeset	1285 y <- length(a_) - (ifelse(nrow(mtxdisdf_) >= 1, 1, nrow(mtxdisdf_)))
42b51a52e308 planemo upload for repository https://github.com/Marie59/champ_blocs commit 0d86db7d42b608c386a54500064f5f9c9d7019a4 ecology parents: diff changeset	1286 a_ <- a_[1:y]
42b51a52e308 planemo upload for repository https://github.com/Marie59/champ_blocs commit 0d86db7d42b608c386a54500064f5f9c9d7019a4 ecology parents: diff changeset	1287 y <- length(b_) - (ifelse(nrow(mtxdisdf_) >= 2, 2, nrow(mtxdisdf_)))
42b51a52e308 planemo upload for repository https://github.com/Marie59/champ_blocs commit 0d86db7d42b608c386a54500064f5f9c9d7019a4 ecology parents: diff changeset	1288 b_ <- b_[1:y]
42b51a52e308 planemo upload for repository https://github.com/Marie59/champ_blocs commit 0d86db7d42b608c386a54500064f5f9c9d7019a4 ecology parents: diff changeset	1289 y <- length(c_) - (ifelse(nrow(mtxdisdf_) >= 3, 3, nrow(mtxdisdf_)))
42b51a52e308 planemo upload for repository https://github.com/Marie59/champ_blocs commit 0d86db7d42b608c386a54500064f5f9c9d7019a4 ecology parents: diff changeset	1290 c_ <- c_[1:y]
42b51a52e308 planemo upload for repository https://github.com/Marie59/champ_blocs commit 0d86db7d42b608c386a54500064f5f9c9d7019a4 ecology parents: diff changeset	1291 y <- length(d_) - (ifelse(nrow(mtxdisdf_) >= 4, 4, nrow(mtxdisdf_)))
42b51a52e308 planemo upload for repository https://github.com/Marie59/champ_blocs commit 0d86db7d42b608c386a54500064f5f9c9d7019a4 ecology parents: diff changeset	1292 d_ <- d_[1:y]
42b51a52e308 planemo upload for repository https://github.com/Marie59/champ_blocs commit 0d86db7d42b608c386a54500064f5f9c9d7019a4 ecology parents: diff changeset	1293 y <- length(e_) - (ifelse(nrow(mtxdisdf_) >= 5, 5, nrow(mtxdisdf_)))
42b51a52e308 planemo upload for repository https://github.com/Marie59/champ_blocs commit 0d86db7d42b608c386a54500064f5f9c9d7019a4 ecology parents: diff changeset	1294 e_ <- e_[1:y]
42b51a52e308 planemo upload for repository https://github.com/Marie59/champ_blocs commit 0d86db7d42b608c386a54500064f5f9c9d7019a4 ecology parents: diff changeset	1295 y <- length(f_) - (ifelse(nrow(mtxdisdf_) >= 6, 6, nrow(mtxdisdf_)))
42b51a52e308 planemo upload for repository https://github.com/Marie59/champ_blocs commit 0d86db7d42b608c386a54500064f5f9c9d7019a4 ecology parents: diff changeset	1296 f_ <- f_[1:y]
42b51a52e308 planemo upload for repository https://github.com/Marie59/champ_blocs commit 0d86db7d42b608c386a54500064f5f9c9d7019a4 ecology parents: diff changeset	1297 y <- length(g_) - (ifelse(nrow(mtxdisdf_) >= 7, 7, nrow(mtxdisdf_)))
42b51a52e308 planemo upload for repository https://github.com/Marie59/champ_blocs commit 0d86db7d42b608c386a54500064f5f9c9d7019a4 ecology parents: diff changeset	1298 g_ <- g_[1:y]
42b51a52e308 planemo upload for repository https://github.com/Marie59/champ_blocs commit 0d86db7d42b608c386a54500064f5f9c9d7019a4 ecology parents: diff changeset	1299 y <- length(h_) - (ifelse(nrow(mtxdisdf_) >= 8, 8, nrow(mtxdisdf_)))
42b51a52e308 planemo upload for repository https://github.com/Marie59/champ_blocs commit 0d86db7d42b608c386a54500064f5f9c9d7019a4 ecology parents: diff changeset	1300 h_ <- h_[1:y]
42b51a52e308 planemo upload for repository https://github.com/Marie59/champ_blocs commit 0d86db7d42b608c386a54500064f5f9c9d7019a4 ecology parents: diff changeset	1301 y <- length(i_) - (ifelse(nrow(mtxdisdf_) >= 9, 9, nrow(mtxdisdf_)))
42b51a52e308 planemo upload for repository https://github.com/Marie59/champ_blocs commit 0d86db7d42b608c386a54500064f5f9c9d7019a4 ecology parents: diff changeset	1302 i_ <- i_[1:y]
42b51a52e308 planemo upload for repository https://github.com/Marie59/champ_blocs commit 0d86db7d42b608c386a54500064f5f9c9d7019a4 ecology parents: diff changeset	1303 y <- length(j_) - (ifelse(nrow(mtxdisdf_) >= 10, 10, nrow(mtxdisdf_)))
42b51a52e308 planemo upload for repository https://github.com/Marie59/champ_blocs commit 0d86db7d42b608c386a54500064f5f9c9d7019a4 ecology parents: diff changeset	1304 j_ <- j_[1:y]
42b51a52e308 planemo upload for repository https://github.com/Marie59/champ_blocs commit 0d86db7d42b608c386a54500064f5f9c9d7019a4 ecology parents: diff changeset	1305 y <- length(k_) - (ifelse(nrow(mtxdisdf_) >= 11, 11, nrow(mtxdisdf_)))
42b51a52e308 planemo upload for repository https://github.com/Marie59/champ_blocs commit 0d86db7d42b608c386a54500064f5f9c9d7019a4 ecology parents: diff changeset	1306 k_ <- k_[1:y]
42b51a52e308 planemo upload for repository https://github.com/Marie59/champ_blocs commit 0d86db7d42b608c386a54500064f5f9c9d7019a4 ecology parents: diff changeset	1307 y <- length(l_) - (ifelse(nrow(mtxdisdf_) >= 12, 12, nrow(mtxdisdf_)))
42b51a52e308 planemo upload for repository https://github.com/Marie59/champ_blocs commit 0d86db7d42b608c386a54500064f5f9c9d7019a4 ecology parents: diff changeset	1308 l_ <- l_[1:y]
42b51a52e308 planemo upload for repository https://github.com/Marie59/champ_blocs commit 0d86db7d42b608c386a54500064f5f9c9d7019a4 ecology parents: diff changeset	1309 y <- length(m_) - (ifelse(nrow(mtxdisdf_) >= 13, 13, nrow(mtxdisdf_)))
42b51a52e308 planemo upload for repository https://github.com/Marie59/champ_blocs commit 0d86db7d42b608c386a54500064f5f9c9d7019a4 ecology parents: diff changeset	1310 m_ <- m_[1:y]
42b51a52e308 planemo upload for repository https://github.com/Marie59/champ_blocs commit 0d86db7d42b608c386a54500064f5f9c9d7019a4 ecology parents: diff changeset	1311 y <- length(n_) - (ifelse(nrow(mtxdisdf_) >= 14, 14, nrow(mtxdisdf_)))
42b51a52e308 planemo upload for repository https://github.com/Marie59/champ_blocs commit 0d86db7d42b608c386a54500064f5f9c9d7019a4 ecology parents: diff changeset	1312 n_ <- n_[1:y]
42b51a52e308 planemo upload for repository https://github.com/Marie59/champ_blocs commit 0d86db7d42b608c386a54500064f5f9c9d7019a4 ecology parents: diff changeset	1313
42b51a52e308 planemo upload for repository https://github.com/Marie59/champ_blocs commit 0d86db7d42b608c386a54500064f5f9c9d7019a4 ecology parents: diff changeset	1314 rm(y)
42b51a52e308 planemo upload for repository https://github.com/Marie59/champ_blocs commit 0d86db7d42b608c386a54500064f5f9c9d7019a4 ecology parents: diff changeset	1315
42b51a52e308 planemo upload for repository https://github.com/Marie59/champ_blocs commit 0d86db7d42b608c386a54500064f5f9c9d7019a4 ecology parents: diff changeset	1316 name_ <- c(a_, b_, c_, d_, e_, f_, g_, h_, i_, j_, k_, l_, m_, n_)
42b51a52e308 planemo upload for repository https://github.com/Marie59/champ_blocs commit 0d86db7d42b608c386a54500064f5f9c9d7019a4 ecology parents: diff changeset	1317 df_ <- data.frame(expand.grid(mtxdis), name_[1:nrow(expand.grid(mtxdis))])
42b51a52e308 planemo upload for repository https://github.com/Marie59/champ_blocs commit 0d86db7d42b608c386a54500064f5f9c9d7019a4 ecology parents: diff changeset	1318 names(df_) <- c("dist.", "name_")
42b51a52e308 planemo upload for repository https://github.com/Marie59/champ_blocs commit 0d86db7d42b608c386a54500064f5f9c9d7019a4 ecology parents: diff changeset	1319
42b51a52e308 planemo upload for repository https://github.com/Marie59/champ_blocs commit 0d86db7d42b608c386a54500064f5f9c9d7019a4 ecology parents: diff changeset	1320 rm(a_, b_, c_, d_, e_, f_, g_, h_, i_, j_, k_, l_, m_, n_)
42b51a52e308 planemo upload for repository https://github.com/Marie59/champ_blocs commit 0d86db7d42b608c386a54500064f5f9c9d7019a4 ecology parents: diff changeset	1321 rm(name_)
42b51a52e308 planemo upload for repository https://github.com/Marie59/champ_blocs commit 0d86db7d42b608c386a54500064f5f9c9d7019a4 ecology parents: diff changeset	1322
42b51a52e308 planemo upload for repository https://github.com/Marie59/champ_blocs commit 0d86db7d42b608c386a54500064f5f9c9d7019a4 ecology parents: diff changeset	1323 q_ <- strsplit(df_$name_, " & ")
42b51a52e308 planemo upload for repository https://github.com/Marie59/champ_blocs commit 0d86db7d42b608c386a54500064f5f9c9d7019a4 ecology parents: diff changeset	1324 mat_ <- matrix(unlist(q_), ncol = 2, byrow = TRUE)
42b51a52e308 planemo upload for repository https://github.com/Marie59/champ_blocs commit 0d86db7d42b608c386a54500064f5f9c9d7019a4 ecology parents: diff changeset	1325 q_df_ <- as.data.frame(matrix(unlist(q_), ncol = 2, byrow = TRUE))
42b51a52e308 planemo upload for repository https://github.com/Marie59/champ_blocs commit 0d86db7d42b608c386a54500064f5f9c9d7019a4 ecology parents: diff changeset	1326 df_ <- dplyr::bind_cols(df_, q_df_)
42b51a52e308 planemo upload for repository https://github.com/Marie59/champ_blocs commit 0d86db7d42b608c386a54500064f5f9c9d7019a4 ecology parents: diff changeset	1327
42b51a52e308 planemo upload for repository https://github.com/Marie59/champ_blocs commit 0d86db7d42b608c386a54500064f5f9c9d7019a4 ecology parents: diff changeset	1328 rm(q_, mat_, q_df_)
42b51a52e308 planemo upload for repository https://github.com/Marie59/champ_blocs commit 0d86db7d42b608c386a54500064f5f9c9d7019a4 ecology parents: diff changeset	1329
42b51a52e308 planemo upload for repository https://github.com/Marie59/champ_blocs commit 0d86db7d42b608c386a54500064f5f9c9d7019a4 ecology parents: diff changeset	1330 split_ <- strsplit(df_$V1, "_")
42b51a52e308 planemo upload for repository https://github.com/Marie59/champ_blocs commit 0d86db7d42b608c386a54500064f5f9c9d7019a4 ecology parents: diff changeset	1331 v1_split_ <- as.data.frame(matrix(unlist(split_), ncol = 4, byrow = TRUE))
42b51a52e308 planemo upload for repository https://github.com/Marie59/champ_blocs commit 0d86db7d42b608c386a54500064f5f9c9d7019a4 ecology parents: diff changeset	1332 split_ <- strsplit(df_$V2, "_")
42b51a52e308 planemo upload for repository https://github.com/Marie59/champ_blocs commit 0d86db7d42b608c386a54500064f5f9c9d7019a4 ecology parents: diff changeset	1333 v2_split_ <- as.data.frame(matrix(unlist(split_), ncol = 4, byrow = TRUE))
42b51a52e308 planemo upload for repository https://github.com/Marie59/champ_blocs commit 0d86db7d42b608c386a54500064f5f9c9d7019a4 ecology parents: diff changeset	1334
42b51a52e308 planemo upload for repository https://github.com/Marie59/champ_blocs commit 0d86db7d42b608c386a54500064f5f9c9d7019a4 ecology parents: diff changeset	1335 df_ <- dplyr::bind_cols(df_, v1_split_)
42b51a52e308 planemo upload for repository https://github.com/Marie59/champ_blocs commit 0d86db7d42b608c386a54500064f5f9c9d7019a4 ecology parents: diff changeset	1336 df_ <- dplyr::bind_cols(df_, v2_split_)
42b51a52e308 planemo upload for repository https://github.com/Marie59/champ_blocs commit 0d86db7d42b608c386a54500064f5f9c9d7019a4 ecology parents: diff changeset	1337 df_red_ <- subset(df_, V4...8 == V4...12 & V1...5 != V1...9)
42b51a52e308 planemo upload for repository https://github.com/Marie59/champ_blocs commit 0d86db7d42b608c386a54500064f5f9c9d7019a4 ecology parents: diff changeset	1338 site_year_month_day <- rep(unique(qecbnato0_x$site_year_month_day), nrow(df_red_))
42b51a52e308 planemo upload for repository https://github.com/Marie59/champ_blocs commit 0d86db7d42b608c386a54500064f5f9c9d7019a4 ecology parents: diff changeset	1339
42b51a52e308 planemo upload for repository https://github.com/Marie59/champ_blocs commit 0d86db7d42b608c386a54500064f5f9c9d7019a4 ecology parents: diff changeset	1340 df_red_ <- tibble::add_column(df_red_, site_year_month_day, .before = "dist.")
42b51a52e308 planemo upload for repository https://github.com/Marie59/champ_blocs commit 0d86db7d42b608c386a54500064f5f9c9d7019a4 ecology parents: diff changeset	1341
42b51a52e308 planemo upload for repository https://github.com/Marie59/champ_blocs commit 0d86db7d42b608c386a54500064f5f9c9d7019a4 ecology parents: diff changeset	1342 rm(split_, v1_split_, v2_split_)
42b51a52e308 planemo upload for repository https://github.com/Marie59/champ_blocs commit 0d86db7d42b608c386a54500064f5f9c9d7019a4 ecology parents: diff changeset	1343 rm(mtxdis, mtxdisdf_, df_, site_year_month_day)
42b51a52e308 planemo upload for repository https://github.com/Marie59/champ_blocs commit 0d86db7d42b608c386a54500064f5f9c9d7019a4 ecology parents: diff changeset	1344
42b51a52e308 planemo upload for repository https://github.com/Marie59/champ_blocs commit 0d86db7d42b608c386a54500064f5f9c9d7019a4 ecology parents: diff changeset	1345 matri_list[[x]] <- df_red_
42b51a52e308 planemo upload for repository https://github.com/Marie59/champ_blocs commit 0d86db7d42b608c386a54500064f5f9c9d7019a4 ecology parents: diff changeset	1346 matri_list <<- matri_list
42b51a52e308 planemo upload for repository https://github.com/Marie59/champ_blocs commit 0d86db7d42b608c386a54500064f5f9c9d7019a4 ecology parents: diff changeset	1347
42b51a52e308 planemo upload for repository https://github.com/Marie59/champ_blocs commit 0d86db7d42b608c386a54500064f5f9c9d7019a4 ecology parents: diff changeset	1348 rm(df_red_, qecbnato0_x, x)
42b51a52e308 planemo upload for repository https://github.com/Marie59/champ_blocs commit 0d86db7d42b608c386a54500064f5f9c9d7019a4 ecology parents: diff changeset	1349
42b51a52e308 planemo upload for repository https://github.com/Marie59/champ_blocs commit 0d86db7d42b608c386a54500064f5f9c9d7019a4 ecology parents: diff changeset	1350 }
42b51a52e308 planemo upload for repository https://github.com/Marie59/champ_blocs commit 0d86db7d42b608c386a54500064f5f9c9d7019a4 ecology parents: diff changeset	1351
42b51a52e308 planemo upload for repository https://github.com/Marie59/champ_blocs commit 0d86db7d42b608c386a54500064f5f9c9d7019a4 ecology parents: diff changeset	1352 matri_df <- do.call("rbind", matri_list)
42b51a52e308 planemo upload for repository https://github.com/Marie59/champ_blocs commit 0d86db7d42b608c386a54500064f5f9c9d7019a4 ecology parents: diff changeset	1353
42b51a52e308 planemo upload for repository https://github.com/Marie59/champ_blocs commit 0d86db7d42b608c386a54500064f5f9c9d7019a4 ecology parents: diff changeset	1354 names(matri_df) <- c("site_year_month_day", "dist.", "name_", "name_left", "name_right", "Type.Bloc.left", "Face.left", "Numéro.Bloc.échantillon.left", "Quadrat.left", "Type.Bloc.right", "Face.right", "Numéro.Bloc.échantillon.right", "Quadrat.right")
42b51a52e308 planemo upload for repository https://github.com/Marie59/champ_blocs commit 0d86db7d42b608c386a54500064f5f9c9d7019a4 ecology parents: diff changeset	1355
42b51a52e308 planemo upload for repository https://github.com/Marie59/champ_blocs commit 0d86db7d42b608c386a54500064f5f9c9d7019a4 ecology parents: diff changeset	1356 matri_df <<- matri_df
42b51a52e308 planemo upload for repository https://github.com/Marie59/champ_blocs commit 0d86db7d42b608c386a54500064f5f9c9d7019a4 ecology parents: diff changeset	1357
42b51a52e308 planemo upload for repository https://github.com/Marie59/champ_blocs commit 0d86db7d42b608c386a54500064f5f9c9d7019a4 ecology parents: diff changeset	1358 hist(matri_df$dist.)
42b51a52e308 planemo upload for repository https://github.com/Marie59/champ_blocs commit 0d86db7d42b608c386a54500064f5f9c9d7019a4 ecology parents: diff changeset	1359
42b51a52e308 planemo upload for repository https://github.com/Marie59/champ_blocs commit 0d86db7d42b608c386a54500064f5f9c9d7019a4 ecology parents: diff changeset	1360 }
42b51a52e308 planemo upload for repository https://github.com/Marie59/champ_blocs commit 0d86db7d42b608c386a54500064f5f9c9d7019a4 ecology parents: diff changeset	1361
42b51a52e308 planemo upload for repository https://github.com/Marie59/champ_blocs commit 0d86db7d42b608c386a54500064f5f9c9d7019a4 ecology parents: diff changeset	1362 data_ <- dplyr::filter(qecbnato0, Face == "face supérieure")
42b51a52e308 planemo upload for repository https://github.com/Marie59/champ_blocs commit 0d86db7d42b608c386a54500064f5f9c9d7019a4 ecology parents: diff changeset	1363 data_$Type.Bloc <- ifelse(as.character(data_$Type.Bloc) == "Roche en place", "Bloc fixé", as.character(data_$Type.Bloc))
42b51a52e308 planemo upload for repository https://github.com/Marie59/champ_blocs commit 0d86db7d42b608c386a54500064f5f9c9d7019a4 ecology parents: diff changeset	1364 matri_list <- vector("list", length(unique(data_$site_year_month_day)))
42b51a52e308 planemo upload for repository https://github.com/Marie59/champ_blocs commit 0d86db7d42b608c386a54500064f5f9c9d7019a4 ecology parents: diff changeset	1365
42b51a52e308 planemo upload for repository https://github.com/Marie59/champ_blocs commit 0d86db7d42b608c386a54500064f5f9c9d7019a4 ecology parents: diff changeset	1366 matri_fct_bmf(data = data_, conca = c(bret_egmp_basq_qecb, egmp_basq_qecb))
42b51a52e308 planemo upload for repository https://github.com/Marie59/champ_blocs commit 0d86db7d42b608c386a54500064f5f9c9d7019a4 ecology parents: diff changeset	1367 hist(matri_df$dist., main = c(paste("Histo. of Bray (0-adjusted) dist. dissimilarity measures"), paste(" (sqrt transfo) - BMfs vs BF -")))
42b51a52e308 planemo upload for repository https://github.com/Marie59/champ_blocs commit 0d86db7d42b608c386a54500064f5f9c9d7019a4 ecology parents: diff changeset	1368
42b51a52e308 planemo upload for repository https://github.com/Marie59/champ_blocs commit 0d86db7d42b608c386a54500064f5f9c9d7019a4 ecology parents: diff changeset	1369 matri_full_bm_bf_fs <- matri_df
42b51a52e308 planemo upload for repository https://github.com/Marie59/champ_blocs commit 0d86db7d42b608c386a54500064f5f9c9d7019a4 ecology parents: diff changeset	1370
42b51a52e308 planemo upload for repository https://github.com/Marie59/champ_blocs commit 0d86db7d42b608c386a54500064f5f9c9d7019a4 ecology parents: diff changeset	1371
42b51a52e308 planemo upload for repository https://github.com/Marie59/champ_blocs commit 0d86db7d42b608c386a54500064f5f9c9d7019a4 ecology parents: diff changeset	1372 rm(data_, matri_df, matri_list)
42b51a52e308 planemo upload for repository https://github.com/Marie59/champ_blocs commit 0d86db7d42b608c386a54500064f5f9c9d7019a4 ecology parents: diff changeset	1373
42b51a52e308 planemo upload for repository https://github.com/Marie59/champ_blocs commit 0d86db7d42b608c386a54500064f5f9c9d7019a4 ecology parents: diff changeset	1374
42b51a52e308 planemo upload for repository https://github.com/Marie59/champ_blocs commit 0d86db7d42b608c386a54500064f5f9c9d7019a4 ecology parents: diff changeset	1375 ### determination of coefficient of dissimilarity between blocs mobiles face sup vs face inf.
42b51a52e308 planemo upload for repository https://github.com/Marie59/champ_blocs commit 0d86db7d42b608c386a54500064f5f9c9d7019a4 ecology parents: diff changeset	1376
42b51a52e308 planemo upload for repository https://github.com/Marie59/champ_blocs commit 0d86db7d42b608c386a54500064f5f9c9d7019a4 ecology parents: diff changeset	1377 # loop in a fct
42b51a52e308 planemo upload for repository https://github.com/Marie59/champ_blocs commit 0d86db7d42b608c386a54500064f5f9c9d7019a4 ecology parents: diff changeset	1378
42b51a52e308 planemo upload for repository https://github.com/Marie59/champ_blocs commit 0d86db7d42b608c386a54500064f5f9c9d7019a4 ecology parents: diff changeset	1379 matri_fct_bmm <- function(data, conca) {
42b51a52e308 planemo upload for repository https://github.com/Marie59/champ_blocs commit 0d86db7d42b608c386a54500064f5f9c9d7019a4 ecology parents: diff changeset	1380
42b51a52e308 planemo upload for repository https://github.com/Marie59/champ_blocs commit 0d86db7d42b608c386a54500064f5f9c9d7019a4 ecology parents: diff changeset	1381 matri_df <- data
42b51a52e308 planemo upload for repository https://github.com/Marie59/champ_blocs commit 0d86db7d42b608c386a54500064f5f9c9d7019a4 ecology parents: diff changeset	1382
42b51a52e308 planemo upload for repository https://github.com/Marie59/champ_blocs commit 0d86db7d42b608c386a54500064f5f9c9d7019a4 ecology parents: diff changeset	1383 for (x in c(1:length(unique(matri_df$site_year_month_day)))) {
42b51a52e308 planemo upload for repository https://github.com/Marie59/champ_blocs commit 0d86db7d42b608c386a54500064f5f9c9d7019a4 ecology parents: diff changeset	1384
42b51a52e308 planemo upload for repository https://github.com/Marie59/champ_blocs commit 0d86db7d42b608c386a54500064f5f9c9d7019a4 ecology parents: diff changeset	1385 qecbnato0_x <- matri_df %>% dplyr::filter(site_year_month_day == unique(matri_df$site_year_month_day)[[x]])
42b51a52e308 planemo upload for repository https://github.com/Marie59/champ_blocs commit 0d86db7d42b608c386a54500064f5f9c9d7019a4 ecology parents: diff changeset	1386
42b51a52e308 planemo upload for repository https://github.com/Marie59/champ_blocs commit 0d86db7d42b608c386a54500064f5f9c9d7019a4 ecology parents: diff changeset	1387 rownames(qecbnato0_x) <- paste0(qecbnato0_x$Type.Bloc, "_", qecbnato0_x$Face, "_", qecbnato0_x$Numéro.Bloc.échantillon, "_", qecbnato0_x$quadrat_bis)
42b51a52e308 planemo upload for repository https://github.com/Marie59/champ_blocs commit 0d86db7d42b608c386a54500064f5f9c9d7019a4 ecology parents: diff changeset	1388
42b51a52e308 planemo upload for repository https://github.com/Marie59/champ_blocs commit 0d86db7d42b608c386a54500064f5f9c9d7019a4 ecology parents: diff changeset	1389
42b51a52e308 planemo upload for repository https://github.com/Marie59/champ_blocs commit 0d86db7d42b608c386a54500064f5f9c9d7019a4 ecology parents: diff changeset	1390 mtxdis <- vegan::vegdist(
42b51a52e308 planemo upload for repository https://github.com/Marie59/champ_blocs commit 0d86db7d42b608c386a54500064f5f9c9d7019a4 ecology parents: diff changeset	1391 sqrt(qecbnato0_x[, c(bret_egmp_basq_qecb)]), #Transform your species abundance data_ Typically, raw abundances are transformed prior to analysis. Usually you will use square root, fourth-root, log(X+1), or presence-absence (square root being least extreme, P/A being most). I would start with square root. (https://stats.stackexchange.com/questions/234495/double-zeroes-problem-with-euclidean-distance-and-abundance-data-is-the-proble)
42b51a52e308 planemo upload for repository https://github.com/Marie59/champ_blocs commit 0d86db7d42b608c386a54500064f5f9c9d7019a4 ecology parents: diff changeset	1392 na.rm = TRUE,
42b51a52e308 planemo upload for repository https://github.com/Marie59/champ_blocs commit 0d86db7d42b608c386a54500064f5f9c9d7019a4 ecology parents: diff changeset	1393 method = "bray" #Construct species abundance dissimilarity matrices with Bray-Curtis. If your data contains samples that are all-zero you will run into the double zero problem. This can be overcome by using a zero-adjusted Bray-Curtis coefficient, which is sometimes referred to as a 'dummy variable' which damps down the similarity fluctuations between samples that are both zero (undefined). => see below for zero-adjusted Bray-Curtis coefficient ; #another possibility, sqrt + 1 ??
42b51a52e308 planemo upload for repository https://github.com/Marie59/champ_blocs commit 0d86db7d42b608c386a54500064f5f9c9d7019a4 ecology parents: diff changeset	1394 )
42b51a52e308 planemo upload for repository https://github.com/Marie59/champ_blocs commit 0d86db7d42b608c386a54500064f5f9c9d7019a4 ecology parents: diff changeset	1395
42b51a52e308 planemo upload for repository https://github.com/Marie59/champ_blocs commit 0d86db7d42b608c386a54500064f5f9c9d7019a4 ecology parents: diff changeset	1396
42b51a52e308 planemo upload for repository https://github.com/Marie59/champ_blocs commit 0d86db7d42b608c386a54500064f5f9c9d7019a4 ecology parents: diff changeset	1397 #mtxdis <- ecole::bray0(
42b51a52e308 planemo upload for repository https://github.com/Marie59/champ_blocs commit 0d86db7d42b608c386a54500064f5f9c9d7019a4 ecology parents: diff changeset	1398 # sqrt(qecbnato0_x[, conca]), na.rm = TRUE)
42b51a52e308 planemo upload for repository https://github.com/Marie59/champ_blocs commit 0d86db7d42b608c386a54500064f5f9c9d7019a4 ecology parents: diff changeset	1399
42b51a52e308 planemo upload for repository https://github.com/Marie59/champ_blocs commit 0d86db7d42b608c386a54500064f5f9c9d7019a4 ecology parents: diff changeset	1400
42b51a52e308 planemo upload for repository https://github.com/Marie59/champ_blocs commit 0d86db7d42b608c386a54500064f5f9c9d7019a4 ecology parents: diff changeset	1401 expand.grid(mtxdis)
42b51a52e308 planemo upload for repository https://github.com/Marie59/champ_blocs commit 0d86db7d42b608c386a54500064f5f9c9d7019a4 ecology parents: diff changeset	1402
42b51a52e308 planemo upload for repository https://github.com/Marie59/champ_blocs commit 0d86db7d42b608c386a54500064f5f9c9d7019a4 ecology parents: diff changeset	1403 mtxdisdf_ <- as.data.frame(as.matrix(mtxdis))
42b51a52e308 planemo upload for repository https://github.com/Marie59/champ_blocs commit 0d86db7d42b608c386a54500064f5f9c9d7019a4 ecology parents: diff changeset	1404
42b51a52e308 planemo upload for repository https://github.com/Marie59/champ_blocs commit 0d86db7d42b608c386a54500064f5f9c9d7019a4 ecology parents: diff changeset	1405 a_ <- NA
42b51a52e308 planemo upload for repository https://github.com/Marie59/champ_blocs commit 0d86db7d42b608c386a54500064f5f9c9d7019a4 ecology parents: diff changeset	1406 b_ <- NA
42b51a52e308 planemo upload for repository https://github.com/Marie59/champ_blocs commit 0d86db7d42b608c386a54500064f5f9c9d7019a4 ecology parents: diff changeset	1407 c_ <- NA
42b51a52e308 planemo upload for repository https://github.com/Marie59/champ_blocs commit 0d86db7d42b608c386a54500064f5f9c9d7019a4 ecology parents: diff changeset	1408 d_ <- NA
42b51a52e308 planemo upload for repository https://github.com/Marie59/champ_blocs commit 0d86db7d42b608c386a54500064f5f9c9d7019a4 ecology parents: diff changeset	1409 e_ <- NA
42b51a52e308 planemo upload for repository https://github.com/Marie59/champ_blocs commit 0d86db7d42b608c386a54500064f5f9c9d7019a4 ecology parents: diff changeset	1410 f_ <- NA
42b51a52e308 planemo upload for repository https://github.com/Marie59/champ_blocs commit 0d86db7d42b608c386a54500064f5f9c9d7019a4 ecology parents: diff changeset	1411 g_ <- NA
42b51a52e308 planemo upload for repository https://github.com/Marie59/champ_blocs commit 0d86db7d42b608c386a54500064f5f9c9d7019a4 ecology parents: diff changeset	1412 h_ <- NA
42b51a52e308 planemo upload for repository https://github.com/Marie59/champ_blocs commit 0d86db7d42b608c386a54500064f5f9c9d7019a4 ecology parents: diff changeset	1413 i_ <- NA
42b51a52e308 planemo upload for repository https://github.com/Marie59/champ_blocs commit 0d86db7d42b608c386a54500064f5f9c9d7019a4 ecology parents: diff changeset	1414 j_ <- NA
42b51a52e308 planemo upload for repository https://github.com/Marie59/champ_blocs commit 0d86db7d42b608c386a54500064f5f9c9d7019a4 ecology parents: diff changeset	1415 k_ <- NA
42b51a52e308 planemo upload for repository https://github.com/Marie59/champ_blocs commit 0d86db7d42b608c386a54500064f5f9c9d7019a4 ecology parents: diff changeset	1416 l_ <- NA
42b51a52e308 planemo upload for repository https://github.com/Marie59/champ_blocs commit 0d86db7d42b608c386a54500064f5f9c9d7019a4 ecology parents: diff changeset	1417 m_ <- NA
42b51a52e308 planemo upload for repository https://github.com/Marie59/champ_blocs commit 0d86db7d42b608c386a54500064f5f9c9d7019a4 ecology parents: diff changeset	1418 n_ <- NA
42b51a52e308 planemo upload for repository https://github.com/Marie59/champ_blocs commit 0d86db7d42b608c386a54500064f5f9c9d7019a4 ecology parents: diff changeset	1419 o_ <- NA
42b51a52e308 planemo upload for repository https://github.com/Marie59/champ_blocs commit 0d86db7d42b608c386a54500064f5f9c9d7019a4 ecology parents: diff changeset	1420 p_ <- NA
42b51a52e308 planemo upload for repository https://github.com/Marie59/champ_blocs commit 0d86db7d42b608c386a54500064f5f9c9d7019a4 ecology parents: diff changeset	1421 q_ <- NA
42b51a52e308 planemo upload for repository https://github.com/Marie59/champ_blocs commit 0d86db7d42b608c386a54500064f5f9c9d7019a4 ecology parents: diff changeset	1422 r_ <- NA
42b51a52e308 planemo upload for repository https://github.com/Marie59/champ_blocs commit 0d86db7d42b608c386a54500064f5f9c9d7019a4 ecology parents: diff changeset	1423 s_ <- NA
42b51a52e308 planemo upload for repository https://github.com/Marie59/champ_blocs commit 0d86db7d42b608c386a54500064f5f9c9d7019a4 ecology parents: diff changeset	1424
42b51a52e308 planemo upload for repository https://github.com/Marie59/champ_blocs commit 0d86db7d42b608c386a54500064f5f9c9d7019a4 ecology parents: diff changeset	1425 for (z in c(1:nrow(mtxdisdf_))) {
42b51a52e308 planemo upload for repository https://github.com/Marie59/champ_blocs commit 0d86db7d42b608c386a54500064f5f9c9d7019a4 ecology parents: diff changeset	1426
42b51a52e308 planemo upload for repository https://github.com/Marie59/champ_blocs commit 0d86db7d42b608c386a54500064f5f9c9d7019a4 ecology parents: diff changeset	1427 a_[[z]] <- (paste0(rownames(mtxdisdf_[z + 1, ]), " & ", ifelse(nrow(mtxdisdf_) >= 1, colnames(mtxdisdf_[1]), NA)))
42b51a52e308 planemo upload for repository https://github.com/Marie59/champ_blocs commit 0d86db7d42b608c386a54500064f5f9c9d7019a4 ecology parents: diff changeset	1428 b_[[z]] <- (paste0(rownames(mtxdisdf_[z + 2, ]), " & ", ifelse(nrow(mtxdisdf_) >= 2, colnames(mtxdisdf_[2]), NA)))
42b51a52e308 planemo upload for repository https://github.com/Marie59/champ_blocs commit 0d86db7d42b608c386a54500064f5f9c9d7019a4 ecology parents: diff changeset	1429 c_[[z]] <- (paste0(rownames(mtxdisdf_[z + 3, ]), " & ", ifelse(nrow(mtxdisdf_) >= 3, colnames(mtxdisdf_[3]), NA)))
42b51a52e308 planemo upload for repository https://github.com/Marie59/champ_blocs commit 0d86db7d42b608c386a54500064f5f9c9d7019a4 ecology parents: diff changeset	1430 d_[[z]] <- (paste0(rownames(mtxdisdf_[z + 4, ]), " & ", ifelse(nrow(mtxdisdf_) >= 4, colnames(mtxdisdf_[4]), NA)))
42b51a52e308 planemo upload for repository https://github.com/Marie59/champ_blocs commit 0d86db7d42b608c386a54500064f5f9c9d7019a4 ecology parents: diff changeset	1431 e_[[z]] <- (paste0(rownames(mtxdisdf_[z + 5, ]), " & ", ifelse(nrow(mtxdisdf_) >= 5, colnames(mtxdisdf_[5]), NA)))
42b51a52e308 planemo upload for repository https://github.com/Marie59/champ_blocs commit 0d86db7d42b608c386a54500064f5f9c9d7019a4 ecology parents: diff changeset	1432 f_[[z]] <- (paste0(rownames(mtxdisdf_[z + 6, ]), " & ", ifelse(nrow(mtxdisdf_) >= 6, colnames(mtxdisdf_[6]), NA)))
42b51a52e308 planemo upload for repository https://github.com/Marie59/champ_blocs commit 0d86db7d42b608c386a54500064f5f9c9d7019a4 ecology parents: diff changeset	1433 g_[[z]] <- (paste0(rownames(mtxdisdf_[z + 7, ]), " & ", ifelse(nrow(mtxdisdf_) >= 7, colnames(mtxdisdf_[7]), NA)))
42b51a52e308 planemo upload for repository https://github.com/Marie59/champ_blocs commit 0d86db7d42b608c386a54500064f5f9c9d7019a4 ecology parents: diff changeset	1434 h_[[z]] <- (paste0(rownames(mtxdisdf_[z + 8, ]), " & ", ifelse(nrow(mtxdisdf_) >= 8, colnames(mtxdisdf_[8]), NA)))
42b51a52e308 planemo upload for repository https://github.com/Marie59/champ_blocs commit 0d86db7d42b608c386a54500064f5f9c9d7019a4 ecology parents: diff changeset	1435 i_[[z]] <- (paste0(rownames(mtxdisdf_[z + 9, ]), " & ", ifelse(nrow(mtxdisdf_) >= 9, colnames(mtxdisdf_[9]), NA)))
42b51a52e308 planemo upload for repository https://github.com/Marie59/champ_blocs commit 0d86db7d42b608c386a54500064f5f9c9d7019a4 ecology parents: diff changeset	1436 j_[[z]] <- (paste0(rownames(mtxdisdf_[z + 10, ]), " & ", ifelse(nrow(mtxdisdf_) >= 10, colnames(mtxdisdf_[10]), NA)))
42b51a52e308 planemo upload for repository https://github.com/Marie59/champ_blocs commit 0d86db7d42b608c386a54500064f5f9c9d7019a4 ecology parents: diff changeset	1437 k_[[z]] <- (paste0(rownames(mtxdisdf_[z + 11, ]), " & ", ifelse(nrow(mtxdisdf_) >= 11, colnames(mtxdisdf_[11]), NA)))
42b51a52e308 planemo upload for repository https://github.com/Marie59/champ_blocs commit 0d86db7d42b608c386a54500064f5f9c9d7019a4 ecology parents: diff changeset	1438 l_[[z]] <- (paste0(rownames(mtxdisdf_[z + 12, ]), " & ", ifelse(nrow(mtxdisdf_) >= 12, colnames(mtxdisdf_[12]), NA)))
42b51a52e308 planemo upload for repository https://github.com/Marie59/champ_blocs commit 0d86db7d42b608c386a54500064f5f9c9d7019a4 ecology parents: diff changeset	1439 m_[[z]] <- (paste0(rownames(mtxdisdf_[z + 13, ]), " & ", ifelse(nrow(mtxdisdf_) >= 13, colnames(mtxdisdf_[13]), NA)))
42b51a52e308 planemo upload for repository https://github.com/Marie59/champ_blocs commit 0d86db7d42b608c386a54500064f5f9c9d7019a4 ecology parents: diff changeset	1440 n_[[z]] <- (paste0(rownames(mtxdisdf_[z + 14, ]), " & ", ifelse(nrow(mtxdisdf_) >= 14, colnames(mtxdisdf_[14]), NA)))
42b51a52e308 planemo upload for repository https://github.com/Marie59/champ_blocs commit 0d86db7d42b608c386a54500064f5f9c9d7019a4 ecology parents: diff changeset	1441 o_[[z]] <- (paste0(rownames(mtxdisdf_[z + 15, ]), " & ", ifelse(nrow(mtxdisdf_) >= 15, colnames(mtxdisdf_[15]), NA)))
42b51a52e308 planemo upload for repository https://github.com/Marie59/champ_blocs commit 0d86db7d42b608c386a54500064f5f9c9d7019a4 ecology parents: diff changeset	1442 p_[[z]] <- (paste0(rownames(mtxdisdf_[z + 16, ]), " & ", ifelse(nrow(mtxdisdf_) >= 16, colnames(mtxdisdf_[16]), NA)))
42b51a52e308 planemo upload for repository https://github.com/Marie59/champ_blocs commit 0d86db7d42b608c386a54500064f5f9c9d7019a4 ecology parents: diff changeset	1443 q_[[z]] <- (paste0(rownames(mtxdisdf_[z + 17, ]), " & ", ifelse(nrow(mtxdisdf_) >= 17, colnames(mtxdisdf_[17]), NA)))
42b51a52e308 planemo upload for repository https://github.com/Marie59/champ_blocs commit 0d86db7d42b608c386a54500064f5f9c9d7019a4 ecology parents: diff changeset	1444 r_[[z]] <- (paste0(rownames(mtxdisdf_[z + 18, ]), " & ", ifelse(nrow(mtxdisdf_) >= 18, colnames(mtxdisdf_[18]), NA)))
42b51a52e308 planemo upload for repository https://github.com/Marie59/champ_blocs commit 0d86db7d42b608c386a54500064f5f9c9d7019a4 ecology parents: diff changeset	1445 s_[[z]] <- (paste0(rownames(mtxdisdf_[z + 19, ]), " & ", ifelse(nrow(mtxdisdf_) >= 19, colnames(mtxdisdf_[19]), NA)))
42b51a52e308 planemo upload for repository https://github.com/Marie59/champ_blocs commit 0d86db7d42b608c386a54500064f5f9c9d7019a4 ecology parents: diff changeset	1446
42b51a52e308 planemo upload for repository https://github.com/Marie59/champ_blocs commit 0d86db7d42b608c386a54500064f5f9c9d7019a4 ecology parents: diff changeset	1447 }
42b51a52e308 planemo upload for repository https://github.com/Marie59/champ_blocs commit 0d86db7d42b608c386a54500064f5f9c9d7019a4 ecology parents: diff changeset	1448
42b51a52e308 planemo upload for repository https://github.com/Marie59/champ_blocs commit 0d86db7d42b608c386a54500064f5f9c9d7019a4 ecology parents: diff changeset	1449 rm(z)
42b51a52e308 planemo upload for repository https://github.com/Marie59/champ_blocs commit 0d86db7d42b608c386a54500064f5f9c9d7019a4 ecology parents: diff changeset	1450
42b51a52e308 planemo upload for repository https://github.com/Marie59/champ_blocs commit 0d86db7d42b608c386a54500064f5f9c9d7019a4 ecology parents: diff changeset	1451 y <- length(a_) - (ifelse(nrow(mtxdisdf_) >= 1, 1, nrow(mtxdisdf_)))
42b51a52e308 planemo upload for repository https://github.com/Marie59/champ_blocs commit 0d86db7d42b608c386a54500064f5f9c9d7019a4 ecology parents: diff changeset	1452 a_ <- a_[1:y]
42b51a52e308 planemo upload for repository https://github.com/Marie59/champ_blocs commit 0d86db7d42b608c386a54500064f5f9c9d7019a4 ecology parents: diff changeset	1453 y <- length(b_) - (ifelse(nrow(mtxdisdf_) >= 2, 2, nrow(mtxdisdf_)))
42b51a52e308 planemo upload for repository https://github.com/Marie59/champ_blocs commit 0d86db7d42b608c386a54500064f5f9c9d7019a4 ecology parents: diff changeset	1454 b_ <- b_[1:y]
42b51a52e308 planemo upload for repository https://github.com/Marie59/champ_blocs commit 0d86db7d42b608c386a54500064f5f9c9d7019a4 ecology parents: diff changeset	1455 y <- length(c_) - (ifelse(nrow(mtxdisdf_) >= 3, 3, nrow(mtxdisdf_)))
42b51a52e308 planemo upload for repository https://github.com/Marie59/champ_blocs commit 0d86db7d42b608c386a54500064f5f9c9d7019a4 ecology parents: diff changeset	1456 c_ <- c_[1:y]
42b51a52e308 planemo upload for repository https://github.com/Marie59/champ_blocs commit 0d86db7d42b608c386a54500064f5f9c9d7019a4 ecology parents: diff changeset	1457 y <- length(d_) - (ifelse(nrow(mtxdisdf_) >= 4, 4, nrow(mtxdisdf_)))
42b51a52e308 planemo upload for repository https://github.com/Marie59/champ_blocs commit 0d86db7d42b608c386a54500064f5f9c9d7019a4 ecology parents: diff changeset	1458 d_ <- d_[1:y]
42b51a52e308 planemo upload for repository https://github.com/Marie59/champ_blocs commit 0d86db7d42b608c386a54500064f5f9c9d7019a4 ecology parents: diff changeset	1459 y <- length(e_) - (ifelse(nrow(mtxdisdf_) >= 5, 5, nrow(mtxdisdf_)))
42b51a52e308 planemo upload for repository https://github.com/Marie59/champ_blocs commit 0d86db7d42b608c386a54500064f5f9c9d7019a4 ecology parents: diff changeset	1460 e_ <- e_[1:y]
42b51a52e308 planemo upload for repository https://github.com/Marie59/champ_blocs commit 0d86db7d42b608c386a54500064f5f9c9d7019a4 ecology parents: diff changeset	1461 y <- length(f_) - (ifelse(nrow(mtxdisdf_) >= 6, 6, nrow(mtxdisdf_)))
42b51a52e308 planemo upload for repository https://github.com/Marie59/champ_blocs commit 0d86db7d42b608c386a54500064f5f9c9d7019a4 ecology parents: diff changeset	1462 f_ <- f_[1:y]
42b51a52e308 planemo upload for repository https://github.com/Marie59/champ_blocs commit 0d86db7d42b608c386a54500064f5f9c9d7019a4 ecology parents: diff changeset	1463 y <- length(g_) - (ifelse(nrow(mtxdisdf_) >= 7, 7, nrow(mtxdisdf_)))
42b51a52e308 planemo upload for repository https://github.com/Marie59/champ_blocs commit 0d86db7d42b608c386a54500064f5f9c9d7019a4 ecology parents: diff changeset	1464 g_ <- g_[1:y]
42b51a52e308 planemo upload for repository https://github.com/Marie59/champ_blocs commit 0d86db7d42b608c386a54500064f5f9c9d7019a4 ecology parents: diff changeset	1465 y <- length(h_) - (ifelse(nrow(mtxdisdf_) >= 8, 8, nrow(mtxdisdf_)))
42b51a52e308 planemo upload for repository https://github.com/Marie59/champ_blocs commit 0d86db7d42b608c386a54500064f5f9c9d7019a4 ecology parents: diff changeset	1466 h_ <- h_[1:y]
42b51a52e308 planemo upload for repository https://github.com/Marie59/champ_blocs commit 0d86db7d42b608c386a54500064f5f9c9d7019a4 ecology parents: diff changeset	1467 y <- length(i_) - (ifelse(nrow(mtxdisdf_) >= 9, 9, nrow(mtxdisdf_)))
42b51a52e308 planemo upload for repository https://github.com/Marie59/champ_blocs commit 0d86db7d42b608c386a54500064f5f9c9d7019a4 ecology parents: diff changeset	1468 i_ <- i_[1:y]
42b51a52e308 planemo upload for repository https://github.com/Marie59/champ_blocs commit 0d86db7d42b608c386a54500064f5f9c9d7019a4 ecology parents: diff changeset	1469 y <- length(j_) - (ifelse(nrow(mtxdisdf_) >= 10, 10, nrow(mtxdisdf_)))
42b51a52e308 planemo upload for repository https://github.com/Marie59/champ_blocs commit 0d86db7d42b608c386a54500064f5f9c9d7019a4 ecology parents: diff changeset	1470 j_ <- j_[1:y]
42b51a52e308 planemo upload for repository https://github.com/Marie59/champ_blocs commit 0d86db7d42b608c386a54500064f5f9c9d7019a4 ecology parents: diff changeset	1471 y <- length(k_) - (ifelse(nrow(mtxdisdf_) >= 11, 11, nrow(mtxdisdf_)))
42b51a52e308 planemo upload for repository https://github.com/Marie59/champ_blocs commit 0d86db7d42b608c386a54500064f5f9c9d7019a4 ecology parents: diff changeset	1472 k_ <- k_[1:y]
42b51a52e308 planemo upload for repository https://github.com/Marie59/champ_blocs commit 0d86db7d42b608c386a54500064f5f9c9d7019a4 ecology parents: diff changeset	1473 y <- length(l_) - (ifelse(nrow(mtxdisdf_) >= 12, 12, nrow(mtxdisdf_)))
42b51a52e308 planemo upload for repository https://github.com/Marie59/champ_blocs commit 0d86db7d42b608c386a54500064f5f9c9d7019a4 ecology parents: diff changeset	1474 l_ <- l_[1:y]
42b51a52e308 planemo upload for repository https://github.com/Marie59/champ_blocs commit 0d86db7d42b608c386a54500064f5f9c9d7019a4 ecology parents: diff changeset	1475 y <- length(m_) - (ifelse(nrow(mtxdisdf_) >= 13, 13, nrow(mtxdisdf_)))
42b51a52e308 planemo upload for repository https://github.com/Marie59/champ_blocs commit 0d86db7d42b608c386a54500064f5f9c9d7019a4 ecology parents: diff changeset	1476 m_ <- m_[1:y]
42b51a52e308 planemo upload for repository https://github.com/Marie59/champ_blocs commit 0d86db7d42b608c386a54500064f5f9c9d7019a4 ecology parents: diff changeset	1477 y <- length(n_) - (ifelse(nrow(mtxdisdf_) >= 14, 14, nrow(mtxdisdf_)))
42b51a52e308 planemo upload for repository https://github.com/Marie59/champ_blocs commit 0d86db7d42b608c386a54500064f5f9c9d7019a4 ecology parents: diff changeset	1478 n_ <- n_[1:y]
42b51a52e308 planemo upload for repository https://github.com/Marie59/champ_blocs commit 0d86db7d42b608c386a54500064f5f9c9d7019a4 ecology parents: diff changeset	1479 y <- length(o_) - (ifelse(nrow(mtxdisdf_) >= 15, 15, nrow(mtxdisdf_)))
42b51a52e308 planemo upload for repository https://github.com/Marie59/champ_blocs commit 0d86db7d42b608c386a54500064f5f9c9d7019a4 ecology parents: diff changeset	1480 o_ <- o_[1:y]
42b51a52e308 planemo upload for repository https://github.com/Marie59/champ_blocs commit 0d86db7d42b608c386a54500064f5f9c9d7019a4 ecology parents: diff changeset	1481 y <- length(p_) - (ifelse(nrow(mtxdisdf_) >= 16, 16, nrow(mtxdisdf_)))
42b51a52e308 planemo upload for repository https://github.com/Marie59/champ_blocs commit 0d86db7d42b608c386a54500064f5f9c9d7019a4 ecology parents: diff changeset	1482 p_ <- p_[1:y]
42b51a52e308 planemo upload for repository https://github.com/Marie59/champ_blocs commit 0d86db7d42b608c386a54500064f5f9c9d7019a4 ecology parents: diff changeset	1483 y <- length(q_) - (ifelse(nrow(mtxdisdf_) >= 17, 17, nrow(mtxdisdf_)))
42b51a52e308 planemo upload for repository https://github.com/Marie59/champ_blocs commit 0d86db7d42b608c386a54500064f5f9c9d7019a4 ecology parents: diff changeset	1484 q_ <- q_[1:y]
42b51a52e308 planemo upload for repository https://github.com/Marie59/champ_blocs commit 0d86db7d42b608c386a54500064f5f9c9d7019a4 ecology parents: diff changeset	1485 y <- length(r_) - (ifelse(nrow(mtxdisdf_) >= 18, 18, nrow(mtxdisdf_)))
42b51a52e308 planemo upload for repository https://github.com/Marie59/champ_blocs commit 0d86db7d42b608c386a54500064f5f9c9d7019a4 ecology parents: diff changeset	1486 r_ <- r_[1:y]
42b51a52e308 planemo upload for repository https://github.com/Marie59/champ_blocs commit 0d86db7d42b608c386a54500064f5f9c9d7019a4 ecology parents: diff changeset	1487 y <- length(s_) - (ifelse(nrow(mtxdisdf_) >= 19, 19, nrow(mtxdisdf_)))
42b51a52e308 planemo upload for repository https://github.com/Marie59/champ_blocs commit 0d86db7d42b608c386a54500064f5f9c9d7019a4 ecology parents: diff changeset	1488 s_ <- s_[1:y]
42b51a52e308 planemo upload for repository https://github.com/Marie59/champ_blocs commit 0d86db7d42b608c386a54500064f5f9c9d7019a4 ecology parents: diff changeset	1489
42b51a52e308 planemo upload for repository https://github.com/Marie59/champ_blocs commit 0d86db7d42b608c386a54500064f5f9c9d7019a4 ecology parents: diff changeset	1490 rm(y)
42b51a52e308 planemo upload for repository https://github.com/Marie59/champ_blocs commit 0d86db7d42b608c386a54500064f5f9c9d7019a4 ecology parents: diff changeset	1491
42b51a52e308 planemo upload for repository https://github.com/Marie59/champ_blocs commit 0d86db7d42b608c386a54500064f5f9c9d7019a4 ecology parents: diff changeset	1492 name_ <- c(a_, b_, c_, d_, e_, f_, g_, h_, i_, j_, k_, l_, m_, n_, o_, p_, q_, r_, s_)
42b51a52e308 planemo upload for repository https://github.com/Marie59/champ_blocs commit 0d86db7d42b608c386a54500064f5f9c9d7019a4 ecology parents: diff changeset	1493 df_ <- data.frame(expand.grid(mtxdis), name_[1:seq_len(nrow(expand.grid(mtxdis)))])
42b51a52e308 planemo upload for repository https://github.com/Marie59/champ_blocs commit 0d86db7d42b608c386a54500064f5f9c9d7019a4 ecology parents: diff changeset	1494 names(df_) <- c("dist.", "name_")
42b51a52e308 planemo upload for repository https://github.com/Marie59/champ_blocs commit 0d86db7d42b608c386a54500064f5f9c9d7019a4 ecology parents: diff changeset	1495
42b51a52e308 planemo upload for repository https://github.com/Marie59/champ_blocs commit 0d86db7d42b608c386a54500064f5f9c9d7019a4 ecology parents: diff changeset	1496 rm(a_, b_, c_, d_, e_, f_, g_, h_, i_, j_, k_, l_, m_, n_, o_, p_, q_, r_, s_)
42b51a52e308 planemo upload for repository https://github.com/Marie59/champ_blocs commit 0d86db7d42b608c386a54500064f5f9c9d7019a4 ecology parents: diff changeset	1497 rm(name_)
42b51a52e308 planemo upload for repository https://github.com/Marie59/champ_blocs commit 0d86db7d42b608c386a54500064f5f9c9d7019a4 ecology parents: diff changeset	1498
42b51a52e308 planemo upload for repository https://github.com/Marie59/champ_blocs commit 0d86db7d42b608c386a54500064f5f9c9d7019a4 ecology parents: diff changeset	1499 q_ <- strsplit(df_$name_, " & ")
42b51a52e308 planemo upload for repository https://github.com/Marie59/champ_blocs commit 0d86db7d42b608c386a54500064f5f9c9d7019a4 ecology parents: diff changeset	1500 mat_ <- matrix(unlist(q_), ncol = 2, byrow = TRUE)
42b51a52e308 planemo upload for repository https://github.com/Marie59/champ_blocs commit 0d86db7d42b608c386a54500064f5f9c9d7019a4 ecology parents: diff changeset	1501 q_df_ <- as.data.frame(matrix(unlist(q_), ncol = 2, byrow = TRUE))
42b51a52e308 planemo upload for repository https://github.com/Marie59/champ_blocs commit 0d86db7d42b608c386a54500064f5f9c9d7019a4 ecology parents: diff changeset	1502 df_ <- dplyr::bind_cols(df_, q_df_)
42b51a52e308 planemo upload for repository https://github.com/Marie59/champ_blocs commit 0d86db7d42b608c386a54500064f5f9c9d7019a4 ecology parents: diff changeset	1503
42b51a52e308 planemo upload for repository https://github.com/Marie59/champ_blocs commit 0d86db7d42b608c386a54500064f5f9c9d7019a4 ecology parents: diff changeset	1504 rm(q_, mat_, q_df_)
42b51a52e308 planemo upload for repository https://github.com/Marie59/champ_blocs commit 0d86db7d42b608c386a54500064f5f9c9d7019a4 ecology parents: diff changeset	1505
42b51a52e308 planemo upload for repository https://github.com/Marie59/champ_blocs commit 0d86db7d42b608c386a54500064f5f9c9d7019a4 ecology parents: diff changeset	1506 split_ <- strsplit(df_$V1, "_")
42b51a52e308 planemo upload for repository https://github.com/Marie59/champ_blocs commit 0d86db7d42b608c386a54500064f5f9c9d7019a4 ecology parents: diff changeset	1507 v1_split_ <- as.data.frame(matrix(unlist(split_), ncol = 4, byrow = TRUE))
42b51a52e308 planemo upload for repository https://github.com/Marie59/champ_blocs commit 0d86db7d42b608c386a54500064f5f9c9d7019a4 ecology parents: diff changeset	1508 split_ <- strsplit(df_$V2, "_")
42b51a52e308 planemo upload for repository https://github.com/Marie59/champ_blocs commit 0d86db7d42b608c386a54500064f5f9c9d7019a4 ecology parents: diff changeset	1509 v2_split_ <- as.data.frame(matrix(unlist(split_), ncol = 4, byrow = TRUE))
42b51a52e308 planemo upload for repository https://github.com/Marie59/champ_blocs commit 0d86db7d42b608c386a54500064f5f9c9d7019a4 ecology parents: diff changeset	1510
42b51a52e308 planemo upload for repository https://github.com/Marie59/champ_blocs commit 0d86db7d42b608c386a54500064f5f9c9d7019a4 ecology parents: diff changeset	1511 df_ <- dplyr::bind_cols(df_, v1_split_)
42b51a52e308 planemo upload for repository https://github.com/Marie59/champ_blocs commit 0d86db7d42b608c386a54500064f5f9c9d7019a4 ecology parents: diff changeset	1512 df_ <- dplyr::bind_cols(df_, v2_split_)
42b51a52e308 planemo upload for repository https://github.com/Marie59/champ_blocs commit 0d86db7d42b608c386a54500064f5f9c9d7019a4 ecology parents: diff changeset	1513 df_red_ <- subset(df_, V4...8 == V4...12 & V3...7 == V3...11)
42b51a52e308 planemo upload for repository https://github.com/Marie59/champ_blocs commit 0d86db7d42b608c386a54500064f5f9c9d7019a4 ecology parents: diff changeset	1514 site_year_month_day <- rep(unique(qecbnato0_x$site_year_month_day), nrow(df_red_))
42b51a52e308 planemo upload for repository https://github.com/Marie59/champ_blocs commit 0d86db7d42b608c386a54500064f5f9c9d7019a4 ecology parents: diff changeset	1515
42b51a52e308 planemo upload for repository https://github.com/Marie59/champ_blocs commit 0d86db7d42b608c386a54500064f5f9c9d7019a4 ecology parents: diff changeset	1516 df_red_ <- tibble::add_column(df_red_, site_year_month_day, .before = "dist.")
42b51a52e308 planemo upload for repository https://github.com/Marie59/champ_blocs commit 0d86db7d42b608c386a54500064f5f9c9d7019a4 ecology parents: diff changeset	1517
42b51a52e308 planemo upload for repository https://github.com/Marie59/champ_blocs commit 0d86db7d42b608c386a54500064f5f9c9d7019a4 ecology parents: diff changeset	1518 rm(split_, v1_split_, v2_split_)
42b51a52e308 planemo upload for repository https://github.com/Marie59/champ_blocs commit 0d86db7d42b608c386a54500064f5f9c9d7019a4 ecology parents: diff changeset	1519 rm(mtxdis, mtxdisdf_, df_, site_year_month_day)
42b51a52e308 planemo upload for repository https://github.com/Marie59/champ_blocs commit 0d86db7d42b608c386a54500064f5f9c9d7019a4 ecology parents: diff changeset	1520
42b51a52e308 planemo upload for repository https://github.com/Marie59/champ_blocs commit 0d86db7d42b608c386a54500064f5f9c9d7019a4 ecology parents: diff changeset	1521 matri_list[[x]] <- df_red_
42b51a52e308 planemo upload for repository https://github.com/Marie59/champ_blocs commit 0d86db7d42b608c386a54500064f5f9c9d7019a4 ecology parents: diff changeset	1522 matri_list <<- matri_list
42b51a52e308 planemo upload for repository https://github.com/Marie59/champ_blocs commit 0d86db7d42b608c386a54500064f5f9c9d7019a4 ecology parents: diff changeset	1523
42b51a52e308 planemo upload for repository https://github.com/Marie59/champ_blocs commit 0d86db7d42b608c386a54500064f5f9c9d7019a4 ecology parents: diff changeset	1524 rm(df_red_, qecbnato0_x, x)
42b51a52e308 planemo upload for repository https://github.com/Marie59/champ_blocs commit 0d86db7d42b608c386a54500064f5f9c9d7019a4 ecology parents: diff changeset	1525
42b51a52e308 planemo upload for repository https://github.com/Marie59/champ_blocs commit 0d86db7d42b608c386a54500064f5f9c9d7019a4 ecology parents: diff changeset	1526 }
42b51a52e308 planemo upload for repository https://github.com/Marie59/champ_blocs commit 0d86db7d42b608c386a54500064f5f9c9d7019a4 ecology parents: diff changeset	1527
42b51a52e308 planemo upload for repository https://github.com/Marie59/champ_blocs commit 0d86db7d42b608c386a54500064f5f9c9d7019a4 ecology parents: diff changeset	1528 matri_df <- do.call("rbind", matri_list)
42b51a52e308 planemo upload for repository https://github.com/Marie59/champ_blocs commit 0d86db7d42b608c386a54500064f5f9c9d7019a4 ecology parents: diff changeset	1529
42b51a52e308 planemo upload for repository https://github.com/Marie59/champ_blocs commit 0d86db7d42b608c386a54500064f5f9c9d7019a4 ecology parents: diff changeset	1530 names(matri_df) <- c("site_year_month_day", "dist.", "name_", "name_left", "name_right", "Type.Bloc.left", "Face.left", "Numéro.Bloc.échantillon.left", "Quadrat.left", "Type.Bloc.right", "Face.right", "Numéro.Bloc.échantillon.right", "Quadrat.right")
42b51a52e308 planemo upload for repository https://github.com/Marie59/champ_blocs commit 0d86db7d42b608c386a54500064f5f9c9d7019a4 ecology parents: diff changeset	1531
42b51a52e308 planemo upload for repository https://github.com/Marie59/champ_blocs commit 0d86db7d42b608c386a54500064f5f9c9d7019a4 ecology parents: diff changeset	1532 matri_df <<- matri_df
42b51a52e308 planemo upload for repository https://github.com/Marie59/champ_blocs commit 0d86db7d42b608c386a54500064f5f9c9d7019a4 ecology parents: diff changeset	1533
42b51a52e308 planemo upload for repository https://github.com/Marie59/champ_blocs commit 0d86db7d42b608c386a54500064f5f9c9d7019a4 ecology parents: diff changeset	1534 hist(matri_df$dist.)
42b51a52e308 planemo upload for repository https://github.com/Marie59/champ_blocs commit 0d86db7d42b608c386a54500064f5f9c9d7019a4 ecology parents: diff changeset	1535
42b51a52e308 planemo upload for repository https://github.com/Marie59/champ_blocs commit 0d86db7d42b608c386a54500064f5f9c9d7019a4 ecology parents: diff changeset	1536 }
42b51a52e308 planemo upload for repository https://github.com/Marie59/champ_blocs commit 0d86db7d42b608c386a54500064f5f9c9d7019a4 ecology parents: diff changeset	1537
42b51a52e308 planemo upload for repository https://github.com/Marie59/champ_blocs commit 0d86db7d42b608c386a54500064f5f9c9d7019a4 ecology parents: diff changeset	1538 data_ <- dplyr::filter(qecbnato0, Type.Bloc == "Bloc mobile")
42b51a52e308 planemo upload for repository https://github.com/Marie59/champ_blocs commit 0d86db7d42b608c386a54500064f5f9c9d7019a4 ecology parents: diff changeset	1539 matri_list <- vector("list", length(unique(data_$site_year_month_day)))
42b51a52e308 planemo upload for repository https://github.com/Marie59/champ_blocs commit 0d86db7d42b608c386a54500064f5f9c9d7019a4 ecology parents: diff changeset	1540
42b51a52e308 planemo upload for repository https://github.com/Marie59/champ_blocs commit 0d86db7d42b608c386a54500064f5f9c9d7019a4 ecology parents: diff changeset	1541 matri_fct_bmm(data = data_, conca = c(bret_egmp_basq_qecb, egmp_basq_qecb))
42b51a52e308 planemo upload for repository https://github.com/Marie59/champ_blocs commit 0d86db7d42b608c386a54500064f5f9c9d7019a4 ecology parents: diff changeset	1542 hist(matri_df$dist., main = c(paste("Histo. of Bray (0-adjusted) dist. dissimilarity measures"), paste(" (sqrt transfo) - BMfs vs BMfi -")))
42b51a52e308 planemo upload for repository https://github.com/Marie59/champ_blocs commit 0d86db7d42b608c386a54500064f5f9c9d7019a4 ecology parents: diff changeset	1543
42b51a52e308 planemo upload for repository https://github.com/Marie59/champ_blocs commit 0d86db7d42b608c386a54500064f5f9c9d7019a4 ecology parents: diff changeset	1544 matri_full_bm_bf_fi <- matri_df
42b51a52e308 planemo upload for repository https://github.com/Marie59/champ_blocs commit 0d86db7d42b608c386a54500064f5f9c9d7019a4 ecology parents: diff changeset	1545
42b51a52e308 planemo upload for repository https://github.com/Marie59/champ_blocs commit 0d86db7d42b608c386a54500064f5f9c9d7019a4 ecology parents: diff changeset	1546 rm(data_, matri_df, matri_list)
42b51a52e308 planemo upload for repository https://github.com/Marie59/champ_blocs commit 0d86db7d42b608c386a54500064f5f9c9d7019a4 ecology parents: diff changeset	1547
42b51a52e308 planemo upload for repository https://github.com/Marie59/champ_blocs commit 0d86db7d42b608c386a54500064f5f9c9d7019a4 ecology parents: diff changeset	1548
42b51a52e308 planemo upload for repository https://github.com/Marie59/champ_blocs commit 0d86db7d42b608c386a54500064f5f9c9d7019a4 ecology parents: diff changeset	1549 #############################################################
42b51a52e308 planemo upload for repository https://github.com/Marie59/champ_blocs commit 0d86db7d42b608c386a54500064f5f9c9d7019a4 ecology parents: diff changeset	1550 # #
42b51a52e308 planemo upload for repository https://github.com/Marie59/champ_blocs commit 0d86db7d42b608c386a54500064f5f9c9d7019a4 ecology parents: diff changeset	1551 # Plot dissimilarity #
42b51a52e308 planemo upload for repository https://github.com/Marie59/champ_blocs commit 0d86db7d42b608c386a54500064f5f9c9d7019a4 ecology parents: diff changeset	1552 # #
42b51a52e308 planemo upload for repository https://github.com/Marie59/champ_blocs commit 0d86db7d42b608c386a54500064f5f9c9d7019a4 ecology parents: diff changeset	1553 #############################################################
42b51a52e308 planemo upload for repository https://github.com/Marie59/champ_blocs commit 0d86db7d42b608c386a54500064f5f9c9d7019a4 ecology parents: diff changeset	1554 ## plot
42b51a52e308 planemo upload for repository https://github.com/Marie59/champ_blocs commit 0d86db7d42b608c386a54500064f5f9c9d7019a4 ecology parents: diff changeset	1555
42b51a52e308 planemo upload for repository https://github.com/Marie59/champ_blocs commit 0d86db7d42b608c386a54500064f5f9c9d7019a4 ecology parents: diff changeset	1556 # activate line
42b51a52e308 planemo upload for repository https://github.com/Marie59/champ_blocs commit 0d86db7d42b608c386a54500064f5f9c9d7019a4 ecology parents: diff changeset	1557
42b51a52e308 planemo upload for repository https://github.com/Marie59/champ_blocs commit 0d86db7d42b608c386a54500064f5f9c9d7019a4 ecology parents: diff changeset	1558 matri_full_bm_bf_fs <- tidyr::separate(matri_full_bm_bf_fs, "site_year_month_day", into = c("departement", "Site", "Year", "Month", "Day"), remove = FALSE)
42b51a52e308 planemo upload for repository https://github.com/Marie59/champ_blocs commit 0d86db7d42b608c386a54500064f5f9c9d7019a4 ecology parents: diff changeset	1559 matri_full_bm_bf_fs$Site <- paste0(matri_full_bm_bf_fs$departement, "_", matri_full_bm_bf_fs$Site)
42b51a52e308 planemo upload for repository https://github.com/Marie59/champ_blocs commit 0d86db7d42b608c386a54500064f5f9c9d7019a4 ecology parents: diff changeset	1560 matri_full_bm_bf_fs <- subset(matri_full_bm_bf_fs, select = - c(departement))
42b51a52e308 planemo upload for repository https://github.com/Marie59/champ_blocs commit 0d86db7d42b608c386a54500064f5f9c9d7019a4 ecology parents: diff changeset	1561
42b51a52e308 planemo upload for repository https://github.com/Marie59/champ_blocs commit 0d86db7d42b608c386a54500064f5f9c9d7019a4 ecology parents: diff changeset	1562 matri_full_bm_bf_fs <- tibble::add_column(matri_full_bm_bf_fs, Date = as.Date(paste0(matri_full_bm_bf_fs$Year, "-", matri_full_bm_bf_fs$Month, "-", matri_full_bm_bf_fs$Day), origin = "1970-01-01"), .after = "Site")
42b51a52e308 planemo upload for repository https://github.com/Marie59/champ_blocs commit 0d86db7d42b608c386a54500064f5f9c9d7019a4 ecology parents: diff changeset	1563 matri_full_bm_bf_fs$Site <- as.factor(matri_full_bm_bf_fs$Site)
42b51a52e308 planemo upload for repository https://github.com/Marie59/champ_blocs commit 0d86db7d42b608c386a54500064f5f9c9d7019a4 ecology parents: diff changeset	1564
42b51a52e308 planemo upload for repository https://github.com/Marie59/champ_blocs commit 0d86db7d42b608c386a54500064f5f9c9d7019a4 ecology parents: diff changeset	1565 matri_full_bm_bf_fi <- tidyr::separate(matri_full_bm_bf_fi, "site_year_month_day", into = c("departement", "Site", "Year", "Month", "Day"), remove = FALSE)
42b51a52e308 planemo upload for repository https://github.com/Marie59/champ_blocs commit 0d86db7d42b608c386a54500064f5f9c9d7019a4 ecology parents: diff changeset	1566 matri_full_bm_bf_fi$Site <- paste0(matri_full_bm_bf_fi$departement, "_", matri_full_bm_bf_fi$Site)
42b51a52e308 planemo upload for repository https://github.com/Marie59/champ_blocs commit 0d86db7d42b608c386a54500064f5f9c9d7019a4 ecology parents: diff changeset	1567 matri_full_bm_bf_fi <- subset(matri_full_bm_bf_fi, select = - c(departement))
42b51a52e308 planemo upload for repository https://github.com/Marie59/champ_blocs commit 0d86db7d42b608c386a54500064f5f9c9d7019a4 ecology parents: diff changeset	1568 matri_full_bm_bf_fi <- tibble::add_column(matri_full_bm_bf_fi, Date = as.Date(paste0(matri_full_bm_bf_fi$Year, "-", matri_full_bm_bf_fi$Month, "-", matri_full_bm_bf_fi$Day), origin = "1970-01-01"), .after = "Site")
42b51a52e308 planemo upload for repository https://github.com/Marie59/champ_blocs commit 0d86db7d42b608c386a54500064f5f9c9d7019a4 ecology parents: diff changeset	1569 matri_full_bm_bf_fi$Site <- as.factor(matri_full_bm_bf_fi$Site)
42b51a52e308 planemo upload for repository https://github.com/Marie59/champ_blocs commit 0d86db7d42b608c386a54500064f5f9c9d7019a4 ecology parents: diff changeset	1570
42b51a52e308 planemo upload for repository https://github.com/Marie59/champ_blocs commit 0d86db7d42b608c386a54500064f5f9c9d7019a4 ecology parents: diff changeset	1571 # if error message "Error in .Call.graphics(C_palette2, .Call(C_palette2, NULL)) : invalid graphics state"
42b51a52e308 planemo upload for repository https://github.com/Marie59/champ_blocs commit 0d86db7d42b608c386a54500064f5f9c9d7019a4 ecology parents: diff changeset	1572
42b51a52e308 planemo upload for repository https://github.com/Marie59/champ_blocs commit 0d86db7d42b608c386a54500064f5f9c9d7019a4 ecology parents: diff changeset	1573
42b51a52e308 planemo upload for repository https://github.com/Marie59/champ_blocs commit 0d86db7d42b608c386a54500064f5f9c9d7019a4 ecology parents: diff changeset	1574 bf_fs_plot <- ggplot2::ggplot(matri_full_bm_bf_fs, ggplot2::aes(x = Site, y = dist.)) +
42b51a52e308 planemo upload for repository https://github.com/Marie59/champ_blocs commit 0d86db7d42b608c386a54500064f5f9c9d7019a4 ecology parents: diff changeset	1575 ggplot2::geom_boxplot() +
42b51a52e308 planemo upload for repository https://github.com/Marie59/champ_blocs commit 0d86db7d42b608c386a54500064f5f9c9d7019a4 ecology parents: diff changeset	1576 #geom_jitter(shape = 16, position=position_jitter(0.2)) +
42b51a52e308 planemo upload for repository https://github.com/Marie59/champ_blocs commit 0d86db7d42b608c386a54500064f5f9c9d7019a4 ecology parents: diff changeset	1577 ggplot2::xlab("") +
42b51a52e308 planemo upload for repository https://github.com/Marie59/champ_blocs commit 0d86db7d42b608c386a54500064f5f9c9d7019a4 ecology parents: diff changeset	1578 ggplot2::ylab("distance diss. BM.BF_FS") +
42b51a52e308 planemo upload for repository https://github.com/Marie59/champ_blocs commit 0d86db7d42b608c386a54500064f5f9c9d7019a4 ecology parents: diff changeset	1579 ggplot2::theme(axis.text.x = ggplot2::element_text(angle = 90, vjust = 0.5, hjust = 1))
42b51a52e308 planemo upload for repository https://github.com/Marie59/champ_blocs commit 0d86db7d42b608c386a54500064f5f9c9d7019a4 ecology parents: diff changeset	1580
42b51a52e308 planemo upload for repository https://github.com/Marie59/champ_blocs commit 0d86db7d42b608c386a54500064f5f9c9d7019a4 ecology parents: diff changeset	1581 ggplot2::ggsave("distance_diss_BF_FS.png", bf_fs_plot, height = 4.5, width = 4)
42b51a52e308 planemo upload for repository https://github.com/Marie59/champ_blocs commit 0d86db7d42b608c386a54500064f5f9c9d7019a4 ecology parents: diff changeset	1582
42b51a52e308 planemo upload for repository https://github.com/Marie59/champ_blocs commit 0d86db7d42b608c386a54500064f5f9c9d7019a4 ecology parents: diff changeset	1583 fs_fi_plot <- ggplot2::ggplot(matri_full_bm_bf_fi, ggplot2::aes(x = Site, y = dist.)) +
42b51a52e308 planemo upload for repository https://github.com/Marie59/champ_blocs commit 0d86db7d42b608c386a54500064f5f9c9d7019a4 ecology parents: diff changeset	1584 ggplot2::geom_boxplot() +
42b51a52e308 planemo upload for repository https://github.com/Marie59/champ_blocs commit 0d86db7d42b608c386a54500064f5f9c9d7019a4 ecology parents: diff changeset	1585 #geom_jitter(shape = 16, position=position_jitter(0.2)) +
42b51a52e308 planemo upload for repository https://github.com/Marie59/champ_blocs commit 0d86db7d42b608c386a54500064f5f9c9d7019a4 ecology parents: diff changeset	1586 ggplot2::xlab("") +
42b51a52e308 planemo upload for repository https://github.com/Marie59/champ_blocs commit 0d86db7d42b608c386a54500064f5f9c9d7019a4 ecology parents: diff changeset	1587 ggplot2::ylab("distance diss. BM_FS.FI") +
42b51a52e308 planemo upload for repository https://github.com/Marie59/champ_blocs commit 0d86db7d42b608c386a54500064f5f9c9d7019a4 ecology parents: diff changeset	1588 ggplot2::theme(axis.text.x = ggplot2::element_text(angle = 90, vjust = 0.5, hjust = 1))
42b51a52e308 planemo upload for repository https://github.com/Marie59/champ_blocs commit 0d86db7d42b608c386a54500064f5f9c9d7019a4 ecology parents: diff changeset	1589
42b51a52e308 planemo upload for repository https://github.com/Marie59/champ_blocs commit 0d86db7d42b608c386a54500064f5f9c9d7019a4 ecology parents: diff changeset	1590 ggplot2::ggsave("distance_diss_FS_FI.png", fs_fi_plot, height = 4.5, width = 4)
42b51a52e308 planemo upload for repository https://github.com/Marie59/champ_blocs commit 0d86db7d42b608c386a54500064f5f9c9d7019a4 ecology parents: diff changeset	1591
42b51a52e308 planemo upload for repository https://github.com/Marie59/champ_blocs commit 0d86db7d42b608c386a54500064f5f9c9d7019a4 ecology parents: diff changeset	1592 # issue with type de bloc, numéro de bloc and quadrat for df_ BM.BF_FS, cfr df_ left vs right variables doesn't give the right combination (variables with left vs right label in names come from the dissimilarity coefficient functions).
42b51a52e308 planemo upload for repository https://github.com/Marie59/champ_blocs commit 0d86db7d42b608c386a54500064f5f9c9d7019a4 ecology parents: diff changeset	1593 matri_full_bm_bf_fs$Quadrat <- NA
42b51a52e308 planemo upload for repository https://github.com/Marie59/champ_blocs commit 0d86db7d42b608c386a54500064f5f9c9d7019a4 ecology parents: diff changeset	1594 for (i in c(1:seq_len(nrow(matri_full_bm_bf_fs)))) {
42b51a52e308 planemo upload for repository https://github.com/Marie59/champ_blocs commit 0d86db7d42b608c386a54500064f5f9c9d7019a4 ecology parents: diff changeset	1595 ifelse(matri_full_bm_bf_fs$Type.Bloc.left[i] == "Bloc mobile", matri_full_bm_bf_fs$Quadrat[i] <- matri_full_bm_bf_fs$Quadrat.left[i], matri_full_bm_bf_fs$Quadrat[i] <- matri_full_bm_bf_fs$Quadrat.right[i])
42b51a52e308 planemo upload for repository https://github.com/Marie59/champ_blocs commit 0d86db7d42b608c386a54500064f5f9c9d7019a4 ecology parents: diff changeset	1596 }
42b51a52e308 planemo upload for repository https://github.com/Marie59/champ_blocs commit 0d86db7d42b608c386a54500064f5f9c9d7019a4 ecology parents: diff changeset	1597 matri_full_bm_bf_fs$Numéro.Bloc <- NA
42b51a52e308 planemo upload for repository https://github.com/Marie59/champ_blocs commit 0d86db7d42b608c386a54500064f5f9c9d7019a4 ecology parents: diff changeset	1598 for (i in c(1:seq_len(nrow(matri_full_bm_bf_fs)))) {
42b51a52e308 planemo upload for repository https://github.com/Marie59/champ_blocs commit 0d86db7d42b608c386a54500064f5f9c9d7019a4 ecology parents: diff changeset	1599 ifelse(matri_full_bm_bf_fs$Type.Bloc.left[i] == "Bloc mobile", matri_full_bm_bf_fs$Numéro.Bloc[i] <- matri_full_bm_bf_fs$Numéro.Bloc.échantillon.left[i], matri_full_bm_bf_fs$Numéro.Bloc[i] <- matri_full_bm_bf_fs$Numéro.Bloc.échantillon.right[i])
42b51a52e308 planemo upload for repository https://github.com/Marie59/champ_blocs commit 0d86db7d42b608c386a54500064f5f9c9d7019a4 ecology parents: diff changeset	1600 }
42b51a52e308 planemo upload for repository https://github.com/Marie59/champ_blocs commit 0d86db7d42b608c386a54500064f5f9c9d7019a4 ecology parents: diff changeset	1601
42b51a52e308 planemo upload for repository https://github.com/Marie59/champ_blocs commit 0d86db7d42b608c386a54500064f5f9c9d7019a4 ecology parents: diff changeset	1602 matri_full_bm_bf_fs <- tibble::add_column(matri_full_bm_bf_fs, site_year_month_day.q_BMnb = paste0(matri_full_bm_bf_fs$site_year_month_day, "_", matri_full_bm_bf_fs$Quadrat, "_", matri_full_bm_bf_fs$Numéro.Bloc), .after = "site_year_month_day")
42b51a52e308 planemo upload for repository https://github.com/Marie59/champ_blocs commit 0d86db7d42b608c386a54500064f5f9c9d7019a4 ecology parents: diff changeset	1603 matri_full_bm_bf_fi <- tibble::add_column(matri_full_bm_bf_fi, site_year_month_day.q_BMnb = paste0(matri_full_bm_bf_fi$site_year_month_day, "_", matri_full_bm_bf_fi$Quadrat.left, "_", matri_full_bm_bf_fi$Numéro.Bloc.échantillon.left), .after = "site_year_month_day")
42b51a52e308 planemo upload for repository https://github.com/Marie59/champ_blocs commit 0d86db7d42b608c386a54500064f5f9c9d7019a4 ecology parents: diff changeset	1604
42b51a52e308 planemo upload for repository https://github.com/Marie59/champ_blocs commit 0d86db7d42b608c386a54500064f5f9c9d7019a4 ecology parents: diff changeset	1605 colnames(matri_full_bm_bf_fs) <- paste("BM.BF_FS", colnames(matri_full_bm_bf_fs), sep = "_")
42b51a52e308 planemo upload for repository https://github.com/Marie59/champ_blocs commit 0d86db7d42b608c386a54500064f5f9c9d7019a4 ecology parents: diff changeset	1606 matri_full_bm_bf_fs <- dplyr::rename(matri_full_bm_bf_fs, site_year_month_day.q_BMnb = BM.BF_FS_site_year_month_day.q_BMnb)
42b51a52e308 planemo upload for repository https://github.com/Marie59/champ_blocs commit 0d86db7d42b608c386a54500064f5f9c9d7019a4 ecology parents: diff changeset	1607 colnames(matri_full_bm_bf_fi) <- paste("BM_FS.FI", colnames(matri_full_bm_bf_fi), sep = "_")
42b51a52e308 planemo upload for repository https://github.com/Marie59/champ_blocs commit 0d86db7d42b608c386a54500064f5f9c9d7019a4 ecology parents: diff changeset	1608 matri_full_bm_bf_fi <- dplyr::rename(matri_full_bm_bf_fi, site_year_month_day.q_BMnb = BM_FS.FI_site_year_month_day.q_BMnb)
42b51a52e308 planemo upload for repository https://github.com/Marie59/champ_blocs commit 0d86db7d42b608c386a54500064f5f9c9d7019a4 ecology parents: diff changeset	1609
42b51a52e308 planemo upload for repository https://github.com/Marie59/champ_blocs commit 0d86db7d42b608c386a54500064f5f9c9d7019a4 ecology parents: diff changeset	1610 matri_full <- dplyr::full_join(matri_full_bm_bf_fs[, c("site_year_month_day.q_BMnb", "BM.BF_FS_dist.")], matri_full_bm_bf_fi[, c("site_year_month_day.q_BMnb", "BM_FS.FI_dist.")])
42b51a52e308 planemo upload for repository https://github.com/Marie59/champ_blocs commit 0d86db7d42b608c386a54500064f5f9c9d7019a4 ecology parents: diff changeset	1611
42b51a52e308 planemo upload for repository https://github.com/Marie59/champ_blocs commit 0d86db7d42b608c386a54500064f5f9c9d7019a4 ecology parents: diff changeset	1612 matri_full <- tidyr::separate(matri_full, "site_year_month_day.q_BMnb", into = c("departement", "Site", "Year", "Month", "Day", "Quadrat", "Bloc Mobile Number"), remove = FALSE)
42b51a52e308 planemo upload for repository https://github.com/Marie59/champ_blocs commit 0d86db7d42b608c386a54500064f5f9c9d7019a4 ecology parents: diff changeset	1613 matri_full$Site <- paste0(matri_full$departement, "_", matri_full$Site)
42b51a52e308 planemo upload for repository https://github.com/Marie59/champ_blocs commit 0d86db7d42b608c386a54500064f5f9c9d7019a4 ecology parents: diff changeset	1614 matri_full <- subset(matri_full, select = - c(departement))
42b51a52e308 planemo upload for repository https://github.com/Marie59/champ_blocs commit 0d86db7d42b608c386a54500064f5f9c9d7019a4 ecology parents: diff changeset	1615 matri_full <- tibble::add_column(matri_full, Date = as.Date(paste0(matri_full$Year, "-", matri_full$Month, "-", matri_full$Day), origin = "1970-01-01"), .after = "Site")
42b51a52e308 planemo upload for repository https://github.com/Marie59/champ_blocs commit 0d86db7d42b608c386a54500064f5f9c9d7019a4 ecology parents: diff changeset	1616
42b51a52e308 planemo upload for repository https://github.com/Marie59/champ_blocs commit 0d86db7d42b608c386a54500064f5f9c9d7019a4 ecology parents: diff changeset	1617 # Name for report/plot
42b51a52e308 planemo upload for repository https://github.com/Marie59/champ_blocs commit 0d86db7d42b608c386a54500064f5f9c9d7019a4 ecology parents: diff changeset	1618
42b51a52e308 planemo upload for repository https://github.com/Marie59/champ_blocs commit 0d86db7d42b608c386a54500064f5f9c9d7019a4 ecology parents: diff changeset	1619 matri_full <- tibble::add_column(matri_full, Site_bis = matri_full$Site, .after = "Site")
42b51a52e308 planemo upload for repository https://github.com/Marie59/champ_blocs commit 0d86db7d42b608c386a54500064f5f9c9d7019a4 ecology parents: diff changeset	1620
42b51a52e308 planemo upload for repository https://github.com/Marie59/champ_blocs commit 0d86db7d42b608c386a54500064f5f9c9d7019a4 ecology parents: diff changeset	1621 matri_full$Site_bis <- ifelse(matri_full$Site == "GDMO_Locmariaquer", "Locmariaquer", matri_full$Site_bis)
42b51a52e308 planemo upload for repository https://github.com/Marie59/champ_blocs commit 0d86db7d42b608c386a54500064f5f9c9d7019a4 ecology parents: diff changeset	1622 matri_full$Site_bis <- ifelse(matri_full$Site == "GDMO_BegLann", "Beg Lann", matri_full$Site_bis)
42b51a52e308 planemo upload for repository https://github.com/Marie59/champ_blocs commit 0d86db7d42b608c386a54500064f5f9c9d7019a4 ecology parents: diff changeset	1623 matri_full$Site_bis <- ifelse(matri_full$Site == "FOUR_PlateauFour", "Plateau du Four", matri_full$Site_bis)
42b51a52e308 planemo upload for repository https://github.com/Marie59/champ_blocs commit 0d86db7d42b608c386a54500064f5f9c9d7019a4 ecology parents: diff changeset	1624 matri_full$Site_bis <- ifelse(matri_full$Site == "EGMP_GroinCou", "Groin du Cou", matri_full$Site_bis)
42b51a52e308 planemo upload for repository https://github.com/Marie59/champ_blocs commit 0d86db7d42b608c386a54500064f5f9c9d7019a4 ecology parents: diff changeset	1625 matri_full$Site_bis <- ifelse(matri_full$Site == "EGMP_PasEmsembert", "Le Pas d'Emsembert", matri_full$Site_bis)
42b51a52e308 planemo upload for repository https://github.com/Marie59/champ_blocs commit 0d86db7d42b608c386a54500064f5f9c9d7019a4 ecology parents: diff changeset	1626 matri_full$Site_bis <- ifelse(matri_full$Site == "EGMP_BreeBains", "La Brée-les-Bains", matri_full$Site_bis)
42b51a52e308 planemo upload for repository https://github.com/Marie59/champ_blocs commit 0d86db7d42b608c386a54500064f5f9c9d7019a4 ecology parents: diff changeset	1627 matri_full$Site_bis <- ifelse(matri_full$Site == "EGMP_PerreAntiochat", "Le Perré d'Antiochat", matri_full$Site_bis)
42b51a52e308 planemo upload for repository https://github.com/Marie59/champ_blocs commit 0d86db7d42b608c386a54500064f5f9c9d7019a4 ecology parents: diff changeset	1628 matri_full$Site_bis <- ifelse(matri_full$Site == "EGMP_Chassiron", "Chassiron", matri_full$Site_bis)
42b51a52e308 planemo upload for repository https://github.com/Marie59/champ_blocs commit 0d86db7d42b608c386a54500064f5f9c9d7019a4 ecology parents: diff changeset	1629 matri_full$Site_bis <- ifelse(matri_full$Site == "BASQ_FlotsBleusZP", "Les Flots Bleus / zone pêcheurs", matri_full$Site_bis)
42b51a52e308 planemo upload for repository https://github.com/Marie59/champ_blocs commit 0d86db7d42b608c386a54500064f5f9c9d7019a4 ecology parents: diff changeset	1630 matri_full$Site_bis <- ifelse(matri_full$Site == "BASQ_FlotsBleusZF", "Les Flots Bleus / zone familles", matri_full$Site_bis)
42b51a52e308 planemo upload for repository https://github.com/Marie59/champ_blocs commit 0d86db7d42b608c386a54500064f5f9c9d7019a4 ecology parents: diff changeset	1631 matri_full$Site_bis <- ifelse(matri_full$Site == "GONB_IlotStMichel", "Îlot Saint-Michel", matri_full$Site_bis)
42b51a52e308 planemo upload for repository https://github.com/Marie59/champ_blocs commit 0d86db7d42b608c386a54500064f5f9c9d7019a4 ecology parents: diff changeset	1632 matri_full$Site_bis <- ifelse(matri_full$Site == "FINS_Quemenes", "Quéménès", matri_full$Site_bis)
42b51a52e308 planemo upload for repository https://github.com/Marie59/champ_blocs commit 0d86db7d42b608c386a54500064f5f9c9d7019a4 ecology parents: diff changeset	1633 matri_full$Site_bis <- ifelse(matri_full$Site == "FINS_SeinGoulenez", "Île de Sein - Goulenez", matri_full$Site_bis)
42b51a52e308 planemo upload for repository https://github.com/Marie59/champ_blocs commit 0d86db7d42b608c386a54500064f5f9c9d7019a4 ecology parents: diff changeset	1634 matri_full$Site_bis <- ifelse(matri_full$Site == "FINS_SeinKilaourou", "Île de Sein - Kilaourou", matri_full$Site_bis)
42b51a52e308 planemo upload for repository https://github.com/Marie59/champ_blocs commit 0d86db7d42b608c386a54500064f5f9c9d7019a4 ecology parents: diff changeset	1635 matri_full$Site_bis <- ifelse(matri_full$Site == "ARMO_Verdelet", "Îlot du Verdelet", matri_full$Site_bis)
42b51a52e308 planemo upload for repository https://github.com/Marie59/champ_blocs commit 0d86db7d42b608c386a54500064f5f9c9d7019a4 ecology parents: diff changeset	1636 matri_full$Site_bis <- ifelse(matri_full$Site == "ARMO_Piegu", "Piégu", matri_full$Site_bis)
42b51a52e308 planemo upload for repository https://github.com/Marie59/champ_blocs commit 0d86db7d42b608c386a54500064f5f9c9d7019a4 ecology parents: diff changeset	1637 matri_full$Site_bis <- ifelse(matri_full$Site == "ARMO_Bilfot", "Pointe de Bilfot", matri_full$Site_bis)
42b51a52e308 planemo upload for repository https://github.com/Marie59/champ_blocs commit 0d86db7d42b608c386a54500064f5f9c9d7019a4 ecology parents: diff changeset	1638 matri_full$Site_bis <- ifelse(matri_full$Site == "ARMO_IlePlate", "Île Plate", matri_full$Site_bis)
42b51a52e308 planemo upload for repository https://github.com/Marie59/champ_blocs commit 0d86db7d42b608c386a54500064f5f9c9d7019a4 ecology parents: diff changeset	1639 matri_full$Site_bis <- ifelse(matri_full$Site == "PDMO_Perharidy", "Perharidy", matri_full$Site_bis)
42b51a52e308 planemo upload for repository https://github.com/Marie59/champ_blocs commit 0d86db7d42b608c386a54500064f5f9c9d7019a4 ecology parents: diff changeset	1640 matri_full$Site_bis <- ifelse(matri_full$Site == "BRES_Keraliou", "Keraliou", matri_full$Site_bis)
42b51a52e308 planemo upload for repository https://github.com/Marie59/champ_blocs commit 0d86db7d42b608c386a54500064f5f9c9d7019a4 ecology parents: diff changeset	1641 matri_full$Site_bis <- ifelse(matri_full$Site == "FINS_Mousterlin", "Pointe de Mousterlin", matri_full$Site_bis)
42b51a52e308 planemo upload for repository https://github.com/Marie59/champ_blocs commit 0d86db7d42b608c386a54500064f5f9c9d7019a4 ecology parents: diff changeset	1642 matri_full$Site_bis <- ifelse(matri_full$Site == "FINS_StNicolasGlenan", "Saint-Nicolas des Glénan", matri_full$Site_bis)
42b51a52e308 planemo upload for repository https://github.com/Marie59/champ_blocs commit 0d86db7d42b608c386a54500064f5f9c9d7019a4 ecology parents: diff changeset	1643 matri_full$Site_bis <- ifelse(matri_full$Site == "FINS_AnseRoz", "Pointe de l'Anse du Roz", matri_full$Site_bis)
42b51a52e308 planemo upload for repository https://github.com/Marie59/champ_blocs commit 0d86db7d42b608c386a54500064f5f9c9d7019a4 ecology parents: diff changeset	1644
42b51a52e308 planemo upload for repository https://github.com/Marie59/champ_blocs commit 0d86db7d42b608c386a54500064f5f9c9d7019a4 ecology parents: diff changeset	1645 saveRDS(matri_full, "matri_full.RDS")
42b51a52e308 planemo upload for repository https://github.com/Marie59/champ_blocs commit 0d86db7d42b608c386a54500064f5f9c9d7019a4 ecology parents: diff changeset	1646
42b51a52e308 planemo upload for repository https://github.com/Marie59/champ_blocs commit 0d86db7d42b608c386a54500064f5f9c9d7019a4 ecology parents: diff changeset	1647 #############################################################
42b51a52e308 planemo upload for repository https://github.com/Marie59/champ_blocs commit 0d86db7d42b608c386a54500064f5f9c9d7019a4 ecology parents: diff changeset	1648 # #
42b51a52e308 planemo upload for repository https://github.com/Marie59/champ_blocs commit 0d86db7d42b608c386a54500064f5f9c9d7019a4 ecology parents: diff changeset	1649 # Plot the dissimilarity per site #
42b51a52e308 planemo upload for repository https://github.com/Marie59/champ_blocs commit 0d86db7d42b608c386a54500064f5f9c9d7019a4 ecology parents: diff changeset	1650 # #
42b51a52e308 planemo upload for repository https://github.com/Marie59/champ_blocs commit 0d86db7d42b608c386a54500064f5f9c9d7019a4 ecology parents: diff changeset	1651 #############################################################
42b51a52e308 planemo upload for repository https://github.com/Marie59/champ_blocs commit 0d86db7d42b608c386a54500064f5f9c9d7019a4 ecology parents: diff changeset	1652 ## plot dissimilarity coefficient
42b51a52e308 planemo upload for repository https://github.com/Marie59/champ_blocs commit 0d86db7d42b608c386a54500064f5f9c9d7019a4 ecology parents: diff changeset	1653
42b51a52e308 planemo upload for repository https://github.com/Marie59/champ_blocs commit 0d86db7d42b608c386a54500064f5f9c9d7019a4 ecology parents: diff changeset	1654 matri_full$Year <- as.integer(matri_full$Year)
42b51a52e308 planemo upload for repository https://github.com/Marie59/champ_blocs commit 0d86db7d42b608c386a54500064f5f9c9d7019a4 ecology parents: diff changeset	1655 matri_full$Month <- as.integer(matri_full$Month)
42b51a52e308 planemo upload for repository https://github.com/Marie59/champ_blocs commit 0d86db7d42b608c386a54500064f5f9c9d7019a4 ecology parents: diff changeset	1656 matri_full$Day <- as.integer(matri_full$Day)
42b51a52e308 planemo upload for repository https://github.com/Marie59/champ_blocs commit 0d86db7d42b608c386a54500064f5f9c9d7019a4 ecology parents: diff changeset	1657
42b51a52e308 planemo upload for repository https://github.com/Marie59/champ_blocs commit 0d86db7d42b608c386a54500064f5f9c9d7019a4 ecology parents: diff changeset	1658
42b51a52e308 planemo upload for repository https://github.com/Marie59/champ_blocs commit 0d86db7d42b608c386a54500064f5f9c9d7019a4 ecology parents: diff changeset	1659 ## BM_FS.FI_dist => mobile boulder upper vs lower faces
42b51a52e308 planemo upload for repository https://github.com/Marie59/champ_blocs commit 0d86db7d42b608c386a54500064f5f9c9d7019a4 ecology parents: diff changeset	1660
42b51a52e308 planemo upload for repository https://github.com/Marie59/champ_blocs commit 0d86db7d42b608c386a54500064f5f9c9d7019a4 ecology parents: diff changeset	1661 # Stats
42b51a52e308 planemo upload for repository https://github.com/Marie59/champ_blocs commit 0d86db7d42b608c386a54500064f5f9c9d7019a4 ecology parents: diff changeset	1662
42b51a52e308 planemo upload for repository https://github.com/Marie59/champ_blocs commit 0d86db7d42b608c386a54500064f5f9c9d7019a4 ecology parents: diff changeset	1663 bm_fs_fi_dist_stat <- matri_full %>% dplyr::group_by(Site, Site_bis, Date, Year, Month, Day) %>% dplyr::summarize(BM_FS.FI_dist.moy = mean(BM_FS.FI_dist., na.rm = TRUE), BM_FS.FI_dist.et = sd(BM_FS.FI_dist., na.rm = TRUE), BM_FS.FI_dist.med = median(BM_FS.FI_dist., na.rm = TRUE), BM_FS.FI_dist.min = min(BM_FS.FI_dist., na.rm = TRUE), BM_FS.FI_dist.max = max(BM_FS.FI_dist., na.rm = TRUE), nb. = dplyr::n(), nb.notNa = sum(!is.na(BM_FS.FI_dist.)))
42b51a52e308 planemo upload for repository https://github.com/Marie59/champ_blocs commit 0d86db7d42b608c386a54500064f5f9c9d7019a4 ecology parents: diff changeset	1664
42b51a52e308 planemo upload for repository https://github.com/Marie59/champ_blocs commit 0d86db7d42b608c386a54500064f5f9c9d7019a4 ecology parents: diff changeset	1665 bm_fs_fi_dist_stat <- dplyr::ungroup(bm_fs_fi_dist_stat)
42b51a52e308 planemo upload for repository https://github.com/Marie59/champ_blocs commit 0d86db7d42b608c386a54500064f5f9c9d7019a4 ecology parents: diff changeset	1666
42b51a52e308 planemo upload for repository https://github.com/Marie59/champ_blocs commit 0d86db7d42b608c386a54500064f5f9c9d7019a4 ecology parents: diff changeset	1667 # Quality scale based on quartiles
42b51a52e308 planemo upload for repository https://github.com/Marie59/champ_blocs commit 0d86db7d42b608c386a54500064f5f9c9d7019a4 ecology parents: diff changeset	1668
42b51a52e308 planemo upload for repository https://github.com/Marie59/champ_blocs commit 0d86db7d42b608c386a54500064f5f9c9d7019a4 ecology parents: diff changeset	1669 if (choice == "N") {
42b51a52e308 planemo upload for repository https://github.com/Marie59/champ_blocs commit 0d86db7d42b608c386a54500064f5f9c9d7019a4 ecology parents: diff changeset	1670 one <- round(mean(unlist(dplyr::filter(matri_full, BM_FS.FI_dist. <= quantile(matri_full$BM_FS.FI_dist., 0.25, na.rm = TRUE))["BM_FS.FI_dist."])), digits = 3)
42b51a52e308 planemo upload for repository https://github.com/Marie59/champ_blocs commit 0d86db7d42b608c386a54500064f5f9c9d7019a4 ecology parents: diff changeset	1671 two <- round(mean(unlist(dplyr::filter(matri_full, BM_FS.FI_dist. > quantile(matri_full$BM_FS.FI_dist., 0.25, na.rm = TRUE) & BM_FS.FI_dist. <= quantile(matri_full$BM_FS.FI_dist., 0.5, na.rm = TRUE))["BM_FS.FI_dist."])), digits = 3)
42b51a52e308 planemo upload for repository https://github.com/Marie59/champ_blocs commit 0d86db7d42b608c386a54500064f5f9c9d7019a4 ecology parents: diff changeset	1672 three <- round(mean(unlist(dplyr::filter(matri_full, BM_FS.FI_dist. > quantile(matri_full$BM_FS.FI_dist., 0.5, na.rm = TRUE) & BM_FS.FI_dist. <= quantile(matri_full$BM_FS.FI_dist., 0.75, na.rm = TRUE))["BM_FS.FI_dist."])), digits = 3)
42b51a52e308 planemo upload for repository https://github.com/Marie59/champ_blocs commit 0d86db7d42b608c386a54500064f5f9c9d7019a4 ecology parents: diff changeset	1673 four <- round(mean(unlist(dplyr::filter(matri_full, BM_FS.FI_dist. > quantile(matri_full$BM_FS.FI_dist., 0.75, na.rm = TRUE))["BM_FS.FI_dist."])), digits = 3)
42b51a52e308 planemo upload for repository https://github.com/Marie59/champ_blocs commit 0d86db7d42b608c386a54500064f5f9c9d7019a4 ecology parents: diff changeset	1674 }else {
42b51a52e308 planemo upload for repository https://github.com/Marie59/champ_blocs commit 0d86db7d42b608c386a54500064f5f9c9d7019a4 ecology parents: diff changeset	1675 one <- 0.47
42b51a52e308 planemo upload for repository https://github.com/Marie59/champ_blocs commit 0d86db7d42b608c386a54500064f5f9c9d7019a4 ecology parents: diff changeset	1676 two <- 0.7
42b51a52e308 planemo upload for repository https://github.com/Marie59/champ_blocs commit 0d86db7d42b608c386a54500064f5f9c9d7019a4 ecology parents: diff changeset	1677 three <- 0.83
42b51a52e308 planemo upload for repository https://github.com/Marie59/champ_blocs commit 0d86db7d42b608c386a54500064f5f9c9d7019a4 ecology parents: diff changeset	1678 four <- 0.98
42b51a52e308 planemo upload for repository https://github.com/Marie59/champ_blocs commit 0d86db7d42b608c386a54500064f5f9c9d7019a4 ecology parents: diff changeset	1679 }
42b51a52e308 planemo upload for repository https://github.com/Marie59/champ_blocs commit 0d86db7d42b608c386a54500064f5f9c9d7019a4 ecology parents: diff changeset	1680
42b51a52e308 planemo upload for repository https://github.com/Marie59/champ_blocs commit 0d86db7d42b608c386a54500064f5f9c9d7019a4 ecology parents: diff changeset	1681 val_xmax <- as.Date(paste0(as.character(choice_date + 1), "-01-01"), origin = "1970-01-01")
42b51a52e308 planemo upload for repository https://github.com/Marie59/champ_blocs commit 0d86db7d42b608c386a54500064f5f9c9d7019a4 ecology parents: diff changeset	1682
42b51a52e308 planemo upload for repository https://github.com/Marie59/champ_blocs commit 0d86db7d42b608c386a54500064f5f9c9d7019a4 ecology parents: diff changeset	1683 for (i in c(1:length(unique(bm_fs_fi_dist_stat$Site)))) {
42b51a52e308 planemo upload for repository https://github.com/Marie59/champ_blocs commit 0d86db7d42b608c386a54500064f5f9c9d7019a4 ecology parents: diff changeset	1684
42b51a52e308 planemo upload for repository https://github.com/Marie59/champ_blocs commit 0d86db7d42b608c386a54500064f5f9c9d7019a4 ecology parents: diff changeset	1685 df1 <- dplyr::filter(bm_fs_fi_dist_stat, bm_fs_fi_dist_stat$Site == unique(bm_fs_fi_dist_stat$Site)[i])
42b51a52e308 planemo upload for repository https://github.com/Marie59/champ_blocs commit 0d86db7d42b608c386a54500064f5f9c9d7019a4 ecology parents: diff changeset	1686
42b51a52e308 planemo upload for repository https://github.com/Marie59/champ_blocs commit 0d86db7d42b608c386a54500064f5f9c9d7019a4 ecology parents: diff changeset	1687 bm_fs_fi_plot <- ggplot2::ggplot() +
42b51a52e308 planemo upload for repository https://github.com/Marie59/champ_blocs commit 0d86db7d42b608c386a54500064f5f9c9d7019a4 ecology parents: diff changeset	1688 ggplot2::geom_point(ggplot2::aes(x = bm_fs_fi_dist_stat$Date, y = bm_fs_fi_dist_stat$BM_FS.FI_dist.med), col = "grey") +
42b51a52e308 planemo upload for repository https://github.com/Marie59/champ_blocs commit 0d86db7d42b608c386a54500064f5f9c9d7019a4 ecology parents: diff changeset	1689 ggplot2::geom_rect(ggplot2::aes(xmin = as.Date("2013-01-01", origin = "1970-01-01"), xmax = val_xmax, ymin = - 0.1, ymax = one, fill = "blue"), alpha = 0.3) +
42b51a52e308 planemo upload for repository https://github.com/Marie59/champ_blocs commit 0d86db7d42b608c386a54500064f5f9c9d7019a4 ecology parents: diff changeset	1690 ggplot2::geom_rect(ggplot2::aes(xmin = as.Date("2013-01-01", origin = "1970-01-01"), xmax = val_xmax, ymin = one, ymax = two, fill = "green"), alpha = 0.3) +
42b51a52e308 planemo upload for repository https://github.com/Marie59/champ_blocs commit 0d86db7d42b608c386a54500064f5f9c9d7019a4 ecology parents: diff changeset	1691 ggplot2::geom_rect(ggplot2::aes(xmin = as.Date("2013-01-01", origin = "1970-01-01"), xmax = val_xmax, ymin = two, ymax = three, fill = "yellow"), alpha = 0.3) +
42b51a52e308 planemo upload for repository https://github.com/Marie59/champ_blocs commit 0d86db7d42b608c386a54500064f5f9c9d7019a4 ecology parents: diff changeset	1692 ggplot2::geom_rect(ggplot2::aes(xmin = as.Date("2013-01-01", origin = "1970-01-01"), xmax = val_xmax, ymin = three, ymax = four, fill = "orange"), alpha = 0.3) +
42b51a52e308 planemo upload for repository https://github.com/Marie59/champ_blocs commit 0d86db7d42b608c386a54500064f5f9c9d7019a4 ecology parents: diff changeset	1693 ggplot2::geom_rect(ggplot2::aes(xmin = as.Date("2013-01-01", origin = "1970-01-01"), xmax = val_xmax, ymin = four, ymax = 1.1, fill = "red"), alpha = 0.3) +
42b51a52e308 planemo upload for repository https://github.com/Marie59/champ_blocs commit 0d86db7d42b608c386a54500064f5f9c9d7019a4 ecology parents: diff changeset	1694 ggplot2::scale_fill_manual(values = c("#FF0000", "#F59404", "#18E125", "#1A1AE8", "#FAFA15")) +
42b51a52e308 planemo upload for repository https://github.com/Marie59/champ_blocs commit 0d86db7d42b608c386a54500064f5f9c9d7019a4 ecology parents: diff changeset	1695 ggplot2::geom_pointrange(ggplot2::aes(x = df1$Date, y = df1$BM_FS.FI_dist.med, ymin = df1$BM_FS.FI_dist.min, ymax = df1$BM_FS.FI_dist.max), col = "black") +
42b51a52e308 planemo upload for repository https://github.com/Marie59/champ_blocs commit 0d86db7d42b608c386a54500064f5f9c9d7019a4 ecology parents: diff changeset	1696 ggplot2::xlab("Date") +
42b51a52e308 planemo upload for repository https://github.com/Marie59/champ_blocs commit 0d86db7d42b608c386a54500064f5f9c9d7019a4 ecology parents: diff changeset	1697 ggplot2::ylab("Coef dissim BM FS-FI") +
42b51a52e308 planemo upload for repository https://github.com/Marie59/champ_blocs commit 0d86db7d42b608c386a54500064f5f9c9d7019a4 ecology parents: diff changeset	1698 ggplot2::ggtitle(unique(df1$Site_bis)) +
42b51a52e308 planemo upload for repository https://github.com/Marie59/champ_blocs commit 0d86db7d42b608c386a54500064f5f9c9d7019a4 ecology parents: diff changeset	1699 ggplot2::theme(axis.text.x = ggplot2::element_text(angle = 90, vjust = 0.5, hjust = 1), legend.position = "none")
42b51a52e308 planemo upload for repository https://github.com/Marie59/champ_blocs commit 0d86db7d42b608c386a54500064f5f9c9d7019a4 ecology parents: diff changeset	1700
42b51a52e308 planemo upload for repository https://github.com/Marie59/champ_blocs commit 0d86db7d42b608c386a54500064f5f9c9d7019a4 ecology parents: diff changeset	1701 ggplot2::ggsave(paste0("fs_fi_", df1$Site, ".png"), device = "png", bm_fs_fi_plot, height = 3, width = 3.5)
42b51a52e308 planemo upload for repository https://github.com/Marie59/champ_blocs commit 0d86db7d42b608c386a54500064f5f9c9d7019a4 ecology parents: diff changeset	1702
42b51a52e308 planemo upload for repository https://github.com/Marie59/champ_blocs commit 0d86db7d42b608c386a54500064f5f9c9d7019a4 ecology parents: diff changeset	1703 }
42b51a52e308 planemo upload for repository https://github.com/Marie59/champ_blocs commit 0d86db7d42b608c386a54500064f5f9c9d7019a4 ecology parents: diff changeset	1704
42b51a52e308 planemo upload for repository https://github.com/Marie59/champ_blocs commit 0d86db7d42b608c386a54500064f5f9c9d7019a4 ecology parents: diff changeset	1705 rm(df1, four, i, one, three, two, xmax_, xmin_, ymax_, ymin_)
42b51a52e308 planemo upload for repository https://github.com/Marie59/champ_blocs commit 0d86db7d42b608c386a54500064f5f9c9d7019a4 ecology parents: diff changeset	1706
42b51a52e308 planemo upload for repository https://github.com/Marie59/champ_blocs commit 0d86db7d42b608c386a54500064f5f9c9d7019a4 ecology parents: diff changeset	1707
42b51a52e308 planemo upload for repository https://github.com/Marie59/champ_blocs commit 0d86db7d42b608c386a54500064f5f9c9d7019a4 ecology parents: diff changeset	1708 ## BM.BF_FS_dist => mobile boulder vs fixed boulder upper faces
42b51a52e308 planemo upload for repository https://github.com/Marie59/champ_blocs commit 0d86db7d42b608c386a54500064f5f9c9d7019a4 ecology parents: diff changeset	1709
42b51a52e308 planemo upload for repository https://github.com/Marie59/champ_blocs commit 0d86db7d42b608c386a54500064f5f9c9d7019a4 ecology parents: diff changeset	1710 # Stats
42b51a52e308 planemo upload for repository https://github.com/Marie59/champ_blocs commit 0d86db7d42b608c386a54500064f5f9c9d7019a4 ecology parents: diff changeset	1711
42b51a52e308 planemo upload for repository https://github.com/Marie59/champ_blocs commit 0d86db7d42b608c386a54500064f5f9c9d7019a4 ecology parents: diff changeset	1712 bm_bf_fs_dist_stat <- matri_full %>% dplyr::group_by(Site, Site_bis, Date, Year, Month, Day) %>% dplyr::summarize(BM.BF_FS_dist.moy = mean(BM.BF_FS_dist., na.rm = TRUE), BM.BF_FS_dist.et = sd(BM.BF_FS_dist., na.rm = TRUE), BM.BF_FS_dist.med = median(BM.BF_FS_dist., na.rm = TRUE), BM.BF_FS_dist.min = min(BM.BF_FS_dist., na.rm = TRUE), BM.BF_FS_dist.max = max(BM.BF_FS_dist., na.rm = TRUE), nb. = dplyr::n(), nb.notNa = sum(!is.na(BM.BF_FS_dist.)))
42b51a52e308 planemo upload for repository https://github.com/Marie59/champ_blocs commit 0d86db7d42b608c386a54500064f5f9c9d7019a4 ecology parents: diff changeset	1713
42b51a52e308 planemo upload for repository https://github.com/Marie59/champ_blocs commit 0d86db7d42b608c386a54500064f5f9c9d7019a4 ecology parents: diff changeset	1714 bm_bf_fs_dist_stat <- dplyr::ungroup(bm_bf_fs_dist_stat)
42b51a52e308 planemo upload for repository https://github.com/Marie59/champ_blocs commit 0d86db7d42b608c386a54500064f5f9c9d7019a4 ecology parents: diff changeset	1715
42b51a52e308 planemo upload for repository https://github.com/Marie59/champ_blocs commit 0d86db7d42b608c386a54500064f5f9c9d7019a4 ecology parents: diff changeset	1716 # Quality scale based on quartiles
42b51a52e308 planemo upload for repository https://github.com/Marie59/champ_blocs commit 0d86db7d42b608c386a54500064f5f9c9d7019a4 ecology parents: diff changeset	1717
42b51a52e308 planemo upload for repository https://github.com/Marie59/champ_blocs commit 0d86db7d42b608c386a54500064f5f9c9d7019a4 ecology parents: diff changeset	1718 if (choice == "N") {
42b51a52e308 planemo upload for repository https://github.com/Marie59/champ_blocs commit 0d86db7d42b608c386a54500064f5f9c9d7019a4 ecology parents: diff changeset	1719 one <- round(mean(unlist(dplyr::filter(matri_full, BM.BF_FS_dist. <= quantile(matri_full$BM.BF_FS_dist., 0.25, na.rm = TRUE))["BM.BF_FS_dist."])), digits = 3)
42b51a52e308 planemo upload for repository https://github.com/Marie59/champ_blocs commit 0d86db7d42b608c386a54500064f5f9c9d7019a4 ecology parents: diff changeset	1720 two <- round(mean(unlist(dplyr::filter(matri_full, BM.BF_FS_dist. > quantile(matri_full$BM.BF_FS_dist., 0.25, na.rm = TRUE) & BM.BF_FS_dist. <= quantile(matri_full$BM.BF_FS_dist., 0.5, na.rm = TRUE))["BM.BF_FS_dist."])), digits = 3)
42b51a52e308 planemo upload for repository https://github.com/Marie59/champ_blocs commit 0d86db7d42b608c386a54500064f5f9c9d7019a4 ecology parents: diff changeset	1721 three <- round(mean(unlist(dplyr::filter(matri_full, BM.BF_FS_dist. > quantile(matri_full$BM.BF_FS_dist., 0.5, na.rm = TRUE) & BM.BF_FS_dist. <= quantile(matri_full$BM.BF_FS_dist., 0.75, na.rm = TRUE))["BM.BF_FS_dist."])), digits = 3)
42b51a52e308 planemo upload for repository https://github.com/Marie59/champ_blocs commit 0d86db7d42b608c386a54500064f5f9c9d7019a4 ecology parents: diff changeset	1722 four <- round(mean(unlist(dplyr::filter(matri_full, BM.BF_FS_dist. > quantile(matri_full$BM.BF_FS_dist., 0.75, na.rm = TRUE))["BM.BF_FS_dist."])), digits = 3)
42b51a52e308 planemo upload for repository https://github.com/Marie59/champ_blocs commit 0d86db7d42b608c386a54500064f5f9c9d7019a4 ecology parents: diff changeset	1723
42b51a52e308 planemo upload for repository https://github.com/Marie59/champ_blocs commit 0d86db7d42b608c386a54500064f5f9c9d7019a4 ecology parents: diff changeset	1724 }else {
42b51a52e308 planemo upload for repository https://github.com/Marie59/champ_blocs commit 0d86db7d42b608c386a54500064f5f9c9d7019a4 ecology parents: diff changeset	1725 one <- 0.19
42b51a52e308 planemo upload for repository https://github.com/Marie59/champ_blocs commit 0d86db7d42b608c386a54500064f5f9c9d7019a4 ecology parents: diff changeset	1726 two <- 0.32
42b51a52e308 planemo upload for repository https://github.com/Marie59/champ_blocs commit 0d86db7d42b608c386a54500064f5f9c9d7019a4 ecology parents: diff changeset	1727 three <- 0.455
42b51a52e308 planemo upload for repository https://github.com/Marie59/champ_blocs commit 0d86db7d42b608c386a54500064f5f9c9d7019a4 ecology parents: diff changeset	1728 four <- 0.735
42b51a52e308 planemo upload for repository https://github.com/Marie59/champ_blocs commit 0d86db7d42b608c386a54500064f5f9c9d7019a4 ecology parents: diff changeset	1729 }
42b51a52e308 planemo upload for repository https://github.com/Marie59/champ_blocs commit 0d86db7d42b608c386a54500064f5f9c9d7019a4 ecology parents: diff changeset	1730 # Plot
42b51a52e308 planemo upload for repository https://github.com/Marie59/champ_blocs commit 0d86db7d42b608c386a54500064f5f9c9d7019a4 ecology parents: diff changeset	1731
42b51a52e308 planemo upload for repository https://github.com/Marie59/champ_blocs commit 0d86db7d42b608c386a54500064f5f9c9d7019a4 ecology parents: diff changeset	1732 for (i in c(1:length(unique(bm_bf_fs_dist_stat$Site)))) {
42b51a52e308 planemo upload for repository https://github.com/Marie59/champ_blocs commit 0d86db7d42b608c386a54500064f5f9c9d7019a4 ecology parents: diff changeset	1733
42b51a52e308 planemo upload for repository https://github.com/Marie59/champ_blocs commit 0d86db7d42b608c386a54500064f5f9c9d7019a4 ecology parents: diff changeset	1734 df1 <- dplyr::filter(bm_bf_fs_dist_stat, bm_bf_fs_dist_stat$Site == unique(bm_bf_fs_dist_stat$Site)[i])
42b51a52e308 planemo upload for repository https://github.com/Marie59/champ_blocs commit 0d86db7d42b608c386a54500064f5f9c9d7019a4 ecology parents: diff changeset	1735
42b51a52e308 planemo upload for repository https://github.com/Marie59/champ_blocs commit 0d86db7d42b608c386a54500064f5f9c9d7019a4 ecology parents: diff changeset	1736 bm_bf_fs_plot <- ggplot2::ggplot() +
42b51a52e308 planemo upload for repository https://github.com/Marie59/champ_blocs commit 0d86db7d42b608c386a54500064f5f9c9d7019a4 ecology parents: diff changeset	1737 ggplot2::geom_point(ggplot2::aes(x = bm_bf_fs_dist_stat$Date, y = bm_bf_fs_dist_stat$BM.BF_FS_dist.med), col = "grey") +
42b51a52e308 planemo upload for repository https://github.com/Marie59/champ_blocs commit 0d86db7d42b608c386a54500064f5f9c9d7019a4 ecology parents: diff changeset	1738 ggplot2::geom_rect(ggplot2::aes(xmin = as.Date("2013-01-01", origin = "1970-01-01"), xmax = val_xmax, ymin = - 0.1, ymax = one, fill = "red"), alpha = 0.3) +
42b51a52e308 planemo upload for repository https://github.com/Marie59/champ_blocs commit 0d86db7d42b608c386a54500064f5f9c9d7019a4 ecology parents: diff changeset	1739 ggplot2::geom_rect(ggplot2::aes(xmin = as.Date("2013-01-01", origin = "1970-01-01"), xmax = val_xmax, ymin = one, ymax = two, fill = "orange"), alpha = 0.3) +
42b51a52e308 planemo upload for repository https://github.com/Marie59/champ_blocs commit 0d86db7d42b608c386a54500064f5f9c9d7019a4 ecology parents: diff changeset	1740 ggplot2::geom_rect(ggplot2::aes(xmin = as.Date("2013-01-01", origin = "1970-01-01"), xmax = val_xmax, ymin = two, ymax = three, fill = "yellow"), alpha = 0.3) +
42b51a52e308 planemo upload for repository https://github.com/Marie59/champ_blocs commit 0d86db7d42b608c386a54500064f5f9c9d7019a4 ecology parents: diff changeset	1741 ggplot2::geom_rect(ggplot2::aes(xmin = as.Date("2013-01-01", origin = "1970-01-01"), xmax = val_xmax, ymin = three, ymax = four, fill = "green"), alpha = 0.3) +
42b51a52e308 planemo upload for repository https://github.com/Marie59/champ_blocs commit 0d86db7d42b608c386a54500064f5f9c9d7019a4 ecology parents: diff changeset	1742 ggplot2::geom_rect(ggplot2::aes(xmin = as.Date("2013-01-01", origin = "1970-01-01"), xmax = val_xmax, ymin = four, ymax = 1.1, fill = "blue"), alpha = 0.3) +
42b51a52e308 planemo upload for repository https://github.com/Marie59/champ_blocs commit 0d86db7d42b608c386a54500064f5f9c9d7019a4 ecology parents: diff changeset	1743 ggplot2::scale_fill_manual(values = c("#FF0000", "#F59404", "#18E125", "#1A1AE8", "#FAFA15")) +
42b51a52e308 planemo upload for repository https://github.com/Marie59/champ_blocs commit 0d86db7d42b608c386a54500064f5f9c9d7019a4 ecology parents: diff changeset	1744 ggplot2::geom_pointrange(ggplot2::aes(x = df1$Date, y = df1$BM.BF_FS_dist.med, ymin = df1$BM.BF_FS_dist.min, ymax = df1$BM.BF_FS_dist.max), col = "black") +
42b51a52e308 planemo upload for repository https://github.com/Marie59/champ_blocs commit 0d86db7d42b608c386a54500064f5f9c9d7019a4 ecology parents: diff changeset	1745 ggplot2::xlab("Date") +
42b51a52e308 planemo upload for repository https://github.com/Marie59/champ_blocs commit 0d86db7d42b608c386a54500064f5f9c9d7019a4 ecology parents: diff changeset	1746 ggplot2::ylab("Coef dissim BM-BF FS") +
42b51a52e308 planemo upload for repository https://github.com/Marie59/champ_blocs commit 0d86db7d42b608c386a54500064f5f9c9d7019a4 ecology parents: diff changeset	1747 ggplot2::ggtitle(unique(df1$Site_bis)) +
42b51a52e308 planemo upload for repository https://github.com/Marie59/champ_blocs commit 0d86db7d42b608c386a54500064f5f9c9d7019a4 ecology parents: diff changeset	1748 ggplot2::theme(axis.text.x = ggplot2::element_text(angle = 90, vjust = 0.5, hjust = 1), legend.position = "none")
42b51a52e308 planemo upload for repository https://github.com/Marie59/champ_blocs commit 0d86db7d42b608c386a54500064f5f9c9d7019a4 ecology parents: diff changeset	1749
42b51a52e308 planemo upload for repository https://github.com/Marie59/champ_blocs commit 0d86db7d42b608c386a54500064f5f9c9d7019a4 ecology parents: diff changeset	1750 ggplot2::ggsave(paste0("bm_bf_", df1$Site, ".png"), device = "png", bm_bf_fs_plot, height = 3, width = 3.5)
42b51a52e308 planemo upload for repository https://github.com/Marie59/champ_blocs commit 0d86db7d42b608c386a54500064f5f9c9d7019a4 ecology parents: diff changeset	1751
42b51a52e308 planemo upload for repository https://github.com/Marie59/champ_blocs commit 0d86db7d42b608c386a54500064f5f9c9d7019a4 ecology parents: diff changeset	1752 }
42b51a52e308 planemo upload for repository https://github.com/Marie59/champ_blocs commit 0d86db7d42b608c386a54500064f5f9c9d7019a4 ecology parents: diff changeset	1753
42b51a52e308 planemo upload for repository https://github.com/Marie59/champ_blocs commit 0d86db7d42b608c386a54500064f5f9c9d7019a4 ecology parents: diff changeset	1754 rm(df1, four, i, one, three, two, xmax_, xmin_, ymax_, ymin_)

Mercurial > repos > ecology > cb_dissim

annotate cb_dissimilarity.r @ 1:f941081e03f0 draft default tip