ecology/cb_ivr: cb_dissimilarity.r annotate

annotate cb_dissimilarity.r @ 1:83a4d3b47184 draft default tip

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

author	ecology
date	Sat, 18 Mar 2023 16:48:40 +0000
parents	89f977a3a256
children

rev	line source
0 89f977a3a256 planemo upload for repository https://github.com/Marie59/champ_blocs commit 0d86db7d42b608c386a54500064f5f9c9d7019a4 ecology parents: diff changeset	1 # author: "Jonathan Richir"
89f977a3a256 planemo upload for repository https://github.com/Marie59/champ_blocs commit 0d86db7d42b608c386a54500064f5f9c9d7019a4 ecology parents: diff changeset	2 # date: "01 October 2022"
89f977a3a256 planemo upload for repository https://github.com/Marie59/champ_blocs commit 0d86db7d42b608c386a54500064f5f9c9d7019a4 ecology parents: diff changeset	3
89f977a3a256 planemo upload for repository https://github.com/Marie59/champ_blocs commit 0d86db7d42b608c386a54500064f5f9c9d7019a4 ecology parents: diff changeset	4
89f977a3a256 planemo upload for repository https://github.com/Marie59/champ_blocs commit 0d86db7d42b608c386a54500064f5f9c9d7019a4 ecology parents: diff changeset	5 #Rscript
89f977a3a256 planemo upload for repository https://github.com/Marie59/champ_blocs commit 0d86db7d42b608c386a54500064f5f9c9d7019a4 ecology parents: diff changeset	6
89f977a3a256 planemo upload for repository https://github.com/Marie59/champ_blocs commit 0d86db7d42b608c386a54500064f5f9c9d7019a4 ecology parents: diff changeset	7 ###############################
89f977a3a256 planemo upload for repository https://github.com/Marie59/champ_blocs commit 0d86db7d42b608c386a54500064f5f9c9d7019a4 ecology parents: diff changeset	8 ## ##
89f977a3a256 planemo upload for repository https://github.com/Marie59/champ_blocs commit 0d86db7d42b608c386a54500064f5f9c9d7019a4 ecology parents: diff changeset	9 ###############################
89f977a3a256 planemo upload for repository https://github.com/Marie59/champ_blocs commit 0d86db7d42b608c386a54500064f5f9c9d7019a4 ecology parents: diff changeset	10
89f977a3a256 planemo upload for repository https://github.com/Marie59/champ_blocs commit 0d86db7d42b608c386a54500064f5f9c9d7019a4 ecology parents: diff changeset	11 #####Packages : dplyr
89f977a3a256 planemo upload for repository https://github.com/Marie59/champ_blocs commit 0d86db7d42b608c386a54500064f5f9c9d7019a4 ecology parents: diff changeset	12 # tidyr
89f977a3a256 planemo upload for repository https://github.com/Marie59/champ_blocs commit 0d86db7d42b608c386a54500064f5f9c9d7019a4 ecology parents: diff changeset	13 # readr
89f977a3a256 planemo upload for repository https://github.com/Marie59/champ_blocs commit 0d86db7d42b608c386a54500064f5f9c9d7019a4 ecology parents: diff changeset	14 # writexl
89f977a3a256 planemo upload for repository https://github.com/Marie59/champ_blocs commit 0d86db7d42b608c386a54500064f5f9c9d7019a4 ecology parents: diff changeset	15 # stringr
89f977a3a256 planemo upload for repository https://github.com/Marie59/champ_blocs commit 0d86db7d42b608c386a54500064f5f9c9d7019a4 ecology parents: diff changeset	16 # readxl
89f977a3a256 planemo upload for repository https://github.com/Marie59/champ_blocs commit 0d86db7d42b608c386a54500064f5f9c9d7019a4 ecology parents: diff changeset	17 # tibble
89f977a3a256 planemo upload for repository https://github.com/Marie59/champ_blocs commit 0d86db7d42b608c386a54500064f5f9c9d7019a4 ecology parents: diff changeset	18 # lubridate
89f977a3a256 planemo upload for repository https://github.com/Marie59/champ_blocs commit 0d86db7d42b608c386a54500064f5f9c9d7019a4 ecology parents: diff changeset	19 # cowplot
89f977a3a256 planemo upload for repository https://github.com/Marie59/champ_blocs commit 0d86db7d42b608c386a54500064f5f9c9d7019a4 ecology parents: diff changeset	20 # magrittr
89f977a3a256 planemo upload for repository https://github.com/Marie59/champ_blocs commit 0d86db7d42b608c386a54500064f5f9c9d7019a4 ecology parents: diff changeset	21 # rmarkdown
89f977a3a256 planemo upload for repository https://github.com/Marie59/champ_blocs commit 0d86db7d42b608c386a54500064f5f9c9d7019a4 ecology parents: diff changeset	22 library(magrittr)
1 83a4d3b47184 planemo upload for repository https://github.com/Marie59/champ_blocs commit 075fd90d1a39ae7912b48549e5537971635b9620 ecology parents: 0 diff changeset	23
0 89f977a3a256 planemo upload for repository https://github.com/Marie59/champ_blocs commit 0d86db7d42b608c386a54500064f5f9c9d7019a4 ecology parents: diff changeset	24 #####Load arguments
89f977a3a256 planemo upload for repository https://github.com/Marie59/champ_blocs commit 0d86db7d42b608c386a54500064f5f9c9d7019a4 ecology parents: diff changeset	25
89f977a3a256 planemo upload for repository https://github.com/Marie59/champ_blocs commit 0d86db7d42b608c386a54500064f5f9c9d7019a4 ecology parents: diff changeset	26 args <- commandArgs(trailingOnly = TRUE)
89f977a3a256 planemo upload for repository https://github.com/Marie59/champ_blocs commit 0d86db7d42b608c386a54500064f5f9c9d7019a4 ecology parents: diff changeset	27
89f977a3a256 planemo upload for repository https://github.com/Marie59/champ_blocs commit 0d86db7d42b608c386a54500064f5f9c9d7019a4 ecology parents: diff changeset	28 #####Import data
89f977a3a256 planemo upload for repository https://github.com/Marie59/champ_blocs commit 0d86db7d42b608c386a54500064f5f9c9d7019a4 ecology parents: diff changeset	29
89f977a3a256 planemo upload for repository https://github.com/Marie59/champ_blocs commit 0d86db7d42b608c386a54500064f5f9c9d7019a4 ecology parents: diff changeset	30 if (length(args) < 1) {
89f977a3a256 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")
89f977a3a256 planemo upload for repository https://github.com/Marie59/champ_blocs commit 0d86db7d42b608c386a54500064f5f9c9d7019a4 ecology parents: diff changeset	32 }else {
89f977a3a256 planemo upload for repository https://github.com/Marie59/champ_blocs commit 0d86db7d42b608c386a54500064f5f9c9d7019a4 ecology parents: diff changeset	33 fiche_val <- args[1]
89f977a3a256 planemo upload for repository https://github.com/Marie59/champ_blocs commit 0d86db7d42b608c386a54500064f5f9c9d7019a4 ecology parents: diff changeset	34 input_data <- args[2]
89f977a3a256 planemo upload for repository https://github.com/Marie59/champ_blocs commit 0d86db7d42b608c386a54500064f5f9c9d7019a4 ecology parents: diff changeset	35 choice <- args[3]
89f977a3a256 planemo upload for repository https://github.com/Marie59/champ_blocs commit 0d86db7d42b608c386a54500064f5f9c9d7019a4 ecology parents: diff changeset	36 choice_date <- as.numeric(args[4])
89f977a3a256 planemo upload for repository https://github.com/Marie59/champ_blocs commit 0d86db7d42b608c386a54500064f5f9c9d7019a4 ecology parents: diff changeset	37 }
89f977a3a256 planemo upload for repository https://github.com/Marie59/champ_blocs commit 0d86db7d42b608c386a54500064f5f9c9d7019a4 ecology parents: diff changeset	38
89f977a3a256 planemo upload for repository https://github.com/Marie59/champ_blocs commit 0d86db7d42b608c386a54500064f5f9c9d7019a4 ecology parents: diff changeset	39 #############################################################
89f977a3a256 planemo upload for repository https://github.com/Marie59/champ_blocs commit 0d86db7d42b608c386a54500064f5f9c9d7019a4 ecology parents: diff changeset	40 # #
89f977a3a256 planemo upload for repository https://github.com/Marie59/champ_blocs commit 0d86db7d42b608c386a54500064f5f9c9d7019a4 ecology parents: diff changeset	41 # Loading and cleaning data #
89f977a3a256 planemo upload for repository https://github.com/Marie59/champ_blocs commit 0d86db7d42b608c386a54500064f5f9c9d7019a4 ecology parents: diff changeset	42 # #
89f977a3a256 planemo upload for repository https://github.com/Marie59/champ_blocs commit 0d86db7d42b608c386a54500064f5f9c9d7019a4 ecology parents: diff changeset	43 #############################################################
89f977a3a256 planemo upload for repository https://github.com/Marie59/champ_blocs commit 0d86db7d42b608c386a54500064f5f9c9d7019a4 ecology parents: diff changeset	44 # load qecb data
89f977a3a256 planemo upload for repository https://github.com/Marie59/champ_blocs commit 0d86db7d42b608c386a54500064f5f9c9d7019a4 ecology parents: diff changeset	45
89f977a3a256 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
89f977a3a256 planemo upload for repository https://github.com/Marie59/champ_blocs commit 0d86db7d42b608c386a54500064f5f9c9d7019a4 ecology parents: diff changeset	47
89f977a3a256 planemo upload for repository https://github.com/Marie59/champ_blocs commit 0d86db7d42b608c386a54500064f5f9c9d7019a4 ecology parents: diff changeset	48 # import csv files ficheterrain
89f977a3a256 planemo upload for repository https://github.com/Marie59/champ_blocs commit 0d86db7d42b608c386a54500064f5f9c9d7019a4 ecology parents: diff changeset	49
89f977a3a256 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
89f977a3a256 planemo upload for repository https://github.com/Marie59/champ_blocs commit 0d86db7d42b608c386a54500064f5f9c9d7019a4 ecology parents: diff changeset	51
89f977a3a256 planemo upload for repository https://github.com/Marie59/champ_blocs commit 0d86db7d42b608c386a54500064f5f9c9d7019a4 ecology parents: diff changeset	52 ## work on "Fiche terrain"
89f977a3a256 planemo upload for repository https://github.com/Marie59/champ_blocs commit 0d86db7d42b608c386a54500064f5f9c9d7019a4 ecology parents: diff changeset	53
89f977a3a256 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$date.sortie, end = 10), origin = "1970-01-01")
89f977a3a256 planemo upload for repository https://github.com/Marie59/champ_blocs commit 0d86db7d42b608c386a54500064f5f9c9d7019a4 ecology parents: diff changeset	55 fiche <- tibble::add_column(fiche, date_fiche, .after = "date.sortie")
89f977a3a256 planemo upload for repository https://github.com/Marie59/champ_blocs commit 0d86db7d42b608c386a54500064f5f9c9d7019a4 ecology parents: diff changeset	56 rm(date_fiche)
89f977a3a256 planemo upload for repository https://github.com/Marie59/champ_blocs commit 0d86db7d42b608c386a54500064f5f9c9d7019a4 ecology parents: diff changeset	57
89f977a3a256 planemo upload for repository https://github.com/Marie59/champ_blocs commit 0d86db7d42b608c386a54500064f5f9c9d7019a4 ecology parents: diff changeset	58 ## qecb vs fiche terrain
89f977a3a256 planemo upload for repository https://github.com/Marie59/champ_blocs commit 0d86db7d42b608c386a54500064f5f9c9d7019a4 ecology parents: diff changeset	59
89f977a3a256 planemo upload for repository https://github.com/Marie59/champ_blocs commit 0d86db7d42b608c386a54500064f5f9c9d7019a4 ecology parents: diff changeset	60 fiche_red <- dplyr::filter(fiche, fiche$ID.Fiche %in% unique(qecb[, c("id")]))
89f977a3a256 planemo upload for repository https://github.com/Marie59/champ_blocs commit 0d86db7d42b608c386a54500064f5f9c9d7019a4 ecology parents: diff changeset	61
89f977a3a256 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()
89f977a3a256 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")
89f977a3a256 planemo upload for repository https://github.com/Marie59/champ_blocs commit 0d86db7d42b608c386a54500064f5f9c9d7019a4 ecology parents: diff changeset	64 id_count <- data.frame(id_count)
89f977a3a256 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)
89f977a3a256 planemo upload for repository https://github.com/Marie59/champ_blocs commit 0d86db7d42b608c386a54500064f5f9c9d7019a4 ecology parents: diff changeset	66
89f977a3a256 planemo upload for repository https://github.com/Marie59/champ_blocs commit 0d86db7d42b608c386a54500064f5f9c9d7019a4 ecology parents: diff changeset	67 # rep fiche terrain information
89f977a3a256 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)]
89f977a3a256 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")
89f977a3a256 planemo upload for repository https://github.com/Marie59/champ_blocs commit 0d86db7d42b608c386a54500064f5f9c9d7019a4 ecology parents: diff changeset	70
89f977a3a256 planemo upload for repository https://github.com/Marie59/champ_blocs commit 0d86db7d42b608c386a54500064f5f9c9d7019a4 ecology parents: diff changeset	71 ## merge qecb data and ficheterrain information
89f977a3a256 planemo upload for repository https://github.com/Marie59/champ_blocs commit 0d86db7d42b608c386a54500064f5f9c9d7019a4 ecology parents: diff changeset	72
89f977a3a256 planemo upload for repository https://github.com/Marie59/champ_blocs commit 0d86db7d42b608c386a54500064f5f9c9d7019a4 ecology parents: diff changeset	73 qecb <- dplyr::bind_cols(qecb, fiche_expanded)
89f977a3a256 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")
89f977a3a256 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")
89f977a3a256 planemo upload for repository https://github.com/Marie59/champ_blocs commit 0d86db7d42b608c386a54500064f5f9c9d7019a4 ecology parents: diff changeset	76
89f977a3a256 planemo upload for repository https://github.com/Marie59/champ_blocs commit 0d86db7d42b608c386a54500064f5f9c9d7019a4 ecology parents: diff changeset	77 rm(fiche_expanded, fiche_red, id_count)
89f977a3a256 planemo upload for repository https://github.com/Marie59/champ_blocs commit 0d86db7d42b608c386a54500064f5f9c9d7019a4 ecology parents: diff changeset	78
89f977a3a256 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)
89f977a3a256 planemo upload for repository https://github.com/Marie59/champ_blocs commit 0d86db7d42b608c386a54500064f5f9c9d7019a4 ecology parents: diff changeset	80
89f977a3a256 planemo upload for repository https://github.com/Marie59/champ_blocs commit 0d86db7d42b608c386a54500064f5f9c9d7019a4 ecology parents: diff changeset	81
89f977a3a256 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
89f977a3a256 planemo upload for repository https://github.com/Marie59/champ_blocs commit 0d86db7d42b608c386a54500064f5f9c9d7019a4 ecology parents: diff changeset	83
89f977a3a256 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]")
89f977a3a256 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")
89f977a3a256 planemo upload for repository https://github.com/Marie59/champ_blocs commit 0d86db7d42b608c386a54500064f5f9c9d7019a4 ecology parents: diff changeset	86 rm(quadrat)
89f977a3a256 planemo upload for repository https://github.com/Marie59/champ_blocs commit 0d86db7d42b608c386a54500064f5f9c9d7019a4 ecology parents: diff changeset	87
89f977a3a256 planemo upload for repository https://github.com/Marie59/champ_blocs commit 0d86db7d42b608c386a54500064f5f9c9d7019a4 ecology parents: diff changeset	88 # check
89f977a3a256 planemo upload for repository https://github.com/Marie59/champ_blocs commit 0d86db7d42b608c386a54500064f5f9c9d7019a4 ecology parents: diff changeset	89 quadrat_bis <- rep(NA, length = nrow(qecb))
89f977a3a256 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")
89f977a3a256 planemo upload for repository https://github.com/Marie59/champ_blocs commit 0d86db7d42b608c386a54500064f5f9c9d7019a4 ecology parents: diff changeset	91 rm(quadrat_bis)
89f977a3a256 planemo upload for repository https://github.com/Marie59/champ_blocs commit 0d86db7d42b608c386a54500064f5f9c9d7019a4 ecology parents: diff changeset	92
89f977a3a256 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)
89f977a3a256 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)
89f977a3a256 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)
89f977a3a256 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)
89f977a3a256 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)
89f977a3a256 planemo upload for repository https://github.com/Marie59/champ_blocs commit 0d86db7d42b608c386a54500064f5f9c9d7019a4 ecology parents: diff changeset	98
89f977a3a256 planemo upload for repository https://github.com/Marie59/champ_blocs commit 0d86db7d42b608c386a54500064f5f9c9d7019a4 ecology parents: diff changeset	99
89f977a3a256 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)
89f977a3a256 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)
89f977a3a256 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)
89f977a3a256 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)
89f977a3a256 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)
89f977a3a256 planemo upload for repository https://github.com/Marie59/champ_blocs commit 0d86db7d42b608c386a54500064f5f9c9d7019a4 ecology parents: diff changeset	105
89f977a3a256 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 !
89f977a3a256 planemo upload for repository https://github.com/Marie59/champ_blocs commit 0d86db7d42b608c386a54500064f5f9c9d7019a4 ecology parents: diff changeset	107
89f977a3a256 planemo upload for repository https://github.com/Marie59/champ_blocs commit 0d86db7d42b608c386a54500064f5f9c9d7019a4 ecology parents: diff changeset	108 # Name for data analysis
89f977a3a256 planemo upload for repository https://github.com/Marie59/champ_blocs commit 0d86db7d42b608c386a54500064f5f9c9d7019a4 ecology parents: diff changeset	109
89f977a3a256 planemo upload for repository https://github.com/Marie59/champ_blocs commit 0d86db7d42b608c386a54500064f5f9c9d7019a4 ecology parents: diff changeset	110 qecb <- tibble::add_column(qecb, Site = qecb$zone.habitat, .after = "ID.Fiche")
89f977a3a256 planemo upload for repository https://github.com/Marie59/champ_blocs commit 0d86db7d42b608c386a54500064f5f9c9d7019a4 ecology parents: diff changeset	111
89f977a3a256 planemo upload for repository https://github.com/Marie59/champ_blocs commit 0d86db7d42b608c386a54500064f5f9c9d7019a4 ecology parents: diff changeset	112 for (x in seq_along(qecb$Site)) {
89f977a3a256 planemo upload for repository https://github.com/Marie59/champ_blocs commit 0d86db7d42b608c386a54500064f5f9c9d7019a4 ecology parents: diff changeset	113 if (grepl(pattern = "Locmariaquer", qecb$Site[x]) == TRUE) {
89f977a3a256 planemo upload for repository https://github.com/Marie59/champ_blocs commit 0d86db7d42b608c386a54500064f5f9c9d7019a4 ecology parents: diff changeset	114 qecb$Site[x] <- "GDMO_Locmariaquer"
89f977a3a256 planemo upload for repository https://github.com/Marie59/champ_blocs commit 0d86db7d42b608c386a54500064f5f9c9d7019a4 ecology parents: diff changeset	115 } else if (grepl(pattern = "Beg Lann", qecb$Site[x]) == TRUE) {
89f977a3a256 planemo upload for repository https://github.com/Marie59/champ_blocs commit 0d86db7d42b608c386a54500064f5f9c9d7019a4 ecology parents: diff changeset	116 qecb$Site[x] <- "GDMO_BegLann"
89f977a3a256 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$Site[x]) == TRUE) {
89f977a3a256 planemo upload for repository https://github.com/Marie59/champ_blocs commit 0d86db7d42b608c386a54500064f5f9c9d7019a4 ecology parents: diff changeset	118 qecb$Site[x] <- "FOUR_PlateauFour"
89f977a3a256 planemo upload for repository https://github.com/Marie59/champ_blocs commit 0d86db7d42b608c386a54500064f5f9c9d7019a4 ecology parents: diff changeset	119 } else if (grepl(pattern = "Grouin", qecb$Site[x]) == TRUE) {
89f977a3a256 planemo upload for repository https://github.com/Marie59/champ_blocs commit 0d86db7d42b608c386a54500064f5f9c9d7019a4 ecology parents: diff changeset	120 qecb$Site[x] <- "EGMP_GroinCou"
89f977a3a256 planemo upload for repository https://github.com/Marie59/champ_blocs commit 0d86db7d42b608c386a54500064f5f9c9d7019a4 ecology parents: diff changeset	121 } else if (grepl(pattern = "Ensembert", qecb$Site[x]) == TRUE) {
89f977a3a256 planemo upload for repository https://github.com/Marie59/champ_blocs commit 0d86db7d42b608c386a54500064f5f9c9d7019a4 ecology parents: diff changeset	122 qecb$Site[x] <- "EGMP_PasEmsembert"
89f977a3a256 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$Site[x]) == TRUE) {
89f977a3a256 planemo upload for repository https://github.com/Marie59/champ_blocs commit 0d86db7d42b608c386a54500064f5f9c9d7019a4 ecology parents: diff changeset	124 qecb$Site[x] <- "EGMP_BreeBains"
89f977a3a256 planemo upload for repository https://github.com/Marie59/champ_blocs commit 0d86db7d42b608c386a54500064f5f9c9d7019a4 ecology parents: diff changeset	125 } else if (grepl(pattern = "Antiochat", qecb$Site[x]) == TRUE) {
89f977a3a256 planemo upload for repository https://github.com/Marie59/champ_blocs commit 0d86db7d42b608c386a54500064f5f9c9d7019a4 ecology parents: diff changeset	126 qecb$Site[x] <- "EGMP_PerreAntiochat"
89f977a3a256 planemo upload for repository https://github.com/Marie59/champ_blocs commit 0d86db7d42b608c386a54500064f5f9c9d7019a4 ecology parents: diff changeset	127 } else if (grepl(pattern = "Chassiron", qecb$Site[x]) == TRUE) {
89f977a3a256 planemo upload for repository https://github.com/Marie59/champ_blocs commit 0d86db7d42b608c386a54500064f5f9c9d7019a4 ecology parents: diff changeset	128 qecb$Site[x] <- "EGMP_Chassiron"
89f977a3a256 planemo upload for repository https://github.com/Marie59/champ_blocs commit 0d86db7d42b608c386a54500064f5f9c9d7019a4 ecology parents: diff changeset	129 } else if (grepl(pattern = "zone p", qecb$Site[x]) == TRUE) {
89f977a3a256 planemo upload for repository https://github.com/Marie59/champ_blocs commit 0d86db7d42b608c386a54500064f5f9c9d7019a4 ecology parents: diff changeset	130 qecb$Site[x] <- "BASQ_FlotsBleusZP"
89f977a3a256 planemo upload for repository https://github.com/Marie59/champ_blocs commit 0d86db7d42b608c386a54500064f5f9c9d7019a4 ecology parents: diff changeset	131 } else if (grepl(pattern = "zone f", qecb$Site[x]) == TRUE) {
89f977a3a256 planemo upload for repository https://github.com/Marie59/champ_blocs commit 0d86db7d42b608c386a54500064f5f9c9d7019a4 ecology parents: diff changeset	132 qecb$Site[x] <- "BASQ_FlotsBleusZF"
89f977a3a256 planemo upload for repository https://github.com/Marie59/champ_blocs commit 0d86db7d42b608c386a54500064f5f9c9d7019a4 ecology parents: diff changeset	133 } else if (grepl(pattern = "Saint-Michel", qecb$Site[x]) == TRUE) {
89f977a3a256 planemo upload for repository https://github.com/Marie59/champ_blocs commit 0d86db7d42b608c386a54500064f5f9c9d7019a4 ecology parents: diff changeset	134 qecb$Site[x] <- "GONB_IlotStMichel"
89f977a3a256 planemo upload for repository https://github.com/Marie59/champ_blocs commit 0d86db7d42b608c386a54500064f5f9c9d7019a4 ecology parents: diff changeset	135 } else if (grepl(pattern = "Quéménès", qecb$Site[x]) == TRUE) {
89f977a3a256 planemo upload for repository https://github.com/Marie59/champ_blocs commit 0d86db7d42b608c386a54500064f5f9c9d7019a4 ecology parents: diff changeset	136 qecb$Site[x] <- "FINS_Quemenes"
89f977a3a256 planemo upload for repository https://github.com/Marie59/champ_blocs commit 0d86db7d42b608c386a54500064f5f9c9d7019a4 ecology parents: diff changeset	137 } else if (grepl(pattern = "Goulenez", qecb$Site[x]) == TRUE) {
89f977a3a256 planemo upload for repository https://github.com/Marie59/champ_blocs commit 0d86db7d42b608c386a54500064f5f9c9d7019a4 ecology parents: diff changeset	138 qecb$Site[x] <- "FINS_SeinGoulenez"
89f977a3a256 planemo upload for repository https://github.com/Marie59/champ_blocs commit 0d86db7d42b608c386a54500064f5f9c9d7019a4 ecology parents: diff changeset	139 } else if (grepl(pattern = "Kilaourou", qecb$Site[x]) == TRUE) {
89f977a3a256 planemo upload for repository https://github.com/Marie59/champ_blocs commit 0d86db7d42b608c386a54500064f5f9c9d7019a4 ecology parents: diff changeset	140 qecb$Site[x] <- "FINS_SeinKilaourou"
89f977a3a256 planemo upload for repository https://github.com/Marie59/champ_blocs commit 0d86db7d42b608c386a54500064f5f9c9d7019a4 ecology parents: diff changeset	141 } else if (grepl(pattern = "Verdelet", qecb$Site[x]) == TRUE) {
89f977a3a256 planemo upload for repository https://github.com/Marie59/champ_blocs commit 0d86db7d42b608c386a54500064f5f9c9d7019a4 ecology parents: diff changeset	142 qecb$Site[x] <- "ARMO_Verdelet"
89f977a3a256 planemo upload for repository https://github.com/Marie59/champ_blocs commit 0d86db7d42b608c386a54500064f5f9c9d7019a4 ecology parents: diff changeset	143 } else if (grepl(pattern = "Piégu", qecb$Site[x]) == TRUE) {
89f977a3a256 planemo upload for repository https://github.com/Marie59/champ_blocs commit 0d86db7d42b608c386a54500064f5f9c9d7019a4 ecology parents: diff changeset	144 qecb$Site[x] <- "ARMO_Piegu"
89f977a3a256 planemo upload for repository https://github.com/Marie59/champ_blocs commit 0d86db7d42b608c386a54500064f5f9c9d7019a4 ecology parents: diff changeset	145 } else if (grepl(pattern = "Bilfot", qecb$Site[x]) == TRUE) {
89f977a3a256 planemo upload for repository https://github.com/Marie59/champ_blocs commit 0d86db7d42b608c386a54500064f5f9c9d7019a4 ecology parents: diff changeset	146 qecb$Site[x] <- "ARMO_Bilfot"
89f977a3a256 planemo upload for repository https://github.com/Marie59/champ_blocs commit 0d86db7d42b608c386a54500064f5f9c9d7019a4 ecology parents: diff changeset	147 } else if (grepl(pattern = "Plate", qecb$Site[x]) == TRUE) {
89f977a3a256 planemo upload for repository https://github.com/Marie59/champ_blocs commit 0d86db7d42b608c386a54500064f5f9c9d7019a4 ecology parents: diff changeset	148 qecb$Site[x] <- "ARMO_IlePlate"
89f977a3a256 planemo upload for repository https://github.com/Marie59/champ_blocs commit 0d86db7d42b608c386a54500064f5f9c9d7019a4 ecology parents: diff changeset	149 } else if (grepl(pattern = "Perharidy", qecb$Site[x]) == TRUE) {
89f977a3a256 planemo upload for repository https://github.com/Marie59/champ_blocs commit 0d86db7d42b608c386a54500064f5f9c9d7019a4 ecology parents: diff changeset	150 qecb$Site[x] <- "PDMO_Perharidy"
89f977a3a256 planemo upload for repository https://github.com/Marie59/champ_blocs commit 0d86db7d42b608c386a54500064f5f9c9d7019a4 ecology parents: diff changeset	151 } else if (grepl(pattern = "Keraliou", qecb$Site[x]) == TRUE) {
89f977a3a256 planemo upload for repository https://github.com/Marie59/champ_blocs commit 0d86db7d42b608c386a54500064f5f9c9d7019a4 ecology parents: diff changeset	152 qecb$Site[x] <- "BRES_Keraliou"
89f977a3a256 planemo upload for repository https://github.com/Marie59/champ_blocs commit 0d86db7d42b608c386a54500064f5f9c9d7019a4 ecology parents: diff changeset	153 } else if (grepl(pattern = "Mousterlin", qecb$Site[x]) == TRUE) {
89f977a3a256 planemo upload for repository https://github.com/Marie59/champ_blocs commit 0d86db7d42b608c386a54500064f5f9c9d7019a4 ecology parents: diff changeset	154 qecb$Site[x] <- "FINS_Mousterlin"
89f977a3a256 planemo upload for repository https://github.com/Marie59/champ_blocs commit 0d86db7d42b608c386a54500064f5f9c9d7019a4 ecology parents: diff changeset	155 } else if (grepl(pattern = "Nicolas", qecb$Site[x]) == TRUE) {
89f977a3a256 planemo upload for repository https://github.com/Marie59/champ_blocs commit 0d86db7d42b608c386a54500064f5f9c9d7019a4 ecology parents: diff changeset	156 qecb$Site[x] <- "FINS_StNicolasGlenan"
89f977a3a256 planemo upload for repository https://github.com/Marie59/champ_blocs commit 0d86db7d42b608c386a54500064f5f9c9d7019a4 ecology parents: diff changeset	157 }
89f977a3a256 planemo upload for repository https://github.com/Marie59/champ_blocs commit 0d86db7d42b608c386a54500064f5f9c9d7019a4 ecology parents: diff changeset	158 if (grepl(pattern = "Roz", qecb$site[x]) == TRUE) {
89f977a3a256 planemo upload for repository https://github.com/Marie59/champ_blocs commit 0d86db7d42b608c386a54500064f5f9c9d7019a4 ecology parents: diff changeset	159 qecb$Site[x] <- "FINS_AnseRoz"
89f977a3a256 planemo upload for repository https://github.com/Marie59/champ_blocs commit 0d86db7d42b608c386a54500064f5f9c9d7019a4 ecology parents: diff changeset	160 }
89f977a3a256 planemo upload for repository https://github.com/Marie59/champ_blocs commit 0d86db7d42b608c386a54500064f5f9c9d7019a4 ecology parents: diff changeset	161 }
89f977a3a256 planemo upload for repository https://github.com/Marie59/champ_blocs commit 0d86db7d42b608c386a54500064f5f9c9d7019a4 ecology parents: diff changeset	162
89f977a3a256 planemo upload for repository https://github.com/Marie59/champ_blocs commit 0d86db7d42b608c386a54500064f5f9c9d7019a4 ecology parents: diff changeset	163 # Name for report/plot
89f977a3a256 planemo upload for repository https://github.com/Marie59/champ_blocs commit 0d86db7d42b608c386a54500064f5f9c9d7019a4 ecology parents: diff changeset	164
89f977a3a256 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$Site, .after = "Site")
89f977a3a256 planemo upload for repository https://github.com/Marie59/champ_blocs commit 0d86db7d42b608c386a54500064f5f9c9d7019a4 ecology parents: diff changeset	166
89f977a3a256 planemo upload for repository https://github.com/Marie59/champ_blocs commit 0d86db7d42b608c386a54500064f5f9c9d7019a4 ecology parents: diff changeset	167 qecb$Site_bis <- ifelse(qecb$Site == "GDMO_Locmariaquer", "Locmariaquer", qecb$Site_bis)
89f977a3a256 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$Site_bis)
89f977a3a256 planemo upload for repository https://github.com/Marie59/champ_blocs commit 0d86db7d42b608c386a54500064f5f9c9d7019a4 ecology parents: diff changeset	169 qecb$Site_bis <- ifelse(qecb$Site == "FOUR_PlateauFour", "Plateau du Four", qecb$Site_bis)
89f977a3a256 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$Site_bis)
89f977a3a256 planemo upload for repository https://github.com/Marie59/champ_blocs commit 0d86db7d42b608c386a54500064f5f9c9d7019a4 ecology parents: diff changeset	171 qecb$Site_bis <- ifelse(qecb$Site == "EGMP_PasEmsembert", "Le Pas d'Emsembert", qecb$Site_bis)
89f977a3a256 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$Site_bis)
89f977a3a256 planemo upload for repository https://github.com/Marie59/champ_blocs commit 0d86db7d42b608c386a54500064f5f9c9d7019a4 ecology parents: diff changeset	173 qecb$Site_bis <- ifelse(qecb$Site == "EGMP_PerreAntiochat", "Le Perré d'Antiochat", qecb$Site_bis)
89f977a3a256 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$Site_bis)
89f977a3a256 planemo upload for repository https://github.com/Marie59/champ_blocs commit 0d86db7d42b608c386a54500064f5f9c9d7019a4 ecology parents: diff changeset	175 qecb$Site_bis <- ifelse(qecb$Site == "BASQ_FlotsBleusZP", "Les Flots Bleus / zone pêcheurs", qecb$Site_bis)
89f977a3a256 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$Site_bis)
89f977a3a256 planemo upload for repository https://github.com/Marie59/champ_blocs commit 0d86db7d42b608c386a54500064f5f9c9d7019a4 ecology parents: diff changeset	177 qecb$Site_bis <- ifelse(qecb$Site == "GONB_IlotStMichel", "Îlot Saint-Michel", qecb$Site_bis)
89f977a3a256 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$Site_bis)
89f977a3a256 planemo upload for repository https://github.com/Marie59/champ_blocs commit 0d86db7d42b608c386a54500064f5f9c9d7019a4 ecology parents: diff changeset	179 qecb$Site_bis <- ifelse(qecb$Site == "FINS_SeinGoulenez", "Île de Sein - Goulenez", qecb$Site_bis)
89f977a3a256 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$Site_bis)
89f977a3a256 planemo upload for repository https://github.com/Marie59/champ_blocs commit 0d86db7d42b608c386a54500064f5f9c9d7019a4 ecology parents: diff changeset	181 qecb$Site_bis <- ifelse(qecb$Site == "ARMO_Verdelet", "Îlot du Verdelet", qecb$Site_bis)
89f977a3a256 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$Site_bis)
89f977a3a256 planemo upload for repository https://github.com/Marie59/champ_blocs commit 0d86db7d42b608c386a54500064f5f9c9d7019a4 ecology parents: diff changeset	183 qecb$Site_bis <- ifelse(qecb$Site == "ARMO_Bilfot", "Pointe de Bilfot", qecb$Site_bis)
89f977a3a256 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$Site_bis)
89f977a3a256 planemo upload for repository https://github.com/Marie59/champ_blocs commit 0d86db7d42b608c386a54500064f5f9c9d7019a4 ecology parents: diff changeset	185 qecb$Site_bis <- ifelse(qecb$Site == "PDMO_Perharidy", "Perharidy", qecb$Site_bis)
89f977a3a256 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$Site_bis)
89f977a3a256 planemo upload for repository https://github.com/Marie59/champ_blocs commit 0d86db7d42b608c386a54500064f5f9c9d7019a4 ecology parents: diff changeset	187 qecb$Site_bis <- ifelse(qecb$Site == "FINS_Mousterlin", "Pointe de Mousterlin", qecb$Site_bis)
89f977a3a256 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$Site_bis)
89f977a3a256 planemo upload for repository https://github.com/Marie59/champ_blocs commit 0d86db7d42b608c386a54500064f5f9c9d7019a4 ecology parents: diff changeset	189 qecb$Site_bis <- ifelse(qecb$Site == "FINS_AnseRoz", "Pointe de l'Anse du Roz", qecb$Site_bis)
89f977a3a256 planemo upload for repository https://github.com/Marie59/champ_blocs commit 0d86db7d42b608c386a54500064f5f9c9d7019a4 ecology parents: diff changeset	190
89f977a3a256 planemo upload for repository https://github.com/Marie59/champ_blocs commit 0d86db7d42b608c386a54500064f5f9c9d7019a4 ecology parents: diff changeset	191 ## change some variables to factor
89f977a3a256 planemo upload for repository https://github.com/Marie59/champ_blocs commit 0d86db7d42b608c386a54500064f5f9c9d7019a4 ecology parents: diff changeset	192
89f977a3a256 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
89f977a3a256 planemo upload for repository https://github.com/Marie59/champ_blocs commit 0d86db7d42b608c386a54500064f5f9c9d7019a4 ecology parents: diff changeset	194 ix <- grep("^X..", names(qecb))
89f977a3a256 planemo upload for repository https://github.com/Marie59/champ_blocs commit 0d86db7d42b608c386a54500064f5f9c9d7019a4 ecology parents: diff changeset	195 qecb[ix] <- lapply(qecb[ix], as.numeric)
89f977a3a256 planemo upload for repository https://github.com/Marie59/champ_blocs commit 0d86db7d42b608c386a54500064f5f9c9d7019a4 ecology parents: diff changeset	196 rm(ix)
89f977a3a256 planemo upload for repository https://github.com/Marie59/champ_blocs commit 0d86db7d42b608c386a54500064f5f9c9d7019a4 ecology parents: diff changeset	197
89f977a3a256 planemo upload for repository https://github.com/Marie59/champ_blocs commit 0d86db7d42b608c386a54500064f5f9c9d7019a4 ecology parents: diff changeset	198
89f977a3a256 planemo upload for repository https://github.com/Marie59/champ_blocs commit 0d86db7d42b608c386a54500064f5f9c9d7019a4 ecology parents: diff changeset	199 ## save the final, complete qecb df_
89f977a3a256 planemo upload for repository https://github.com/Marie59/champ_blocs commit 0d86db7d42b608c386a54500064f5f9c9d7019a4 ecology parents: diff changeset	200
89f977a3a256 planemo upload for repository https://github.com/Marie59/champ_blocs commit 0d86db7d42b608c386a54500064f5f9c9d7019a4 ecology parents: diff changeset	201 qecb <- qecb[, c(72:107, 1:71)]
89f977a3a256 planemo upload for repository https://github.com/Marie59/champ_blocs commit 0d86db7d42b608c386a54500064f5f9c9d7019a4 ecology parents: diff changeset	202
89f977a3a256 planemo upload for repository https://github.com/Marie59/champ_blocs commit 0d86db7d42b608c386a54500064f5f9c9d7019a4 ecology parents: diff changeset	203 ## qecb df preparation prior qecb calculation
89f977a3a256 planemo upload for repository https://github.com/Marie59/champ_blocs commit 0d86db7d42b608c386a54500064f5f9c9d7019a4 ecology parents: diff changeset	204
89f977a3a256 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
89f977a3a256 planemo upload for repository https://github.com/Marie59/champ_blocs commit 0d86db7d42b608c386a54500064f5f9c9d7019a4 ecology parents: diff changeset	206
89f977a3a256 planemo upload for repository https://github.com/Marie59/champ_blocs commit 0d86db7d42b608c386a54500064f5f9c9d7019a4 ecology parents: diff changeset	207
89f977a3a256 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"))
89f977a3a256 planemo upload for repository https://github.com/Marie59/champ_blocs commit 0d86db7d42b608c386a54500064f5f9c9d7019a4 ecology parents: diff changeset	209
89f977a3a256 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"))
89f977a3a256 planemo upload for repository https://github.com/Marie59/champ_blocs commit 0d86db7d42b608c386a54500064f5f9c9d7019a4 ecology parents: diff changeset	211
89f977a3a256 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)
89f977a3a256 planemo upload for repository https://github.com/Marie59/champ_blocs commit 0d86db7d42b608c386a54500064f5f9c9d7019a4 ecology parents: diff changeset	213
89f977a3a256 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")
89f977a3a256 planemo upload for repository https://github.com/Marie59/champ_blocs commit 0d86db7d42b608c386a54500064f5f9c9d7019a4 ecology parents: diff changeset	215
89f977a3a256 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
89f977a3a256 planemo upload for repository https://github.com/Marie59/champ_blocs commit 0d86db7d42b608c386a54500064f5f9c9d7019a4 ecology parents: diff changeset	217
89f977a3a256 planemo upload for repository https://github.com/Marie59/champ_blocs commit 0d86db7d42b608c386a54500064f5f9c9d7019a4 ecology parents: diff changeset	218 qecbnew <- qecb
89f977a3a256 planemo upload for repository https://github.com/Marie59/champ_blocs commit 0d86db7d42b608c386a54500064f5f9c9d7019a4 ecology parents: diff changeset	219
89f977a3a256 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
89f977a3a256 planemo upload for repository https://github.com/Marie59/champ_blocs commit 0d86db7d42b608c386a54500064f5f9c9d7019a4 ecology parents: diff changeset	221
89f977a3a256 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$site_year_month_day),
89f977a3a256 planemo upload for repository https://github.com/Marie59/champ_blocs commit 0d86db7d42b608c386a54500064f5f9c9d7019a4 ecology parents: diff changeset	223 "loop nb" = c(1:seq_along(unique(qecbnew$site_year_month_day))))
89f977a3a256 planemo upload for repository https://github.com/Marie59/champ_blocs commit 0d86db7d42b608c386a54500064f5f9c9d7019a4 ecology parents: diff changeset	224
89f977a3a256 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.
89f977a3a256 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.
89f977a3a256 planemo upload for repository https://github.com/Marie59/champ_blocs commit 0d86db7d42b608c386a54500064f5f9c9d7019a4 ecology parents: diff changeset	227
89f977a3a256 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
89f977a3a256 planemo upload for repository https://github.com/Marie59/champ_blocs commit 0d86db7d42b608c386a54500064f5f9c9d7019a4 ecology parents: diff changeset	229 qecbnew$Face <- as.character(qecbnew$Face)
89f977a3a256 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)
89f977a3a256 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)
89f977a3a256 planemo upload for repository https://github.com/Marie59/champ_blocs commit 0d86db7d42b608c386a54500064f5f9c9d7019a4 ecology parents: diff changeset	232 qecbnew$Face <- as.factor(qecbnew$Face)
89f977a3a256 planemo upload for repository https://github.com/Marie59/champ_blocs commit 0d86db7d42b608c386a54500064f5f9c9d7019a4 ecology parents: diff changeset	233
89f977a3a256 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
89f977a3a256 planemo upload for repository https://github.com/Marie59/champ_blocs commit 0d86db7d42b608c386a54500064f5f9c9d7019a4 ecology parents: diff changeset	235 qecbnew$Face <- as.character(qecbnew$Face)
89f977a3a256 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)
89f977a3a256 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)
89f977a3a256 planemo upload for repository https://github.com/Marie59/champ_blocs commit 0d86db7d42b608c386a54500064f5f9c9d7019a4 ecology parents: diff changeset	238 qecbnew$Face <- as.factor(qecbnew$Face)
89f977a3a256 planemo upload for repository https://github.com/Marie59/champ_blocs commit 0d86db7d42b608c386a54500064f5f9c9d7019a4 ecology parents: diff changeset	239
89f977a3a256 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
89f977a3a256 planemo upload for repository https://github.com/Marie59/champ_blocs commit 0d86db7d42b608c386a54500064f5f9c9d7019a4 ecology parents: diff changeset	241 qecbnew$Face <- as.character(qecbnew$Face)
89f977a3a256 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)
89f977a3a256 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)
89f977a3a256 planemo upload for repository https://github.com/Marie59/champ_blocs commit 0d86db7d42b608c386a54500064f5f9c9d7019a4 ecology parents: diff changeset	244 qecbnew$Face <- as.factor(qecbnew$Face)
89f977a3a256 planemo upload for repository https://github.com/Marie59/champ_blocs commit 0d86db7d42b608c386a54500064f5f9c9d7019a4 ecology parents: diff changeset	245
89f977a3a256 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
89f977a3a256 planemo upload for repository https://github.com/Marie59/champ_blocs commit 0d86db7d42b608c386a54500064f5f9c9d7019a4 ecology parents: diff changeset	247 qecbnew$Face <- as.character(qecbnew$Face)
89f977a3a256 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)
89f977a3a256 planemo upload for repository https://github.com/Marie59/champ_blocs commit 0d86db7d42b608c386a54500064f5f9c9d7019a4 ecology parents: diff changeset	249 qecbnew$Face <- as.factor(qecbnew$Face)
89f977a3a256 planemo upload for repository https://github.com/Marie59/champ_blocs commit 0d86db7d42b608c386a54500064f5f9c9d7019a4 ecology parents: diff changeset	250
89f977a3a256 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"
89f977a3a256 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)
89f977a3a256 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)
89f977a3a256 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)
89f977a3a256 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)
89f977a3a256 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 == ""))
89f977a3a256 planemo upload for repository https://github.com/Marie59/champ_blocs commit 0d86db7d42b608c386a54500064f5f9c9d7019a4 ecology parents: diff changeset	257
89f977a3a256 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.
89f977a3a256 planemo upload for repository https://github.com/Marie59/champ_blocs commit 0d86db7d42b608c386a54500064f5f9c9d7019a4 ecology parents: diff changeset	259
89f977a3a256 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 !
89f977a3a256 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")
89f977a3a256 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
89f977a3a256 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")
89f977a3a256 planemo upload for repository https://github.com/Marie59/champ_blocs commit 0d86db7d42b608c386a54500064f5f9c9d7019a4 ecology parents: diff changeset	264 rm(df_list_loop, qecb_i)
89f977a3a256 planemo upload for repository https://github.com/Marie59/champ_blocs commit 0d86db7d42b608c386a54500064f5f9c9d7019a4 ecology parents: diff changeset	265
89f977a3a256 planemo upload for repository https://github.com/Marie59/champ_blocs commit 0d86db7d42b608c386a54500064f5f9c9d7019a4 ecology parents: diff changeset	266
89f977a3a256 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)
89f977a3a256 planemo upload for repository https://github.com/Marie59/champ_blocs commit 0d86db7d42b608c386a54500064f5f9c9d7019a4 ecology parents: diff changeset	268
89f977a3a256 planemo upload for repository https://github.com/Marie59/champ_blocs commit 0d86db7d42b608c386a54500064f5f9c9d7019a4 ecology parents: diff changeset	269 # first for Spirobranchus
89f977a3a256 planemo upload for repository https://github.com/Marie59/champ_blocs commit 0d86db7d42b608c386a54500064f5f9c9d7019a4 ecology parents: diff changeset	270
89f977a3a256 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
89f977a3a256 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)
89f977a3a256 planemo upload for repository https://github.com/Marie59/champ_blocs commit 0d86db7d42b608c386a54500064f5f9c9d7019a4 ecology parents: diff changeset	273
89f977a3a256 planemo upload for repository https://github.com/Marie59/champ_blocs commit 0d86db7d42b608c386a54500064f5f9c9d7019a4 ecology parents: diff changeset	274
89f977a3a256 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")))
89f977a3a256 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)
89f977a3a256 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$Nb.Spirobranchus.lamarckii.5B))[, c("site_year_month_day", "Nb.Spirobranchus.lamarckii.1B", "Nb.Spirobranchus.lamarckii.2B", "Nb.Spirobranchus.lamarckii.3B", "Nb.Spirobranchus.lamarckii.4B", "Nb.Spirobranchus.lamarckii.5B", "Nb.Spirobranchus.lamarckii.total")])
89f977a3a256 planemo upload for repository https://github.com/Marie59/champ_blocs commit 0d86db7d42b608c386a54500064f5f9c9d7019a4 ecology parents: diff changeset	278
89f977a3a256 planemo upload for repository https://github.com/Marie59/champ_blocs commit 0d86db7d42b608c386a54500064f5f9c9d7019a4 ecology parents: diff changeset	279 quemenes <- dplyr::filter(qecbnew, Site == "FINS_Quemenes")
89f977a3a256 planemo upload for repository https://github.com/Marie59/champ_blocs commit 0d86db7d42b608c386a54500064f5f9c9d7019a4 ecology parents: diff changeset	280 quemenes <- dplyr::arrange(quemenes, date_fiche)
89f977a3a256 planemo upload for repository https://github.com/Marie59/champ_blocs commit 0d86db7d42b608c386a54500064f5f9c9d7019a4 ecology parents: diff changeset	281 # for Quemenes, issue because for sampling date "FINS_Quemenes.2015.09.30" the 5 counts of Spirobranchus were encoded in 1B instead of total !!! I noticed this issue when mining data (see below), therefore I corrected before running below script for Spirobranchus.
89f977a3a256 planemo upload for repository https://github.com/Marie59/champ_blocs commit 0d86db7d42b608c386a54500064f5f9c9d7019a4 ecology parents: diff changeset	282 qecbnew$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)
89f977a3a256 planemo upload for repository https://github.com/Marie59/champ_blocs commit 0d86db7d42b608c386a54500064f5f9c9d7019a4 ecology parents: diff changeset	283
89f977a3a256 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")])
89f977a3a256 planemo upload for repository https://github.com/Marie59/champ_blocs commit 0d86db7d42b608c386a54500064f5f9c9d7019a4 ecology parents: diff changeset	285 rm(quemenes)
89f977a3a256 planemo upload for repository https://github.com/Marie59/champ_blocs commit 0d86db7d42b608c386a54500064f5f9c9d7019a4 ecology parents: diff changeset	286
89f977a3a256 planemo upload for repository https://github.com/Marie59/champ_blocs commit 0d86db7d42b608c386a54500064f5f9c9d7019a4 ecology parents: diff changeset	287 seinkilaourou <- dplyr::filter(qecbnew, Site == "FINS_SeinKilaourou")
89f977a3a256 planemo upload for repository https://github.com/Marie59/champ_blocs commit 0d86db7d42b608c386a54500064f5f9c9d7019a4 ecology parents: diff changeset	288 seinkilaourou <- dplyr::arrange(seinkilaourou, date_fiche)
89f977a3a256 planemo upload for repository https://github.com/Marie59/champ_blocs commit 0d86db7d42b608c386a54500064f5f9c9d7019a4 ecology parents: diff changeset	289 # same issue with SeinKilaourou
89f977a3a256 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$Nb.Spirobranchus.lamarckii.total)
89f977a3a256 planemo upload for repository https://github.com/Marie59/champ_blocs commit 0d86db7d42b608c386a54500064f5f9c9d7019a4 ecology parents: diff changeset	291 (seinkilaourou <- dplyr::filter(qecbnew, site_year_month_day == "FINS_SeinKilaourou.2015.04.21")[, c("site_year_month_day", "Nb.Spirobranchus.lamarckii.1B", "Nb.Spirobranchus.lamarckii.2B", "Nb.Spirobranchus.lamarckii.3B", "Nb.Spirobranchus.lamarckii.4B", "Nb.Spirobranchus.lamarckii.5B", "Nb.Spirobranchus.lamarckii.total")])
89f977a3a256 planemo upload for repository https://github.com/Marie59/champ_blocs commit 0d86db7d42b608c386a54500064f5f9c9d7019a4 ecology parents: diff changeset	292 rm(seinkilaourou)
89f977a3a256 planemo upload for repository https://github.com/Marie59/champ_blocs commit 0d86db7d42b608c386a54500064f5f9c9d7019a4 ecology parents: diff changeset	293
89f977a3a256 planemo upload for repository https://github.com/Marie59/champ_blocs commit 0d86db7d42b608c386a54500064f5f9c9d7019a4 ecology parents: diff changeset	294 # some more issues however with "x100"count data
89f977a3a256 planemo upload for repository https://github.com/Marie59/champ_blocs commit 0d86db7d42b608c386a54500064f5f9c9d7019a4 ecology parents: diff changeset	295 spirobranchus <- subset(qecbnew, !is.na(qecbnew$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$Nb.Spirobranchus.lamarckii.total))[, c("site_year_month_day", "Nb.Spirobranchus.lamarckii.1B", "Nb.Spirobranchus.lamarckii.2B", "Nb.Spirobranchus.lamarckii.3B", "Nb.Spirobranchus.lamarckii.4B", "Nb.Spirobranchus.lamarckii.5B", "Nb.Spirobranchus.lamarckii.total")]
89f977a3a256 planemo upload for repository https://github.com/Marie59/champ_blocs commit 0d86db7d42b608c386a54500064f5f9c9d7019a4 ecology parents: diff changeset	296
89f977a3a256 planemo upload for repository https://github.com/Marie59/champ_blocs commit 0d86db7d42b608c386a54500064f5f9c9d7019a4 ecology parents: diff changeset	297 for (i in c(1:nrow(spirobranchus))) {
89f977a3a256 planemo upload for repository https://github.com/Marie59/champ_blocs commit 0d86db7d42b608c386a54500064f5f9c9d7019a4 ecology parents: diff changeset	298 spirobranchus$mean.x.100[[i]] <- sum(spirobranchus[i, c(2:6)], na.rm = TRUE) / sum(!is.na(spirobranchus[i, c(2:6)])) * 100
89f977a3a256 planemo upload for repository https://github.com/Marie59/champ_blocs commit 0d86db7d42b608c386a54500064f5f9c9d7019a4 ecology parents: diff changeset	299 }
89f977a3a256 planemo upload for repository https://github.com/Marie59/champ_blocs commit 0d86db7d42b608c386a54500064f5f9c9d7019a4 ecology parents: diff changeset	300
89f977a3a256 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)
89f977a3a256 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)
89f977a3a256 planemo upload for repository https://github.com/Marie59/champ_blocs commit 0d86db7d42b608c386a54500064f5f9c9d7019a4 ecology parents: diff changeset	303 for (i in c(1:nrow(spirobranchus))) {
89f977a3a256 planemo upload for repository https://github.com/Marie59/champ_blocs commit 0d86db7d42b608c386a54500064f5f9c9d7019a4 ecology parents: diff changeset	304 spirobranchus$diff[[i]] <- spirobranchus[i, "Nb.Spirobranchus.lamarckii.total"] - spirobranchus[i, "mean.x.100"]
89f977a3a256 planemo upload for repository https://github.com/Marie59/champ_blocs commit 0d86db7d42b608c386a54500064f5f9c9d7019a4 ecology parents: diff changeset	305 }
89f977a3a256 planemo upload for repository https://github.com/Marie59/champ_blocs commit 0d86db7d42b608c386a54500064f5f9c9d7019a4 ecology parents: diff changeset	306
89f977a3a256 planemo upload for repository https://github.com/Marie59/champ_blocs commit 0d86db7d42b608c386a54500064f5f9c9d7019a4 ecology parents: diff changeset	307 spirobranchus$diff <- abs(as.integer(spirobranchus$diff))
89f977a3a256 planemo upload for repository https://github.com/Marie59/champ_blocs commit 0d86db7d42b608c386a54500064f5f9c9d7019a4 ecology parents: diff changeset	308 spirobranchus <- dplyr::arrange(spirobranchus, desc(diff), mean.x.100)
89f977a3a256 planemo upload for repository https://github.com/Marie59/champ_blocs commit 0d86db7d42b608c386a54500064f5f9c9d7019a4 ecology parents: diff changeset	309 spirobranchus <- dplyr::arrange(dplyr::filter(spirobranchus, diff != 0 & mean.x.100 != 0), desc(diff))
89f977a3a256 planemo upload for repository https://github.com/Marie59/champ_blocs commit 0d86db7d42b608c386a54500064f5f9c9d7019a4 ecology parents: diff changeset	310
89f977a3a256 planemo upload for repository https://github.com/Marie59/champ_blocs commit 0d86db7d42b608c386a54500064f5f9c9d7019a4 ecology parents: diff changeset	311 # check it all in the qecbnew df
89f977a3a256 planemo upload for repository https://github.com/Marie59/champ_blocs commit 0d86db7d42b608c386a54500064f5f9c9d7019a4 ecology parents: diff changeset	312
89f977a3a256 planemo upload for repository https://github.com/Marie59/champ_blocs commit 0d86db7d42b608c386a54500064f5f9c9d7019a4 ecology parents: diff changeset	313 for (i in c(1:nrow(qecbnew))) {
89f977a3a256 planemo upload for repository https://github.com/Marie59/champ_blocs commit 0d86db7d42b608c386a54500064f5f9c9d7019a4 ecology parents: diff changeset	314 qecbnew$mean.x.100[[i]] <-
89f977a3a256 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
89f977a3a256 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
89f977a3a256 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)
89f977a3a256 planemo upload for repository https://github.com/Marie59/champ_blocs commit 0d86db7d42b608c386a54500064f5f9c9d7019a4 ecology parents: diff changeset	318
89f977a3a256 planemo upload for repository https://github.com/Marie59/champ_blocs commit 0d86db7d42b608c386a54500064f5f9c9d7019a4 ecology parents: diff changeset	319
89f977a3a256 planemo upload for repository https://github.com/Marie59/champ_blocs commit 0d86db7d42b608c386a54500064f5f9c9d7019a4 ecology parents: diff changeset	320 for (i in c(1:nrow(qecbnew))) {
89f977a3a256 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$mean.x.100[[i]])
89f977a3a256 planemo upload for repository https://github.com/Marie59/champ_blocs commit 0d86db7d42b608c386a54500064f5f9c9d7019a4 ecology parents: diff changeset	322 }
89f977a3a256 planemo upload for repository https://github.com/Marie59/champ_blocs commit 0d86db7d42b608c386a54500064f5f9c9d7019a4 ecology parents: diff changeset	323 qecbnew$mean.x.100 <- as.integer(qecbnew$mean.x.100)
89f977a3a256 planemo upload for repository https://github.com/Marie59/champ_blocs commit 0d86db7d42b608c386a54500064f5f9c9d7019a4 ecology parents: diff changeset	324
89f977a3a256 planemo upload for repository https://github.com/Marie59/champ_blocs commit 0d86db7d42b608c386a54500064f5f9c9d7019a4 ecology parents: diff changeset	325 qecbnew$Nb.Spirobranchus.lamarckii.total <- as.integer(qecbnew$Nb.Spirobranchus.lamarckii.total)
89f977a3a256 planemo upload for repository https://github.com/Marie59/champ_blocs commit 0d86db7d42b608c386a54500064f5f9c9d7019a4 ecology parents: diff changeset	326 qecbnew$Nb.Spirobranchus.lamarckii.total.diff <- abs((qecbnew$Nb.Spirobranchus.lamarckii.total - qecbnew$mean.x.100))
89f977a3a256 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")]
89f977a3a256 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)
89f977a3a256 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))
89f977a3a256 planemo upload for repository https://github.com/Marie59/champ_blocs commit 0d86db7d42b608c386a54500064f5f9c9d7019a4 ecology parents: diff changeset	330
89f977a3a256 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$Nb.Spirobranchus.lamarckii.total)
89f977a3a256 planemo upload for repository https://github.com/Marie59/champ_blocs commit 0d86db7d42b608c386a54500064f5f9c9d7019a4 ecology parents: diff changeset	332 spirobranchus_diff <- qecbnew[, c("Nb.Spirobranchus.lamarckii.1B", "Nb.Spirobranchus.lamarckii.2B", "Nb.Spirobranchus.lamarckii.3B", "Nb.Spirobranchus.lamarckii.4B", "Nb.Spirobranchus.lamarckii.5B", "Nb.Spirobranchus.lamarckii.total", "Nb.Spirobranchus.lamarckii.total.ini", "mean.x.100", "Nb.Spirobranchus.lamarckii.total.diff")]
89f977a3a256 planemo upload for repository https://github.com/Marie59/champ_blocs commit 0d86db7d42b608c386a54500064f5f9c9d7019a4 ecology parents: diff changeset	333 spirobranchus_diff$Nb.Spirobranchus.lamarckii.total.diff <- abs(as.integer(spirobranchus_diff$Nb.Spirobranchus.lamarckii.total.diff))
89f977a3a256 planemo upload for repository https://github.com/Marie59/champ_blocs commit 0d86db7d42b608c386a54500064f5f9c9d7019a4 ecology parents: diff changeset	334 spirobranchus_diff <- dplyr::arrange(spirobranchus_diff, desc(Nb.Spirobranchus.lamarckii.total.diff), mean.x.100)
89f977a3a256 planemo upload for repository https://github.com/Marie59/champ_blocs commit 0d86db7d42b608c386a54500064f5f9c9d7019a4 ecology parents: diff changeset	335 spirobranchus_diff <- dplyr::arrange(dplyr::filter(spirobranchus_diff, Nb.Spirobranchus.lamarckii.total.diff != 0 & mean.x.100 != 0), desc(Nb.Spirobranchus.lamarckii.total.diff))
89f977a3a256 planemo upload for repository https://github.com/Marie59/champ_blocs commit 0d86db7d42b608c386a54500064f5f9c9d7019a4 ecology parents: diff changeset	336 # ok, change made when data x 100 was not correct.
89f977a3a256 planemo upload for repository https://github.com/Marie59/champ_blocs commit 0d86db7d42b608c386a54500064f5f9c9d7019a4 ecology parents: diff changeset	337
89f977a3a256 planemo upload for repository https://github.com/Marie59/champ_blocs commit 0d86db7d42b608c386a54500064f5f9c9d7019a4 ecology parents: diff changeset	338 # finally, change NA by mean.x100 for Spirobranchus total
89f977a3a256 planemo upload for repository https://github.com/Marie59/champ_blocs commit 0d86db7d42b608c386a54500064f5f9c9d7019a4 ecology parents: diff changeset	339 qecbnew$Nb.Spirobranchus.lamarckii.total <- as.character(qecbnew$Nb.Spirobranchus.lamarckii.total)
89f977a3a256 planemo upload for repository https://github.com/Marie59/champ_blocs commit 0d86db7d42b608c386a54500064f5f9c9d7019a4 ecology parents: diff changeset	340 for (i in c(1:nrow(qecbnew))) {
89f977a3a256 planemo upload for repository https://github.com/Marie59/champ_blocs commit 0d86db7d42b608c386a54500064f5f9c9d7019a4 ecology parents: diff changeset	341 qecbnew$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]])
89f977a3a256 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
89f977a3a256 planemo upload for repository https://github.com/Marie59/champ_blocs commit 0d86db7d42b608c386a54500064f5f9c9d7019a4 ecology parents: diff changeset	343
89f977a3a256 planemo upload for repository https://github.com/Marie59/champ_blocs commit 0d86db7d42b608c386a54500064f5f9c9d7019a4 ecology parents: diff changeset	344
89f977a3a256 planemo upload for repository https://github.com/Marie59/champ_blocs commit 0d86db7d42b608c386a54500064f5f9c9d7019a4 ecology parents: diff changeset	345 for (i in c(1:nrow(qecbnew))) {
89f977a3a256 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$Nb.Spirobranchus.lamarckii.total[[i]])
89f977a3a256 planemo upload for repository https://github.com/Marie59/champ_blocs commit 0d86db7d42b608c386a54500064f5f9c9d7019a4 ecology parents: diff changeset	347 }
89f977a3a256 planemo upload for repository https://github.com/Marie59/champ_blocs commit 0d86db7d42b608c386a54500064f5f9c9d7019a4 ecology parents: diff changeset	348
89f977a3a256 planemo upload for repository https://github.com/Marie59/champ_blocs commit 0d86db7d42b608c386a54500064f5f9c9d7019a4 ecology parents: diff changeset	349 qecbnew$Nb.Spirobranchus.lamarckii.total <- as.integer(qecbnew$Nb.Spirobranchus.lamarckii.total)
89f977a3a256 planemo upload for repository https://github.com/Marie59/champ_blocs commit 0d86db7d42b608c386a54500064f5f9c9d7019a4 ecology parents: diff changeset	350
89f977a3a256 planemo upload for repository https://github.com/Marie59/champ_blocs commit 0d86db7d42b608c386a54500064f5f9c9d7019a4 ecology parents: diff changeset	351 qecbnew$Nb.Spirobranchus.lamarckii.total.diff <- abs(qecbnew$Nb.Spirobranchus.lamarckii.total - qecbnew$Nb.Spirobranchus.lamarckii.total.ini)
89f977a3a256 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")]
89f977a3a256 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)
89f977a3a256 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))
89f977a3a256 planemo upload for repository https://github.com/Marie59/champ_blocs commit 0d86db7d42b608c386a54500064f5f9c9d7019a4 ecology parents: diff changeset	355
89f977a3a256 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))
89f977a3a256 planemo upload for repository https://github.com/Marie59/champ_blocs commit 0d86db7d42b608c386a54500064f5f9c9d7019a4 ecology parents: diff changeset	357
89f977a3a256 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)
89f977a3a256 planemo upload for repository https://github.com/Marie59/champ_blocs commit 0d86db7d42b608c386a54500064f5f9c9d7019a4 ecology parents: diff changeset	359
89f977a3a256 planemo upload for repository https://github.com/Marie59/champ_blocs commit 0d86db7d42b608c386a54500064f5f9c9d7019a4 ecology parents: diff changeset	360 # do the same for spirorbis
89f977a3a256 planemo upload for repository https://github.com/Marie59/champ_blocs commit 0d86db7d42b608c386a54500064f5f9c9d7019a4 ecology parents: diff changeset	361
89f977a3a256 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
89f977a3a256 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)
89f977a3a256 planemo upload for repository https://github.com/Marie59/champ_blocs commit 0d86db7d42b608c386a54500064f5f9c9d7019a4 ecology parents: diff changeset	364
89f977a3a256 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")))
89f977a3a256 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)
89f977a3a256 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$Nb.spirorbis.5A))[, c("site_year_month_day", "Nb.spirorbis.1A", "Nb.spirorbis.2A", "Nb.spirorbis.3A", "Nb.spirorbis.4A", "Nb.spirorbis.5A", "Nb.spirorbis.total")])
89f977a3a256 planemo upload for repository https://github.com/Marie59/champ_blocs commit 0d86db7d42b608c386a54500064f5f9c9d7019a4 ecology parents: diff changeset	368
89f977a3a256 planemo upload for repository https://github.com/Marie59/champ_blocs commit 0d86db7d42b608c386a54500064f5f9c9d7019a4 ecology parents: diff changeset	369 # In contrast to Spirobranchus data, no encoding issues for spirorbis data, cfr when sub-quadrat 1A-5A are ALL encoded, NA for total.
89f977a3a256 planemo upload for repository https://github.com/Marie59/champ_blocs commit 0d86db7d42b608c386a54500064f5f9c9d7019a4 ecology parents: diff changeset	370
89f977a3a256 planemo upload for repository https://github.com/Marie59/champ_blocs commit 0d86db7d42b608c386a54500064f5f9c9d7019a4 ecology parents: diff changeset	371 # some more issues however with "x200"count data
89f977a3a256 planemo upload for repository https://github.com/Marie59/champ_blocs commit 0d86db7d42b608c386a54500064f5f9c9d7019a4 ecology parents: diff changeset	372
89f977a3a256 planemo upload for repository https://github.com/Marie59/champ_blocs commit 0d86db7d42b608c386a54500064f5f9c9d7019a4 ecology parents: diff changeset	373 spirorbis <- subset(qecbnew, !is.na(qecbnew$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$Nb.spirorbis.total))[, c("site_year_month_day", "Nb.spirorbis.1A", "Nb.spirorbis.2A", "Nb.spirorbis.3A", "Nb.spirorbis.4A", "Nb.spirorbis.5A", "Nb.spirorbis.total")]
89f977a3a256 planemo upload for repository https://github.com/Marie59/champ_blocs commit 0d86db7d42b608c386a54500064f5f9c9d7019a4 ecology parents: diff changeset	374 for (i in c(1:nrow(spirorbis))) {
89f977a3a256 planemo upload for repository https://github.com/Marie59/champ_blocs commit 0d86db7d42b608c386a54500064f5f9c9d7019a4 ecology parents: diff changeset	375 spirorbis$mean.x.200[[i]] <- sum(spirorbis[i, c(2:6)], na.rm = TRUE) / sum(!is.na(spirorbis[i, c(2:6)])) * 200
89f977a3a256 planemo upload for repository https://github.com/Marie59/champ_blocs commit 0d86db7d42b608c386a54500064f5f9c9d7019a4 ecology parents: diff changeset	376 }
89f977a3a256 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)
89f977a3a256 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)
89f977a3a256 planemo upload for repository https://github.com/Marie59/champ_blocs commit 0d86db7d42b608c386a54500064f5f9c9d7019a4 ecology parents: diff changeset	379 for (i in c(1:nrow(spirorbis))) {
89f977a3a256 planemo upload for repository https://github.com/Marie59/champ_blocs commit 0d86db7d42b608c386a54500064f5f9c9d7019a4 ecology parents: diff changeset	380 spirorbis$diff[[i]] <- spirorbis[i, "Nb.spirorbis.total"] - spirorbis[i, "mean.x.200"]
89f977a3a256 planemo upload for repository https://github.com/Marie59/champ_blocs commit 0d86db7d42b608c386a54500064f5f9c9d7019a4 ecology parents: diff changeset	381 }
89f977a3a256 planemo upload for repository https://github.com/Marie59/champ_blocs commit 0d86db7d42b608c386a54500064f5f9c9d7019a4 ecology parents: diff changeset	382 spirorbis$diff <- abs(as.integer(spirorbis$diff))
89f977a3a256 planemo upload for repository https://github.com/Marie59/champ_blocs commit 0d86db7d42b608c386a54500064f5f9c9d7019a4 ecology parents: diff changeset	383 spirorbis <- dplyr::arrange(spirorbis, desc(diff), mean.x.200)
89f977a3a256 planemo upload for repository https://github.com/Marie59/champ_blocs commit 0d86db7d42b608c386a54500064f5f9c9d7019a4 ecology parents: diff changeset	384 (gonb_ilotstmichel_2015_04_18 <- dplyr::filter(spirorbis, site_year_month_day == "GONB_IlotStMichel.2015.04.18"))
89f977a3a256 planemo upload for repository https://github.com/Marie59/champ_blocs commit 0d86db7d42b608c386a54500064f5f9c9d7019a4 ecology parents: diff changeset	385 rm(gonb_ilotstmichel_2015_04_18)
89f977a3a256 planemo upload for repository https://github.com/Marie59/champ_blocs commit 0d86db7d42b608c386a54500064f5f9c9d7019a4 ecology parents: diff changeset	386 spirorbis <- dplyr::arrange(dplyr::filter(spirorbis, diff != 0 & mean.x.200 != 0), desc(diff))
89f977a3a256 planemo upload for repository https://github.com/Marie59/champ_blocs commit 0d86db7d42b608c386a54500064f5f9c9d7019a4 ecology parents: diff changeset	387
89f977a3a256 planemo upload for repository https://github.com/Marie59/champ_blocs commit 0d86db7d42b608c386a54500064f5f9c9d7019a4 ecology parents: diff changeset	388 # check it all in the qecbnew df
89f977a3a256 planemo upload for repository https://github.com/Marie59/champ_blocs commit 0d86db7d42b608c386a54500064f5f9c9d7019a4 ecology parents: diff changeset	389
89f977a3a256 planemo upload for repository https://github.com/Marie59/champ_blocs commit 0d86db7d42b608c386a54500064f5f9c9d7019a4 ecology parents: diff changeset	390 for (i in c(1:nrow(qecbnew))) {
89f977a3a256 planemo upload for repository https://github.com/Marie59/champ_blocs commit 0d86db7d42b608c386a54500064f5f9c9d7019a4 ecology parents: diff changeset	391 qecbnew$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
89f977a3a256 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
89f977a3a256 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)
89f977a3a256 planemo upload for repository https://github.com/Marie59/champ_blocs commit 0d86db7d42b608c386a54500064f5f9c9d7019a4 ecology parents: diff changeset	394
89f977a3a256 planemo upload for repository https://github.com/Marie59/champ_blocs commit 0d86db7d42b608c386a54500064f5f9c9d7019a4 ecology parents: diff changeset	395 for (i in c(1:nrow(qecbnew))) {
89f977a3a256 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$mean.x.200[[i]])
89f977a3a256 planemo upload for repository https://github.com/Marie59/champ_blocs commit 0d86db7d42b608c386a54500064f5f9c9d7019a4 ecology parents: diff changeset	397 }
89f977a3a256 planemo upload for repository https://github.com/Marie59/champ_blocs commit 0d86db7d42b608c386a54500064f5f9c9d7019a4 ecology parents: diff changeset	398
89f977a3a256 planemo upload for repository https://github.com/Marie59/champ_blocs commit 0d86db7d42b608c386a54500064f5f9c9d7019a4 ecology parents: diff changeset	399 qecbnew$mean.x.200 <- as.integer(qecbnew$mean.x.200)
89f977a3a256 planemo upload for repository https://github.com/Marie59/champ_blocs commit 0d86db7d42b608c386a54500064f5f9c9d7019a4 ecology parents: diff changeset	400
89f977a3a256 planemo upload for repository https://github.com/Marie59/champ_blocs commit 0d86db7d42b608c386a54500064f5f9c9d7019a4 ecology parents: diff changeset	401 qecbnew$Nb.spirorbis.total <- as.integer(qecbnew$Nb.spirorbis.total)
89f977a3a256 planemo upload for repository https://github.com/Marie59/champ_blocs commit 0d86db7d42b608c386a54500064f5f9c9d7019a4 ecology parents: diff changeset	402 qecbnew$Nb.spirorbis.total.diff <- abs((qecbnew$Nb.spirorbis.total - qecbnew$mean.x.200))
89f977a3a256 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")]
89f977a3a256 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)
89f977a3a256 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))
89f977a3a256 planemo upload for repository https://github.com/Marie59/champ_blocs commit 0d86db7d42b608c386a54500064f5f9c9d7019a4 ecology parents: diff changeset	406
89f977a3a256 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$Nb.spirorbis.total)
89f977a3a256 planemo upload for repository https://github.com/Marie59/champ_blocs commit 0d86db7d42b608c386a54500064f5f9c9d7019a4 ecology parents: diff changeset	408 spirorbis_diff <- qecbnew[, c("Nb.spirorbis.1A", "Nb.spirorbis.2A", "Nb.spirorbis.3A", "Nb.spirorbis.4A", "Nb.spirorbis.5A", "Nb.spirorbis.total", "Nb.spirorbis.total.ini", "mean.x.200", "Nb.spirorbis.total.diff")]
89f977a3a256 planemo upload for repository https://github.com/Marie59/champ_blocs commit 0d86db7d42b608c386a54500064f5f9c9d7019a4 ecology parents: diff changeset	409 spirorbis_diff$Nb.spirorbis.total.diff <- abs(as.integer(spirorbis_diff$Nb.spirorbis.total.diff))
89f977a3a256 planemo upload for repository https://github.com/Marie59/champ_blocs commit 0d86db7d42b608c386a54500064f5f9c9d7019a4 ecology parents: diff changeset	410 spirorbis_diff <- dplyr::arrange(spirorbis_diff, desc(Nb.spirorbis.total.diff), mean.x.200)
89f977a3a256 planemo upload for repository https://github.com/Marie59/champ_blocs commit 0d86db7d42b608c386a54500064f5f9c9d7019a4 ecology parents: diff changeset	411 spirorbis_diff <- dplyr::arrange(dplyr::filter(spirorbis_diff, Nb.spirorbis.total.diff != 0 & mean.x.200 != 0), desc(Nb.spirorbis.total.diff))
89f977a3a256 planemo upload for repository https://github.com/Marie59/champ_blocs commit 0d86db7d42b608c386a54500064f5f9c9d7019a4 ecology parents: diff changeset	412 # ok, change made when data x 200 was not correct.
89f977a3a256 planemo upload for repository https://github.com/Marie59/champ_blocs commit 0d86db7d42b608c386a54500064f5f9c9d7019a4 ecology parents: diff changeset	413
89f977a3a256 planemo upload for repository https://github.com/Marie59/champ_blocs commit 0d86db7d42b608c386a54500064f5f9c9d7019a4 ecology parents: diff changeset	414 # finally, change NA by mean.x200 for spirorbis total
89f977a3a256 planemo upload for repository https://github.com/Marie59/champ_blocs commit 0d86db7d42b608c386a54500064f5f9c9d7019a4 ecology parents: diff changeset	415 qecbnew$Nb.spirorbis.total <- as.character(qecbnew$Nb.spirorbis.total)
89f977a3a256 planemo upload for repository https://github.com/Marie59/champ_blocs commit 0d86db7d42b608c386a54500064f5f9c9d7019a4 ecology parents: diff changeset	416 for (i in c(1:nrow(qecbnew))) {
89f977a3a256 planemo upload for repository https://github.com/Marie59/champ_blocs commit 0d86db7d42b608c386a54500064f5f9c9d7019a4 ecology parents: diff changeset	417 qecbnew$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]])
89f977a3a256 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
89f977a3a256 planemo upload for repository https://github.com/Marie59/champ_blocs commit 0d86db7d42b608c386a54500064f5f9c9d7019a4 ecology parents: diff changeset	419
89f977a3a256 planemo upload for repository https://github.com/Marie59/champ_blocs commit 0d86db7d42b608c386a54500064f5f9c9d7019a4 ecology parents: diff changeset	420 for (i in c(1:nrow(qecbnew))) {
89f977a3a256 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$Nb.spirorbis.total[[i]])
89f977a3a256 planemo upload for repository https://github.com/Marie59/champ_blocs commit 0d86db7d42b608c386a54500064f5f9c9d7019a4 ecology parents: diff changeset	422 }
89f977a3a256 planemo upload for repository https://github.com/Marie59/champ_blocs commit 0d86db7d42b608c386a54500064f5f9c9d7019a4 ecology parents: diff changeset	423
89f977a3a256 planemo upload for repository https://github.com/Marie59/champ_blocs commit 0d86db7d42b608c386a54500064f5f9c9d7019a4 ecology parents: diff changeset	424 qecbnew$Nb.spirorbis.total <- as.integer(qecbnew$Nb.spirorbis.total)
89f977a3a256 planemo upload for repository https://github.com/Marie59/champ_blocs commit 0d86db7d42b608c386a54500064f5f9c9d7019a4 ecology parents: diff changeset	425
89f977a3a256 planemo upload for repository https://github.com/Marie59/champ_blocs commit 0d86db7d42b608c386a54500064f5f9c9d7019a4 ecology parents: diff changeset	426 qecbnew$Nb.spirorbis.total.diff <- abs(qecbnew$Nb.spirorbis.total - qecbnew$Nb.spirorbis.total.ini)
89f977a3a256 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")]
89f977a3a256 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)
89f977a3a256 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))
89f977a3a256 planemo upload for repository https://github.com/Marie59/champ_blocs commit 0d86db7d42b608c386a54500064f5f9c9d7019a4 ecology parents: diff changeset	430
89f977a3a256 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))
89f977a3a256 planemo upload for repository https://github.com/Marie59/champ_blocs commit 0d86db7d42b608c386a54500064f5f9c9d7019a4 ecology parents: diff changeset	432
89f977a3a256 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)
89f977a3a256 planemo upload for repository https://github.com/Marie59/champ_blocs commit 0d86db7d42b608c386a54500064f5f9c9d7019a4 ecology parents: diff changeset	434
89f977a3a256 planemo upload for repository https://github.com/Marie59/champ_blocs commit 0d86db7d42b608c386a54500064f5f9c9d7019a4 ecology parents: diff changeset	435
89f977a3a256 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
89f977a3a256 planemo upload for repository https://github.com/Marie59/champ_blocs commit 0d86db7d42b608c386a54500064f5f9c9d7019a4 ecology parents: diff changeset	437
89f977a3a256 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")]
89f977a3a256 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$X..algues.brunes)
89f977a3a256 planemo upload for repository https://github.com/Marie59/champ_blocs commit 0d86db7d42b608c386a54500064f5f9c9d7019a4 ecology parents: diff changeset	440 dplyr::filter(qecbnew, X..algues.rouges > 100)[, c("Site", "date_fiche", "Type.Bloc", "Numéro.Bloc.échantillon", "Face", "X..algues.rouges")]
89f977a3a256 planemo upload for repository https://github.com/Marie59/champ_blocs commit 0d86db7d42b608c386a54500064f5f9c9d7019a4 ecology parents: diff changeset	441 qecbnew$X..algues.rouges <- ifelse(qecbnew$X..algues.rouges > 100, 100, qecbnew$X..algues.rouges)
89f977a3a256 planemo upload for repository https://github.com/Marie59/champ_blocs commit 0d86db7d42b608c386a54500064f5f9c9d7019a4 ecology parents: diff changeset	442
89f977a3a256 planemo upload for repository https://github.com/Marie59/champ_blocs commit 0d86db7d42b608c386a54500064f5f9c9d7019a4 ecology parents: diff changeset	443
89f977a3a256 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
89f977a3a256 planemo upload for repository https://github.com/Marie59/champ_blocs commit 0d86db7d42b608c386a54500064f5f9c9d7019a4 ecology parents: diff changeset	445
89f977a3a256 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 ...
89f977a3a256 planemo upload for repository https://github.com/Marie59/champ_blocs commit 0d86db7d42b608c386a54500064f5f9c9d7019a4 ecology parents: diff changeset	447 # I theregore change these NAs by 0
89f977a3a256 planemo upload for repository https://github.com/Marie59/champ_blocs commit 0d86db7d42b608c386a54500064f5f9c9d7019a4 ecology parents: diff changeset	448
89f977a3a256 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
89f977a3a256 planemo upload for repository https://github.com/Marie59/champ_blocs commit 0d86db7d42b608c386a54500064f5f9c9d7019a4 ecology parents: diff changeset	450 qecbnew[, c("X..algues.brunes",
89f977a3a256 planemo upload for repository https://github.com/Marie59/champ_blocs commit 0d86db7d42b608c386a54500064f5f9c9d7019a4 ecology parents: diff changeset	451 "X..algues.rouges",
89f977a3a256 planemo upload for repository https://github.com/Marie59/champ_blocs commit 0d86db7d42b608c386a54500064f5f9c9d7019a4 ecology parents: diff changeset	452 "X..Lithophyllum",
89f977a3a256 planemo upload for repository https://github.com/Marie59/champ_blocs commit 0d86db7d42b608c386a54500064f5f9c9d7019a4 ecology parents: diff changeset	453 "X..Cladophora",
89f977a3a256 planemo upload for repository https://github.com/Marie59/champ_blocs commit 0d86db7d42b608c386a54500064f5f9c9d7019a4 ecology parents: diff changeset	454 "Nb.Littorina.obtusata",
89f977a3a256 planemo upload for repository https://github.com/Marie59/champ_blocs commit 0d86db7d42b608c386a54500064f5f9c9d7019a4 ecology parents: diff changeset	455 "Nb.Gibbula.cineraria",
89f977a3a256 planemo upload for repository https://github.com/Marie59/champ_blocs commit 0d86db7d42b608c386a54500064f5f9c9d7019a4 ecology parents: diff changeset	456 "Nb.Gibbula.pennanti",
89f977a3a256 planemo upload for repository https://github.com/Marie59/champ_blocs commit 0d86db7d42b608c386a54500064f5f9c9d7019a4 ecology parents: diff changeset	457 "Nb.Gibbula.umbilicalis",
89f977a3a256 planemo upload for repository https://github.com/Marie59/champ_blocs commit 0d86db7d42b608c386a54500064f5f9c9d7019a4 ecology parents: diff changeset	458 "X..Eponges",
89f977a3a256 planemo upload for repository https://github.com/Marie59/champ_blocs commit 0d86db7d42b608c386a54500064f5f9c9d7019a4 ecology parents: diff changeset	459 "X..Ascidies.Coloniales",
89f977a3a256 planemo upload for repository https://github.com/Marie59/champ_blocs commit 0d86db7d42b608c386a54500064f5f9c9d7019a4 ecology parents: diff changeset	460 "X..Ascidies.Solitaires",
89f977a3a256 planemo upload for repository https://github.com/Marie59/champ_blocs commit 0d86db7d42b608c386a54500064f5f9c9d7019a4 ecology parents: diff changeset	461 "X..Bryozoaires.Dresses",
89f977a3a256 planemo upload for repository https://github.com/Marie59/champ_blocs commit 0d86db7d42b608c386a54500064f5f9c9d7019a4 ecology parents: diff changeset	462 "X..algues.vertes",
89f977a3a256 planemo upload for repository https://github.com/Marie59/champ_blocs commit 0d86db7d42b608c386a54500064f5f9c9d7019a4 ecology parents: diff changeset	463 "X..Roche.Nue",
89f977a3a256 planemo upload for repository https://github.com/Marie59/champ_blocs commit 0d86db7d42b608c386a54500064f5f9c9d7019a4 ecology parents: diff changeset	464 "Nb.spirorbis.total",
89f977a3a256 planemo upload for repository https://github.com/Marie59/champ_blocs commit 0d86db7d42b608c386a54500064f5f9c9d7019a4 ecology parents: diff changeset	465 "X..Balanes.Vivantes",
89f977a3a256 planemo upload for repository https://github.com/Marie59/champ_blocs commit 0d86db7d42b608c386a54500064f5f9c9d7019a4 ecology parents: diff changeset	466 "Nb.Spirobranchus.lamarckii.total",
89f977a3a256 planemo upload for repository https://github.com/Marie59/champ_blocs commit 0d86db7d42b608c386a54500064f5f9c9d7019a4 ecology parents: diff changeset	467 "X..Surface.Accolement")] <- lapply(qecbnew[,
89f977a3a256 planemo upload for repository https://github.com/Marie59/champ_blocs commit 0d86db7d42b608c386a54500064f5f9c9d7019a4 ecology parents: diff changeset	468 c("X..algues.brunes",
89f977a3a256 planemo upload for repository https://github.com/Marie59/champ_blocs commit 0d86db7d42b608c386a54500064f5f9c9d7019a4 ecology parents: diff changeset	469 "X..algues.rouges",
89f977a3a256 planemo upload for repository https://github.com/Marie59/champ_blocs commit 0d86db7d42b608c386a54500064f5f9c9d7019a4 ecology parents: diff changeset	470 "X..Lithophyllum",
89f977a3a256 planemo upload for repository https://github.com/Marie59/champ_blocs commit 0d86db7d42b608c386a54500064f5f9c9d7019a4 ecology parents: diff changeset	471 "X..Cladophora",
89f977a3a256 planemo upload for repository https://github.com/Marie59/champ_blocs commit 0d86db7d42b608c386a54500064f5f9c9d7019a4 ecology parents: diff changeset	472 "Nb.Littorina.obtusata",
89f977a3a256 planemo upload for repository https://github.com/Marie59/champ_blocs commit 0d86db7d42b608c386a54500064f5f9c9d7019a4 ecology parents: diff changeset	473 "Nb.Gibbula.cineraria",
89f977a3a256 planemo upload for repository https://github.com/Marie59/champ_blocs commit 0d86db7d42b608c386a54500064f5f9c9d7019a4 ecology parents: diff changeset	474 "Nb.Gibbula.pennanti",
89f977a3a256 planemo upload for repository https://github.com/Marie59/champ_blocs commit 0d86db7d42b608c386a54500064f5f9c9d7019a4 ecology parents: diff changeset	475 "Nb.Gibbula.umbilicalis",
89f977a3a256 planemo upload for repository https://github.com/Marie59/champ_blocs commit 0d86db7d42b608c386a54500064f5f9c9d7019a4 ecology parents: diff changeset	476 "X..Eponges",
89f977a3a256 planemo upload for repository https://github.com/Marie59/champ_blocs commit 0d86db7d42b608c386a54500064f5f9c9d7019a4 ecology parents: diff changeset	477 "X..Ascidies.Coloniales",
89f977a3a256 planemo upload for repository https://github.com/Marie59/champ_blocs commit 0d86db7d42b608c386a54500064f5f9c9d7019a4 ecology parents: diff changeset	478 "X..Ascidies.Solitaires",
89f977a3a256 planemo upload for repository https://github.com/Marie59/champ_blocs commit 0d86db7d42b608c386a54500064f5f9c9d7019a4 ecology parents: diff changeset	479 "X..Bryozoaires.Dresses",
89f977a3a256 planemo upload for repository https://github.com/Marie59/champ_blocs commit 0d86db7d42b608c386a54500064f5f9c9d7019a4 ecology parents: diff changeset	480 "X..algues.vertes",
89f977a3a256 planemo upload for repository https://github.com/Marie59/champ_blocs commit 0d86db7d42b608c386a54500064f5f9c9d7019a4 ecology parents: diff changeset	481 "X..Roche.Nue",
89f977a3a256 planemo upload for repository https://github.com/Marie59/champ_blocs commit 0d86db7d42b608c386a54500064f5f9c9d7019a4 ecology parents: diff changeset	482 "Nb.spirorbis.total",
89f977a3a256 planemo upload for repository https://github.com/Marie59/champ_blocs commit 0d86db7d42b608c386a54500064f5f9c9d7019a4 ecology parents: diff changeset	483 "X..Balanes.Vivantes",
89f977a3a256 planemo upload for repository https://github.com/Marie59/champ_blocs commit 0d86db7d42b608c386a54500064f5f9c9d7019a4 ecology parents: diff changeset	484 "Nb.Spirobranchus.lamarckii.total",
89f977a3a256 planemo upload for repository https://github.com/Marie59/champ_blocs commit 0d86db7d42b608c386a54500064f5f9c9d7019a4 ecology parents: diff changeset	485 "X..Surface.Accolement")],
89f977a3a256 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))
89f977a3a256 planemo upload for repository https://github.com/Marie59/champ_blocs commit 0d86db7d42b608c386a54500064f5f9c9d7019a4 ecology parents: diff changeset	487
89f977a3a256 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.
89f977a3a256 planemo upload for repository https://github.com/Marie59/champ_blocs commit 0d86db7d42b608c386a54500064f5f9c9d7019a4 ecology parents: diff changeset	489
89f977a3a256 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.)
89f977a3a256 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)
89f977a3a256 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)
89f977a3a256 planemo upload for repository https://github.com/Marie59/champ_blocs commit 0d86db7d42b608c386a54500064f5f9c9d7019a4 ecology parents: diff changeset	493
89f977a3a256 planemo upload for repository https://github.com/Marie59/champ_blocs commit 0d86db7d42b608c386a54500064f5f9c9d7019a4 ecology parents: diff changeset	494
89f977a3a256 planemo upload for repository https://github.com/Marie59/champ_blocs commit 0d86db7d42b608c386a54500064f5f9c9d7019a4 ecology parents: diff changeset	495 # add a region variable
89f977a3a256 planemo upload for repository https://github.com/Marie59/champ_blocs commit 0d86db7d42b608c386a54500064f5f9c9d7019a4 ecology parents: diff changeset	496 region <- rep(NA, nrow(qecbnew))
89f977a3a256 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")
89f977a3a256 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")
89f977a3a256 planemo upload for repository https://github.com/Marie59/champ_blocs commit 0d86db7d42b608c386a54500064f5f9c9d7019a4 ecology parents: diff changeset	499 rm(region)
89f977a3a256 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)
89f977a3a256 planemo upload for repository https://github.com/Marie59/champ_blocs commit 0d86db7d42b608c386a54500064f5f9c9d7019a4 ecology parents: diff changeset	501
89f977a3a256 planemo upload for repository https://github.com/Marie59/champ_blocs commit 0d86db7d42b608c386a54500064f5f9c9d7019a4 ecology parents: diff changeset	502 # accolement function according to recent 'retournement'
89f977a3a256 planemo upload for repository https://github.com/Marie59/champ_blocs commit 0d86db7d42b608c386a54500064f5f9c9d7019a4 ecology parents: diff changeset	503
89f977a3a256 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 !!
89f977a3a256 planemo upload for repository https://github.com/Marie59/champ_blocs commit 0d86db7d42b608c386a54500064f5f9c9d7019a4 ecology parents: diff changeset	505
89f977a3a256 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.
89f977a3a256 planemo upload for repository https://github.com/Marie59/champ_blocs commit 0d86db7d42b608c386a54500064f5f9c9d7019a4 ecology parents: diff changeset	507
89f977a3a256 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$Site, 1, 4), .after = "Site_bis")
89f977a3a256 planemo upload for repository https://github.com/Marie59/champ_blocs commit 0d86db7d42b608c386a54500064f5f9c9d7019a4 ecology parents: diff changeset	509
89f977a3a256 planemo upload for repository https://github.com/Marie59/champ_blocs commit 0d86db7d42b608c386a54500064f5f9c9d7019a4 ecology parents: diff changeset	510 qecbnew$X..Eponges_ini <- qecbnew$X..Eponges
89f977a3a256 planemo upload for repository https://github.com/Marie59/champ_blocs commit 0d86db7d42b608c386a54500064f5f9c9d7019a4 ecology parents: diff changeset	511 qecbnew$X..Ascidies.Coloniales_ini <- qecbnew$X..Ascidies.Coloniales
89f977a3a256 planemo upload for repository https://github.com/Marie59/champ_blocs commit 0d86db7d42b608c386a54500064f5f9c9d7019a4 ecology parents: diff changeset	512 qecbnew$X..Ascidies.Solitaires_ini <- qecbnew$X..Ascidies.Solitaires
89f977a3a256 planemo upload for repository https://github.com/Marie59/champ_blocs commit 0d86db7d42b608c386a54500064f5f9c9d7019a4 ecology parents: diff changeset	513 qecbnew$X..Bryozoaires.Dresses_ini <- qecbnew$X..Bryozoaires.Dresses
89f977a3a256 planemo upload for repository https://github.com/Marie59/champ_blocs commit 0d86db7d42b608c386a54500064f5f9c9d7019a4 ecology parents: diff changeset	514 qecbnew$X..Lithophyllum_ini <- qecbnew$X..Lithophyllum
89f977a3a256 planemo upload for repository https://github.com/Marie59/champ_blocs commit 0d86db7d42b608c386a54500064f5f9c9d7019a4 ecology parents: diff changeset	515 qecbnew$X..Balanes.Vivantes_ini <- qecbnew$X..Balanes.Vivantes
89f977a3a256 planemo upload for repository https://github.com/Marie59/champ_blocs commit 0d86db7d42b608c386a54500064f5f9c9d7019a4 ecology parents: diff changeset	516
89f977a3a256 planemo upload for repository https://github.com/Marie59/champ_blocs commit 0d86db7d42b608c386a54500064f5f9c9d7019a4 ecology parents: diff changeset	517 df_bm_fs <- qecbnew %>% dplyr::filter(Type.Bloc == "Bloc mobile" & Face == "face supérieure")
89f977a3a256 planemo upload for repository https://github.com/Marie59/champ_blocs commit 0d86db7d42b608c386a54500064f5f9c9d7019a4 ecology parents: diff changeset	518 df_bm_fi <- qecbnew %>% dplyr::filter(Type.Bloc == "Bloc mobile" & Face == "face inférieure")
89f977a3a256 planemo upload for repository https://github.com/Marie59/champ_blocs commit 0d86db7d42b608c386a54500064f5f9c9d7019a4 ecology parents: diff changeset	519 df_bf <- qecbnew %>% dplyr::filter(Type.Bloc != "Bloc mobile")
89f977a3a256 planemo upload for repository https://github.com/Marie59/champ_blocs commit 0d86db7d42b608c386a54500064f5f9c9d7019a4 ecology parents: diff changeset	520
89f977a3a256 planemo upload for repository https://github.com/Marie59/champ_blocs commit 0d86db7d42b608c386a54500064f5f9c9d7019a4 ecology parents: diff changeset	521 `%notin%` <- Negate(`%in%`)
89f977a3a256 planemo upload for repository https://github.com/Marie59/champ_blocs commit 0d86db7d42b608c386a54500064f5f9c9d7019a4 ecology parents: diff changeset	522
89f977a3a256 planemo upload for repository https://github.com/Marie59/champ_blocs commit 0d86db7d42b608c386a54500064f5f9c9d7019a4 ecology parents: diff changeset	523 acco_fct <- function(var_) {
89f977a3a256 planemo upload for repository https://github.com/Marie59/champ_blocs commit 0d86db7d42b608c386a54500064f5f9c9d7019a4 ecology parents: diff changeset	524
89f977a3a256 planemo upload for repository https://github.com/Marie59/champ_blocs commit 0d86db7d42b608c386a54500064f5f9c9d7019a4 ecology parents: diff changeset	525 df_bm_fi$var_cor.acco. <<- NA
89f977a3a256 planemo upload for repository https://github.com/Marie59/champ_blocs commit 0d86db7d42b608c386a54500064f5f9c9d7019a4 ecology parents: diff changeset	526
89f977a3a256 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))) {
89f977a3a256 planemo upload for repository https://github.com/Marie59/champ_blocs commit 0d86db7d42b608c386a54500064f5f9c9d7019a4 ecology parents: diff changeset	528
89f977a3a256 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")) {
89f977a3a256 planemo upload for repository https://github.com/Marie59/champ_blocs commit 0d86db7d42b608c386a54500064f5f9c9d7019a4 ecology parents: diff changeset	530 ifelse(#df_$Couleur.dominante %in% c("Rouge", "Brune", "Brune-Rouge") \|\|
89f977a3a256 planemo upload for repository https://github.com/Marie59/champ_blocs commit 0d86db7d42b608c386a54500064f5f9c9d7019a4 ecology parents: diff changeset	531 df_bm_fs$Couleur.dominante[[i]] %in% c("Blanche", "Verte", "Blanche-Verte", "Colorée"), df_bm_fi[i, var_] / (100 - df_bm_fi$X..Surface.Accolement[[i]]) * 100, df_bm_fi[i, var_])
89f977a3a256 planemo upload for repository https://github.com/Marie59/champ_blocs commit 0d86db7d42b608c386a54500064f5f9c9d7019a4 ecology parents: diff changeset	532 } else {
89f977a3a256 planemo upload for repository https://github.com/Marie59/champ_blocs commit 0d86db7d42b608c386a54500064f5f9c9d7019a4 ecology parents: diff changeset	533 ifelse(df_bm_fs$Couleur.dominante[[i]] %in% c("Blanche", "Verte", "Blanche-Verte", "Colorée")
89f977a3a256 planemo upload for repository https://github.com/Marie59/champ_blocs commit 0d86db7d42b608c386a54500064f5f9c9d7019a4 ecology parents: diff changeset	534 & df_bm_fi$X..Surface.Accolement[[i]] != 0 # I have to use it in dplyr::filter this time as well for EGMP- BASQ (but not for Bretagne, although could be added, same result); identical/repeated measure for BM.FI and BM.FS
89f977a3a256 planemo upload for repository https://github.com/Marie59/champ_blocs commit 0d86db7d42b608c386a54500064f5f9c9d7019a4 ecology parents: diff changeset	535 & df_bm_fs$X..Mytilus.sp.[[i]] == 0, df_bm_fi[i, var_] / (100 - df_bm_fi$X..Surface.Accolement[[i]]) * 100, df_bm_fi[i, var_])
89f977a3a256 planemo upload for repository https://github.com/Marie59/champ_blocs commit 0d86db7d42b608c386a54500064f5f9c9d7019a4 ecology parents: diff changeset	536 }
89f977a3a256 planemo upload for repository https://github.com/Marie59/champ_blocs commit 0d86db7d42b608c386a54500064f5f9c9d7019a4 ecology parents: diff changeset	537
89f977a3a256 planemo upload for repository https://github.com/Marie59/champ_blocs commit 0d86db7d42b608c386a54500064f5f9c9d7019a4 ecology parents: diff changeset	538 }
89f977a3a256 planemo upload for repository https://github.com/Marie59/champ_blocs commit 0d86db7d42b608c386a54500064f5f9c9d7019a4 ecology parents: diff changeset	539
89f977a3a256 planemo upload for repository https://github.com/Marie59/champ_blocs commit 0d86db7d42b608c386a54500064f5f9c9d7019a4 ecology parents: diff changeset	540 }
89f977a3a256 planemo upload for repository https://github.com/Marie59/champ_blocs commit 0d86db7d42b608c386a54500064f5f9c9d7019a4 ecology parents: diff changeset	541
89f977a3a256 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 !!!
89f977a3a256 planemo upload for repository https://github.com/Marie59/champ_blocs commit 0d86db7d42b608c386a54500064f5f9c9d7019a4 ecology parents: diff changeset	543
89f977a3a256 planemo upload for repository https://github.com/Marie59/champ_blocs commit 0d86db7d42b608c386a54500064f5f9c9d7019a4 ecology parents: diff changeset	544
89f977a3a256 planemo upload for repository https://github.com/Marie59/champ_blocs commit 0d86db7d42b608c386a54500064f5f9c9d7019a4 ecology parents: diff changeset	545 # apply acco_fct to BM.FI variables
89f977a3a256 planemo upload for repository https://github.com/Marie59/champ_blocs commit 0d86db7d42b608c386a54500064f5f9c9d7019a4 ecology parents: diff changeset	546
89f977a3a256 planemo upload for repository https://github.com/Marie59/champ_blocs commit 0d86db7d42b608c386a54500064f5f9c9d7019a4 ecology parents: diff changeset	547 apply_acco_fct <- function(var_) {
89f977a3a256 planemo upload for repository https://github.com/Marie59/champ_blocs commit 0d86db7d42b608c386a54500064f5f9c9d7019a4 ecology parents: diff changeset	548
89f977a3a256 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])
89f977a3a256 planemo upload for repository https://github.com/Marie59/champ_blocs commit 0d86db7d42b608c386a54500064f5f9c9d7019a4 ecology parents: diff changeset	550 pre_ <- as.vector(df_bm_fi[, var_])
89f977a3a256 planemo upload for repository https://github.com/Marie59/champ_blocs commit 0d86db7d42b608c386a54500064f5f9c9d7019a4 ecology parents: diff changeset	551 acco_fct(var_)
89f977a3a256 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_)
89f977a3a256 planemo upload for repository https://github.com/Marie59/champ_blocs commit 0d86db7d42b608c386a54500064f5f9c9d7019a4 ecology parents: diff changeset	553 show(sort(df_bm_fi$var_cor., decreasing = TRUE, index.return = FALSE)[1:50])
89f977a3a256 planemo upload for repository https://github.com/Marie59/champ_blocs commit 0d86db7d42b608c386a54500064f5f9c9d7019a4 ecology parents: diff changeset	554 df_bm_fi$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.)))
89f977a3a256 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$var_cor.)
89f977a3a256 planemo upload for repository https://github.com/Marie59/champ_blocs commit 0d86db7d42b608c386a54500064f5f9c9d7019a4 ecology parents: diff changeset	556 show(sort(df_bm_fi$var_cor., decreasing = TRUE, index.return = FALSE)[1:50])
89f977a3a256 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)
89f977a3a256 planemo upload for repository https://github.com/Marie59/champ_blocs commit 0d86db7d42b608c386a54500064f5f9c9d7019a4 ecology parents: diff changeset	558 par(mfrow = c(1, 3))
89f977a3a256 planemo upload for repository https://github.com/Marie59/champ_blocs commit 0d86db7d42b608c386a54500064f5f9c9d7019a4 ecology parents: diff changeset	559 hist(pre_, main = var_, xlab = "pre-corection")
89f977a3a256 planemo upload for repository https://github.com/Marie59/champ_blocs commit 0d86db7d42b608c386a54500064f5f9c9d7019a4 ecology parents: diff changeset	560 hist(df_bm_fi$var_cor., main = var_, xlab = "post-corection")
89f977a3a256 planemo upload for repository https://github.com/Marie59/champ_blocs commit 0d86db7d42b608c386a54500064f5f9c9d7019a4 ecology parents: diff changeset	561 hist(df_bm_fi[as.vector(which(abs(as.vector(df_bm_fi$var_cor.) - pre_) != 0)), var_], main = var_, xlab = "diff. post-pre != 0")
89f977a3a256 planemo upload for repository https://github.com/Marie59/champ_blocs commit 0d86db7d42b608c386a54500064f5f9c9d7019a4 ecology parents: diff changeset	562 par(mfrow = c(1, 1))
89f977a3a256 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."))]
89f977a3a256 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_
89f977a3a256 planemo upload for repository https://github.com/Marie59/champ_blocs commit 0d86db7d42b608c386a54500064f5f9c9d7019a4 ecology parents: diff changeset	565
89f977a3a256 planemo upload for repository https://github.com/Marie59/champ_blocs commit 0d86db7d42b608c386a54500064f5f9c9d7019a4 ecology parents: diff changeset	566 rm(pre_)
89f977a3a256 planemo upload for repository https://github.com/Marie59/champ_blocs commit 0d86db7d42b608c386a54500064f5f9c9d7019a4 ecology parents: diff changeset	567
89f977a3a256 planemo upload for repository https://github.com/Marie59/champ_blocs commit 0d86db7d42b608c386a54500064f5f9c9d7019a4 ecology parents: diff changeset	568 }
89f977a3a256 planemo upload for repository https://github.com/Marie59/champ_blocs commit 0d86db7d42b608c386a54500064f5f9c9d7019a4 ecology parents: diff changeset	569
89f977a3a256 planemo upload for repository https://github.com/Marie59/champ_blocs commit 0d86db7d42b608c386a54500064f5f9c9d7019a4 ecology parents: diff changeset	570 apply_acco_fct("X..Eponges")
89f977a3a256 planemo upload for repository https://github.com/Marie59/champ_blocs commit 0d86db7d42b608c386a54500064f5f9c9d7019a4 ecology parents: diff changeset	571 apply_acco_fct("X..Ascidies.Coloniales")
89f977a3a256 planemo upload for repository https://github.com/Marie59/champ_blocs commit 0d86db7d42b608c386a54500064f5f9c9d7019a4 ecology parents: diff changeset	572 apply_acco_fct("X..Ascidies.Solitaires")
89f977a3a256 planemo upload for repository https://github.com/Marie59/champ_blocs commit 0d86db7d42b608c386a54500064f5f9c9d7019a4 ecology parents: diff changeset	573 apply_acco_fct("X..Bryozoaires.Dresses")
89f977a3a256 planemo upload for repository https://github.com/Marie59/champ_blocs commit 0d86db7d42b608c386a54500064f5f9c9d7019a4 ecology parents: diff changeset	574 apply_acco_fct("X..Lithophyllum")
89f977a3a256 planemo upload for repository https://github.com/Marie59/champ_blocs commit 0d86db7d42b608c386a54500064f5f9c9d7019a4 ecology parents: diff changeset	575 apply_acco_fct("X..Balanes.Vivantes")
89f977a3a256 planemo upload for repository https://github.com/Marie59/champ_blocs commit 0d86db7d42b608c386a54500064f5f9c9d7019a4 ecology parents: diff changeset	576
89f977a3a256 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)
89f977a3a256 planemo upload for repository https://github.com/Marie59/champ_blocs commit 0d86db7d42b608c386a54500064f5f9c9d7019a4 ecology parents: diff changeset	578 qecbnew <- dplyr::bind_rows(qecbnew, df_bf)
89f977a3a256 planemo upload for repository https://github.com/Marie59/champ_blocs commit 0d86db7d42b608c386a54500064f5f9c9d7019a4 ecology parents: diff changeset	579
89f977a3a256 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)
89f977a3a256 planemo upload for repository https://github.com/Marie59/champ_blocs commit 0d86db7d42b608c386a54500064f5f9c9d7019a4 ecology parents: diff changeset	581
89f977a3a256 planemo upload for repository https://github.com/Marie59/champ_blocs commit 0d86db7d42b608c386a54500064f5f9c9d7019a4 ecology parents: diff changeset	582 # do remove some more data ...
89f977a3a256 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
89f977a3a256 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")
89f977a3a256 planemo upload for repository https://github.com/Marie59/champ_blocs commit 0d86db7d42b608c386a54500064f5f9c9d7019a4 ecology parents: diff changeset	585
89f977a3a256 planemo upload for repository https://github.com/Marie59/champ_blocs commit 0d86db7d42b608c386a54500064f5f9c9d7019a4 ecology parents: diff changeset	586 # save the final qecbnew df_
89f977a3a256 planemo upload for repository https://github.com/Marie59/champ_blocs commit 0d86db7d42b608c386a54500064f5f9c9d7019a4 ecology parents: diff changeset	587
89f977a3a256 planemo upload for repository https://github.com/Marie59/champ_blocs commit 0d86db7d42b608c386a54500064f5f9c9d7019a4 ecology parents: diff changeset	588 qecb <- qecbnew
89f977a3a256 planemo upload for repository https://github.com/Marie59/champ_blocs commit 0d86db7d42b608c386a54500064f5f9c9d7019a4 ecology parents: diff changeset	589
89f977a3a256 planemo upload for repository https://github.com/Marie59/champ_blocs commit 0d86db7d42b608c386a54500064f5f9c9d7019a4 ecology parents: diff changeset	590
89f977a3a256 planemo upload for repository https://github.com/Marie59/champ_blocs commit 0d86db7d42b608c386a54500064f5f9c9d7019a4 ecology parents: diff changeset	591 `%notin%` <- Negate(`%in%`)
89f977a3a256 planemo upload for repository https://github.com/Marie59/champ_blocs commit 0d86db7d42b608c386a54500064f5f9c9d7019a4 ecology parents: diff changeset	592
89f977a3a256 planemo upload for repository https://github.com/Marie59/champ_blocs commit 0d86db7d42b608c386a54500064f5f9c9d7019a4 ecology parents: diff changeset	593 ## reorder and/or create new variables
89f977a3a256 planemo upload for repository https://github.com/Marie59/champ_blocs commit 0d86db7d42b608c386a54500064f5f9c9d7019a4 ecology parents: diff changeset	594
89f977a3a256 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
89f977a3a256 planemo upload for repository https://github.com/Marie59/champ_blocs commit 0d86db7d42b608c386a54500064f5f9c9d7019a4 ecology parents: diff changeset	596 qecb <- tibble::add_column(qecb, qecb$site_year_month_day, .after = "Site_bis")
89f977a3a256 planemo upload for repository https://github.com/Marie59/champ_blocs commit 0d86db7d42b608c386a54500064f5f9c9d7019a4 ecology parents: diff changeset	597 qecb <- qecb[, -which(names(qecb) %in% c("site_year_month_day"))]
89f977a3a256 planemo upload for repository https://github.com/Marie59/champ_blocs commit 0d86db7d42b608c386a54500064f5f9c9d7019a4 ecology parents: diff changeset	598 qecb <- dplyr::rename(qecb, site_year_month_day = `qecb$site_year_month_day`)
89f977a3a256 planemo upload for repository https://github.com/Marie59/champ_blocs commit 0d86db7d42b608c386a54500064f5f9c9d7019a4 ecology parents: diff changeset	599
89f977a3a256 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)
89f977a3a256 planemo upload for repository https://github.com/Marie59/champ_blocs commit 0d86db7d42b608c386a54500064f5f9c9d7019a4 ecology parents: diff changeset	601 period <- rep(NA, nrow(qecb))
89f977a3a256 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")
89f977a3a256 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")
89f977a3a256 planemo upload for repository https://github.com/Marie59/champ_blocs commit 0d86db7d42b608c386a54500064f5f9c9d7019a4 ecology parents: diff changeset	604 qecb$period <- as.factor(qecb$period)
89f977a3a256 planemo upload for repository https://github.com/Marie59/champ_blocs commit 0d86db7d42b608c386a54500064f5f9c9d7019a4 ecology parents: diff changeset	605 rm(period)
89f977a3a256 planemo upload for repository https://github.com/Marie59/champ_blocs commit 0d86db7d42b608c386a54500064f5f9c9d7019a4 ecology parents: diff changeset	606
89f977a3a256 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)
89f977a3a256 planemo upload for repository https://github.com/Marie59/champ_blocs commit 0d86db7d42b608c386a54500064f5f9c9d7019a4 ecology parents: diff changeset	608
89f977a3a256 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 ...)
89f977a3a256 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.
89f977a3a256 planemo upload for repository https://github.com/Marie59/champ_blocs commit 0d86db7d42b608c386a54500064f5f9c9d7019a4 ecology parents: diff changeset	611
89f977a3a256 planemo upload for repository https://github.com/Marie59/champ_blocs commit 0d86db7d42b608c386a54500064f5f9c9d7019a4 ecology parents: diff changeset	612 ## SCRIPT I - NAs <- 0
89f977a3a256 planemo upload for repository https://github.com/Marie59/champ_blocs commit 0d86db7d42b608c386a54500064f5f9c9d7019a4 ecology parents: diff changeset	613
89f977a3a256 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 ...
89f977a3a256 planemo upload for repository https://github.com/Marie59/champ_blocs commit 0d86db7d42b608c386a54500064f5f9c9d7019a4 ecology parents: diff changeset	615
89f977a3a256 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")
89f977a3a256 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"))
89f977a3a256 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")
89f977a3a256 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"))
89f977a3a256 planemo upload for repository https://github.com/Marie59/champ_blocs commit 0d86db7d42b608c386a54500064f5f9c9d7019a4 ecology parents: diff changeset	620
89f977a3a256 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
89f977a3a256 planemo upload for repository https://github.com/Marie59/champ_blocs commit 0d86db7d42b608c386a54500064f5f9c9d7019a4 ecology parents: diff changeset	622
89f977a3a256 planemo upload for repository https://github.com/Marie59/champ_blocs commit 0d86db7d42b608c386a54500064f5f9c9d7019a4 ecology parents: diff changeset	623 bretagne_bm[, c(
89f977a3a256 planemo upload for repository https://github.com/Marie59/champ_blocs commit 0d86db7d42b608c386a54500064f5f9c9d7019a4 ecology parents: diff changeset	624 "X..algues.brunes",
89f977a3a256 planemo upload for repository https://github.com/Marie59/champ_blocs commit 0d86db7d42b608c386a54500064f5f9c9d7019a4 ecology parents: diff changeset	625 "Strate.algues.brunes",
89f977a3a256 planemo upload for repository https://github.com/Marie59/champ_blocs commit 0d86db7d42b608c386a54500064f5f9c9d7019a4 ecology parents: diff changeset	626 "X..algues.rouges",
89f977a3a256 planemo upload for repository https://github.com/Marie59/champ_blocs commit 0d86db7d42b608c386a54500064f5f9c9d7019a4 ecology parents: diff changeset	627 "Strate.algues.rouges",
89f977a3a256 planemo upload for repository https://github.com/Marie59/champ_blocs commit 0d86db7d42b608c386a54500064f5f9c9d7019a4 ecology parents: diff changeset	628 "X..algues.vertes",
89f977a3a256 planemo upload for repository https://github.com/Marie59/champ_blocs commit 0d86db7d42b608c386a54500064f5f9c9d7019a4 ecology parents: diff changeset	629 "Strate.algues.vertes",
89f977a3a256 planemo upload for repository https://github.com/Marie59/champ_blocs commit 0d86db7d42b608c386a54500064f5f9c9d7019a4 ecology parents: diff changeset	630 "X..Cladophora",
89f977a3a256 planemo upload for repository https://github.com/Marie59/champ_blocs commit 0d86db7d42b608c386a54500064f5f9c9d7019a4 ecology parents: diff changeset	631 "X..Lithophyllum",
89f977a3a256 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.
89f977a3a256 planemo upload for repository https://github.com/Marie59/champ_blocs commit 0d86db7d42b608c386a54500064f5f9c9d7019a4 ecology parents: diff changeset	633 #"Type.Sediment",
89f977a3a256 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.
89f977a3a256 planemo upload for repository https://github.com/Marie59/champ_blocs commit 0d86db7d42b608c386a54500064f5f9c9d7019a4 ecology parents: diff changeset	635 "Nb.Littorina.obtusata",
89f977a3a256 planemo upload for repository https://github.com/Marie59/champ_blocs commit 0d86db7d42b608c386a54500064f5f9c9d7019a4 ecology parents: diff changeset	636 "Nb.Gibbula.cineraria",
89f977a3a256 planemo upload for repository https://github.com/Marie59/champ_blocs commit 0d86db7d42b608c386a54500064f5f9c9d7019a4 ecology parents: diff changeset	637 "Nb.Gibbula.pennanti",
89f977a3a256 planemo upload for repository https://github.com/Marie59/champ_blocs commit 0d86db7d42b608c386a54500064f5f9c9d7019a4 ecology parents: diff changeset	638 "Nb.Gibbula.umbilicalis",
89f977a3a256 planemo upload for repository https://github.com/Marie59/champ_blocs commit 0d86db7d42b608c386a54500064f5f9c9d7019a4 ecology parents: diff changeset	639 "Nb.Phallusia.mamillata",
89f977a3a256 planemo upload for repository https://github.com/Marie59/champ_blocs commit 0d86db7d42b608c386a54500064f5f9c9d7019a4 ecology parents: diff changeset	640 "Nb.Tethya.aurantium",
89f977a3a256 planemo upload for repository https://github.com/Marie59/champ_blocs commit 0d86db7d42b608c386a54500064f5f9c9d7019a4 ecology parents: diff changeset	641 #"Nb.Spirobranchus.lamarckii.1B",
89f977a3a256 planemo upload for repository https://github.com/Marie59/champ_blocs commit 0d86db7d42b608c386a54500064f5f9c9d7019a4 ecology parents: diff changeset	642 #"Nb.Spirobranchus.lamarckii.2B",
89f977a3a256 planemo upload for repository https://github.com/Marie59/champ_blocs commit 0d86db7d42b608c386a54500064f5f9c9d7019a4 ecology parents: diff changeset	643 #"Nb.Spirobranchus.lamarckii.3B",
89f977a3a256 planemo upload for repository https://github.com/Marie59/champ_blocs commit 0d86db7d42b608c386a54500064f5f9c9d7019a4 ecology parents: diff changeset	644 #"Nb.Spirobranchus.lamarckii.4B",
89f977a3a256 planemo upload for repository https://github.com/Marie59/champ_blocs commit 0d86db7d42b608c386a54500064f5f9c9d7019a4 ecology parents: diff changeset	645 #"Nb.Spirobranchus.lamarckii.5B",
89f977a3a256 planemo upload for repository https://github.com/Marie59/champ_blocs commit 0d86db7d42b608c386a54500064f5f9c9d7019a4 ecology parents: diff changeset	646 "Nb.Spirobranchus.lamarckii.total",
89f977a3a256 planemo upload for repository https://github.com/Marie59/champ_blocs commit 0d86db7d42b608c386a54500064f5f9c9d7019a4 ecology parents: diff changeset	647 #"Nb.spirorbis.1A",
89f977a3a256 planemo upload for repository https://github.com/Marie59/champ_blocs commit 0d86db7d42b608c386a54500064f5f9c9d7019a4 ecology parents: diff changeset	648 #"Nb.spirorbis.2A",
89f977a3a256 planemo upload for repository https://github.com/Marie59/champ_blocs commit 0d86db7d42b608c386a54500064f5f9c9d7019a4 ecology parents: diff changeset	649 #"Nb.spirorbis.3A",
89f977a3a256 planemo upload for repository https://github.com/Marie59/champ_blocs commit 0d86db7d42b608c386a54500064f5f9c9d7019a4 ecology parents: diff changeset	650 #"Nb.spirorbis.4A",
89f977a3a256 planemo upload for repository https://github.com/Marie59/champ_blocs commit 0d86db7d42b608c386a54500064f5f9c9d7019a4 ecology parents: diff changeset	651 #"Nb.spirorbis.5A",
89f977a3a256 planemo upload for repository https://github.com/Marie59/champ_blocs commit 0d86db7d42b608c386a54500064f5f9c9d7019a4 ecology parents: diff changeset	652 "Nb.spirorbis.total",
89f977a3a256 planemo upload for repository https://github.com/Marie59/champ_blocs commit 0d86db7d42b608c386a54500064f5f9c9d7019a4 ecology parents: diff changeset	653 #.."Nb.Crassostrea.gigas",
89f977a3a256 planemo upload for repository https://github.com/Marie59/champ_blocs commit 0d86db7d42b608c386a54500064f5f9c9d7019a4 ecology parents: diff changeset	654 #.."Nb.Ostrea.edulis",
89f977a3a256 planemo upload for repository https://github.com/Marie59/champ_blocs commit 0d86db7d42b608c386a54500064f5f9c9d7019a4 ecology parents: diff changeset	655 #.."X..Mytilus.sp.",
89f977a3a256 planemo upload for repository https://github.com/Marie59/champ_blocs commit 0d86db7d42b608c386a54500064f5f9c9d7019a4 ecology parents: diff changeset	656 #.."X..Hermelles",
89f977a3a256 planemo upload for repository https://github.com/Marie59/champ_blocs commit 0d86db7d42b608c386a54500064f5f9c9d7019a4 ecology parents: diff changeset	657 #.."X..Hydraires",
89f977a3a256 planemo upload for repository https://github.com/Marie59/champ_blocs commit 0d86db7d42b608c386a54500064f5f9c9d7019a4 ecology parents: diff changeset	658 "X..Eponges",
89f977a3a256 planemo upload for repository https://github.com/Marie59/champ_blocs commit 0d86db7d42b608c386a54500064f5f9c9d7019a4 ecology parents: diff changeset	659 "X..Ascidies.Coloniales",
89f977a3a256 planemo upload for repository https://github.com/Marie59/champ_blocs commit 0d86db7d42b608c386a54500064f5f9c9d7019a4 ecology parents: diff changeset	660 "X..Ascidies.Solitaires",
89f977a3a256 planemo upload for repository https://github.com/Marie59/champ_blocs commit 0d86db7d42b608c386a54500064f5f9c9d7019a4 ecology parents: diff changeset	661 "X..Bryozoaires.Dresses",
89f977a3a256 planemo upload for repository https://github.com/Marie59/champ_blocs commit 0d86db7d42b608c386a54500064f5f9c9d7019a4 ecology parents: diff changeset	662 "X..Balanes.Vivantes",
89f977a3a256 planemo upload for repository https://github.com/Marie59/champ_blocs commit 0d86db7d42b608c386a54500064f5f9c9d7019a4 ecology parents: diff changeset	663 #"Commentaires.Avant",
89f977a3a256 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.
89f977a3a256 planemo upload for repository https://github.com/Marie59/champ_blocs commit 0d86db7d42b608c386a54500064f5f9c9d7019a4 ecology parents: diff changeset	665 #"Type.sustrat.observé",
89f977a3a256 planemo upload for repository https://github.com/Marie59/champ_blocs commit 0d86db7d42b608c386a54500064f5f9c9d7019a4 ecology parents: diff changeset	666 #"Commentaires",
89f977a3a256 planemo upload for repository https://github.com/Marie59/champ_blocs commit 0d86db7d42b608c386a54500064f5f9c9d7019a4 ecology parents: diff changeset	667 "Nb.Cancer.pagurus..Tourteau.",
89f977a3a256 planemo upload for repository https://github.com/Marie59/champ_blocs commit 0d86db7d42b608c386a54500064f5f9c9d7019a4 ecology parents: diff changeset	668 "Nb.Necora.puber..Etrille.",
89f977a3a256 planemo upload for repository https://github.com/Marie59/champ_blocs commit 0d86db7d42b608c386a54500064f5f9c9d7019a4 ecology parents: diff changeset	669 "Nb.Carcinus.maenas..Crabe.vert.",
89f977a3a256 planemo upload for repository https://github.com/Marie59/champ_blocs commit 0d86db7d42b608c386a54500064f5f9c9d7019a4 ecology parents: diff changeset	670 "Nb.Nucella.lapilus..Pourpre.",
89f977a3a256 planemo upload for repository https://github.com/Marie59/champ_blocs commit 0d86db7d42b608c386a54500064f5f9c9d7019a4 ecology parents: diff changeset	671 #.."Nb.Eriphia.verrucosa..Crabe.verruqueux.",
89f977a3a256 planemo upload for repository https://github.com/Marie59/champ_blocs commit 0d86db7d42b608c386a54500064f5f9c9d7019a4 ecology parents: diff changeset	672 #.."Nb.Octopus.vulgaris..Poulpe.",
89f977a3a256 planemo upload for repository https://github.com/Marie59/champ_blocs commit 0d86db7d42b608c386a54500064f5f9c9d7019a4 ecology parents: diff changeset	673 "Nb.Galathea..Galathées.",
89f977a3a256 planemo upload for repository https://github.com/Marie59/champ_blocs commit 0d86db7d42b608c386a54500064f5f9c9d7019a4 ecology parents: diff changeset	674 #.."Nb.Paracentrotus.lividus..Oursin.",
89f977a3a256 planemo upload for repository https://github.com/Marie59/champ_blocs commit 0d86db7d42b608c386a54500064f5f9c9d7019a4 ecology parents: diff changeset	675 "Nb.Lophozozymus.incisus..ancien.Xantho.incisus.",
89f977a3a256 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.",
89f977a3a256 planemo upload for repository https://github.com/Marie59/champ_blocs commit 0d86db7d42b608c386a54500064f5f9c9d7019a4 ecology parents: diff changeset	677 "Nb.Haliotis.tuberculata..Ormeau.",
89f977a3a256 planemo upload for repository https://github.com/Marie59/champ_blocs commit 0d86db7d42b608c386a54500064f5f9c9d7019a4 ecology parents: diff changeset	678 #"Nb.Stramonita.haemastoma..Pourpre.bouche.de.sang.",
89f977a3a256 planemo upload for repository https://github.com/Marie59/champ_blocs commit 0d86db7d42b608c386a54500064f5f9c9d7019a4 ecology parents: diff changeset	679 "Nb.Littorina.littorea..Bigorneau.",
89f977a3a256 planemo upload for repository https://github.com/Marie59/champ_blocs commit 0d86db7d42b608c386a54500064f5f9c9d7019a4 ecology parents: diff changeset	680 "Nb.Xantho.pilipes..Xanthe.poilu.",
89f977a3a256 planemo upload for repository https://github.com/Marie59/champ_blocs commit 0d86db7d42b608c386a54500064f5f9c9d7019a4 ecology parents: diff changeset	681 "Nb.Mimachlamys.varia..Pétoncle.noir."
89f977a3a256 planemo upload for repository https://github.com/Marie59/champ_blocs commit 0d86db7d42b608c386a54500064f5f9c9d7019a4 ecology parents: diff changeset	682 )
89f977a3a256 planemo upload for repository https://github.com/Marie59/champ_blocs commit 0d86db7d42b608c386a54500064f5f9c9d7019a4 ecology parents: diff changeset	683 ] <- lapply(bretagne_bm[, c(
89f977a3a256 planemo upload for repository https://github.com/Marie59/champ_blocs commit 0d86db7d42b608c386a54500064f5f9c9d7019a4 ecology parents: diff changeset	684 "X..algues.brunes",
89f977a3a256 planemo upload for repository https://github.com/Marie59/champ_blocs commit 0d86db7d42b608c386a54500064f5f9c9d7019a4 ecology parents: diff changeset	685 "Strate.algues.brunes",
89f977a3a256 planemo upload for repository https://github.com/Marie59/champ_blocs commit 0d86db7d42b608c386a54500064f5f9c9d7019a4 ecology parents: diff changeset	686 "X..algues.rouges",
89f977a3a256 planemo upload for repository https://github.com/Marie59/champ_blocs commit 0d86db7d42b608c386a54500064f5f9c9d7019a4 ecology parents: diff changeset	687 "Strate.algues.rouges",
89f977a3a256 planemo upload for repository https://github.com/Marie59/champ_blocs commit 0d86db7d42b608c386a54500064f5f9c9d7019a4 ecology parents: diff changeset	688 "X..algues.vertes",
89f977a3a256 planemo upload for repository https://github.com/Marie59/champ_blocs commit 0d86db7d42b608c386a54500064f5f9c9d7019a4 ecology parents: diff changeset	689 "Strate.algues.vertes",
89f977a3a256 planemo upload for repository https://github.com/Marie59/champ_blocs commit 0d86db7d42b608c386a54500064f5f9c9d7019a4 ecology parents: diff changeset	690 "X..Cladophora",
89f977a3a256 planemo upload for repository https://github.com/Marie59/champ_blocs commit 0d86db7d42b608c386a54500064f5f9c9d7019a4 ecology parents: diff changeset	691 "X..Lithophyllum",
89f977a3a256 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.
89f977a3a256 planemo upload for repository https://github.com/Marie59/champ_blocs commit 0d86db7d42b608c386a54500064f5f9c9d7019a4 ecology parents: diff changeset	693 #"Type.Sediment",
89f977a3a256 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.
89f977a3a256 planemo upload for repository https://github.com/Marie59/champ_blocs commit 0d86db7d42b608c386a54500064f5f9c9d7019a4 ecology parents: diff changeset	695 "Nb.Littorina.obtusata",
89f977a3a256 planemo upload for repository https://github.com/Marie59/champ_blocs commit 0d86db7d42b608c386a54500064f5f9c9d7019a4 ecology parents: diff changeset	696 "Nb.Gibbula.cineraria",
89f977a3a256 planemo upload for repository https://github.com/Marie59/champ_blocs commit 0d86db7d42b608c386a54500064f5f9c9d7019a4 ecology parents: diff changeset	697 "Nb.Gibbula.pennanti",
89f977a3a256 planemo upload for repository https://github.com/Marie59/champ_blocs commit 0d86db7d42b608c386a54500064f5f9c9d7019a4 ecology parents: diff changeset	698 "Nb.Gibbula.umbilicalis",
89f977a3a256 planemo upload for repository https://github.com/Marie59/champ_blocs commit 0d86db7d42b608c386a54500064f5f9c9d7019a4 ecology parents: diff changeset	699 "Nb.Phallusia.mamillata",
89f977a3a256 planemo upload for repository https://github.com/Marie59/champ_blocs commit 0d86db7d42b608c386a54500064f5f9c9d7019a4 ecology parents: diff changeset	700 "Nb.Tethya.aurantium",
89f977a3a256 planemo upload for repository https://github.com/Marie59/champ_blocs commit 0d86db7d42b608c386a54500064f5f9c9d7019a4 ecology parents: diff changeset	701 #"Nb.Spirobranchus.lamarckii.1B",
89f977a3a256 planemo upload for repository https://github.com/Marie59/champ_blocs commit 0d86db7d42b608c386a54500064f5f9c9d7019a4 ecology parents: diff changeset	702 #"Nb.Spirobranchus.lamarckii.2B",
89f977a3a256 planemo upload for repository https://github.com/Marie59/champ_blocs commit 0d86db7d42b608c386a54500064f5f9c9d7019a4 ecology parents: diff changeset	703 #"Nb.Spirobranchus.lamarckii.3B",
89f977a3a256 planemo upload for repository https://github.com/Marie59/champ_blocs commit 0d86db7d42b608c386a54500064f5f9c9d7019a4 ecology parents: diff changeset	704 #"Nb.Spirobranchus.lamarckii.4B",
89f977a3a256 planemo upload for repository https://github.com/Marie59/champ_blocs commit 0d86db7d42b608c386a54500064f5f9c9d7019a4 ecology parents: diff changeset	705 #"Nb.Spirobranchus.lamarckii.5B",
89f977a3a256 planemo upload for repository https://github.com/Marie59/champ_blocs commit 0d86db7d42b608c386a54500064f5f9c9d7019a4 ecology parents: diff changeset	706 "Nb.Spirobranchus.lamarckii.total",
89f977a3a256 planemo upload for repository https://github.com/Marie59/champ_blocs commit 0d86db7d42b608c386a54500064f5f9c9d7019a4 ecology parents: diff changeset	707 #"Nb.spirorbis.1A",
89f977a3a256 planemo upload for repository https://github.com/Marie59/champ_blocs commit 0d86db7d42b608c386a54500064f5f9c9d7019a4 ecology parents: diff changeset	708 #"Nb.spirorbis.2A",
89f977a3a256 planemo upload for repository https://github.com/Marie59/champ_blocs commit 0d86db7d42b608c386a54500064f5f9c9d7019a4 ecology parents: diff changeset	709 #"Nb.spirorbis.3A",
89f977a3a256 planemo upload for repository https://github.com/Marie59/champ_blocs commit 0d86db7d42b608c386a54500064f5f9c9d7019a4 ecology parents: diff changeset	710 #"Nb.spirorbis.4A",
89f977a3a256 planemo upload for repository https://github.com/Marie59/champ_blocs commit 0d86db7d42b608c386a54500064f5f9c9d7019a4 ecology parents: diff changeset	711 #"Nb.spirorbis.5A",
89f977a3a256 planemo upload for repository https://github.com/Marie59/champ_blocs commit 0d86db7d42b608c386a54500064f5f9c9d7019a4 ecology parents: diff changeset	712 "Nb.spirorbis.total",
89f977a3a256 planemo upload for repository https://github.com/Marie59/champ_blocs commit 0d86db7d42b608c386a54500064f5f9c9d7019a4 ecology parents: diff changeset	713 #.."Nb.Crassostrea.gigas",
89f977a3a256 planemo upload for repository https://github.com/Marie59/champ_blocs commit 0d86db7d42b608c386a54500064f5f9c9d7019a4 ecology parents: diff changeset	714 #.."Nb.Ostrea.edulis",
89f977a3a256 planemo upload for repository https://github.com/Marie59/champ_blocs commit 0d86db7d42b608c386a54500064f5f9c9d7019a4 ecology parents: diff changeset	715 #.."X..Mytilus.sp.",
89f977a3a256 planemo upload for repository https://github.com/Marie59/champ_blocs commit 0d86db7d42b608c386a54500064f5f9c9d7019a4 ecology parents: diff changeset	716 #.."X..Hermelles",
89f977a3a256 planemo upload for repository https://github.com/Marie59/champ_blocs commit 0d86db7d42b608c386a54500064f5f9c9d7019a4 ecology parents: diff changeset	717 #.."X..Hydraires",
89f977a3a256 planemo upload for repository https://github.com/Marie59/champ_blocs commit 0d86db7d42b608c386a54500064f5f9c9d7019a4 ecology parents: diff changeset	718 "X..Eponges",
89f977a3a256 planemo upload for repository https://github.com/Marie59/champ_blocs commit 0d86db7d42b608c386a54500064f5f9c9d7019a4 ecology parents: diff changeset	719 "X..Ascidies.Coloniales",
89f977a3a256 planemo upload for repository https://github.com/Marie59/champ_blocs commit 0d86db7d42b608c386a54500064f5f9c9d7019a4 ecology parents: diff changeset	720 "X..Ascidies.Solitaires",
89f977a3a256 planemo upload for repository https://github.com/Marie59/champ_blocs commit 0d86db7d42b608c386a54500064f5f9c9d7019a4 ecology parents: diff changeset	721 "X..Bryozoaires.Dresses",
89f977a3a256 planemo upload for repository https://github.com/Marie59/champ_blocs commit 0d86db7d42b608c386a54500064f5f9c9d7019a4 ecology parents: diff changeset	722 "X..Balanes.Vivantes",
89f977a3a256 planemo upload for repository https://github.com/Marie59/champ_blocs commit 0d86db7d42b608c386a54500064f5f9c9d7019a4 ecology parents: diff changeset	723 #"Commentaires.Avant",
89f977a3a256 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.
89f977a3a256 planemo upload for repository https://github.com/Marie59/champ_blocs commit 0d86db7d42b608c386a54500064f5f9c9d7019a4 ecology parents: diff changeset	725 #"Type.sustrat.observé",
89f977a3a256 planemo upload for repository https://github.com/Marie59/champ_blocs commit 0d86db7d42b608c386a54500064f5f9c9d7019a4 ecology parents: diff changeset	726 #"Commentaires",
89f977a3a256 planemo upload for repository https://github.com/Marie59/champ_blocs commit 0d86db7d42b608c386a54500064f5f9c9d7019a4 ecology parents: diff changeset	727 "Nb.Cancer.pagurus..Tourteau.",
89f977a3a256 planemo upload for repository https://github.com/Marie59/champ_blocs commit 0d86db7d42b608c386a54500064f5f9c9d7019a4 ecology parents: diff changeset	728 "Nb.Necora.puber..Etrille.",
89f977a3a256 planemo upload for repository https://github.com/Marie59/champ_blocs commit 0d86db7d42b608c386a54500064f5f9c9d7019a4 ecology parents: diff changeset	729 "Nb.Carcinus.maenas..Crabe.vert.",
89f977a3a256 planemo upload for repository https://github.com/Marie59/champ_blocs commit 0d86db7d42b608c386a54500064f5f9c9d7019a4 ecology parents: diff changeset	730 "Nb.Nucella.lapilus..Pourpre.",
89f977a3a256 planemo upload for repository https://github.com/Marie59/champ_blocs commit 0d86db7d42b608c386a54500064f5f9c9d7019a4 ecology parents: diff changeset	731 #.."Nb.Eriphia.verrucosa..Crabe.verruqueux.",
89f977a3a256 planemo upload for repository https://github.com/Marie59/champ_blocs commit 0d86db7d42b608c386a54500064f5f9c9d7019a4 ecology parents: diff changeset	732 #.."Nb.Octopus.vulgaris..Poulpe.",
89f977a3a256 planemo upload for repository https://github.com/Marie59/champ_blocs commit 0d86db7d42b608c386a54500064f5f9c9d7019a4 ecology parents: diff changeset	733 "Nb.Galathea..Galathées.",
89f977a3a256 planemo upload for repository https://github.com/Marie59/champ_blocs commit 0d86db7d42b608c386a54500064f5f9c9d7019a4 ecology parents: diff changeset	734 #.."Nb.Paracentrotus.lividus..Oursin.",
89f977a3a256 planemo upload for repository https://github.com/Marie59/champ_blocs commit 0d86db7d42b608c386a54500064f5f9c9d7019a4 ecology parents: diff changeset	735 "Nb.Lophozozymus.incisus..ancien.Xantho.incisus.",
89f977a3a256 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.",
89f977a3a256 planemo upload for repository https://github.com/Marie59/champ_blocs commit 0d86db7d42b608c386a54500064f5f9c9d7019a4 ecology parents: diff changeset	737 "Nb.Haliotis.tuberculata..Ormeau.",
89f977a3a256 planemo upload for repository https://github.com/Marie59/champ_blocs commit 0d86db7d42b608c386a54500064f5f9c9d7019a4 ecology parents: diff changeset	738 #"Nb.Stramonita.haemastoma..Pourpre.bouche.de.sang.",
89f977a3a256 planemo upload for repository https://github.com/Marie59/champ_blocs commit 0d86db7d42b608c386a54500064f5f9c9d7019a4 ecology parents: diff changeset	739 "Nb.Littorina.littorea..Bigorneau.",
89f977a3a256 planemo upload for repository https://github.com/Marie59/champ_blocs commit 0d86db7d42b608c386a54500064f5f9c9d7019a4 ecology parents: diff changeset	740 "Nb.Xantho.pilipes..Xanthe.poilu.",
89f977a3a256 planemo upload for repository https://github.com/Marie59/champ_blocs commit 0d86db7d42b608c386a54500064f5f9c9d7019a4 ecology parents: diff changeset	741 "Nb.Mimachlamys.varia..Pétoncle.noir."
89f977a3a256 planemo upload for repository https://github.com/Marie59/champ_blocs commit 0d86db7d42b608c386a54500064f5f9c9d7019a4 ecology parents: diff changeset	742 )
89f977a3a256 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))
89f977a3a256 planemo upload for repository https://github.com/Marie59/champ_blocs commit 0d86db7d42b608c386a54500064f5f9c9d7019a4 ecology parents: diff changeset	744
89f977a3a256 planemo upload for repository https://github.com/Marie59/champ_blocs commit 0d86db7d42b608c386a54500064f5f9c9d7019a4 ecology parents: diff changeset	745
89f977a3a256 planemo upload for repository https://github.com/Marie59/champ_blocs commit 0d86db7d42b608c386a54500064f5f9c9d7019a4 ecology parents: diff changeset	746 # bretagne_bf
89f977a3a256 planemo upload for repository https://github.com/Marie59/champ_blocs commit 0d86db7d42b608c386a54500064f5f9c9d7019a4 ecology parents: diff changeset	747 bretagne_bf[, c(
89f977a3a256 planemo upload for repository https://github.com/Marie59/champ_blocs commit 0d86db7d42b608c386a54500064f5f9c9d7019a4 ecology parents: diff changeset	748 "X..algues.brunes",
89f977a3a256 planemo upload for repository https://github.com/Marie59/champ_blocs commit 0d86db7d42b608c386a54500064f5f9c9d7019a4 ecology parents: diff changeset	749 "Strate.algues.brunes",
89f977a3a256 planemo upload for repository https://github.com/Marie59/champ_blocs commit 0d86db7d42b608c386a54500064f5f9c9d7019a4 ecology parents: diff changeset	750 "X..algues.rouges",
89f977a3a256 planemo upload for repository https://github.com/Marie59/champ_blocs commit 0d86db7d42b608c386a54500064f5f9c9d7019a4 ecology parents: diff changeset	751 "Strate.algues.rouges",
89f977a3a256 planemo upload for repository https://github.com/Marie59/champ_blocs commit 0d86db7d42b608c386a54500064f5f9c9d7019a4 ecology parents: diff changeset	752 "X..algues.vertes",
89f977a3a256 planemo upload for repository https://github.com/Marie59/champ_blocs commit 0d86db7d42b608c386a54500064f5f9c9d7019a4 ecology parents: diff changeset	753 "Strate.algues.vertes",
89f977a3a256 planemo upload for repository https://github.com/Marie59/champ_blocs commit 0d86db7d42b608c386a54500064f5f9c9d7019a4 ecology parents: diff changeset	754 "X..Cladophora",
89f977a3a256 planemo upload for repository https://github.com/Marie59/champ_blocs commit 0d86db7d42b608c386a54500064f5f9c9d7019a4 ecology parents: diff changeset	755 "X..Lithophyllum",
89f977a3a256 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.
89f977a3a256 planemo upload for repository https://github.com/Marie59/champ_blocs commit 0d86db7d42b608c386a54500064f5f9c9d7019a4 ecology parents: diff changeset	757 #"Type.Sediment",
89f977a3a256 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.
89f977a3a256 planemo upload for repository https://github.com/Marie59/champ_blocs commit 0d86db7d42b608c386a54500064f5f9c9d7019a4 ecology parents: diff changeset	759 "Nb.Littorina.obtusata",
89f977a3a256 planemo upload for repository https://github.com/Marie59/champ_blocs commit 0d86db7d42b608c386a54500064f5f9c9d7019a4 ecology parents: diff changeset	760 "Nb.Gibbula.cineraria",
89f977a3a256 planemo upload for repository https://github.com/Marie59/champ_blocs commit 0d86db7d42b608c386a54500064f5f9c9d7019a4 ecology parents: diff changeset	761 "Nb.Gibbula.pennanti",
89f977a3a256 planemo upload for repository https://github.com/Marie59/champ_blocs commit 0d86db7d42b608c386a54500064f5f9c9d7019a4 ecology parents: diff changeset	762 "Nb.Gibbula.umbilicalis",
89f977a3a256 planemo upload for repository https://github.com/Marie59/champ_blocs commit 0d86db7d42b608c386a54500064f5f9c9d7019a4 ecology parents: diff changeset	763 "Nb.Phallusia.mamillata",
89f977a3a256 planemo upload for repository https://github.com/Marie59/champ_blocs commit 0d86db7d42b608c386a54500064f5f9c9d7019a4 ecology parents: diff changeset	764 "Nb.Tethya.aurantium",
89f977a3a256 planemo upload for repository https://github.com/Marie59/champ_blocs commit 0d86db7d42b608c386a54500064f5f9c9d7019a4 ecology parents: diff changeset	765 #"Nb.Spirobranchus.lamarckii.1B",
89f977a3a256 planemo upload for repository https://github.com/Marie59/champ_blocs commit 0d86db7d42b608c386a54500064f5f9c9d7019a4 ecology parents: diff changeset	766 #"Nb.Spirobranchus.lamarckii.2B",
89f977a3a256 planemo upload for repository https://github.com/Marie59/champ_blocs commit 0d86db7d42b608c386a54500064f5f9c9d7019a4 ecology parents: diff changeset	767 #"Nb.Spirobranchus.lamarckii.3B",
89f977a3a256 planemo upload for repository https://github.com/Marie59/champ_blocs commit 0d86db7d42b608c386a54500064f5f9c9d7019a4 ecology parents: diff changeset	768 #"Nb.Spirobranchus.lamarckii.4B",
89f977a3a256 planemo upload for repository https://github.com/Marie59/champ_blocs commit 0d86db7d42b608c386a54500064f5f9c9d7019a4 ecology parents: diff changeset	769 #"Nb.Spirobranchus.lamarckii.5B",
89f977a3a256 planemo upload for repository https://github.com/Marie59/champ_blocs commit 0d86db7d42b608c386a54500064f5f9c9d7019a4 ecology parents: diff changeset	770 "Nb.Spirobranchus.lamarckii.total",
89f977a3a256 planemo upload for repository https://github.com/Marie59/champ_blocs commit 0d86db7d42b608c386a54500064f5f9c9d7019a4 ecology parents: diff changeset	771 #"Nb.spirorbis.1A",
89f977a3a256 planemo upload for repository https://github.com/Marie59/champ_blocs commit 0d86db7d42b608c386a54500064f5f9c9d7019a4 ecology parents: diff changeset	772 #"Nb.spirorbis.2A",
89f977a3a256 planemo upload for repository https://github.com/Marie59/champ_blocs commit 0d86db7d42b608c386a54500064f5f9c9d7019a4 ecology parents: diff changeset	773 #"Nb.spirorbis.3A",
89f977a3a256 planemo upload for repository https://github.com/Marie59/champ_blocs commit 0d86db7d42b608c386a54500064f5f9c9d7019a4 ecology parents: diff changeset	774 #"Nb.spirorbis.4A",
89f977a3a256 planemo upload for repository https://github.com/Marie59/champ_blocs commit 0d86db7d42b608c386a54500064f5f9c9d7019a4 ecology parents: diff changeset	775 #"Nb.spirorbis.5A",
89f977a3a256 planemo upload for repository https://github.com/Marie59/champ_blocs commit 0d86db7d42b608c386a54500064f5f9c9d7019a4 ecology parents: diff changeset	776 "Nb.spirorbis.total",
89f977a3a256 planemo upload for repository https://github.com/Marie59/champ_blocs commit 0d86db7d42b608c386a54500064f5f9c9d7019a4 ecology parents: diff changeset	777 #.."Nb.Crassostrea.gigas",
89f977a3a256 planemo upload for repository https://github.com/Marie59/champ_blocs commit 0d86db7d42b608c386a54500064f5f9c9d7019a4 ecology parents: diff changeset	778 #.."Nb.Ostrea.edulis",
89f977a3a256 planemo upload for repository https://github.com/Marie59/champ_blocs commit 0d86db7d42b608c386a54500064f5f9c9d7019a4 ecology parents: diff changeset	779 #.."X..Mytilus.sp.",
89f977a3a256 planemo upload for repository https://github.com/Marie59/champ_blocs commit 0d86db7d42b608c386a54500064f5f9c9d7019a4 ecology parents: diff changeset	780 #.."X..Hermelles",
89f977a3a256 planemo upload for repository https://github.com/Marie59/champ_blocs commit 0d86db7d42b608c386a54500064f5f9c9d7019a4 ecology parents: diff changeset	781 #.."X..Hydraires",
89f977a3a256 planemo upload for repository https://github.com/Marie59/champ_blocs commit 0d86db7d42b608c386a54500064f5f9c9d7019a4 ecology parents: diff changeset	782 "X..Eponges",
89f977a3a256 planemo upload for repository https://github.com/Marie59/champ_blocs commit 0d86db7d42b608c386a54500064f5f9c9d7019a4 ecology parents: diff changeset	783 "X..Ascidies.Coloniales",
89f977a3a256 planemo upload for repository https://github.com/Marie59/champ_blocs commit 0d86db7d42b608c386a54500064f5f9c9d7019a4 ecology parents: diff changeset	784 "X..Ascidies.Solitaires",
89f977a3a256 planemo upload for repository https://github.com/Marie59/champ_blocs commit 0d86db7d42b608c386a54500064f5f9c9d7019a4 ecology parents: diff changeset	785 "X..Bryozoaires.Dresses",
89f977a3a256 planemo upload for repository https://github.com/Marie59/champ_blocs commit 0d86db7d42b608c386a54500064f5f9c9d7019a4 ecology parents: diff changeset	786 "X..Balanes.Vivantes",
89f977a3a256 planemo upload for repository https://github.com/Marie59/champ_blocs commit 0d86db7d42b608c386a54500064f5f9c9d7019a4 ecology parents: diff changeset	787 #"Commentaires.Avant",
89f977a3a256 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.
89f977a3a256 planemo upload for repository https://github.com/Marie59/champ_blocs commit 0d86db7d42b608c386a54500064f5f9c9d7019a4 ecology parents: diff changeset	789 #"Type.sustrat.observé",
89f977a3a256 planemo upload for repository https://github.com/Marie59/champ_blocs commit 0d86db7d42b608c386a54500064f5f9c9d7019a4 ecology parents: diff changeset	790 #"Commentaires",
89f977a3a256 planemo upload for repository https://github.com/Marie59/champ_blocs commit 0d86db7d42b608c386a54500064f5f9c9d7019a4 ecology parents: diff changeset	791 #."Nb.Cancer.pagurus..Tourteau.",
89f977a3a256 planemo upload for repository https://github.com/Marie59/champ_blocs commit 0d86db7d42b608c386a54500064f5f9c9d7019a4 ecology parents: diff changeset	792 #.."Nb.Necora.puber..Etrille.",
89f977a3a256 planemo upload for repository https://github.com/Marie59/champ_blocs commit 0d86db7d42b608c386a54500064f5f9c9d7019a4 ecology parents: diff changeset	793 #."Nb.Carcinus.maenas..Crabe.vert.",
89f977a3a256 planemo upload for repository https://github.com/Marie59/champ_blocs commit 0d86db7d42b608c386a54500064f5f9c9d7019a4 ecology parents: diff changeset	794 #."Nb.Nucella.lapilus..Pourpre.",
89f977a3a256 planemo upload for repository https://github.com/Marie59/champ_blocs commit 0d86db7d42b608c386a54500064f5f9c9d7019a4 ecology parents: diff changeset	795 #.."Nb.Eriphia.verrucosa..Crabe.verruqueux.",
89f977a3a256 planemo upload for repository https://github.com/Marie59/champ_blocs commit 0d86db7d42b608c386a54500064f5f9c9d7019a4 ecology parents: diff changeset	796 #.."Nb.Octopus.vulgaris..Poulpe.",
89f977a3a256 planemo upload for repository https://github.com/Marie59/champ_blocs commit 0d86db7d42b608c386a54500064f5f9c9d7019a4 ecology parents: diff changeset	797 #."Nb.Galathea..Galathées.",
89f977a3a256 planemo upload for repository https://github.com/Marie59/champ_blocs commit 0d86db7d42b608c386a54500064f5f9c9d7019a4 ecology parents: diff changeset	798 #.."Nb.Paracentrotus.lividus..Oursin.",
89f977a3a256 planemo upload for repository https://github.com/Marie59/champ_blocs commit 0d86db7d42b608c386a54500064f5f9c9d7019a4 ecology parents: diff changeset	799 #."Nb.Lophozozymus.incisus..ancien.Xantho.incisus.",
89f977a3a256 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.",
89f977a3a256 planemo upload for repository https://github.com/Marie59/champ_blocs commit 0d86db7d42b608c386a54500064f5f9c9d7019a4 ecology parents: diff changeset	801 #."Nb.Haliotis.tuberculata..Ormeau.",
89f977a3a256 planemo upload for repository https://github.com/Marie59/champ_blocs commit 0d86db7d42b608c386a54500064f5f9c9d7019a4 ecology parents: diff changeset	802 #."Nb.Stramonita.haemastoma..Pourpre.bouche.de.sang.",
89f977a3a256 planemo upload for repository https://github.com/Marie59/champ_blocs commit 0d86db7d42b608c386a54500064f5f9c9d7019a4 ecology parents: diff changeset	803 #."Nb.Littorina.littorea..Bigorneau.",
89f977a3a256 planemo upload for repository https://github.com/Marie59/champ_blocs commit 0d86db7d42b608c386a54500064f5f9c9d7019a4 ecology parents: diff changeset	804 #."Nb.Xantho.pilipes..Xanthe.poilu.",
89f977a3a256 planemo upload for repository https://github.com/Marie59/champ_blocs commit 0d86db7d42b608c386a54500064f5f9c9d7019a4 ecology parents: diff changeset	805 #."Nb.Mimachlamys.varia..Pétoncle.noir."
89f977a3a256 planemo upload for repository https://github.com/Marie59/champ_blocs commit 0d86db7d42b608c386a54500064f5f9c9d7019a4 ecology parents: diff changeset	806 )
89f977a3a256 planemo upload for repository https://github.com/Marie59/champ_blocs commit 0d86db7d42b608c386a54500064f5f9c9d7019a4 ecology parents: diff changeset	807 ] <- lapply(bretagne_bf[, c(
89f977a3a256 planemo upload for repository https://github.com/Marie59/champ_blocs commit 0d86db7d42b608c386a54500064f5f9c9d7019a4 ecology parents: diff changeset	808 "X..algues.brunes",
89f977a3a256 planemo upload for repository https://github.com/Marie59/champ_blocs commit 0d86db7d42b608c386a54500064f5f9c9d7019a4 ecology parents: diff changeset	809 "Strate.algues.brunes",
89f977a3a256 planemo upload for repository https://github.com/Marie59/champ_blocs commit 0d86db7d42b608c386a54500064f5f9c9d7019a4 ecology parents: diff changeset	810 "X..algues.rouges",
89f977a3a256 planemo upload for repository https://github.com/Marie59/champ_blocs commit 0d86db7d42b608c386a54500064f5f9c9d7019a4 ecology parents: diff changeset	811 "Strate.algues.rouges",
89f977a3a256 planemo upload for repository https://github.com/Marie59/champ_blocs commit 0d86db7d42b608c386a54500064f5f9c9d7019a4 ecology parents: diff changeset	812 "X..algues.vertes",
89f977a3a256 planemo upload for repository https://github.com/Marie59/champ_blocs commit 0d86db7d42b608c386a54500064f5f9c9d7019a4 ecology parents: diff changeset	813 "Strate.algues.vertes",
89f977a3a256 planemo upload for repository https://github.com/Marie59/champ_blocs commit 0d86db7d42b608c386a54500064f5f9c9d7019a4 ecology parents: diff changeset	814 "X..Cladophora",
89f977a3a256 planemo upload for repository https://github.com/Marie59/champ_blocs commit 0d86db7d42b608c386a54500064f5f9c9d7019a4 ecology parents: diff changeset	815 "X..Lithophyllum",
89f977a3a256 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.
89f977a3a256 planemo upload for repository https://github.com/Marie59/champ_blocs commit 0d86db7d42b608c386a54500064f5f9c9d7019a4 ecology parents: diff changeset	817 #"Type.Sediment",
89f977a3a256 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.
89f977a3a256 planemo upload for repository https://github.com/Marie59/champ_blocs commit 0d86db7d42b608c386a54500064f5f9c9d7019a4 ecology parents: diff changeset	819 "Nb.Littorina.obtusata",
89f977a3a256 planemo upload for repository https://github.com/Marie59/champ_blocs commit 0d86db7d42b608c386a54500064f5f9c9d7019a4 ecology parents: diff changeset	820 "Nb.Gibbula.cineraria",
89f977a3a256 planemo upload for repository https://github.com/Marie59/champ_blocs commit 0d86db7d42b608c386a54500064f5f9c9d7019a4 ecology parents: diff changeset	821 "Nb.Gibbula.pennanti",
89f977a3a256 planemo upload for repository https://github.com/Marie59/champ_blocs commit 0d86db7d42b608c386a54500064f5f9c9d7019a4 ecology parents: diff changeset	822 "Nb.Gibbula.umbilicalis",
89f977a3a256 planemo upload for repository https://github.com/Marie59/champ_blocs commit 0d86db7d42b608c386a54500064f5f9c9d7019a4 ecology parents: diff changeset	823 "Nb.Phallusia.mamillata",
89f977a3a256 planemo upload for repository https://github.com/Marie59/champ_blocs commit 0d86db7d42b608c386a54500064f5f9c9d7019a4 ecology parents: diff changeset	824 "Nb.Tethya.aurantium",
89f977a3a256 planemo upload for repository https://github.com/Marie59/champ_blocs commit 0d86db7d42b608c386a54500064f5f9c9d7019a4 ecology parents: diff changeset	825 #"Nb.Spirobranchus.lamarckii.1B",
89f977a3a256 planemo upload for repository https://github.com/Marie59/champ_blocs commit 0d86db7d42b608c386a54500064f5f9c9d7019a4 ecology parents: diff changeset	826 #"Nb.Spirobranchus.lamarckii.2B",
89f977a3a256 planemo upload for repository https://github.com/Marie59/champ_blocs commit 0d86db7d42b608c386a54500064f5f9c9d7019a4 ecology parents: diff changeset	827 #"Nb.Spirobranchus.lamarckii.3B",
89f977a3a256 planemo upload for repository https://github.com/Marie59/champ_blocs commit 0d86db7d42b608c386a54500064f5f9c9d7019a4 ecology parents: diff changeset	828 #"Nb.Spirobranchus.lamarckii.4B",
89f977a3a256 planemo upload for repository https://github.com/Marie59/champ_blocs commit 0d86db7d42b608c386a54500064f5f9c9d7019a4 ecology parents: diff changeset	829 #"Nb.Spirobranchus.lamarckii.5B",
89f977a3a256 planemo upload for repository https://github.com/Marie59/champ_blocs commit 0d86db7d42b608c386a54500064f5f9c9d7019a4 ecology parents: diff changeset	830 "Nb.Spirobranchus.lamarckii.total",
89f977a3a256 planemo upload for repository https://github.com/Marie59/champ_blocs commit 0d86db7d42b608c386a54500064f5f9c9d7019a4 ecology parents: diff changeset	831 #"Nb.spirorbis.1A",
89f977a3a256 planemo upload for repository https://github.com/Marie59/champ_blocs commit 0d86db7d42b608c386a54500064f5f9c9d7019a4 ecology parents: diff changeset	832 #"Nb.spirorbis.2A",
89f977a3a256 planemo upload for repository https://github.com/Marie59/champ_blocs commit 0d86db7d42b608c386a54500064f5f9c9d7019a4 ecology parents: diff changeset	833 #"Nb.spirorbis.3A",
89f977a3a256 planemo upload for repository https://github.com/Marie59/champ_blocs commit 0d86db7d42b608c386a54500064f5f9c9d7019a4 ecology parents: diff changeset	834 #"Nb.spirorbis.4A",
89f977a3a256 planemo upload for repository https://github.com/Marie59/champ_blocs commit 0d86db7d42b608c386a54500064f5f9c9d7019a4 ecology parents: diff changeset	835 #"Nb.spirorbis.5A",
89f977a3a256 planemo upload for repository https://github.com/Marie59/champ_blocs commit 0d86db7d42b608c386a54500064f5f9c9d7019a4 ecology parents: diff changeset	836 "Nb.spirorbis.total",
89f977a3a256 planemo upload for repository https://github.com/Marie59/champ_blocs commit 0d86db7d42b608c386a54500064f5f9c9d7019a4 ecology parents: diff changeset	837 #.."Nb.Crassostrea.gigas",
89f977a3a256 planemo upload for repository https://github.com/Marie59/champ_blocs commit 0d86db7d42b608c386a54500064f5f9c9d7019a4 ecology parents: diff changeset	838 #.."Nb.Ostrea.edulis",
89f977a3a256 planemo upload for repository https://github.com/Marie59/champ_blocs commit 0d86db7d42b608c386a54500064f5f9c9d7019a4 ecology parents: diff changeset	839 #.."X..Mytilus.sp.",
89f977a3a256 planemo upload for repository https://github.com/Marie59/champ_blocs commit 0d86db7d42b608c386a54500064f5f9c9d7019a4 ecology parents: diff changeset	840 #.."X..Hermelles",
89f977a3a256 planemo upload for repository https://github.com/Marie59/champ_blocs commit 0d86db7d42b608c386a54500064f5f9c9d7019a4 ecology parents: diff changeset	841 #.."X..Hydraires",
89f977a3a256 planemo upload for repository https://github.com/Marie59/champ_blocs commit 0d86db7d42b608c386a54500064f5f9c9d7019a4 ecology parents: diff changeset	842 "X..Eponges",
89f977a3a256 planemo upload for repository https://github.com/Marie59/champ_blocs commit 0d86db7d42b608c386a54500064f5f9c9d7019a4 ecology parents: diff changeset	843 "X..Ascidies.Coloniales",
89f977a3a256 planemo upload for repository https://github.com/Marie59/champ_blocs commit 0d86db7d42b608c386a54500064f5f9c9d7019a4 ecology parents: diff changeset	844 "X..Ascidies.Solitaires",
89f977a3a256 planemo upload for repository https://github.com/Marie59/champ_blocs commit 0d86db7d42b608c386a54500064f5f9c9d7019a4 ecology parents: diff changeset	845 "X..Bryozoaires.Dresses",
89f977a3a256 planemo upload for repository https://github.com/Marie59/champ_blocs commit 0d86db7d42b608c386a54500064f5f9c9d7019a4 ecology parents: diff changeset	846 "X..Balanes.Vivantes",
89f977a3a256 planemo upload for repository https://github.com/Marie59/champ_blocs commit 0d86db7d42b608c386a54500064f5f9c9d7019a4 ecology parents: diff changeset	847 #"Commentaires.Avant",
89f977a3a256 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.
89f977a3a256 planemo upload for repository https://github.com/Marie59/champ_blocs commit 0d86db7d42b608c386a54500064f5f9c9d7019a4 ecology parents: diff changeset	849 #"Type.sustrat.observé",
89f977a3a256 planemo upload for repository https://github.com/Marie59/champ_blocs commit 0d86db7d42b608c386a54500064f5f9c9d7019a4 ecology parents: diff changeset	850 #"Commentaires",
89f977a3a256 planemo upload for repository https://github.com/Marie59/champ_blocs commit 0d86db7d42b608c386a54500064f5f9c9d7019a4 ecology parents: diff changeset	851 #."Nb.Cancer.pagurus..Tourteau.",
89f977a3a256 planemo upload for repository https://github.com/Marie59/champ_blocs commit 0d86db7d42b608c386a54500064f5f9c9d7019a4 ecology parents: diff changeset	852 #.."Nb.Necora.puber..Etrille.",
89f977a3a256 planemo upload for repository https://github.com/Marie59/champ_blocs commit 0d86db7d42b608c386a54500064f5f9c9d7019a4 ecology parents: diff changeset	853 #."Nb.Carcinus.maenas..Crabe.vert.",
89f977a3a256 planemo upload for repository https://github.com/Marie59/champ_blocs commit 0d86db7d42b608c386a54500064f5f9c9d7019a4 ecology parents: diff changeset	854 #."Nb.Nucella.lapilus..Pourpre.",
89f977a3a256 planemo upload for repository https://github.com/Marie59/champ_blocs commit 0d86db7d42b608c386a54500064f5f9c9d7019a4 ecology parents: diff changeset	855 #.."Nb.Eriphia.verrucosa..Crabe.verruqueux.",
89f977a3a256 planemo upload for repository https://github.com/Marie59/champ_blocs commit 0d86db7d42b608c386a54500064f5f9c9d7019a4 ecology parents: diff changeset	856 #.."Nb.Octopus.vulgaris..Poulpe.",
89f977a3a256 planemo upload for repository https://github.com/Marie59/champ_blocs commit 0d86db7d42b608c386a54500064f5f9c9d7019a4 ecology parents: diff changeset	857 #."Nb.Galathea..Galathées.",
89f977a3a256 planemo upload for repository https://github.com/Marie59/champ_blocs commit 0d86db7d42b608c386a54500064f5f9c9d7019a4 ecology parents: diff changeset	858 #.."Nb.Paracentrotus.lividus..Oursin.",
89f977a3a256 planemo upload for repository https://github.com/Marie59/champ_blocs commit 0d86db7d42b608c386a54500064f5f9c9d7019a4 ecology parents: diff changeset	859 #."Nb.Lophozozymus.incisus..ancien.Xantho.incisus.",
89f977a3a256 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.",
89f977a3a256 planemo upload for repository https://github.com/Marie59/champ_blocs commit 0d86db7d42b608c386a54500064f5f9c9d7019a4 ecology parents: diff changeset	861 #."Nb.Haliotis.tuberculata..Ormeau.",
89f977a3a256 planemo upload for repository https://github.com/Marie59/champ_blocs commit 0d86db7d42b608c386a54500064f5f9c9d7019a4 ecology parents: diff changeset	862 #."Nb.Stramonita.haemastoma..Pourpre.bouche.de.sang.",
89f977a3a256 planemo upload for repository https://github.com/Marie59/champ_blocs commit 0d86db7d42b608c386a54500064f5f9c9d7019a4 ecology parents: diff changeset	863 #."Nb.Littorina.littorea..Bigorneau.",
89f977a3a256 planemo upload for repository https://github.com/Marie59/champ_blocs commit 0d86db7d42b608c386a54500064f5f9c9d7019a4 ecology parents: diff changeset	864 #."Nb.Xantho.pilipes..Xanthe.poilu.",
89f977a3a256 planemo upload for repository https://github.com/Marie59/champ_blocs commit 0d86db7d42b608c386a54500064f5f9c9d7019a4 ecology parents: diff changeset	865 #."Nb.Mimachlamys.varia..Pétoncle.noir."
89f977a3a256 planemo upload for repository https://github.com/Marie59/champ_blocs commit 0d86db7d42b608c386a54500064f5f9c9d7019a4 ecology parents: diff changeset	866 )
89f977a3a256 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))
89f977a3a256 planemo upload for repository https://github.com/Marie59/champ_blocs commit 0d86db7d42b608c386a54500064f5f9c9d7019a4 ecology parents: diff changeset	868
89f977a3a256 planemo upload for repository https://github.com/Marie59/champ_blocs commit 0d86db7d42b608c386a54500064f5f9c9d7019a4 ecology parents: diff changeset	869
89f977a3a256 planemo upload for repository https://github.com/Marie59/champ_blocs commit 0d86db7d42b608c386a54500064f5f9c9d7019a4 ecology parents: diff changeset	870 # egmp_basq_bm
89f977a3a256 planemo upload for repository https://github.com/Marie59/champ_blocs commit 0d86db7d42b608c386a54500064f5f9c9d7019a4 ecology parents: diff changeset	871 egmp_basq_bm[, c(
89f977a3a256 planemo upload for repository https://github.com/Marie59/champ_blocs commit 0d86db7d42b608c386a54500064f5f9c9d7019a4 ecology parents: diff changeset	872 "X..algues.brunes",
89f977a3a256 planemo upload for repository https://github.com/Marie59/champ_blocs commit 0d86db7d42b608c386a54500064f5f9c9d7019a4 ecology parents: diff changeset	873 "Strate.algues.brunes",
89f977a3a256 planemo upload for repository https://github.com/Marie59/champ_blocs commit 0d86db7d42b608c386a54500064f5f9c9d7019a4 ecology parents: diff changeset	874 "X..algues.rouges",
89f977a3a256 planemo upload for repository https://github.com/Marie59/champ_blocs commit 0d86db7d42b608c386a54500064f5f9c9d7019a4 ecology parents: diff changeset	875 "Strate.algues.rouges",
89f977a3a256 planemo upload for repository https://github.com/Marie59/champ_blocs commit 0d86db7d42b608c386a54500064f5f9c9d7019a4 ecology parents: diff changeset	876 "X..algues.vertes",
89f977a3a256 planemo upload for repository https://github.com/Marie59/champ_blocs commit 0d86db7d42b608c386a54500064f5f9c9d7019a4 ecology parents: diff changeset	877 "Strate.algues.vertes",
89f977a3a256 planemo upload for repository https://github.com/Marie59/champ_blocs commit 0d86db7d42b608c386a54500064f5f9c9d7019a4 ecology parents: diff changeset	878 "X..Cladophora",
89f977a3a256 planemo upload for repository https://github.com/Marie59/champ_blocs commit 0d86db7d42b608c386a54500064f5f9c9d7019a4 ecology parents: diff changeset	879 "X..Lithophyllum",
89f977a3a256 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.
89f977a3a256 planemo upload for repository https://github.com/Marie59/champ_blocs commit 0d86db7d42b608c386a54500064f5f9c9d7019a4 ecology parents: diff changeset	881 #"Type.Sediment",
89f977a3a256 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.
89f977a3a256 planemo upload for repository https://github.com/Marie59/champ_blocs commit 0d86db7d42b608c386a54500064f5f9c9d7019a4 ecology parents: diff changeset	883 "Nb.Littorina.obtusata",
89f977a3a256 planemo upload for repository https://github.com/Marie59/champ_blocs commit 0d86db7d42b608c386a54500064f5f9c9d7019a4 ecology parents: diff changeset	884 "Nb.Gibbula.cineraria",
89f977a3a256 planemo upload for repository https://github.com/Marie59/champ_blocs commit 0d86db7d42b608c386a54500064f5f9c9d7019a4 ecology parents: diff changeset	885 "Nb.Gibbula.pennanti",
89f977a3a256 planemo upload for repository https://github.com/Marie59/champ_blocs commit 0d86db7d42b608c386a54500064f5f9c9d7019a4 ecology parents: diff changeset	886 "Nb.Gibbula.umbilicalis",
89f977a3a256 planemo upload for repository https://github.com/Marie59/champ_blocs commit 0d86db7d42b608c386a54500064f5f9c9d7019a4 ecology parents: diff changeset	887 "Nb.Phallusia.mamillata",
89f977a3a256 planemo upload for repository https://github.com/Marie59/champ_blocs commit 0d86db7d42b608c386a54500064f5f9c9d7019a4 ecology parents: diff changeset	888 "Nb.Tethya.aurantium",
89f977a3a256 planemo upload for repository https://github.com/Marie59/champ_blocs commit 0d86db7d42b608c386a54500064f5f9c9d7019a4 ecology parents: diff changeset	889 #"Nb.Spirobranchus.lamarckii.1B",
89f977a3a256 planemo upload for repository https://github.com/Marie59/champ_blocs commit 0d86db7d42b608c386a54500064f5f9c9d7019a4 ecology parents: diff changeset	890 #"Nb.Spirobranchus.lamarckii.2B",
89f977a3a256 planemo upload for repository https://github.com/Marie59/champ_blocs commit 0d86db7d42b608c386a54500064f5f9c9d7019a4 ecology parents: diff changeset	891 #"Nb.Spirobranchus.lamarckii.3B",
89f977a3a256 planemo upload for repository https://github.com/Marie59/champ_blocs commit 0d86db7d42b608c386a54500064f5f9c9d7019a4 ecology parents: diff changeset	892 #"Nb.Spirobranchus.lamarckii.4B",
89f977a3a256 planemo upload for repository https://github.com/Marie59/champ_blocs commit 0d86db7d42b608c386a54500064f5f9c9d7019a4 ecology parents: diff changeset	893 #"Nb.Spirobranchus.lamarckii.5B",
89f977a3a256 planemo upload for repository https://github.com/Marie59/champ_blocs commit 0d86db7d42b608c386a54500064f5f9c9d7019a4 ecology parents: diff changeset	894 "Nb.Spirobranchus.lamarckii.total",
89f977a3a256 planemo upload for repository https://github.com/Marie59/champ_blocs commit 0d86db7d42b608c386a54500064f5f9c9d7019a4 ecology parents: diff changeset	895 #"Nb.spirorbis.1A",
89f977a3a256 planemo upload for repository https://github.com/Marie59/champ_blocs commit 0d86db7d42b608c386a54500064f5f9c9d7019a4 ecology parents: diff changeset	896 #"Nb.spirorbis.2A",
89f977a3a256 planemo upload for repository https://github.com/Marie59/champ_blocs commit 0d86db7d42b608c386a54500064f5f9c9d7019a4 ecology parents: diff changeset	897 #"Nb.spirorbis.3A",
89f977a3a256 planemo upload for repository https://github.com/Marie59/champ_blocs commit 0d86db7d42b608c386a54500064f5f9c9d7019a4 ecology parents: diff changeset	898 #"Nb.spirorbis.4A",
89f977a3a256 planemo upload for repository https://github.com/Marie59/champ_blocs commit 0d86db7d42b608c386a54500064f5f9c9d7019a4 ecology parents: diff changeset	899 #"Nb.spirorbis.5A",
89f977a3a256 planemo upload for repository https://github.com/Marie59/champ_blocs commit 0d86db7d42b608c386a54500064f5f9c9d7019a4 ecology parents: diff changeset	900 "Nb.spirorbis.total",
89f977a3a256 planemo upload for repository https://github.com/Marie59/champ_blocs commit 0d86db7d42b608c386a54500064f5f9c9d7019a4 ecology parents: diff changeset	901 "Nb.Crassostrea.gigas",
89f977a3a256 planemo upload for repository https://github.com/Marie59/champ_blocs commit 0d86db7d42b608c386a54500064f5f9c9d7019a4 ecology parents: diff changeset	902 "Nb.Ostrea.edulis",
89f977a3a256 planemo upload for repository https://github.com/Marie59/champ_blocs commit 0d86db7d42b608c386a54500064f5f9c9d7019a4 ecology parents: diff changeset	903 "X..Mytilus.sp.",
89f977a3a256 planemo upload for repository https://github.com/Marie59/champ_blocs commit 0d86db7d42b608c386a54500064f5f9c9d7019a4 ecology parents: diff changeset	904 "X..Hermelles",
89f977a3a256 planemo upload for repository https://github.com/Marie59/champ_blocs commit 0d86db7d42b608c386a54500064f5f9c9d7019a4 ecology parents: diff changeset	905 "X..Hydraires",
89f977a3a256 planemo upload for repository https://github.com/Marie59/champ_blocs commit 0d86db7d42b608c386a54500064f5f9c9d7019a4 ecology parents: diff changeset	906 "X..Eponges",
89f977a3a256 planemo upload for repository https://github.com/Marie59/champ_blocs commit 0d86db7d42b608c386a54500064f5f9c9d7019a4 ecology parents: diff changeset	907 "X..Ascidies.Coloniales",
89f977a3a256 planemo upload for repository https://github.com/Marie59/champ_blocs commit 0d86db7d42b608c386a54500064f5f9c9d7019a4 ecology parents: diff changeset	908 "X..Ascidies.Solitaires",
89f977a3a256 planemo upload for repository https://github.com/Marie59/champ_blocs commit 0d86db7d42b608c386a54500064f5f9c9d7019a4 ecology parents: diff changeset	909 "X..Bryozoaires.Dresses",
89f977a3a256 planemo upload for repository https://github.com/Marie59/champ_blocs commit 0d86db7d42b608c386a54500064f5f9c9d7019a4 ecology parents: diff changeset	910 "X..Balanes.Vivantes",
89f977a3a256 planemo upload for repository https://github.com/Marie59/champ_blocs commit 0d86db7d42b608c386a54500064f5f9c9d7019a4 ecology parents: diff changeset	911 #"Commentaires.Avant",
89f977a3a256 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.
89f977a3a256 planemo upload for repository https://github.com/Marie59/champ_blocs commit 0d86db7d42b608c386a54500064f5f9c9d7019a4 ecology parents: diff changeset	913 #"Type.sustrat.observé",
89f977a3a256 planemo upload for repository https://github.com/Marie59/champ_blocs commit 0d86db7d42b608c386a54500064f5f9c9d7019a4 ecology parents: diff changeset	914 #"Commentaires",
89f977a3a256 planemo upload for repository https://github.com/Marie59/champ_blocs commit 0d86db7d42b608c386a54500064f5f9c9d7019a4 ecology parents: diff changeset	915 "Nb.Cancer.pagurus..Tourteau.",
89f977a3a256 planemo upload for repository https://github.com/Marie59/champ_blocs commit 0d86db7d42b608c386a54500064f5f9c9d7019a4 ecology parents: diff changeset	916 "Nb.Necora.puber..Etrille.",
89f977a3a256 planemo upload for repository https://github.com/Marie59/champ_blocs commit 0d86db7d42b608c386a54500064f5f9c9d7019a4 ecology parents: diff changeset	917 "Nb.Carcinus.maenas..Crabe.vert.",
89f977a3a256 planemo upload for repository https://github.com/Marie59/champ_blocs commit 0d86db7d42b608c386a54500064f5f9c9d7019a4 ecology parents: diff changeset	918 "Nb.Nucella.lapilus..Pourpre.",
89f977a3a256 planemo upload for repository https://github.com/Marie59/champ_blocs commit 0d86db7d42b608c386a54500064f5f9c9d7019a4 ecology parents: diff changeset	919 "Nb.Eriphia.verrucosa..Crabe.verruqueux.",
89f977a3a256 planemo upload for repository https://github.com/Marie59/champ_blocs commit 0d86db7d42b608c386a54500064f5f9c9d7019a4 ecology parents: diff changeset	920 "Nb.Octopus.vulgaris..Poulpe.",
89f977a3a256 planemo upload for repository https://github.com/Marie59/champ_blocs commit 0d86db7d42b608c386a54500064f5f9c9d7019a4 ecology parents: diff changeset	921 "Nb.Galathea..Galathées.",
89f977a3a256 planemo upload for repository https://github.com/Marie59/champ_blocs commit 0d86db7d42b608c386a54500064f5f9c9d7019a4 ecology parents: diff changeset	922 "Nb.Paracentrotus.lividus..Oursin.",
89f977a3a256 planemo upload for repository https://github.com/Marie59/champ_blocs commit 0d86db7d42b608c386a54500064f5f9c9d7019a4 ecology parents: diff changeset	923 "Nb.Lophozozymus.incisus..ancien.Xantho.incisus.",
89f977a3a256 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.",
89f977a3a256 planemo upload for repository https://github.com/Marie59/champ_blocs commit 0d86db7d42b608c386a54500064f5f9c9d7019a4 ecology parents: diff changeset	925 "Nb.Haliotis.tuberculata..Ormeau.",
89f977a3a256 planemo upload for repository https://github.com/Marie59/champ_blocs commit 0d86db7d42b608c386a54500064f5f9c9d7019a4 ecology parents: diff changeset	926 "Nb.Stramonita.haemastoma..Pourpre.bouche.de.sang.",
89f977a3a256 planemo upload for repository https://github.com/Marie59/champ_blocs commit 0d86db7d42b608c386a54500064f5f9c9d7019a4 ecology parents: diff changeset	927 "Nb.Littorina.littorea..Bigorneau.",
89f977a3a256 planemo upload for repository https://github.com/Marie59/champ_blocs commit 0d86db7d42b608c386a54500064f5f9c9d7019a4 ecology parents: diff changeset	928 "Nb.Xantho.pilipes..Xanthe.poilu.",
89f977a3a256 planemo upload for repository https://github.com/Marie59/champ_blocs commit 0d86db7d42b608c386a54500064f5f9c9d7019a4 ecology parents: diff changeset	929 "Nb.Mimachlamys.varia..Pétoncle.noir."
89f977a3a256 planemo upload for repository https://github.com/Marie59/champ_blocs commit 0d86db7d42b608c386a54500064f5f9c9d7019a4 ecology parents: diff changeset	930 )
89f977a3a256 planemo upload for repository https://github.com/Marie59/champ_blocs commit 0d86db7d42b608c386a54500064f5f9c9d7019a4 ecology parents: diff changeset	931 ] <- lapply(egmp_basq_bm[, c(
89f977a3a256 planemo upload for repository https://github.com/Marie59/champ_blocs commit 0d86db7d42b608c386a54500064f5f9c9d7019a4 ecology parents: diff changeset	932 "X..algues.brunes",
89f977a3a256 planemo upload for repository https://github.com/Marie59/champ_blocs commit 0d86db7d42b608c386a54500064f5f9c9d7019a4 ecology parents: diff changeset	933 "Strate.algues.brunes",
89f977a3a256 planemo upload for repository https://github.com/Marie59/champ_blocs commit 0d86db7d42b608c386a54500064f5f9c9d7019a4 ecology parents: diff changeset	934 "X..algues.rouges",
89f977a3a256 planemo upload for repository https://github.com/Marie59/champ_blocs commit 0d86db7d42b608c386a54500064f5f9c9d7019a4 ecology parents: diff changeset	935 "Strate.algues.rouges",
89f977a3a256 planemo upload for repository https://github.com/Marie59/champ_blocs commit 0d86db7d42b608c386a54500064f5f9c9d7019a4 ecology parents: diff changeset	936 "X..algues.vertes",
89f977a3a256 planemo upload for repository https://github.com/Marie59/champ_blocs commit 0d86db7d42b608c386a54500064f5f9c9d7019a4 ecology parents: diff changeset	937 "Strate.algues.vertes",
89f977a3a256 planemo upload for repository https://github.com/Marie59/champ_blocs commit 0d86db7d42b608c386a54500064f5f9c9d7019a4 ecology parents: diff changeset	938 "X..Cladophora",
89f977a3a256 planemo upload for repository https://github.com/Marie59/champ_blocs commit 0d86db7d42b608c386a54500064f5f9c9d7019a4 ecology parents: diff changeset	939 "X..Lithophyllum",
89f977a3a256 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.
89f977a3a256 planemo upload for repository https://github.com/Marie59/champ_blocs commit 0d86db7d42b608c386a54500064f5f9c9d7019a4 ecology parents: diff changeset	941 #"Type.Sediment",
89f977a3a256 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.
89f977a3a256 planemo upload for repository https://github.com/Marie59/champ_blocs commit 0d86db7d42b608c386a54500064f5f9c9d7019a4 ecology parents: diff changeset	943 "Nb.Littorina.obtusata",
89f977a3a256 planemo upload for repository https://github.com/Marie59/champ_blocs commit 0d86db7d42b608c386a54500064f5f9c9d7019a4 ecology parents: diff changeset	944 "Nb.Gibbula.cineraria",
89f977a3a256 planemo upload for repository https://github.com/Marie59/champ_blocs commit 0d86db7d42b608c386a54500064f5f9c9d7019a4 ecology parents: diff changeset	945 "Nb.Gibbula.pennanti",
89f977a3a256 planemo upload for repository https://github.com/Marie59/champ_blocs commit 0d86db7d42b608c386a54500064f5f9c9d7019a4 ecology parents: diff changeset	946 "Nb.Gibbula.umbilicalis",
89f977a3a256 planemo upload for repository https://github.com/Marie59/champ_blocs commit 0d86db7d42b608c386a54500064f5f9c9d7019a4 ecology parents: diff changeset	947 "Nb.Phallusia.mamillata",
89f977a3a256 planemo upload for repository https://github.com/Marie59/champ_blocs commit 0d86db7d42b608c386a54500064f5f9c9d7019a4 ecology parents: diff changeset	948 "Nb.Tethya.aurantium",
89f977a3a256 planemo upload for repository https://github.com/Marie59/champ_blocs commit 0d86db7d42b608c386a54500064f5f9c9d7019a4 ecology parents: diff changeset	949 #"Nb.Spirobranchus.lamarckii.1B",
89f977a3a256 planemo upload for repository https://github.com/Marie59/champ_blocs commit 0d86db7d42b608c386a54500064f5f9c9d7019a4 ecology parents: diff changeset	950 #"Nb.Spirobranchus.lamarckii.2B",
89f977a3a256 planemo upload for repository https://github.com/Marie59/champ_blocs commit 0d86db7d42b608c386a54500064f5f9c9d7019a4 ecology parents: diff changeset	951 #"Nb.Spirobranchus.lamarckii.3B",
89f977a3a256 planemo upload for repository https://github.com/Marie59/champ_blocs commit 0d86db7d42b608c386a54500064f5f9c9d7019a4 ecology parents: diff changeset	952 #"Nb.Spirobranchus.lamarckii.4B",
89f977a3a256 planemo upload for repository https://github.com/Marie59/champ_blocs commit 0d86db7d42b608c386a54500064f5f9c9d7019a4 ecology parents: diff changeset	953 #"Nb.Spirobranchus.lamarckii.5B",
89f977a3a256 planemo upload for repository https://github.com/Marie59/champ_blocs commit 0d86db7d42b608c386a54500064f5f9c9d7019a4 ecology parents: diff changeset	954 "Nb.Spirobranchus.lamarckii.total",
89f977a3a256 planemo upload for repository https://github.com/Marie59/champ_blocs commit 0d86db7d42b608c386a54500064f5f9c9d7019a4 ecology parents: diff changeset	955 #"Nb.spirorbis.1A",
89f977a3a256 planemo upload for repository https://github.com/Marie59/champ_blocs commit 0d86db7d42b608c386a54500064f5f9c9d7019a4 ecology parents: diff changeset	956 #"Nb.spirorbis.2A",
89f977a3a256 planemo upload for repository https://github.com/Marie59/champ_blocs commit 0d86db7d42b608c386a54500064f5f9c9d7019a4 ecology parents: diff changeset	957 #"Nb.spirorbis.3A",
89f977a3a256 planemo upload for repository https://github.com/Marie59/champ_blocs commit 0d86db7d42b608c386a54500064f5f9c9d7019a4 ecology parents: diff changeset	958 #"Nb.spirorbis.4A",
89f977a3a256 planemo upload for repository https://github.com/Marie59/champ_blocs commit 0d86db7d42b608c386a54500064f5f9c9d7019a4 ecology parents: diff changeset	959 #"Nb.spirorbis.5A",
89f977a3a256 planemo upload for repository https://github.com/Marie59/champ_blocs commit 0d86db7d42b608c386a54500064f5f9c9d7019a4 ecology parents: diff changeset	960 "Nb.spirorbis.total",
89f977a3a256 planemo upload for repository https://github.com/Marie59/champ_blocs commit 0d86db7d42b608c386a54500064f5f9c9d7019a4 ecology parents: diff changeset	961 "Nb.Crassostrea.gigas",
89f977a3a256 planemo upload for repository https://github.com/Marie59/champ_blocs commit 0d86db7d42b608c386a54500064f5f9c9d7019a4 ecology parents: diff changeset	962 "Nb.Ostrea.edulis",
89f977a3a256 planemo upload for repository https://github.com/Marie59/champ_blocs commit 0d86db7d42b608c386a54500064f5f9c9d7019a4 ecology parents: diff changeset	963 "X..Mytilus.sp.",
89f977a3a256 planemo upload for repository https://github.com/Marie59/champ_blocs commit 0d86db7d42b608c386a54500064f5f9c9d7019a4 ecology parents: diff changeset	964 "X..Hermelles",
89f977a3a256 planemo upload for repository https://github.com/Marie59/champ_blocs commit 0d86db7d42b608c386a54500064f5f9c9d7019a4 ecology parents: diff changeset	965 "X..Hydraires",
89f977a3a256 planemo upload for repository https://github.com/Marie59/champ_blocs commit 0d86db7d42b608c386a54500064f5f9c9d7019a4 ecology parents: diff changeset	966 "X..Eponges",
89f977a3a256 planemo upload for repository https://github.com/Marie59/champ_blocs commit 0d86db7d42b608c386a54500064f5f9c9d7019a4 ecology parents: diff changeset	967 "X..Ascidies.Coloniales",
89f977a3a256 planemo upload for repository https://github.com/Marie59/champ_blocs commit 0d86db7d42b608c386a54500064f5f9c9d7019a4 ecology parents: diff changeset	968 "X..Ascidies.Solitaires",
89f977a3a256 planemo upload for repository https://github.com/Marie59/champ_blocs commit 0d86db7d42b608c386a54500064f5f9c9d7019a4 ecology parents: diff changeset	969 "X..Bryozoaires.Dresses",
89f977a3a256 planemo upload for repository https://github.com/Marie59/champ_blocs commit 0d86db7d42b608c386a54500064f5f9c9d7019a4 ecology parents: diff changeset	970 "X..Balanes.Vivantes",
89f977a3a256 planemo upload for repository https://github.com/Marie59/champ_blocs commit 0d86db7d42b608c386a54500064f5f9c9d7019a4 ecology parents: diff changeset	971 #"Commentaires.Avant",
89f977a3a256 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.
89f977a3a256 planemo upload for repository https://github.com/Marie59/champ_blocs commit 0d86db7d42b608c386a54500064f5f9c9d7019a4 ecology parents: diff changeset	973 #"Type.sustrat.observé",
89f977a3a256 planemo upload for repository https://github.com/Marie59/champ_blocs commit 0d86db7d42b608c386a54500064f5f9c9d7019a4 ecology parents: diff changeset	974 #"Commentaires",
89f977a3a256 planemo upload for repository https://github.com/Marie59/champ_blocs commit 0d86db7d42b608c386a54500064f5f9c9d7019a4 ecology parents: diff changeset	975 "Nb.Cancer.pagurus..Tourteau.",
89f977a3a256 planemo upload for repository https://github.com/Marie59/champ_blocs commit 0d86db7d42b608c386a54500064f5f9c9d7019a4 ecology parents: diff changeset	976 "Nb.Necora.puber..Etrille.",
89f977a3a256 planemo upload for repository https://github.com/Marie59/champ_blocs commit 0d86db7d42b608c386a54500064f5f9c9d7019a4 ecology parents: diff changeset	977 "Nb.Carcinus.maenas..Crabe.vert.",
89f977a3a256 planemo upload for repository https://github.com/Marie59/champ_blocs commit 0d86db7d42b608c386a54500064f5f9c9d7019a4 ecology parents: diff changeset	978 "Nb.Nucella.lapilus..Pourpre.",
89f977a3a256 planemo upload for repository https://github.com/Marie59/champ_blocs commit 0d86db7d42b608c386a54500064f5f9c9d7019a4 ecology parents: diff changeset	979 "Nb.Eriphia.verrucosa..Crabe.verruqueux.",
89f977a3a256 planemo upload for repository https://github.com/Marie59/champ_blocs commit 0d86db7d42b608c386a54500064f5f9c9d7019a4 ecology parents: diff changeset	980 "Nb.Octopus.vulgaris..Poulpe.",
89f977a3a256 planemo upload for repository https://github.com/Marie59/champ_blocs commit 0d86db7d42b608c386a54500064f5f9c9d7019a4 ecology parents: diff changeset	981 "Nb.Galathea..Galathées.",
89f977a3a256 planemo upload for repository https://github.com/Marie59/champ_blocs commit 0d86db7d42b608c386a54500064f5f9c9d7019a4 ecology parents: diff changeset	982 "Nb.Paracentrotus.lividus..Oursin.",
89f977a3a256 planemo upload for repository https://github.com/Marie59/champ_blocs commit 0d86db7d42b608c386a54500064f5f9c9d7019a4 ecology parents: diff changeset	983 "Nb.Lophozozymus.incisus..ancien.Xantho.incisus.",
89f977a3a256 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.",
89f977a3a256 planemo upload for repository https://github.com/Marie59/champ_blocs commit 0d86db7d42b608c386a54500064f5f9c9d7019a4 ecology parents: diff changeset	985 "Nb.Haliotis.tuberculata..Ormeau.",
89f977a3a256 planemo upload for repository https://github.com/Marie59/champ_blocs commit 0d86db7d42b608c386a54500064f5f9c9d7019a4 ecology parents: diff changeset	986 "Nb.Stramonita.haemastoma..Pourpre.bouche.de.sang.",
89f977a3a256 planemo upload for repository https://github.com/Marie59/champ_blocs commit 0d86db7d42b608c386a54500064f5f9c9d7019a4 ecology parents: diff changeset	987 "Nb.Littorina.littorea..Bigorneau.",
89f977a3a256 planemo upload for repository https://github.com/Marie59/champ_blocs commit 0d86db7d42b608c386a54500064f5f9c9d7019a4 ecology parents: diff changeset	988 "Nb.Xantho.pilipes..Xanthe.poilu.",
89f977a3a256 planemo upload for repository https://github.com/Marie59/champ_blocs commit 0d86db7d42b608c386a54500064f5f9c9d7019a4 ecology parents: diff changeset	989 "Nb.Mimachlamys.varia..Pétoncle.noir."
89f977a3a256 planemo upload for repository https://github.com/Marie59/champ_blocs commit 0d86db7d42b608c386a54500064f5f9c9d7019a4 ecology parents: diff changeset	990 )
89f977a3a256 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))
89f977a3a256 planemo upload for repository https://github.com/Marie59/champ_blocs commit 0d86db7d42b608c386a54500064f5f9c9d7019a4 ecology parents: diff changeset	992
89f977a3a256 planemo upload for repository https://github.com/Marie59/champ_blocs commit 0d86db7d42b608c386a54500064f5f9c9d7019a4 ecology parents: diff changeset	993
89f977a3a256 planemo upload for repository https://github.com/Marie59/champ_blocs commit 0d86db7d42b608c386a54500064f5f9c9d7019a4 ecology parents: diff changeset	994 # egmp_basq_bf
89f977a3a256 planemo upload for repository https://github.com/Marie59/champ_blocs commit 0d86db7d42b608c386a54500064f5f9c9d7019a4 ecology parents: diff changeset	995 egmp_basq_bf[, c(
89f977a3a256 planemo upload for repository https://github.com/Marie59/champ_blocs commit 0d86db7d42b608c386a54500064f5f9c9d7019a4 ecology parents: diff changeset	996 "X..algues.brunes",
89f977a3a256 planemo upload for repository https://github.com/Marie59/champ_blocs commit 0d86db7d42b608c386a54500064f5f9c9d7019a4 ecology parents: diff changeset	997 "Strate.algues.brunes",
89f977a3a256 planemo upload for repository https://github.com/Marie59/champ_blocs commit 0d86db7d42b608c386a54500064f5f9c9d7019a4 ecology parents: diff changeset	998 "X..algues.rouges",
89f977a3a256 planemo upload for repository https://github.com/Marie59/champ_blocs commit 0d86db7d42b608c386a54500064f5f9c9d7019a4 ecology parents: diff changeset	999 "Strate.algues.rouges",
89f977a3a256 planemo upload for repository https://github.com/Marie59/champ_blocs commit 0d86db7d42b608c386a54500064f5f9c9d7019a4 ecology parents: diff changeset	1000 "X..algues.vertes",
89f977a3a256 planemo upload for repository https://github.com/Marie59/champ_blocs commit 0d86db7d42b608c386a54500064f5f9c9d7019a4 ecology parents: diff changeset	1001 "Strate.algues.vertes",
89f977a3a256 planemo upload for repository https://github.com/Marie59/champ_blocs commit 0d86db7d42b608c386a54500064f5f9c9d7019a4 ecology parents: diff changeset	1002 "X..Cladophora",
89f977a3a256 planemo upload for repository https://github.com/Marie59/champ_blocs commit 0d86db7d42b608c386a54500064f5f9c9d7019a4 ecology parents: diff changeset	1003 "X..Lithophyllum",
89f977a3a256 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.
89f977a3a256 planemo upload for repository https://github.com/Marie59/champ_blocs commit 0d86db7d42b608c386a54500064f5f9c9d7019a4 ecology parents: diff changeset	1005 #"Type.Sediment",
89f977a3a256 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.
89f977a3a256 planemo upload for repository https://github.com/Marie59/champ_blocs commit 0d86db7d42b608c386a54500064f5f9c9d7019a4 ecology parents: diff changeset	1007 "Nb.Littorina.obtusata",
89f977a3a256 planemo upload for repository https://github.com/Marie59/champ_blocs commit 0d86db7d42b608c386a54500064f5f9c9d7019a4 ecology parents: diff changeset	1008 "Nb.Gibbula.cineraria",
89f977a3a256 planemo upload for repository https://github.com/Marie59/champ_blocs commit 0d86db7d42b608c386a54500064f5f9c9d7019a4 ecology parents: diff changeset	1009 "Nb.Gibbula.pennanti",
89f977a3a256 planemo upload for repository https://github.com/Marie59/champ_blocs commit 0d86db7d42b608c386a54500064f5f9c9d7019a4 ecology parents: diff changeset	1010 "Nb.Gibbula.umbilicalis",
89f977a3a256 planemo upload for repository https://github.com/Marie59/champ_blocs commit 0d86db7d42b608c386a54500064f5f9c9d7019a4 ecology parents: diff changeset	1011 "Nb.Phallusia.mamillata",
89f977a3a256 planemo upload for repository https://github.com/Marie59/champ_blocs commit 0d86db7d42b608c386a54500064f5f9c9d7019a4 ecology parents: diff changeset	1012 "Nb.Tethya.aurantium",
89f977a3a256 planemo upload for repository https://github.com/Marie59/champ_blocs commit 0d86db7d42b608c386a54500064f5f9c9d7019a4 ecology parents: diff changeset	1013 #"Nb.Spirobranchus.lamarckii.1B",
89f977a3a256 planemo upload for repository https://github.com/Marie59/champ_blocs commit 0d86db7d42b608c386a54500064f5f9c9d7019a4 ecology parents: diff changeset	1014 #"Nb.Spirobranchus.lamarckii.2B",
89f977a3a256 planemo upload for repository https://github.com/Marie59/champ_blocs commit 0d86db7d42b608c386a54500064f5f9c9d7019a4 ecology parents: diff changeset	1015 #"Nb.Spirobranchus.lamarckii.3B",
89f977a3a256 planemo upload for repository https://github.com/Marie59/champ_blocs commit 0d86db7d42b608c386a54500064f5f9c9d7019a4 ecology parents: diff changeset	1016 #"Nb.Spirobranchus.lamarckii.4B",
89f977a3a256 planemo upload for repository https://github.com/Marie59/champ_blocs commit 0d86db7d42b608c386a54500064f5f9c9d7019a4 ecology parents: diff changeset	1017 #"Nb.Spirobranchus.lamarckii.5B",
89f977a3a256 planemo upload for repository https://github.com/Marie59/champ_blocs commit 0d86db7d42b608c386a54500064f5f9c9d7019a4 ecology parents: diff changeset	1018 "Nb.Spirobranchus.lamarckii.total",
89f977a3a256 planemo upload for repository https://github.com/Marie59/champ_blocs commit 0d86db7d42b608c386a54500064f5f9c9d7019a4 ecology parents: diff changeset	1019 #"Nb.spirorbis.1A",
89f977a3a256 planemo upload for repository https://github.com/Marie59/champ_blocs commit 0d86db7d42b608c386a54500064f5f9c9d7019a4 ecology parents: diff changeset	1020 #"Nb.spirorbis.2A",
89f977a3a256 planemo upload for repository https://github.com/Marie59/champ_blocs commit 0d86db7d42b608c386a54500064f5f9c9d7019a4 ecology parents: diff changeset	1021 #"Nb.spirorbis.3A",
89f977a3a256 planemo upload for repository https://github.com/Marie59/champ_blocs commit 0d86db7d42b608c386a54500064f5f9c9d7019a4 ecology parents: diff changeset	1022 #"Nb.spirorbis.4A",
89f977a3a256 planemo upload for repository https://github.com/Marie59/champ_blocs commit 0d86db7d42b608c386a54500064f5f9c9d7019a4 ecology parents: diff changeset	1023 #"Nb.spirorbis.5A",
89f977a3a256 planemo upload for repository https://github.com/Marie59/champ_blocs commit 0d86db7d42b608c386a54500064f5f9c9d7019a4 ecology parents: diff changeset	1024 "Nb.spirorbis.total",
89f977a3a256 planemo upload for repository https://github.com/Marie59/champ_blocs commit 0d86db7d42b608c386a54500064f5f9c9d7019a4 ecology parents: diff changeset	1025 "Nb.Crassostrea.gigas",
89f977a3a256 planemo upload for repository https://github.com/Marie59/champ_blocs commit 0d86db7d42b608c386a54500064f5f9c9d7019a4 ecology parents: diff changeset	1026 "Nb.Ostrea.edulis",
89f977a3a256 planemo upload for repository https://github.com/Marie59/champ_blocs commit 0d86db7d42b608c386a54500064f5f9c9d7019a4 ecology parents: diff changeset	1027 "X..Mytilus.sp.",
89f977a3a256 planemo upload for repository https://github.com/Marie59/champ_blocs commit 0d86db7d42b608c386a54500064f5f9c9d7019a4 ecology parents: diff changeset	1028 "X..Hermelles",
89f977a3a256 planemo upload for repository https://github.com/Marie59/champ_blocs commit 0d86db7d42b608c386a54500064f5f9c9d7019a4 ecology parents: diff changeset	1029 "X..Hydraires",
89f977a3a256 planemo upload for repository https://github.com/Marie59/champ_blocs commit 0d86db7d42b608c386a54500064f5f9c9d7019a4 ecology parents: diff changeset	1030 "X..Eponges",
89f977a3a256 planemo upload for repository https://github.com/Marie59/champ_blocs commit 0d86db7d42b608c386a54500064f5f9c9d7019a4 ecology parents: diff changeset	1031 "X..Ascidies.Coloniales",
89f977a3a256 planemo upload for repository https://github.com/Marie59/champ_blocs commit 0d86db7d42b608c386a54500064f5f9c9d7019a4 ecology parents: diff changeset	1032 "X..Ascidies.Solitaires",
89f977a3a256 planemo upload for repository https://github.com/Marie59/champ_blocs commit 0d86db7d42b608c386a54500064f5f9c9d7019a4 ecology parents: diff changeset	1033 "X..Bryozoaires.Dresses",
89f977a3a256 planemo upload for repository https://github.com/Marie59/champ_blocs commit 0d86db7d42b608c386a54500064f5f9c9d7019a4 ecology parents: diff changeset	1034 "X..Balanes.Vivantes",
89f977a3a256 planemo upload for repository https://github.com/Marie59/champ_blocs commit 0d86db7d42b608c386a54500064f5f9c9d7019a4 ecology parents: diff changeset	1035 #"Commentaires.Avant",
89f977a3a256 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.
89f977a3a256 planemo upload for repository https://github.com/Marie59/champ_blocs commit 0d86db7d42b608c386a54500064f5f9c9d7019a4 ecology parents: diff changeset	1037 #"Type.sustrat.observé",
89f977a3a256 planemo upload for repository https://github.com/Marie59/champ_blocs commit 0d86db7d42b608c386a54500064f5f9c9d7019a4 ecology parents: diff changeset	1038 #"Commentaires",
89f977a3a256 planemo upload for repository https://github.com/Marie59/champ_blocs commit 0d86db7d42b608c386a54500064f5f9c9d7019a4 ecology parents: diff changeset	1039 #."Nb.Cancer.pagurus..Tourteau.",
89f977a3a256 planemo upload for repository https://github.com/Marie59/champ_blocs commit 0d86db7d42b608c386a54500064f5f9c9d7019a4 ecology parents: diff changeset	1040 #.."Nb.Necora.puber..Etrille.",
89f977a3a256 planemo upload for repository https://github.com/Marie59/champ_blocs commit 0d86db7d42b608c386a54500064f5f9c9d7019a4 ecology parents: diff changeset	1041 #."Nb.Carcinus.maenas..Crabe.vert.",
89f977a3a256 planemo upload for repository https://github.com/Marie59/champ_blocs commit 0d86db7d42b608c386a54500064f5f9c9d7019a4 ecology parents: diff changeset	1042 #."Nb.Nucella.lapilus..Pourpre.",
89f977a3a256 planemo upload for repository https://github.com/Marie59/champ_blocs commit 0d86db7d42b608c386a54500064f5f9c9d7019a4 ecology parents: diff changeset	1043 #.."Nb.Eriphia.verrucosa..Crabe.verruqueux.",
89f977a3a256 planemo upload for repository https://github.com/Marie59/champ_blocs commit 0d86db7d42b608c386a54500064f5f9c9d7019a4 ecology parents: diff changeset	1044 #.."Nb.Octopus.vulgaris..Poulpe.",
89f977a3a256 planemo upload for repository https://github.com/Marie59/champ_blocs commit 0d86db7d42b608c386a54500064f5f9c9d7019a4 ecology parents: diff changeset	1045 #."Nb.Galathea..Galathées.",
89f977a3a256 planemo upload for repository https://github.com/Marie59/champ_blocs commit 0d86db7d42b608c386a54500064f5f9c9d7019a4 ecology parents: diff changeset	1046 #.."Nb.Paracentrotus.lividus..Oursin.",
89f977a3a256 planemo upload for repository https://github.com/Marie59/champ_blocs commit 0d86db7d42b608c386a54500064f5f9c9d7019a4 ecology parents: diff changeset	1047 #."Nb.Lophozozymus.incisus..ancien.Xantho.incisus.",
89f977a3a256 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.",
89f977a3a256 planemo upload for repository https://github.com/Marie59/champ_blocs commit 0d86db7d42b608c386a54500064f5f9c9d7019a4 ecology parents: diff changeset	1049 #."Nb.Haliotis.tuberculata..Ormeau.",
89f977a3a256 planemo upload for repository https://github.com/Marie59/champ_blocs commit 0d86db7d42b608c386a54500064f5f9c9d7019a4 ecology parents: diff changeset	1050 #."Nb.Stramonita.haemastoma..Pourpre.bouche.de.sang.",
89f977a3a256 planemo upload for repository https://github.com/Marie59/champ_blocs commit 0d86db7d42b608c386a54500064f5f9c9d7019a4 ecology parents: diff changeset	1051 #."Nb.Littorina.littorea..Bigorneau.",
89f977a3a256 planemo upload for repository https://github.com/Marie59/champ_blocs commit 0d86db7d42b608c386a54500064f5f9c9d7019a4 ecology parents: diff changeset	1052 #."Nb.Xantho.pilipes..Xanthe.poilu.",
89f977a3a256 planemo upload for repository https://github.com/Marie59/champ_blocs commit 0d86db7d42b608c386a54500064f5f9c9d7019a4 ecology parents: diff changeset	1053 #."Nb.Mimachlamys.varia..Pétoncle.noir."
89f977a3a256 planemo upload for repository https://github.com/Marie59/champ_blocs commit 0d86db7d42b608c386a54500064f5f9c9d7019a4 ecology parents: diff changeset	1054 )
89f977a3a256 planemo upload for repository https://github.com/Marie59/champ_blocs commit 0d86db7d42b608c386a54500064f5f9c9d7019a4 ecology parents: diff changeset	1055 ] <- lapply(egmp_basq_bf[, c(
89f977a3a256 planemo upload for repository https://github.com/Marie59/champ_blocs commit 0d86db7d42b608c386a54500064f5f9c9d7019a4 ecology parents: diff changeset	1056 "X..algues.brunes",
89f977a3a256 planemo upload for repository https://github.com/Marie59/champ_blocs commit 0d86db7d42b608c386a54500064f5f9c9d7019a4 ecology parents: diff changeset	1057 "Strate.algues.brunes",
89f977a3a256 planemo upload for repository https://github.com/Marie59/champ_blocs commit 0d86db7d42b608c386a54500064f5f9c9d7019a4 ecology parents: diff changeset	1058 "X..algues.rouges",
89f977a3a256 planemo upload for repository https://github.com/Marie59/champ_blocs commit 0d86db7d42b608c386a54500064f5f9c9d7019a4 ecology parents: diff changeset	1059 "Strate.algues.rouges",
89f977a3a256 planemo upload for repository https://github.com/Marie59/champ_blocs commit 0d86db7d42b608c386a54500064f5f9c9d7019a4 ecology parents: diff changeset	1060 "X..algues.vertes",
89f977a3a256 planemo upload for repository https://github.com/Marie59/champ_blocs commit 0d86db7d42b608c386a54500064f5f9c9d7019a4 ecology parents: diff changeset	1061 "Strate.algues.vertes",
89f977a3a256 planemo upload for repository https://github.com/Marie59/champ_blocs commit 0d86db7d42b608c386a54500064f5f9c9d7019a4 ecology parents: diff changeset	1062 "X..Cladophora",
89f977a3a256 planemo upload for repository https://github.com/Marie59/champ_blocs commit 0d86db7d42b608c386a54500064f5f9c9d7019a4 ecology parents: diff changeset	1063 "X..Lithophyllum",
89f977a3a256 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.
89f977a3a256 planemo upload for repository https://github.com/Marie59/champ_blocs commit 0d86db7d42b608c386a54500064f5f9c9d7019a4 ecology parents: diff changeset	1065 #"Type.Sediment",
89f977a3a256 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.
89f977a3a256 planemo upload for repository https://github.com/Marie59/champ_blocs commit 0d86db7d42b608c386a54500064f5f9c9d7019a4 ecology parents: diff changeset	1067 "Nb.Littorina.obtusata",
89f977a3a256 planemo upload for repository https://github.com/Marie59/champ_blocs commit 0d86db7d42b608c386a54500064f5f9c9d7019a4 ecology parents: diff changeset	1068 "Nb.Gibbula.cineraria",
89f977a3a256 planemo upload for repository https://github.com/Marie59/champ_blocs commit 0d86db7d42b608c386a54500064f5f9c9d7019a4 ecology parents: diff changeset	1069 "Nb.Gibbula.pennanti",
89f977a3a256 planemo upload for repository https://github.com/Marie59/champ_blocs commit 0d86db7d42b608c386a54500064f5f9c9d7019a4 ecology parents: diff changeset	1070 "Nb.Gibbula.umbilicalis",
89f977a3a256 planemo upload for repository https://github.com/Marie59/champ_blocs commit 0d86db7d42b608c386a54500064f5f9c9d7019a4 ecology parents: diff changeset	1071 "Nb.Phallusia.mamillata",
89f977a3a256 planemo upload for repository https://github.com/Marie59/champ_blocs commit 0d86db7d42b608c386a54500064f5f9c9d7019a4 ecology parents: diff changeset	1072 "Nb.Tethya.aurantium",
89f977a3a256 planemo upload for repository https://github.com/Marie59/champ_blocs commit 0d86db7d42b608c386a54500064f5f9c9d7019a4 ecology parents: diff changeset	1073 #"Nb.Spirobranchus.lamarckii.1B",
89f977a3a256 planemo upload for repository https://github.com/Marie59/champ_blocs commit 0d86db7d42b608c386a54500064f5f9c9d7019a4 ecology parents: diff changeset	1074 #"Nb.Spirobranchus.lamarckii.2B",
89f977a3a256 planemo upload for repository https://github.com/Marie59/champ_blocs commit 0d86db7d42b608c386a54500064f5f9c9d7019a4 ecology parents: diff changeset	1075 #"Nb.Spirobranchus.lamarckii.3B",
89f977a3a256 planemo upload for repository https://github.com/Marie59/champ_blocs commit 0d86db7d42b608c386a54500064f5f9c9d7019a4 ecology parents: diff changeset	1076 #"Nb.Spirobranchus.lamarckii.4B",
89f977a3a256 planemo upload for repository https://github.com/Marie59/champ_blocs commit 0d86db7d42b608c386a54500064f5f9c9d7019a4 ecology parents: diff changeset	1077 #"Nb.Spirobranchus.lamarckii.5B",
89f977a3a256 planemo upload for repository https://github.com/Marie59/champ_blocs commit 0d86db7d42b608c386a54500064f5f9c9d7019a4 ecology parents: diff changeset	1078 "Nb.Spirobranchus.lamarckii.total",
89f977a3a256 planemo upload for repository https://github.com/Marie59/champ_blocs commit 0d86db7d42b608c386a54500064f5f9c9d7019a4 ecology parents: diff changeset	1079 #"Nb.spirorbis.1A",
89f977a3a256 planemo upload for repository https://github.com/Marie59/champ_blocs commit 0d86db7d42b608c386a54500064f5f9c9d7019a4 ecology parents: diff changeset	1080 #"Nb.spirorbis.2A",
89f977a3a256 planemo upload for repository https://github.com/Marie59/champ_blocs commit 0d86db7d42b608c386a54500064f5f9c9d7019a4 ecology parents: diff changeset	1081 #"Nb.spirorbis.3A",
89f977a3a256 planemo upload for repository https://github.com/Marie59/champ_blocs commit 0d86db7d42b608c386a54500064f5f9c9d7019a4 ecology parents: diff changeset	1082 #"Nb.spirorbis.4A",
89f977a3a256 planemo upload for repository https://github.com/Marie59/champ_blocs commit 0d86db7d42b608c386a54500064f5f9c9d7019a4 ecology parents: diff changeset	1083 #"Nb.spirorbis.5A",
89f977a3a256 planemo upload for repository https://github.com/Marie59/champ_blocs commit 0d86db7d42b608c386a54500064f5f9c9d7019a4 ecology parents: diff changeset	1084 "Nb.spirorbis.total",
89f977a3a256 planemo upload for repository https://github.com/Marie59/champ_blocs commit 0d86db7d42b608c386a54500064f5f9c9d7019a4 ecology parents: diff changeset	1085 "Nb.Crassostrea.gigas",
89f977a3a256 planemo upload for repository https://github.com/Marie59/champ_blocs commit 0d86db7d42b608c386a54500064f5f9c9d7019a4 ecology parents: diff changeset	1086 "Nb.Ostrea.edulis",
89f977a3a256 planemo upload for repository https://github.com/Marie59/champ_blocs commit 0d86db7d42b608c386a54500064f5f9c9d7019a4 ecology parents: diff changeset	1087 "X..Mytilus.sp.",
89f977a3a256 planemo upload for repository https://github.com/Marie59/champ_blocs commit 0d86db7d42b608c386a54500064f5f9c9d7019a4 ecology parents: diff changeset	1088 "X..Hermelles",
89f977a3a256 planemo upload for repository https://github.com/Marie59/champ_blocs commit 0d86db7d42b608c386a54500064f5f9c9d7019a4 ecology parents: diff changeset	1089 "X..Hydraires",
89f977a3a256 planemo upload for repository https://github.com/Marie59/champ_blocs commit 0d86db7d42b608c386a54500064f5f9c9d7019a4 ecology parents: diff changeset	1090 "X..Eponges",
89f977a3a256 planemo upload for repository https://github.com/Marie59/champ_blocs commit 0d86db7d42b608c386a54500064f5f9c9d7019a4 ecology parents: diff changeset	1091 "X..Ascidies.Coloniales",
89f977a3a256 planemo upload for repository https://github.com/Marie59/champ_blocs commit 0d86db7d42b608c386a54500064f5f9c9d7019a4 ecology parents: diff changeset	1092 "X..Ascidies.Solitaires",
89f977a3a256 planemo upload for repository https://github.com/Marie59/champ_blocs commit 0d86db7d42b608c386a54500064f5f9c9d7019a4 ecology parents: diff changeset	1093 "X..Bryozoaires.Dresses",
89f977a3a256 planemo upload for repository https://github.com/Marie59/champ_blocs commit 0d86db7d42b608c386a54500064f5f9c9d7019a4 ecology parents: diff changeset	1094 "X..Balanes.Vivantes",
89f977a3a256 planemo upload for repository https://github.com/Marie59/champ_blocs commit 0d86db7d42b608c386a54500064f5f9c9d7019a4 ecology parents: diff changeset	1095 #"Commentaires.Avant",
89f977a3a256 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.
89f977a3a256 planemo upload for repository https://github.com/Marie59/champ_blocs commit 0d86db7d42b608c386a54500064f5f9c9d7019a4 ecology parents: diff changeset	1097 #"Type.sustrat.observé",
89f977a3a256 planemo upload for repository https://github.com/Marie59/champ_blocs commit 0d86db7d42b608c386a54500064f5f9c9d7019a4 ecology parents: diff changeset	1098 #"Commentaires",
89f977a3a256 planemo upload for repository https://github.com/Marie59/champ_blocs commit 0d86db7d42b608c386a54500064f5f9c9d7019a4 ecology parents: diff changeset	1099 #."Nb.Cancer.pagurus..Tourteau.",
89f977a3a256 planemo upload for repository https://github.com/Marie59/champ_blocs commit 0d86db7d42b608c386a54500064f5f9c9d7019a4 ecology parents: diff changeset	1100 #.."Nb.Necora.puber..Etrille.",
89f977a3a256 planemo upload for repository https://github.com/Marie59/champ_blocs commit 0d86db7d42b608c386a54500064f5f9c9d7019a4 ecology parents: diff changeset	1101 #."Nb.Carcinus.maenas..Crabe.vert.",
89f977a3a256 planemo upload for repository https://github.com/Marie59/champ_blocs commit 0d86db7d42b608c386a54500064f5f9c9d7019a4 ecology parents: diff changeset	1102 #."Nb.Nucella.lapilus..Pourpre.",
89f977a3a256 planemo upload for repository https://github.com/Marie59/champ_blocs commit 0d86db7d42b608c386a54500064f5f9c9d7019a4 ecology parents: diff changeset	1103 #.."Nb.Eriphia.verrucosa..Crabe.verruqueux.",
89f977a3a256 planemo upload for repository https://github.com/Marie59/champ_blocs commit 0d86db7d42b608c386a54500064f5f9c9d7019a4 ecology parents: diff changeset	1104 #.."Nb.Octopus.vulgaris..Poulpe.",
89f977a3a256 planemo upload for repository https://github.com/Marie59/champ_blocs commit 0d86db7d42b608c386a54500064f5f9c9d7019a4 ecology parents: diff changeset	1105 #."Nb.Galathea..Galathées.",
89f977a3a256 planemo upload for repository https://github.com/Marie59/champ_blocs commit 0d86db7d42b608c386a54500064f5f9c9d7019a4 ecology parents: diff changeset	1106 #.."Nb.Paracentrotus.lividus..Oursin.",
89f977a3a256 planemo upload for repository https://github.com/Marie59/champ_blocs commit 0d86db7d42b608c386a54500064f5f9c9d7019a4 ecology parents: diff changeset	1107 #."Nb.Lophozozymus.incisus..ancien.Xantho.incisus.",
89f977a3a256 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.",
89f977a3a256 planemo upload for repository https://github.com/Marie59/champ_blocs commit 0d86db7d42b608c386a54500064f5f9c9d7019a4 ecology parents: diff changeset	1109 #."Nb.Haliotis.tuberculata..Ormeau.",
89f977a3a256 planemo upload for repository https://github.com/Marie59/champ_blocs commit 0d86db7d42b608c386a54500064f5f9c9d7019a4 ecology parents: diff changeset	1110 #."Nb.Stramonita.haemastoma..Pourpre.bouche.de.sang.",
89f977a3a256 planemo upload for repository https://github.com/Marie59/champ_blocs commit 0d86db7d42b608c386a54500064f5f9c9d7019a4 ecology parents: diff changeset	1111 #."Nb.Littorina.littorea..Bigorneau.",
89f977a3a256 planemo upload for repository https://github.com/Marie59/champ_blocs commit 0d86db7d42b608c386a54500064f5f9c9d7019a4 ecology parents: diff changeset	1112 #."Nb.Xantho.pilipes..Xanthe.poilu.",
89f977a3a256 planemo upload for repository https://github.com/Marie59/champ_blocs commit 0d86db7d42b608c386a54500064f5f9c9d7019a4 ecology parents: diff changeset	1113 #."Nb.Mimachlamys.varia..Pétoncle.noir."
89f977a3a256 planemo upload for repository https://github.com/Marie59/champ_blocs commit 0d86db7d42b608c386a54500064f5f9c9d7019a4 ecology parents: diff changeset	1114 )
89f977a3a256 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))
89f977a3a256 planemo upload for repository https://github.com/Marie59/champ_blocs commit 0d86db7d42b608c386a54500064f5f9c9d7019a4 ecology parents: diff changeset	1116
89f977a3a256 planemo upload for repository https://github.com/Marie59/champ_blocs commit 0d86db7d42b608c386a54500064f5f9c9d7019a4 ecology parents: diff changeset	1117
89f977a3a256 planemo upload for repository https://github.com/Marie59/champ_blocs commit 0d86db7d42b608c386a54500064f5f9c9d7019a4 ecology parents: diff changeset	1118 # merge dfs.
89f977a3a256 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)
89f977a3a256 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)
89f977a3a256 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)
89f977a3a256 planemo upload for repository https://github.com/Marie59/champ_blocs commit 0d86db7d42b608c386a54500064f5f9c9d7019a4 ecology parents: diff changeset	1122
89f977a3a256 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)
89f977a3a256 planemo upload for repository https://github.com/Marie59/champ_blocs commit 0d86db7d42b608c386a54500064f5f9c9d7019a4 ecology parents: diff changeset	1124
89f977a3a256 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)
89f977a3a256 planemo upload for repository https://github.com/Marie59/champ_blocs commit 0d86db7d42b608c386a54500064f5f9c9d7019a4 ecology parents: diff changeset	1126
89f977a3a256 planemo upload for repository https://github.com/Marie59/champ_blocs commit 0d86db7d42b608c386a54500064f5f9c9d7019a4 ecology parents: diff changeset	1127
89f977a3a256 planemo upload for repository https://github.com/Marie59/champ_blocs commit 0d86db7d42b608c386a54500064f5f9c9d7019a4 ecology parents: diff changeset	1128 ## analyse matricielle
89f977a3a256 planemo upload for repository https://github.com/Marie59/champ_blocs commit 0d86db7d42b608c386a54500064f5f9c9d7019a4 ecology parents: diff changeset	1129
89f977a3a256 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.
89f977a3a256 planemo upload for repository https://github.com/Marie59/champ_blocs commit 0d86db7d42b608c386a54500064f5f9c9d7019a4 ecology parents: diff changeset	1131
89f977a3a256 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")
89f977a3a256 planemo upload for repository https://github.com/Marie59/champ_blocs commit 0d86db7d42b608c386a54500064f5f9c9d7019a4 ecology parents: diff changeset	1133
89f977a3a256 planemo upload for repository https://github.com/Marie59/champ_blocs commit 0d86db7d42b608c386a54500064f5f9c9d7019a4 ecology parents: diff changeset	1134
89f977a3a256 planemo upload for repository https://github.com/Marie59/champ_blocs commit 0d86db7d42b608c386a54500064f5f9c9d7019a4 ecology parents: diff changeset	1135 numero_quadrat <- stringr::str_sub(qecbnato0$quadrat_bis, start = -1)
89f977a3a256 planemo upload for repository https://github.com/Marie59/champ_blocs commit 0d86db7d42b608c386a54500064f5f9c9d7019a4 ecology parents: diff changeset	1136 qecbnato0 <- tibble::add_column(qecbnato0, numero_quadrat, .after = "quadrat_bis")
89f977a3a256 planemo upload for repository https://github.com/Marie59/champ_blocs commit 0d86db7d42b608c386a54500064f5f9c9d7019a4 ecology parents: diff changeset	1137 rm(numero_quadrat)
89f977a3a256 planemo upload for repository https://github.com/Marie59/champ_blocs commit 0d86db7d42b608c386a54500064f5f9c9d7019a4 ecology parents: diff changeset	1138 qecbnato0$numero_quadrat <- as.integer(qecbnato0$numero_quadrat)
89f977a3a256 planemo upload for repository https://github.com/Marie59/champ_blocs commit 0d86db7d42b608c386a54500064f5f9c9d7019a4 ecology parents: diff changeset	1139
89f977a3a256 planemo upload for repository https://github.com/Marie59/champ_blocs commit 0d86db7d42b608c386a54500064f5f9c9d7019a4 ecology parents: diff changeset	1140
89f977a3a256 planemo upload for repository https://github.com/Marie59/champ_blocs commit 0d86db7d42b608c386a54500064f5f9c9d7019a4 ecology parents: diff changeset	1141 qecbnato0$Year <- as.integer(qecbnato0$Year)
89f977a3a256 planemo upload for repository https://github.com/Marie59/champ_blocs commit 0d86db7d42b608c386a54500064f5f9c9d7019a4 ecology parents: diff changeset	1142 qecbnato0$Month <- as.integer(qecbnato0$Month)
89f977a3a256 planemo upload for repository https://github.com/Marie59/champ_blocs commit 0d86db7d42b608c386a54500064f5f9c9d7019a4 ecology parents: diff changeset	1143 qecbnato0$Day <- as.integer(qecbnato0$Day)
89f977a3a256 planemo upload for repository https://github.com/Marie59/champ_blocs commit 0d86db7d42b608c386a54500064f5f9c9d7019a4 ecology parents: diff changeset	1144
89f977a3a256 planemo upload for repository https://github.com/Marie59/champ_blocs commit 0d86db7d42b608c386a54500064f5f9c9d7019a4 ecology parents: diff changeset	1145 ############################################################
89f977a3a256 planemo upload for repository https://github.com/Marie59/champ_blocs commit 0d86db7d42b608c386a54500064f5f9c9d7019a4 ecology parents: diff changeset	1146 #!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!
89f977a3a256 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_
89f977a3a256 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")
89f977a3a256 planemo upload for repository https://github.com/Marie59/champ_blocs commit 0d86db7d42b608c386a54500064f5f9c9d7019a4 ecology parents: diff changeset	1149 ############################################################
89f977a3a256 planemo upload for repository https://github.com/Marie59/champ_blocs commit 0d86db7d42b608c386a54500064f5f9c9d7019a4 ecology parents: diff changeset	1150
89f977a3a256 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
89f977a3a256 planemo upload for repository https://github.com/Marie59/champ_blocs commit 0d86db7d42b608c386a54500064f5f9c9d7019a4 ecology parents: diff changeset	1152
89f977a3a256 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")
89f977a3a256 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")
89f977a3a256 planemo upload for repository https://github.com/Marie59/champ_blocs commit 0d86db7d42b608c386a54500064f5f9c9d7019a4 ecology parents: diff changeset	1155
89f977a3a256 planemo upload for repository https://github.com/Marie59/champ_blocs commit 0d86db7d42b608c386a54500064f5f9c9d7019a4 ecology parents: diff changeset	1156 saveRDS(qecbnato0, "qecbnato0.RDS")
89f977a3a256 planemo upload for repository https://github.com/Marie59/champ_blocs commit 0d86db7d42b608c386a54500064f5f9c9d7019a4 ecology parents: diff changeset	1157
89f977a3a256 planemo upload for repository https://github.com/Marie59/champ_blocs commit 0d86db7d42b608c386a54500064f5f9c9d7019a4 ecology parents: diff changeset	1158
89f977a3a256 planemo upload for repository https://github.com/Marie59/champ_blocs commit 0d86db7d42b608c386a54500064f5f9c9d7019a4 ecology parents: diff changeset	1159 ###############################################################
89f977a3a256 planemo upload for repository https://github.com/Marie59/champ_blocs commit 0d86db7d42b608c386a54500064f5f9c9d7019a4 ecology parents: diff changeset	1160 # #
89f977a3a256 planemo upload for repository https://github.com/Marie59/champ_blocs commit 0d86db7d42b608c386a54500064f5f9c9d7019a4 ecology parents: diff changeset	1161 # Start dissimilarity calculation with some data handling #
89f977a3a256 planemo upload for repository https://github.com/Marie59/champ_blocs commit 0d86db7d42b608c386a54500064f5f9c9d7019a4 ecology parents: diff changeset	1162 # #
89f977a3a256 planemo upload for repository https://github.com/Marie59/champ_blocs commit 0d86db7d42b608c386a54500064f5f9c9d7019a4 ecology parents: diff changeset	1163 ###############################################################
89f977a3a256 planemo upload for repository https://github.com/Marie59/champ_blocs commit 0d86db7d42b608c386a54500064f5f9c9d7019a4 ecology parents: diff changeset	1164
89f977a3a256 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)
89f977a3a256 planemo upload for repository https://github.com/Marie59/champ_blocs commit 0d86db7d42b608c386a54500064f5f9c9d7019a4 ecology parents: diff changeset	1166
89f977a3a256 planemo upload for repository https://github.com/Marie59/champ_blocs commit 0d86db7d42b608c386a54500064f5f9c9d7019a4 ecology parents: diff changeset	1167 bret_egmp_basq_qecb <- c(
89f977a3a256 planemo upload for repository https://github.com/Marie59/champ_blocs commit 0d86db7d42b608c386a54500064f5f9c9d7019a4 ecology parents: diff changeset	1168 "X..algues.brunes",
89f977a3a256 planemo upload for repository https://github.com/Marie59/champ_blocs commit 0d86db7d42b608c386a54500064f5f9c9d7019a4 ecology parents: diff changeset	1169 "X..algues.rouges",
89f977a3a256 planemo upload for repository https://github.com/Marie59/champ_blocs commit 0d86db7d42b608c386a54500064f5f9c9d7019a4 ecology parents: diff changeset	1170 "X..algues.vertes",
89f977a3a256 planemo upload for repository https://github.com/Marie59/champ_blocs commit 0d86db7d42b608c386a54500064f5f9c9d7019a4 ecology parents: diff changeset	1171 "X..Cladophora",
89f977a3a256 planemo upload for repository https://github.com/Marie59/champ_blocs commit 0d86db7d42b608c386a54500064f5f9c9d7019a4 ecology parents: diff changeset	1172 "X..Lithophyllum",
89f977a3a256 planemo upload for repository https://github.com/Marie59/champ_blocs commit 0d86db7d42b608c386a54500064f5f9c9d7019a4 ecology parents: diff changeset	1173 "Nb.Littorina.obtusata",
89f977a3a256 planemo upload for repository https://github.com/Marie59/champ_blocs commit 0d86db7d42b608c386a54500064f5f9c9d7019a4 ecology parents: diff changeset	1174 "Nb.Gibbula.cineraria",
89f977a3a256 planemo upload for repository https://github.com/Marie59/champ_blocs commit 0d86db7d42b608c386a54500064f5f9c9d7019a4 ecology parents: diff changeset	1175 "Nb.Gibbula.pennanti",
89f977a3a256 planemo upload for repository https://github.com/Marie59/champ_blocs commit 0d86db7d42b608c386a54500064f5f9c9d7019a4 ecology parents: diff changeset	1176 "Nb.Gibbula.umbilicalis",
89f977a3a256 planemo upload for repository https://github.com/Marie59/champ_blocs commit 0d86db7d42b608c386a54500064f5f9c9d7019a4 ecology parents: diff changeset	1177 "Nb.Phallusia.mamillata",
89f977a3a256 planemo upload for repository https://github.com/Marie59/champ_blocs commit 0d86db7d42b608c386a54500064f5f9c9d7019a4 ecology parents: diff changeset	1178 "Nb.Tethya.aurantium",
89f977a3a256 planemo upload for repository https://github.com/Marie59/champ_blocs commit 0d86db7d42b608c386a54500064f5f9c9d7019a4 ecology parents: diff changeset	1179 "Nb.Spirobranchus.lamarckii.total",
89f977a3a256 planemo upload for repository https://github.com/Marie59/champ_blocs commit 0d86db7d42b608c386a54500064f5f9c9d7019a4 ecology parents: diff changeset	1180 "Nb.spirorbis.total",
89f977a3a256 planemo upload for repository https://github.com/Marie59/champ_blocs commit 0d86db7d42b608c386a54500064f5f9c9d7019a4 ecology parents: diff changeset	1181 "X..Eponges",
89f977a3a256 planemo upload for repository https://github.com/Marie59/champ_blocs commit 0d86db7d42b608c386a54500064f5f9c9d7019a4 ecology parents: diff changeset	1182 "X..Ascidies.Coloniales",
89f977a3a256 planemo upload for repository https://github.com/Marie59/champ_blocs commit 0d86db7d42b608c386a54500064f5f9c9d7019a4 ecology parents: diff changeset	1183 "X..Ascidies.Solitaires",
89f977a3a256 planemo upload for repository https://github.com/Marie59/champ_blocs commit 0d86db7d42b608c386a54500064f5f9c9d7019a4 ecology parents: diff changeset	1184 "X..Bryozoaires.Dresses",
89f977a3a256 planemo upload for repository https://github.com/Marie59/champ_blocs commit 0d86db7d42b608c386a54500064f5f9c9d7019a4 ecology parents: diff changeset	1185 "X..Balanes.Vivantes"
89f977a3a256 planemo upload for repository https://github.com/Marie59/champ_blocs commit 0d86db7d42b608c386a54500064f5f9c9d7019a4 ecology parents: diff changeset	1186 #, "X..Recouvrement.Sediment"
89f977a3a256 planemo upload for repository https://github.com/Marie59/champ_blocs commit 0d86db7d42b608c386a54500064f5f9c9d7019a4 ecology parents: diff changeset	1187 #, "X..Roche.Nue"
89f977a3a256 planemo upload for repository https://github.com/Marie59/champ_blocs commit 0d86db7d42b608c386a54500064f5f9c9d7019a4 ecology parents: diff changeset	1188 #, "X..Surface.Accolement"
89f977a3a256 planemo upload for repository https://github.com/Marie59/champ_blocs commit 0d86db7d42b608c386a54500064f5f9c9d7019a4 ecology parents: diff changeset	1189 )
89f977a3a256 planemo upload for repository https://github.com/Marie59/champ_blocs commit 0d86db7d42b608c386a54500064f5f9c9d7019a4 ecology parents: diff changeset	1190
89f977a3a256 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")
89f977a3a256 planemo upload for repository https://github.com/Marie59/champ_blocs commit 0d86db7d42b608c386a54500064f5f9c9d7019a4 ecology parents: diff changeset	1192
89f977a3a256 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.",
89f977a3a256 planemo upload for repository https://github.com/Marie59/champ_blocs commit 0d86db7d42b608c386a54500064f5f9c9d7019a4 ecology parents: diff changeset	1194 "Nb.Necora.puber..Etrille.",
89f977a3a256 planemo upload for repository https://github.com/Marie59/champ_blocs commit 0d86db7d42b608c386a54500064f5f9c9d7019a4 ecology parents: diff changeset	1195 "Nb.Carcinus.maenas..Crabe.vert.",
89f977a3a256 planemo upload for repository https://github.com/Marie59/champ_blocs commit 0d86db7d42b608c386a54500064f5f9c9d7019a4 ecology parents: diff changeset	1196 "Nb.Nucella.lapilus..Pourpre.",
89f977a3a256 planemo upload for repository https://github.com/Marie59/champ_blocs commit 0d86db7d42b608c386a54500064f5f9c9d7019a4 ecology parents: diff changeset	1197 "Nb.Galathea..Galathées.",
89f977a3a256 planemo upload for repository https://github.com/Marie59/champ_blocs commit 0d86db7d42b608c386a54500064f5f9c9d7019a4 ecology parents: diff changeset	1198 "Nb.Lophozozymus.incisus..ancien.Xantho.incisus.",
89f977a3a256 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.",
89f977a3a256 planemo upload for repository https://github.com/Marie59/champ_blocs commit 0d86db7d42b608c386a54500064f5f9c9d7019a4 ecology parents: diff changeset	1200 "Nb.Haliotis.tuberculata..Ormeau.",
89f977a3a256 planemo upload for repository https://github.com/Marie59/champ_blocs commit 0d86db7d42b608c386a54500064f5f9c9d7019a4 ecology parents: diff changeset	1201 "Nb.Littorina.littorea..Bigorneau.",
89f977a3a256 planemo upload for repository https://github.com/Marie59/champ_blocs commit 0d86db7d42b608c386a54500064f5f9c9d7019a4 ecology parents: diff changeset	1202 "Nb.Xantho.pilipes..Xanthe.poilu.",
89f977a3a256 planemo upload for repository https://github.com/Marie59/champ_blocs commit 0d86db7d42b608c386a54500064f5f9c9d7019a4 ecology parents: diff changeset	1203 "Nb.Mimachlamys.varia..Pétoncle.noir.")
89f977a3a256 planemo upload for repository https://github.com/Marie59/champ_blocs commit 0d86db7d42b608c386a54500064f5f9c9d7019a4 ecology parents: diff changeset	1204
89f977a3a256 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.")
89f977a3a256 planemo upload for repository https://github.com/Marie59/champ_blocs commit 0d86db7d42b608c386a54500064f5f9c9d7019a4 ecology parents: diff changeset	1206
89f977a3a256 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
89f977a3a256 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")
89f977a3a256 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")
89f977a3a256 planemo upload for repository https://github.com/Marie59/champ_blocs commit 0d86db7d42b608c386a54500064f5f9c9d7019a4 ecology parents: diff changeset	1210
89f977a3a256 planemo upload for repository https://github.com/Marie59/champ_blocs commit 0d86db7d42b608c386a54500064f5f9c9d7019a4 ecology parents: diff changeset	1211
89f977a3a256 planemo upload for repository https://github.com/Marie59/champ_blocs commit 0d86db7d42b608c386a54500064f5f9c9d7019a4 ecology parents: diff changeset	1212 #############################################################
89f977a3a256 planemo upload for repository https://github.com/Marie59/champ_blocs commit 0d86db7d42b608c386a54500064f5f9c9d7019a4 ecology parents: diff changeset	1213 # #
89f977a3a256 planemo upload for repository https://github.com/Marie59/champ_blocs commit 0d86db7d42b608c386a54500064f5f9c9d7019a4 ecology parents: diff changeset	1214 # Compute dissimilarity #
89f977a3a256 planemo upload for repository https://github.com/Marie59/champ_blocs commit 0d86db7d42b608c386a54500064f5f9c9d7019a4 ecology parents: diff changeset	1215 # #
89f977a3a256 planemo upload for repository https://github.com/Marie59/champ_blocs commit 0d86db7d42b608c386a54500064f5f9c9d7019a4 ecology parents: diff changeset	1216 #############################################################
89f977a3a256 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
89f977a3a256 planemo upload for repository https://github.com/Marie59/champ_blocs commit 0d86db7d42b608c386a54500064f5f9c9d7019a4 ecology parents: diff changeset	1218
89f977a3a256 planemo upload for repository https://github.com/Marie59/champ_blocs commit 0d86db7d42b608c386a54500064f5f9c9d7019a4 ecology parents: diff changeset	1219 # loop in a fct
89f977a3a256 planemo upload for repository https://github.com/Marie59/champ_blocs commit 0d86db7d42b608c386a54500064f5f9c9d7019a4 ecology parents: diff changeset	1220
89f977a3a256 planemo upload for repository https://github.com/Marie59/champ_blocs commit 0d86db7d42b608c386a54500064f5f9c9d7019a4 ecology parents: diff changeset	1221 matri_fct_bmf <- function(data, conca) {
89f977a3a256 planemo upload for repository https://github.com/Marie59/champ_blocs commit 0d86db7d42b608c386a54500064f5f9c9d7019a4 ecology parents: diff changeset	1222
89f977a3a256 planemo upload for repository https://github.com/Marie59/champ_blocs commit 0d86db7d42b608c386a54500064f5f9c9d7019a4 ecology parents: diff changeset	1223 matri_df <- data
89f977a3a256 planemo upload for repository https://github.com/Marie59/champ_blocs commit 0d86db7d42b608c386a54500064f5f9c9d7019a4 ecology parents: diff changeset	1224
89f977a3a256 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)))) {
89f977a3a256 planemo upload for repository https://github.com/Marie59/champ_blocs commit 0d86db7d42b608c386a54500064f5f9c9d7019a4 ecology parents: diff changeset	1226
89f977a3a256 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$site_year_month_day)[[x]])
89f977a3a256 planemo upload for repository https://github.com/Marie59/champ_blocs commit 0d86db7d42b608c386a54500064f5f9c9d7019a4 ecology parents: diff changeset	1228
89f977a3a256 planemo upload for repository https://github.com/Marie59/champ_blocs commit 0d86db7d42b608c386a54500064f5f9c9d7019a4 ecology parents: diff changeset	1229 rownames(qecbnato0_x) <- paste0(qecbnato0_x$Type.Bloc, "_", qecbnato0_x$Face, "_", qecbnato0_x$Numéro.Bloc.échantillon, "_", qecbnato0_x$quadrat_bis)
89f977a3a256 planemo upload for repository https://github.com/Marie59/champ_blocs commit 0d86db7d42b608c386a54500064f5f9c9d7019a4 ecology parents: diff changeset	1230
89f977a3a256 planemo upload for repository https://github.com/Marie59/champ_blocs commit 0d86db7d42b608c386a54500064f5f9c9d7019a4 ecology parents: diff changeset	1231
89f977a3a256 planemo upload for repository https://github.com/Marie59/champ_blocs commit 0d86db7d42b608c386a54500064f5f9c9d7019a4 ecology parents: diff changeset	1232 mtxdis <- vegan::vegdist(
89f977a3a256 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)
89f977a3a256 planemo upload for repository https://github.com/Marie59/champ_blocs commit 0d86db7d42b608c386a54500064f5f9c9d7019a4 ecology parents: diff changeset	1234
89f977a3a256 planemo upload for repository https://github.com/Marie59/champ_blocs commit 0d86db7d42b608c386a54500064f5f9c9d7019a4 ecology parents: diff changeset	1235 na.rm = TRUE,
89f977a3a256 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 ??
89f977a3a256 planemo upload for repository https://github.com/Marie59/champ_blocs commit 0d86db7d42b608c386a54500064f5f9c9d7019a4 ecology parents: diff changeset	1237 )
89f977a3a256 planemo upload for repository https://github.com/Marie59/champ_blocs commit 0d86db7d42b608c386a54500064f5f9c9d7019a4 ecology parents: diff changeset	1238
89f977a3a256 planemo upload for repository https://github.com/Marie59/champ_blocs commit 0d86db7d42b608c386a54500064f5f9c9d7019a4 ecology parents: diff changeset	1239
89f977a3a256 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
89f977a3a256 planemo upload for repository https://github.com/Marie59/champ_blocs commit 0d86db7d42b608c386a54500064f5f9c9d7019a4 ecology parents: diff changeset	1241 # mtxdis <- ecole::bray0(
89f977a3a256 planemo upload for repository https://github.com/Marie59/champ_blocs commit 0d86db7d42b608c386a54500064f5f9c9d7019a4 ecology parents: diff changeset	1242 # sqrt
89f977a3a256 planemo upload for repository https://github.com/Marie59/champ_blocs commit 0d86db7d42b608c386a54500064f5f9c9d7019a4 ecology parents: diff changeset	1243 # (qecbnato0_x[,conca]), na.rm = TRUE)
89f977a3a256 planemo upload for repository https://github.com/Marie59/champ_blocs commit 0d86db7d42b608c386a54500064f5f9c9d7019a4 ecology parents: diff changeset	1244
89f977a3a256 planemo upload for repository https://github.com/Marie59/champ_blocs commit 0d86db7d42b608c386a54500064f5f9c9d7019a4 ecology parents: diff changeset	1245 expand.grid(mtxdis)
89f977a3a256 planemo upload for repository https://github.com/Marie59/champ_blocs commit 0d86db7d42b608c386a54500064f5f9c9d7019a4 ecology parents: diff changeset	1246
89f977a3a256 planemo upload for repository https://github.com/Marie59/champ_blocs commit 0d86db7d42b608c386a54500064f5f9c9d7019a4 ecology parents: diff changeset	1247 mtxdisdf_ <- as.data.frame(as.matrix(mtxdis))
89f977a3a256 planemo upload for repository https://github.com/Marie59/champ_blocs commit 0d86db7d42b608c386a54500064f5f9c9d7019a4 ecology parents: diff changeset	1248
89f977a3a256 planemo upload for repository https://github.com/Marie59/champ_blocs commit 0d86db7d42b608c386a54500064f5f9c9d7019a4 ecology parents: diff changeset	1249 a_ <- NA
89f977a3a256 planemo upload for repository https://github.com/Marie59/champ_blocs commit 0d86db7d42b608c386a54500064f5f9c9d7019a4 ecology parents: diff changeset	1250 b_ <- NA
89f977a3a256 planemo upload for repository https://github.com/Marie59/champ_blocs commit 0d86db7d42b608c386a54500064f5f9c9d7019a4 ecology parents: diff changeset	1251 c_ <- NA
89f977a3a256 planemo upload for repository https://github.com/Marie59/champ_blocs commit 0d86db7d42b608c386a54500064f5f9c9d7019a4 ecology parents: diff changeset	1252 d_ <- NA
89f977a3a256 planemo upload for repository https://github.com/Marie59/champ_blocs commit 0d86db7d42b608c386a54500064f5f9c9d7019a4 ecology parents: diff changeset	1253 e_ <- NA
89f977a3a256 planemo upload for repository https://github.com/Marie59/champ_blocs commit 0d86db7d42b608c386a54500064f5f9c9d7019a4 ecology parents: diff changeset	1254 f_ <- NA
89f977a3a256 planemo upload for repository https://github.com/Marie59/champ_blocs commit 0d86db7d42b608c386a54500064f5f9c9d7019a4 ecology parents: diff changeset	1255 g_ <- NA
89f977a3a256 planemo upload for repository https://github.com/Marie59/champ_blocs commit 0d86db7d42b608c386a54500064f5f9c9d7019a4 ecology parents: diff changeset	1256 h_ <- NA
89f977a3a256 planemo upload for repository https://github.com/Marie59/champ_blocs commit 0d86db7d42b608c386a54500064f5f9c9d7019a4 ecology parents: diff changeset	1257 i_ <- NA
89f977a3a256 planemo upload for repository https://github.com/Marie59/champ_blocs commit 0d86db7d42b608c386a54500064f5f9c9d7019a4 ecology parents: diff changeset	1258 j_ <- NA
89f977a3a256 planemo upload for repository https://github.com/Marie59/champ_blocs commit 0d86db7d42b608c386a54500064f5f9c9d7019a4 ecology parents: diff changeset	1259 k_ <- NA
89f977a3a256 planemo upload for repository https://github.com/Marie59/champ_blocs commit 0d86db7d42b608c386a54500064f5f9c9d7019a4 ecology parents: diff changeset	1260 l_ <- NA
89f977a3a256 planemo upload for repository https://github.com/Marie59/champ_blocs commit 0d86db7d42b608c386a54500064f5f9c9d7019a4 ecology parents: diff changeset	1261 m_ <- NA
89f977a3a256 planemo upload for repository https://github.com/Marie59/champ_blocs commit 0d86db7d42b608c386a54500064f5f9c9d7019a4 ecology parents: diff changeset	1262 n_ <- NA
89f977a3a256 planemo upload for repository https://github.com/Marie59/champ_blocs commit 0d86db7d42b608c386a54500064f5f9c9d7019a4 ecology parents: diff changeset	1263
89f977a3a256 planemo upload for repository https://github.com/Marie59/champ_blocs commit 0d86db7d42b608c386a54500064f5f9c9d7019a4 ecology parents: diff changeset	1264 for (z in c(1:nrow(mtxdisdf_))) {
89f977a3a256 planemo upload for repository https://github.com/Marie59/champ_blocs commit 0d86db7d42b608c386a54500064f5f9c9d7019a4 ecology parents: diff changeset	1265
89f977a3a256 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)))
89f977a3a256 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)))
89f977a3a256 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)))
89f977a3a256 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)))
89f977a3a256 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)))
89f977a3a256 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)))
89f977a3a256 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)))
89f977a3a256 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)))
89f977a3a256 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)))
89f977a3a256 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)))
89f977a3a256 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)))
89f977a3a256 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)))
89f977a3a256 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)))
89f977a3a256 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)))
89f977a3a256 planemo upload for repository https://github.com/Marie59/champ_blocs commit 0d86db7d42b608c386a54500064f5f9c9d7019a4 ecology parents: diff changeset	1280
89f977a3a256 planemo upload for repository https://github.com/Marie59/champ_blocs commit 0d86db7d42b608c386a54500064f5f9c9d7019a4 ecology parents: diff changeset	1281 }
89f977a3a256 planemo upload for repository https://github.com/Marie59/champ_blocs commit 0d86db7d42b608c386a54500064f5f9c9d7019a4 ecology parents: diff changeset	1282
89f977a3a256 planemo upload for repository https://github.com/Marie59/champ_blocs commit 0d86db7d42b608c386a54500064f5f9c9d7019a4 ecology parents: diff changeset	1283 rm(z)
89f977a3a256 planemo upload for repository https://github.com/Marie59/champ_blocs commit 0d86db7d42b608c386a54500064f5f9c9d7019a4 ecology parents: diff changeset	1284
89f977a3a256 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_)))
89f977a3a256 planemo upload for repository https://github.com/Marie59/champ_blocs commit 0d86db7d42b608c386a54500064f5f9c9d7019a4 ecology parents: diff changeset	1286 a_ <- a_[1:y]
89f977a3a256 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_)))
89f977a3a256 planemo upload for repository https://github.com/Marie59/champ_blocs commit 0d86db7d42b608c386a54500064f5f9c9d7019a4 ecology parents: diff changeset	1288 b_ <- b_[1:y]
89f977a3a256 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_)))
89f977a3a256 planemo upload for repository https://github.com/Marie59/champ_blocs commit 0d86db7d42b608c386a54500064f5f9c9d7019a4 ecology parents: diff changeset	1290 c_ <- c_[1:y]
89f977a3a256 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_)))
89f977a3a256 planemo upload for repository https://github.com/Marie59/champ_blocs commit 0d86db7d42b608c386a54500064f5f9c9d7019a4 ecology parents: diff changeset	1292 d_ <- d_[1:y]
89f977a3a256 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_)))
89f977a3a256 planemo upload for repository https://github.com/Marie59/champ_blocs commit 0d86db7d42b608c386a54500064f5f9c9d7019a4 ecology parents: diff changeset	1294 e_ <- e_[1:y]
89f977a3a256 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_)))
89f977a3a256 planemo upload for repository https://github.com/Marie59/champ_blocs commit 0d86db7d42b608c386a54500064f5f9c9d7019a4 ecology parents: diff changeset	1296 f_ <- f_[1:y]
89f977a3a256 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_)))
89f977a3a256 planemo upload for repository https://github.com/Marie59/champ_blocs commit 0d86db7d42b608c386a54500064f5f9c9d7019a4 ecology parents: diff changeset	1298 g_ <- g_[1:y]
89f977a3a256 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_)))
89f977a3a256 planemo upload for repository https://github.com/Marie59/champ_blocs commit 0d86db7d42b608c386a54500064f5f9c9d7019a4 ecology parents: diff changeset	1300 h_ <- h_[1:y]
89f977a3a256 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_)))
89f977a3a256 planemo upload for repository https://github.com/Marie59/champ_blocs commit 0d86db7d42b608c386a54500064f5f9c9d7019a4 ecology parents: diff changeset	1302 i_ <- i_[1:y]
89f977a3a256 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_)))
89f977a3a256 planemo upload for repository https://github.com/Marie59/champ_blocs commit 0d86db7d42b608c386a54500064f5f9c9d7019a4 ecology parents: diff changeset	1304 j_ <- j_[1:y]
89f977a3a256 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_)))
89f977a3a256 planemo upload for repository https://github.com/Marie59/champ_blocs commit 0d86db7d42b608c386a54500064f5f9c9d7019a4 ecology parents: diff changeset	1306 k_ <- k_[1:y]
89f977a3a256 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_)))
89f977a3a256 planemo upload for repository https://github.com/Marie59/champ_blocs commit 0d86db7d42b608c386a54500064f5f9c9d7019a4 ecology parents: diff changeset	1308 l_ <- l_[1:y]
89f977a3a256 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_)))
89f977a3a256 planemo upload for repository https://github.com/Marie59/champ_blocs commit 0d86db7d42b608c386a54500064f5f9c9d7019a4 ecology parents: diff changeset	1310 m_ <- m_[1:y]
89f977a3a256 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_)))
89f977a3a256 planemo upload for repository https://github.com/Marie59/champ_blocs commit 0d86db7d42b608c386a54500064f5f9c9d7019a4 ecology parents: diff changeset	1312 n_ <- n_[1:y]
89f977a3a256 planemo upload for repository https://github.com/Marie59/champ_blocs commit 0d86db7d42b608c386a54500064f5f9c9d7019a4 ecology parents: diff changeset	1313
89f977a3a256 planemo upload for repository https://github.com/Marie59/champ_blocs commit 0d86db7d42b608c386a54500064f5f9c9d7019a4 ecology parents: diff changeset	1314 rm(y)
89f977a3a256 planemo upload for repository https://github.com/Marie59/champ_blocs commit 0d86db7d42b608c386a54500064f5f9c9d7019a4 ecology parents: diff changeset	1315
89f977a3a256 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_)
89f977a3a256 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))])
89f977a3a256 planemo upload for repository https://github.com/Marie59/champ_blocs commit 0d86db7d42b608c386a54500064f5f9c9d7019a4 ecology parents: diff changeset	1318 names(df_) <- c("dist.", "name_")
89f977a3a256 planemo upload for repository https://github.com/Marie59/champ_blocs commit 0d86db7d42b608c386a54500064f5f9c9d7019a4 ecology parents: diff changeset	1319
89f977a3a256 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_)
89f977a3a256 planemo upload for repository https://github.com/Marie59/champ_blocs commit 0d86db7d42b608c386a54500064f5f9c9d7019a4 ecology parents: diff changeset	1321 rm(name_)
89f977a3a256 planemo upload for repository https://github.com/Marie59/champ_blocs commit 0d86db7d42b608c386a54500064f5f9c9d7019a4 ecology parents: diff changeset	1322
89f977a3a256 planemo upload for repository https://github.com/Marie59/champ_blocs commit 0d86db7d42b608c386a54500064f5f9c9d7019a4 ecology parents: diff changeset	1323 q_ <- strsplit(df_$name_, " & ")
89f977a3a256 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)
89f977a3a256 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))
89f977a3a256 planemo upload for repository https://github.com/Marie59/champ_blocs commit 0d86db7d42b608c386a54500064f5f9c9d7019a4 ecology parents: diff changeset	1326 df_ <- dplyr::bind_cols(df_, q_df_)
89f977a3a256 planemo upload for repository https://github.com/Marie59/champ_blocs commit 0d86db7d42b608c386a54500064f5f9c9d7019a4 ecology parents: diff changeset	1327
89f977a3a256 planemo upload for repository https://github.com/Marie59/champ_blocs commit 0d86db7d42b608c386a54500064f5f9c9d7019a4 ecology parents: diff changeset	1328 rm(q_, mat_, q_df_)
89f977a3a256 planemo upload for repository https://github.com/Marie59/champ_blocs commit 0d86db7d42b608c386a54500064f5f9c9d7019a4 ecology parents: diff changeset	1329
89f977a3a256 planemo upload for repository https://github.com/Marie59/champ_blocs commit 0d86db7d42b608c386a54500064f5f9c9d7019a4 ecology parents: diff changeset	1330 split_ <- strsplit(df_$V1, "_")
89f977a3a256 planemo upload for repository https://github.com/Marie59/champ_blocs commit 0d86db7d42b608c386a54500064f5f9c9d7019a4 ecology parents: diff changeset	1331 v1_split_ <- as.data.frame(matrix(unlist(split_), ncol = 4, byrow = TRUE))
89f977a3a256 planemo upload for repository https://github.com/Marie59/champ_blocs commit 0d86db7d42b608c386a54500064f5f9c9d7019a4 ecology parents: diff changeset	1332 split_ <- strsplit(df_$V2, "_")
89f977a3a256 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))
89f977a3a256 planemo upload for repository https://github.com/Marie59/champ_blocs commit 0d86db7d42b608c386a54500064f5f9c9d7019a4 ecology parents: diff changeset	1334
89f977a3a256 planemo upload for repository https://github.com/Marie59/champ_blocs commit 0d86db7d42b608c386a54500064f5f9c9d7019a4 ecology parents: diff changeset	1335 df_ <- dplyr::bind_cols(df_, v1_split_)
89f977a3a256 planemo upload for repository https://github.com/Marie59/champ_blocs commit 0d86db7d42b608c386a54500064f5f9c9d7019a4 ecology parents: diff changeset	1336 df_ <- dplyr::bind_cols(df_, v2_split_)
89f977a3a256 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)
89f977a3a256 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_))
89f977a3a256 planemo upload for repository https://github.com/Marie59/champ_blocs commit 0d86db7d42b608c386a54500064f5f9c9d7019a4 ecology parents: diff changeset	1339
89f977a3a256 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.")
89f977a3a256 planemo upload for repository https://github.com/Marie59/champ_blocs commit 0d86db7d42b608c386a54500064f5f9c9d7019a4 ecology parents: diff changeset	1341
89f977a3a256 planemo upload for repository https://github.com/Marie59/champ_blocs commit 0d86db7d42b608c386a54500064f5f9c9d7019a4 ecology parents: diff changeset	1342 rm(split_, v1_split_, v2_split_)
89f977a3a256 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)
89f977a3a256 planemo upload for repository https://github.com/Marie59/champ_blocs commit 0d86db7d42b608c386a54500064f5f9c9d7019a4 ecology parents: diff changeset	1344
89f977a3a256 planemo upload for repository https://github.com/Marie59/champ_blocs commit 0d86db7d42b608c386a54500064f5f9c9d7019a4 ecology parents: diff changeset	1345 matri_list[[x]] <- df_red_
89f977a3a256 planemo upload for repository https://github.com/Marie59/champ_blocs commit 0d86db7d42b608c386a54500064f5f9c9d7019a4 ecology parents: diff changeset	1346 matri_list <<- matri_list
89f977a3a256 planemo upload for repository https://github.com/Marie59/champ_blocs commit 0d86db7d42b608c386a54500064f5f9c9d7019a4 ecology parents: diff changeset	1347
89f977a3a256 planemo upload for repository https://github.com/Marie59/champ_blocs commit 0d86db7d42b608c386a54500064f5f9c9d7019a4 ecology parents: diff changeset	1348 rm(df_red_, qecbnato0_x, x)
89f977a3a256 planemo upload for repository https://github.com/Marie59/champ_blocs commit 0d86db7d42b608c386a54500064f5f9c9d7019a4 ecology parents: diff changeset	1349
89f977a3a256 planemo upload for repository https://github.com/Marie59/champ_blocs commit 0d86db7d42b608c386a54500064f5f9c9d7019a4 ecology parents: diff changeset	1350 }
89f977a3a256 planemo upload for repository https://github.com/Marie59/champ_blocs commit 0d86db7d42b608c386a54500064f5f9c9d7019a4 ecology parents: diff changeset	1351
89f977a3a256 planemo upload for repository https://github.com/Marie59/champ_blocs commit 0d86db7d42b608c386a54500064f5f9c9d7019a4 ecology parents: diff changeset	1352 matri_df <- do.call("rbind", matri_list)
89f977a3a256 planemo upload for repository https://github.com/Marie59/champ_blocs commit 0d86db7d42b608c386a54500064f5f9c9d7019a4 ecology parents: diff changeset	1353
89f977a3a256 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")
89f977a3a256 planemo upload for repository https://github.com/Marie59/champ_blocs commit 0d86db7d42b608c386a54500064f5f9c9d7019a4 ecology parents: diff changeset	1355
89f977a3a256 planemo upload for repository https://github.com/Marie59/champ_blocs commit 0d86db7d42b608c386a54500064f5f9c9d7019a4 ecology parents: diff changeset	1356 matri_df <<- matri_df
89f977a3a256 planemo upload for repository https://github.com/Marie59/champ_blocs commit 0d86db7d42b608c386a54500064f5f9c9d7019a4 ecology parents: diff changeset	1357
89f977a3a256 planemo upload for repository https://github.com/Marie59/champ_blocs commit 0d86db7d42b608c386a54500064f5f9c9d7019a4 ecology parents: diff changeset	1358 hist(matri_df$dist.)
89f977a3a256 planemo upload for repository https://github.com/Marie59/champ_blocs commit 0d86db7d42b608c386a54500064f5f9c9d7019a4 ecology parents: diff changeset	1359
89f977a3a256 planemo upload for repository https://github.com/Marie59/champ_blocs commit 0d86db7d42b608c386a54500064f5f9c9d7019a4 ecology parents: diff changeset	1360 }
89f977a3a256 planemo upload for repository https://github.com/Marie59/champ_blocs commit 0d86db7d42b608c386a54500064f5f9c9d7019a4 ecology parents: diff changeset	1361
89f977a3a256 planemo upload for repository https://github.com/Marie59/champ_blocs commit 0d86db7d42b608c386a54500064f5f9c9d7019a4 ecology parents: diff changeset	1362 data_ <- dplyr::filter(qecbnato0, Face == "face supérieure")
89f977a3a256 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_$Type.Bloc))
89f977a3a256 planemo upload for repository https://github.com/Marie59/champ_blocs commit 0d86db7d42b608c386a54500064f5f9c9d7019a4 ecology parents: diff changeset	1364 matri_list <- vector("list", length(unique(data_$site_year_month_day)))
89f977a3a256 planemo upload for repository https://github.com/Marie59/champ_blocs commit 0d86db7d42b608c386a54500064f5f9c9d7019a4 ecology parents: diff changeset	1365
89f977a3a256 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))
89f977a3a256 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 -")))
89f977a3a256 planemo upload for repository https://github.com/Marie59/champ_blocs commit 0d86db7d42b608c386a54500064f5f9c9d7019a4 ecology parents: diff changeset	1368
89f977a3a256 planemo upload for repository https://github.com/Marie59/champ_blocs commit 0d86db7d42b608c386a54500064f5f9c9d7019a4 ecology parents: diff changeset	1369 matri_full_bm_bf_fs <- matri_df
89f977a3a256 planemo upload for repository https://github.com/Marie59/champ_blocs commit 0d86db7d42b608c386a54500064f5f9c9d7019a4 ecology parents: diff changeset	1370
89f977a3a256 planemo upload for repository https://github.com/Marie59/champ_blocs commit 0d86db7d42b608c386a54500064f5f9c9d7019a4 ecology parents: diff changeset	1371
89f977a3a256 planemo upload for repository https://github.com/Marie59/champ_blocs commit 0d86db7d42b608c386a54500064f5f9c9d7019a4 ecology parents: diff changeset	1372 rm(data_, matri_df, matri_list)
89f977a3a256 planemo upload for repository https://github.com/Marie59/champ_blocs commit 0d86db7d42b608c386a54500064f5f9c9d7019a4 ecology parents: diff changeset	1373
89f977a3a256 planemo upload for repository https://github.com/Marie59/champ_blocs commit 0d86db7d42b608c386a54500064f5f9c9d7019a4 ecology parents: diff changeset	1374
89f977a3a256 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.
89f977a3a256 planemo upload for repository https://github.com/Marie59/champ_blocs commit 0d86db7d42b608c386a54500064f5f9c9d7019a4 ecology parents: diff changeset	1376
89f977a3a256 planemo upload for repository https://github.com/Marie59/champ_blocs commit 0d86db7d42b608c386a54500064f5f9c9d7019a4 ecology parents: diff changeset	1377 # loop in a fct
89f977a3a256 planemo upload for repository https://github.com/Marie59/champ_blocs commit 0d86db7d42b608c386a54500064f5f9c9d7019a4 ecology parents: diff changeset	1378
89f977a3a256 planemo upload for repository https://github.com/Marie59/champ_blocs commit 0d86db7d42b608c386a54500064f5f9c9d7019a4 ecology parents: diff changeset	1379 matri_fct_bmm <- function(data, conca) {
89f977a3a256 planemo upload for repository https://github.com/Marie59/champ_blocs commit 0d86db7d42b608c386a54500064f5f9c9d7019a4 ecology parents: diff changeset	1380
89f977a3a256 planemo upload for repository https://github.com/Marie59/champ_blocs commit 0d86db7d42b608c386a54500064f5f9c9d7019a4 ecology parents: diff changeset	1381 matri_df <- data
89f977a3a256 planemo upload for repository https://github.com/Marie59/champ_blocs commit 0d86db7d42b608c386a54500064f5f9c9d7019a4 ecology parents: diff changeset	1382
89f977a3a256 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)))) {
89f977a3a256 planemo upload for repository https://github.com/Marie59/champ_blocs commit 0d86db7d42b608c386a54500064f5f9c9d7019a4 ecology parents: diff changeset	1384
89f977a3a256 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$site_year_month_day)[[x]])
89f977a3a256 planemo upload for repository https://github.com/Marie59/champ_blocs commit 0d86db7d42b608c386a54500064f5f9c9d7019a4 ecology parents: diff changeset	1386
89f977a3a256 planemo upload for repository https://github.com/Marie59/champ_blocs commit 0d86db7d42b608c386a54500064f5f9c9d7019a4 ecology parents: diff changeset	1387 rownames(qecbnato0_x) <- paste0(qecbnato0_x$Type.Bloc, "_", qecbnato0_x$Face, "_", qecbnato0_x$Numéro.Bloc.échantillon, "_", qecbnato0_x$quadrat_bis)
89f977a3a256 planemo upload for repository https://github.com/Marie59/champ_blocs commit 0d86db7d42b608c386a54500064f5f9c9d7019a4 ecology parents: diff changeset	1388
89f977a3a256 planemo upload for repository https://github.com/Marie59/champ_blocs commit 0d86db7d42b608c386a54500064f5f9c9d7019a4 ecology parents: diff changeset	1389
89f977a3a256 planemo upload for repository https://github.com/Marie59/champ_blocs commit 0d86db7d42b608c386a54500064f5f9c9d7019a4 ecology parents: diff changeset	1390 mtxdis <- vegan::vegdist(
89f977a3a256 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)
89f977a3a256 planemo upload for repository https://github.com/Marie59/champ_blocs commit 0d86db7d42b608c386a54500064f5f9c9d7019a4 ecology parents: diff changeset	1392 na.rm = TRUE,
89f977a3a256 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 ??
89f977a3a256 planemo upload for repository https://github.com/Marie59/champ_blocs commit 0d86db7d42b608c386a54500064f5f9c9d7019a4 ecology parents: diff changeset	1394 )
89f977a3a256 planemo upload for repository https://github.com/Marie59/champ_blocs commit 0d86db7d42b608c386a54500064f5f9c9d7019a4 ecology parents: diff changeset	1395
89f977a3a256 planemo upload for repository https://github.com/Marie59/champ_blocs commit 0d86db7d42b608c386a54500064f5f9c9d7019a4 ecology parents: diff changeset	1396
89f977a3a256 planemo upload for repository https://github.com/Marie59/champ_blocs commit 0d86db7d42b608c386a54500064f5f9c9d7019a4 ecology parents: diff changeset	1397 #mtxdis <- ecole::bray0(
89f977a3a256 planemo upload for repository https://github.com/Marie59/champ_blocs commit 0d86db7d42b608c386a54500064f5f9c9d7019a4 ecology parents: diff changeset	1398 # sqrt(qecbnato0_x[, conca]), na.rm = TRUE)
89f977a3a256 planemo upload for repository https://github.com/Marie59/champ_blocs commit 0d86db7d42b608c386a54500064f5f9c9d7019a4 ecology parents: diff changeset	1399
89f977a3a256 planemo upload for repository https://github.com/Marie59/champ_blocs commit 0d86db7d42b608c386a54500064f5f9c9d7019a4 ecology parents: diff changeset	1400
89f977a3a256 planemo upload for repository https://github.com/Marie59/champ_blocs commit 0d86db7d42b608c386a54500064f5f9c9d7019a4 ecology parents: diff changeset	1401 expand.grid(mtxdis)
89f977a3a256 planemo upload for repository https://github.com/Marie59/champ_blocs commit 0d86db7d42b608c386a54500064f5f9c9d7019a4 ecology parents: diff changeset	1402
89f977a3a256 planemo upload for repository https://github.com/Marie59/champ_blocs commit 0d86db7d42b608c386a54500064f5f9c9d7019a4 ecology parents: diff changeset	1403 mtxdisdf_ <- as.data.frame(as.matrix(mtxdis))
89f977a3a256 planemo upload for repository https://github.com/Marie59/champ_blocs commit 0d86db7d42b608c386a54500064f5f9c9d7019a4 ecology parents: diff changeset	1404
89f977a3a256 planemo upload for repository https://github.com/Marie59/champ_blocs commit 0d86db7d42b608c386a54500064f5f9c9d7019a4 ecology parents: diff changeset	1405 a_ <- NA
89f977a3a256 planemo upload for repository https://github.com/Marie59/champ_blocs commit 0d86db7d42b608c386a54500064f5f9c9d7019a4 ecology parents: diff changeset	1406 b_ <- NA
89f977a3a256 planemo upload for repository https://github.com/Marie59/champ_blocs commit 0d86db7d42b608c386a54500064f5f9c9d7019a4 ecology parents: diff changeset	1407 c_ <- NA
89f977a3a256 planemo upload for repository https://github.com/Marie59/champ_blocs commit 0d86db7d42b608c386a54500064f5f9c9d7019a4 ecology parents: diff changeset	1408 d_ <- NA
89f977a3a256 planemo upload for repository https://github.com/Marie59/champ_blocs commit 0d86db7d42b608c386a54500064f5f9c9d7019a4 ecology parents: diff changeset	1409 e_ <- NA
89f977a3a256 planemo upload for repository https://github.com/Marie59/champ_blocs commit 0d86db7d42b608c386a54500064f5f9c9d7019a4 ecology parents: diff changeset	1410 f_ <- NA
89f977a3a256 planemo upload for repository https://github.com/Marie59/champ_blocs commit 0d86db7d42b608c386a54500064f5f9c9d7019a4 ecology parents: diff changeset	1411 g_ <- NA
89f977a3a256 planemo upload for repository https://github.com/Marie59/champ_blocs commit 0d86db7d42b608c386a54500064f5f9c9d7019a4 ecology parents: diff changeset	1412 h_ <- NA
89f977a3a256 planemo upload for repository https://github.com/Marie59/champ_blocs commit 0d86db7d42b608c386a54500064f5f9c9d7019a4 ecology parents: diff changeset	1413 i_ <- NA
89f977a3a256 planemo upload for repository https://github.com/Marie59/champ_blocs commit 0d86db7d42b608c386a54500064f5f9c9d7019a4 ecology parents: diff changeset	1414 j_ <- NA
89f977a3a256 planemo upload for repository https://github.com/Marie59/champ_blocs commit 0d86db7d42b608c386a54500064f5f9c9d7019a4 ecology parents: diff changeset	1415 k_ <- NA
89f977a3a256 planemo upload for repository https://github.com/Marie59/champ_blocs commit 0d86db7d42b608c386a54500064f5f9c9d7019a4 ecology parents: diff changeset	1416 l_ <- NA
89f977a3a256 planemo upload for repository https://github.com/Marie59/champ_blocs commit 0d86db7d42b608c386a54500064f5f9c9d7019a4 ecology parents: diff changeset	1417 m_ <- NA
89f977a3a256 planemo upload for repository https://github.com/Marie59/champ_blocs commit 0d86db7d42b608c386a54500064f5f9c9d7019a4 ecology parents: diff changeset	1418 n_ <- NA
89f977a3a256 planemo upload for repository https://github.com/Marie59/champ_blocs commit 0d86db7d42b608c386a54500064f5f9c9d7019a4 ecology parents: diff changeset	1419 o_ <- NA
89f977a3a256 planemo upload for repository https://github.com/Marie59/champ_blocs commit 0d86db7d42b608c386a54500064f5f9c9d7019a4 ecology parents: diff changeset	1420 p_ <- NA
89f977a3a256 planemo upload for repository https://github.com/Marie59/champ_blocs commit 0d86db7d42b608c386a54500064f5f9c9d7019a4 ecology parents: diff changeset	1421 q_ <- NA
89f977a3a256 planemo upload for repository https://github.com/Marie59/champ_blocs commit 0d86db7d42b608c386a54500064f5f9c9d7019a4 ecology parents: diff changeset	1422 r_ <- NA
89f977a3a256 planemo upload for repository https://github.com/Marie59/champ_blocs commit 0d86db7d42b608c386a54500064f5f9c9d7019a4 ecology parents: diff changeset	1423 s_ <- NA
89f977a3a256 planemo upload for repository https://github.com/Marie59/champ_blocs commit 0d86db7d42b608c386a54500064f5f9c9d7019a4 ecology parents: diff changeset	1424
89f977a3a256 planemo upload for repository https://github.com/Marie59/champ_blocs commit 0d86db7d42b608c386a54500064f5f9c9d7019a4 ecology parents: diff changeset	1425 for (z in c(1:nrow(mtxdisdf_))) {
89f977a3a256 planemo upload for repository https://github.com/Marie59/champ_blocs commit 0d86db7d42b608c386a54500064f5f9c9d7019a4 ecology parents: diff changeset	1426
89f977a3a256 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)))
89f977a3a256 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)))
89f977a3a256 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)))
89f977a3a256 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)))
89f977a3a256 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)))
89f977a3a256 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)))
89f977a3a256 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)))
89f977a3a256 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)))
89f977a3a256 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)))
89f977a3a256 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)))
89f977a3a256 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)))
89f977a3a256 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)))
89f977a3a256 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)))
89f977a3a256 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)))
89f977a3a256 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)))
89f977a3a256 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)))
89f977a3a256 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)))
89f977a3a256 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)))
89f977a3a256 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)))
89f977a3a256 planemo upload for repository https://github.com/Marie59/champ_blocs commit 0d86db7d42b608c386a54500064f5f9c9d7019a4 ecology parents: diff changeset	1446
89f977a3a256 planemo upload for repository https://github.com/Marie59/champ_blocs commit 0d86db7d42b608c386a54500064f5f9c9d7019a4 ecology parents: diff changeset	1447 }
89f977a3a256 planemo upload for repository https://github.com/Marie59/champ_blocs commit 0d86db7d42b608c386a54500064f5f9c9d7019a4 ecology parents: diff changeset	1448
89f977a3a256 planemo upload for repository https://github.com/Marie59/champ_blocs commit 0d86db7d42b608c386a54500064f5f9c9d7019a4 ecology parents: diff changeset	1449 rm(z)
89f977a3a256 planemo upload for repository https://github.com/Marie59/champ_blocs commit 0d86db7d42b608c386a54500064f5f9c9d7019a4 ecology parents: diff changeset	1450
89f977a3a256 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_)))
89f977a3a256 planemo upload for repository https://github.com/Marie59/champ_blocs commit 0d86db7d42b608c386a54500064f5f9c9d7019a4 ecology parents: diff changeset	1452 a_ <- a_[1:y]
89f977a3a256 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_)))
89f977a3a256 planemo upload for repository https://github.com/Marie59/champ_blocs commit 0d86db7d42b608c386a54500064f5f9c9d7019a4 ecology parents: diff changeset	1454 b_ <- b_[1:y]
89f977a3a256 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_)))
89f977a3a256 planemo upload for repository https://github.com/Marie59/champ_blocs commit 0d86db7d42b608c386a54500064f5f9c9d7019a4 ecology parents: diff changeset	1456 c_ <- c_[1:y]
89f977a3a256 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_)))
89f977a3a256 planemo upload for repository https://github.com/Marie59/champ_blocs commit 0d86db7d42b608c386a54500064f5f9c9d7019a4 ecology parents: diff changeset	1458 d_ <- d_[1:y]
89f977a3a256 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_)))
89f977a3a256 planemo upload for repository https://github.com/Marie59/champ_blocs commit 0d86db7d42b608c386a54500064f5f9c9d7019a4 ecology parents: diff changeset	1460 e_ <- e_[1:y]
89f977a3a256 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_)))
89f977a3a256 planemo upload for repository https://github.com/Marie59/champ_blocs commit 0d86db7d42b608c386a54500064f5f9c9d7019a4 ecology parents: diff changeset	1462 f_ <- f_[1:y]
89f977a3a256 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_)))
89f977a3a256 planemo upload for repository https://github.com/Marie59/champ_blocs commit 0d86db7d42b608c386a54500064f5f9c9d7019a4 ecology parents: diff changeset	1464 g_ <- g_[1:y]
89f977a3a256 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_)))
89f977a3a256 planemo upload for repository https://github.com/Marie59/champ_blocs commit 0d86db7d42b608c386a54500064f5f9c9d7019a4 ecology parents: diff changeset	1466 h_ <- h_[1:y]
89f977a3a256 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_)))
89f977a3a256 planemo upload for repository https://github.com/Marie59/champ_blocs commit 0d86db7d42b608c386a54500064f5f9c9d7019a4 ecology parents: diff changeset	1468 i_ <- i_[1:y]
89f977a3a256 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_)))
89f977a3a256 planemo upload for repository https://github.com/Marie59/champ_blocs commit 0d86db7d42b608c386a54500064f5f9c9d7019a4 ecology parents: diff changeset	1470 j_ <- j_[1:y]
89f977a3a256 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_)))
89f977a3a256 planemo upload for repository https://github.com/Marie59/champ_blocs commit 0d86db7d42b608c386a54500064f5f9c9d7019a4 ecology parents: diff changeset	1472 k_ <- k_[1:y]
89f977a3a256 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_)))
89f977a3a256 planemo upload for repository https://github.com/Marie59/champ_blocs commit 0d86db7d42b608c386a54500064f5f9c9d7019a4 ecology parents: diff changeset	1474 l_ <- l_[1:y]
89f977a3a256 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_)))
89f977a3a256 planemo upload for repository https://github.com/Marie59/champ_blocs commit 0d86db7d42b608c386a54500064f5f9c9d7019a4 ecology parents: diff changeset	1476 m_ <- m_[1:y]
89f977a3a256 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_)))
89f977a3a256 planemo upload for repository https://github.com/Marie59/champ_blocs commit 0d86db7d42b608c386a54500064f5f9c9d7019a4 ecology parents: diff changeset	1478 n_ <- n_[1:y]
89f977a3a256 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_)))
89f977a3a256 planemo upload for repository https://github.com/Marie59/champ_blocs commit 0d86db7d42b608c386a54500064f5f9c9d7019a4 ecology parents: diff changeset	1480 o_ <- o_[1:y]
89f977a3a256 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_)))
89f977a3a256 planemo upload for repository https://github.com/Marie59/champ_blocs commit 0d86db7d42b608c386a54500064f5f9c9d7019a4 ecology parents: diff changeset	1482 p_ <- p_[1:y]
89f977a3a256 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_)))
89f977a3a256 planemo upload for repository https://github.com/Marie59/champ_blocs commit 0d86db7d42b608c386a54500064f5f9c9d7019a4 ecology parents: diff changeset	1484 q_ <- q_[1:y]
89f977a3a256 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_)))
89f977a3a256 planemo upload for repository https://github.com/Marie59/champ_blocs commit 0d86db7d42b608c386a54500064f5f9c9d7019a4 ecology parents: diff changeset	1486 r_ <- r_[1:y]
89f977a3a256 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_)))
89f977a3a256 planemo upload for repository https://github.com/Marie59/champ_blocs commit 0d86db7d42b608c386a54500064f5f9c9d7019a4 ecology parents: diff changeset	1488 s_ <- s_[1:y]
89f977a3a256 planemo upload for repository https://github.com/Marie59/champ_blocs commit 0d86db7d42b608c386a54500064f5f9c9d7019a4 ecology parents: diff changeset	1489
89f977a3a256 planemo upload for repository https://github.com/Marie59/champ_blocs commit 0d86db7d42b608c386a54500064f5f9c9d7019a4 ecology parents: diff changeset	1490 rm(y)
89f977a3a256 planemo upload for repository https://github.com/Marie59/champ_blocs commit 0d86db7d42b608c386a54500064f5f9c9d7019a4 ecology parents: diff changeset	1491
89f977a3a256 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_)
89f977a3a256 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)))])
89f977a3a256 planemo upload for repository https://github.com/Marie59/champ_blocs commit 0d86db7d42b608c386a54500064f5f9c9d7019a4 ecology parents: diff changeset	1494 names(df_) <- c("dist.", "name_")
89f977a3a256 planemo upload for repository https://github.com/Marie59/champ_blocs commit 0d86db7d42b608c386a54500064f5f9c9d7019a4 ecology parents: diff changeset	1495
89f977a3a256 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_)
89f977a3a256 planemo upload for repository https://github.com/Marie59/champ_blocs commit 0d86db7d42b608c386a54500064f5f9c9d7019a4 ecology parents: diff changeset	1497 rm(name_)
89f977a3a256 planemo upload for repository https://github.com/Marie59/champ_blocs commit 0d86db7d42b608c386a54500064f5f9c9d7019a4 ecology parents: diff changeset	1498
89f977a3a256 planemo upload for repository https://github.com/Marie59/champ_blocs commit 0d86db7d42b608c386a54500064f5f9c9d7019a4 ecology parents: diff changeset	1499 q_ <- strsplit(df_$name_, " & ")
89f977a3a256 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)
89f977a3a256 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))
89f977a3a256 planemo upload for repository https://github.com/Marie59/champ_blocs commit 0d86db7d42b608c386a54500064f5f9c9d7019a4 ecology parents: diff changeset	1502 df_ <- dplyr::bind_cols(df_, q_df_)
89f977a3a256 planemo upload for repository https://github.com/Marie59/champ_blocs commit 0d86db7d42b608c386a54500064f5f9c9d7019a4 ecology parents: diff changeset	1503
89f977a3a256 planemo upload for repository https://github.com/Marie59/champ_blocs commit 0d86db7d42b608c386a54500064f5f9c9d7019a4 ecology parents: diff changeset	1504 rm(q_, mat_, q_df_)
89f977a3a256 planemo upload for repository https://github.com/Marie59/champ_blocs commit 0d86db7d42b608c386a54500064f5f9c9d7019a4 ecology parents: diff changeset	1505
89f977a3a256 planemo upload for repository https://github.com/Marie59/champ_blocs commit 0d86db7d42b608c386a54500064f5f9c9d7019a4 ecology parents: diff changeset	1506 split_ <- strsplit(df_$V1, "_")
89f977a3a256 planemo upload for repository https://github.com/Marie59/champ_blocs commit 0d86db7d42b608c386a54500064f5f9c9d7019a4 ecology parents: diff changeset	1507 v1_split_ <- as.data.frame(matrix(unlist(split_), ncol = 4, byrow = TRUE))
89f977a3a256 planemo upload for repository https://github.com/Marie59/champ_blocs commit 0d86db7d42b608c386a54500064f5f9c9d7019a4 ecology parents: diff changeset	1508 split_ <- strsplit(df_$V2, "_")
89f977a3a256 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))
89f977a3a256 planemo upload for repository https://github.com/Marie59/champ_blocs commit 0d86db7d42b608c386a54500064f5f9c9d7019a4 ecology parents: diff changeset	1510
89f977a3a256 planemo upload for repository https://github.com/Marie59/champ_blocs commit 0d86db7d42b608c386a54500064f5f9c9d7019a4 ecology parents: diff changeset	1511 df_ <- dplyr::bind_cols(df_, v1_split_)
89f977a3a256 planemo upload for repository https://github.com/Marie59/champ_blocs commit 0d86db7d42b608c386a54500064f5f9c9d7019a4 ecology parents: diff changeset	1512 df_ <- dplyr::bind_cols(df_, v2_split_)
89f977a3a256 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)
89f977a3a256 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_))
89f977a3a256 planemo upload for repository https://github.com/Marie59/champ_blocs commit 0d86db7d42b608c386a54500064f5f9c9d7019a4 ecology parents: diff changeset	1515
89f977a3a256 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.")
89f977a3a256 planemo upload for repository https://github.com/Marie59/champ_blocs commit 0d86db7d42b608c386a54500064f5f9c9d7019a4 ecology parents: diff changeset	1517
89f977a3a256 planemo upload for repository https://github.com/Marie59/champ_blocs commit 0d86db7d42b608c386a54500064f5f9c9d7019a4 ecology parents: diff changeset	1518 rm(split_, v1_split_, v2_split_)
89f977a3a256 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)
89f977a3a256 planemo upload for repository https://github.com/Marie59/champ_blocs commit 0d86db7d42b608c386a54500064f5f9c9d7019a4 ecology parents: diff changeset	1520
89f977a3a256 planemo upload for repository https://github.com/Marie59/champ_blocs commit 0d86db7d42b608c386a54500064f5f9c9d7019a4 ecology parents: diff changeset	1521 matri_list[[x]] <- df_red_
89f977a3a256 planemo upload for repository https://github.com/Marie59/champ_blocs commit 0d86db7d42b608c386a54500064f5f9c9d7019a4 ecology parents: diff changeset	1522 matri_list <<- matri_list
89f977a3a256 planemo upload for repository https://github.com/Marie59/champ_blocs commit 0d86db7d42b608c386a54500064f5f9c9d7019a4 ecology parents: diff changeset	1523
89f977a3a256 planemo upload for repository https://github.com/Marie59/champ_blocs commit 0d86db7d42b608c386a54500064f5f9c9d7019a4 ecology parents: diff changeset	1524 rm(df_red_, qecbnato0_x, x)
89f977a3a256 planemo upload for repository https://github.com/Marie59/champ_blocs commit 0d86db7d42b608c386a54500064f5f9c9d7019a4 ecology parents: diff changeset	1525
89f977a3a256 planemo upload for repository https://github.com/Marie59/champ_blocs commit 0d86db7d42b608c386a54500064f5f9c9d7019a4 ecology parents: diff changeset	1526 }
89f977a3a256 planemo upload for repository https://github.com/Marie59/champ_blocs commit 0d86db7d42b608c386a54500064f5f9c9d7019a4 ecology parents: diff changeset	1527
89f977a3a256 planemo upload for repository https://github.com/Marie59/champ_blocs commit 0d86db7d42b608c386a54500064f5f9c9d7019a4 ecology parents: diff changeset	1528 matri_df <- do.call("rbind", matri_list)
89f977a3a256 planemo upload for repository https://github.com/Marie59/champ_blocs commit 0d86db7d42b608c386a54500064f5f9c9d7019a4 ecology parents: diff changeset	1529
89f977a3a256 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")
89f977a3a256 planemo upload for repository https://github.com/Marie59/champ_blocs commit 0d86db7d42b608c386a54500064f5f9c9d7019a4 ecology parents: diff changeset	1531
89f977a3a256 planemo upload for repository https://github.com/Marie59/champ_blocs commit 0d86db7d42b608c386a54500064f5f9c9d7019a4 ecology parents: diff changeset	1532 matri_df <<- matri_df
89f977a3a256 planemo upload for repository https://github.com/Marie59/champ_blocs commit 0d86db7d42b608c386a54500064f5f9c9d7019a4 ecology parents: diff changeset	1533
89f977a3a256 planemo upload for repository https://github.com/Marie59/champ_blocs commit 0d86db7d42b608c386a54500064f5f9c9d7019a4 ecology parents: diff changeset	1534 hist(matri_df$dist.)
89f977a3a256 planemo upload for repository https://github.com/Marie59/champ_blocs commit 0d86db7d42b608c386a54500064f5f9c9d7019a4 ecology parents: diff changeset	1535
89f977a3a256 planemo upload for repository https://github.com/Marie59/champ_blocs commit 0d86db7d42b608c386a54500064f5f9c9d7019a4 ecology parents: diff changeset	1536 }
89f977a3a256 planemo upload for repository https://github.com/Marie59/champ_blocs commit 0d86db7d42b608c386a54500064f5f9c9d7019a4 ecology parents: diff changeset	1537
89f977a3a256 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")
89f977a3a256 planemo upload for repository https://github.com/Marie59/champ_blocs commit 0d86db7d42b608c386a54500064f5f9c9d7019a4 ecology parents: diff changeset	1539 matri_list <- vector("list", length(unique(data_$site_year_month_day)))
89f977a3a256 planemo upload for repository https://github.com/Marie59/champ_blocs commit 0d86db7d42b608c386a54500064f5f9c9d7019a4 ecology parents: diff changeset	1540
89f977a3a256 planemo upload for repository https://github.com/Marie59/champ_blocs commit 0d86db7d42b608c386a54500064f5f9c9d7019a4 ecology parents: diff changeset	1541 matri_fct_bmm(data = data_, conca = c(bret_egmp_basq_qecb, egmp_basq_qecb))
89f977a3a256 planemo upload for repository https://github.com/Marie59/champ_blocs commit 0d86db7d42b608c386a54500064f5f9c9d7019a4 ecology parents: diff changeset	1542 hist(matri_df$dist., main = c(paste("Histo. of Bray (0-adjusted) dist. dissimilarity measures"), paste(" (sqrt transfo) - BMfs vs BMfi -")))
89f977a3a256 planemo upload for repository https://github.com/Marie59/champ_blocs commit 0d86db7d42b608c386a54500064f5f9c9d7019a4 ecology parents: diff changeset	1543
89f977a3a256 planemo upload for repository https://github.com/Marie59/champ_blocs commit 0d86db7d42b608c386a54500064f5f9c9d7019a4 ecology parents: diff changeset	1544 matri_full_bm_bf_fi <- matri_df
89f977a3a256 planemo upload for repository https://github.com/Marie59/champ_blocs commit 0d86db7d42b608c386a54500064f5f9c9d7019a4 ecology parents: diff changeset	1545
89f977a3a256 planemo upload for repository https://github.com/Marie59/champ_blocs commit 0d86db7d42b608c386a54500064f5f9c9d7019a4 ecology parents: diff changeset	1546 rm(data_, matri_df, matri_list)
89f977a3a256 planemo upload for repository https://github.com/Marie59/champ_blocs commit 0d86db7d42b608c386a54500064f5f9c9d7019a4 ecology parents: diff changeset	1547
89f977a3a256 planemo upload for repository https://github.com/Marie59/champ_blocs commit 0d86db7d42b608c386a54500064f5f9c9d7019a4 ecology parents: diff changeset	1548
89f977a3a256 planemo upload for repository https://github.com/Marie59/champ_blocs commit 0d86db7d42b608c386a54500064f5f9c9d7019a4 ecology parents: diff changeset	1549 #############################################################
89f977a3a256 planemo upload for repository https://github.com/Marie59/champ_blocs commit 0d86db7d42b608c386a54500064f5f9c9d7019a4 ecology parents: diff changeset	1550 # #
89f977a3a256 planemo upload for repository https://github.com/Marie59/champ_blocs commit 0d86db7d42b608c386a54500064f5f9c9d7019a4 ecology parents: diff changeset	1551 # Plot dissimilarity #
89f977a3a256 planemo upload for repository https://github.com/Marie59/champ_blocs commit 0d86db7d42b608c386a54500064f5f9c9d7019a4 ecology parents: diff changeset	1552 # #
89f977a3a256 planemo upload for repository https://github.com/Marie59/champ_blocs commit 0d86db7d42b608c386a54500064f5f9c9d7019a4 ecology parents: diff changeset	1553 #############################################################
89f977a3a256 planemo upload for repository https://github.com/Marie59/champ_blocs commit 0d86db7d42b608c386a54500064f5f9c9d7019a4 ecology parents: diff changeset	1554 ## plot
89f977a3a256 planemo upload for repository https://github.com/Marie59/champ_blocs commit 0d86db7d42b608c386a54500064f5f9c9d7019a4 ecology parents: diff changeset	1555
89f977a3a256 planemo upload for repository https://github.com/Marie59/champ_blocs commit 0d86db7d42b608c386a54500064f5f9c9d7019a4 ecology parents: diff changeset	1556 # activate line
89f977a3a256 planemo upload for repository https://github.com/Marie59/champ_blocs commit 0d86db7d42b608c386a54500064f5f9c9d7019a4 ecology parents: diff changeset	1557
89f977a3a256 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)
89f977a3a256 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$Site)
89f977a3a256 planemo upload for repository https://github.com/Marie59/champ_blocs commit 0d86db7d42b608c386a54500064f5f9c9d7019a4 ecology parents: diff changeset	1560 matri_full_bm_bf_fs <- subset(matri_full_bm_bf_fs, select = - c(departement))
89f977a3a256 planemo upload for repository https://github.com/Marie59/champ_blocs commit 0d86db7d42b608c386a54500064f5f9c9d7019a4 ecology parents: diff changeset	1561
89f977a3a256 planemo upload for repository https://github.com/Marie59/champ_blocs commit 0d86db7d42b608c386a54500064f5f9c9d7019a4 ecology parents: diff changeset	1562 matri_full_bm_bf_fs <- tibble::add_column(matri_full_bm_bf_fs, Date = as.Date(paste0(matri_full_bm_bf_fs$Year, "-", matri_full_bm_bf_fs$Month, "-", matri_full_bm_bf_fs$Day), origin = "1970-01-01"), .after = "Site")
89f977a3a256 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)
89f977a3a256 planemo upload for repository https://github.com/Marie59/champ_blocs commit 0d86db7d42b608c386a54500064f5f9c9d7019a4 ecology parents: diff changeset	1564
89f977a3a256 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)
89f977a3a256 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$Site)
89f977a3a256 planemo upload for repository https://github.com/Marie59/champ_blocs commit 0d86db7d42b608c386a54500064f5f9c9d7019a4 ecology parents: diff changeset	1567 matri_full_bm_bf_fi <- subset(matri_full_bm_bf_fi, select = - c(departement))
89f977a3a256 planemo upload for repository https://github.com/Marie59/champ_blocs commit 0d86db7d42b608c386a54500064f5f9c9d7019a4 ecology parents: diff changeset	1568 matri_full_bm_bf_fi <- tibble::add_column(matri_full_bm_bf_fi, Date = as.Date(paste0(matri_full_bm_bf_fi$Year, "-", matri_full_bm_bf_fi$Month, "-", matri_full_bm_bf_fi$Day), origin = "1970-01-01"), .after = "Site")
89f977a3a256 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)
89f977a3a256 planemo upload for repository https://github.com/Marie59/champ_blocs commit 0d86db7d42b608c386a54500064f5f9c9d7019a4 ecology parents: diff changeset	1570
89f977a3a256 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"
89f977a3a256 planemo upload for repository https://github.com/Marie59/champ_blocs commit 0d86db7d42b608c386a54500064f5f9c9d7019a4 ecology parents: diff changeset	1572
89f977a3a256 planemo upload for repository https://github.com/Marie59/champ_blocs commit 0d86db7d42b608c386a54500064f5f9c9d7019a4 ecology parents: diff changeset	1573
89f977a3a256 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.)) +
89f977a3a256 planemo upload for repository https://github.com/Marie59/champ_blocs commit 0d86db7d42b608c386a54500064f5f9c9d7019a4 ecology parents: diff changeset	1575 ggplot2::geom_boxplot() +
89f977a3a256 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)) +
89f977a3a256 planemo upload for repository https://github.com/Marie59/champ_blocs commit 0d86db7d42b608c386a54500064f5f9c9d7019a4 ecology parents: diff changeset	1577 ggplot2::xlab("") +
89f977a3a256 planemo upload for repository https://github.com/Marie59/champ_blocs commit 0d86db7d42b608c386a54500064f5f9c9d7019a4 ecology parents: diff changeset	1578 ggplot2::ylab("distance diss. BM.BF_FS") +
89f977a3a256 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))
89f977a3a256 planemo upload for repository https://github.com/Marie59/champ_blocs commit 0d86db7d42b608c386a54500064f5f9c9d7019a4 ecology parents: diff changeset	1580
89f977a3a256 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)
89f977a3a256 planemo upload for repository https://github.com/Marie59/champ_blocs commit 0d86db7d42b608c386a54500064f5f9c9d7019a4 ecology parents: diff changeset	1582
89f977a3a256 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.)) +
89f977a3a256 planemo upload for repository https://github.com/Marie59/champ_blocs commit 0d86db7d42b608c386a54500064f5f9c9d7019a4 ecology parents: diff changeset	1584 ggplot2::geom_boxplot() +
89f977a3a256 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)) +
89f977a3a256 planemo upload for repository https://github.com/Marie59/champ_blocs commit 0d86db7d42b608c386a54500064f5f9c9d7019a4 ecology parents: diff changeset	1586 ggplot2::xlab("") +
89f977a3a256 planemo upload for repository https://github.com/Marie59/champ_blocs commit 0d86db7d42b608c386a54500064f5f9c9d7019a4 ecology parents: diff changeset	1587 ggplot2::ylab("distance diss. BM_FS.FI") +
89f977a3a256 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))
89f977a3a256 planemo upload for repository https://github.com/Marie59/champ_blocs commit 0d86db7d42b608c386a54500064f5f9c9d7019a4 ecology parents: diff changeset	1589
89f977a3a256 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)
89f977a3a256 planemo upload for repository https://github.com/Marie59/champ_blocs commit 0d86db7d42b608c386a54500064f5f9c9d7019a4 ecology parents: diff changeset	1591
89f977a3a256 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).
89f977a3a256 planemo upload for repository https://github.com/Marie59/champ_blocs commit 0d86db7d42b608c386a54500064f5f9c9d7019a4 ecology parents: diff changeset	1593 matri_full_bm_bf_fs$Quadrat <- NA
89f977a3a256 planemo upload for repository https://github.com/Marie59/champ_blocs commit 0d86db7d42b608c386a54500064f5f9c9d7019a4 ecology parents: diff changeset	1594 for (i in c(1:seq_len(nrow(matri_full_bm_bf_fs)))) {
89f977a3a256 planemo upload for repository https://github.com/Marie59/champ_blocs commit 0d86db7d42b608c386a54500064f5f9c9d7019a4 ecology parents: diff changeset	1595 ifelse(matri_full_bm_bf_fs$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])
89f977a3a256 planemo upload for repository https://github.com/Marie59/champ_blocs commit 0d86db7d42b608c386a54500064f5f9c9d7019a4 ecology parents: diff changeset	1596 }
89f977a3a256 planemo upload for repository https://github.com/Marie59/champ_blocs commit 0d86db7d42b608c386a54500064f5f9c9d7019a4 ecology parents: diff changeset	1597 matri_full_bm_bf_fs$Numéro.Bloc <- NA
89f977a3a256 planemo upload for repository https://github.com/Marie59/champ_blocs commit 0d86db7d42b608c386a54500064f5f9c9d7019a4 ecology parents: diff changeset	1598 for (i in c(1:seq_len(nrow(matri_full_bm_bf_fs)))) {
89f977a3a256 planemo upload for repository https://github.com/Marie59/champ_blocs commit 0d86db7d42b608c386a54500064f5f9c9d7019a4 ecology parents: diff changeset	1599 ifelse(matri_full_bm_bf_fs$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])
89f977a3a256 planemo upload for repository https://github.com/Marie59/champ_blocs commit 0d86db7d42b608c386a54500064f5f9c9d7019a4 ecology parents: diff changeset	1600 }
89f977a3a256 planemo upload for repository https://github.com/Marie59/champ_blocs commit 0d86db7d42b608c386a54500064f5f9c9d7019a4 ecology parents: diff changeset	1601
89f977a3a256 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$Numéro.Bloc), .after = "site_year_month_day")
89f977a3a256 planemo upload for repository https://github.com/Marie59/champ_blocs commit 0d86db7d42b608c386a54500064f5f9c9d7019a4 ecology parents: diff changeset	1603 matri_full_bm_bf_fi <- tibble::add_column(matri_full_bm_bf_fi, site_year_month_day.q_BMnb = paste0(matri_full_bm_bf_fi$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")
89f977a3a256 planemo upload for repository https://github.com/Marie59/champ_blocs commit 0d86db7d42b608c386a54500064f5f9c9d7019a4 ecology parents: diff changeset	1604
89f977a3a256 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 = "_")
89f977a3a256 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)
89f977a3a256 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 = "_")
89f977a3a256 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)
89f977a3a256 planemo upload for repository https://github.com/Marie59/champ_blocs commit 0d86db7d42b608c386a54500064f5f9c9d7019a4 ecology parents: diff changeset	1609
89f977a3a256 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.")])
89f977a3a256 planemo upload for repository https://github.com/Marie59/champ_blocs commit 0d86db7d42b608c386a54500064f5f9c9d7019a4 ecology parents: diff changeset	1611
89f977a3a256 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)
89f977a3a256 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$Site)
89f977a3a256 planemo upload for repository https://github.com/Marie59/champ_blocs commit 0d86db7d42b608c386a54500064f5f9c9d7019a4 ecology parents: diff changeset	1614 matri_full <- subset(matri_full, select = - c(departement))
89f977a3a256 planemo upload for repository https://github.com/Marie59/champ_blocs commit 0d86db7d42b608c386a54500064f5f9c9d7019a4 ecology parents: diff changeset	1615 matri_full <- tibble::add_column(matri_full, Date = as.Date(paste0(matri_full$Year, "-", matri_full$Month, "-", matri_full$Day), origin = "1970-01-01"), .after = "Site")
89f977a3a256 planemo upload for repository https://github.com/Marie59/champ_blocs commit 0d86db7d42b608c386a54500064f5f9c9d7019a4 ecology parents: diff changeset	1616
89f977a3a256 planemo upload for repository https://github.com/Marie59/champ_blocs commit 0d86db7d42b608c386a54500064f5f9c9d7019a4 ecology parents: diff changeset	1617 # Name for report/plot
89f977a3a256 planemo upload for repository https://github.com/Marie59/champ_blocs commit 0d86db7d42b608c386a54500064f5f9c9d7019a4 ecology parents: diff changeset	1618
89f977a3a256 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$Site, .after = "Site")
89f977a3a256 planemo upload for repository https://github.com/Marie59/champ_blocs commit 0d86db7d42b608c386a54500064f5f9c9d7019a4 ecology parents: diff changeset	1620
89f977a3a256 planemo upload for repository https://github.com/Marie59/champ_blocs commit 0d86db7d42b608c386a54500064f5f9c9d7019a4 ecology parents: diff changeset	1621 matri_full$Site_bis <- ifelse(matri_full$Site == "GDMO_Locmariaquer", "Locmariaquer", matri_full$Site_bis)
89f977a3a256 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$Site_bis)
89f977a3a256 planemo upload for repository https://github.com/Marie59/champ_blocs commit 0d86db7d42b608c386a54500064f5f9c9d7019a4 ecology parents: diff changeset	1623 matri_full$Site_bis <- ifelse(matri_full$Site == "FOUR_PlateauFour", "Plateau du Four", matri_full$Site_bis)
89f977a3a256 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$Site_bis)
89f977a3a256 planemo upload for repository https://github.com/Marie59/champ_blocs commit 0d86db7d42b608c386a54500064f5f9c9d7019a4 ecology parents: diff changeset	1625 matri_full$Site_bis <- ifelse(matri_full$Site == "EGMP_PasEmsembert", "Le Pas d'Emsembert", matri_full$Site_bis)
89f977a3a256 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$Site_bis)
89f977a3a256 planemo upload for repository https://github.com/Marie59/champ_blocs commit 0d86db7d42b608c386a54500064f5f9c9d7019a4 ecology parents: diff changeset	1627 matri_full$Site_bis <- ifelse(matri_full$Site == "EGMP_PerreAntiochat", "Le Perré d'Antiochat", matri_full$Site_bis)
89f977a3a256 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$Site_bis)
89f977a3a256 planemo upload for repository https://github.com/Marie59/champ_blocs commit 0d86db7d42b608c386a54500064f5f9c9d7019a4 ecology parents: diff changeset	1629 matri_full$Site_bis <- ifelse(matri_full$Site == "BASQ_FlotsBleusZP", "Les Flots Bleus / zone pêcheurs", matri_full$Site_bis)
89f977a3a256 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$Site_bis)
89f977a3a256 planemo upload for repository https://github.com/Marie59/champ_blocs commit 0d86db7d42b608c386a54500064f5f9c9d7019a4 ecology parents: diff changeset	1631 matri_full$Site_bis <- ifelse(matri_full$Site == "GONB_IlotStMichel", "Îlot Saint-Michel", matri_full$Site_bis)
89f977a3a256 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$Site_bis)
89f977a3a256 planemo upload for repository https://github.com/Marie59/champ_blocs commit 0d86db7d42b608c386a54500064f5f9c9d7019a4 ecology parents: diff changeset	1633 matri_full$Site_bis <- ifelse(matri_full$Site == "FINS_SeinGoulenez", "Île de Sein - Goulenez", matri_full$Site_bis)
89f977a3a256 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$Site_bis)
89f977a3a256 planemo upload for repository https://github.com/Marie59/champ_blocs commit 0d86db7d42b608c386a54500064f5f9c9d7019a4 ecology parents: diff changeset	1635 matri_full$Site_bis <- ifelse(matri_full$Site == "ARMO_Verdelet", "Îlot du Verdelet", matri_full$Site_bis)
89f977a3a256 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$Site_bis)
89f977a3a256 planemo upload for repository https://github.com/Marie59/champ_blocs commit 0d86db7d42b608c386a54500064f5f9c9d7019a4 ecology parents: diff changeset	1637 matri_full$Site_bis <- ifelse(matri_full$Site == "ARMO_Bilfot", "Pointe de Bilfot", matri_full$Site_bis)
89f977a3a256 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$Site_bis)
89f977a3a256 planemo upload for repository https://github.com/Marie59/champ_blocs commit 0d86db7d42b608c386a54500064f5f9c9d7019a4 ecology parents: diff changeset	1639 matri_full$Site_bis <- ifelse(matri_full$Site == "PDMO_Perharidy", "Perharidy", matri_full$Site_bis)
89f977a3a256 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$Site_bis)
89f977a3a256 planemo upload for repository https://github.com/Marie59/champ_blocs commit 0d86db7d42b608c386a54500064f5f9c9d7019a4 ecology parents: diff changeset	1641 matri_full$Site_bis <- ifelse(matri_full$Site == "FINS_Mousterlin", "Pointe de Mousterlin", matri_full$Site_bis)
89f977a3a256 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$Site_bis)
89f977a3a256 planemo upload for repository https://github.com/Marie59/champ_blocs commit 0d86db7d42b608c386a54500064f5f9c9d7019a4 ecology parents: diff changeset	1643 matri_full$Site_bis <- ifelse(matri_full$Site == "FINS_AnseRoz", "Pointe de l'Anse du Roz", matri_full$Site_bis)
89f977a3a256 planemo upload for repository https://github.com/Marie59/champ_blocs commit 0d86db7d42b608c386a54500064f5f9c9d7019a4 ecology parents: diff changeset	1644
89f977a3a256 planemo upload for repository https://github.com/Marie59/champ_blocs commit 0d86db7d42b608c386a54500064f5f9c9d7019a4 ecology parents: diff changeset	1645 saveRDS(matri_full, "matri_full.RDS")
89f977a3a256 planemo upload for repository https://github.com/Marie59/champ_blocs commit 0d86db7d42b608c386a54500064f5f9c9d7019a4 ecology parents: diff changeset	1646
89f977a3a256 planemo upload for repository https://github.com/Marie59/champ_blocs commit 0d86db7d42b608c386a54500064f5f9c9d7019a4 ecology parents: diff changeset	1647 #############################################################
89f977a3a256 planemo upload for repository https://github.com/Marie59/champ_blocs commit 0d86db7d42b608c386a54500064f5f9c9d7019a4 ecology parents: diff changeset	1648 # #
89f977a3a256 planemo upload for repository https://github.com/Marie59/champ_blocs commit 0d86db7d42b608c386a54500064f5f9c9d7019a4 ecology parents: diff changeset	1649 # Plot the dissimilarity per site #
89f977a3a256 planemo upload for repository https://github.com/Marie59/champ_blocs commit 0d86db7d42b608c386a54500064f5f9c9d7019a4 ecology parents: diff changeset	1650 # #
89f977a3a256 planemo upload for repository https://github.com/Marie59/champ_blocs commit 0d86db7d42b608c386a54500064f5f9c9d7019a4 ecology parents: diff changeset	1651 #############################################################
89f977a3a256 planemo upload for repository https://github.com/Marie59/champ_blocs commit 0d86db7d42b608c386a54500064f5f9c9d7019a4 ecology parents: diff changeset	1652 ## plot dissimilarity coefficient
89f977a3a256 planemo upload for repository https://github.com/Marie59/champ_blocs commit 0d86db7d42b608c386a54500064f5f9c9d7019a4 ecology parents: diff changeset	1653
89f977a3a256 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)
89f977a3a256 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)
89f977a3a256 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)
89f977a3a256 planemo upload for repository https://github.com/Marie59/champ_blocs commit 0d86db7d42b608c386a54500064f5f9c9d7019a4 ecology parents: diff changeset	1657
89f977a3a256 planemo upload for repository https://github.com/Marie59/champ_blocs commit 0d86db7d42b608c386a54500064f5f9c9d7019a4 ecology parents: diff changeset	1658
89f977a3a256 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
89f977a3a256 planemo upload for repository https://github.com/Marie59/champ_blocs commit 0d86db7d42b608c386a54500064f5f9c9d7019a4 ecology parents: diff changeset	1660
89f977a3a256 planemo upload for repository https://github.com/Marie59/champ_blocs commit 0d86db7d42b608c386a54500064f5f9c9d7019a4 ecology parents: diff changeset	1661 # Stats
89f977a3a256 planemo upload for repository https://github.com/Marie59/champ_blocs commit 0d86db7d42b608c386a54500064f5f9c9d7019a4 ecology parents: diff changeset	1662
89f977a3a256 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.)))
89f977a3a256 planemo upload for repository https://github.com/Marie59/champ_blocs commit 0d86db7d42b608c386a54500064f5f9c9d7019a4 ecology parents: diff changeset	1664
89f977a3a256 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)
89f977a3a256 planemo upload for repository https://github.com/Marie59/champ_blocs commit 0d86db7d42b608c386a54500064f5f9c9d7019a4 ecology parents: diff changeset	1666
89f977a3a256 planemo upload for repository https://github.com/Marie59/champ_blocs commit 0d86db7d42b608c386a54500064f5f9c9d7019a4 ecology parents: diff changeset	1667 # Quality scale based on quartiles
89f977a3a256 planemo upload for repository https://github.com/Marie59/champ_blocs commit 0d86db7d42b608c386a54500064f5f9c9d7019a4 ecology parents: diff changeset	1668
89f977a3a256 planemo upload for repository https://github.com/Marie59/champ_blocs commit 0d86db7d42b608c386a54500064f5f9c9d7019a4 ecology parents: diff changeset	1669 if (choice == "N") {
89f977a3a256 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$BM_FS.FI_dist., 0.25, na.rm = TRUE))["BM_FS.FI_dist."])), digits = 3)
89f977a3a256 planemo upload for repository https://github.com/Marie59/champ_blocs commit 0d86db7d42b608c386a54500064f5f9c9d7019a4 ecology parents: diff changeset	1671 two <- round(mean(unlist(dplyr::filter(matri_full, BM_FS.FI_dist. > quantile(matri_full$BM_FS.FI_dist., 0.25, na.rm = TRUE) & BM_FS.FI_dist. <= quantile(matri_full$BM_FS.FI_dist., 0.5, na.rm = TRUE))["BM_FS.FI_dist."])), digits = 3)
89f977a3a256 planemo upload for repository https://github.com/Marie59/champ_blocs commit 0d86db7d42b608c386a54500064f5f9c9d7019a4 ecology parents: diff changeset	1672 three <- round(mean(unlist(dplyr::filter(matri_full, BM_FS.FI_dist. > quantile(matri_full$BM_FS.FI_dist., 0.5, na.rm = TRUE) & BM_FS.FI_dist. <= quantile(matri_full$BM_FS.FI_dist., 0.75, na.rm = TRUE))["BM_FS.FI_dist."])), digits = 3)
89f977a3a256 planemo upload for repository https://github.com/Marie59/champ_blocs commit 0d86db7d42b608c386a54500064f5f9c9d7019a4 ecology parents: diff changeset	1673 four <- round(mean(unlist(dplyr::filter(matri_full, BM_FS.FI_dist. > quantile(matri_full$BM_FS.FI_dist., 0.75, na.rm = TRUE))["BM_FS.FI_dist."])), digits = 3)
89f977a3a256 planemo upload for repository https://github.com/Marie59/champ_blocs commit 0d86db7d42b608c386a54500064f5f9c9d7019a4 ecology parents: diff changeset	1674 }else {
89f977a3a256 planemo upload for repository https://github.com/Marie59/champ_blocs commit 0d86db7d42b608c386a54500064f5f9c9d7019a4 ecology parents: diff changeset	1675 one <- 0.47
89f977a3a256 planemo upload for repository https://github.com/Marie59/champ_blocs commit 0d86db7d42b608c386a54500064f5f9c9d7019a4 ecology parents: diff changeset	1676 two <- 0.7
89f977a3a256 planemo upload for repository https://github.com/Marie59/champ_blocs commit 0d86db7d42b608c386a54500064f5f9c9d7019a4 ecology parents: diff changeset	1677 three <- 0.83
89f977a3a256 planemo upload for repository https://github.com/Marie59/champ_blocs commit 0d86db7d42b608c386a54500064f5f9c9d7019a4 ecology parents: diff changeset	1678 four <- 0.98
89f977a3a256 planemo upload for repository https://github.com/Marie59/champ_blocs commit 0d86db7d42b608c386a54500064f5f9c9d7019a4 ecology parents: diff changeset	1679 }
89f977a3a256 planemo upload for repository https://github.com/Marie59/champ_blocs commit 0d86db7d42b608c386a54500064f5f9c9d7019a4 ecology parents: diff changeset	1680
89f977a3a256 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")
89f977a3a256 planemo upload for repository https://github.com/Marie59/champ_blocs commit 0d86db7d42b608c386a54500064f5f9c9d7019a4 ecology parents: diff changeset	1682
89f977a3a256 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$Site)))) {
89f977a3a256 planemo upload for repository https://github.com/Marie59/champ_blocs commit 0d86db7d42b608c386a54500064f5f9c9d7019a4 ecology parents: diff changeset	1684
89f977a3a256 planemo upload for repository https://github.com/Marie59/champ_blocs commit 0d86db7d42b608c386a54500064f5f9c9d7019a4 ecology parents: diff changeset	1685 df1 <- dplyr::filter(bm_fs_fi_dist_stat, bm_fs_fi_dist_stat$Site == unique(bm_fs_fi_dist_stat$Site)[i])
89f977a3a256 planemo upload for repository https://github.com/Marie59/champ_blocs commit 0d86db7d42b608c386a54500064f5f9c9d7019a4 ecology parents: diff changeset	1686
89f977a3a256 planemo upload for repository https://github.com/Marie59/champ_blocs commit 0d86db7d42b608c386a54500064f5f9c9d7019a4 ecology parents: diff changeset	1687 bm_fs_fi_plot <- ggplot2::ggplot() +
89f977a3a256 planemo upload for repository https://github.com/Marie59/champ_blocs commit 0d86db7d42b608c386a54500064f5f9c9d7019a4 ecology parents: diff changeset	1688 ggplot2::geom_point(ggplot2::aes(x = bm_fs_fi_dist_stat$Date, y = bm_fs_fi_dist_stat$BM_FS.FI_dist.med), col = "grey") +
89f977a3a256 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) +
89f977a3a256 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) +
89f977a3a256 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) +
89f977a3a256 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) +
89f977a3a256 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) +
89f977a3a256 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")) +
89f977a3a256 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$BM_FS.FI_dist.max), col = "black") +
89f977a3a256 planemo upload for repository https://github.com/Marie59/champ_blocs commit 0d86db7d42b608c386a54500064f5f9c9d7019a4 ecology parents: diff changeset	1696 ggplot2::xlab("Date") +
89f977a3a256 planemo upload for repository https://github.com/Marie59/champ_blocs commit 0d86db7d42b608c386a54500064f5f9c9d7019a4 ecology parents: diff changeset	1697 ggplot2::ylab("Coef dissim BM FS-FI") +
89f977a3a256 planemo upload for repository https://github.com/Marie59/champ_blocs commit 0d86db7d42b608c386a54500064f5f9c9d7019a4 ecology parents: diff changeset	1698 ggplot2::ggtitle(unique(df1$Site_bis)) +
89f977a3a256 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")
89f977a3a256 planemo upload for repository https://github.com/Marie59/champ_blocs commit 0d86db7d42b608c386a54500064f5f9c9d7019a4 ecology parents: diff changeset	1700
89f977a3a256 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)
89f977a3a256 planemo upload for repository https://github.com/Marie59/champ_blocs commit 0d86db7d42b608c386a54500064f5f9c9d7019a4 ecology parents: diff changeset	1702
89f977a3a256 planemo upload for repository https://github.com/Marie59/champ_blocs commit 0d86db7d42b608c386a54500064f5f9c9d7019a4 ecology parents: diff changeset	1703 }
89f977a3a256 planemo upload for repository https://github.com/Marie59/champ_blocs commit 0d86db7d42b608c386a54500064f5f9c9d7019a4 ecology parents: diff changeset	1704
89f977a3a256 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_)
89f977a3a256 planemo upload for repository https://github.com/Marie59/champ_blocs commit 0d86db7d42b608c386a54500064f5f9c9d7019a4 ecology parents: diff changeset	1706
89f977a3a256 planemo upload for repository https://github.com/Marie59/champ_blocs commit 0d86db7d42b608c386a54500064f5f9c9d7019a4 ecology parents: diff changeset	1707
89f977a3a256 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
89f977a3a256 planemo upload for repository https://github.com/Marie59/champ_blocs commit 0d86db7d42b608c386a54500064f5f9c9d7019a4 ecology parents: diff changeset	1709
89f977a3a256 planemo upload for repository https://github.com/Marie59/champ_blocs commit 0d86db7d42b608c386a54500064f5f9c9d7019a4 ecology parents: diff changeset	1710 # Stats
89f977a3a256 planemo upload for repository https://github.com/Marie59/champ_blocs commit 0d86db7d42b608c386a54500064f5f9c9d7019a4 ecology parents: diff changeset	1711
89f977a3a256 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.)))
89f977a3a256 planemo upload for repository https://github.com/Marie59/champ_blocs commit 0d86db7d42b608c386a54500064f5f9c9d7019a4 ecology parents: diff changeset	1713
89f977a3a256 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)
89f977a3a256 planemo upload for repository https://github.com/Marie59/champ_blocs commit 0d86db7d42b608c386a54500064f5f9c9d7019a4 ecology parents: diff changeset	1715
89f977a3a256 planemo upload for repository https://github.com/Marie59/champ_blocs commit 0d86db7d42b608c386a54500064f5f9c9d7019a4 ecology parents: diff changeset	1716 # Quality scale based on quartiles
89f977a3a256 planemo upload for repository https://github.com/Marie59/champ_blocs commit 0d86db7d42b608c386a54500064f5f9c9d7019a4 ecology parents: diff changeset	1717
89f977a3a256 planemo upload for repository https://github.com/Marie59/champ_blocs commit 0d86db7d42b608c386a54500064f5f9c9d7019a4 ecology parents: diff changeset	1718 if (choice == "N") {
89f977a3a256 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)
89f977a3a256 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)
89f977a3a256 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)
89f977a3a256 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$BM.BF_FS_dist., 0.75, na.rm = TRUE))["BM.BF_FS_dist."])), digits = 3)
89f977a3a256 planemo upload for repository https://github.com/Marie59/champ_blocs commit 0d86db7d42b608c386a54500064f5f9c9d7019a4 ecology parents: diff changeset	1723
89f977a3a256 planemo upload for repository https://github.com/Marie59/champ_blocs commit 0d86db7d42b608c386a54500064f5f9c9d7019a4 ecology parents: diff changeset	1724 }else {
89f977a3a256 planemo upload for repository https://github.com/Marie59/champ_blocs commit 0d86db7d42b608c386a54500064f5f9c9d7019a4 ecology parents: diff changeset	1725 one <- 0.19
89f977a3a256 planemo upload for repository https://github.com/Marie59/champ_blocs commit 0d86db7d42b608c386a54500064f5f9c9d7019a4 ecology parents: diff changeset	1726 two <- 0.32
89f977a3a256 planemo upload for repository https://github.com/Marie59/champ_blocs commit 0d86db7d42b608c386a54500064f5f9c9d7019a4 ecology parents: diff changeset	1727 three <- 0.455
89f977a3a256 planemo upload for repository https://github.com/Marie59/champ_blocs commit 0d86db7d42b608c386a54500064f5f9c9d7019a4 ecology parents: diff changeset	1728 four <- 0.735
89f977a3a256 planemo upload for repository https://github.com/Marie59/champ_blocs commit 0d86db7d42b608c386a54500064f5f9c9d7019a4 ecology parents: diff changeset	1729 }
89f977a3a256 planemo upload for repository https://github.com/Marie59/champ_blocs commit 0d86db7d42b608c386a54500064f5f9c9d7019a4 ecology parents: diff changeset	1730 # Plot
89f977a3a256 planemo upload for repository https://github.com/Marie59/champ_blocs commit 0d86db7d42b608c386a54500064f5f9c9d7019a4 ecology parents: diff changeset	1731
89f977a3a256 planemo upload for repository https://github.com/Marie59/champ_blocs commit 0d86db7d42b608c386a54500064f5f9c9d7019a4 ecology parents: diff changeset	1732 for (i in c(1:length(unique(bm_bf_fs_dist_stat$Site)))) {
89f977a3a256 planemo upload for repository https://github.com/Marie59/champ_blocs commit 0d86db7d42b608c386a54500064f5f9c9d7019a4 ecology parents: diff changeset	1733
89f977a3a256 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])
89f977a3a256 planemo upload for repository https://github.com/Marie59/champ_blocs commit 0d86db7d42b608c386a54500064f5f9c9d7019a4 ecology parents: diff changeset	1735
89f977a3a256 planemo upload for repository https://github.com/Marie59/champ_blocs commit 0d86db7d42b608c386a54500064f5f9c9d7019a4 ecology parents: diff changeset	1736 bm_bf_fs_plot <- ggplot2::ggplot() +
89f977a3a256 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") +
89f977a3a256 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) +
89f977a3a256 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) +
89f977a3a256 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) +
89f977a3a256 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) +
89f977a3a256 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) +
89f977a3a256 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")) +
89f977a3a256 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") +
89f977a3a256 planemo upload for repository https://github.com/Marie59/champ_blocs commit 0d86db7d42b608c386a54500064f5f9c9d7019a4 ecology parents: diff changeset	1745 ggplot2::xlab("Date") +
89f977a3a256 planemo upload for repository https://github.com/Marie59/champ_blocs commit 0d86db7d42b608c386a54500064f5f9c9d7019a4 ecology parents: diff changeset	1746 ggplot2::ylab("Coef dissim BM-BF FS") +
89f977a3a256 planemo upload for repository https://github.com/Marie59/champ_blocs commit 0d86db7d42b608c386a54500064f5f9c9d7019a4 ecology parents: diff changeset	1747 ggplot2::ggtitle(unique(df1$Site_bis)) +
89f977a3a256 planemo upload for repository https://github.com/Marie59/champ_blocs commit 0d86db7d42b608c386a54500064f5f9c9d7019a4 ecology parents: diff changeset	1748 ggplot2::theme(axis.text.x = ggplot2::element_text(angle = 90, vjust = 0.5, hjust = 1), legend.position = "none")
89f977a3a256 planemo upload for repository https://github.com/Marie59/champ_blocs commit 0d86db7d42b608c386a54500064f5f9c9d7019a4 ecology parents: diff changeset	1749
89f977a3a256 planemo upload for repository https://github.com/Marie59/champ_blocs commit 0d86db7d42b608c386a54500064f5f9c9d7019a4 ecology parents: diff changeset	1750 ggplot2::ggsave(paste0("bm_bf_", df1$Site, ".png"), device = "png", bm_bf_fs_plot, height = 3, width = 3.5)
89f977a3a256 planemo upload for repository https://github.com/Marie59/champ_blocs commit 0d86db7d42b608c386a54500064f5f9c9d7019a4 ecology parents: diff changeset	1751
89f977a3a256 planemo upload for repository https://github.com/Marie59/champ_blocs commit 0d86db7d42b608c386a54500064f5f9c9d7019a4 ecology parents: diff changeset	1752 }
89f977a3a256 planemo upload for repository https://github.com/Marie59/champ_blocs commit 0d86db7d42b608c386a54500064f5f9c9d7019a4 ecology parents: diff changeset	1753
89f977a3a256 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_ivr

annotate cb_dissimilarity.r @ 1:83a4d3b47184 draft default tip