ecology/cb_dissim: cb_dissimilarity.r annotate

annotate cb_dissimilarity.r @ 0:42b51a52e308 draft

planemo upload for repository https://github.com/Marie59/champ_blocs commit 0d86db7d42b608c386a54500064f5f9c9d7019a4

author	ecology
date	Wed, 04 Jan 2023 13:21:14 +0000
parents
children	f941081e03f0

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

Mercurial > repos > ecology > cb_dissim

annotate cb_dissimilarity.r @ 0:42b51a52e308 draft