ecology/cb_ivr: cb_dissimilarity.r annotate

annotate cb_dissimilarity.r @ 0:89f977a3a256 draft

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

author	ecology
date	Wed, 04 Jan 2023 13:20:53 +0000
parents
children	83a4d3b47184

rev	line source
0 89f977a3a256 planemo upload for repository https://github.com/Marie59/champ_blocs commit 0d86db7d42b608c386a54500064f5f9c9d7019a4 ecology parents: diff changeset	1 # author: "Jonathan Richir"
89f977a3a256 planemo upload for repository https://github.com/Marie59/champ_blocs commit 0d86db7d42b608c386a54500064f5f9c9d7019a4 ecology parents: diff changeset	2 # date: "01 October 2022"
89f977a3a256 planemo upload for repository https://github.com/Marie59/champ_blocs commit 0d86db7d42b608c386a54500064f5f9c9d7019a4 ecology parents: diff changeset	3
89f977a3a256 planemo upload for repository https://github.com/Marie59/champ_blocs commit 0d86db7d42b608c386a54500064f5f9c9d7019a4 ecology parents: diff changeset	4
89f977a3a256 planemo upload for repository https://github.com/Marie59/champ_blocs commit 0d86db7d42b608c386a54500064f5f9c9d7019a4 ecology parents: diff changeset	5 #Rscript
89f977a3a256 planemo upload for repository https://github.com/Marie59/champ_blocs commit 0d86db7d42b608c386a54500064f5f9c9d7019a4 ecology parents: diff changeset	6
89f977a3a256 planemo upload for repository https://github.com/Marie59/champ_blocs commit 0d86db7d42b608c386a54500064f5f9c9d7019a4 ecology parents: diff changeset	7 ###############################
89f977a3a256 planemo upload for repository https://github.com/Marie59/champ_blocs commit 0d86db7d42b608c386a54500064f5f9c9d7019a4 ecology parents: diff changeset	8 ## ##
89f977a3a256 planemo upload for repository https://github.com/Marie59/champ_blocs commit 0d86db7d42b608c386a54500064f5f9c9d7019a4 ecology parents: diff changeset	9 ###############################
89f977a3a256 planemo upload for repository https://github.com/Marie59/champ_blocs commit 0d86db7d42b608c386a54500064f5f9c9d7019a4 ecology parents: diff changeset	10
89f977a3a256 planemo upload for repository https://github.com/Marie59/champ_blocs commit 0d86db7d42b608c386a54500064f5f9c9d7019a4 ecology parents: diff changeset	11 #####Packages : dplyr
89f977a3a256 planemo upload for repository https://github.com/Marie59/champ_blocs commit 0d86db7d42b608c386a54500064f5f9c9d7019a4 ecology parents: diff changeset	12 # tidyr
89f977a3a256 planemo upload for repository https://github.com/Marie59/champ_blocs commit 0d86db7d42b608c386a54500064f5f9c9d7019a4 ecology parents: diff changeset	13 # readr
89f977a3a256 planemo upload for repository https://github.com/Marie59/champ_blocs commit 0d86db7d42b608c386a54500064f5f9c9d7019a4 ecology parents: diff changeset	14 # writexl
89f977a3a256 planemo upload for repository https://github.com/Marie59/champ_blocs commit 0d86db7d42b608c386a54500064f5f9c9d7019a4 ecology parents: diff changeset	15 # stringr
89f977a3a256 planemo upload for repository https://github.com/Marie59/champ_blocs commit 0d86db7d42b608c386a54500064f5f9c9d7019a4 ecology parents: diff changeset	16 # readxl
89f977a3a256 planemo upload for repository https://github.com/Marie59/champ_blocs commit 0d86db7d42b608c386a54500064f5f9c9d7019a4 ecology parents: diff changeset	17 # tibble
89f977a3a256 planemo upload for repository https://github.com/Marie59/champ_blocs commit 0d86db7d42b608c386a54500064f5f9c9d7019a4 ecology parents: diff changeset	18 # lubridate
89f977a3a256 planemo upload for repository https://github.com/Marie59/champ_blocs commit 0d86db7d42b608c386a54500064f5f9c9d7019a4 ecology parents: diff changeset	19 # cowplot
89f977a3a256 planemo upload for repository https://github.com/Marie59/champ_blocs commit 0d86db7d42b608c386a54500064f5f9c9d7019a4 ecology parents: diff changeset	20 # magrittr
89f977a3a256 planemo upload for repository https://github.com/Marie59/champ_blocs commit 0d86db7d42b608c386a54500064f5f9c9d7019a4 ecology parents: diff changeset	21 # rmarkdown
89f977a3a256 planemo upload for repository https://github.com/Marie59/champ_blocs commit 0d86db7d42b608c386a54500064f5f9c9d7019a4 ecology parents: diff changeset	22 library(magrittr)
89f977a3a256 planemo upload for repository https://github.com/Marie59/champ_blocs commit 0d86db7d42b608c386a54500064f5f9c9d7019a4 ecology parents: diff changeset	23 #####Load arguments
89f977a3a256 planemo upload for repository https://github.com/Marie59/champ_blocs commit 0d86db7d42b608c386a54500064f5f9c9d7019a4 ecology parents: diff changeset	24
89f977a3a256 planemo upload for repository https://github.com/Marie59/champ_blocs commit 0d86db7d42b608c386a54500064f5f9c9d7019a4 ecology parents: diff changeset	25 args <- commandArgs(trailingOnly = TRUE)
89f977a3a256 planemo upload for repository https://github.com/Marie59/champ_blocs commit 0d86db7d42b608c386a54500064f5f9c9d7019a4 ecology parents: diff changeset	26
89f977a3a256 planemo upload for repository https://github.com/Marie59/champ_blocs commit 0d86db7d42b608c386a54500064f5f9c9d7019a4 ecology parents: diff changeset	27 #####Import data
89f977a3a256 planemo upload for repository https://github.com/Marie59/champ_blocs commit 0d86db7d42b608c386a54500064f5f9c9d7019a4 ecology parents: diff changeset	28
89f977a3a256 planemo upload for repository https://github.com/Marie59/champ_blocs commit 0d86db7d42b608c386a54500064f5f9c9d7019a4 ecology parents: diff changeset	29 if (length(args) < 1) {
89f977a3a256 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")
89f977a3a256 planemo upload for repository https://github.com/Marie59/champ_blocs commit 0d86db7d42b608c386a54500064f5f9c9d7019a4 ecology parents: diff changeset	31 }else {
89f977a3a256 planemo upload for repository https://github.com/Marie59/champ_blocs commit 0d86db7d42b608c386a54500064f5f9c9d7019a4 ecology parents: diff changeset	32 fiche_val <- args[1]
89f977a3a256 planemo upload for repository https://github.com/Marie59/champ_blocs commit 0d86db7d42b608c386a54500064f5f9c9d7019a4 ecology parents: diff changeset	33 input_data <- args[2]
89f977a3a256 planemo upload for repository https://github.com/Marie59/champ_blocs commit 0d86db7d42b608c386a54500064f5f9c9d7019a4 ecology parents: diff changeset	34 choice <- args[3]
89f977a3a256 planemo upload for repository https://github.com/Marie59/champ_blocs commit 0d86db7d42b608c386a54500064f5f9c9d7019a4 ecology parents: diff changeset	35 choice_date <- as.numeric(args[4])
89f977a3a256 planemo upload for repository https://github.com/Marie59/champ_blocs commit 0d86db7d42b608c386a54500064f5f9c9d7019a4 ecology parents: diff changeset	36 }
89f977a3a256 planemo upload for repository https://github.com/Marie59/champ_blocs commit 0d86db7d42b608c386a54500064f5f9c9d7019a4 ecology parents: diff changeset	37
89f977a3a256 planemo upload for repository https://github.com/Marie59/champ_blocs commit 0d86db7d42b608c386a54500064f5f9c9d7019a4 ecology parents: diff changeset	38 #############################################################
89f977a3a256 planemo upload for repository https://github.com/Marie59/champ_blocs commit 0d86db7d42b608c386a54500064f5f9c9d7019a4 ecology parents: diff changeset	39 # #
89f977a3a256 planemo upload for repository https://github.com/Marie59/champ_blocs commit 0d86db7d42b608c386a54500064f5f9c9d7019a4 ecology parents: diff changeset	40 # Loading and cleaning data #
89f977a3a256 planemo upload for repository https://github.com/Marie59/champ_blocs commit 0d86db7d42b608c386a54500064f5f9c9d7019a4 ecology parents: diff changeset	41 # #
89f977a3a256 planemo upload for repository https://github.com/Marie59/champ_blocs commit 0d86db7d42b608c386a54500064f5f9c9d7019a4 ecology parents: diff changeset	42 #############################################################
89f977a3a256 planemo upload for repository https://github.com/Marie59/champ_blocs commit 0d86db7d42b608c386a54500064f5f9c9d7019a4 ecology parents: diff changeset	43 # load qecb data
89f977a3a256 planemo upload for repository https://github.com/Marie59/champ_blocs commit 0d86db7d42b608c386a54500064f5f9c9d7019a4 ecology parents: diff changeset	44
89f977a3a256 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
89f977a3a256 planemo upload for repository https://github.com/Marie59/champ_blocs commit 0d86db7d42b608c386a54500064f5f9c9d7019a4 ecology parents: diff changeset	46
89f977a3a256 planemo upload for repository https://github.com/Marie59/champ_blocs commit 0d86db7d42b608c386a54500064f5f9c9d7019a4 ecology parents: diff changeset	47 # import csv files ficheterrain
89f977a3a256 planemo upload for repository https://github.com/Marie59/champ_blocs commit 0d86db7d42b608c386a54500064f5f9c9d7019a4 ecology parents: diff changeset	48
89f977a3a256 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
89f977a3a256 planemo upload for repository https://github.com/Marie59/champ_blocs commit 0d86db7d42b608c386a54500064f5f9c9d7019a4 ecology parents: diff changeset	50
89f977a3a256 planemo upload for repository https://github.com/Marie59/champ_blocs commit 0d86db7d42b608c386a54500064f5f9c9d7019a4 ecology parents: diff changeset	51 ## work on "Fiche terrain"
89f977a3a256 planemo upload for repository https://github.com/Marie59/champ_blocs commit 0d86db7d42b608c386a54500064f5f9c9d7019a4 ecology parents: diff changeset	52
89f977a3a256 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$date.sortie, end = 10), origin = "1970-01-01")
89f977a3a256 planemo upload for repository https://github.com/Marie59/champ_blocs commit 0d86db7d42b608c386a54500064f5f9c9d7019a4 ecology parents: diff changeset	54 fiche <- tibble::add_column(fiche, date_fiche, .after = "date.sortie")
89f977a3a256 planemo upload for repository https://github.com/Marie59/champ_blocs commit 0d86db7d42b608c386a54500064f5f9c9d7019a4 ecology parents: diff changeset	55 rm(date_fiche)
89f977a3a256 planemo upload for repository https://github.com/Marie59/champ_blocs commit 0d86db7d42b608c386a54500064f5f9c9d7019a4 ecology parents: diff changeset	56
89f977a3a256 planemo upload for repository https://github.com/Marie59/champ_blocs commit 0d86db7d42b608c386a54500064f5f9c9d7019a4 ecology parents: diff changeset	57 ## qecb vs fiche terrain
89f977a3a256 planemo upload for repository https://github.com/Marie59/champ_blocs commit 0d86db7d42b608c386a54500064f5f9c9d7019a4 ecology parents: diff changeset	58
89f977a3a256 planemo upload for repository https://github.com/Marie59/champ_blocs commit 0d86db7d42b608c386a54500064f5f9c9d7019a4 ecology parents: diff changeset	59 fiche_red <- dplyr::filter(fiche, fiche$ID.Fiche %in% unique(qecb[, c("id")]))
89f977a3a256 planemo upload for repository https://github.com/Marie59/champ_blocs commit 0d86db7d42b608c386a54500064f5f9c9d7019a4 ecology parents: diff changeset	60
89f977a3a256 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()
89f977a3a256 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")
89f977a3a256 planemo upload for repository https://github.com/Marie59/champ_blocs commit 0d86db7d42b608c386a54500064f5f9c9d7019a4 ecology parents: diff changeset	63 id_count <- data.frame(id_count)
89f977a3a256 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)
89f977a3a256 planemo upload for repository https://github.com/Marie59/champ_blocs commit 0d86db7d42b608c386a54500064f5f9c9d7019a4 ecology parents: diff changeset	65
89f977a3a256 planemo upload for repository https://github.com/Marie59/champ_blocs commit 0d86db7d42b608c386a54500064f5f9c9d7019a4 ecology parents: diff changeset	66 # rep fiche terrain information
89f977a3a256 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)]
89f977a3a256 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")
89f977a3a256 planemo upload for repository https://github.com/Marie59/champ_blocs commit 0d86db7d42b608c386a54500064f5f9c9d7019a4 ecology parents: diff changeset	69
89f977a3a256 planemo upload for repository https://github.com/Marie59/champ_blocs commit 0d86db7d42b608c386a54500064f5f9c9d7019a4 ecology parents: diff changeset	70 ## merge qecb data and ficheterrain information
89f977a3a256 planemo upload for repository https://github.com/Marie59/champ_blocs commit 0d86db7d42b608c386a54500064f5f9c9d7019a4 ecology parents: diff changeset	71
89f977a3a256 planemo upload for repository https://github.com/Marie59/champ_blocs commit 0d86db7d42b608c386a54500064f5f9c9d7019a4 ecology parents: diff changeset	72 qecb <- dplyr::bind_cols(qecb, fiche_expanded)
89f977a3a256 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")
89f977a3a256 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")
89f977a3a256 planemo upload for repository https://github.com/Marie59/champ_blocs commit 0d86db7d42b608c386a54500064f5f9c9d7019a4 ecology parents: diff changeset	75
89f977a3a256 planemo upload for repository https://github.com/Marie59/champ_blocs commit 0d86db7d42b608c386a54500064f5f9c9d7019a4 ecology parents: diff changeset	76 rm(fiche_expanded, fiche_red, id_count)
89f977a3a256 planemo upload for repository https://github.com/Marie59/champ_blocs commit 0d86db7d42b608c386a54500064f5f9c9d7019a4 ecology parents: diff changeset	77
89f977a3a256 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)
89f977a3a256 planemo upload for repository https://github.com/Marie59/champ_blocs commit 0d86db7d42b608c386a54500064f5f9c9d7019a4 ecology parents: diff changeset	79
89f977a3a256 planemo upload for repository https://github.com/Marie59/champ_blocs commit 0d86db7d42b608c386a54500064f5f9c9d7019a4 ecology parents: diff changeset	80
89f977a3a256 planemo upload for repository https://github.com/Marie59/champ_blocs commit 0d86db7d42b608c386a54500064f5f9c9d7019a4 ecology parents: diff changeset	81 ## quadrat nb : in contrast to ivr df, quadrat number is missing for many observations in qecb df ; but from the Numero.Photo variable (boulder photo associated to field data collection), I could get back most missing quadrat numbers
89f977a3a256 planemo upload for repository https://github.com/Marie59/champ_blocs commit 0d86db7d42b608c386a54500064f5f9c9d7019a4 ecology parents: diff changeset	82
89f977a3a256 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]")
89f977a3a256 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")
89f977a3a256 planemo upload for repository https://github.com/Marie59/champ_blocs commit 0d86db7d42b608c386a54500064f5f9c9d7019a4 ecology parents: diff changeset	85 rm(quadrat)
89f977a3a256 planemo upload for repository https://github.com/Marie59/champ_blocs commit 0d86db7d42b608c386a54500064f5f9c9d7019a4 ecology parents: diff changeset	86
89f977a3a256 planemo upload for repository https://github.com/Marie59/champ_blocs commit 0d86db7d42b608c386a54500064f5f9c9d7019a4 ecology parents: diff changeset	87 # check
89f977a3a256 planemo upload for repository https://github.com/Marie59/champ_blocs commit 0d86db7d42b608c386a54500064f5f9c9d7019a4 ecology parents: diff changeset	88 quadrat_bis <- rep(NA, length = nrow(qecb))
89f977a3a256 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")
89f977a3a256 planemo upload for repository https://github.com/Marie59/champ_blocs commit 0d86db7d42b608c386a54500064f5f9c9d7019a4 ecology parents: diff changeset	90 rm(quadrat_bis)
89f977a3a256 planemo upload for repository https://github.com/Marie59/champ_blocs commit 0d86db7d42b608c386a54500064f5f9c9d7019a4 ecology parents: diff changeset	91
89f977a3a256 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)
89f977a3a256 planemo upload for repository https://github.com/Marie59/champ_blocs commit 0d86db7d42b608c386a54500064f5f9c9d7019a4 ecology parents: diff changeset	93 qecb$quadrat_bis <- ifelse(qecb$Numéro.Bloc.échantillon %in% c(3, 4) & qecb$Type.Bloc == "Bloc mobile", "Q2", qecb$quadrat_bis)
89f977a3a256 planemo upload for repository https://github.com/Marie59/champ_blocs commit 0d86db7d42b608c386a54500064f5f9c9d7019a4 ecology parents: diff changeset	94 qecb$quadrat_bis <- ifelse(qecb$Numéro.Bloc.échantillon %in% c(5, 6) & qecb$Type.Bloc == "Bloc mobile", "Q3", qecb$quadrat_bis)
89f977a3a256 planemo upload for repository https://github.com/Marie59/champ_blocs commit 0d86db7d42b608c386a54500064f5f9c9d7019a4 ecology parents: diff changeset	95 qecb$quadrat_bis <- ifelse(qecb$Numéro.Bloc.échantillon %in% c(7, 8) & qecb$Type.Bloc == "Bloc mobile", "Q4", qecb$quadrat_bis)
89f977a3a256 planemo upload for repository https://github.com/Marie59/champ_blocs commit 0d86db7d42b608c386a54500064f5f9c9d7019a4 ecology parents: diff changeset	96 qecb$quadrat_bis <- ifelse(qecb$Numéro.Bloc.échantillon %in% c(9, 10) & qecb$Type.Bloc == "Bloc mobile", "Q5", qecb$quadrat_bis)
89f977a3a256 planemo upload for repository https://github.com/Marie59/champ_blocs commit 0d86db7d42b608c386a54500064f5f9c9d7019a4 ecology parents: diff changeset	97
89f977a3a256 planemo upload for repository https://github.com/Marie59/champ_blocs commit 0d86db7d42b608c386a54500064f5f9c9d7019a4 ecology parents: diff changeset	98
89f977a3a256 planemo upload for repository https://github.com/Marie59/champ_blocs commit 0d86db7d42b608c386a54500064f5f9c9d7019a4 ecology parents: diff changeset	99 qecb$quadrat_bis <- ifelse(qecb$Numéro.Bloc.échantillon == 1 & qecb$Type.Bloc %in% c("Bloc fixé", "Roche en place"), "Q1", qecb$quadrat_bis)
89f977a3a256 planemo upload for repository https://github.com/Marie59/champ_blocs commit 0d86db7d42b608c386a54500064f5f9c9d7019a4 ecology parents: diff changeset	100 qecb$quadrat_bis <- ifelse(qecb$Numéro.Bloc.échantillon == 2 & qecb$Type.Bloc %in% c("Bloc fixé", "Roche en place"), "Q2", qecb$quadrat_bis)
89f977a3a256 planemo upload for repository https://github.com/Marie59/champ_blocs commit 0d86db7d42b608c386a54500064f5f9c9d7019a4 ecology parents: diff changeset	101 qecb$quadrat_bis <- ifelse(qecb$Numéro.Bloc.échantillon == 3 & qecb$Type.Bloc %in% c("Bloc fixé", "Roche en place"), "Q3", qecb$quadrat_bis)
89f977a3a256 planemo upload for repository https://github.com/Marie59/champ_blocs commit 0d86db7d42b608c386a54500064f5f9c9d7019a4 ecology parents: diff changeset	102 qecb$quadrat_bis <- ifelse(qecb$Numéro.Bloc.échantillon == 4 & qecb$Type.Bloc %in% c("Bloc fixé", "Roche en place"), "Q4", qecb$quadrat_bis)
89f977a3a256 planemo upload for repository https://github.com/Marie59/champ_blocs commit 0d86db7d42b608c386a54500064f5f9c9d7019a4 ecology parents: diff changeset	103 qecb$quadrat_bis <- ifelse(qecb$Numéro.Bloc.échantillon == 5 & qecb$Type.Bloc %in% c("Bloc fixé", "Roche en place"), "Q5", qecb$quadrat_bis)
89f977a3a256 planemo upload for repository https://github.com/Marie59/champ_blocs commit 0d86db7d42b608c386a54500064f5f9c9d7019a4 ecology parents: diff changeset	104
89f977a3a256 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 !
89f977a3a256 planemo upload for repository https://github.com/Marie59/champ_blocs commit 0d86db7d42b608c386a54500064f5f9c9d7019a4 ecology parents: diff changeset	106
89f977a3a256 planemo upload for repository https://github.com/Marie59/champ_blocs commit 0d86db7d42b608c386a54500064f5f9c9d7019a4 ecology parents: diff changeset	107 # Name for data analysis
89f977a3a256 planemo upload for repository https://github.com/Marie59/champ_blocs commit 0d86db7d42b608c386a54500064f5f9c9d7019a4 ecology parents: diff changeset	108
89f977a3a256 planemo upload for repository https://github.com/Marie59/champ_blocs commit 0d86db7d42b608c386a54500064f5f9c9d7019a4 ecology parents: diff changeset	109 qecb <- tibble::add_column(qecb, Site = qecb$zone.habitat, .after = "ID.Fiche")
89f977a3a256 planemo upload for repository https://github.com/Marie59/champ_blocs commit 0d86db7d42b608c386a54500064f5f9c9d7019a4 ecology parents: diff changeset	110
89f977a3a256 planemo upload for repository https://github.com/Marie59/champ_blocs commit 0d86db7d42b608c386a54500064f5f9c9d7019a4 ecology parents: diff changeset	111 for (x in seq_along(qecb$Site)) {
89f977a3a256 planemo upload for repository https://github.com/Marie59/champ_blocs commit 0d86db7d42b608c386a54500064f5f9c9d7019a4 ecology parents: diff changeset	112 if (grepl(pattern = "Locmariaquer", qecb$Site[x]) == TRUE) {
89f977a3a256 planemo upload for repository https://github.com/Marie59/champ_blocs commit 0d86db7d42b608c386a54500064f5f9c9d7019a4 ecology parents: diff changeset	113 qecb$Site[x] <- "GDMO_Locmariaquer"
89f977a3a256 planemo upload for repository https://github.com/Marie59/champ_blocs commit 0d86db7d42b608c386a54500064f5f9c9d7019a4 ecology parents: diff changeset	114 } else if (grepl(pattern = "Beg Lann", qecb$Site[x]) == TRUE) {
89f977a3a256 planemo upload for repository https://github.com/Marie59/champ_blocs commit 0d86db7d42b608c386a54500064f5f9c9d7019a4 ecology parents: diff changeset	115 qecb$Site[x] <- "GDMO_BegLann"
89f977a3a256 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$Site[x]) == TRUE) {
89f977a3a256 planemo upload for repository https://github.com/Marie59/champ_blocs commit 0d86db7d42b608c386a54500064f5f9c9d7019a4 ecology parents: diff changeset	117 qecb$Site[x] <- "FOUR_PlateauFour"
89f977a3a256 planemo upload for repository https://github.com/Marie59/champ_blocs commit 0d86db7d42b608c386a54500064f5f9c9d7019a4 ecology parents: diff changeset	118 } else if (grepl(pattern = "Grouin", qecb$Site[x]) == TRUE) {
89f977a3a256 planemo upload for repository https://github.com/Marie59/champ_blocs commit 0d86db7d42b608c386a54500064f5f9c9d7019a4 ecology parents: diff changeset	119 qecb$Site[x] <- "EGMP_GroinCou"
89f977a3a256 planemo upload for repository https://github.com/Marie59/champ_blocs commit 0d86db7d42b608c386a54500064f5f9c9d7019a4 ecology parents: diff changeset	120 } else if (grepl(pattern = "Ensembert", qecb$Site[x]) == TRUE) {
89f977a3a256 planemo upload for repository https://github.com/Marie59/champ_blocs commit 0d86db7d42b608c386a54500064f5f9c9d7019a4 ecology parents: diff changeset	121 qecb$Site[x] <- "EGMP_PasEmsembert"
89f977a3a256 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$Site[x]) == TRUE) {
89f977a3a256 planemo upload for repository https://github.com/Marie59/champ_blocs commit 0d86db7d42b608c386a54500064f5f9c9d7019a4 ecology parents: diff changeset	123 qecb$Site[x] <- "EGMP_BreeBains"
89f977a3a256 planemo upload for repository https://github.com/Marie59/champ_blocs commit 0d86db7d42b608c386a54500064f5f9c9d7019a4 ecology parents: diff changeset	124 } else if (grepl(pattern = "Antiochat", qecb$Site[x]) == TRUE) {
89f977a3a256 planemo upload for repository https://github.com/Marie59/champ_blocs commit 0d86db7d42b608c386a54500064f5f9c9d7019a4 ecology parents: diff changeset	125 qecb$Site[x] <- "EGMP_PerreAntiochat"
89f977a3a256 planemo upload for repository https://github.com/Marie59/champ_blocs commit 0d86db7d42b608c386a54500064f5f9c9d7019a4 ecology parents: diff changeset	126 } else if (grepl(pattern = "Chassiron", qecb$Site[x]) == TRUE) {
89f977a3a256 planemo upload for repository https://github.com/Marie59/champ_blocs commit 0d86db7d42b608c386a54500064f5f9c9d7019a4 ecology parents: diff changeset	127 qecb$Site[x] <- "EGMP_Chassiron"
89f977a3a256 planemo upload for repository https://github.com/Marie59/champ_blocs commit 0d86db7d42b608c386a54500064f5f9c9d7019a4 ecology parents: diff changeset	128 } else if (grepl(pattern = "zone p", qecb$Site[x]) == TRUE) {
89f977a3a256 planemo upload for repository https://github.com/Marie59/champ_blocs commit 0d86db7d42b608c386a54500064f5f9c9d7019a4 ecology parents: diff changeset	129 qecb$Site[x] <- "BASQ_FlotsBleusZP"
89f977a3a256 planemo upload for repository https://github.com/Marie59/champ_blocs commit 0d86db7d42b608c386a54500064f5f9c9d7019a4 ecology parents: diff changeset	130 } else if (grepl(pattern = "zone f", qecb$Site[x]) == TRUE) {
89f977a3a256 planemo upload for repository https://github.com/Marie59/champ_blocs commit 0d86db7d42b608c386a54500064f5f9c9d7019a4 ecology parents: diff changeset	131 qecb$Site[x] <- "BASQ_FlotsBleusZF"
89f977a3a256 planemo upload for repository https://github.com/Marie59/champ_blocs commit 0d86db7d42b608c386a54500064f5f9c9d7019a4 ecology parents: diff changeset	132 } else if (grepl(pattern = "Saint-Michel", qecb$Site[x]) == TRUE) {
89f977a3a256 planemo upload for repository https://github.com/Marie59/champ_blocs commit 0d86db7d42b608c386a54500064f5f9c9d7019a4 ecology parents: diff changeset	133 qecb$Site[x] <- "GONB_IlotStMichel"
89f977a3a256 planemo upload for repository https://github.com/Marie59/champ_blocs commit 0d86db7d42b608c386a54500064f5f9c9d7019a4 ecology parents: diff changeset	134 } else if (grepl(pattern = "Quéménès", qecb$Site[x]) == TRUE) {
89f977a3a256 planemo upload for repository https://github.com/Marie59/champ_blocs commit 0d86db7d42b608c386a54500064f5f9c9d7019a4 ecology parents: diff changeset	135 qecb$Site[x] <- "FINS_Quemenes"
89f977a3a256 planemo upload for repository https://github.com/Marie59/champ_blocs commit 0d86db7d42b608c386a54500064f5f9c9d7019a4 ecology parents: diff changeset	136 } else if (grepl(pattern = "Goulenez", qecb$Site[x]) == TRUE) {
89f977a3a256 planemo upload for repository https://github.com/Marie59/champ_blocs commit 0d86db7d42b608c386a54500064f5f9c9d7019a4 ecology parents: diff changeset	137 qecb$Site[x] <- "FINS_SeinGoulenez"
89f977a3a256 planemo upload for repository https://github.com/Marie59/champ_blocs commit 0d86db7d42b608c386a54500064f5f9c9d7019a4 ecology parents: diff changeset	138 } else if (grepl(pattern = "Kilaourou", qecb$Site[x]) == TRUE) {
89f977a3a256 planemo upload for repository https://github.com/Marie59/champ_blocs commit 0d86db7d42b608c386a54500064f5f9c9d7019a4 ecology parents: diff changeset	139 qecb$Site[x] <- "FINS_SeinKilaourou"
89f977a3a256 planemo upload for repository https://github.com/Marie59/champ_blocs commit 0d86db7d42b608c386a54500064f5f9c9d7019a4 ecology parents: diff changeset	140 } else if (grepl(pattern = "Verdelet", qecb$Site[x]) == TRUE) {
89f977a3a256 planemo upload for repository https://github.com/Marie59/champ_blocs commit 0d86db7d42b608c386a54500064f5f9c9d7019a4 ecology parents: diff changeset	141 qecb$Site[x] <- "ARMO_Verdelet"
89f977a3a256 planemo upload for repository https://github.com/Marie59/champ_blocs commit 0d86db7d42b608c386a54500064f5f9c9d7019a4 ecology parents: diff changeset	142 } else if (grepl(pattern = "Piégu", qecb$Site[x]) == TRUE) {
89f977a3a256 planemo upload for repository https://github.com/Marie59/champ_blocs commit 0d86db7d42b608c386a54500064f5f9c9d7019a4 ecology parents: diff changeset	143 qecb$Site[x] <- "ARMO_Piegu"
89f977a3a256 planemo upload for repository https://github.com/Marie59/champ_blocs commit 0d86db7d42b608c386a54500064f5f9c9d7019a4 ecology parents: diff changeset	144 } else if (grepl(pattern = "Bilfot", qecb$Site[x]) == TRUE) {
89f977a3a256 planemo upload for repository https://github.com/Marie59/champ_blocs commit 0d86db7d42b608c386a54500064f5f9c9d7019a4 ecology parents: diff changeset	145 qecb$Site[x] <- "ARMO_Bilfot"
89f977a3a256 planemo upload for repository https://github.com/Marie59/champ_blocs commit 0d86db7d42b608c386a54500064f5f9c9d7019a4 ecology parents: diff changeset	146 } else if (grepl(pattern = "Plate", qecb$Site[x]) == TRUE) {
89f977a3a256 planemo upload for repository https://github.com/Marie59/champ_blocs commit 0d86db7d42b608c386a54500064f5f9c9d7019a4 ecology parents: diff changeset	147 qecb$Site[x] <- "ARMO_IlePlate"
89f977a3a256 planemo upload for repository https://github.com/Marie59/champ_blocs commit 0d86db7d42b608c386a54500064f5f9c9d7019a4 ecology parents: diff changeset	148 } else if (grepl(pattern = "Perharidy", qecb$Site[x]) == TRUE) {
89f977a3a256 planemo upload for repository https://github.com/Marie59/champ_blocs commit 0d86db7d42b608c386a54500064f5f9c9d7019a4 ecology parents: diff changeset	149 qecb$Site[x] <- "PDMO_Perharidy"
89f977a3a256 planemo upload for repository https://github.com/Marie59/champ_blocs commit 0d86db7d42b608c386a54500064f5f9c9d7019a4 ecology parents: diff changeset	150 } else if (grepl(pattern = "Keraliou", qecb$Site[x]) == TRUE) {
89f977a3a256 planemo upload for repository https://github.com/Marie59/champ_blocs commit 0d86db7d42b608c386a54500064f5f9c9d7019a4 ecology parents: diff changeset	151 qecb$Site[x] <- "BRES_Keraliou"
89f977a3a256 planemo upload for repository https://github.com/Marie59/champ_blocs commit 0d86db7d42b608c386a54500064f5f9c9d7019a4 ecology parents: diff changeset	152 } else if (grepl(pattern = "Mousterlin", qecb$Site[x]) == TRUE) {
89f977a3a256 planemo upload for repository https://github.com/Marie59/champ_blocs commit 0d86db7d42b608c386a54500064f5f9c9d7019a4 ecology parents: diff changeset	153 qecb$Site[x] <- "FINS_Mousterlin"
89f977a3a256 planemo upload for repository https://github.com/Marie59/champ_blocs commit 0d86db7d42b608c386a54500064f5f9c9d7019a4 ecology parents: diff changeset	154 } else if (grepl(pattern = "Nicolas", qecb$Site[x]) == TRUE) {
89f977a3a256 planemo upload for repository https://github.com/Marie59/champ_blocs commit 0d86db7d42b608c386a54500064f5f9c9d7019a4 ecology parents: diff changeset	155 qecb$Site[x] <- "FINS_StNicolasGlenan"
89f977a3a256 planemo upload for repository https://github.com/Marie59/champ_blocs commit 0d86db7d42b608c386a54500064f5f9c9d7019a4 ecology parents: diff changeset	156 }
89f977a3a256 planemo upload for repository https://github.com/Marie59/champ_blocs commit 0d86db7d42b608c386a54500064f5f9c9d7019a4 ecology parents: diff changeset	157 if (grepl(pattern = "Roz", qecb$site[x]) == TRUE) {
89f977a3a256 planemo upload for repository https://github.com/Marie59/champ_blocs commit 0d86db7d42b608c386a54500064f5f9c9d7019a4 ecology parents: diff changeset	158 qecb$Site[x] <- "FINS_AnseRoz"
89f977a3a256 planemo upload for repository https://github.com/Marie59/champ_blocs commit 0d86db7d42b608c386a54500064f5f9c9d7019a4 ecology parents: diff changeset	159 }
89f977a3a256 planemo upload for repository https://github.com/Marie59/champ_blocs commit 0d86db7d42b608c386a54500064f5f9c9d7019a4 ecology parents: diff changeset	160 }
89f977a3a256 planemo upload for repository https://github.com/Marie59/champ_blocs commit 0d86db7d42b608c386a54500064f5f9c9d7019a4 ecology parents: diff changeset	161
89f977a3a256 planemo upload for repository https://github.com/Marie59/champ_blocs commit 0d86db7d42b608c386a54500064f5f9c9d7019a4 ecology parents: diff changeset	162 # Name for report/plot
89f977a3a256 planemo upload for repository https://github.com/Marie59/champ_blocs commit 0d86db7d42b608c386a54500064f5f9c9d7019a4 ecology parents: diff changeset	163
89f977a3a256 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$Site, .after = "Site")
89f977a3a256 planemo upload for repository https://github.com/Marie59/champ_blocs commit 0d86db7d42b608c386a54500064f5f9c9d7019a4 ecology parents: diff changeset	165
89f977a3a256 planemo upload for repository https://github.com/Marie59/champ_blocs commit 0d86db7d42b608c386a54500064f5f9c9d7019a4 ecology parents: diff changeset	166 qecb$Site_bis <- ifelse(qecb$Site == "GDMO_Locmariaquer", "Locmariaquer", qecb$Site_bis)
89f977a3a256 planemo upload for repository https://github.com/Marie59/champ_blocs commit 0d86db7d42b608c386a54500064f5f9c9d7019a4 ecology parents: diff changeset	167 qecb$Site_bis <- ifelse(qecb$Site == "GDMO_BegLann", "Beg Lann", qecb$Site_bis)
89f977a3a256 planemo upload for repository https://github.com/Marie59/champ_blocs commit 0d86db7d42b608c386a54500064f5f9c9d7019a4 ecology parents: diff changeset	168 qecb$Site_bis <- ifelse(qecb$Site == "FOUR_PlateauFour", "Plateau du Four", qecb$Site_bis)
89f977a3a256 planemo upload for repository https://github.com/Marie59/champ_blocs commit 0d86db7d42b608c386a54500064f5f9c9d7019a4 ecology parents: diff changeset	169 qecb$Site_bis <- ifelse(qecb$Site == "EGMP_GroinCou", "Groin du Cou", qecb$Site_bis)
89f977a3a256 planemo upload for repository https://github.com/Marie59/champ_blocs commit 0d86db7d42b608c386a54500064f5f9c9d7019a4 ecology parents: diff changeset	170 qecb$Site_bis <- ifelse(qecb$Site == "EGMP_PasEmsembert", "Le Pas d'Emsembert", qecb$Site_bis)
89f977a3a256 planemo upload for repository https://github.com/Marie59/champ_blocs commit 0d86db7d42b608c386a54500064f5f9c9d7019a4 ecology parents: diff changeset	171 qecb$Site_bis <- ifelse(qecb$Site == "EGMP_BreeBains", "La Brée-les-Bains", qecb$Site_bis)
89f977a3a256 planemo upload for repository https://github.com/Marie59/champ_blocs commit 0d86db7d42b608c386a54500064f5f9c9d7019a4 ecology parents: diff changeset	172 qecb$Site_bis <- ifelse(qecb$Site == "EGMP_PerreAntiochat", "Le Perré d'Antiochat", qecb$Site_bis)
89f977a3a256 planemo upload for repository https://github.com/Marie59/champ_blocs commit 0d86db7d42b608c386a54500064f5f9c9d7019a4 ecology parents: diff changeset	173 qecb$Site_bis <- ifelse(qecb$Site == "EGMP_Chassiron", "Chassiron", qecb$Site_bis)
89f977a3a256 planemo upload for repository https://github.com/Marie59/champ_blocs commit 0d86db7d42b608c386a54500064f5f9c9d7019a4 ecology parents: diff changeset	174 qecb$Site_bis <- ifelse(qecb$Site == "BASQ_FlotsBleusZP", "Les Flots Bleus / zone pêcheurs", qecb$Site_bis)
89f977a3a256 planemo upload for repository https://github.com/Marie59/champ_blocs commit 0d86db7d42b608c386a54500064f5f9c9d7019a4 ecology parents: diff changeset	175 qecb$Site_bis <- ifelse(qecb$Site == "BASQ_FlotsBleusZF", "Les Flots Bleus / zone familles", qecb$Site_bis)
89f977a3a256 planemo upload for repository https://github.com/Marie59/champ_blocs commit 0d86db7d42b608c386a54500064f5f9c9d7019a4 ecology parents: diff changeset	176 qecb$Site_bis <- ifelse(qecb$Site == "GONB_IlotStMichel", "Îlot Saint-Michel", qecb$Site_bis)
89f977a3a256 planemo upload for repository https://github.com/Marie59/champ_blocs commit 0d86db7d42b608c386a54500064f5f9c9d7019a4 ecology parents: diff changeset	177 qecb$Site_bis <- ifelse(qecb$Site == "FINS_Quemenes", "Quéménès", qecb$Site_bis)
89f977a3a256 planemo upload for repository https://github.com/Marie59/champ_blocs commit 0d86db7d42b608c386a54500064f5f9c9d7019a4 ecology parents: diff changeset	178 qecb$Site_bis <- ifelse(qecb$Site == "FINS_SeinGoulenez", "Île de Sein - Goulenez", qecb$Site_bis)
89f977a3a256 planemo upload for repository https://github.com/Marie59/champ_blocs commit 0d86db7d42b608c386a54500064f5f9c9d7019a4 ecology parents: diff changeset	179 qecb$Site_bis <- ifelse(qecb$Site == "FINS_SeinKilaourou", "Île de Sein - Kilaourou", qecb$Site_bis)
89f977a3a256 planemo upload for repository https://github.com/Marie59/champ_blocs commit 0d86db7d42b608c386a54500064f5f9c9d7019a4 ecology parents: diff changeset	180 qecb$Site_bis <- ifelse(qecb$Site == "ARMO_Verdelet", "Îlot du Verdelet", qecb$Site_bis)
89f977a3a256 planemo upload for repository https://github.com/Marie59/champ_blocs commit 0d86db7d42b608c386a54500064f5f9c9d7019a4 ecology parents: diff changeset	181 qecb$Site_bis <- ifelse(qecb$Site == "ARMO_Piegu", "Piégu", qecb$Site_bis)
89f977a3a256 planemo upload for repository https://github.com/Marie59/champ_blocs commit 0d86db7d42b608c386a54500064f5f9c9d7019a4 ecology parents: diff changeset	182 qecb$Site_bis <- ifelse(qecb$Site == "ARMO_Bilfot", "Pointe de Bilfot", qecb$Site_bis)
89f977a3a256 planemo upload for repository https://github.com/Marie59/champ_blocs commit 0d86db7d42b608c386a54500064f5f9c9d7019a4 ecology parents: diff changeset	183 qecb$Site_bis <- ifelse(qecb$Site == "ARMO_IlePlate", "Île Plate", qecb$Site_bis)
89f977a3a256 planemo upload for repository https://github.com/Marie59/champ_blocs commit 0d86db7d42b608c386a54500064f5f9c9d7019a4 ecology parents: diff changeset	184 qecb$Site_bis <- ifelse(qecb$Site == "PDMO_Perharidy", "Perharidy", qecb$Site_bis)
89f977a3a256 planemo upload for repository https://github.com/Marie59/champ_blocs commit 0d86db7d42b608c386a54500064f5f9c9d7019a4 ecology parents: diff changeset	185 qecb$Site_bis <- ifelse(qecb$Site == "BRES_Keraliou", "Keraliou", qecb$Site_bis)
89f977a3a256 planemo upload for repository https://github.com/Marie59/champ_blocs commit 0d86db7d42b608c386a54500064f5f9c9d7019a4 ecology parents: diff changeset	186 qecb$Site_bis <- ifelse(qecb$Site == "FINS_Mousterlin", "Pointe de Mousterlin", qecb$Site_bis)
89f977a3a256 planemo upload for repository https://github.com/Marie59/champ_blocs commit 0d86db7d42b608c386a54500064f5f9c9d7019a4 ecology parents: diff changeset	187 qecb$Site_bis <- ifelse(qecb$Site == "FINS_StNicolasGlenan", "Saint-Nicolas des Glénan", qecb$Site_bis)
89f977a3a256 planemo upload for repository https://github.com/Marie59/champ_blocs commit 0d86db7d42b608c386a54500064f5f9c9d7019a4 ecology parents: diff changeset	188 qecb$Site_bis <- ifelse(qecb$Site == "FINS_AnseRoz", "Pointe de l'Anse du Roz", qecb$Site_bis)
89f977a3a256 planemo upload for repository https://github.com/Marie59/champ_blocs commit 0d86db7d42b608c386a54500064f5f9c9d7019a4 ecology parents: diff changeset	189
89f977a3a256 planemo upload for repository https://github.com/Marie59/champ_blocs commit 0d86db7d42b608c386a54500064f5f9c9d7019a4 ecology parents: diff changeset	190 ## change some variables to factor
89f977a3a256 planemo upload for repository https://github.com/Marie59/champ_blocs commit 0d86db7d42b608c386a54500064f5f9c9d7019a4 ecology parents: diff changeset	191
89f977a3a256 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
89f977a3a256 planemo upload for repository https://github.com/Marie59/champ_blocs commit 0d86db7d42b608c386a54500064f5f9c9d7019a4 ecology parents: diff changeset	193 ix <- grep("^X..", names(qecb))
89f977a3a256 planemo upload for repository https://github.com/Marie59/champ_blocs commit 0d86db7d42b608c386a54500064f5f9c9d7019a4 ecology parents: diff changeset	194 qecb[ix] <- lapply(qecb[ix], as.numeric)
89f977a3a256 planemo upload for repository https://github.com/Marie59/champ_blocs commit 0d86db7d42b608c386a54500064f5f9c9d7019a4 ecology parents: diff changeset	195 rm(ix)
89f977a3a256 planemo upload for repository https://github.com/Marie59/champ_blocs commit 0d86db7d42b608c386a54500064f5f9c9d7019a4 ecology parents: diff changeset	196
89f977a3a256 planemo upload for repository https://github.com/Marie59/champ_blocs commit 0d86db7d42b608c386a54500064f5f9c9d7019a4 ecology parents: diff changeset	197
89f977a3a256 planemo upload for repository https://github.com/Marie59/champ_blocs commit 0d86db7d42b608c386a54500064f5f9c9d7019a4 ecology parents: diff changeset	198 ## save the final, complete qecb df_
89f977a3a256 planemo upload for repository https://github.com/Marie59/champ_blocs commit 0d86db7d42b608c386a54500064f5f9c9d7019a4 ecology parents: diff changeset	199
89f977a3a256 planemo upload for repository https://github.com/Marie59/champ_blocs commit 0d86db7d42b608c386a54500064f5f9c9d7019a4 ecology parents: diff changeset	200 qecb <- qecb[, c(72:107, 1:71)]
89f977a3a256 planemo upload for repository https://github.com/Marie59/champ_blocs commit 0d86db7d42b608c386a54500064f5f9c9d7019a4 ecology parents: diff changeset	201
89f977a3a256 planemo upload for repository https://github.com/Marie59/champ_blocs commit 0d86db7d42b608c386a54500064f5f9c9d7019a4 ecology parents: diff changeset	202 ## qecb df preparation prior qecb calculation
89f977a3a256 planemo upload for repository https://github.com/Marie59/champ_blocs commit 0d86db7d42b608c386a54500064f5f9c9d7019a4 ecology parents: diff changeset	203
89f977a3a256 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
89f977a3a256 planemo upload for repository https://github.com/Marie59/champ_blocs commit 0d86db7d42b608c386a54500064f5f9c9d7019a4 ecology parents: diff changeset	205
89f977a3a256 planemo upload for repository https://github.com/Marie59/champ_blocs commit 0d86db7d42b608c386a54500064f5f9c9d7019a4 ecology parents: diff changeset	206
89f977a3a256 planemo upload for repository https://github.com/Marie59/champ_blocs commit 0d86db7d42b608c386a54500064f5f9c9d7019a4 ecology parents: diff changeset	207 qecb$Type.Bloc <- factor(qecb$Type.Bloc, levels = c("Bloc mobile", "Bloc fixé", "Roche en place"))
89f977a3a256 planemo upload for repository https://github.com/Marie59/champ_blocs commit 0d86db7d42b608c386a54500064f5f9c9d7019a4 ecology parents: diff changeset	208
89f977a3a256 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"))
89f977a3a256 planemo upload for repository https://github.com/Marie59/champ_blocs commit 0d86db7d42b608c386a54500064f5f9c9d7019a4 ecology parents: diff changeset	210
89f977a3a256 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)
89f977a3a256 planemo upload for repository https://github.com/Marie59/champ_blocs commit 0d86db7d42b608c386a54500064f5f9c9d7019a4 ecology parents: diff changeset	212
89f977a3a256 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")
89f977a3a256 planemo upload for repository https://github.com/Marie59/champ_blocs commit 0d86db7d42b608c386a54500064f5f9c9d7019a4 ecology parents: diff changeset	214
89f977a3a256 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
89f977a3a256 planemo upload for repository https://github.com/Marie59/champ_blocs commit 0d86db7d42b608c386a54500064f5f9c9d7019a4 ecology parents: diff changeset	216
89f977a3a256 planemo upload for repository https://github.com/Marie59/champ_blocs commit 0d86db7d42b608c386a54500064f5f9c9d7019a4 ecology parents: diff changeset	217 qecbnew <- qecb
89f977a3a256 planemo upload for repository https://github.com/Marie59/champ_blocs commit 0d86db7d42b608c386a54500064f5f9c9d7019a4 ecology parents: diff changeset	218
89f977a3a256 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
89f977a3a256 planemo upload for repository https://github.com/Marie59/champ_blocs commit 0d86db7d42b608c386a54500064f5f9c9d7019a4 ecology parents: diff changeset	220
89f977a3a256 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$site_year_month_day),
89f977a3a256 planemo upload for repository https://github.com/Marie59/champ_blocs commit 0d86db7d42b608c386a54500064f5f9c9d7019a4 ecology parents: diff changeset	222 "loop nb" = c(1:seq_along(unique(qecbnew$site_year_month_day))))
89f977a3a256 planemo upload for repository https://github.com/Marie59/champ_blocs commit 0d86db7d42b608c386a54500064f5f9c9d7019a4 ecology parents: diff changeset	223
89f977a3a256 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.
89f977a3a256 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.
89f977a3a256 planemo upload for repository https://github.com/Marie59/champ_blocs commit 0d86db7d42b608c386a54500064f5f9c9d7019a4 ecology parents: diff changeset	226
89f977a3a256 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
89f977a3a256 planemo upload for repository https://github.com/Marie59/champ_blocs commit 0d86db7d42b608c386a54500064f5f9c9d7019a4 ecology parents: diff changeset	228 qecbnew$Face <- as.character(qecbnew$Face)
89f977a3a256 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)
89f977a3a256 planemo upload for repository https://github.com/Marie59/champ_blocs commit 0d86db7d42b608c386a54500064f5f9c9d7019a4 ecology parents: diff changeset	230 qecbnew$Face <- ifelse(qecbnew$ID.Fiche == "BDD_IVR&QECB_La Bree_20160406_VImport.xlsx" & qecbnew$Référence.bloc == "avr16-LaBreeB10sup", "face supérieure", qecbnew$Face)
89f977a3a256 planemo upload for repository https://github.com/Marie59/champ_blocs commit 0d86db7d42b608c386a54500064f5f9c9d7019a4 ecology parents: diff changeset	231 qecbnew$Face <- as.factor(qecbnew$Face)
89f977a3a256 planemo upload for repository https://github.com/Marie59/champ_blocs commit 0d86db7d42b608c386a54500064f5f9c9d7019a4 ecology parents: diff changeset	232
89f977a3a256 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
89f977a3a256 planemo upload for repository https://github.com/Marie59/champ_blocs commit 0d86db7d42b608c386a54500064f5f9c9d7019a4 ecology parents: diff changeset	234 qecbnew$Face <- as.character(qecbnew$Face)
89f977a3a256 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)
89f977a3a256 planemo upload for repository https://github.com/Marie59/champ_blocs commit 0d86db7d42b608c386a54500064f5f9c9d7019a4 ecology parents: diff changeset	236 qecbnew$Face <- ifelse(qecbnew$ID.Fiche == "BDD_IVR&QECB_PerAnt_20160407_VImport.xlsx" & qecbnew$Référence.bloc == "avr16-PerAntB10sup", "face supérieure", qecbnew$Face)
89f977a3a256 planemo upload for repository https://github.com/Marie59/champ_blocs commit 0d86db7d42b608c386a54500064f5f9c9d7019a4 ecology parents: diff changeset	237 qecbnew$Face <- as.factor(qecbnew$Face)
89f977a3a256 planemo upload for repository https://github.com/Marie59/champ_blocs commit 0d86db7d42b608c386a54500064f5f9c9d7019a4 ecology parents: diff changeset	238
89f977a3a256 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
89f977a3a256 planemo upload for repository https://github.com/Marie59/champ_blocs commit 0d86db7d42b608c386a54500064f5f9c9d7019a4 ecology parents: diff changeset	240 qecbnew$Face <- as.character(qecbnew$Face)
89f977a3a256 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)
89f977a3a256 planemo upload for repository https://github.com/Marie59/champ_blocs commit 0d86db7d42b608c386a54500064f5f9c9d7019a4 ecology parents: diff changeset	242 qecbnew$Face <- ifelse(qecbnew$ID.Fiche == "BDD_IVR&QECB_Chassiron_20160309&10_VImport.xlsx" & qecbnew$Référence.bloc == "mars16-ChasB10sup", "face supérieure", qecbnew$Face)
89f977a3a256 planemo upload for repository https://github.com/Marie59/champ_blocs commit 0d86db7d42b608c386a54500064f5f9c9d7019a4 ecology parents: diff changeset	243 qecbnew$Face <- as.factor(qecbnew$Face)
89f977a3a256 planemo upload for repository https://github.com/Marie59/champ_blocs commit 0d86db7d42b608c386a54500064f5f9c9d7019a4 ecology parents: diff changeset	244
89f977a3a256 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
89f977a3a256 planemo upload for repository https://github.com/Marie59/champ_blocs commit 0d86db7d42b608c386a54500064f5f9c9d7019a4 ecology parents: diff changeset	246 qecbnew$Face <- as.character(qecbnew$Face)
89f977a3a256 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)
89f977a3a256 planemo upload for repository https://github.com/Marie59/champ_blocs commit 0d86db7d42b608c386a54500064f5f9c9d7019a4 ecology parents: diff changeset	248 qecbnew$Face <- as.factor(qecbnew$Face)
89f977a3a256 planemo upload for repository https://github.com/Marie59/champ_blocs commit 0d86db7d42b608c386a54500064f5f9c9d7019a4 ecology parents: diff changeset	249
89f977a3a256 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"
89f977a3a256 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)
89f977a3a256 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)
89f977a3a256 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)
89f977a3a256 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)
89f977a3a256 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 == ""))
89f977a3a256 planemo upload for repository https://github.com/Marie59/champ_blocs commit 0d86db7d42b608c386a54500064f5f9c9d7019a4 ecology parents: diff changeset	256
89f977a3a256 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.
89f977a3a256 planemo upload for repository https://github.com/Marie59/champ_blocs commit 0d86db7d42b608c386a54500064f5f9c9d7019a4 ecology parents: diff changeset	258
89f977a3a256 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 !
89f977a3a256 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")
89f977a3a256 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
89f977a3a256 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")
89f977a3a256 planemo upload for repository https://github.com/Marie59/champ_blocs commit 0d86db7d42b608c386a54500064f5f9c9d7019a4 ecology parents: diff changeset	263 rm(df_list_loop, qecb_i)
89f977a3a256 planemo upload for repository https://github.com/Marie59/champ_blocs commit 0d86db7d42b608c386a54500064f5f9c9d7019a4 ecology parents: diff changeset	264
89f977a3a256 planemo upload for repository https://github.com/Marie59/champ_blocs commit 0d86db7d42b608c386a54500064f5f9c9d7019a4 ecology parents: diff changeset	265
89f977a3a256 planemo upload for repository https://github.com/Marie59/champ_blocs commit 0d86db7d42b608c386a54500064f5f9c9d7019a4 ecology parents: diff changeset	266 # check for species with count within sub-0.1m^2-quadrat (i.e. reduced size quadrat compare to most organisms on boulder to count them, because abundant ; then some extrapolation)
89f977a3a256 planemo upload for repository https://github.com/Marie59/champ_blocs commit 0d86db7d42b608c386a54500064f5f9c9d7019a4 ecology parents: diff changeset	267
89f977a3a256 planemo upload for repository https://github.com/Marie59/champ_blocs commit 0d86db7d42b608c386a54500064f5f9c9d7019a4 ecology parents: diff changeset	268 # first for Spirobranchus
89f977a3a256 planemo upload for repository https://github.com/Marie59/champ_blocs commit 0d86db7d42b608c386a54500064f5f9c9d7019a4 ecology parents: diff changeset	269
89f977a3a256 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
89f977a3a256 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)
89f977a3a256 planemo upload for repository https://github.com/Marie59/champ_blocs commit 0d86db7d42b608c386a54500064f5f9c9d7019a4 ecology parents: diff changeset	272
89f977a3a256 planemo upload for repository https://github.com/Marie59/champ_blocs commit 0d86db7d42b608c386a54500064f5f9c9d7019a4 ecology parents: diff changeset	273
89f977a3a256 planemo upload for repository https://github.com/Marie59/champ_blocs commit 0d86db7d42b608c386a54500064f5f9c9d7019a4 ecology parents: diff changeset	274 qecbnew_spirobranchus <- (dplyr::filter(qecbnew, Nb.Spirobranchus.lamarckii.total %in% c(NA, "NaN", "Inf", "-Inf")))
89f977a3a256 planemo upload for repository https://github.com/Marie59/champ_blocs commit 0d86db7d42b608c386a54500064f5f9c9d7019a4 ecology parents: diff changeset	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)
89f977a3a256 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$Nb.Spirobranchus.lamarckii.5B))[, c("site_year_month_day", "Nb.Spirobranchus.lamarckii.1B", "Nb.Spirobranchus.lamarckii.2B", "Nb.Spirobranchus.lamarckii.3B", "Nb.Spirobranchus.lamarckii.4B", "Nb.Spirobranchus.lamarckii.5B", "Nb.Spirobranchus.lamarckii.total")])
89f977a3a256 planemo upload for repository https://github.com/Marie59/champ_blocs commit 0d86db7d42b608c386a54500064f5f9c9d7019a4 ecology parents: diff changeset	277
89f977a3a256 planemo upload for repository https://github.com/Marie59/champ_blocs commit 0d86db7d42b608c386a54500064f5f9c9d7019a4 ecology parents: diff changeset	278 quemenes <- dplyr::filter(qecbnew, Site == "FINS_Quemenes")
89f977a3a256 planemo upload for repository https://github.com/Marie59/champ_blocs commit 0d86db7d42b608c386a54500064f5f9c9d7019a4 ecology parents: diff changeset	279 quemenes <- dplyr::arrange(quemenes, date_fiche)
89f977a3a256 planemo upload for repository https://github.com/Marie59/champ_blocs commit 0d86db7d42b608c386a54500064f5f9c9d7019a4 ecology parents: diff changeset	280 # for Quemenes, issue because for sampling date "FINS_Quemenes.2015.09.30" the 5 counts of Spirobranchus were encoded in 1B instead of total !!! I noticed this issue when mining data (see below), therefore I corrected before running below script for Spirobranchus.
89f977a3a256 planemo upload for repository https://github.com/Marie59/champ_blocs commit 0d86db7d42b608c386a54500064f5f9c9d7019a4 ecology parents: diff changeset	281 qecbnew$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)
89f977a3a256 planemo upload for repository https://github.com/Marie59/champ_blocs commit 0d86db7d42b608c386a54500064f5f9c9d7019a4 ecology parents: diff changeset	282
89f977a3a256 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")])
89f977a3a256 planemo upload for repository https://github.com/Marie59/champ_blocs commit 0d86db7d42b608c386a54500064f5f9c9d7019a4 ecology parents: diff changeset	284 rm(quemenes)
89f977a3a256 planemo upload for repository https://github.com/Marie59/champ_blocs commit 0d86db7d42b608c386a54500064f5f9c9d7019a4 ecology parents: diff changeset	285
89f977a3a256 planemo upload for repository https://github.com/Marie59/champ_blocs commit 0d86db7d42b608c386a54500064f5f9c9d7019a4 ecology parents: diff changeset	286 seinkilaourou <- dplyr::filter(qecbnew, Site == "FINS_SeinKilaourou")
89f977a3a256 planemo upload for repository https://github.com/Marie59/champ_blocs commit 0d86db7d42b608c386a54500064f5f9c9d7019a4 ecology parents: diff changeset	287 seinkilaourou <- dplyr::arrange(seinkilaourou, date_fiche)
89f977a3a256 planemo upload for repository https://github.com/Marie59/champ_blocs commit 0d86db7d42b608c386a54500064f5f9c9d7019a4 ecology parents: diff changeset	288 # same issue with SeinKilaourou
89f977a3a256 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$Nb.Spirobranchus.lamarckii.total)
89f977a3a256 planemo upload for repository https://github.com/Marie59/champ_blocs commit 0d86db7d42b608c386a54500064f5f9c9d7019a4 ecology parents: diff changeset	290 (seinkilaourou <- dplyr::filter(qecbnew, site_year_month_day == "FINS_SeinKilaourou.2015.04.21")[, c("site_year_month_day", "Nb.Spirobranchus.lamarckii.1B", "Nb.Spirobranchus.lamarckii.2B", "Nb.Spirobranchus.lamarckii.3B", "Nb.Spirobranchus.lamarckii.4B", "Nb.Spirobranchus.lamarckii.5B", "Nb.Spirobranchus.lamarckii.total")])
89f977a3a256 planemo upload for repository https://github.com/Marie59/champ_blocs commit 0d86db7d42b608c386a54500064f5f9c9d7019a4 ecology parents: diff changeset	291 rm(seinkilaourou)
89f977a3a256 planemo upload for repository https://github.com/Marie59/champ_blocs commit 0d86db7d42b608c386a54500064f5f9c9d7019a4 ecology parents: diff changeset	292
89f977a3a256 planemo upload for repository https://github.com/Marie59/champ_blocs commit 0d86db7d42b608c386a54500064f5f9c9d7019a4 ecology parents: diff changeset	293 # some more issues however with "x100"count data
89f977a3a256 planemo upload for repository https://github.com/Marie59/champ_blocs commit 0d86db7d42b608c386a54500064f5f9c9d7019a4 ecology parents: diff changeset	294 spirobranchus <- subset(qecbnew, !is.na(qecbnew$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$Nb.Spirobranchus.lamarckii.total))[, c("site_year_month_day", "Nb.Spirobranchus.lamarckii.1B", "Nb.Spirobranchus.lamarckii.2B", "Nb.Spirobranchus.lamarckii.3B", "Nb.Spirobranchus.lamarckii.4B", "Nb.Spirobranchus.lamarckii.5B", "Nb.Spirobranchus.lamarckii.total")]
89f977a3a256 planemo upload for repository https://github.com/Marie59/champ_blocs commit 0d86db7d42b608c386a54500064f5f9c9d7019a4 ecology parents: diff changeset	295
89f977a3a256 planemo upload for repository https://github.com/Marie59/champ_blocs commit 0d86db7d42b608c386a54500064f5f9c9d7019a4 ecology parents: diff changeset	296 for (i in c(1:nrow(spirobranchus))) {
89f977a3a256 planemo upload for repository https://github.com/Marie59/champ_blocs commit 0d86db7d42b608c386a54500064f5f9c9d7019a4 ecology parents: diff changeset	297 spirobranchus$mean.x.100[[i]] <- sum(spirobranchus[i, c(2:6)], na.rm = TRUE) / sum(!is.na(spirobranchus[i, c(2:6)])) * 100
89f977a3a256 planemo upload for repository https://github.com/Marie59/champ_blocs commit 0d86db7d42b608c386a54500064f5f9c9d7019a4 ecology parents: diff changeset	298 }
89f977a3a256 planemo upload for repository https://github.com/Marie59/champ_blocs commit 0d86db7d42b608c386a54500064f5f9c9d7019a4 ecology parents: diff changeset	299
89f977a3a256 planemo upload for repository https://github.com/Marie59/champ_blocs commit 0d86db7d42b608c386a54500064f5f9c9d7019a4 ecology parents: diff changeset	300 spirobranchus$mean.x.100 <- unlist(spirobranchus$mean.x.100)
89f977a3a256 planemo upload for repository https://github.com/Marie59/champ_blocs commit 0d86db7d42b608c386a54500064f5f9c9d7019a4 ecology parents: diff changeset	301 spirobranchus$Nb.Spirobranchus.lamarckii.total <- as.numeric(spirobranchus$Nb.Spirobranchus.lamarckii.total)
89f977a3a256 planemo upload for repository https://github.com/Marie59/champ_blocs commit 0d86db7d42b608c386a54500064f5f9c9d7019a4 ecology parents: diff changeset	302 for (i in c(1:nrow(spirobranchus))) {
89f977a3a256 planemo upload for repository https://github.com/Marie59/champ_blocs commit 0d86db7d42b608c386a54500064f5f9c9d7019a4 ecology parents: diff changeset	303 spirobranchus$diff[[i]] <- spirobranchus[i, "Nb.Spirobranchus.lamarckii.total"] - spirobranchus[i, "mean.x.100"]
89f977a3a256 planemo upload for repository https://github.com/Marie59/champ_blocs commit 0d86db7d42b608c386a54500064f5f9c9d7019a4 ecology parents: diff changeset	304 }
89f977a3a256 planemo upload for repository https://github.com/Marie59/champ_blocs commit 0d86db7d42b608c386a54500064f5f9c9d7019a4 ecology parents: diff changeset	305
89f977a3a256 planemo upload for repository https://github.com/Marie59/champ_blocs commit 0d86db7d42b608c386a54500064f5f9c9d7019a4 ecology parents: diff changeset	306 spirobranchus$diff <- abs(as.integer(spirobranchus$diff))
89f977a3a256 planemo upload for repository https://github.com/Marie59/champ_blocs commit 0d86db7d42b608c386a54500064f5f9c9d7019a4 ecology parents: diff changeset	307 spirobranchus <- dplyr::arrange(spirobranchus, desc(diff), mean.x.100)
89f977a3a256 planemo upload for repository https://github.com/Marie59/champ_blocs commit 0d86db7d42b608c386a54500064f5f9c9d7019a4 ecology parents: diff changeset	308 spirobranchus <- dplyr::arrange(dplyr::filter(spirobranchus, diff != 0 & mean.x.100 != 0), desc(diff))
89f977a3a256 planemo upload for repository https://github.com/Marie59/champ_blocs commit 0d86db7d42b608c386a54500064f5f9c9d7019a4 ecology parents: diff changeset	309
89f977a3a256 planemo upload for repository https://github.com/Marie59/champ_blocs commit 0d86db7d42b608c386a54500064f5f9c9d7019a4 ecology parents: diff changeset	310 # check it all in the qecbnew df
89f977a3a256 planemo upload for repository https://github.com/Marie59/champ_blocs commit 0d86db7d42b608c386a54500064f5f9c9d7019a4 ecology parents: diff changeset	311
89f977a3a256 planemo upload for repository https://github.com/Marie59/champ_blocs commit 0d86db7d42b608c386a54500064f5f9c9d7019a4 ecology parents: diff changeset	312 for (i in c(1:nrow(qecbnew))) {
89f977a3a256 planemo upload for repository https://github.com/Marie59/champ_blocs commit 0d86db7d42b608c386a54500064f5f9c9d7019a4 ecology parents: diff changeset	313 qecbnew$mean.x.100[[i]] <-
89f977a3a256 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
89f977a3a256 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
89f977a3a256 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)
89f977a3a256 planemo upload for repository https://github.com/Marie59/champ_blocs commit 0d86db7d42b608c386a54500064f5f9c9d7019a4 ecology parents: diff changeset	317
89f977a3a256 planemo upload for repository https://github.com/Marie59/champ_blocs commit 0d86db7d42b608c386a54500064f5f9c9d7019a4 ecology parents: diff changeset	318
89f977a3a256 planemo upload for repository https://github.com/Marie59/champ_blocs commit 0d86db7d42b608c386a54500064f5f9c9d7019a4 ecology parents: diff changeset	319 for (i in c(1:nrow(qecbnew))) {
89f977a3a256 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$mean.x.100[[i]])
89f977a3a256 planemo upload for repository https://github.com/Marie59/champ_blocs commit 0d86db7d42b608c386a54500064f5f9c9d7019a4 ecology parents: diff changeset	321 }
89f977a3a256 planemo upload for repository https://github.com/Marie59/champ_blocs commit 0d86db7d42b608c386a54500064f5f9c9d7019a4 ecology parents: diff changeset	322 qecbnew$mean.x.100 <- as.integer(qecbnew$mean.x.100)
89f977a3a256 planemo upload for repository https://github.com/Marie59/champ_blocs commit 0d86db7d42b608c386a54500064f5f9c9d7019a4 ecology parents: diff changeset	323
89f977a3a256 planemo upload for repository https://github.com/Marie59/champ_blocs commit 0d86db7d42b608c386a54500064f5f9c9d7019a4 ecology parents: diff changeset	324 qecbnew$Nb.Spirobranchus.lamarckii.total <- as.integer(qecbnew$Nb.Spirobranchus.lamarckii.total)
89f977a3a256 planemo upload for repository https://github.com/Marie59/champ_blocs commit 0d86db7d42b608c386a54500064f5f9c9d7019a4 ecology parents: diff changeset	325 qecbnew$Nb.Spirobranchus.lamarckii.total.diff <- abs((qecbnew$Nb.Spirobranchus.lamarckii.total - qecbnew$mean.x.100))
89f977a3a256 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")]
89f977a3a256 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)
89f977a3a256 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))
89f977a3a256 planemo upload for repository https://github.com/Marie59/champ_blocs commit 0d86db7d42b608c386a54500064f5f9c9d7019a4 ecology parents: diff changeset	329
89f977a3a256 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$Nb.Spirobranchus.lamarckii.total)
89f977a3a256 planemo upload for repository https://github.com/Marie59/champ_blocs commit 0d86db7d42b608c386a54500064f5f9c9d7019a4 ecology parents: diff changeset	331 spirobranchus_diff <- qecbnew[, c("Nb.Spirobranchus.lamarckii.1B", "Nb.Spirobranchus.lamarckii.2B", "Nb.Spirobranchus.lamarckii.3B", "Nb.Spirobranchus.lamarckii.4B", "Nb.Spirobranchus.lamarckii.5B", "Nb.Spirobranchus.lamarckii.total", "Nb.Spirobranchus.lamarckii.total.ini", "mean.x.100", "Nb.Spirobranchus.lamarckii.total.diff")]
89f977a3a256 planemo upload for repository https://github.com/Marie59/champ_blocs commit 0d86db7d42b608c386a54500064f5f9c9d7019a4 ecology parents: diff changeset	332 spirobranchus_diff$Nb.Spirobranchus.lamarckii.total.diff <- abs(as.integer(spirobranchus_diff$Nb.Spirobranchus.lamarckii.total.diff))
89f977a3a256 planemo upload for repository https://github.com/Marie59/champ_blocs commit 0d86db7d42b608c386a54500064f5f9c9d7019a4 ecology parents: diff changeset	333 spirobranchus_diff <- dplyr::arrange(spirobranchus_diff, desc(Nb.Spirobranchus.lamarckii.total.diff), mean.x.100)
89f977a3a256 planemo upload for repository https://github.com/Marie59/champ_blocs commit 0d86db7d42b608c386a54500064f5f9c9d7019a4 ecology parents: diff changeset	334 spirobranchus_diff <- dplyr::arrange(dplyr::filter(spirobranchus_diff, Nb.Spirobranchus.lamarckii.total.diff != 0 & mean.x.100 != 0), desc(Nb.Spirobranchus.lamarckii.total.diff))
89f977a3a256 planemo upload for repository https://github.com/Marie59/champ_blocs commit 0d86db7d42b608c386a54500064f5f9c9d7019a4 ecology parents: diff changeset	335 # ok, change made when data x 100 was not correct.
89f977a3a256 planemo upload for repository https://github.com/Marie59/champ_blocs commit 0d86db7d42b608c386a54500064f5f9c9d7019a4 ecology parents: diff changeset	336
89f977a3a256 planemo upload for repository https://github.com/Marie59/champ_blocs commit 0d86db7d42b608c386a54500064f5f9c9d7019a4 ecology parents: diff changeset	337 # finally, change NA by mean.x100 for Spirobranchus total
89f977a3a256 planemo upload for repository https://github.com/Marie59/champ_blocs commit 0d86db7d42b608c386a54500064f5f9c9d7019a4 ecology parents: diff changeset	338 qecbnew$Nb.Spirobranchus.lamarckii.total <- as.character(qecbnew$Nb.Spirobranchus.lamarckii.total)
89f977a3a256 planemo upload for repository https://github.com/Marie59/champ_blocs commit 0d86db7d42b608c386a54500064f5f9c9d7019a4 ecology parents: diff changeset	339 for (i in c(1:nrow(qecbnew))) {
89f977a3a256 planemo upload for repository https://github.com/Marie59/champ_blocs commit 0d86db7d42b608c386a54500064f5f9c9d7019a4 ecology parents: diff changeset	340 qecbnew$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]])
89f977a3a256 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
89f977a3a256 planemo upload for repository https://github.com/Marie59/champ_blocs commit 0d86db7d42b608c386a54500064f5f9c9d7019a4 ecology parents: diff changeset	342
89f977a3a256 planemo upload for repository https://github.com/Marie59/champ_blocs commit 0d86db7d42b608c386a54500064f5f9c9d7019a4 ecology parents: diff changeset	343
89f977a3a256 planemo upload for repository https://github.com/Marie59/champ_blocs commit 0d86db7d42b608c386a54500064f5f9c9d7019a4 ecology parents: diff changeset	344 for (i in c(1:nrow(qecbnew))) {
89f977a3a256 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$Nb.Spirobranchus.lamarckii.total[[i]])
89f977a3a256 planemo upload for repository https://github.com/Marie59/champ_blocs commit 0d86db7d42b608c386a54500064f5f9c9d7019a4 ecology parents: diff changeset	346 }
89f977a3a256 planemo upload for repository https://github.com/Marie59/champ_blocs commit 0d86db7d42b608c386a54500064f5f9c9d7019a4 ecology parents: diff changeset	347
89f977a3a256 planemo upload for repository https://github.com/Marie59/champ_blocs commit 0d86db7d42b608c386a54500064f5f9c9d7019a4 ecology parents: diff changeset	348 qecbnew$Nb.Spirobranchus.lamarckii.total <- as.integer(qecbnew$Nb.Spirobranchus.lamarckii.total)
89f977a3a256 planemo upload for repository https://github.com/Marie59/champ_blocs commit 0d86db7d42b608c386a54500064f5f9c9d7019a4 ecology parents: diff changeset	349
89f977a3a256 planemo upload for repository https://github.com/Marie59/champ_blocs commit 0d86db7d42b608c386a54500064f5f9c9d7019a4 ecology parents: diff changeset	350 qecbnew$Nb.Spirobranchus.lamarckii.total.diff <- abs(qecbnew$Nb.Spirobranchus.lamarckii.total - qecbnew$Nb.Spirobranchus.lamarckii.total.ini)
89f977a3a256 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")]
89f977a3a256 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)
89f977a3a256 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))
89f977a3a256 planemo upload for repository https://github.com/Marie59/champ_blocs commit 0d86db7d42b608c386a54500064f5f9c9d7019a4 ecology parents: diff changeset	354
89f977a3a256 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))
89f977a3a256 planemo upload for repository https://github.com/Marie59/champ_blocs commit 0d86db7d42b608c386a54500064f5f9c9d7019a4 ecology parents: diff changeset	356
89f977a3a256 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)
89f977a3a256 planemo upload for repository https://github.com/Marie59/champ_blocs commit 0d86db7d42b608c386a54500064f5f9c9d7019a4 ecology parents: diff changeset	358
89f977a3a256 planemo upload for repository https://github.com/Marie59/champ_blocs commit 0d86db7d42b608c386a54500064f5f9c9d7019a4 ecology parents: diff changeset	359 # do the same for spirorbis
89f977a3a256 planemo upload for repository https://github.com/Marie59/champ_blocs commit 0d86db7d42b608c386a54500064f5f9c9d7019a4 ecology parents: diff changeset	360
89f977a3a256 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
89f977a3a256 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)
89f977a3a256 planemo upload for repository https://github.com/Marie59/champ_blocs commit 0d86db7d42b608c386a54500064f5f9c9d7019a4 ecology parents: diff changeset	363
89f977a3a256 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")))
89f977a3a256 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)
89f977a3a256 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$Nb.spirorbis.5A))[, c("site_year_month_day", "Nb.spirorbis.1A", "Nb.spirorbis.2A", "Nb.spirorbis.3A", "Nb.spirorbis.4A", "Nb.spirorbis.5A", "Nb.spirorbis.total")])
89f977a3a256 planemo upload for repository https://github.com/Marie59/champ_blocs commit 0d86db7d42b608c386a54500064f5f9c9d7019a4 ecology parents: diff changeset	367
89f977a3a256 planemo upload for repository https://github.com/Marie59/champ_blocs commit 0d86db7d42b608c386a54500064f5f9c9d7019a4 ecology parents: diff changeset	368 # In contrast to Spirobranchus data, no encoding issues for spirorbis data, cfr when sub-quadrat 1A-5A are ALL encoded, NA for total.
89f977a3a256 planemo upload for repository https://github.com/Marie59/champ_blocs commit 0d86db7d42b608c386a54500064f5f9c9d7019a4 ecology parents: diff changeset	369
89f977a3a256 planemo upload for repository https://github.com/Marie59/champ_blocs commit 0d86db7d42b608c386a54500064f5f9c9d7019a4 ecology parents: diff changeset	370 # some more issues however with "x200"count data
89f977a3a256 planemo upload for repository https://github.com/Marie59/champ_blocs commit 0d86db7d42b608c386a54500064f5f9c9d7019a4 ecology parents: diff changeset	371
89f977a3a256 planemo upload for repository https://github.com/Marie59/champ_blocs commit 0d86db7d42b608c386a54500064f5f9c9d7019a4 ecology parents: diff changeset	372 spirorbis <- subset(qecbnew, !is.na(qecbnew$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$Nb.spirorbis.total))[, c("site_year_month_day", "Nb.spirorbis.1A", "Nb.spirorbis.2A", "Nb.spirorbis.3A", "Nb.spirorbis.4A", "Nb.spirorbis.5A", "Nb.spirorbis.total")]
89f977a3a256 planemo upload for repository https://github.com/Marie59/champ_blocs commit 0d86db7d42b608c386a54500064f5f9c9d7019a4 ecology parents: diff changeset	373 for (i in c(1:nrow(spirorbis))) {
89f977a3a256 planemo upload for repository https://github.com/Marie59/champ_blocs commit 0d86db7d42b608c386a54500064f5f9c9d7019a4 ecology parents: diff changeset	374 spirorbis$mean.x.200[[i]] <- sum(spirorbis[i, c(2:6)], na.rm = TRUE) / sum(!is.na(spirorbis[i, c(2:6)])) * 200
89f977a3a256 planemo upload for repository https://github.com/Marie59/champ_blocs commit 0d86db7d42b608c386a54500064f5f9c9d7019a4 ecology parents: diff changeset	375 }
89f977a3a256 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)
89f977a3a256 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)
89f977a3a256 planemo upload for repository https://github.com/Marie59/champ_blocs commit 0d86db7d42b608c386a54500064f5f9c9d7019a4 ecology parents: diff changeset	378 for (i in c(1:nrow(spirorbis))) {
89f977a3a256 planemo upload for repository https://github.com/Marie59/champ_blocs commit 0d86db7d42b608c386a54500064f5f9c9d7019a4 ecology parents: diff changeset	379 spirorbis$diff[[i]] <- spirorbis[i, "Nb.spirorbis.total"] - spirorbis[i, "mean.x.200"]
89f977a3a256 planemo upload for repository https://github.com/Marie59/champ_blocs commit 0d86db7d42b608c386a54500064f5f9c9d7019a4 ecology parents: diff changeset	380 }
89f977a3a256 planemo upload for repository https://github.com/Marie59/champ_blocs commit 0d86db7d42b608c386a54500064f5f9c9d7019a4 ecology parents: diff changeset	381 spirorbis$diff <- abs(as.integer(spirorbis$diff))
89f977a3a256 planemo upload for repository https://github.com/Marie59/champ_blocs commit 0d86db7d42b608c386a54500064f5f9c9d7019a4 ecology parents: diff changeset	382 spirorbis <- dplyr::arrange(spirorbis, desc(diff), mean.x.200)
89f977a3a256 planemo upload for repository https://github.com/Marie59/champ_blocs commit 0d86db7d42b608c386a54500064f5f9c9d7019a4 ecology parents: diff changeset	383 (gonb_ilotstmichel_2015_04_18 <- dplyr::filter(spirorbis, site_year_month_day == "GONB_IlotStMichel.2015.04.18"))
89f977a3a256 planemo upload for repository https://github.com/Marie59/champ_blocs commit 0d86db7d42b608c386a54500064f5f9c9d7019a4 ecology parents: diff changeset	384 rm(gonb_ilotstmichel_2015_04_18)
89f977a3a256 planemo upload for repository https://github.com/Marie59/champ_blocs commit 0d86db7d42b608c386a54500064f5f9c9d7019a4 ecology parents: diff changeset	385 spirorbis <- dplyr::arrange(dplyr::filter(spirorbis, diff != 0 & mean.x.200 != 0), desc(diff))
89f977a3a256 planemo upload for repository https://github.com/Marie59/champ_blocs commit 0d86db7d42b608c386a54500064f5f9c9d7019a4 ecology parents: diff changeset	386
89f977a3a256 planemo upload for repository https://github.com/Marie59/champ_blocs commit 0d86db7d42b608c386a54500064f5f9c9d7019a4 ecology parents: diff changeset	387 # check it all in the qecbnew df
89f977a3a256 planemo upload for repository https://github.com/Marie59/champ_blocs commit 0d86db7d42b608c386a54500064f5f9c9d7019a4 ecology parents: diff changeset	388
89f977a3a256 planemo upload for repository https://github.com/Marie59/champ_blocs commit 0d86db7d42b608c386a54500064f5f9c9d7019a4 ecology parents: diff changeset	389 for (i in c(1:nrow(qecbnew))) {
89f977a3a256 planemo upload for repository https://github.com/Marie59/champ_blocs commit 0d86db7d42b608c386a54500064f5f9c9d7019a4 ecology parents: diff changeset	390 qecbnew$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
89f977a3a256 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
89f977a3a256 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)
89f977a3a256 planemo upload for repository https://github.com/Marie59/champ_blocs commit 0d86db7d42b608c386a54500064f5f9c9d7019a4 ecology parents: diff changeset	393
89f977a3a256 planemo upload for repository https://github.com/Marie59/champ_blocs commit 0d86db7d42b608c386a54500064f5f9c9d7019a4 ecology parents: diff changeset	394 for (i in c(1:nrow(qecbnew))) {
89f977a3a256 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$mean.x.200[[i]])
89f977a3a256 planemo upload for repository https://github.com/Marie59/champ_blocs commit 0d86db7d42b608c386a54500064f5f9c9d7019a4 ecology parents: diff changeset	396 }
89f977a3a256 planemo upload for repository https://github.com/Marie59/champ_blocs commit 0d86db7d42b608c386a54500064f5f9c9d7019a4 ecology parents: diff changeset	397
89f977a3a256 planemo upload for repository https://github.com/Marie59/champ_blocs commit 0d86db7d42b608c386a54500064f5f9c9d7019a4 ecology parents: diff changeset	398 qecbnew$mean.x.200 <- as.integer(qecbnew$mean.x.200)
89f977a3a256 planemo upload for repository https://github.com/Marie59/champ_blocs commit 0d86db7d42b608c386a54500064f5f9c9d7019a4 ecology parents: diff changeset	399
89f977a3a256 planemo upload for repository https://github.com/Marie59/champ_blocs commit 0d86db7d42b608c386a54500064f5f9c9d7019a4 ecology parents: diff changeset	400 qecbnew$Nb.spirorbis.total <- as.integer(qecbnew$Nb.spirorbis.total)
89f977a3a256 planemo upload for repository https://github.com/Marie59/champ_blocs commit 0d86db7d42b608c386a54500064f5f9c9d7019a4 ecology parents: diff changeset	401 qecbnew$Nb.spirorbis.total.diff <- abs((qecbnew$Nb.spirorbis.total - qecbnew$mean.x.200))
89f977a3a256 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")]
89f977a3a256 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)
89f977a3a256 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))
89f977a3a256 planemo upload for repository https://github.com/Marie59/champ_blocs commit 0d86db7d42b608c386a54500064f5f9c9d7019a4 ecology parents: diff changeset	405
89f977a3a256 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$Nb.spirorbis.total)
89f977a3a256 planemo upload for repository https://github.com/Marie59/champ_blocs commit 0d86db7d42b608c386a54500064f5f9c9d7019a4 ecology parents: diff changeset	407 spirorbis_diff <- qecbnew[, c("Nb.spirorbis.1A", "Nb.spirorbis.2A", "Nb.spirorbis.3A", "Nb.spirorbis.4A", "Nb.spirorbis.5A", "Nb.spirorbis.total", "Nb.spirorbis.total.ini", "mean.x.200", "Nb.spirorbis.total.diff")]
89f977a3a256 planemo upload for repository https://github.com/Marie59/champ_blocs commit 0d86db7d42b608c386a54500064f5f9c9d7019a4 ecology parents: diff changeset	408 spirorbis_diff$Nb.spirorbis.total.diff <- abs(as.integer(spirorbis_diff$Nb.spirorbis.total.diff))
89f977a3a256 planemo upload for repository https://github.com/Marie59/champ_blocs commit 0d86db7d42b608c386a54500064f5f9c9d7019a4 ecology parents: diff changeset	409 spirorbis_diff <- dplyr::arrange(spirorbis_diff, desc(Nb.spirorbis.total.diff), mean.x.200)
89f977a3a256 planemo upload for repository https://github.com/Marie59/champ_blocs commit 0d86db7d42b608c386a54500064f5f9c9d7019a4 ecology parents: diff changeset	410 spirorbis_diff <- dplyr::arrange(dplyr::filter(spirorbis_diff, Nb.spirorbis.total.diff != 0 & mean.x.200 != 0), desc(Nb.spirorbis.total.diff))
89f977a3a256 planemo upload for repository https://github.com/Marie59/champ_blocs commit 0d86db7d42b608c386a54500064f5f9c9d7019a4 ecology parents: diff changeset	411 # ok, change made when data x 200 was not correct.
89f977a3a256 planemo upload for repository https://github.com/Marie59/champ_blocs commit 0d86db7d42b608c386a54500064f5f9c9d7019a4 ecology parents: diff changeset	412
89f977a3a256 planemo upload for repository https://github.com/Marie59/champ_blocs commit 0d86db7d42b608c386a54500064f5f9c9d7019a4 ecology parents: diff changeset	413 # finally, change NA by mean.x200 for spirorbis total
89f977a3a256 planemo upload for repository https://github.com/Marie59/champ_blocs commit 0d86db7d42b608c386a54500064f5f9c9d7019a4 ecology parents: diff changeset	414 qecbnew$Nb.spirorbis.total <- as.character(qecbnew$Nb.spirorbis.total)
89f977a3a256 planemo upload for repository https://github.com/Marie59/champ_blocs commit 0d86db7d42b608c386a54500064f5f9c9d7019a4 ecology parents: diff changeset	415 for (i in c(1:nrow(qecbnew))) {
89f977a3a256 planemo upload for repository https://github.com/Marie59/champ_blocs commit 0d86db7d42b608c386a54500064f5f9c9d7019a4 ecology parents: diff changeset	416 qecbnew$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]])
89f977a3a256 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
89f977a3a256 planemo upload for repository https://github.com/Marie59/champ_blocs commit 0d86db7d42b608c386a54500064f5f9c9d7019a4 ecology parents: diff changeset	418
89f977a3a256 planemo upload for repository https://github.com/Marie59/champ_blocs commit 0d86db7d42b608c386a54500064f5f9c9d7019a4 ecology parents: diff changeset	419 for (i in c(1:nrow(qecbnew))) {
89f977a3a256 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$Nb.spirorbis.total[[i]])
89f977a3a256 planemo upload for repository https://github.com/Marie59/champ_blocs commit 0d86db7d42b608c386a54500064f5f9c9d7019a4 ecology parents: diff changeset	421 }
89f977a3a256 planemo upload for repository https://github.com/Marie59/champ_blocs commit 0d86db7d42b608c386a54500064f5f9c9d7019a4 ecology parents: diff changeset	422
89f977a3a256 planemo upload for repository https://github.com/Marie59/champ_blocs commit 0d86db7d42b608c386a54500064f5f9c9d7019a4 ecology parents: diff changeset	423 qecbnew$Nb.spirorbis.total <- as.integer(qecbnew$Nb.spirorbis.total)
89f977a3a256 planemo upload for repository https://github.com/Marie59/champ_blocs commit 0d86db7d42b608c386a54500064f5f9c9d7019a4 ecology parents: diff changeset	424
89f977a3a256 planemo upload for repository https://github.com/Marie59/champ_blocs commit 0d86db7d42b608c386a54500064f5f9c9d7019a4 ecology parents: diff changeset	425 qecbnew$Nb.spirorbis.total.diff <- abs(qecbnew$Nb.spirorbis.total - qecbnew$Nb.spirorbis.total.ini)
89f977a3a256 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")]
89f977a3a256 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)
89f977a3a256 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))
89f977a3a256 planemo upload for repository https://github.com/Marie59/champ_blocs commit 0d86db7d42b608c386a54500064f5f9c9d7019a4 ecology parents: diff changeset	429
89f977a3a256 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))
89f977a3a256 planemo upload for repository https://github.com/Marie59/champ_blocs commit 0d86db7d42b608c386a54500064f5f9c9d7019a4 ecology parents: diff changeset	431
89f977a3a256 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)
89f977a3a256 planemo upload for repository https://github.com/Marie59/champ_blocs commit 0d86db7d42b608c386a54500064f5f9c9d7019a4 ecology parents: diff changeset	433
89f977a3a256 planemo upload for repository https://github.com/Marie59/champ_blocs commit 0d86db7d42b608c386a54500064f5f9c9d7019a4 ecology parents: diff changeset	434
89f977a3a256 planemo upload for repository https://github.com/Marie59/champ_blocs commit 0d86db7d42b608c386a54500064f5f9c9d7019a4 ecology parents: diff changeset	435 # dplyr::filter for abnormal data, based on histogram distribution of data
89f977a3a256 planemo upload for repository https://github.com/Marie59/champ_blocs commit 0d86db7d42b608c386a54500064f5f9c9d7019a4 ecology parents: diff changeset	436
89f977a3a256 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")]
89f977a3a256 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$X..algues.brunes)
89f977a3a256 planemo upload for repository https://github.com/Marie59/champ_blocs commit 0d86db7d42b608c386a54500064f5f9c9d7019a4 ecology parents: diff changeset	439 dplyr::filter(qecbnew, X..algues.rouges > 100)[, c("Site", "date_fiche", "Type.Bloc", "Numéro.Bloc.échantillon", "Face", "X..algues.rouges")]
89f977a3a256 planemo upload for repository https://github.com/Marie59/champ_blocs commit 0d86db7d42b608c386a54500064f5f9c9d7019a4 ecology parents: diff changeset	440 qecbnew$X..algues.rouges <- ifelse(qecbnew$X..algues.rouges > 100, 100, qecbnew$X..algues.rouges)
89f977a3a256 planemo upload for repository https://github.com/Marie59/champ_blocs commit 0d86db7d42b608c386a54500064f5f9c9d7019a4 ecology parents: diff changeset	441
89f977a3a256 planemo upload for repository https://github.com/Marie59/champ_blocs commit 0d86db7d42b608c386a54500064f5f9c9d7019a4 ecology parents: diff changeset	442
89f977a3a256 planemo upload for repository https://github.com/Marie59/champ_blocs commit 0d86db7d42b608c386a54500064f5f9c9d7019a4 ecology parents: diff changeset	443 ## SCRIPT I - NAs <- 0 ; cfr previous comment makes no sense to have NA encoded when the presence of an organism is in reality = 0
89f977a3a256 planemo upload for repository https://github.com/Marie59/champ_blocs commit 0d86db7d42b608c386a54500064f5f9c9d7019a4 ecology parents: diff changeset	444
89f977a3a256 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 ...
89f977a3a256 planemo upload for repository https://github.com/Marie59/champ_blocs commit 0d86db7d42b608c386a54500064f5f9c9d7019a4 ecology parents: diff changeset	446 # I theregore change these NAs by 0
89f977a3a256 planemo upload for repository https://github.com/Marie59/champ_blocs commit 0d86db7d42b608c386a54500064f5f9c9d7019a4 ecology parents: diff changeset	447
89f977a3a256 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
89f977a3a256 planemo upload for repository https://github.com/Marie59/champ_blocs commit 0d86db7d42b608c386a54500064f5f9c9d7019a4 ecology parents: diff changeset	449 qecbnew[, c("X..algues.brunes",
89f977a3a256 planemo upload for repository https://github.com/Marie59/champ_blocs commit 0d86db7d42b608c386a54500064f5f9c9d7019a4 ecology parents: diff changeset	450 "X..algues.rouges",
89f977a3a256 planemo upload for repository https://github.com/Marie59/champ_blocs commit 0d86db7d42b608c386a54500064f5f9c9d7019a4 ecology parents: diff changeset	451 "X..Lithophyllum",
89f977a3a256 planemo upload for repository https://github.com/Marie59/champ_blocs commit 0d86db7d42b608c386a54500064f5f9c9d7019a4 ecology parents: diff changeset	452 "X..Cladophora",
89f977a3a256 planemo upload for repository https://github.com/Marie59/champ_blocs commit 0d86db7d42b608c386a54500064f5f9c9d7019a4 ecology parents: diff changeset	453 "Nb.Littorina.obtusata",
89f977a3a256 planemo upload for repository https://github.com/Marie59/champ_blocs commit 0d86db7d42b608c386a54500064f5f9c9d7019a4 ecology parents: diff changeset	454 "Nb.Gibbula.cineraria",
89f977a3a256 planemo upload for repository https://github.com/Marie59/champ_blocs commit 0d86db7d42b608c386a54500064f5f9c9d7019a4 ecology parents: diff changeset	455 "Nb.Gibbula.pennanti",
89f977a3a256 planemo upload for repository https://github.com/Marie59/champ_blocs commit 0d86db7d42b608c386a54500064f5f9c9d7019a4 ecology parents: diff changeset	456 "Nb.Gibbula.umbilicalis",
89f977a3a256 planemo upload for repository https://github.com/Marie59/champ_blocs commit 0d86db7d42b608c386a54500064f5f9c9d7019a4 ecology parents: diff changeset	457 "X..Eponges",
89f977a3a256 planemo upload for repository https://github.com/Marie59/champ_blocs commit 0d86db7d42b608c386a54500064f5f9c9d7019a4 ecology parents: diff changeset	458 "X..Ascidies.Coloniales",
89f977a3a256 planemo upload for repository https://github.com/Marie59/champ_blocs commit 0d86db7d42b608c386a54500064f5f9c9d7019a4 ecology parents: diff changeset	459 "X..Ascidies.Solitaires",
89f977a3a256 planemo upload for repository https://github.com/Marie59/champ_blocs commit 0d86db7d42b608c386a54500064f5f9c9d7019a4 ecology parents: diff changeset	460 "X..Bryozoaires.Dresses",
89f977a3a256 planemo upload for repository https://github.com/Marie59/champ_blocs commit 0d86db7d42b608c386a54500064f5f9c9d7019a4 ecology parents: diff changeset	461 "X..algues.vertes",
89f977a3a256 planemo upload for repository https://github.com/Marie59/champ_blocs commit 0d86db7d42b608c386a54500064f5f9c9d7019a4 ecology parents: diff changeset	462 "X..Roche.Nue",
89f977a3a256 planemo upload for repository https://github.com/Marie59/champ_blocs commit 0d86db7d42b608c386a54500064f5f9c9d7019a4 ecology parents: diff changeset	463 "Nb.spirorbis.total",
89f977a3a256 planemo upload for repository https://github.com/Marie59/champ_blocs commit 0d86db7d42b608c386a54500064f5f9c9d7019a4 ecology parents: diff changeset	464 "X..Balanes.Vivantes",
89f977a3a256 planemo upload for repository https://github.com/Marie59/champ_blocs commit 0d86db7d42b608c386a54500064f5f9c9d7019a4 ecology parents: diff changeset	465 "Nb.Spirobranchus.lamarckii.total",
89f977a3a256 planemo upload for repository https://github.com/Marie59/champ_blocs commit 0d86db7d42b608c386a54500064f5f9c9d7019a4 ecology parents: diff changeset	466 "X..Surface.Accolement")] <- lapply(qecbnew[,
89f977a3a256 planemo upload for repository https://github.com/Marie59/champ_blocs commit 0d86db7d42b608c386a54500064f5f9c9d7019a4 ecology parents: diff changeset	467 c("X..algues.brunes",
89f977a3a256 planemo upload for repository https://github.com/Marie59/champ_blocs commit 0d86db7d42b608c386a54500064f5f9c9d7019a4 ecology parents: diff changeset	468 "X..algues.rouges",
89f977a3a256 planemo upload for repository https://github.com/Marie59/champ_blocs commit 0d86db7d42b608c386a54500064f5f9c9d7019a4 ecology parents: diff changeset	469 "X..Lithophyllum",
89f977a3a256 planemo upload for repository https://github.com/Marie59/champ_blocs commit 0d86db7d42b608c386a54500064f5f9c9d7019a4 ecology parents: diff changeset	470 "X..Cladophora",
89f977a3a256 planemo upload for repository https://github.com/Marie59/champ_blocs commit 0d86db7d42b608c386a54500064f5f9c9d7019a4 ecology parents: diff changeset	471 "Nb.Littorina.obtusata",
89f977a3a256 planemo upload for repository https://github.com/Marie59/champ_blocs commit 0d86db7d42b608c386a54500064f5f9c9d7019a4 ecology parents: diff changeset	472 "Nb.Gibbula.cineraria",
89f977a3a256 planemo upload for repository https://github.com/Marie59/champ_blocs commit 0d86db7d42b608c386a54500064f5f9c9d7019a4 ecology parents: diff changeset	473 "Nb.Gibbula.pennanti",
89f977a3a256 planemo upload for repository https://github.com/Marie59/champ_blocs commit 0d86db7d42b608c386a54500064f5f9c9d7019a4 ecology parents: diff changeset	474 "Nb.Gibbula.umbilicalis",
89f977a3a256 planemo upload for repository https://github.com/Marie59/champ_blocs commit 0d86db7d42b608c386a54500064f5f9c9d7019a4 ecology parents: diff changeset	475 "X..Eponges",
89f977a3a256 planemo upload for repository https://github.com/Marie59/champ_blocs commit 0d86db7d42b608c386a54500064f5f9c9d7019a4 ecology parents: diff changeset	476 "X..Ascidies.Coloniales",
89f977a3a256 planemo upload for repository https://github.com/Marie59/champ_blocs commit 0d86db7d42b608c386a54500064f5f9c9d7019a4 ecology parents: diff changeset	477 "X..Ascidies.Solitaires",
89f977a3a256 planemo upload for repository https://github.com/Marie59/champ_blocs commit 0d86db7d42b608c386a54500064f5f9c9d7019a4 ecology parents: diff changeset	478 "X..Bryozoaires.Dresses",
89f977a3a256 planemo upload for repository https://github.com/Marie59/champ_blocs commit 0d86db7d42b608c386a54500064f5f9c9d7019a4 ecology parents: diff changeset	479 "X..algues.vertes",
89f977a3a256 planemo upload for repository https://github.com/Marie59/champ_blocs commit 0d86db7d42b608c386a54500064f5f9c9d7019a4 ecology parents: diff changeset	480 "X..Roche.Nue",
89f977a3a256 planemo upload for repository https://github.com/Marie59/champ_blocs commit 0d86db7d42b608c386a54500064f5f9c9d7019a4 ecology parents: diff changeset	481 "Nb.spirorbis.total",
89f977a3a256 planemo upload for repository https://github.com/Marie59/champ_blocs commit 0d86db7d42b608c386a54500064f5f9c9d7019a4 ecology parents: diff changeset	482 "X..Balanes.Vivantes",
89f977a3a256 planemo upload for repository https://github.com/Marie59/champ_blocs commit 0d86db7d42b608c386a54500064f5f9c9d7019a4 ecology parents: diff changeset	483 "Nb.Spirobranchus.lamarckii.total",
89f977a3a256 planemo upload for repository https://github.com/Marie59/champ_blocs commit 0d86db7d42b608c386a54500064f5f9c9d7019a4 ecology parents: diff changeset	484 "X..Surface.Accolement")],
89f977a3a256 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))
89f977a3a256 planemo upload for repository https://github.com/Marie59/champ_blocs commit 0d86db7d42b608c386a54500064f5f9c9d7019a4 ecology parents: diff changeset	486
89f977a3a256 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.
89f977a3a256 planemo upload for repository https://github.com/Marie59/champ_blocs commit 0d86db7d42b608c386a54500064f5f9c9d7019a4 ecology parents: diff changeset	488
89f977a3a256 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.)
89f977a3a256 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)
89f977a3a256 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)
89f977a3a256 planemo upload for repository https://github.com/Marie59/champ_blocs commit 0d86db7d42b608c386a54500064f5f9c9d7019a4 ecology parents: diff changeset	492
89f977a3a256 planemo upload for repository https://github.com/Marie59/champ_blocs commit 0d86db7d42b608c386a54500064f5f9c9d7019a4 ecology parents: diff changeset	493
89f977a3a256 planemo upload for repository https://github.com/Marie59/champ_blocs commit 0d86db7d42b608c386a54500064f5f9c9d7019a4 ecology parents: diff changeset	494 # add a region variable
89f977a3a256 planemo upload for repository https://github.com/Marie59/champ_blocs commit 0d86db7d42b608c386a54500064f5f9c9d7019a4 ecology parents: diff changeset	495 region <- rep(NA, nrow(qecbnew))
89f977a3a256 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")
89f977a3a256 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")
89f977a3a256 planemo upload for repository https://github.com/Marie59/champ_blocs commit 0d86db7d42b608c386a54500064f5f9c9d7019a4 ecology parents: diff changeset	498 rm(region)
89f977a3a256 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)
89f977a3a256 planemo upload for repository https://github.com/Marie59/champ_blocs commit 0d86db7d42b608c386a54500064f5f9c9d7019a4 ecology parents: diff changeset	500
89f977a3a256 planemo upload for repository https://github.com/Marie59/champ_blocs commit 0d86db7d42b608c386a54500064f5f9c9d7019a4 ecology parents: diff changeset	501 # accolement function according to recent 'retournement'
89f977a3a256 planemo upload for repository https://github.com/Marie59/champ_blocs commit 0d86db7d42b608c386a54500064f5f9c9d7019a4 ecology parents: diff changeset	502
89f977a3a256 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 !!
89f977a3a256 planemo upload for repository https://github.com/Marie59/champ_blocs commit 0d86db7d42b608c386a54500064f5f9c9d7019a4 ecology parents: diff changeset	504
89f977a3a256 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.
89f977a3a256 planemo upload for repository https://github.com/Marie59/champ_blocs commit 0d86db7d42b608c386a54500064f5f9c9d7019a4 ecology parents: diff changeset	506
89f977a3a256 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$Site, 1, 4), .after = "Site_bis")
89f977a3a256 planemo upload for repository https://github.com/Marie59/champ_blocs commit 0d86db7d42b608c386a54500064f5f9c9d7019a4 ecology parents: diff changeset	508
89f977a3a256 planemo upload for repository https://github.com/Marie59/champ_blocs commit 0d86db7d42b608c386a54500064f5f9c9d7019a4 ecology parents: diff changeset	509 qecbnew$X..Eponges_ini <- qecbnew$X..Eponges
89f977a3a256 planemo upload for repository https://github.com/Marie59/champ_blocs commit 0d86db7d42b608c386a54500064f5f9c9d7019a4 ecology parents: diff changeset	510 qecbnew$X..Ascidies.Coloniales_ini <- qecbnew$X..Ascidies.Coloniales
89f977a3a256 planemo upload for repository https://github.com/Marie59/champ_blocs commit 0d86db7d42b608c386a54500064f5f9c9d7019a4 ecology parents: diff changeset	511 qecbnew$X..Ascidies.Solitaires_ini <- qecbnew$X..Ascidies.Solitaires
89f977a3a256 planemo upload for repository https://github.com/Marie59/champ_blocs commit 0d86db7d42b608c386a54500064f5f9c9d7019a4 ecology parents: diff changeset	512 qecbnew$X..Bryozoaires.Dresses_ini <- qecbnew$X..Bryozoaires.Dresses
89f977a3a256 planemo upload for repository https://github.com/Marie59/champ_blocs commit 0d86db7d42b608c386a54500064f5f9c9d7019a4 ecology parents: diff changeset	513 qecbnew$X..Lithophyllum_ini <- qecbnew$X..Lithophyllum
89f977a3a256 planemo upload for repository https://github.com/Marie59/champ_blocs commit 0d86db7d42b608c386a54500064f5f9c9d7019a4 ecology parents: diff changeset	514 qecbnew$X..Balanes.Vivantes_ini <- qecbnew$X..Balanes.Vivantes
89f977a3a256 planemo upload for repository https://github.com/Marie59/champ_blocs commit 0d86db7d42b608c386a54500064f5f9c9d7019a4 ecology parents: diff changeset	515
89f977a3a256 planemo upload for repository https://github.com/Marie59/champ_blocs commit 0d86db7d42b608c386a54500064f5f9c9d7019a4 ecology parents: diff changeset	516 df_bm_fs <- qecbnew %>% dplyr::filter(Type.Bloc == "Bloc mobile" & Face == "face supérieure")
89f977a3a256 planemo upload for repository https://github.com/Marie59/champ_blocs commit 0d86db7d42b608c386a54500064f5f9c9d7019a4 ecology parents: diff changeset	517 df_bm_fi <- qecbnew %>% dplyr::filter(Type.Bloc == "Bloc mobile" & Face == "face inférieure")
89f977a3a256 planemo upload for repository https://github.com/Marie59/champ_blocs commit 0d86db7d42b608c386a54500064f5f9c9d7019a4 ecology parents: diff changeset	518 df_bf <- qecbnew %>% dplyr::filter(Type.Bloc != "Bloc mobile")
89f977a3a256 planemo upload for repository https://github.com/Marie59/champ_blocs commit 0d86db7d42b608c386a54500064f5f9c9d7019a4 ecology parents: diff changeset	519
89f977a3a256 planemo upload for repository https://github.com/Marie59/champ_blocs commit 0d86db7d42b608c386a54500064f5f9c9d7019a4 ecology parents: diff changeset	520 `%notin%` <- Negate(`%in%`)
89f977a3a256 planemo upload for repository https://github.com/Marie59/champ_blocs commit 0d86db7d42b608c386a54500064f5f9c9d7019a4 ecology parents: diff changeset	521
89f977a3a256 planemo upload for repository https://github.com/Marie59/champ_blocs commit 0d86db7d42b608c386a54500064f5f9c9d7019a4 ecology parents: diff changeset	522 acco_fct <- function(var_) {
89f977a3a256 planemo upload for repository https://github.com/Marie59/champ_blocs commit 0d86db7d42b608c386a54500064f5f9c9d7019a4 ecology parents: diff changeset	523
89f977a3a256 planemo upload for repository https://github.com/Marie59/champ_blocs commit 0d86db7d42b608c386a54500064f5f9c9d7019a4 ecology parents: diff changeset	524 df_bm_fi$var_cor.acco. <<- NA
89f977a3a256 planemo upload for repository https://github.com/Marie59/champ_blocs commit 0d86db7d42b608c386a54500064f5f9c9d7019a4 ecology parents: diff changeset	525
89f977a3a256 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))) {
89f977a3a256 planemo upload for repository https://github.com/Marie59/champ_blocs commit 0d86db7d42b608c386a54500064f5f9c9d7019a4 ecology parents: diff changeset	527
89f977a3a256 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")) {
89f977a3a256 planemo upload for repository https://github.com/Marie59/champ_blocs commit 0d86db7d42b608c386a54500064f5f9c9d7019a4 ecology parents: diff changeset	529 ifelse(#df_$Couleur.dominante %in% c("Rouge", "Brune", "Brune-Rouge") \|\|
89f977a3a256 planemo upload for repository https://github.com/Marie59/champ_blocs commit 0d86db7d42b608c386a54500064f5f9c9d7019a4 ecology parents: diff changeset	530 df_bm_fs$Couleur.dominante[[i]] %in% c("Blanche", "Verte", "Blanche-Verte", "Colorée"), df_bm_fi[i, var_] / (100 - df_bm_fi$X..Surface.Accolement[[i]]) * 100, df_bm_fi[i, var_])
89f977a3a256 planemo upload for repository https://github.com/Marie59/champ_blocs commit 0d86db7d42b608c386a54500064f5f9c9d7019a4 ecology parents: diff changeset	531 } else {
89f977a3a256 planemo upload for repository https://github.com/Marie59/champ_blocs commit 0d86db7d42b608c386a54500064f5f9c9d7019a4 ecology parents: diff changeset	532 ifelse(df_bm_fs$Couleur.dominante[[i]] %in% c("Blanche", "Verte", "Blanche-Verte", "Colorée")
89f977a3a256 planemo upload for repository https://github.com/Marie59/champ_blocs commit 0d86db7d42b608c386a54500064f5f9c9d7019a4 ecology parents: diff changeset	533 & df_bm_fi$X..Surface.Accolement[[i]] != 0 # I have to use it in dplyr::filter this time as well for EGMP- BASQ (but not for Bretagne, although could be added, same result); identical/repeated measure for BM.FI and BM.FS
89f977a3a256 planemo upload for repository https://github.com/Marie59/champ_blocs commit 0d86db7d42b608c386a54500064f5f9c9d7019a4 ecology parents: diff changeset	534 & df_bm_fs$X..Mytilus.sp.[[i]] == 0, df_bm_fi[i, var_] / (100 - df_bm_fi$X..Surface.Accolement[[i]]) * 100, df_bm_fi[i, var_])
89f977a3a256 planemo upload for repository https://github.com/Marie59/champ_blocs commit 0d86db7d42b608c386a54500064f5f9c9d7019a4 ecology parents: diff changeset	535 }
89f977a3a256 planemo upload for repository https://github.com/Marie59/champ_blocs commit 0d86db7d42b608c386a54500064f5f9c9d7019a4 ecology parents: diff changeset	536
89f977a3a256 planemo upload for repository https://github.com/Marie59/champ_blocs commit 0d86db7d42b608c386a54500064f5f9c9d7019a4 ecology parents: diff changeset	537 }
89f977a3a256 planemo upload for repository https://github.com/Marie59/champ_blocs commit 0d86db7d42b608c386a54500064f5f9c9d7019a4 ecology parents: diff changeset	538
89f977a3a256 planemo upload for repository https://github.com/Marie59/champ_blocs commit 0d86db7d42b608c386a54500064f5f9c9d7019a4 ecology parents: diff changeset	539 }
89f977a3a256 planemo upload for repository https://github.com/Marie59/champ_blocs commit 0d86db7d42b608c386a54500064f5f9c9d7019a4 ecology parents: diff changeset	540
89f977a3a256 planemo upload for repository https://github.com/Marie59/champ_blocs commit 0d86db7d42b608c386a54500064f5f9c9d7019a4 ecology parents: diff changeset	541 # I would only consider colors in c("Rouge", "Brune", "Brune-Rouge") for BM.FI correction [ and not the series c("Blanche-Brune", "Rouge", "Brune", "Blanche-Rouge", "Brune-Rouge", "Rouge-Verte", "Brune-Verte") ] ; and for BM.FS, the list c("Blanche", "Verte", "Colorée") => we do the correction for BM.FI accollement based on BM.FS color !!!
89f977a3a256 planemo upload for repository https://github.com/Marie59/champ_blocs commit 0d86db7d42b608c386a54500064f5f9c9d7019a4 ecology parents: diff changeset	542
89f977a3a256 planemo upload for repository https://github.com/Marie59/champ_blocs commit 0d86db7d42b608c386a54500064f5f9c9d7019a4 ecology parents: diff changeset	543
89f977a3a256 planemo upload for repository https://github.com/Marie59/champ_blocs commit 0d86db7d42b608c386a54500064f5f9c9d7019a4 ecology parents: diff changeset	544 # apply acco_fct to BM.FI variables
89f977a3a256 planemo upload for repository https://github.com/Marie59/champ_blocs commit 0d86db7d42b608c386a54500064f5f9c9d7019a4 ecology parents: diff changeset	545
89f977a3a256 planemo upload for repository https://github.com/Marie59/champ_blocs commit 0d86db7d42b608c386a54500064f5f9c9d7019a4 ecology parents: diff changeset	546 apply_acco_fct <- function(var_) {
89f977a3a256 planemo upload for repository https://github.com/Marie59/champ_blocs commit 0d86db7d42b608c386a54500064f5f9c9d7019a4 ecology parents: diff changeset	547
89f977a3a256 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])
89f977a3a256 planemo upload for repository https://github.com/Marie59/champ_blocs commit 0d86db7d42b608c386a54500064f5f9c9d7019a4 ecology parents: diff changeset	549 pre_ <- as.vector(df_bm_fi[, var_])
89f977a3a256 planemo upload for repository https://github.com/Marie59/champ_blocs commit 0d86db7d42b608c386a54500064f5f9c9d7019a4 ecology parents: diff changeset	550 acco_fct(var_)
89f977a3a256 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_)
89f977a3a256 planemo upload for repository https://github.com/Marie59/champ_blocs commit 0d86db7d42b608c386a54500064f5f9c9d7019a4 ecology parents: diff changeset	552 show(sort(df_bm_fi$var_cor., decreasing = TRUE, index.return = FALSE)[1:50])
89f977a3a256 planemo upload for repository https://github.com/Marie59/champ_blocs commit 0d86db7d42b608c386a54500064f5f9c9d7019a4 ecology parents: diff changeset	553 df_bm_fi$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.)))
89f977a3a256 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$var_cor.)
89f977a3a256 planemo upload for repository https://github.com/Marie59/champ_blocs commit 0d86db7d42b608c386a54500064f5f9c9d7019a4 ecology parents: diff changeset	555 show(sort(df_bm_fi$var_cor., decreasing = TRUE, index.return = FALSE)[1:50])
89f977a3a256 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)
89f977a3a256 planemo upload for repository https://github.com/Marie59/champ_blocs commit 0d86db7d42b608c386a54500064f5f9c9d7019a4 ecology parents: diff changeset	557 par(mfrow = c(1, 3))
89f977a3a256 planemo upload for repository https://github.com/Marie59/champ_blocs commit 0d86db7d42b608c386a54500064f5f9c9d7019a4 ecology parents: diff changeset	558 hist(pre_, main = var_, xlab = "pre-corection")
89f977a3a256 planemo upload for repository https://github.com/Marie59/champ_blocs commit 0d86db7d42b608c386a54500064f5f9c9d7019a4 ecology parents: diff changeset	559 hist(df_bm_fi$var_cor., main = var_, xlab = "post-corection")
89f977a3a256 planemo upload for repository https://github.com/Marie59/champ_blocs commit 0d86db7d42b608c386a54500064f5f9c9d7019a4 ecology parents: diff changeset	560 hist(df_bm_fi[as.vector(which(abs(as.vector(df_bm_fi$var_cor.) - pre_) != 0)), var_], main = var_, xlab = "diff. post-pre != 0")
89f977a3a256 planemo upload for repository https://github.com/Marie59/champ_blocs commit 0d86db7d42b608c386a54500064f5f9c9d7019a4 ecology parents: diff changeset	561 par(mfrow = c(1, 1))
89f977a3a256 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."))]
89f977a3a256 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_
89f977a3a256 planemo upload for repository https://github.com/Marie59/champ_blocs commit 0d86db7d42b608c386a54500064f5f9c9d7019a4 ecology parents: diff changeset	564
89f977a3a256 planemo upload for repository https://github.com/Marie59/champ_blocs commit 0d86db7d42b608c386a54500064f5f9c9d7019a4 ecology parents: diff changeset	565 rm(pre_)
89f977a3a256 planemo upload for repository https://github.com/Marie59/champ_blocs commit 0d86db7d42b608c386a54500064f5f9c9d7019a4 ecology parents: diff changeset	566
89f977a3a256 planemo upload for repository https://github.com/Marie59/champ_blocs commit 0d86db7d42b608c386a54500064f5f9c9d7019a4 ecology parents: diff changeset	567 }
89f977a3a256 planemo upload for repository https://github.com/Marie59/champ_blocs commit 0d86db7d42b608c386a54500064f5f9c9d7019a4 ecology parents: diff changeset	568
89f977a3a256 planemo upload for repository https://github.com/Marie59/champ_blocs commit 0d86db7d42b608c386a54500064f5f9c9d7019a4 ecology parents: diff changeset	569 apply_acco_fct("X..Eponges")
89f977a3a256 planemo upload for repository https://github.com/Marie59/champ_blocs commit 0d86db7d42b608c386a54500064f5f9c9d7019a4 ecology parents: diff changeset	570 apply_acco_fct("X..Ascidies.Coloniales")
89f977a3a256 planemo upload for repository https://github.com/Marie59/champ_blocs commit 0d86db7d42b608c386a54500064f5f9c9d7019a4 ecology parents: diff changeset	571 apply_acco_fct("X..Ascidies.Solitaires")
89f977a3a256 planemo upload for repository https://github.com/Marie59/champ_blocs commit 0d86db7d42b608c386a54500064f5f9c9d7019a4 ecology parents: diff changeset	572 apply_acco_fct("X..Bryozoaires.Dresses")
89f977a3a256 planemo upload for repository https://github.com/Marie59/champ_blocs commit 0d86db7d42b608c386a54500064f5f9c9d7019a4 ecology parents: diff changeset	573 apply_acco_fct("X..Lithophyllum")
89f977a3a256 planemo upload for repository https://github.com/Marie59/champ_blocs commit 0d86db7d42b608c386a54500064f5f9c9d7019a4 ecology parents: diff changeset	574 apply_acco_fct("X..Balanes.Vivantes")
89f977a3a256 planemo upload for repository https://github.com/Marie59/champ_blocs commit 0d86db7d42b608c386a54500064f5f9c9d7019a4 ecology parents: diff changeset	575
89f977a3a256 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)
89f977a3a256 planemo upload for repository https://github.com/Marie59/champ_blocs commit 0d86db7d42b608c386a54500064f5f9c9d7019a4 ecology parents: diff changeset	577 qecbnew <- dplyr::bind_rows(qecbnew, df_bf)
89f977a3a256 planemo upload for repository https://github.com/Marie59/champ_blocs commit 0d86db7d42b608c386a54500064f5f9c9d7019a4 ecology parents: diff changeset	578
89f977a3a256 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)
89f977a3a256 planemo upload for repository https://github.com/Marie59/champ_blocs commit 0d86db7d42b608c386a54500064f5f9c9d7019a4 ecology parents: diff changeset	580
89f977a3a256 planemo upload for repository https://github.com/Marie59/champ_blocs commit 0d86db7d42b608c386a54500064f5f9c9d7019a4 ecology parents: diff changeset	581 # do remove some more data ...
89f977a3a256 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
89f977a3a256 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")
89f977a3a256 planemo upload for repository https://github.com/Marie59/champ_blocs commit 0d86db7d42b608c386a54500064f5f9c9d7019a4 ecology parents: diff changeset	584
89f977a3a256 planemo upload for repository https://github.com/Marie59/champ_blocs commit 0d86db7d42b608c386a54500064f5f9c9d7019a4 ecology parents: diff changeset	585 # save the final qecbnew df_
89f977a3a256 planemo upload for repository https://github.com/Marie59/champ_blocs commit 0d86db7d42b608c386a54500064f5f9c9d7019a4 ecology parents: diff changeset	586
89f977a3a256 planemo upload for repository https://github.com/Marie59/champ_blocs commit 0d86db7d42b608c386a54500064f5f9c9d7019a4 ecology parents: diff changeset	587 qecb <- qecbnew
89f977a3a256 planemo upload for repository https://github.com/Marie59/champ_blocs commit 0d86db7d42b608c386a54500064f5f9c9d7019a4 ecology parents: diff changeset	588
89f977a3a256 planemo upload for repository https://github.com/Marie59/champ_blocs commit 0d86db7d42b608c386a54500064f5f9c9d7019a4 ecology parents: diff changeset	589
89f977a3a256 planemo upload for repository https://github.com/Marie59/champ_blocs commit 0d86db7d42b608c386a54500064f5f9c9d7019a4 ecology parents: diff changeset	590 `%notin%` <- Negate(`%in%`)
89f977a3a256 planemo upload for repository https://github.com/Marie59/champ_blocs commit 0d86db7d42b608c386a54500064f5f9c9d7019a4 ecology parents: diff changeset	591
89f977a3a256 planemo upload for repository https://github.com/Marie59/champ_blocs commit 0d86db7d42b608c386a54500064f5f9c9d7019a4 ecology parents: diff changeset	592 ## reorder and/or create new variables
89f977a3a256 planemo upload for repository https://github.com/Marie59/champ_blocs commit 0d86db7d42b608c386a54500064f5f9c9d7019a4 ecology parents: diff changeset	593
89f977a3a256 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
89f977a3a256 planemo upload for repository https://github.com/Marie59/champ_blocs commit 0d86db7d42b608c386a54500064f5f9c9d7019a4 ecology parents: diff changeset	595 qecb <- tibble::add_column(qecb, qecb$site_year_month_day, .after = "Site_bis")
89f977a3a256 planemo upload for repository https://github.com/Marie59/champ_blocs commit 0d86db7d42b608c386a54500064f5f9c9d7019a4 ecology parents: diff changeset	596 qecb <- qecb[, -which(names(qecb) %in% c("site_year_month_day"))]
89f977a3a256 planemo upload for repository https://github.com/Marie59/champ_blocs commit 0d86db7d42b608c386a54500064f5f9c9d7019a4 ecology parents: diff changeset	597 qecb <- dplyr::rename(qecb, site_year_month_day = `qecb$site_year_month_day`)
89f977a3a256 planemo upload for repository https://github.com/Marie59/champ_blocs commit 0d86db7d42b608c386a54500064f5f9c9d7019a4 ecology parents: diff changeset	598
89f977a3a256 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)
89f977a3a256 planemo upload for repository https://github.com/Marie59/champ_blocs commit 0d86db7d42b608c386a54500064f5f9c9d7019a4 ecology parents: diff changeset	600 period <- rep(NA, nrow(qecb))
89f977a3a256 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")
89f977a3a256 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")
89f977a3a256 planemo upload for repository https://github.com/Marie59/champ_blocs commit 0d86db7d42b608c386a54500064f5f9c9d7019a4 ecology parents: diff changeset	603 qecb$period <- as.factor(qecb$period)
89f977a3a256 planemo upload for repository https://github.com/Marie59/champ_blocs commit 0d86db7d42b608c386a54500064f5f9c9d7019a4 ecology parents: diff changeset	604 rm(period)
89f977a3a256 planemo upload for repository https://github.com/Marie59/champ_blocs commit 0d86db7d42b608c386a54500064f5f9c9d7019a4 ecology parents: diff changeset	605
89f977a3a256 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)
89f977a3a256 planemo upload for repository https://github.com/Marie59/champ_blocs commit 0d86db7d42b608c386a54500064f5f9c9d7019a4 ecology parents: diff changeset	607
89f977a3a256 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 ...)
89f977a3a256 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.
89f977a3a256 planemo upload for repository https://github.com/Marie59/champ_blocs commit 0d86db7d42b608c386a54500064f5f9c9d7019a4 ecology parents: diff changeset	610
89f977a3a256 planemo upload for repository https://github.com/Marie59/champ_blocs commit 0d86db7d42b608c386a54500064f5f9c9d7019a4 ecology parents: diff changeset	611 ## SCRIPT I - NAs <- 0
89f977a3a256 planemo upload for repository https://github.com/Marie59/champ_blocs commit 0d86db7d42b608c386a54500064f5f9c9d7019a4 ecology parents: diff changeset	612
89f977a3a256 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 ...
89f977a3a256 planemo upload for repository https://github.com/Marie59/champ_blocs commit 0d86db7d42b608c386a54500064f5f9c9d7019a4 ecology parents: diff changeset	614
89f977a3a256 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")
89f977a3a256 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"))
89f977a3a256 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")
89f977a3a256 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"))
89f977a3a256 planemo upload for repository https://github.com/Marie59/champ_blocs commit 0d86db7d42b608c386a54500064f5f9c9d7019a4 ecology parents: diff changeset	619
89f977a3a256 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
89f977a3a256 planemo upload for repository https://github.com/Marie59/champ_blocs commit 0d86db7d42b608c386a54500064f5f9c9d7019a4 ecology parents: diff changeset	621
89f977a3a256 planemo upload for repository https://github.com/Marie59/champ_blocs commit 0d86db7d42b608c386a54500064f5f9c9d7019a4 ecology parents: diff changeset	622 bretagne_bm[, c(
89f977a3a256 planemo upload for repository https://github.com/Marie59/champ_blocs commit 0d86db7d42b608c386a54500064f5f9c9d7019a4 ecology parents: diff changeset	623 "X..algues.brunes",
89f977a3a256 planemo upload for repository https://github.com/Marie59/champ_blocs commit 0d86db7d42b608c386a54500064f5f9c9d7019a4 ecology parents: diff changeset	624 "Strate.algues.brunes",
89f977a3a256 planemo upload for repository https://github.com/Marie59/champ_blocs commit 0d86db7d42b608c386a54500064f5f9c9d7019a4 ecology parents: diff changeset	625 "X..algues.rouges",
89f977a3a256 planemo upload for repository https://github.com/Marie59/champ_blocs commit 0d86db7d42b608c386a54500064f5f9c9d7019a4 ecology parents: diff changeset	626 "Strate.algues.rouges",
89f977a3a256 planemo upload for repository https://github.com/Marie59/champ_blocs commit 0d86db7d42b608c386a54500064f5f9c9d7019a4 ecology parents: diff changeset	627 "X..algues.vertes",
89f977a3a256 planemo upload for repository https://github.com/Marie59/champ_blocs commit 0d86db7d42b608c386a54500064f5f9c9d7019a4 ecology parents: diff changeset	628 "Strate.algues.vertes",
89f977a3a256 planemo upload for repository https://github.com/Marie59/champ_blocs commit 0d86db7d42b608c386a54500064f5f9c9d7019a4 ecology parents: diff changeset	629 "X..Cladophora",
89f977a3a256 planemo upload for repository https://github.com/Marie59/champ_blocs commit 0d86db7d42b608c386a54500064f5f9c9d7019a4 ecology parents: diff changeset	630 "X..Lithophyllum",
89f977a3a256 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.
89f977a3a256 planemo upload for repository https://github.com/Marie59/champ_blocs commit 0d86db7d42b608c386a54500064f5f9c9d7019a4 ecology parents: diff changeset	632 #"Type.Sediment",
89f977a3a256 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.
89f977a3a256 planemo upload for repository https://github.com/Marie59/champ_blocs commit 0d86db7d42b608c386a54500064f5f9c9d7019a4 ecology parents: diff changeset	634 "Nb.Littorina.obtusata",
89f977a3a256 planemo upload for repository https://github.com/Marie59/champ_blocs commit 0d86db7d42b608c386a54500064f5f9c9d7019a4 ecology parents: diff changeset	635 "Nb.Gibbula.cineraria",
89f977a3a256 planemo upload for repository https://github.com/Marie59/champ_blocs commit 0d86db7d42b608c386a54500064f5f9c9d7019a4 ecology parents: diff changeset	636 "Nb.Gibbula.pennanti",
89f977a3a256 planemo upload for repository https://github.com/Marie59/champ_blocs commit 0d86db7d42b608c386a54500064f5f9c9d7019a4 ecology parents: diff changeset	637 "Nb.Gibbula.umbilicalis",
89f977a3a256 planemo upload for repository https://github.com/Marie59/champ_blocs commit 0d86db7d42b608c386a54500064f5f9c9d7019a4 ecology parents: diff changeset	638 "Nb.Phallusia.mamillata",
89f977a3a256 planemo upload for repository https://github.com/Marie59/champ_blocs commit 0d86db7d42b608c386a54500064f5f9c9d7019a4 ecology parents: diff changeset	639 "Nb.Tethya.aurantium",
89f977a3a256 planemo upload for repository https://github.com/Marie59/champ_blocs commit 0d86db7d42b608c386a54500064f5f9c9d7019a4 ecology parents: diff changeset	640 #"Nb.Spirobranchus.lamarckii.1B",
89f977a3a256 planemo upload for repository https://github.com/Marie59/champ_blocs commit 0d86db7d42b608c386a54500064f5f9c9d7019a4 ecology parents: diff changeset	641 #"Nb.Spirobranchus.lamarckii.2B",
89f977a3a256 planemo upload for repository https://github.com/Marie59/champ_blocs commit 0d86db7d42b608c386a54500064f5f9c9d7019a4 ecology parents: diff changeset	642 #"Nb.Spirobranchus.lamarckii.3B",
89f977a3a256 planemo upload for repository https://github.com/Marie59/champ_blocs commit 0d86db7d42b608c386a54500064f5f9c9d7019a4 ecology parents: diff changeset	643 #"Nb.Spirobranchus.lamarckii.4B",
89f977a3a256 planemo upload for repository https://github.com/Marie59/champ_blocs commit 0d86db7d42b608c386a54500064f5f9c9d7019a4 ecology parents: diff changeset	644 #"Nb.Spirobranchus.lamarckii.5B",
89f977a3a256 planemo upload for repository https://github.com/Marie59/champ_blocs commit 0d86db7d42b608c386a54500064f5f9c9d7019a4 ecology parents: diff changeset	645 "Nb.Spirobranchus.lamarckii.total",
89f977a3a256 planemo upload for repository https://github.com/Marie59/champ_blocs commit 0d86db7d42b608c386a54500064f5f9c9d7019a4 ecology parents: diff changeset	646 #"Nb.spirorbis.1A",
89f977a3a256 planemo upload for repository https://github.com/Marie59/champ_blocs commit 0d86db7d42b608c386a54500064f5f9c9d7019a4 ecology parents: diff changeset	647 #"Nb.spirorbis.2A",
89f977a3a256 planemo upload for repository https://github.com/Marie59/champ_blocs commit 0d86db7d42b608c386a54500064f5f9c9d7019a4 ecology parents: diff changeset	648 #"Nb.spirorbis.3A",
89f977a3a256 planemo upload for repository https://github.com/Marie59/champ_blocs commit 0d86db7d42b608c386a54500064f5f9c9d7019a4 ecology parents: diff changeset	649 #"Nb.spirorbis.4A",
89f977a3a256 planemo upload for repository https://github.com/Marie59/champ_blocs commit 0d86db7d42b608c386a54500064f5f9c9d7019a4 ecology parents: diff changeset	650 #"Nb.spirorbis.5A",
89f977a3a256 planemo upload for repository https://github.com/Marie59/champ_blocs commit 0d86db7d42b608c386a54500064f5f9c9d7019a4 ecology parents: diff changeset	651 "Nb.spirorbis.total",
89f977a3a256 planemo upload for repository https://github.com/Marie59/champ_blocs commit 0d86db7d42b608c386a54500064f5f9c9d7019a4 ecology parents: diff changeset	652 #.."Nb.Crassostrea.gigas",
89f977a3a256 planemo upload for repository https://github.com/Marie59/champ_blocs commit 0d86db7d42b608c386a54500064f5f9c9d7019a4 ecology parents: diff changeset	653 #.."Nb.Ostrea.edulis",
89f977a3a256 planemo upload for repository https://github.com/Marie59/champ_blocs commit 0d86db7d42b608c386a54500064f5f9c9d7019a4 ecology parents: diff changeset	654 #.."X..Mytilus.sp.",
89f977a3a256 planemo upload for repository https://github.com/Marie59/champ_blocs commit 0d86db7d42b608c386a54500064f5f9c9d7019a4 ecology parents: diff changeset	655 #.."X..Hermelles",
89f977a3a256 planemo upload for repository https://github.com/Marie59/champ_blocs commit 0d86db7d42b608c386a54500064f5f9c9d7019a4 ecology parents: diff changeset	656 #.."X..Hydraires",
89f977a3a256 planemo upload for repository https://github.com/Marie59/champ_blocs commit 0d86db7d42b608c386a54500064f5f9c9d7019a4 ecology parents: diff changeset	657 "X..Eponges",
89f977a3a256 planemo upload for repository https://github.com/Marie59/champ_blocs commit 0d86db7d42b608c386a54500064f5f9c9d7019a4 ecology parents: diff changeset	658 "X..Ascidies.Coloniales",
89f977a3a256 planemo upload for repository https://github.com/Marie59/champ_blocs commit 0d86db7d42b608c386a54500064f5f9c9d7019a4 ecology parents: diff changeset	659 "X..Ascidies.Solitaires",
89f977a3a256 planemo upload for repository https://github.com/Marie59/champ_blocs commit 0d86db7d42b608c386a54500064f5f9c9d7019a4 ecology parents: diff changeset	660 "X..Bryozoaires.Dresses",
89f977a3a256 planemo upload for repository https://github.com/Marie59/champ_blocs commit 0d86db7d42b608c386a54500064f5f9c9d7019a4 ecology parents: diff changeset	661 "X..Balanes.Vivantes",
89f977a3a256 planemo upload for repository https://github.com/Marie59/champ_blocs commit 0d86db7d42b608c386a54500064f5f9c9d7019a4 ecology parents: diff changeset	662 #"Commentaires.Avant",
89f977a3a256 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.
89f977a3a256 planemo upload for repository https://github.com/Marie59/champ_blocs commit 0d86db7d42b608c386a54500064f5f9c9d7019a4 ecology parents: diff changeset	664 #"Type.sustrat.observé",
89f977a3a256 planemo upload for repository https://github.com/Marie59/champ_blocs commit 0d86db7d42b608c386a54500064f5f9c9d7019a4 ecology parents: diff changeset	665 #"Commentaires",
89f977a3a256 planemo upload for repository https://github.com/Marie59/champ_blocs commit 0d86db7d42b608c386a54500064f5f9c9d7019a4 ecology parents: diff changeset	666 "Nb.Cancer.pagurus..Tourteau.",
89f977a3a256 planemo upload for repository https://github.com/Marie59/champ_blocs commit 0d86db7d42b608c386a54500064f5f9c9d7019a4 ecology parents: diff changeset	667 "Nb.Necora.puber..Etrille.",
89f977a3a256 planemo upload for repository https://github.com/Marie59/champ_blocs commit 0d86db7d42b608c386a54500064f5f9c9d7019a4 ecology parents: diff changeset	668 "Nb.Carcinus.maenas..Crabe.vert.",
89f977a3a256 planemo upload for repository https://github.com/Marie59/champ_blocs commit 0d86db7d42b608c386a54500064f5f9c9d7019a4 ecology parents: diff changeset	669 "Nb.Nucella.lapilus..Pourpre.",
89f977a3a256 planemo upload for repository https://github.com/Marie59/champ_blocs commit 0d86db7d42b608c386a54500064f5f9c9d7019a4 ecology parents: diff changeset	670 #.."Nb.Eriphia.verrucosa..Crabe.verruqueux.",
89f977a3a256 planemo upload for repository https://github.com/Marie59/champ_blocs commit 0d86db7d42b608c386a54500064f5f9c9d7019a4 ecology parents: diff changeset	671 #.."Nb.Octopus.vulgaris..Poulpe.",
89f977a3a256 planemo upload for repository https://github.com/Marie59/champ_blocs commit 0d86db7d42b608c386a54500064f5f9c9d7019a4 ecology parents: diff changeset	672 "Nb.Galathea..Galathées.",
89f977a3a256 planemo upload for repository https://github.com/Marie59/champ_blocs commit 0d86db7d42b608c386a54500064f5f9c9d7019a4 ecology parents: diff changeset	673 #.."Nb.Paracentrotus.lividus..Oursin.",
89f977a3a256 planemo upload for repository https://github.com/Marie59/champ_blocs commit 0d86db7d42b608c386a54500064f5f9c9d7019a4 ecology parents: diff changeset	674 "Nb.Lophozozymus.incisus..ancien.Xantho.incisus.",
89f977a3a256 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.",
89f977a3a256 planemo upload for repository https://github.com/Marie59/champ_blocs commit 0d86db7d42b608c386a54500064f5f9c9d7019a4 ecology parents: diff changeset	676 "Nb.Haliotis.tuberculata..Ormeau.",
89f977a3a256 planemo upload for repository https://github.com/Marie59/champ_blocs commit 0d86db7d42b608c386a54500064f5f9c9d7019a4 ecology parents: diff changeset	677 #"Nb.Stramonita.haemastoma..Pourpre.bouche.de.sang.",
89f977a3a256 planemo upload for repository https://github.com/Marie59/champ_blocs commit 0d86db7d42b608c386a54500064f5f9c9d7019a4 ecology parents: diff changeset	678 "Nb.Littorina.littorea..Bigorneau.",
89f977a3a256 planemo upload for repository https://github.com/Marie59/champ_blocs commit 0d86db7d42b608c386a54500064f5f9c9d7019a4 ecology parents: diff changeset	679 "Nb.Xantho.pilipes..Xanthe.poilu.",
89f977a3a256 planemo upload for repository https://github.com/Marie59/champ_blocs commit 0d86db7d42b608c386a54500064f5f9c9d7019a4 ecology parents: diff changeset	680 "Nb.Mimachlamys.varia..Pétoncle.noir."
89f977a3a256 planemo upload for repository https://github.com/Marie59/champ_blocs commit 0d86db7d42b608c386a54500064f5f9c9d7019a4 ecology parents: diff changeset	681 )
89f977a3a256 planemo upload for repository https://github.com/Marie59/champ_blocs commit 0d86db7d42b608c386a54500064f5f9c9d7019a4 ecology parents: diff changeset	682 ] <- lapply(bretagne_bm[, c(
89f977a3a256 planemo upload for repository https://github.com/Marie59/champ_blocs commit 0d86db7d42b608c386a54500064f5f9c9d7019a4 ecology parents: diff changeset	683 "X..algues.brunes",
89f977a3a256 planemo upload for repository https://github.com/Marie59/champ_blocs commit 0d86db7d42b608c386a54500064f5f9c9d7019a4 ecology parents: diff changeset	684 "Strate.algues.brunes",
89f977a3a256 planemo upload for repository https://github.com/Marie59/champ_blocs commit 0d86db7d42b608c386a54500064f5f9c9d7019a4 ecology parents: diff changeset	685 "X..algues.rouges",
89f977a3a256 planemo upload for repository https://github.com/Marie59/champ_blocs commit 0d86db7d42b608c386a54500064f5f9c9d7019a4 ecology parents: diff changeset	686 "Strate.algues.rouges",
89f977a3a256 planemo upload for repository https://github.com/Marie59/champ_blocs commit 0d86db7d42b608c386a54500064f5f9c9d7019a4 ecology parents: diff changeset	687 "X..algues.vertes",
89f977a3a256 planemo upload for repository https://github.com/Marie59/champ_blocs commit 0d86db7d42b608c386a54500064f5f9c9d7019a4 ecology parents: diff changeset	688 "Strate.algues.vertes",
89f977a3a256 planemo upload for repository https://github.com/Marie59/champ_blocs commit 0d86db7d42b608c386a54500064f5f9c9d7019a4 ecology parents: diff changeset	689 "X..Cladophora",
89f977a3a256 planemo upload for repository https://github.com/Marie59/champ_blocs commit 0d86db7d42b608c386a54500064f5f9c9d7019a4 ecology parents: diff changeset	690 "X..Lithophyllum",
89f977a3a256 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.
89f977a3a256 planemo upload for repository https://github.com/Marie59/champ_blocs commit 0d86db7d42b608c386a54500064f5f9c9d7019a4 ecology parents: diff changeset	692 #"Type.Sediment",
89f977a3a256 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.
89f977a3a256 planemo upload for repository https://github.com/Marie59/champ_blocs commit 0d86db7d42b608c386a54500064f5f9c9d7019a4 ecology parents: diff changeset	694 "Nb.Littorina.obtusata",
89f977a3a256 planemo upload for repository https://github.com/Marie59/champ_blocs commit 0d86db7d42b608c386a54500064f5f9c9d7019a4 ecology parents: diff changeset	695 "Nb.Gibbula.cineraria",
89f977a3a256 planemo upload for repository https://github.com/Marie59/champ_blocs commit 0d86db7d42b608c386a54500064f5f9c9d7019a4 ecology parents: diff changeset	696 "Nb.Gibbula.pennanti",
89f977a3a256 planemo upload for repository https://github.com/Marie59/champ_blocs commit 0d86db7d42b608c386a54500064f5f9c9d7019a4 ecology parents: diff changeset	697 "Nb.Gibbula.umbilicalis",
89f977a3a256 planemo upload for repository https://github.com/Marie59/champ_blocs commit 0d86db7d42b608c386a54500064f5f9c9d7019a4 ecology parents: diff changeset	698 "Nb.Phallusia.mamillata",
89f977a3a256 planemo upload for repository https://github.com/Marie59/champ_blocs commit 0d86db7d42b608c386a54500064f5f9c9d7019a4 ecology parents: diff changeset	699 "Nb.Tethya.aurantium",
89f977a3a256 planemo upload for repository https://github.com/Marie59/champ_blocs commit 0d86db7d42b608c386a54500064f5f9c9d7019a4 ecology parents: diff changeset	700 #"Nb.Spirobranchus.lamarckii.1B",
89f977a3a256 planemo upload for repository https://github.com/Marie59/champ_blocs commit 0d86db7d42b608c386a54500064f5f9c9d7019a4 ecology parents: diff changeset	701 #"Nb.Spirobranchus.lamarckii.2B",
89f977a3a256 planemo upload for repository https://github.com/Marie59/champ_blocs commit 0d86db7d42b608c386a54500064f5f9c9d7019a4 ecology parents: diff changeset	702 #"Nb.Spirobranchus.lamarckii.3B",
89f977a3a256 planemo upload for repository https://github.com/Marie59/champ_blocs commit 0d86db7d42b608c386a54500064f5f9c9d7019a4 ecology parents: diff changeset	703 #"Nb.Spirobranchus.lamarckii.4B",
89f977a3a256 planemo upload for repository https://github.com/Marie59/champ_blocs commit 0d86db7d42b608c386a54500064f5f9c9d7019a4 ecology parents: diff changeset	704 #"Nb.Spirobranchus.lamarckii.5B",
89f977a3a256 planemo upload for repository https://github.com/Marie59/champ_blocs commit 0d86db7d42b608c386a54500064f5f9c9d7019a4 ecology parents: diff changeset	705 "Nb.Spirobranchus.lamarckii.total",
89f977a3a256 planemo upload for repository https://github.com/Marie59/champ_blocs commit 0d86db7d42b608c386a54500064f5f9c9d7019a4 ecology parents: diff changeset	706 #"Nb.spirorbis.1A",
89f977a3a256 planemo upload for repository https://github.com/Marie59/champ_blocs commit 0d86db7d42b608c386a54500064f5f9c9d7019a4 ecology parents: diff changeset	707 #"Nb.spirorbis.2A",
89f977a3a256 planemo upload for repository https://github.com/Marie59/champ_blocs commit 0d86db7d42b608c386a54500064f5f9c9d7019a4 ecology parents: diff changeset	708 #"Nb.spirorbis.3A",
89f977a3a256 planemo upload for repository https://github.com/Marie59/champ_blocs commit 0d86db7d42b608c386a54500064f5f9c9d7019a4 ecology parents: diff changeset	709 #"Nb.spirorbis.4A",
89f977a3a256 planemo upload for repository https://github.com/Marie59/champ_blocs commit 0d86db7d42b608c386a54500064f5f9c9d7019a4 ecology parents: diff changeset	710 #"Nb.spirorbis.5A",
89f977a3a256 planemo upload for repository https://github.com/Marie59/champ_blocs commit 0d86db7d42b608c386a54500064f5f9c9d7019a4 ecology parents: diff changeset	711 "Nb.spirorbis.total",
89f977a3a256 planemo upload for repository https://github.com/Marie59/champ_blocs commit 0d86db7d42b608c386a54500064f5f9c9d7019a4 ecology parents: diff changeset	712 #.."Nb.Crassostrea.gigas",
89f977a3a256 planemo upload for repository https://github.com/Marie59/champ_blocs commit 0d86db7d42b608c386a54500064f5f9c9d7019a4 ecology parents: diff changeset	713 #.."Nb.Ostrea.edulis",
89f977a3a256 planemo upload for repository https://github.com/Marie59/champ_blocs commit 0d86db7d42b608c386a54500064f5f9c9d7019a4 ecology parents: diff changeset	714 #.."X..Mytilus.sp.",
89f977a3a256 planemo upload for repository https://github.com/Marie59/champ_blocs commit 0d86db7d42b608c386a54500064f5f9c9d7019a4 ecology parents: diff changeset	715 #.."X..Hermelles",
89f977a3a256 planemo upload for repository https://github.com/Marie59/champ_blocs commit 0d86db7d42b608c386a54500064f5f9c9d7019a4 ecology parents: diff changeset	716 #.."X..Hydraires",
89f977a3a256 planemo upload for repository https://github.com/Marie59/champ_blocs commit 0d86db7d42b608c386a54500064f5f9c9d7019a4 ecology parents: diff changeset	717 "X..Eponges",
89f977a3a256 planemo upload for repository https://github.com/Marie59/champ_blocs commit 0d86db7d42b608c386a54500064f5f9c9d7019a4 ecology parents: diff changeset	718 "X..Ascidies.Coloniales",
89f977a3a256 planemo upload for repository https://github.com/Marie59/champ_blocs commit 0d86db7d42b608c386a54500064f5f9c9d7019a4 ecology parents: diff changeset	719 "X..Ascidies.Solitaires",
89f977a3a256 planemo upload for repository https://github.com/Marie59/champ_blocs commit 0d86db7d42b608c386a54500064f5f9c9d7019a4 ecology parents: diff changeset	720 "X..Bryozoaires.Dresses",
89f977a3a256 planemo upload for repository https://github.com/Marie59/champ_blocs commit 0d86db7d42b608c386a54500064f5f9c9d7019a4 ecology parents: diff changeset	721 "X..Balanes.Vivantes",
89f977a3a256 planemo upload for repository https://github.com/Marie59/champ_blocs commit 0d86db7d42b608c386a54500064f5f9c9d7019a4 ecology parents: diff changeset	722 #"Commentaires.Avant",
89f977a3a256 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.
89f977a3a256 planemo upload for repository https://github.com/Marie59/champ_blocs commit 0d86db7d42b608c386a54500064f5f9c9d7019a4 ecology parents: diff changeset	724 #"Type.sustrat.observé",
89f977a3a256 planemo upload for repository https://github.com/Marie59/champ_blocs commit 0d86db7d42b608c386a54500064f5f9c9d7019a4 ecology parents: diff changeset	725 #"Commentaires",
89f977a3a256 planemo upload for repository https://github.com/Marie59/champ_blocs commit 0d86db7d42b608c386a54500064f5f9c9d7019a4 ecology parents: diff changeset	726 "Nb.Cancer.pagurus..Tourteau.",
89f977a3a256 planemo upload for repository https://github.com/Marie59/champ_blocs commit 0d86db7d42b608c386a54500064f5f9c9d7019a4 ecology parents: diff changeset	727 "Nb.Necora.puber..Etrille.",
89f977a3a256 planemo upload for repository https://github.com/Marie59/champ_blocs commit 0d86db7d42b608c386a54500064f5f9c9d7019a4 ecology parents: diff changeset	728 "Nb.Carcinus.maenas..Crabe.vert.",
89f977a3a256 planemo upload for repository https://github.com/Marie59/champ_blocs commit 0d86db7d42b608c386a54500064f5f9c9d7019a4 ecology parents: diff changeset	729 "Nb.Nucella.lapilus..Pourpre.",
89f977a3a256 planemo upload for repository https://github.com/Marie59/champ_blocs commit 0d86db7d42b608c386a54500064f5f9c9d7019a4 ecology parents: diff changeset	730 #.."Nb.Eriphia.verrucosa..Crabe.verruqueux.",
89f977a3a256 planemo upload for repository https://github.com/Marie59/champ_blocs commit 0d86db7d42b608c386a54500064f5f9c9d7019a4 ecology parents: diff changeset	731 #.."Nb.Octopus.vulgaris..Poulpe.",
89f977a3a256 planemo upload for repository https://github.com/Marie59/champ_blocs commit 0d86db7d42b608c386a54500064f5f9c9d7019a4 ecology parents: diff changeset	732 "Nb.Galathea..Galathées.",
89f977a3a256 planemo upload for repository https://github.com/Marie59/champ_blocs commit 0d86db7d42b608c386a54500064f5f9c9d7019a4 ecology parents: diff changeset	733 #.."Nb.Paracentrotus.lividus..Oursin.",
89f977a3a256 planemo upload for repository https://github.com/Marie59/champ_blocs commit 0d86db7d42b608c386a54500064f5f9c9d7019a4 ecology parents: diff changeset	734 "Nb.Lophozozymus.incisus..ancien.Xantho.incisus.",
89f977a3a256 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.",
89f977a3a256 planemo upload for repository https://github.com/Marie59/champ_blocs commit 0d86db7d42b608c386a54500064f5f9c9d7019a4 ecology parents: diff changeset	736 "Nb.Haliotis.tuberculata..Ormeau.",
89f977a3a256 planemo upload for repository https://github.com/Marie59/champ_blocs commit 0d86db7d42b608c386a54500064f5f9c9d7019a4 ecology parents: diff changeset	737 #"Nb.Stramonita.haemastoma..Pourpre.bouche.de.sang.",
89f977a3a256 planemo upload for repository https://github.com/Marie59/champ_blocs commit 0d86db7d42b608c386a54500064f5f9c9d7019a4 ecology parents: diff changeset	738 "Nb.Littorina.littorea..Bigorneau.",
89f977a3a256 planemo upload for repository https://github.com/Marie59/champ_blocs commit 0d86db7d42b608c386a54500064f5f9c9d7019a4 ecology parents: diff changeset	739 "Nb.Xantho.pilipes..Xanthe.poilu.",
89f977a3a256 planemo upload for repository https://github.com/Marie59/champ_blocs commit 0d86db7d42b608c386a54500064f5f9c9d7019a4 ecology parents: diff changeset	740 "Nb.Mimachlamys.varia..Pétoncle.noir."
89f977a3a256 planemo upload for repository https://github.com/Marie59/champ_blocs commit 0d86db7d42b608c386a54500064f5f9c9d7019a4 ecology parents: diff changeset	741 )
89f977a3a256 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))
89f977a3a256 planemo upload for repository https://github.com/Marie59/champ_blocs commit 0d86db7d42b608c386a54500064f5f9c9d7019a4 ecology parents: diff changeset	743
89f977a3a256 planemo upload for repository https://github.com/Marie59/champ_blocs commit 0d86db7d42b608c386a54500064f5f9c9d7019a4 ecology parents: diff changeset	744
89f977a3a256 planemo upload for repository https://github.com/Marie59/champ_blocs commit 0d86db7d42b608c386a54500064f5f9c9d7019a4 ecology parents: diff changeset	745 # bretagne_bf
89f977a3a256 planemo upload for repository https://github.com/Marie59/champ_blocs commit 0d86db7d42b608c386a54500064f5f9c9d7019a4 ecology parents: diff changeset	746 bretagne_bf[, c(
89f977a3a256 planemo upload for repository https://github.com/Marie59/champ_blocs commit 0d86db7d42b608c386a54500064f5f9c9d7019a4 ecology parents: diff changeset	747 "X..algues.brunes",
89f977a3a256 planemo upload for repository https://github.com/Marie59/champ_blocs commit 0d86db7d42b608c386a54500064f5f9c9d7019a4 ecology parents: diff changeset	748 "Strate.algues.brunes",
89f977a3a256 planemo upload for repository https://github.com/Marie59/champ_blocs commit 0d86db7d42b608c386a54500064f5f9c9d7019a4 ecology parents: diff changeset	749 "X..algues.rouges",
89f977a3a256 planemo upload for repository https://github.com/Marie59/champ_blocs commit 0d86db7d42b608c386a54500064f5f9c9d7019a4 ecology parents: diff changeset	750 "Strate.algues.rouges",
89f977a3a256 planemo upload for repository https://github.com/Marie59/champ_blocs commit 0d86db7d42b608c386a54500064f5f9c9d7019a4 ecology parents: diff changeset	751 "X..algues.vertes",
89f977a3a256 planemo upload for repository https://github.com/Marie59/champ_blocs commit 0d86db7d42b608c386a54500064f5f9c9d7019a4 ecology parents: diff changeset	752 "Strate.algues.vertes",
89f977a3a256 planemo upload for repository https://github.com/Marie59/champ_blocs commit 0d86db7d42b608c386a54500064f5f9c9d7019a4 ecology parents: diff changeset	753 "X..Cladophora",
89f977a3a256 planemo upload for repository https://github.com/Marie59/champ_blocs commit 0d86db7d42b608c386a54500064f5f9c9d7019a4 ecology parents: diff changeset	754 "X..Lithophyllum",
89f977a3a256 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.
89f977a3a256 planemo upload for repository https://github.com/Marie59/champ_blocs commit 0d86db7d42b608c386a54500064f5f9c9d7019a4 ecology parents: diff changeset	756 #"Type.Sediment",
89f977a3a256 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.
89f977a3a256 planemo upload for repository https://github.com/Marie59/champ_blocs commit 0d86db7d42b608c386a54500064f5f9c9d7019a4 ecology parents: diff changeset	758 "Nb.Littorina.obtusata",
89f977a3a256 planemo upload for repository https://github.com/Marie59/champ_blocs commit 0d86db7d42b608c386a54500064f5f9c9d7019a4 ecology parents: diff changeset	759 "Nb.Gibbula.cineraria",
89f977a3a256 planemo upload for repository https://github.com/Marie59/champ_blocs commit 0d86db7d42b608c386a54500064f5f9c9d7019a4 ecology parents: diff changeset	760 "Nb.Gibbula.pennanti",
89f977a3a256 planemo upload for repository https://github.com/Marie59/champ_blocs commit 0d86db7d42b608c386a54500064f5f9c9d7019a4 ecology parents: diff changeset	761 "Nb.Gibbula.umbilicalis",
89f977a3a256 planemo upload for repository https://github.com/Marie59/champ_blocs commit 0d86db7d42b608c386a54500064f5f9c9d7019a4 ecology parents: diff changeset	762 "Nb.Phallusia.mamillata",
89f977a3a256 planemo upload for repository https://github.com/Marie59/champ_blocs commit 0d86db7d42b608c386a54500064f5f9c9d7019a4 ecology parents: diff changeset	763 "Nb.Tethya.aurantium",
89f977a3a256 planemo upload for repository https://github.com/Marie59/champ_blocs commit 0d86db7d42b608c386a54500064f5f9c9d7019a4 ecology parents: diff changeset	764 #"Nb.Spirobranchus.lamarckii.1B",
89f977a3a256 planemo upload for repository https://github.com/Marie59/champ_blocs commit 0d86db7d42b608c386a54500064f5f9c9d7019a4 ecology parents: diff changeset	765 #"Nb.Spirobranchus.lamarckii.2B",
89f977a3a256 planemo upload for repository https://github.com/Marie59/champ_blocs commit 0d86db7d42b608c386a54500064f5f9c9d7019a4 ecology parents: diff changeset	766 #"Nb.Spirobranchus.lamarckii.3B",
89f977a3a256 planemo upload for repository https://github.com/Marie59/champ_blocs commit 0d86db7d42b608c386a54500064f5f9c9d7019a4 ecology parents: diff changeset	767 #"Nb.Spirobranchus.lamarckii.4B",
89f977a3a256 planemo upload for repository https://github.com/Marie59/champ_blocs commit 0d86db7d42b608c386a54500064f5f9c9d7019a4 ecology parents: diff changeset	768 #"Nb.Spirobranchus.lamarckii.5B",
89f977a3a256 planemo upload for repository https://github.com/Marie59/champ_blocs commit 0d86db7d42b608c386a54500064f5f9c9d7019a4 ecology parents: diff changeset	769 "Nb.Spirobranchus.lamarckii.total",
89f977a3a256 planemo upload for repository https://github.com/Marie59/champ_blocs commit 0d86db7d42b608c386a54500064f5f9c9d7019a4 ecology parents: diff changeset	770 #"Nb.spirorbis.1A",
89f977a3a256 planemo upload for repository https://github.com/Marie59/champ_blocs commit 0d86db7d42b608c386a54500064f5f9c9d7019a4 ecology parents: diff changeset	771 #"Nb.spirorbis.2A",
89f977a3a256 planemo upload for repository https://github.com/Marie59/champ_blocs commit 0d86db7d42b608c386a54500064f5f9c9d7019a4 ecology parents: diff changeset	772 #"Nb.spirorbis.3A",
89f977a3a256 planemo upload for repository https://github.com/Marie59/champ_blocs commit 0d86db7d42b608c386a54500064f5f9c9d7019a4 ecology parents: diff changeset	773 #"Nb.spirorbis.4A",
89f977a3a256 planemo upload for repository https://github.com/Marie59/champ_blocs commit 0d86db7d42b608c386a54500064f5f9c9d7019a4 ecology parents: diff changeset	774 #"Nb.spirorbis.5A",
89f977a3a256 planemo upload for repository https://github.com/Marie59/champ_blocs commit 0d86db7d42b608c386a54500064f5f9c9d7019a4 ecology parents: diff changeset	775 "Nb.spirorbis.total",
89f977a3a256 planemo upload for repository https://github.com/Marie59/champ_blocs commit 0d86db7d42b608c386a54500064f5f9c9d7019a4 ecology parents: diff changeset	776 #.."Nb.Crassostrea.gigas",
89f977a3a256 planemo upload for repository https://github.com/Marie59/champ_blocs commit 0d86db7d42b608c386a54500064f5f9c9d7019a4 ecology parents: diff changeset	777 #.."Nb.Ostrea.edulis",
89f977a3a256 planemo upload for repository https://github.com/Marie59/champ_blocs commit 0d86db7d42b608c386a54500064f5f9c9d7019a4 ecology parents: diff changeset	778 #.."X..Mytilus.sp.",
89f977a3a256 planemo upload for repository https://github.com/Marie59/champ_blocs commit 0d86db7d42b608c386a54500064f5f9c9d7019a4 ecology parents: diff changeset	779 #.."X..Hermelles",
89f977a3a256 planemo upload for repository https://github.com/Marie59/champ_blocs commit 0d86db7d42b608c386a54500064f5f9c9d7019a4 ecology parents: diff changeset	780 #.."X..Hydraires",
89f977a3a256 planemo upload for repository https://github.com/Marie59/champ_blocs commit 0d86db7d42b608c386a54500064f5f9c9d7019a4 ecology parents: diff changeset	781 "X..Eponges",
89f977a3a256 planemo upload for repository https://github.com/Marie59/champ_blocs commit 0d86db7d42b608c386a54500064f5f9c9d7019a4 ecology parents: diff changeset	782 "X..Ascidies.Coloniales",
89f977a3a256 planemo upload for repository https://github.com/Marie59/champ_blocs commit 0d86db7d42b608c386a54500064f5f9c9d7019a4 ecology parents: diff changeset	783 "X..Ascidies.Solitaires",
89f977a3a256 planemo upload for repository https://github.com/Marie59/champ_blocs commit 0d86db7d42b608c386a54500064f5f9c9d7019a4 ecology parents: diff changeset	784 "X..Bryozoaires.Dresses",
89f977a3a256 planemo upload for repository https://github.com/Marie59/champ_blocs commit 0d86db7d42b608c386a54500064f5f9c9d7019a4 ecology parents: diff changeset	785 "X..Balanes.Vivantes",
89f977a3a256 planemo upload for repository https://github.com/Marie59/champ_blocs commit 0d86db7d42b608c386a54500064f5f9c9d7019a4 ecology parents: diff changeset	786 #"Commentaires.Avant",
89f977a3a256 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.
89f977a3a256 planemo upload for repository https://github.com/Marie59/champ_blocs commit 0d86db7d42b608c386a54500064f5f9c9d7019a4 ecology parents: diff changeset	788 #"Type.sustrat.observé",
89f977a3a256 planemo upload for repository https://github.com/Marie59/champ_blocs commit 0d86db7d42b608c386a54500064f5f9c9d7019a4 ecology parents: diff changeset	789 #"Commentaires",
89f977a3a256 planemo upload for repository https://github.com/Marie59/champ_blocs commit 0d86db7d42b608c386a54500064f5f9c9d7019a4 ecology parents: diff changeset	790 #."Nb.Cancer.pagurus..Tourteau.",
89f977a3a256 planemo upload for repository https://github.com/Marie59/champ_blocs commit 0d86db7d42b608c386a54500064f5f9c9d7019a4 ecology parents: diff changeset	791 #.."Nb.Necora.puber..Etrille.",
89f977a3a256 planemo upload for repository https://github.com/Marie59/champ_blocs commit 0d86db7d42b608c386a54500064f5f9c9d7019a4 ecology parents: diff changeset	792 #."Nb.Carcinus.maenas..Crabe.vert.",
89f977a3a256 planemo upload for repository https://github.com/Marie59/champ_blocs commit 0d86db7d42b608c386a54500064f5f9c9d7019a4 ecology parents: diff changeset	793 #."Nb.Nucella.lapilus..Pourpre.",
89f977a3a256 planemo upload for repository https://github.com/Marie59/champ_blocs commit 0d86db7d42b608c386a54500064f5f9c9d7019a4 ecology parents: diff changeset	794 #.."Nb.Eriphia.verrucosa..Crabe.verruqueux.",
89f977a3a256 planemo upload for repository https://github.com/Marie59/champ_blocs commit 0d86db7d42b608c386a54500064f5f9c9d7019a4 ecology parents: diff changeset	795 #.."Nb.Octopus.vulgaris..Poulpe.",
89f977a3a256 planemo upload for repository https://github.com/Marie59/champ_blocs commit 0d86db7d42b608c386a54500064f5f9c9d7019a4 ecology parents: diff changeset	796 #."Nb.Galathea..Galathées.",
89f977a3a256 planemo upload for repository https://github.com/Marie59/champ_blocs commit 0d86db7d42b608c386a54500064f5f9c9d7019a4 ecology parents: diff changeset	797 #.."Nb.Paracentrotus.lividus..Oursin.",
89f977a3a256 planemo upload for repository https://github.com/Marie59/champ_blocs commit 0d86db7d42b608c386a54500064f5f9c9d7019a4 ecology parents: diff changeset	798 #."Nb.Lophozozymus.incisus..ancien.Xantho.incisus.",
89f977a3a256 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.",
89f977a3a256 planemo upload for repository https://github.com/Marie59/champ_blocs commit 0d86db7d42b608c386a54500064f5f9c9d7019a4 ecology parents: diff changeset	800 #."Nb.Haliotis.tuberculata..Ormeau.",
89f977a3a256 planemo upload for repository https://github.com/Marie59/champ_blocs commit 0d86db7d42b608c386a54500064f5f9c9d7019a4 ecology parents: diff changeset	801 #."Nb.Stramonita.haemastoma..Pourpre.bouche.de.sang.",
89f977a3a256 planemo upload for repository https://github.com/Marie59/champ_blocs commit 0d86db7d42b608c386a54500064f5f9c9d7019a4 ecology parents: diff changeset	802 #."Nb.Littorina.littorea..Bigorneau.",
89f977a3a256 planemo upload for repository https://github.com/Marie59/champ_blocs commit 0d86db7d42b608c386a54500064f5f9c9d7019a4 ecology parents: diff changeset	803 #."Nb.Xantho.pilipes..Xanthe.poilu.",
89f977a3a256 planemo upload for repository https://github.com/Marie59/champ_blocs commit 0d86db7d42b608c386a54500064f5f9c9d7019a4 ecology parents: diff changeset	804 #."Nb.Mimachlamys.varia..Pétoncle.noir."
89f977a3a256 planemo upload for repository https://github.com/Marie59/champ_blocs commit 0d86db7d42b608c386a54500064f5f9c9d7019a4 ecology parents: diff changeset	805 )
89f977a3a256 planemo upload for repository https://github.com/Marie59/champ_blocs commit 0d86db7d42b608c386a54500064f5f9c9d7019a4 ecology parents: diff changeset	806 ] <- lapply(bretagne_bf[, c(
89f977a3a256 planemo upload for repository https://github.com/Marie59/champ_blocs commit 0d86db7d42b608c386a54500064f5f9c9d7019a4 ecology parents: diff changeset	807 "X..algues.brunes",
89f977a3a256 planemo upload for repository https://github.com/Marie59/champ_blocs commit 0d86db7d42b608c386a54500064f5f9c9d7019a4 ecology parents: diff changeset	808 "Strate.algues.brunes",
89f977a3a256 planemo upload for repository https://github.com/Marie59/champ_blocs commit 0d86db7d42b608c386a54500064f5f9c9d7019a4 ecology parents: diff changeset	809 "X..algues.rouges",
89f977a3a256 planemo upload for repository https://github.com/Marie59/champ_blocs commit 0d86db7d42b608c386a54500064f5f9c9d7019a4 ecology parents: diff changeset	810 "Strate.algues.rouges",
89f977a3a256 planemo upload for repository https://github.com/Marie59/champ_blocs commit 0d86db7d42b608c386a54500064f5f9c9d7019a4 ecology parents: diff changeset	811 "X..algues.vertes",
89f977a3a256 planemo upload for repository https://github.com/Marie59/champ_blocs commit 0d86db7d42b608c386a54500064f5f9c9d7019a4 ecology parents: diff changeset	812 "Strate.algues.vertes",
89f977a3a256 planemo upload for repository https://github.com/Marie59/champ_blocs commit 0d86db7d42b608c386a54500064f5f9c9d7019a4 ecology parents: diff changeset	813 "X..Cladophora",
89f977a3a256 planemo upload for repository https://github.com/Marie59/champ_blocs commit 0d86db7d42b608c386a54500064f5f9c9d7019a4 ecology parents: diff changeset	814 "X..Lithophyllum",
89f977a3a256 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.
89f977a3a256 planemo upload for repository https://github.com/Marie59/champ_blocs commit 0d86db7d42b608c386a54500064f5f9c9d7019a4 ecology parents: diff changeset	816 #"Type.Sediment",
89f977a3a256 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.
89f977a3a256 planemo upload for repository https://github.com/Marie59/champ_blocs commit 0d86db7d42b608c386a54500064f5f9c9d7019a4 ecology parents: diff changeset	818 "Nb.Littorina.obtusata",
89f977a3a256 planemo upload for repository https://github.com/Marie59/champ_blocs commit 0d86db7d42b608c386a54500064f5f9c9d7019a4 ecology parents: diff changeset	819 "Nb.Gibbula.cineraria",
89f977a3a256 planemo upload for repository https://github.com/Marie59/champ_blocs commit 0d86db7d42b608c386a54500064f5f9c9d7019a4 ecology parents: diff changeset	820 "Nb.Gibbula.pennanti",
89f977a3a256 planemo upload for repository https://github.com/Marie59/champ_blocs commit 0d86db7d42b608c386a54500064f5f9c9d7019a4 ecology parents: diff changeset	821 "Nb.Gibbula.umbilicalis",
89f977a3a256 planemo upload for repository https://github.com/Marie59/champ_blocs commit 0d86db7d42b608c386a54500064f5f9c9d7019a4 ecology parents: diff changeset	822 "Nb.Phallusia.mamillata",
89f977a3a256 planemo upload for repository https://github.com/Marie59/champ_blocs commit 0d86db7d42b608c386a54500064f5f9c9d7019a4 ecology parents: diff changeset	823 "Nb.Tethya.aurantium",
89f977a3a256 planemo upload for repository https://github.com/Marie59/champ_blocs commit 0d86db7d42b608c386a54500064f5f9c9d7019a4 ecology parents: diff changeset	824 #"Nb.Spirobranchus.lamarckii.1B",
89f977a3a256 planemo upload for repository https://github.com/Marie59/champ_blocs commit 0d86db7d42b608c386a54500064f5f9c9d7019a4 ecology parents: diff changeset	825 #"Nb.Spirobranchus.lamarckii.2B",
89f977a3a256 planemo upload for repository https://github.com/Marie59/champ_blocs commit 0d86db7d42b608c386a54500064f5f9c9d7019a4 ecology parents: diff changeset	826 #"Nb.Spirobranchus.lamarckii.3B",
89f977a3a256 planemo upload for repository https://github.com/Marie59/champ_blocs commit 0d86db7d42b608c386a54500064f5f9c9d7019a4 ecology parents: diff changeset	827 #"Nb.Spirobranchus.lamarckii.4B",
89f977a3a256 planemo upload for repository https://github.com/Marie59/champ_blocs commit 0d86db7d42b608c386a54500064f5f9c9d7019a4 ecology parents: diff changeset	828 #"Nb.Spirobranchus.lamarckii.5B",
89f977a3a256 planemo upload for repository https://github.com/Marie59/champ_blocs commit 0d86db7d42b608c386a54500064f5f9c9d7019a4 ecology parents: diff changeset	829 "Nb.Spirobranchus.lamarckii.total",
89f977a3a256 planemo upload for repository https://github.com/Marie59/champ_blocs commit 0d86db7d42b608c386a54500064f5f9c9d7019a4 ecology parents: diff changeset	830 #"Nb.spirorbis.1A",
89f977a3a256 planemo upload for repository https://github.com/Marie59/champ_blocs commit 0d86db7d42b608c386a54500064f5f9c9d7019a4 ecology parents: diff changeset	831 #"Nb.spirorbis.2A",
89f977a3a256 planemo upload for repository https://github.com/Marie59/champ_blocs commit 0d86db7d42b608c386a54500064f5f9c9d7019a4 ecology parents: diff changeset	832 #"Nb.spirorbis.3A",
89f977a3a256 planemo upload for repository https://github.com/Marie59/champ_blocs commit 0d86db7d42b608c386a54500064f5f9c9d7019a4 ecology parents: diff changeset	833 #"Nb.spirorbis.4A",
89f977a3a256 planemo upload for repository https://github.com/Marie59/champ_blocs commit 0d86db7d42b608c386a54500064f5f9c9d7019a4 ecology parents: diff changeset	834 #"Nb.spirorbis.5A",
89f977a3a256 planemo upload for repository https://github.com/Marie59/champ_blocs commit 0d86db7d42b608c386a54500064f5f9c9d7019a4 ecology parents: diff changeset	835 "Nb.spirorbis.total",
89f977a3a256 planemo upload for repository https://github.com/Marie59/champ_blocs commit 0d86db7d42b608c386a54500064f5f9c9d7019a4 ecology parents: diff changeset	836 #.."Nb.Crassostrea.gigas",
89f977a3a256 planemo upload for repository https://github.com/Marie59/champ_blocs commit 0d86db7d42b608c386a54500064f5f9c9d7019a4 ecology parents: diff changeset	837 #.."Nb.Ostrea.edulis",
89f977a3a256 planemo upload for repository https://github.com/Marie59/champ_blocs commit 0d86db7d42b608c386a54500064f5f9c9d7019a4 ecology parents: diff changeset	838 #.."X..Mytilus.sp.",
89f977a3a256 planemo upload for repository https://github.com/Marie59/champ_blocs commit 0d86db7d42b608c386a54500064f5f9c9d7019a4 ecology parents: diff changeset	839 #.."X..Hermelles",
89f977a3a256 planemo upload for repository https://github.com/Marie59/champ_blocs commit 0d86db7d42b608c386a54500064f5f9c9d7019a4 ecology parents: diff changeset	840 #.."X..Hydraires",
89f977a3a256 planemo upload for repository https://github.com/Marie59/champ_blocs commit 0d86db7d42b608c386a54500064f5f9c9d7019a4 ecology parents: diff changeset	841 "X..Eponges",
89f977a3a256 planemo upload for repository https://github.com/Marie59/champ_blocs commit 0d86db7d42b608c386a54500064f5f9c9d7019a4 ecology parents: diff changeset	842 "X..Ascidies.Coloniales",
89f977a3a256 planemo upload for repository https://github.com/Marie59/champ_blocs commit 0d86db7d42b608c386a54500064f5f9c9d7019a4 ecology parents: diff changeset	843 "X..Ascidies.Solitaires",
89f977a3a256 planemo upload for repository https://github.com/Marie59/champ_blocs commit 0d86db7d42b608c386a54500064f5f9c9d7019a4 ecology parents: diff changeset	844 "X..Bryozoaires.Dresses",
89f977a3a256 planemo upload for repository https://github.com/Marie59/champ_blocs commit 0d86db7d42b608c386a54500064f5f9c9d7019a4 ecology parents: diff changeset	845 "X..Balanes.Vivantes",
89f977a3a256 planemo upload for repository https://github.com/Marie59/champ_blocs commit 0d86db7d42b608c386a54500064f5f9c9d7019a4 ecology parents: diff changeset	846 #"Commentaires.Avant",
89f977a3a256 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.
89f977a3a256 planemo upload for repository https://github.com/Marie59/champ_blocs commit 0d86db7d42b608c386a54500064f5f9c9d7019a4 ecology parents: diff changeset	848 #"Type.sustrat.observé",
89f977a3a256 planemo upload for repository https://github.com/Marie59/champ_blocs commit 0d86db7d42b608c386a54500064f5f9c9d7019a4 ecology parents: diff changeset	849 #"Commentaires",
89f977a3a256 planemo upload for repository https://github.com/Marie59/champ_blocs commit 0d86db7d42b608c386a54500064f5f9c9d7019a4 ecology parents: diff changeset	850 #."Nb.Cancer.pagurus..Tourteau.",
89f977a3a256 planemo upload for repository https://github.com/Marie59/champ_blocs commit 0d86db7d42b608c386a54500064f5f9c9d7019a4 ecology parents: diff changeset	851 #.."Nb.Necora.puber..Etrille.",
89f977a3a256 planemo upload for repository https://github.com/Marie59/champ_blocs commit 0d86db7d42b608c386a54500064f5f9c9d7019a4 ecology parents: diff changeset	852 #."Nb.Carcinus.maenas..Crabe.vert.",
89f977a3a256 planemo upload for repository https://github.com/Marie59/champ_blocs commit 0d86db7d42b608c386a54500064f5f9c9d7019a4 ecology parents: diff changeset	853 #."Nb.Nucella.lapilus..Pourpre.",
89f977a3a256 planemo upload for repository https://github.com/Marie59/champ_blocs commit 0d86db7d42b608c386a54500064f5f9c9d7019a4 ecology parents: diff changeset	854 #.."Nb.Eriphia.verrucosa..Crabe.verruqueux.",
89f977a3a256 planemo upload for repository https://github.com/Marie59/champ_blocs commit 0d86db7d42b608c386a54500064f5f9c9d7019a4 ecology parents: diff changeset	855 #.."Nb.Octopus.vulgaris..Poulpe.",
89f977a3a256 planemo upload for repository https://github.com/Marie59/champ_blocs commit 0d86db7d42b608c386a54500064f5f9c9d7019a4 ecology parents: diff changeset	856 #."Nb.Galathea..Galathées.",
89f977a3a256 planemo upload for repository https://github.com/Marie59/champ_blocs commit 0d86db7d42b608c386a54500064f5f9c9d7019a4 ecology parents: diff changeset	857 #.."Nb.Paracentrotus.lividus..Oursin.",
89f977a3a256 planemo upload for repository https://github.com/Marie59/champ_blocs commit 0d86db7d42b608c386a54500064f5f9c9d7019a4 ecology parents: diff changeset	858 #."Nb.Lophozozymus.incisus..ancien.Xantho.incisus.",
89f977a3a256 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.",
89f977a3a256 planemo upload for repository https://github.com/Marie59/champ_blocs commit 0d86db7d42b608c386a54500064f5f9c9d7019a4 ecology parents: diff changeset	860 #."Nb.Haliotis.tuberculata..Ormeau.",
89f977a3a256 planemo upload for repository https://github.com/Marie59/champ_blocs commit 0d86db7d42b608c386a54500064f5f9c9d7019a4 ecology parents: diff changeset	861 #."Nb.Stramonita.haemastoma..Pourpre.bouche.de.sang.",
89f977a3a256 planemo upload for repository https://github.com/Marie59/champ_blocs commit 0d86db7d42b608c386a54500064f5f9c9d7019a4 ecology parents: diff changeset	862 #."Nb.Littorina.littorea..Bigorneau.",
89f977a3a256 planemo upload for repository https://github.com/Marie59/champ_blocs commit 0d86db7d42b608c386a54500064f5f9c9d7019a4 ecology parents: diff changeset	863 #."Nb.Xantho.pilipes..Xanthe.poilu.",
89f977a3a256 planemo upload for repository https://github.com/Marie59/champ_blocs commit 0d86db7d42b608c386a54500064f5f9c9d7019a4 ecology parents: diff changeset	864 #."Nb.Mimachlamys.varia..Pétoncle.noir."
89f977a3a256 planemo upload for repository https://github.com/Marie59/champ_blocs commit 0d86db7d42b608c386a54500064f5f9c9d7019a4 ecology parents: diff changeset	865 )
89f977a3a256 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))
89f977a3a256 planemo upload for repository https://github.com/Marie59/champ_blocs commit 0d86db7d42b608c386a54500064f5f9c9d7019a4 ecology parents: diff changeset	867
89f977a3a256 planemo upload for repository https://github.com/Marie59/champ_blocs commit 0d86db7d42b608c386a54500064f5f9c9d7019a4 ecology parents: diff changeset	868
89f977a3a256 planemo upload for repository https://github.com/Marie59/champ_blocs commit 0d86db7d42b608c386a54500064f5f9c9d7019a4 ecology parents: diff changeset	869 # egmp_basq_bm
89f977a3a256 planemo upload for repository https://github.com/Marie59/champ_blocs commit 0d86db7d42b608c386a54500064f5f9c9d7019a4 ecology parents: diff changeset	870 egmp_basq_bm[, c(
89f977a3a256 planemo upload for repository https://github.com/Marie59/champ_blocs commit 0d86db7d42b608c386a54500064f5f9c9d7019a4 ecology parents: diff changeset	871 "X..algues.brunes",
89f977a3a256 planemo upload for repository https://github.com/Marie59/champ_blocs commit 0d86db7d42b608c386a54500064f5f9c9d7019a4 ecology parents: diff changeset	872 "Strate.algues.brunes",
89f977a3a256 planemo upload for repository https://github.com/Marie59/champ_blocs commit 0d86db7d42b608c386a54500064f5f9c9d7019a4 ecology parents: diff changeset	873 "X..algues.rouges",
89f977a3a256 planemo upload for repository https://github.com/Marie59/champ_blocs commit 0d86db7d42b608c386a54500064f5f9c9d7019a4 ecology parents: diff changeset	874 "Strate.algues.rouges",
89f977a3a256 planemo upload for repository https://github.com/Marie59/champ_blocs commit 0d86db7d42b608c386a54500064f5f9c9d7019a4 ecology parents: diff changeset	875 "X..algues.vertes",
89f977a3a256 planemo upload for repository https://github.com/Marie59/champ_blocs commit 0d86db7d42b608c386a54500064f5f9c9d7019a4 ecology parents: diff changeset	876 "Strate.algues.vertes",
89f977a3a256 planemo upload for repository https://github.com/Marie59/champ_blocs commit 0d86db7d42b608c386a54500064f5f9c9d7019a4 ecology parents: diff changeset	877 "X..Cladophora",
89f977a3a256 planemo upload for repository https://github.com/Marie59/champ_blocs commit 0d86db7d42b608c386a54500064f5f9c9d7019a4 ecology parents: diff changeset	878 "X..Lithophyllum",
89f977a3a256 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.
89f977a3a256 planemo upload for repository https://github.com/Marie59/champ_blocs commit 0d86db7d42b608c386a54500064f5f9c9d7019a4 ecology parents: diff changeset	880 #"Type.Sediment",
89f977a3a256 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.
89f977a3a256 planemo upload for repository https://github.com/Marie59/champ_blocs commit 0d86db7d42b608c386a54500064f5f9c9d7019a4 ecology parents: diff changeset	882 "Nb.Littorina.obtusata",
89f977a3a256 planemo upload for repository https://github.com/Marie59/champ_blocs commit 0d86db7d42b608c386a54500064f5f9c9d7019a4 ecology parents: diff changeset	883 "Nb.Gibbula.cineraria",
89f977a3a256 planemo upload for repository https://github.com/Marie59/champ_blocs commit 0d86db7d42b608c386a54500064f5f9c9d7019a4 ecology parents: diff changeset	884 "Nb.Gibbula.pennanti",
89f977a3a256 planemo upload for repository https://github.com/Marie59/champ_blocs commit 0d86db7d42b608c386a54500064f5f9c9d7019a4 ecology parents: diff changeset	885 "Nb.Gibbula.umbilicalis",
89f977a3a256 planemo upload for repository https://github.com/Marie59/champ_blocs commit 0d86db7d42b608c386a54500064f5f9c9d7019a4 ecology parents: diff changeset	886 "Nb.Phallusia.mamillata",
89f977a3a256 planemo upload for repository https://github.com/Marie59/champ_blocs commit 0d86db7d42b608c386a54500064f5f9c9d7019a4 ecology parents: diff changeset	887 "Nb.Tethya.aurantium",
89f977a3a256 planemo upload for repository https://github.com/Marie59/champ_blocs commit 0d86db7d42b608c386a54500064f5f9c9d7019a4 ecology parents: diff changeset	888 #"Nb.Spirobranchus.lamarckii.1B",
89f977a3a256 planemo upload for repository https://github.com/Marie59/champ_blocs commit 0d86db7d42b608c386a54500064f5f9c9d7019a4 ecology parents: diff changeset	889 #"Nb.Spirobranchus.lamarckii.2B",
89f977a3a256 planemo upload for repository https://github.com/Marie59/champ_blocs commit 0d86db7d42b608c386a54500064f5f9c9d7019a4 ecology parents: diff changeset	890 #"Nb.Spirobranchus.lamarckii.3B",
89f977a3a256 planemo upload for repository https://github.com/Marie59/champ_blocs commit 0d86db7d42b608c386a54500064f5f9c9d7019a4 ecology parents: diff changeset	891 #"Nb.Spirobranchus.lamarckii.4B",
89f977a3a256 planemo upload for repository https://github.com/Marie59/champ_blocs commit 0d86db7d42b608c386a54500064f5f9c9d7019a4 ecology parents: diff changeset	892 #"Nb.Spirobranchus.lamarckii.5B",
89f977a3a256 planemo upload for repository https://github.com/Marie59/champ_blocs commit 0d86db7d42b608c386a54500064f5f9c9d7019a4 ecology parents: diff changeset	893 "Nb.Spirobranchus.lamarckii.total",
89f977a3a256 planemo upload for repository https://github.com/Marie59/champ_blocs commit 0d86db7d42b608c386a54500064f5f9c9d7019a4 ecology parents: diff changeset	894 #"Nb.spirorbis.1A",
89f977a3a256 planemo upload for repository https://github.com/Marie59/champ_blocs commit 0d86db7d42b608c386a54500064f5f9c9d7019a4 ecology parents: diff changeset	895 #"Nb.spirorbis.2A",
89f977a3a256 planemo upload for repository https://github.com/Marie59/champ_blocs commit 0d86db7d42b608c386a54500064f5f9c9d7019a4 ecology parents: diff changeset	896 #"Nb.spirorbis.3A",
89f977a3a256 planemo upload for repository https://github.com/Marie59/champ_blocs commit 0d86db7d42b608c386a54500064f5f9c9d7019a4 ecology parents: diff changeset	897 #"Nb.spirorbis.4A",
89f977a3a256 planemo upload for repository https://github.com/Marie59/champ_blocs commit 0d86db7d42b608c386a54500064f5f9c9d7019a4 ecology parents: diff changeset	898 #"Nb.spirorbis.5A",
89f977a3a256 planemo upload for repository https://github.com/Marie59/champ_blocs commit 0d86db7d42b608c386a54500064f5f9c9d7019a4 ecology parents: diff changeset	899 "Nb.spirorbis.total",
89f977a3a256 planemo upload for repository https://github.com/Marie59/champ_blocs commit 0d86db7d42b608c386a54500064f5f9c9d7019a4 ecology parents: diff changeset	900 "Nb.Crassostrea.gigas",
89f977a3a256 planemo upload for repository https://github.com/Marie59/champ_blocs commit 0d86db7d42b608c386a54500064f5f9c9d7019a4 ecology parents: diff changeset	901 "Nb.Ostrea.edulis",
89f977a3a256 planemo upload for repository https://github.com/Marie59/champ_blocs commit 0d86db7d42b608c386a54500064f5f9c9d7019a4 ecology parents: diff changeset	902 "X..Mytilus.sp.",
89f977a3a256 planemo upload for repository https://github.com/Marie59/champ_blocs commit 0d86db7d42b608c386a54500064f5f9c9d7019a4 ecology parents: diff changeset	903 "X..Hermelles",
89f977a3a256 planemo upload for repository https://github.com/Marie59/champ_blocs commit 0d86db7d42b608c386a54500064f5f9c9d7019a4 ecology parents: diff changeset	904 "X..Hydraires",
89f977a3a256 planemo upload for repository https://github.com/Marie59/champ_blocs commit 0d86db7d42b608c386a54500064f5f9c9d7019a4 ecology parents: diff changeset	905 "X..Eponges",
89f977a3a256 planemo upload for repository https://github.com/Marie59/champ_blocs commit 0d86db7d42b608c386a54500064f5f9c9d7019a4 ecology parents: diff changeset	906 "X..Ascidies.Coloniales",
89f977a3a256 planemo upload for repository https://github.com/Marie59/champ_blocs commit 0d86db7d42b608c386a54500064f5f9c9d7019a4 ecology parents: diff changeset	907 "X..Ascidies.Solitaires",
89f977a3a256 planemo upload for repository https://github.com/Marie59/champ_blocs commit 0d86db7d42b608c386a54500064f5f9c9d7019a4 ecology parents: diff changeset	908 "X..Bryozoaires.Dresses",
89f977a3a256 planemo upload for repository https://github.com/Marie59/champ_blocs commit 0d86db7d42b608c386a54500064f5f9c9d7019a4 ecology parents: diff changeset	909 "X..Balanes.Vivantes",
89f977a3a256 planemo upload for repository https://github.com/Marie59/champ_blocs commit 0d86db7d42b608c386a54500064f5f9c9d7019a4 ecology parents: diff changeset	910 #"Commentaires.Avant",
89f977a3a256 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.
89f977a3a256 planemo upload for repository https://github.com/Marie59/champ_blocs commit 0d86db7d42b608c386a54500064f5f9c9d7019a4 ecology parents: diff changeset	912 #"Type.sustrat.observé",
89f977a3a256 planemo upload for repository https://github.com/Marie59/champ_blocs commit 0d86db7d42b608c386a54500064f5f9c9d7019a4 ecology parents: diff changeset	913 #"Commentaires",
89f977a3a256 planemo upload for repository https://github.com/Marie59/champ_blocs commit 0d86db7d42b608c386a54500064f5f9c9d7019a4 ecology parents: diff changeset	914 "Nb.Cancer.pagurus..Tourteau.",
89f977a3a256 planemo upload for repository https://github.com/Marie59/champ_blocs commit 0d86db7d42b608c386a54500064f5f9c9d7019a4 ecology parents: diff changeset	915 "Nb.Necora.puber..Etrille.",
89f977a3a256 planemo upload for repository https://github.com/Marie59/champ_blocs commit 0d86db7d42b608c386a54500064f5f9c9d7019a4 ecology parents: diff changeset	916 "Nb.Carcinus.maenas..Crabe.vert.",
89f977a3a256 planemo upload for repository https://github.com/Marie59/champ_blocs commit 0d86db7d42b608c386a54500064f5f9c9d7019a4 ecology parents: diff changeset	917 "Nb.Nucella.lapilus..Pourpre.",
89f977a3a256 planemo upload for repository https://github.com/Marie59/champ_blocs commit 0d86db7d42b608c386a54500064f5f9c9d7019a4 ecology parents: diff changeset	918 "Nb.Eriphia.verrucosa..Crabe.verruqueux.",
89f977a3a256 planemo upload for repository https://github.com/Marie59/champ_blocs commit 0d86db7d42b608c386a54500064f5f9c9d7019a4 ecology parents: diff changeset	919 "Nb.Octopus.vulgaris..Poulpe.",
89f977a3a256 planemo upload for repository https://github.com/Marie59/champ_blocs commit 0d86db7d42b608c386a54500064f5f9c9d7019a4 ecology parents: diff changeset	920 "Nb.Galathea..Galathées.",
89f977a3a256 planemo upload for repository https://github.com/Marie59/champ_blocs commit 0d86db7d42b608c386a54500064f5f9c9d7019a4 ecology parents: diff changeset	921 "Nb.Paracentrotus.lividus..Oursin.",
89f977a3a256 planemo upload for repository https://github.com/Marie59/champ_blocs commit 0d86db7d42b608c386a54500064f5f9c9d7019a4 ecology parents: diff changeset	922 "Nb.Lophozozymus.incisus..ancien.Xantho.incisus.",
89f977a3a256 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.",
89f977a3a256 planemo upload for repository https://github.com/Marie59/champ_blocs commit 0d86db7d42b608c386a54500064f5f9c9d7019a4 ecology parents: diff changeset	924 "Nb.Haliotis.tuberculata..Ormeau.",
89f977a3a256 planemo upload for repository https://github.com/Marie59/champ_blocs commit 0d86db7d42b608c386a54500064f5f9c9d7019a4 ecology parents: diff changeset	925 "Nb.Stramonita.haemastoma..Pourpre.bouche.de.sang.",
89f977a3a256 planemo upload for repository https://github.com/Marie59/champ_blocs commit 0d86db7d42b608c386a54500064f5f9c9d7019a4 ecology parents: diff changeset	926 "Nb.Littorina.littorea..Bigorneau.",
89f977a3a256 planemo upload for repository https://github.com/Marie59/champ_blocs commit 0d86db7d42b608c386a54500064f5f9c9d7019a4 ecology parents: diff changeset	927 "Nb.Xantho.pilipes..Xanthe.poilu.",
89f977a3a256 planemo upload for repository https://github.com/Marie59/champ_blocs commit 0d86db7d42b608c386a54500064f5f9c9d7019a4 ecology parents: diff changeset	928 "Nb.Mimachlamys.varia..Pétoncle.noir."
89f977a3a256 planemo upload for repository https://github.com/Marie59/champ_blocs commit 0d86db7d42b608c386a54500064f5f9c9d7019a4 ecology parents: diff changeset	929 )
89f977a3a256 planemo upload for repository https://github.com/Marie59/champ_blocs commit 0d86db7d42b608c386a54500064f5f9c9d7019a4 ecology parents: diff changeset	930 ] <- lapply(egmp_basq_bm[, c(
89f977a3a256 planemo upload for repository https://github.com/Marie59/champ_blocs commit 0d86db7d42b608c386a54500064f5f9c9d7019a4 ecology parents: diff changeset	931 "X..algues.brunes",
89f977a3a256 planemo upload for repository https://github.com/Marie59/champ_blocs commit 0d86db7d42b608c386a54500064f5f9c9d7019a4 ecology parents: diff changeset	932 "Strate.algues.brunes",
89f977a3a256 planemo upload for repository https://github.com/Marie59/champ_blocs commit 0d86db7d42b608c386a54500064f5f9c9d7019a4 ecology parents: diff changeset	933 "X..algues.rouges",
89f977a3a256 planemo upload for repository https://github.com/Marie59/champ_blocs commit 0d86db7d42b608c386a54500064f5f9c9d7019a4 ecology parents: diff changeset	934 "Strate.algues.rouges",
89f977a3a256 planemo upload for repository https://github.com/Marie59/champ_blocs commit 0d86db7d42b608c386a54500064f5f9c9d7019a4 ecology parents: diff changeset	935 "X..algues.vertes",
89f977a3a256 planemo upload for repository https://github.com/Marie59/champ_blocs commit 0d86db7d42b608c386a54500064f5f9c9d7019a4 ecology parents: diff changeset	936 "Strate.algues.vertes",
89f977a3a256 planemo upload for repository https://github.com/Marie59/champ_blocs commit 0d86db7d42b608c386a54500064f5f9c9d7019a4 ecology parents: diff changeset	937 "X..Cladophora",
89f977a3a256 planemo upload for repository https://github.com/Marie59/champ_blocs commit 0d86db7d42b608c386a54500064f5f9c9d7019a4 ecology parents: diff changeset	938 "X..Lithophyllum",
89f977a3a256 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.
89f977a3a256 planemo upload for repository https://github.com/Marie59/champ_blocs commit 0d86db7d42b608c386a54500064f5f9c9d7019a4 ecology parents: diff changeset	940 #"Type.Sediment",
89f977a3a256 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.
89f977a3a256 planemo upload for repository https://github.com/Marie59/champ_blocs commit 0d86db7d42b608c386a54500064f5f9c9d7019a4 ecology parents: diff changeset	942 "Nb.Littorina.obtusata",
89f977a3a256 planemo upload for repository https://github.com/Marie59/champ_blocs commit 0d86db7d42b608c386a54500064f5f9c9d7019a4 ecology parents: diff changeset	943 "Nb.Gibbula.cineraria",
89f977a3a256 planemo upload for repository https://github.com/Marie59/champ_blocs commit 0d86db7d42b608c386a54500064f5f9c9d7019a4 ecology parents: diff changeset	944 "Nb.Gibbula.pennanti",
89f977a3a256 planemo upload for repository https://github.com/Marie59/champ_blocs commit 0d86db7d42b608c386a54500064f5f9c9d7019a4 ecology parents: diff changeset	945 "Nb.Gibbula.umbilicalis",
89f977a3a256 planemo upload for repository https://github.com/Marie59/champ_blocs commit 0d86db7d42b608c386a54500064f5f9c9d7019a4 ecology parents: diff changeset	946 "Nb.Phallusia.mamillata",
89f977a3a256 planemo upload for repository https://github.com/Marie59/champ_blocs commit 0d86db7d42b608c386a54500064f5f9c9d7019a4 ecology parents: diff changeset	947 "Nb.Tethya.aurantium",
89f977a3a256 planemo upload for repository https://github.com/Marie59/champ_blocs commit 0d86db7d42b608c386a54500064f5f9c9d7019a4 ecology parents: diff changeset	948 #"Nb.Spirobranchus.lamarckii.1B",
89f977a3a256 planemo upload for repository https://github.com/Marie59/champ_blocs commit 0d86db7d42b608c386a54500064f5f9c9d7019a4 ecology parents: diff changeset	949 #"Nb.Spirobranchus.lamarckii.2B",
89f977a3a256 planemo upload for repository https://github.com/Marie59/champ_blocs commit 0d86db7d42b608c386a54500064f5f9c9d7019a4 ecology parents: diff changeset	950 #"Nb.Spirobranchus.lamarckii.3B",
89f977a3a256 planemo upload for repository https://github.com/Marie59/champ_blocs commit 0d86db7d42b608c386a54500064f5f9c9d7019a4 ecology parents: diff changeset	951 #"Nb.Spirobranchus.lamarckii.4B",
89f977a3a256 planemo upload for repository https://github.com/Marie59/champ_blocs commit 0d86db7d42b608c386a54500064f5f9c9d7019a4 ecology parents: diff changeset	952 #"Nb.Spirobranchus.lamarckii.5B",
89f977a3a256 planemo upload for repository https://github.com/Marie59/champ_blocs commit 0d86db7d42b608c386a54500064f5f9c9d7019a4 ecology parents: diff changeset	953 "Nb.Spirobranchus.lamarckii.total",
89f977a3a256 planemo upload for repository https://github.com/Marie59/champ_blocs commit 0d86db7d42b608c386a54500064f5f9c9d7019a4 ecology parents: diff changeset	954 #"Nb.spirorbis.1A",
89f977a3a256 planemo upload for repository https://github.com/Marie59/champ_blocs commit 0d86db7d42b608c386a54500064f5f9c9d7019a4 ecology parents: diff changeset	955 #"Nb.spirorbis.2A",
89f977a3a256 planemo upload for repository https://github.com/Marie59/champ_blocs commit 0d86db7d42b608c386a54500064f5f9c9d7019a4 ecology parents: diff changeset	956 #"Nb.spirorbis.3A",
89f977a3a256 planemo upload for repository https://github.com/Marie59/champ_blocs commit 0d86db7d42b608c386a54500064f5f9c9d7019a4 ecology parents: diff changeset	957 #"Nb.spirorbis.4A",
89f977a3a256 planemo upload for repository https://github.com/Marie59/champ_blocs commit 0d86db7d42b608c386a54500064f5f9c9d7019a4 ecology parents: diff changeset	958 #"Nb.spirorbis.5A",
89f977a3a256 planemo upload for repository https://github.com/Marie59/champ_blocs commit 0d86db7d42b608c386a54500064f5f9c9d7019a4 ecology parents: diff changeset	959 "Nb.spirorbis.total",
89f977a3a256 planemo upload for repository https://github.com/Marie59/champ_blocs commit 0d86db7d42b608c386a54500064f5f9c9d7019a4 ecology parents: diff changeset	960 "Nb.Crassostrea.gigas",
89f977a3a256 planemo upload for repository https://github.com/Marie59/champ_blocs commit 0d86db7d42b608c386a54500064f5f9c9d7019a4 ecology parents: diff changeset	961 "Nb.Ostrea.edulis",
89f977a3a256 planemo upload for repository https://github.com/Marie59/champ_blocs commit 0d86db7d42b608c386a54500064f5f9c9d7019a4 ecology parents: diff changeset	962 "X..Mytilus.sp.",
89f977a3a256 planemo upload for repository https://github.com/Marie59/champ_blocs commit 0d86db7d42b608c386a54500064f5f9c9d7019a4 ecology parents: diff changeset	963 "X..Hermelles",
89f977a3a256 planemo upload for repository https://github.com/Marie59/champ_blocs commit 0d86db7d42b608c386a54500064f5f9c9d7019a4 ecology parents: diff changeset	964 "X..Hydraires",
89f977a3a256 planemo upload for repository https://github.com/Marie59/champ_blocs commit 0d86db7d42b608c386a54500064f5f9c9d7019a4 ecology parents: diff changeset	965 "X..Eponges",
89f977a3a256 planemo upload for repository https://github.com/Marie59/champ_blocs commit 0d86db7d42b608c386a54500064f5f9c9d7019a4 ecology parents: diff changeset	966 "X..Ascidies.Coloniales",
89f977a3a256 planemo upload for repository https://github.com/Marie59/champ_blocs commit 0d86db7d42b608c386a54500064f5f9c9d7019a4 ecology parents: diff changeset	967 "X..Ascidies.Solitaires",
89f977a3a256 planemo upload for repository https://github.com/Marie59/champ_blocs commit 0d86db7d42b608c386a54500064f5f9c9d7019a4 ecology parents: diff changeset	968 "X..Bryozoaires.Dresses",
89f977a3a256 planemo upload for repository https://github.com/Marie59/champ_blocs commit 0d86db7d42b608c386a54500064f5f9c9d7019a4 ecology parents: diff changeset	969 "X..Balanes.Vivantes",
89f977a3a256 planemo upload for repository https://github.com/Marie59/champ_blocs commit 0d86db7d42b608c386a54500064f5f9c9d7019a4 ecology parents: diff changeset	970 #"Commentaires.Avant",
89f977a3a256 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.
89f977a3a256 planemo upload for repository https://github.com/Marie59/champ_blocs commit 0d86db7d42b608c386a54500064f5f9c9d7019a4 ecology parents: diff changeset	972 #"Type.sustrat.observé",
89f977a3a256 planemo upload for repository https://github.com/Marie59/champ_blocs commit 0d86db7d42b608c386a54500064f5f9c9d7019a4 ecology parents: diff changeset	973 #"Commentaires",
89f977a3a256 planemo upload for repository https://github.com/Marie59/champ_blocs commit 0d86db7d42b608c386a54500064f5f9c9d7019a4 ecology parents: diff changeset	974 "Nb.Cancer.pagurus..Tourteau.",
89f977a3a256 planemo upload for repository https://github.com/Marie59/champ_blocs commit 0d86db7d42b608c386a54500064f5f9c9d7019a4 ecology parents: diff changeset	975 "Nb.Necora.puber..Etrille.",
89f977a3a256 planemo upload for repository https://github.com/Marie59/champ_blocs commit 0d86db7d42b608c386a54500064f5f9c9d7019a4 ecology parents: diff changeset	976 "Nb.Carcinus.maenas..Crabe.vert.",
89f977a3a256 planemo upload for repository https://github.com/Marie59/champ_blocs commit 0d86db7d42b608c386a54500064f5f9c9d7019a4 ecology parents: diff changeset	977 "Nb.Nucella.lapilus..Pourpre.",
89f977a3a256 planemo upload for repository https://github.com/Marie59/champ_blocs commit 0d86db7d42b608c386a54500064f5f9c9d7019a4 ecology parents: diff changeset	978 "Nb.Eriphia.verrucosa..Crabe.verruqueux.",
89f977a3a256 planemo upload for repository https://github.com/Marie59/champ_blocs commit 0d86db7d42b608c386a54500064f5f9c9d7019a4 ecology parents: diff changeset	979 "Nb.Octopus.vulgaris..Poulpe.",
89f977a3a256 planemo upload for repository https://github.com/Marie59/champ_blocs commit 0d86db7d42b608c386a54500064f5f9c9d7019a4 ecology parents: diff changeset	980 "Nb.Galathea..Galathées.",
89f977a3a256 planemo upload for repository https://github.com/Marie59/champ_blocs commit 0d86db7d42b608c386a54500064f5f9c9d7019a4 ecology parents: diff changeset	981 "Nb.Paracentrotus.lividus..Oursin.",
89f977a3a256 planemo upload for repository https://github.com/Marie59/champ_blocs commit 0d86db7d42b608c386a54500064f5f9c9d7019a4 ecology parents: diff changeset	982 "Nb.Lophozozymus.incisus..ancien.Xantho.incisus.",
89f977a3a256 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.",
89f977a3a256 planemo upload for repository https://github.com/Marie59/champ_blocs commit 0d86db7d42b608c386a54500064f5f9c9d7019a4 ecology parents: diff changeset	984 "Nb.Haliotis.tuberculata..Ormeau.",
89f977a3a256 planemo upload for repository https://github.com/Marie59/champ_blocs commit 0d86db7d42b608c386a54500064f5f9c9d7019a4 ecology parents: diff changeset	985 "Nb.Stramonita.haemastoma..Pourpre.bouche.de.sang.",
89f977a3a256 planemo upload for repository https://github.com/Marie59/champ_blocs commit 0d86db7d42b608c386a54500064f5f9c9d7019a4 ecology parents: diff changeset	986 "Nb.Littorina.littorea..Bigorneau.",
89f977a3a256 planemo upload for repository https://github.com/Marie59/champ_blocs commit 0d86db7d42b608c386a54500064f5f9c9d7019a4 ecology parents: diff changeset	987 "Nb.Xantho.pilipes..Xanthe.poilu.",
89f977a3a256 planemo upload for repository https://github.com/Marie59/champ_blocs commit 0d86db7d42b608c386a54500064f5f9c9d7019a4 ecology parents: diff changeset	988 "Nb.Mimachlamys.varia..Pétoncle.noir."
89f977a3a256 planemo upload for repository https://github.com/Marie59/champ_blocs commit 0d86db7d42b608c386a54500064f5f9c9d7019a4 ecology parents: diff changeset	989 )
89f977a3a256 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))
89f977a3a256 planemo upload for repository https://github.com/Marie59/champ_blocs commit 0d86db7d42b608c386a54500064f5f9c9d7019a4 ecology parents: diff changeset	991
89f977a3a256 planemo upload for repository https://github.com/Marie59/champ_blocs commit 0d86db7d42b608c386a54500064f5f9c9d7019a4 ecology parents: diff changeset	992
89f977a3a256 planemo upload for repository https://github.com/Marie59/champ_blocs commit 0d86db7d42b608c386a54500064f5f9c9d7019a4 ecology parents: diff changeset	993 # egmp_basq_bf
89f977a3a256 planemo upload for repository https://github.com/Marie59/champ_blocs commit 0d86db7d42b608c386a54500064f5f9c9d7019a4 ecology parents: diff changeset	994 egmp_basq_bf[, c(
89f977a3a256 planemo upload for repository https://github.com/Marie59/champ_blocs commit 0d86db7d42b608c386a54500064f5f9c9d7019a4 ecology parents: diff changeset	995 "X..algues.brunes",
89f977a3a256 planemo upload for repository https://github.com/Marie59/champ_blocs commit 0d86db7d42b608c386a54500064f5f9c9d7019a4 ecology parents: diff changeset	996 "Strate.algues.brunes",
89f977a3a256 planemo upload for repository https://github.com/Marie59/champ_blocs commit 0d86db7d42b608c386a54500064f5f9c9d7019a4 ecology parents: diff changeset	997 "X..algues.rouges",
89f977a3a256 planemo upload for repository https://github.com/Marie59/champ_blocs commit 0d86db7d42b608c386a54500064f5f9c9d7019a4 ecology parents: diff changeset	998 "Strate.algues.rouges",
89f977a3a256 planemo upload for repository https://github.com/Marie59/champ_blocs commit 0d86db7d42b608c386a54500064f5f9c9d7019a4 ecology parents: diff changeset	999 "X..algues.vertes",
89f977a3a256 planemo upload for repository https://github.com/Marie59/champ_blocs commit 0d86db7d42b608c386a54500064f5f9c9d7019a4 ecology parents: diff changeset	1000 "Strate.algues.vertes",
89f977a3a256 planemo upload for repository https://github.com/Marie59/champ_blocs commit 0d86db7d42b608c386a54500064f5f9c9d7019a4 ecology parents: diff changeset	1001 "X..Cladophora",
89f977a3a256 planemo upload for repository https://github.com/Marie59/champ_blocs commit 0d86db7d42b608c386a54500064f5f9c9d7019a4 ecology parents: diff changeset	1002 "X..Lithophyllum",
89f977a3a256 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.
89f977a3a256 planemo upload for repository https://github.com/Marie59/champ_blocs commit 0d86db7d42b608c386a54500064f5f9c9d7019a4 ecology parents: diff changeset	1004 #"Type.Sediment",
89f977a3a256 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.
89f977a3a256 planemo upload for repository https://github.com/Marie59/champ_blocs commit 0d86db7d42b608c386a54500064f5f9c9d7019a4 ecology parents: diff changeset	1006 "Nb.Littorina.obtusata",
89f977a3a256 planemo upload for repository https://github.com/Marie59/champ_blocs commit 0d86db7d42b608c386a54500064f5f9c9d7019a4 ecology parents: diff changeset	1007 "Nb.Gibbula.cineraria",
89f977a3a256 planemo upload for repository https://github.com/Marie59/champ_blocs commit 0d86db7d42b608c386a54500064f5f9c9d7019a4 ecology parents: diff changeset	1008 "Nb.Gibbula.pennanti",
89f977a3a256 planemo upload for repository https://github.com/Marie59/champ_blocs commit 0d86db7d42b608c386a54500064f5f9c9d7019a4 ecology parents: diff changeset	1009 "Nb.Gibbula.umbilicalis",
89f977a3a256 planemo upload for repository https://github.com/Marie59/champ_blocs commit 0d86db7d42b608c386a54500064f5f9c9d7019a4 ecology parents: diff changeset	1010 "Nb.Phallusia.mamillata",
89f977a3a256 planemo upload for repository https://github.com/Marie59/champ_blocs commit 0d86db7d42b608c386a54500064f5f9c9d7019a4 ecology parents: diff changeset	1011 "Nb.Tethya.aurantium",
89f977a3a256 planemo upload for repository https://github.com/Marie59/champ_blocs commit 0d86db7d42b608c386a54500064f5f9c9d7019a4 ecology parents: diff changeset	1012 #"Nb.Spirobranchus.lamarckii.1B",
89f977a3a256 planemo upload for repository https://github.com/Marie59/champ_blocs commit 0d86db7d42b608c386a54500064f5f9c9d7019a4 ecology parents: diff changeset	1013 #"Nb.Spirobranchus.lamarckii.2B",
89f977a3a256 planemo upload for repository https://github.com/Marie59/champ_blocs commit 0d86db7d42b608c386a54500064f5f9c9d7019a4 ecology parents: diff changeset	1014 #"Nb.Spirobranchus.lamarckii.3B",
89f977a3a256 planemo upload for repository https://github.com/Marie59/champ_blocs commit 0d86db7d42b608c386a54500064f5f9c9d7019a4 ecology parents: diff changeset	1015 #"Nb.Spirobranchus.lamarckii.4B",
89f977a3a256 planemo upload for repository https://github.com/Marie59/champ_blocs commit 0d86db7d42b608c386a54500064f5f9c9d7019a4 ecology parents: diff changeset	1016 #"Nb.Spirobranchus.lamarckii.5B",
89f977a3a256 planemo upload for repository https://github.com/Marie59/champ_blocs commit 0d86db7d42b608c386a54500064f5f9c9d7019a4 ecology parents: diff changeset	1017 "Nb.Spirobranchus.lamarckii.total",
89f977a3a256 planemo upload for repository https://github.com/Marie59/champ_blocs commit 0d86db7d42b608c386a54500064f5f9c9d7019a4 ecology parents: diff changeset	1018 #"Nb.spirorbis.1A",
89f977a3a256 planemo upload for repository https://github.com/Marie59/champ_blocs commit 0d86db7d42b608c386a54500064f5f9c9d7019a4 ecology parents: diff changeset	1019 #"Nb.spirorbis.2A",
89f977a3a256 planemo upload for repository https://github.com/Marie59/champ_blocs commit 0d86db7d42b608c386a54500064f5f9c9d7019a4 ecology parents: diff changeset	1020 #"Nb.spirorbis.3A",
89f977a3a256 planemo upload for repository https://github.com/Marie59/champ_blocs commit 0d86db7d42b608c386a54500064f5f9c9d7019a4 ecology parents: diff changeset	1021 #"Nb.spirorbis.4A",
89f977a3a256 planemo upload for repository https://github.com/Marie59/champ_blocs commit 0d86db7d42b608c386a54500064f5f9c9d7019a4 ecology parents: diff changeset	1022 #"Nb.spirorbis.5A",
89f977a3a256 planemo upload for repository https://github.com/Marie59/champ_blocs commit 0d86db7d42b608c386a54500064f5f9c9d7019a4 ecology parents: diff changeset	1023 "Nb.spirorbis.total",
89f977a3a256 planemo upload for repository https://github.com/Marie59/champ_blocs commit 0d86db7d42b608c386a54500064f5f9c9d7019a4 ecology parents: diff changeset	1024 "Nb.Crassostrea.gigas",
89f977a3a256 planemo upload for repository https://github.com/Marie59/champ_blocs commit 0d86db7d42b608c386a54500064f5f9c9d7019a4 ecology parents: diff changeset	1025 "Nb.Ostrea.edulis",
89f977a3a256 planemo upload for repository https://github.com/Marie59/champ_blocs commit 0d86db7d42b608c386a54500064f5f9c9d7019a4 ecology parents: diff changeset	1026 "X..Mytilus.sp.",
89f977a3a256 planemo upload for repository https://github.com/Marie59/champ_blocs commit 0d86db7d42b608c386a54500064f5f9c9d7019a4 ecology parents: diff changeset	1027 "X..Hermelles",
89f977a3a256 planemo upload for repository https://github.com/Marie59/champ_blocs commit 0d86db7d42b608c386a54500064f5f9c9d7019a4 ecology parents: diff changeset	1028 "X..Hydraires",
89f977a3a256 planemo upload for repository https://github.com/Marie59/champ_blocs commit 0d86db7d42b608c386a54500064f5f9c9d7019a4 ecology parents: diff changeset	1029 "X..Eponges",
89f977a3a256 planemo upload for repository https://github.com/Marie59/champ_blocs commit 0d86db7d42b608c386a54500064f5f9c9d7019a4 ecology parents: diff changeset	1030 "X..Ascidies.Coloniales",
89f977a3a256 planemo upload for repository https://github.com/Marie59/champ_blocs commit 0d86db7d42b608c386a54500064f5f9c9d7019a4 ecology parents: diff changeset	1031 "X..Ascidies.Solitaires",
89f977a3a256 planemo upload for repository https://github.com/Marie59/champ_blocs commit 0d86db7d42b608c386a54500064f5f9c9d7019a4 ecology parents: diff changeset	1032 "X..Bryozoaires.Dresses",
89f977a3a256 planemo upload for repository https://github.com/Marie59/champ_blocs commit 0d86db7d42b608c386a54500064f5f9c9d7019a4 ecology parents: diff changeset	1033 "X..Balanes.Vivantes",
89f977a3a256 planemo upload for repository https://github.com/Marie59/champ_blocs commit 0d86db7d42b608c386a54500064f5f9c9d7019a4 ecology parents: diff changeset	1034 #"Commentaires.Avant",
89f977a3a256 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.
89f977a3a256 planemo upload for repository https://github.com/Marie59/champ_blocs commit 0d86db7d42b608c386a54500064f5f9c9d7019a4 ecology parents: diff changeset	1036 #"Type.sustrat.observé",
89f977a3a256 planemo upload for repository https://github.com/Marie59/champ_blocs commit 0d86db7d42b608c386a54500064f5f9c9d7019a4 ecology parents: diff changeset	1037 #"Commentaires",
89f977a3a256 planemo upload for repository https://github.com/Marie59/champ_blocs commit 0d86db7d42b608c386a54500064f5f9c9d7019a4 ecology parents: diff changeset	1038 #."Nb.Cancer.pagurus..Tourteau.",
89f977a3a256 planemo upload for repository https://github.com/Marie59/champ_blocs commit 0d86db7d42b608c386a54500064f5f9c9d7019a4 ecology parents: diff changeset	1039 #.."Nb.Necora.puber..Etrille.",
89f977a3a256 planemo upload for repository https://github.com/Marie59/champ_blocs commit 0d86db7d42b608c386a54500064f5f9c9d7019a4 ecology parents: diff changeset	1040 #."Nb.Carcinus.maenas..Crabe.vert.",
89f977a3a256 planemo upload for repository https://github.com/Marie59/champ_blocs commit 0d86db7d42b608c386a54500064f5f9c9d7019a4 ecology parents: diff changeset	1041 #."Nb.Nucella.lapilus..Pourpre.",
89f977a3a256 planemo upload for repository https://github.com/Marie59/champ_blocs commit 0d86db7d42b608c386a54500064f5f9c9d7019a4 ecology parents: diff changeset	1042 #.."Nb.Eriphia.verrucosa..Crabe.verruqueux.",
89f977a3a256 planemo upload for repository https://github.com/Marie59/champ_blocs commit 0d86db7d42b608c386a54500064f5f9c9d7019a4 ecology parents: diff changeset	1043 #.."Nb.Octopus.vulgaris..Poulpe.",
89f977a3a256 planemo upload for repository https://github.com/Marie59/champ_blocs commit 0d86db7d42b608c386a54500064f5f9c9d7019a4 ecology parents: diff changeset	1044 #."Nb.Galathea..Galathées.",
89f977a3a256 planemo upload for repository https://github.com/Marie59/champ_blocs commit 0d86db7d42b608c386a54500064f5f9c9d7019a4 ecology parents: diff changeset	1045 #.."Nb.Paracentrotus.lividus..Oursin.",
89f977a3a256 planemo upload for repository https://github.com/Marie59/champ_blocs commit 0d86db7d42b608c386a54500064f5f9c9d7019a4 ecology parents: diff changeset	1046 #."Nb.Lophozozymus.incisus..ancien.Xantho.incisus.",
89f977a3a256 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.",
89f977a3a256 planemo upload for repository https://github.com/Marie59/champ_blocs commit 0d86db7d42b608c386a54500064f5f9c9d7019a4 ecology parents: diff changeset	1048 #."Nb.Haliotis.tuberculata..Ormeau.",
89f977a3a256 planemo upload for repository https://github.com/Marie59/champ_blocs commit 0d86db7d42b608c386a54500064f5f9c9d7019a4 ecology parents: diff changeset	1049 #."Nb.Stramonita.haemastoma..Pourpre.bouche.de.sang.",
89f977a3a256 planemo upload for repository https://github.com/Marie59/champ_blocs commit 0d86db7d42b608c386a54500064f5f9c9d7019a4 ecology parents: diff changeset	1050 #."Nb.Littorina.littorea..Bigorneau.",
89f977a3a256 planemo upload for repository https://github.com/Marie59/champ_blocs commit 0d86db7d42b608c386a54500064f5f9c9d7019a4 ecology parents: diff changeset	1051 #."Nb.Xantho.pilipes..Xanthe.poilu.",
89f977a3a256 planemo upload for repository https://github.com/Marie59/champ_blocs commit 0d86db7d42b608c386a54500064f5f9c9d7019a4 ecology parents: diff changeset	1052 #."Nb.Mimachlamys.varia..Pétoncle.noir."
89f977a3a256 planemo upload for repository https://github.com/Marie59/champ_blocs commit 0d86db7d42b608c386a54500064f5f9c9d7019a4 ecology parents: diff changeset	1053 )
89f977a3a256 planemo upload for repository https://github.com/Marie59/champ_blocs commit 0d86db7d42b608c386a54500064f5f9c9d7019a4 ecology parents: diff changeset	1054 ] <- lapply(egmp_basq_bf[, c(
89f977a3a256 planemo upload for repository https://github.com/Marie59/champ_blocs commit 0d86db7d42b608c386a54500064f5f9c9d7019a4 ecology parents: diff changeset	1055 "X..algues.brunes",
89f977a3a256 planemo upload for repository https://github.com/Marie59/champ_blocs commit 0d86db7d42b608c386a54500064f5f9c9d7019a4 ecology parents: diff changeset	1056 "Strate.algues.brunes",
89f977a3a256 planemo upload for repository https://github.com/Marie59/champ_blocs commit 0d86db7d42b608c386a54500064f5f9c9d7019a4 ecology parents: diff changeset	1057 "X..algues.rouges",
89f977a3a256 planemo upload for repository https://github.com/Marie59/champ_blocs commit 0d86db7d42b608c386a54500064f5f9c9d7019a4 ecology parents: diff changeset	1058 "Strate.algues.rouges",
89f977a3a256 planemo upload for repository https://github.com/Marie59/champ_blocs commit 0d86db7d42b608c386a54500064f5f9c9d7019a4 ecology parents: diff changeset	1059 "X..algues.vertes",
89f977a3a256 planemo upload for repository https://github.com/Marie59/champ_blocs commit 0d86db7d42b608c386a54500064f5f9c9d7019a4 ecology parents: diff changeset	1060 "Strate.algues.vertes",
89f977a3a256 planemo upload for repository https://github.com/Marie59/champ_blocs commit 0d86db7d42b608c386a54500064f5f9c9d7019a4 ecology parents: diff changeset	1061 "X..Cladophora",
89f977a3a256 planemo upload for repository https://github.com/Marie59/champ_blocs commit 0d86db7d42b608c386a54500064f5f9c9d7019a4 ecology parents: diff changeset	1062 "X..Lithophyllum",
89f977a3a256 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.
89f977a3a256 planemo upload for repository https://github.com/Marie59/champ_blocs commit 0d86db7d42b608c386a54500064f5f9c9d7019a4 ecology parents: diff changeset	1064 #"Type.Sediment",
89f977a3a256 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.
89f977a3a256 planemo upload for repository https://github.com/Marie59/champ_blocs commit 0d86db7d42b608c386a54500064f5f9c9d7019a4 ecology parents: diff changeset	1066 "Nb.Littorina.obtusata",
89f977a3a256 planemo upload for repository https://github.com/Marie59/champ_blocs commit 0d86db7d42b608c386a54500064f5f9c9d7019a4 ecology parents: diff changeset	1067 "Nb.Gibbula.cineraria",
89f977a3a256 planemo upload for repository https://github.com/Marie59/champ_blocs commit 0d86db7d42b608c386a54500064f5f9c9d7019a4 ecology parents: diff changeset	1068 "Nb.Gibbula.pennanti",
89f977a3a256 planemo upload for repository https://github.com/Marie59/champ_blocs commit 0d86db7d42b608c386a54500064f5f9c9d7019a4 ecology parents: diff changeset	1069 "Nb.Gibbula.umbilicalis",
89f977a3a256 planemo upload for repository https://github.com/Marie59/champ_blocs commit 0d86db7d42b608c386a54500064f5f9c9d7019a4 ecology parents: diff changeset	1070 "Nb.Phallusia.mamillata",
89f977a3a256 planemo upload for repository https://github.com/Marie59/champ_blocs commit 0d86db7d42b608c386a54500064f5f9c9d7019a4 ecology parents: diff changeset	1071 "Nb.Tethya.aurantium",
89f977a3a256 planemo upload for repository https://github.com/Marie59/champ_blocs commit 0d86db7d42b608c386a54500064f5f9c9d7019a4 ecology parents: diff changeset	1072 #"Nb.Spirobranchus.lamarckii.1B",
89f977a3a256 planemo upload for repository https://github.com/Marie59/champ_blocs commit 0d86db7d42b608c386a54500064f5f9c9d7019a4 ecology parents: diff changeset	1073 #"Nb.Spirobranchus.lamarckii.2B",
89f977a3a256 planemo upload for repository https://github.com/Marie59/champ_blocs commit 0d86db7d42b608c386a54500064f5f9c9d7019a4 ecology parents: diff changeset	1074 #"Nb.Spirobranchus.lamarckii.3B",
89f977a3a256 planemo upload for repository https://github.com/Marie59/champ_blocs commit 0d86db7d42b608c386a54500064f5f9c9d7019a4 ecology parents: diff changeset	1075 #"Nb.Spirobranchus.lamarckii.4B",
89f977a3a256 planemo upload for repository https://github.com/Marie59/champ_blocs commit 0d86db7d42b608c386a54500064f5f9c9d7019a4 ecology parents: diff changeset	1076 #"Nb.Spirobranchus.lamarckii.5B",
89f977a3a256 planemo upload for repository https://github.com/Marie59/champ_blocs commit 0d86db7d42b608c386a54500064f5f9c9d7019a4 ecology parents: diff changeset	1077 "Nb.Spirobranchus.lamarckii.total",
89f977a3a256 planemo upload for repository https://github.com/Marie59/champ_blocs commit 0d86db7d42b608c386a54500064f5f9c9d7019a4 ecology parents: diff changeset	1078 #"Nb.spirorbis.1A",
89f977a3a256 planemo upload for repository https://github.com/Marie59/champ_blocs commit 0d86db7d42b608c386a54500064f5f9c9d7019a4 ecology parents: diff changeset	1079 #"Nb.spirorbis.2A",
89f977a3a256 planemo upload for repository https://github.com/Marie59/champ_blocs commit 0d86db7d42b608c386a54500064f5f9c9d7019a4 ecology parents: diff changeset	1080 #"Nb.spirorbis.3A",
89f977a3a256 planemo upload for repository https://github.com/Marie59/champ_blocs commit 0d86db7d42b608c386a54500064f5f9c9d7019a4 ecology parents: diff changeset	1081 #"Nb.spirorbis.4A",
89f977a3a256 planemo upload for repository https://github.com/Marie59/champ_blocs commit 0d86db7d42b608c386a54500064f5f9c9d7019a4 ecology parents: diff changeset	1082 #"Nb.spirorbis.5A",
89f977a3a256 planemo upload for repository https://github.com/Marie59/champ_blocs commit 0d86db7d42b608c386a54500064f5f9c9d7019a4 ecology parents: diff changeset	1083 "Nb.spirorbis.total",
89f977a3a256 planemo upload for repository https://github.com/Marie59/champ_blocs commit 0d86db7d42b608c386a54500064f5f9c9d7019a4 ecology parents: diff changeset	1084 "Nb.Crassostrea.gigas",
89f977a3a256 planemo upload for repository https://github.com/Marie59/champ_blocs commit 0d86db7d42b608c386a54500064f5f9c9d7019a4 ecology parents: diff changeset	1085 "Nb.Ostrea.edulis",
89f977a3a256 planemo upload for repository https://github.com/Marie59/champ_blocs commit 0d86db7d42b608c386a54500064f5f9c9d7019a4 ecology parents: diff changeset	1086 "X..Mytilus.sp.",
89f977a3a256 planemo upload for repository https://github.com/Marie59/champ_blocs commit 0d86db7d42b608c386a54500064f5f9c9d7019a4 ecology parents: diff changeset	1087 "X..Hermelles",
89f977a3a256 planemo upload for repository https://github.com/Marie59/champ_blocs commit 0d86db7d42b608c386a54500064f5f9c9d7019a4 ecology parents: diff changeset	1088 "X..Hydraires",
89f977a3a256 planemo upload for repository https://github.com/Marie59/champ_blocs commit 0d86db7d42b608c386a54500064f5f9c9d7019a4 ecology parents: diff changeset	1089 "X..Eponges",
89f977a3a256 planemo upload for repository https://github.com/Marie59/champ_blocs commit 0d86db7d42b608c386a54500064f5f9c9d7019a4 ecology parents: diff changeset	1090 "X..Ascidies.Coloniales",
89f977a3a256 planemo upload for repository https://github.com/Marie59/champ_blocs commit 0d86db7d42b608c386a54500064f5f9c9d7019a4 ecology parents: diff changeset	1091 "X..Ascidies.Solitaires",
89f977a3a256 planemo upload for repository https://github.com/Marie59/champ_blocs commit 0d86db7d42b608c386a54500064f5f9c9d7019a4 ecology parents: diff changeset	1092 "X..Bryozoaires.Dresses",
89f977a3a256 planemo upload for repository https://github.com/Marie59/champ_blocs commit 0d86db7d42b608c386a54500064f5f9c9d7019a4 ecology parents: diff changeset	1093 "X..Balanes.Vivantes",
89f977a3a256 planemo upload for repository https://github.com/Marie59/champ_blocs commit 0d86db7d42b608c386a54500064f5f9c9d7019a4 ecology parents: diff changeset	1094 #"Commentaires.Avant",
89f977a3a256 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.
89f977a3a256 planemo upload for repository https://github.com/Marie59/champ_blocs commit 0d86db7d42b608c386a54500064f5f9c9d7019a4 ecology parents: diff changeset	1096 #"Type.sustrat.observé",
89f977a3a256 planemo upload for repository https://github.com/Marie59/champ_blocs commit 0d86db7d42b608c386a54500064f5f9c9d7019a4 ecology parents: diff changeset	1097 #"Commentaires",
89f977a3a256 planemo upload for repository https://github.com/Marie59/champ_blocs commit 0d86db7d42b608c386a54500064f5f9c9d7019a4 ecology parents: diff changeset	1098 #."Nb.Cancer.pagurus..Tourteau.",
89f977a3a256 planemo upload for repository https://github.com/Marie59/champ_blocs commit 0d86db7d42b608c386a54500064f5f9c9d7019a4 ecology parents: diff changeset	1099 #.."Nb.Necora.puber..Etrille.",
89f977a3a256 planemo upload for repository https://github.com/Marie59/champ_blocs commit 0d86db7d42b608c386a54500064f5f9c9d7019a4 ecology parents: diff changeset	1100 #."Nb.Carcinus.maenas..Crabe.vert.",
89f977a3a256 planemo upload for repository https://github.com/Marie59/champ_blocs commit 0d86db7d42b608c386a54500064f5f9c9d7019a4 ecology parents: diff changeset	1101 #."Nb.Nucella.lapilus..Pourpre.",
89f977a3a256 planemo upload for repository https://github.com/Marie59/champ_blocs commit 0d86db7d42b608c386a54500064f5f9c9d7019a4 ecology parents: diff changeset	1102 #.."Nb.Eriphia.verrucosa..Crabe.verruqueux.",
89f977a3a256 planemo upload for repository https://github.com/Marie59/champ_blocs commit 0d86db7d42b608c386a54500064f5f9c9d7019a4 ecology parents: diff changeset	1103 #.."Nb.Octopus.vulgaris..Poulpe.",
89f977a3a256 planemo upload for repository https://github.com/Marie59/champ_blocs commit 0d86db7d42b608c386a54500064f5f9c9d7019a4 ecology parents: diff changeset	1104 #."Nb.Galathea..Galathées.",
89f977a3a256 planemo upload for repository https://github.com/Marie59/champ_blocs commit 0d86db7d42b608c386a54500064f5f9c9d7019a4 ecology parents: diff changeset	1105 #.."Nb.Paracentrotus.lividus..Oursin.",
89f977a3a256 planemo upload for repository https://github.com/Marie59/champ_blocs commit 0d86db7d42b608c386a54500064f5f9c9d7019a4 ecology parents: diff changeset	1106 #."Nb.Lophozozymus.incisus..ancien.Xantho.incisus.",
89f977a3a256 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.",
89f977a3a256 planemo upload for repository https://github.com/Marie59/champ_blocs commit 0d86db7d42b608c386a54500064f5f9c9d7019a4 ecology parents: diff changeset	1108 #."Nb.Haliotis.tuberculata..Ormeau.",
89f977a3a256 planemo upload for repository https://github.com/Marie59/champ_blocs commit 0d86db7d42b608c386a54500064f5f9c9d7019a4 ecology parents: diff changeset	1109 #."Nb.Stramonita.haemastoma..Pourpre.bouche.de.sang.",
89f977a3a256 planemo upload for repository https://github.com/Marie59/champ_blocs commit 0d86db7d42b608c386a54500064f5f9c9d7019a4 ecology parents: diff changeset	1110 #."Nb.Littorina.littorea..Bigorneau.",
89f977a3a256 planemo upload for repository https://github.com/Marie59/champ_blocs commit 0d86db7d42b608c386a54500064f5f9c9d7019a4 ecology parents: diff changeset	1111 #."Nb.Xantho.pilipes..Xanthe.poilu.",
89f977a3a256 planemo upload for repository https://github.com/Marie59/champ_blocs commit 0d86db7d42b608c386a54500064f5f9c9d7019a4 ecology parents: diff changeset	1112 #."Nb.Mimachlamys.varia..Pétoncle.noir."
89f977a3a256 planemo upload for repository https://github.com/Marie59/champ_blocs commit 0d86db7d42b608c386a54500064f5f9c9d7019a4 ecology parents: diff changeset	1113 )
89f977a3a256 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))
89f977a3a256 planemo upload for repository https://github.com/Marie59/champ_blocs commit 0d86db7d42b608c386a54500064f5f9c9d7019a4 ecology parents: diff changeset	1115
89f977a3a256 planemo upload for repository https://github.com/Marie59/champ_blocs commit 0d86db7d42b608c386a54500064f5f9c9d7019a4 ecology parents: diff changeset	1116
89f977a3a256 planemo upload for repository https://github.com/Marie59/champ_blocs commit 0d86db7d42b608c386a54500064f5f9c9d7019a4 ecology parents: diff changeset	1117 # merge dfs.
89f977a3a256 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)
89f977a3a256 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)
89f977a3a256 planemo upload for repository https://github.com/Marie59/champ_blocs commit 0d86db7d42b608c386a54500064f5f9c9d7019a4 ecology parents: diff changeset	1120 qecbnato0 <- dplyr::bind_rows(qecbnato0, egmp_basq_bf)
89f977a3a256 planemo upload for repository https://github.com/Marie59/champ_blocs commit 0d86db7d42b608c386a54500064f5f9c9d7019a4 ecology parents: diff changeset	1121
89f977a3a256 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)
89f977a3a256 planemo upload for repository https://github.com/Marie59/champ_blocs commit 0d86db7d42b608c386a54500064f5f9c9d7019a4 ecology parents: diff changeset	1123
89f977a3a256 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)
89f977a3a256 planemo upload for repository https://github.com/Marie59/champ_blocs commit 0d86db7d42b608c386a54500064f5f9c9d7019a4 ecology parents: diff changeset	1125
89f977a3a256 planemo upload for repository https://github.com/Marie59/champ_blocs commit 0d86db7d42b608c386a54500064f5f9c9d7019a4 ecology parents: diff changeset	1126
89f977a3a256 planemo upload for repository https://github.com/Marie59/champ_blocs commit 0d86db7d42b608c386a54500064f5f9c9d7019a4 ecology parents: diff changeset	1127 ## analyse matricielle
89f977a3a256 planemo upload for repository https://github.com/Marie59/champ_blocs commit 0d86db7d42b608c386a54500064f5f9c9d7019a4 ecology parents: diff changeset	1128
89f977a3a256 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.
89f977a3a256 planemo upload for repository https://github.com/Marie59/champ_blocs commit 0d86db7d42b608c386a54500064f5f9c9d7019a4 ecology parents: diff changeset	1130
89f977a3a256 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")
89f977a3a256 planemo upload for repository https://github.com/Marie59/champ_blocs commit 0d86db7d42b608c386a54500064f5f9c9d7019a4 ecology parents: diff changeset	1132
89f977a3a256 planemo upload for repository https://github.com/Marie59/champ_blocs commit 0d86db7d42b608c386a54500064f5f9c9d7019a4 ecology parents: diff changeset	1133
89f977a3a256 planemo upload for repository https://github.com/Marie59/champ_blocs commit 0d86db7d42b608c386a54500064f5f9c9d7019a4 ecology parents: diff changeset	1134 numero_quadrat <- stringr::str_sub(qecbnato0$quadrat_bis, start = -1)
89f977a3a256 planemo upload for repository https://github.com/Marie59/champ_blocs commit 0d86db7d42b608c386a54500064f5f9c9d7019a4 ecology parents: diff changeset	1135 qecbnato0 <- tibble::add_column(qecbnato0, numero_quadrat, .after = "quadrat_bis")
89f977a3a256 planemo upload for repository https://github.com/Marie59/champ_blocs commit 0d86db7d42b608c386a54500064f5f9c9d7019a4 ecology parents: diff changeset	1136 rm(numero_quadrat)
89f977a3a256 planemo upload for repository https://github.com/Marie59/champ_blocs commit 0d86db7d42b608c386a54500064f5f9c9d7019a4 ecology parents: diff changeset	1137 qecbnato0$numero_quadrat <- as.integer(qecbnato0$numero_quadrat)
89f977a3a256 planemo upload for repository https://github.com/Marie59/champ_blocs commit 0d86db7d42b608c386a54500064f5f9c9d7019a4 ecology parents: diff changeset	1138
89f977a3a256 planemo upload for repository https://github.com/Marie59/champ_blocs commit 0d86db7d42b608c386a54500064f5f9c9d7019a4 ecology parents: diff changeset	1139
89f977a3a256 planemo upload for repository https://github.com/Marie59/champ_blocs commit 0d86db7d42b608c386a54500064f5f9c9d7019a4 ecology parents: diff changeset	1140 qecbnato0$Year <- as.integer(qecbnato0$Year)
89f977a3a256 planemo upload for repository https://github.com/Marie59/champ_blocs commit 0d86db7d42b608c386a54500064f5f9c9d7019a4 ecology parents: diff changeset	1141 qecbnato0$Month <- as.integer(qecbnato0$Month)
89f977a3a256 planemo upload for repository https://github.com/Marie59/champ_blocs commit 0d86db7d42b608c386a54500064f5f9c9d7019a4 ecology parents: diff changeset	1142 qecbnato0$Day <- as.integer(qecbnato0$Day)
89f977a3a256 planemo upload for repository https://github.com/Marie59/champ_blocs commit 0d86db7d42b608c386a54500064f5f9c9d7019a4 ecology parents: diff changeset	1143
89f977a3a256 planemo upload for repository https://github.com/Marie59/champ_blocs commit 0d86db7d42b608c386a54500064f5f9c9d7019a4 ecology parents: diff changeset	1144 ############################################################
89f977a3a256 planemo upload for repository https://github.com/Marie59/champ_blocs commit 0d86db7d42b608c386a54500064f5f9c9d7019a4 ecology parents: diff changeset	1145 #!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!
89f977a3a256 planemo upload for repository https://github.com/Marie59/champ_blocs commit 0d86db7d42b608c386a54500064f5f9c9d7019a4 ecology parents: diff changeset	1146 # Anna still hasn't corrected for boulder nb in FINS_Quemenes.2020.10.16 data encoding ! removed from the df_
89f977a3a256 planemo upload for repository https://github.com/Marie59/champ_blocs commit 0d86db7d42b608c386a54500064f5f9c9d7019a4 ecology parents: diff changeset	1147 qecbnato0 <- qecbnato0 %>% dplyr::filter(site_year_month_day != "FINS_Quemenes.2020.10.16")
89f977a3a256 planemo upload for repository https://github.com/Marie59/champ_blocs commit 0d86db7d42b608c386a54500064f5f9c9d7019a4 ecology parents: diff changeset	1148 ############################################################
89f977a3a256 planemo upload for repository https://github.com/Marie59/champ_blocs commit 0d86db7d42b608c386a54500064f5f9c9d7019a4 ecology parents: diff changeset	1149
89f977a3a256 planemo upload for repository https://github.com/Marie59/champ_blocs commit 0d86db7d42b608c386a54500064f5f9c9d7019a4 ecology parents: diff changeset	1150 # what to do with spirorbes & Nb.Spirobranchus.lamarckii.total? log10 transformation
89f977a3a256 planemo upload for repository https://github.com/Marie59/champ_blocs commit 0d86db7d42b608c386a54500064f5f9c9d7019a4 ecology parents: diff changeset	1151
89f977a3a256 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")
89f977a3a256 planemo upload for repository https://github.com/Marie59/champ_blocs commit 0d86db7d42b608c386a54500064f5f9c9d7019a4 ecology parents: diff changeset	1153 qecbnato0 <- tibble::add_column(qecbnato0, log10.Nb.Spirobranchus.lamarckii.total = log10(qecbnato0$Nb.Spirobranchus.lamarckii.total + 1), .after = "Nb.Spirobranchus.lamarckii.total")
89f977a3a256 planemo upload for repository https://github.com/Marie59/champ_blocs commit 0d86db7d42b608c386a54500064f5f9c9d7019a4 ecology parents: diff changeset	1154
89f977a3a256 planemo upload for repository https://github.com/Marie59/champ_blocs commit 0d86db7d42b608c386a54500064f5f9c9d7019a4 ecology parents: diff changeset	1155 saveRDS(qecbnato0, "qecbnato0.RDS")
89f977a3a256 planemo upload for repository https://github.com/Marie59/champ_blocs commit 0d86db7d42b608c386a54500064f5f9c9d7019a4 ecology parents: diff changeset	1156
89f977a3a256 planemo upload for repository https://github.com/Marie59/champ_blocs commit 0d86db7d42b608c386a54500064f5f9c9d7019a4 ecology parents: diff changeset	1157
89f977a3a256 planemo upload for repository https://github.com/Marie59/champ_blocs commit 0d86db7d42b608c386a54500064f5f9c9d7019a4 ecology parents: diff changeset	1158 ###############################################################
89f977a3a256 planemo upload for repository https://github.com/Marie59/champ_blocs commit 0d86db7d42b608c386a54500064f5f9c9d7019a4 ecology parents: diff changeset	1159 # #
89f977a3a256 planemo upload for repository https://github.com/Marie59/champ_blocs commit 0d86db7d42b608c386a54500064f5f9c9d7019a4 ecology parents: diff changeset	1160 # Start dissimilarity calculation with some data handling #
89f977a3a256 planemo upload for repository https://github.com/Marie59/champ_blocs commit 0d86db7d42b608c386a54500064f5f9c9d7019a4 ecology parents: diff changeset	1161 # #
89f977a3a256 planemo upload for repository https://github.com/Marie59/champ_blocs commit 0d86db7d42b608c386a54500064f5f9c9d7019a4 ecology parents: diff changeset	1162 ###############################################################
89f977a3a256 planemo upload for repository https://github.com/Marie59/champ_blocs commit 0d86db7d42b608c386a54500064f5f9c9d7019a4 ecology parents: diff changeset	1163
89f977a3a256 planemo upload for repository https://github.com/Marie59/champ_blocs commit 0d86db7d42b608c386a54500064f5f9c9d7019a4 ecology parents: diff changeset	1164 # first, create vector (4) for qecb and fishing by region (same as above)
89f977a3a256 planemo upload for repository https://github.com/Marie59/champ_blocs commit 0d86db7d42b608c386a54500064f5f9c9d7019a4 ecology parents: diff changeset	1165
89f977a3a256 planemo upload for repository https://github.com/Marie59/champ_blocs commit 0d86db7d42b608c386a54500064f5f9c9d7019a4 ecology parents: diff changeset	1166 bret_egmp_basq_qecb <- c(
89f977a3a256 planemo upload for repository https://github.com/Marie59/champ_blocs commit 0d86db7d42b608c386a54500064f5f9c9d7019a4 ecology parents: diff changeset	1167 "X..algues.brunes",
89f977a3a256 planemo upload for repository https://github.com/Marie59/champ_blocs commit 0d86db7d42b608c386a54500064f5f9c9d7019a4 ecology parents: diff changeset	1168 "X..algues.rouges",
89f977a3a256 planemo upload for repository https://github.com/Marie59/champ_blocs commit 0d86db7d42b608c386a54500064f5f9c9d7019a4 ecology parents: diff changeset	1169 "X..algues.vertes",
89f977a3a256 planemo upload for repository https://github.com/Marie59/champ_blocs commit 0d86db7d42b608c386a54500064f5f9c9d7019a4 ecology parents: diff changeset	1170 "X..Cladophora",
89f977a3a256 planemo upload for repository https://github.com/Marie59/champ_blocs commit 0d86db7d42b608c386a54500064f5f9c9d7019a4 ecology parents: diff changeset	1171 "X..Lithophyllum",
89f977a3a256 planemo upload for repository https://github.com/Marie59/champ_blocs commit 0d86db7d42b608c386a54500064f5f9c9d7019a4 ecology parents: diff changeset	1172 "Nb.Littorina.obtusata",
89f977a3a256 planemo upload for repository https://github.com/Marie59/champ_blocs commit 0d86db7d42b608c386a54500064f5f9c9d7019a4 ecology parents: diff changeset	1173 "Nb.Gibbula.cineraria",
89f977a3a256 planemo upload for repository https://github.com/Marie59/champ_blocs commit 0d86db7d42b608c386a54500064f5f9c9d7019a4 ecology parents: diff changeset	1174 "Nb.Gibbula.pennanti",
89f977a3a256 planemo upload for repository https://github.com/Marie59/champ_blocs commit 0d86db7d42b608c386a54500064f5f9c9d7019a4 ecology parents: diff changeset	1175 "Nb.Gibbula.umbilicalis",
89f977a3a256 planemo upload for repository https://github.com/Marie59/champ_blocs commit 0d86db7d42b608c386a54500064f5f9c9d7019a4 ecology parents: diff changeset	1176 "Nb.Phallusia.mamillata",
89f977a3a256 planemo upload for repository https://github.com/Marie59/champ_blocs commit 0d86db7d42b608c386a54500064f5f9c9d7019a4 ecology parents: diff changeset	1177 "Nb.Tethya.aurantium",
89f977a3a256 planemo upload for repository https://github.com/Marie59/champ_blocs commit 0d86db7d42b608c386a54500064f5f9c9d7019a4 ecology parents: diff changeset	1178 "Nb.Spirobranchus.lamarckii.total",
89f977a3a256 planemo upload for repository https://github.com/Marie59/champ_blocs commit 0d86db7d42b608c386a54500064f5f9c9d7019a4 ecology parents: diff changeset	1179 "Nb.spirorbis.total",
89f977a3a256 planemo upload for repository https://github.com/Marie59/champ_blocs commit 0d86db7d42b608c386a54500064f5f9c9d7019a4 ecology parents: diff changeset	1180 "X..Eponges",
89f977a3a256 planemo upload for repository https://github.com/Marie59/champ_blocs commit 0d86db7d42b608c386a54500064f5f9c9d7019a4 ecology parents: diff changeset	1181 "X..Ascidies.Coloniales",
89f977a3a256 planemo upload for repository https://github.com/Marie59/champ_blocs commit 0d86db7d42b608c386a54500064f5f9c9d7019a4 ecology parents: diff changeset	1182 "X..Ascidies.Solitaires",
89f977a3a256 planemo upload for repository https://github.com/Marie59/champ_blocs commit 0d86db7d42b608c386a54500064f5f9c9d7019a4 ecology parents: diff changeset	1183 "X..Bryozoaires.Dresses",
89f977a3a256 planemo upload for repository https://github.com/Marie59/champ_blocs commit 0d86db7d42b608c386a54500064f5f9c9d7019a4 ecology parents: diff changeset	1184 "X..Balanes.Vivantes"
89f977a3a256 planemo upload for repository https://github.com/Marie59/champ_blocs commit 0d86db7d42b608c386a54500064f5f9c9d7019a4 ecology parents: diff changeset	1185 #, "X..Recouvrement.Sediment"
89f977a3a256 planemo upload for repository https://github.com/Marie59/champ_blocs commit 0d86db7d42b608c386a54500064f5f9c9d7019a4 ecology parents: diff changeset	1186 #, "X..Roche.Nue"
89f977a3a256 planemo upload for repository https://github.com/Marie59/champ_blocs commit 0d86db7d42b608c386a54500064f5f9c9d7019a4 ecology parents: diff changeset	1187 #, "X..Surface.Accolement"
89f977a3a256 planemo upload for repository https://github.com/Marie59/champ_blocs commit 0d86db7d42b608c386a54500064f5f9c9d7019a4 ecology parents: diff changeset	1188 )
89f977a3a256 planemo upload for repository https://github.com/Marie59/champ_blocs commit 0d86db7d42b608c386a54500064f5f9c9d7019a4 ecology parents: diff changeset	1189
89f977a3a256 planemo upload for repository https://github.com/Marie59/champ_blocs commit 0d86db7d42b608c386a54500064f5f9c9d7019a4 ecology parents: diff changeset	1190 egmp_basq_qecb <- c("Nb.Crassostrea.gigas", "Nb.Ostrea.edulis", "X..Mytilus.sp.", "X..Hermelles", "X..Hydraires")
89f977a3a256 planemo upload for repository https://github.com/Marie59/champ_blocs commit 0d86db7d42b608c386a54500064f5f9c9d7019a4 ecology parents: diff changeset	1191
89f977a3a256 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.",
89f977a3a256 planemo upload for repository https://github.com/Marie59/champ_blocs commit 0d86db7d42b608c386a54500064f5f9c9d7019a4 ecology parents: diff changeset	1193 "Nb.Necora.puber..Etrille.",
89f977a3a256 planemo upload for repository https://github.com/Marie59/champ_blocs commit 0d86db7d42b608c386a54500064f5f9c9d7019a4 ecology parents: diff changeset	1194 "Nb.Carcinus.maenas..Crabe.vert.",
89f977a3a256 planemo upload for repository https://github.com/Marie59/champ_blocs commit 0d86db7d42b608c386a54500064f5f9c9d7019a4 ecology parents: diff changeset	1195 "Nb.Nucella.lapilus..Pourpre.",
89f977a3a256 planemo upload for repository https://github.com/Marie59/champ_blocs commit 0d86db7d42b608c386a54500064f5f9c9d7019a4 ecology parents: diff changeset	1196 "Nb.Galathea..Galathées.",
89f977a3a256 planemo upload for repository https://github.com/Marie59/champ_blocs commit 0d86db7d42b608c386a54500064f5f9c9d7019a4 ecology parents: diff changeset	1197 "Nb.Lophozozymus.incisus..ancien.Xantho.incisus.",
89f977a3a256 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.",
89f977a3a256 planemo upload for repository https://github.com/Marie59/champ_blocs commit 0d86db7d42b608c386a54500064f5f9c9d7019a4 ecology parents: diff changeset	1199 "Nb.Haliotis.tuberculata..Ormeau.",
89f977a3a256 planemo upload for repository https://github.com/Marie59/champ_blocs commit 0d86db7d42b608c386a54500064f5f9c9d7019a4 ecology parents: diff changeset	1200 "Nb.Littorina.littorea..Bigorneau.",
89f977a3a256 planemo upload for repository https://github.com/Marie59/champ_blocs commit 0d86db7d42b608c386a54500064f5f9c9d7019a4 ecology parents: diff changeset	1201 "Nb.Xantho.pilipes..Xanthe.poilu.",
89f977a3a256 planemo upload for repository https://github.com/Marie59/champ_blocs commit 0d86db7d42b608c386a54500064f5f9c9d7019a4 ecology parents: diff changeset	1202 "Nb.Mimachlamys.varia..Pétoncle.noir.")
89f977a3a256 planemo upload for repository https://github.com/Marie59/champ_blocs commit 0d86db7d42b608c386a54500064f5f9c9d7019a4 ecology parents: diff changeset	1203
89f977a3a256 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.")
89f977a3a256 planemo upload for repository https://github.com/Marie59/champ_blocs commit 0d86db7d42b608c386a54500064f5f9c9d7019a4 ecology parents: diff changeset	1205
89f977a3a256 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
89f977a3a256 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")
89f977a3a256 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")
89f977a3a256 planemo upload for repository https://github.com/Marie59/champ_blocs commit 0d86db7d42b608c386a54500064f5f9c9d7019a4 ecology parents: diff changeset	1209
89f977a3a256 planemo upload for repository https://github.com/Marie59/champ_blocs commit 0d86db7d42b608c386a54500064f5f9c9d7019a4 ecology parents: diff changeset	1210
89f977a3a256 planemo upload for repository https://github.com/Marie59/champ_blocs commit 0d86db7d42b608c386a54500064f5f9c9d7019a4 ecology parents: diff changeset	1211 #############################################################
89f977a3a256 planemo upload for repository https://github.com/Marie59/champ_blocs commit 0d86db7d42b608c386a54500064f5f9c9d7019a4 ecology parents: diff changeset	1212 # #
89f977a3a256 planemo upload for repository https://github.com/Marie59/champ_blocs commit 0d86db7d42b608c386a54500064f5f9c9d7019a4 ecology parents: diff changeset	1213 # Compute dissimilarity #
89f977a3a256 planemo upload for repository https://github.com/Marie59/champ_blocs commit 0d86db7d42b608c386a54500064f5f9c9d7019a4 ecology parents: diff changeset	1214 # #
89f977a3a256 planemo upload for repository https://github.com/Marie59/champ_blocs commit 0d86db7d42b608c386a54500064f5f9c9d7019a4 ecology parents: diff changeset	1215 #############################################################
89f977a3a256 planemo upload for repository https://github.com/Marie59/champ_blocs commit 0d86db7d42b608c386a54500064f5f9c9d7019a4 ecology parents: diff changeset	1216 ### determination of coefficient of dissimilarity face sup mobile bloc vs fixed bloc
89f977a3a256 planemo upload for repository https://github.com/Marie59/champ_blocs commit 0d86db7d42b608c386a54500064f5f9c9d7019a4 ecology parents: diff changeset	1217
89f977a3a256 planemo upload for repository https://github.com/Marie59/champ_blocs commit 0d86db7d42b608c386a54500064f5f9c9d7019a4 ecology parents: diff changeset	1218 # loop in a fct
89f977a3a256 planemo upload for repository https://github.com/Marie59/champ_blocs commit 0d86db7d42b608c386a54500064f5f9c9d7019a4 ecology parents: diff changeset	1219
89f977a3a256 planemo upload for repository https://github.com/Marie59/champ_blocs commit 0d86db7d42b608c386a54500064f5f9c9d7019a4 ecology parents: diff changeset	1220 matri_fct_bmf <- function(data, conca) {
89f977a3a256 planemo upload for repository https://github.com/Marie59/champ_blocs commit 0d86db7d42b608c386a54500064f5f9c9d7019a4 ecology parents: diff changeset	1221
89f977a3a256 planemo upload for repository https://github.com/Marie59/champ_blocs commit 0d86db7d42b608c386a54500064f5f9c9d7019a4 ecology parents: diff changeset	1222 matri_df <- data
89f977a3a256 planemo upload for repository https://github.com/Marie59/champ_blocs commit 0d86db7d42b608c386a54500064f5f9c9d7019a4 ecology parents: diff changeset	1223
89f977a3a256 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)))) {
89f977a3a256 planemo upload for repository https://github.com/Marie59/champ_blocs commit 0d86db7d42b608c386a54500064f5f9c9d7019a4 ecology parents: diff changeset	1225
89f977a3a256 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$site_year_month_day)[[x]])
89f977a3a256 planemo upload for repository https://github.com/Marie59/champ_blocs commit 0d86db7d42b608c386a54500064f5f9c9d7019a4 ecology parents: diff changeset	1227
89f977a3a256 planemo upload for repository https://github.com/Marie59/champ_blocs commit 0d86db7d42b608c386a54500064f5f9c9d7019a4 ecology parents: diff changeset	1228 rownames(qecbnato0_x) <- paste0(qecbnato0_x$Type.Bloc, "_", qecbnato0_x$Face, "_", qecbnato0_x$Numéro.Bloc.échantillon, "_", qecbnato0_x$quadrat_bis)
89f977a3a256 planemo upload for repository https://github.com/Marie59/champ_blocs commit 0d86db7d42b608c386a54500064f5f9c9d7019a4 ecology parents: diff changeset	1229
89f977a3a256 planemo upload for repository https://github.com/Marie59/champ_blocs commit 0d86db7d42b608c386a54500064f5f9c9d7019a4 ecology parents: diff changeset	1230
89f977a3a256 planemo upload for repository https://github.com/Marie59/champ_blocs commit 0d86db7d42b608c386a54500064f5f9c9d7019a4 ecology parents: diff changeset	1231 mtxdis <- vegan::vegdist(
89f977a3a256 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)
89f977a3a256 planemo upload for repository https://github.com/Marie59/champ_blocs commit 0d86db7d42b608c386a54500064f5f9c9d7019a4 ecology parents: diff changeset	1233
89f977a3a256 planemo upload for repository https://github.com/Marie59/champ_blocs commit 0d86db7d42b608c386a54500064f5f9c9d7019a4 ecology parents: diff changeset	1234 na.rm = TRUE,
89f977a3a256 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 ??
89f977a3a256 planemo upload for repository https://github.com/Marie59/champ_blocs commit 0d86db7d42b608c386a54500064f5f9c9d7019a4 ecology parents: diff changeset	1236 )
89f977a3a256 planemo upload for repository https://github.com/Marie59/champ_blocs commit 0d86db7d42b608c386a54500064f5f9c9d7019a4 ecology parents: diff changeset	1237
89f977a3a256 planemo upload for repository https://github.com/Marie59/champ_blocs commit 0d86db7d42b608c386a54500064f5f9c9d7019a4 ecology parents: diff changeset	1238
89f977a3a256 planemo upload for repository https://github.com/Marie59/champ_blocs commit 0d86db7d42b608c386a54500064f5f9c9d7019a4 ecology parents: diff changeset	1239 #https://rdrr.io/github/phytomosaic/ecole/man/bray0.html
89f977a3a256 planemo upload for repository https://github.com/Marie59/champ_blocs commit 0d86db7d42b608c386a54500064f5f9c9d7019a4 ecology parents: diff changeset	1240 # mtxdis <- ecole::bray0(
89f977a3a256 planemo upload for repository https://github.com/Marie59/champ_blocs commit 0d86db7d42b608c386a54500064f5f9c9d7019a4 ecology parents: diff changeset	1241 # sqrt
89f977a3a256 planemo upload for repository https://github.com/Marie59/champ_blocs commit 0d86db7d42b608c386a54500064f5f9c9d7019a4 ecology parents: diff changeset	1242 # (qecbnato0_x[,conca]), na.rm = TRUE)
89f977a3a256 planemo upload for repository https://github.com/Marie59/champ_blocs commit 0d86db7d42b608c386a54500064f5f9c9d7019a4 ecology parents: diff changeset	1243
89f977a3a256 planemo upload for repository https://github.com/Marie59/champ_blocs commit 0d86db7d42b608c386a54500064f5f9c9d7019a4 ecology parents: diff changeset	1244 expand.grid(mtxdis)
89f977a3a256 planemo upload for repository https://github.com/Marie59/champ_blocs commit 0d86db7d42b608c386a54500064f5f9c9d7019a4 ecology parents: diff changeset	1245
89f977a3a256 planemo upload for repository https://github.com/Marie59/champ_blocs commit 0d86db7d42b608c386a54500064f5f9c9d7019a4 ecology parents: diff changeset	1246 mtxdisdf_ <- as.data.frame(as.matrix(mtxdis))
89f977a3a256 planemo upload for repository https://github.com/Marie59/champ_blocs commit 0d86db7d42b608c386a54500064f5f9c9d7019a4 ecology parents: diff changeset	1247
89f977a3a256 planemo upload for repository https://github.com/Marie59/champ_blocs commit 0d86db7d42b608c386a54500064f5f9c9d7019a4 ecology parents: diff changeset	1248 a_ <- NA
89f977a3a256 planemo upload for repository https://github.com/Marie59/champ_blocs commit 0d86db7d42b608c386a54500064f5f9c9d7019a4 ecology parents: diff changeset	1249 b_ <- NA
89f977a3a256 planemo upload for repository https://github.com/Marie59/champ_blocs commit 0d86db7d42b608c386a54500064f5f9c9d7019a4 ecology parents: diff changeset	1250 c_ <- NA
89f977a3a256 planemo upload for repository https://github.com/Marie59/champ_blocs commit 0d86db7d42b608c386a54500064f5f9c9d7019a4 ecology parents: diff changeset	1251 d_ <- NA
89f977a3a256 planemo upload for repository https://github.com/Marie59/champ_blocs commit 0d86db7d42b608c386a54500064f5f9c9d7019a4 ecology parents: diff changeset	1252 e_ <- NA
89f977a3a256 planemo upload for repository https://github.com/Marie59/champ_blocs commit 0d86db7d42b608c386a54500064f5f9c9d7019a4 ecology parents: diff changeset	1253 f_ <- NA
89f977a3a256 planemo upload for repository https://github.com/Marie59/champ_blocs commit 0d86db7d42b608c386a54500064f5f9c9d7019a4 ecology parents: diff changeset	1254 g_ <- NA
89f977a3a256 planemo upload for repository https://github.com/Marie59/champ_blocs commit 0d86db7d42b608c386a54500064f5f9c9d7019a4 ecology parents: diff changeset	1255 h_ <- NA
89f977a3a256 planemo upload for repository https://github.com/Marie59/champ_blocs commit 0d86db7d42b608c386a54500064f5f9c9d7019a4 ecology parents: diff changeset	1256 i_ <- NA
89f977a3a256 planemo upload for repository https://github.com/Marie59/champ_blocs commit 0d86db7d42b608c386a54500064f5f9c9d7019a4 ecology parents: diff changeset	1257 j_ <- NA
89f977a3a256 planemo upload for repository https://github.com/Marie59/champ_blocs commit 0d86db7d42b608c386a54500064f5f9c9d7019a4 ecology parents: diff changeset	1258 k_ <- NA
89f977a3a256 planemo upload for repository https://github.com/Marie59/champ_blocs commit 0d86db7d42b608c386a54500064f5f9c9d7019a4 ecology parents: diff changeset	1259 l_ <- NA
89f977a3a256 planemo upload for repository https://github.com/Marie59/champ_blocs commit 0d86db7d42b608c386a54500064f5f9c9d7019a4 ecology parents: diff changeset	1260 m_ <- NA
89f977a3a256 planemo upload for repository https://github.com/Marie59/champ_blocs commit 0d86db7d42b608c386a54500064f5f9c9d7019a4 ecology parents: diff changeset	1261 n_ <- NA
89f977a3a256 planemo upload for repository https://github.com/Marie59/champ_blocs commit 0d86db7d42b608c386a54500064f5f9c9d7019a4 ecology parents: diff changeset	1262
89f977a3a256 planemo upload for repository https://github.com/Marie59/champ_blocs commit 0d86db7d42b608c386a54500064f5f9c9d7019a4 ecology parents: diff changeset	1263 for (z in c(1:nrow(mtxdisdf_))) {
89f977a3a256 planemo upload for repository https://github.com/Marie59/champ_blocs commit 0d86db7d42b608c386a54500064f5f9c9d7019a4 ecology parents: diff changeset	1264
89f977a3a256 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)))
89f977a3a256 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)))
89f977a3a256 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)))
89f977a3a256 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)))
89f977a3a256 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)))
89f977a3a256 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)))
89f977a3a256 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)))
89f977a3a256 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)))
89f977a3a256 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)))
89f977a3a256 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)))
89f977a3a256 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)))
89f977a3a256 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)))
89f977a3a256 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)))
89f977a3a256 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)))
89f977a3a256 planemo upload for repository https://github.com/Marie59/champ_blocs commit 0d86db7d42b608c386a54500064f5f9c9d7019a4 ecology parents: diff changeset	1279
89f977a3a256 planemo upload for repository https://github.com/Marie59/champ_blocs commit 0d86db7d42b608c386a54500064f5f9c9d7019a4 ecology parents: diff changeset	1280 }
89f977a3a256 planemo upload for repository https://github.com/Marie59/champ_blocs commit 0d86db7d42b608c386a54500064f5f9c9d7019a4 ecology parents: diff changeset	1281
89f977a3a256 planemo upload for repository https://github.com/Marie59/champ_blocs commit 0d86db7d42b608c386a54500064f5f9c9d7019a4 ecology parents: diff changeset	1282 rm(z)
89f977a3a256 planemo upload for repository https://github.com/Marie59/champ_blocs commit 0d86db7d42b608c386a54500064f5f9c9d7019a4 ecology parents: diff changeset	1283
89f977a3a256 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_)))
89f977a3a256 planemo upload for repository https://github.com/Marie59/champ_blocs commit 0d86db7d42b608c386a54500064f5f9c9d7019a4 ecology parents: diff changeset	1285 a_ <- a_[1:y]
89f977a3a256 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_)))
89f977a3a256 planemo upload for repository https://github.com/Marie59/champ_blocs commit 0d86db7d42b608c386a54500064f5f9c9d7019a4 ecology parents: diff changeset	1287 b_ <- b_[1:y]
89f977a3a256 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_)))
89f977a3a256 planemo upload for repository https://github.com/Marie59/champ_blocs commit 0d86db7d42b608c386a54500064f5f9c9d7019a4 ecology parents: diff changeset	1289 c_ <- c_[1:y]
89f977a3a256 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_)))
89f977a3a256 planemo upload for repository https://github.com/Marie59/champ_blocs commit 0d86db7d42b608c386a54500064f5f9c9d7019a4 ecology parents: diff changeset	1291 d_ <- d_[1:y]
89f977a3a256 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_)))
89f977a3a256 planemo upload for repository https://github.com/Marie59/champ_blocs commit 0d86db7d42b608c386a54500064f5f9c9d7019a4 ecology parents: diff changeset	1293 e_ <- e_[1:y]
89f977a3a256 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_)))
89f977a3a256 planemo upload for repository https://github.com/Marie59/champ_blocs commit 0d86db7d42b608c386a54500064f5f9c9d7019a4 ecology parents: diff changeset	1295 f_ <- f_[1:y]
89f977a3a256 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_)))
89f977a3a256 planemo upload for repository https://github.com/Marie59/champ_blocs commit 0d86db7d42b608c386a54500064f5f9c9d7019a4 ecology parents: diff changeset	1297 g_ <- g_[1:y]
89f977a3a256 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_)))
89f977a3a256 planemo upload for repository https://github.com/Marie59/champ_blocs commit 0d86db7d42b608c386a54500064f5f9c9d7019a4 ecology parents: diff changeset	1299 h_ <- h_[1:y]
89f977a3a256 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_)))
89f977a3a256 planemo upload for repository https://github.com/Marie59/champ_blocs commit 0d86db7d42b608c386a54500064f5f9c9d7019a4 ecology parents: diff changeset	1301 i_ <- i_[1:y]
89f977a3a256 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_)))
89f977a3a256 planemo upload for repository https://github.com/Marie59/champ_blocs commit 0d86db7d42b608c386a54500064f5f9c9d7019a4 ecology parents: diff changeset	1303 j_ <- j_[1:y]
89f977a3a256 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_)))
89f977a3a256 planemo upload for repository https://github.com/Marie59/champ_blocs commit 0d86db7d42b608c386a54500064f5f9c9d7019a4 ecology parents: diff changeset	1305 k_ <- k_[1:y]
89f977a3a256 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_)))
89f977a3a256 planemo upload for repository https://github.com/Marie59/champ_blocs commit 0d86db7d42b608c386a54500064f5f9c9d7019a4 ecology parents: diff changeset	1307 l_ <- l_[1:y]
89f977a3a256 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_)))
89f977a3a256 planemo upload for repository https://github.com/Marie59/champ_blocs commit 0d86db7d42b608c386a54500064f5f9c9d7019a4 ecology parents: diff changeset	1309 m_ <- m_[1:y]
89f977a3a256 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_)))
89f977a3a256 planemo upload for repository https://github.com/Marie59/champ_blocs commit 0d86db7d42b608c386a54500064f5f9c9d7019a4 ecology parents: diff changeset	1311 n_ <- n_[1:y]
89f977a3a256 planemo upload for repository https://github.com/Marie59/champ_blocs commit 0d86db7d42b608c386a54500064f5f9c9d7019a4 ecology parents: diff changeset	1312
89f977a3a256 planemo upload for repository https://github.com/Marie59/champ_blocs commit 0d86db7d42b608c386a54500064f5f9c9d7019a4 ecology parents: diff changeset	1313 rm(y)
89f977a3a256 planemo upload for repository https://github.com/Marie59/champ_blocs commit 0d86db7d42b608c386a54500064f5f9c9d7019a4 ecology parents: diff changeset	1314
89f977a3a256 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_)
89f977a3a256 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))])
89f977a3a256 planemo upload for repository https://github.com/Marie59/champ_blocs commit 0d86db7d42b608c386a54500064f5f9c9d7019a4 ecology parents: diff changeset	1317 names(df_) <- c("dist.", "name_")
89f977a3a256 planemo upload for repository https://github.com/Marie59/champ_blocs commit 0d86db7d42b608c386a54500064f5f9c9d7019a4 ecology parents: diff changeset	1318
89f977a3a256 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_)
89f977a3a256 planemo upload for repository https://github.com/Marie59/champ_blocs commit 0d86db7d42b608c386a54500064f5f9c9d7019a4 ecology parents: diff changeset	1320 rm(name_)
89f977a3a256 planemo upload for repository https://github.com/Marie59/champ_blocs commit 0d86db7d42b608c386a54500064f5f9c9d7019a4 ecology parents: diff changeset	1321
89f977a3a256 planemo upload for repository https://github.com/Marie59/champ_blocs commit 0d86db7d42b608c386a54500064f5f9c9d7019a4 ecology parents: diff changeset	1322 q_ <- strsplit(df_$name_, " & ")
89f977a3a256 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)
89f977a3a256 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))
89f977a3a256 planemo upload for repository https://github.com/Marie59/champ_blocs commit 0d86db7d42b608c386a54500064f5f9c9d7019a4 ecology parents: diff changeset	1325 df_ <- dplyr::bind_cols(df_, q_df_)
89f977a3a256 planemo upload for repository https://github.com/Marie59/champ_blocs commit 0d86db7d42b608c386a54500064f5f9c9d7019a4 ecology parents: diff changeset	1326
89f977a3a256 planemo upload for repository https://github.com/Marie59/champ_blocs commit 0d86db7d42b608c386a54500064f5f9c9d7019a4 ecology parents: diff changeset	1327 rm(q_, mat_, q_df_)
89f977a3a256 planemo upload for repository https://github.com/Marie59/champ_blocs commit 0d86db7d42b608c386a54500064f5f9c9d7019a4 ecology parents: diff changeset	1328
89f977a3a256 planemo upload for repository https://github.com/Marie59/champ_blocs commit 0d86db7d42b608c386a54500064f5f9c9d7019a4 ecology parents: diff changeset	1329 split_ <- strsplit(df_$V1, "_")
89f977a3a256 planemo upload for repository https://github.com/Marie59/champ_blocs commit 0d86db7d42b608c386a54500064f5f9c9d7019a4 ecology parents: diff changeset	1330 v1_split_ <- as.data.frame(matrix(unlist(split_), ncol = 4, byrow = TRUE))
89f977a3a256 planemo upload for repository https://github.com/Marie59/champ_blocs commit 0d86db7d42b608c386a54500064f5f9c9d7019a4 ecology parents: diff changeset	1331 split_ <- strsplit(df_$V2, "_")
89f977a3a256 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))
89f977a3a256 planemo upload for repository https://github.com/Marie59/champ_blocs commit 0d86db7d42b608c386a54500064f5f9c9d7019a4 ecology parents: diff changeset	1333
89f977a3a256 planemo upload for repository https://github.com/Marie59/champ_blocs commit 0d86db7d42b608c386a54500064f5f9c9d7019a4 ecology parents: diff changeset	1334 df_ <- dplyr::bind_cols(df_, v1_split_)
89f977a3a256 planemo upload for repository https://github.com/Marie59/champ_blocs commit 0d86db7d42b608c386a54500064f5f9c9d7019a4 ecology parents: diff changeset	1335 df_ <- dplyr::bind_cols(df_, v2_split_)
89f977a3a256 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)
89f977a3a256 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_))
89f977a3a256 planemo upload for repository https://github.com/Marie59/champ_blocs commit 0d86db7d42b608c386a54500064f5f9c9d7019a4 ecology parents: diff changeset	1338
89f977a3a256 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.")
89f977a3a256 planemo upload for repository https://github.com/Marie59/champ_blocs commit 0d86db7d42b608c386a54500064f5f9c9d7019a4 ecology parents: diff changeset	1340
89f977a3a256 planemo upload for repository https://github.com/Marie59/champ_blocs commit 0d86db7d42b608c386a54500064f5f9c9d7019a4 ecology parents: diff changeset	1341 rm(split_, v1_split_, v2_split_)
89f977a3a256 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)
89f977a3a256 planemo upload for repository https://github.com/Marie59/champ_blocs commit 0d86db7d42b608c386a54500064f5f9c9d7019a4 ecology parents: diff changeset	1343
89f977a3a256 planemo upload for repository https://github.com/Marie59/champ_blocs commit 0d86db7d42b608c386a54500064f5f9c9d7019a4 ecology parents: diff changeset	1344 matri_list[[x]] <- df_red_
89f977a3a256 planemo upload for repository https://github.com/Marie59/champ_blocs commit 0d86db7d42b608c386a54500064f5f9c9d7019a4 ecology parents: diff changeset	1345 matri_list <<- matri_list
89f977a3a256 planemo upload for repository https://github.com/Marie59/champ_blocs commit 0d86db7d42b608c386a54500064f5f9c9d7019a4 ecology parents: diff changeset	1346
89f977a3a256 planemo upload for repository https://github.com/Marie59/champ_blocs commit 0d86db7d42b608c386a54500064f5f9c9d7019a4 ecology parents: diff changeset	1347 rm(df_red_, qecbnato0_x, x)
89f977a3a256 planemo upload for repository https://github.com/Marie59/champ_blocs commit 0d86db7d42b608c386a54500064f5f9c9d7019a4 ecology parents: diff changeset	1348
89f977a3a256 planemo upload for repository https://github.com/Marie59/champ_blocs commit 0d86db7d42b608c386a54500064f5f9c9d7019a4 ecology parents: diff changeset	1349 }
89f977a3a256 planemo upload for repository https://github.com/Marie59/champ_blocs commit 0d86db7d42b608c386a54500064f5f9c9d7019a4 ecology parents: diff changeset	1350
89f977a3a256 planemo upload for repository https://github.com/Marie59/champ_blocs commit 0d86db7d42b608c386a54500064f5f9c9d7019a4 ecology parents: diff changeset	1351 matri_df <- do.call("rbind", matri_list)
89f977a3a256 planemo upload for repository https://github.com/Marie59/champ_blocs commit 0d86db7d42b608c386a54500064f5f9c9d7019a4 ecology parents: diff changeset	1352
89f977a3a256 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")
89f977a3a256 planemo upload for repository https://github.com/Marie59/champ_blocs commit 0d86db7d42b608c386a54500064f5f9c9d7019a4 ecology parents: diff changeset	1354
89f977a3a256 planemo upload for repository https://github.com/Marie59/champ_blocs commit 0d86db7d42b608c386a54500064f5f9c9d7019a4 ecology parents: diff changeset	1355 matri_df <<- matri_df
89f977a3a256 planemo upload for repository https://github.com/Marie59/champ_blocs commit 0d86db7d42b608c386a54500064f5f9c9d7019a4 ecology parents: diff changeset	1356
89f977a3a256 planemo upload for repository https://github.com/Marie59/champ_blocs commit 0d86db7d42b608c386a54500064f5f9c9d7019a4 ecology parents: diff changeset	1357 hist(matri_df$dist.)
89f977a3a256 planemo upload for repository https://github.com/Marie59/champ_blocs commit 0d86db7d42b608c386a54500064f5f9c9d7019a4 ecology parents: diff changeset	1358
89f977a3a256 planemo upload for repository https://github.com/Marie59/champ_blocs commit 0d86db7d42b608c386a54500064f5f9c9d7019a4 ecology parents: diff changeset	1359 }
89f977a3a256 planemo upload for repository https://github.com/Marie59/champ_blocs commit 0d86db7d42b608c386a54500064f5f9c9d7019a4 ecology parents: diff changeset	1360
89f977a3a256 planemo upload for repository https://github.com/Marie59/champ_blocs commit 0d86db7d42b608c386a54500064f5f9c9d7019a4 ecology parents: diff changeset	1361 data_ <- dplyr::filter(qecbnato0, Face == "face supérieure")
89f977a3a256 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_$Type.Bloc))
89f977a3a256 planemo upload for repository https://github.com/Marie59/champ_blocs commit 0d86db7d42b608c386a54500064f5f9c9d7019a4 ecology parents: diff changeset	1363 matri_list <- vector("list", length(unique(data_$site_year_month_day)))
89f977a3a256 planemo upload for repository https://github.com/Marie59/champ_blocs commit 0d86db7d42b608c386a54500064f5f9c9d7019a4 ecology parents: diff changeset	1364
89f977a3a256 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))
89f977a3a256 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 -")))
89f977a3a256 planemo upload for repository https://github.com/Marie59/champ_blocs commit 0d86db7d42b608c386a54500064f5f9c9d7019a4 ecology parents: diff changeset	1367
89f977a3a256 planemo upload for repository https://github.com/Marie59/champ_blocs commit 0d86db7d42b608c386a54500064f5f9c9d7019a4 ecology parents: diff changeset	1368 matri_full_bm_bf_fs <- matri_df
89f977a3a256 planemo upload for repository https://github.com/Marie59/champ_blocs commit 0d86db7d42b608c386a54500064f5f9c9d7019a4 ecology parents: diff changeset	1369
89f977a3a256 planemo upload for repository https://github.com/Marie59/champ_blocs commit 0d86db7d42b608c386a54500064f5f9c9d7019a4 ecology parents: diff changeset	1370
89f977a3a256 planemo upload for repository https://github.com/Marie59/champ_blocs commit 0d86db7d42b608c386a54500064f5f9c9d7019a4 ecology parents: diff changeset	1371 rm(data_, matri_df, matri_list)
89f977a3a256 planemo upload for repository https://github.com/Marie59/champ_blocs commit 0d86db7d42b608c386a54500064f5f9c9d7019a4 ecology parents: diff changeset	1372
89f977a3a256 planemo upload for repository https://github.com/Marie59/champ_blocs commit 0d86db7d42b608c386a54500064f5f9c9d7019a4 ecology parents: diff changeset	1373
89f977a3a256 planemo upload for repository https://github.com/Marie59/champ_blocs commit 0d86db7d42b608c386a54500064f5f9c9d7019a4 ecology parents: diff changeset	1374 ### determination of coefficient of dissimilarity between blocs mobiles face sup vs face inf.
89f977a3a256 planemo upload for repository https://github.com/Marie59/champ_blocs commit 0d86db7d42b608c386a54500064f5f9c9d7019a4 ecology parents: diff changeset	1375
89f977a3a256 planemo upload for repository https://github.com/Marie59/champ_blocs commit 0d86db7d42b608c386a54500064f5f9c9d7019a4 ecology parents: diff changeset	1376 # loop in a fct
89f977a3a256 planemo upload for repository https://github.com/Marie59/champ_blocs commit 0d86db7d42b608c386a54500064f5f9c9d7019a4 ecology parents: diff changeset	1377
89f977a3a256 planemo upload for repository https://github.com/Marie59/champ_blocs commit 0d86db7d42b608c386a54500064f5f9c9d7019a4 ecology parents: diff changeset	1378 matri_fct_bmm <- function(data, conca) {
89f977a3a256 planemo upload for repository https://github.com/Marie59/champ_blocs commit 0d86db7d42b608c386a54500064f5f9c9d7019a4 ecology parents: diff changeset	1379
89f977a3a256 planemo upload for repository https://github.com/Marie59/champ_blocs commit 0d86db7d42b608c386a54500064f5f9c9d7019a4 ecology parents: diff changeset	1380 matri_df <- data
89f977a3a256 planemo upload for repository https://github.com/Marie59/champ_blocs commit 0d86db7d42b608c386a54500064f5f9c9d7019a4 ecology parents: diff changeset	1381
89f977a3a256 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)))) {
89f977a3a256 planemo upload for repository https://github.com/Marie59/champ_blocs commit 0d86db7d42b608c386a54500064f5f9c9d7019a4 ecology parents: diff changeset	1383
89f977a3a256 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$site_year_month_day)[[x]])
89f977a3a256 planemo upload for repository https://github.com/Marie59/champ_blocs commit 0d86db7d42b608c386a54500064f5f9c9d7019a4 ecology parents: diff changeset	1385
89f977a3a256 planemo upload for repository https://github.com/Marie59/champ_blocs commit 0d86db7d42b608c386a54500064f5f9c9d7019a4 ecology parents: diff changeset	1386 rownames(qecbnato0_x) <- paste0(qecbnato0_x$Type.Bloc, "_", qecbnato0_x$Face, "_", qecbnato0_x$Numéro.Bloc.échantillon, "_", qecbnato0_x$quadrat_bis)
89f977a3a256 planemo upload for repository https://github.com/Marie59/champ_blocs commit 0d86db7d42b608c386a54500064f5f9c9d7019a4 ecology parents: diff changeset	1387
89f977a3a256 planemo upload for repository https://github.com/Marie59/champ_blocs commit 0d86db7d42b608c386a54500064f5f9c9d7019a4 ecology parents: diff changeset	1388
89f977a3a256 planemo upload for repository https://github.com/Marie59/champ_blocs commit 0d86db7d42b608c386a54500064f5f9c9d7019a4 ecology parents: diff changeset	1389 mtxdis <- vegan::vegdist(
89f977a3a256 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)
89f977a3a256 planemo upload for repository https://github.com/Marie59/champ_blocs commit 0d86db7d42b608c386a54500064f5f9c9d7019a4 ecology parents: diff changeset	1391 na.rm = TRUE,
89f977a3a256 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 ??
89f977a3a256 planemo upload for repository https://github.com/Marie59/champ_blocs commit 0d86db7d42b608c386a54500064f5f9c9d7019a4 ecology parents: diff changeset	1393 )
89f977a3a256 planemo upload for repository https://github.com/Marie59/champ_blocs commit 0d86db7d42b608c386a54500064f5f9c9d7019a4 ecology parents: diff changeset	1394
89f977a3a256 planemo upload for repository https://github.com/Marie59/champ_blocs commit 0d86db7d42b608c386a54500064f5f9c9d7019a4 ecology parents: diff changeset	1395
89f977a3a256 planemo upload for repository https://github.com/Marie59/champ_blocs commit 0d86db7d42b608c386a54500064f5f9c9d7019a4 ecology parents: diff changeset	1396 #mtxdis <- ecole::bray0(
89f977a3a256 planemo upload for repository https://github.com/Marie59/champ_blocs commit 0d86db7d42b608c386a54500064f5f9c9d7019a4 ecology parents: diff changeset	1397 # sqrt(qecbnato0_x[, conca]), na.rm = TRUE)
89f977a3a256 planemo upload for repository https://github.com/Marie59/champ_blocs commit 0d86db7d42b608c386a54500064f5f9c9d7019a4 ecology parents: diff changeset	1398
89f977a3a256 planemo upload for repository https://github.com/Marie59/champ_blocs commit 0d86db7d42b608c386a54500064f5f9c9d7019a4 ecology parents: diff changeset	1399
89f977a3a256 planemo upload for repository https://github.com/Marie59/champ_blocs commit 0d86db7d42b608c386a54500064f5f9c9d7019a4 ecology parents: diff changeset	1400 expand.grid(mtxdis)
89f977a3a256 planemo upload for repository https://github.com/Marie59/champ_blocs commit 0d86db7d42b608c386a54500064f5f9c9d7019a4 ecology parents: diff changeset	1401
89f977a3a256 planemo upload for repository https://github.com/Marie59/champ_blocs commit 0d86db7d42b608c386a54500064f5f9c9d7019a4 ecology parents: diff changeset	1402 mtxdisdf_ <- as.data.frame(as.matrix(mtxdis))
89f977a3a256 planemo upload for repository https://github.com/Marie59/champ_blocs commit 0d86db7d42b608c386a54500064f5f9c9d7019a4 ecology parents: diff changeset	1403
89f977a3a256 planemo upload for repository https://github.com/Marie59/champ_blocs commit 0d86db7d42b608c386a54500064f5f9c9d7019a4 ecology parents: diff changeset	1404 a_ <- NA
89f977a3a256 planemo upload for repository https://github.com/Marie59/champ_blocs commit 0d86db7d42b608c386a54500064f5f9c9d7019a4 ecology parents: diff changeset	1405 b_ <- NA
89f977a3a256 planemo upload for repository https://github.com/Marie59/champ_blocs commit 0d86db7d42b608c386a54500064f5f9c9d7019a4 ecology parents: diff changeset	1406 c_ <- NA
89f977a3a256 planemo upload for repository https://github.com/Marie59/champ_blocs commit 0d86db7d42b608c386a54500064f5f9c9d7019a4 ecology parents: diff changeset	1407 d_ <- NA
89f977a3a256 planemo upload for repository https://github.com/Marie59/champ_blocs commit 0d86db7d42b608c386a54500064f5f9c9d7019a4 ecology parents: diff changeset	1408 e_ <- NA
89f977a3a256 planemo upload for repository https://github.com/Marie59/champ_blocs commit 0d86db7d42b608c386a54500064f5f9c9d7019a4 ecology parents: diff changeset	1409 f_ <- NA
89f977a3a256 planemo upload for repository https://github.com/Marie59/champ_blocs commit 0d86db7d42b608c386a54500064f5f9c9d7019a4 ecology parents: diff changeset	1410 g_ <- NA
89f977a3a256 planemo upload for repository https://github.com/Marie59/champ_blocs commit 0d86db7d42b608c386a54500064f5f9c9d7019a4 ecology parents: diff changeset	1411 h_ <- NA
89f977a3a256 planemo upload for repository https://github.com/Marie59/champ_blocs commit 0d86db7d42b608c386a54500064f5f9c9d7019a4 ecology parents: diff changeset	1412 i_ <- NA
89f977a3a256 planemo upload for repository https://github.com/Marie59/champ_blocs commit 0d86db7d42b608c386a54500064f5f9c9d7019a4 ecology parents: diff changeset	1413 j_ <- NA
89f977a3a256 planemo upload for repository https://github.com/Marie59/champ_blocs commit 0d86db7d42b608c386a54500064f5f9c9d7019a4 ecology parents: diff changeset	1414 k_ <- NA
89f977a3a256 planemo upload for repository https://github.com/Marie59/champ_blocs commit 0d86db7d42b608c386a54500064f5f9c9d7019a4 ecology parents: diff changeset	1415 l_ <- NA
89f977a3a256 planemo upload for repository https://github.com/Marie59/champ_blocs commit 0d86db7d42b608c386a54500064f5f9c9d7019a4 ecology parents: diff changeset	1416 m_ <- NA
89f977a3a256 planemo upload for repository https://github.com/Marie59/champ_blocs commit 0d86db7d42b608c386a54500064f5f9c9d7019a4 ecology parents: diff changeset	1417 n_ <- NA
89f977a3a256 planemo upload for repository https://github.com/Marie59/champ_blocs commit 0d86db7d42b608c386a54500064f5f9c9d7019a4 ecology parents: diff changeset	1418 o_ <- NA
89f977a3a256 planemo upload for repository https://github.com/Marie59/champ_blocs commit 0d86db7d42b608c386a54500064f5f9c9d7019a4 ecology parents: diff changeset	1419 p_ <- NA
89f977a3a256 planemo upload for repository https://github.com/Marie59/champ_blocs commit 0d86db7d42b608c386a54500064f5f9c9d7019a4 ecology parents: diff changeset	1420 q_ <- NA
89f977a3a256 planemo upload for repository https://github.com/Marie59/champ_blocs commit 0d86db7d42b608c386a54500064f5f9c9d7019a4 ecology parents: diff changeset	1421 r_ <- NA
89f977a3a256 planemo upload for repository https://github.com/Marie59/champ_blocs commit 0d86db7d42b608c386a54500064f5f9c9d7019a4 ecology parents: diff changeset	1422 s_ <- NA
89f977a3a256 planemo upload for repository https://github.com/Marie59/champ_blocs commit 0d86db7d42b608c386a54500064f5f9c9d7019a4 ecology parents: diff changeset	1423
89f977a3a256 planemo upload for repository https://github.com/Marie59/champ_blocs commit 0d86db7d42b608c386a54500064f5f9c9d7019a4 ecology parents: diff changeset	1424 for (z in c(1:nrow(mtxdisdf_))) {
89f977a3a256 planemo upload for repository https://github.com/Marie59/champ_blocs commit 0d86db7d42b608c386a54500064f5f9c9d7019a4 ecology parents: diff changeset	1425
89f977a3a256 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)))
89f977a3a256 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)))
89f977a3a256 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)))
89f977a3a256 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)))
89f977a3a256 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)))
89f977a3a256 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)))
89f977a3a256 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)))
89f977a3a256 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)))
89f977a3a256 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)))
89f977a3a256 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)))
89f977a3a256 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)))
89f977a3a256 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)))
89f977a3a256 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)))
89f977a3a256 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)))
89f977a3a256 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)))
89f977a3a256 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)))
89f977a3a256 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)))
89f977a3a256 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)))
89f977a3a256 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)))
89f977a3a256 planemo upload for repository https://github.com/Marie59/champ_blocs commit 0d86db7d42b608c386a54500064f5f9c9d7019a4 ecology parents: diff changeset	1445
89f977a3a256 planemo upload for repository https://github.com/Marie59/champ_blocs commit 0d86db7d42b608c386a54500064f5f9c9d7019a4 ecology parents: diff changeset	1446 }
89f977a3a256 planemo upload for repository https://github.com/Marie59/champ_blocs commit 0d86db7d42b608c386a54500064f5f9c9d7019a4 ecology parents: diff changeset	1447
89f977a3a256 planemo upload for repository https://github.com/Marie59/champ_blocs commit 0d86db7d42b608c386a54500064f5f9c9d7019a4 ecology parents: diff changeset	1448 rm(z)
89f977a3a256 planemo upload for repository https://github.com/Marie59/champ_blocs commit 0d86db7d42b608c386a54500064f5f9c9d7019a4 ecology parents: diff changeset	1449
89f977a3a256 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_)))
89f977a3a256 planemo upload for repository https://github.com/Marie59/champ_blocs commit 0d86db7d42b608c386a54500064f5f9c9d7019a4 ecology parents: diff changeset	1451 a_ <- a_[1:y]
89f977a3a256 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_)))
89f977a3a256 planemo upload for repository https://github.com/Marie59/champ_blocs commit 0d86db7d42b608c386a54500064f5f9c9d7019a4 ecology parents: diff changeset	1453 b_ <- b_[1:y]
89f977a3a256 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_)))
89f977a3a256 planemo upload for repository https://github.com/Marie59/champ_blocs commit 0d86db7d42b608c386a54500064f5f9c9d7019a4 ecology parents: diff changeset	1455 c_ <- c_[1:y]
89f977a3a256 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_)))
89f977a3a256 planemo upload for repository https://github.com/Marie59/champ_blocs commit 0d86db7d42b608c386a54500064f5f9c9d7019a4 ecology parents: diff changeset	1457 d_ <- d_[1:y]
89f977a3a256 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_)))
89f977a3a256 planemo upload for repository https://github.com/Marie59/champ_blocs commit 0d86db7d42b608c386a54500064f5f9c9d7019a4 ecology parents: diff changeset	1459 e_ <- e_[1:y]
89f977a3a256 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_)))
89f977a3a256 planemo upload for repository https://github.com/Marie59/champ_blocs commit 0d86db7d42b608c386a54500064f5f9c9d7019a4 ecology parents: diff changeset	1461 f_ <- f_[1:y]
89f977a3a256 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_)))
89f977a3a256 planemo upload for repository https://github.com/Marie59/champ_blocs commit 0d86db7d42b608c386a54500064f5f9c9d7019a4 ecology parents: diff changeset	1463 g_ <- g_[1:y]
89f977a3a256 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_)))
89f977a3a256 planemo upload for repository https://github.com/Marie59/champ_blocs commit 0d86db7d42b608c386a54500064f5f9c9d7019a4 ecology parents: diff changeset	1465 h_ <- h_[1:y]
89f977a3a256 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_)))
89f977a3a256 planemo upload for repository https://github.com/Marie59/champ_blocs commit 0d86db7d42b608c386a54500064f5f9c9d7019a4 ecology parents: diff changeset	1467 i_ <- i_[1:y]
89f977a3a256 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_)))
89f977a3a256 planemo upload for repository https://github.com/Marie59/champ_blocs commit 0d86db7d42b608c386a54500064f5f9c9d7019a4 ecology parents: diff changeset	1469 j_ <- j_[1:y]
89f977a3a256 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_)))
89f977a3a256 planemo upload for repository https://github.com/Marie59/champ_blocs commit 0d86db7d42b608c386a54500064f5f9c9d7019a4 ecology parents: diff changeset	1471 k_ <- k_[1:y]
89f977a3a256 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_)))
89f977a3a256 planemo upload for repository https://github.com/Marie59/champ_blocs commit 0d86db7d42b608c386a54500064f5f9c9d7019a4 ecology parents: diff changeset	1473 l_ <- l_[1:y]
89f977a3a256 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_)))
89f977a3a256 planemo upload for repository https://github.com/Marie59/champ_blocs commit 0d86db7d42b608c386a54500064f5f9c9d7019a4 ecology parents: diff changeset	1475 m_ <- m_[1:y]
89f977a3a256 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_)))
89f977a3a256 planemo upload for repository https://github.com/Marie59/champ_blocs commit 0d86db7d42b608c386a54500064f5f9c9d7019a4 ecology parents: diff changeset	1477 n_ <- n_[1:y]
89f977a3a256 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_)))
89f977a3a256 planemo upload for repository https://github.com/Marie59/champ_blocs commit 0d86db7d42b608c386a54500064f5f9c9d7019a4 ecology parents: diff changeset	1479 o_ <- o_[1:y]
89f977a3a256 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_)))
89f977a3a256 planemo upload for repository https://github.com/Marie59/champ_blocs commit 0d86db7d42b608c386a54500064f5f9c9d7019a4 ecology parents: diff changeset	1481 p_ <- p_[1:y]
89f977a3a256 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_)))
89f977a3a256 planemo upload for repository https://github.com/Marie59/champ_blocs commit 0d86db7d42b608c386a54500064f5f9c9d7019a4 ecology parents: diff changeset	1483 q_ <- q_[1:y]
89f977a3a256 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_)))
89f977a3a256 planemo upload for repository https://github.com/Marie59/champ_blocs commit 0d86db7d42b608c386a54500064f5f9c9d7019a4 ecology parents: diff changeset	1485 r_ <- r_[1:y]
89f977a3a256 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_)))
89f977a3a256 planemo upload for repository https://github.com/Marie59/champ_blocs commit 0d86db7d42b608c386a54500064f5f9c9d7019a4 ecology parents: diff changeset	1487 s_ <- s_[1:y]
89f977a3a256 planemo upload for repository https://github.com/Marie59/champ_blocs commit 0d86db7d42b608c386a54500064f5f9c9d7019a4 ecology parents: diff changeset	1488
89f977a3a256 planemo upload for repository https://github.com/Marie59/champ_blocs commit 0d86db7d42b608c386a54500064f5f9c9d7019a4 ecology parents: diff changeset	1489 rm(y)
89f977a3a256 planemo upload for repository https://github.com/Marie59/champ_blocs commit 0d86db7d42b608c386a54500064f5f9c9d7019a4 ecology parents: diff changeset	1490
89f977a3a256 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_)
89f977a3a256 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)))])
89f977a3a256 planemo upload for repository https://github.com/Marie59/champ_blocs commit 0d86db7d42b608c386a54500064f5f9c9d7019a4 ecology parents: diff changeset	1493 names(df_) <- c("dist.", "name_")
89f977a3a256 planemo upload for repository https://github.com/Marie59/champ_blocs commit 0d86db7d42b608c386a54500064f5f9c9d7019a4 ecology parents: diff changeset	1494
89f977a3a256 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_)
89f977a3a256 planemo upload for repository https://github.com/Marie59/champ_blocs commit 0d86db7d42b608c386a54500064f5f9c9d7019a4 ecology parents: diff changeset	1496 rm(name_)
89f977a3a256 planemo upload for repository https://github.com/Marie59/champ_blocs commit 0d86db7d42b608c386a54500064f5f9c9d7019a4 ecology parents: diff changeset	1497
89f977a3a256 planemo upload for repository https://github.com/Marie59/champ_blocs commit 0d86db7d42b608c386a54500064f5f9c9d7019a4 ecology parents: diff changeset	1498 q_ <- strsplit(df_$name_, " & ")
89f977a3a256 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)
89f977a3a256 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))
89f977a3a256 planemo upload for repository https://github.com/Marie59/champ_blocs commit 0d86db7d42b608c386a54500064f5f9c9d7019a4 ecology parents: diff changeset	1501 df_ <- dplyr::bind_cols(df_, q_df_)
89f977a3a256 planemo upload for repository https://github.com/Marie59/champ_blocs commit 0d86db7d42b608c386a54500064f5f9c9d7019a4 ecology parents: diff changeset	1502
89f977a3a256 planemo upload for repository https://github.com/Marie59/champ_blocs commit 0d86db7d42b608c386a54500064f5f9c9d7019a4 ecology parents: diff changeset	1503 rm(q_, mat_, q_df_)
89f977a3a256 planemo upload for repository https://github.com/Marie59/champ_blocs commit 0d86db7d42b608c386a54500064f5f9c9d7019a4 ecology parents: diff changeset	1504
89f977a3a256 planemo upload for repository https://github.com/Marie59/champ_blocs commit 0d86db7d42b608c386a54500064f5f9c9d7019a4 ecology parents: diff changeset	1505 split_ <- strsplit(df_$V1, "_")
89f977a3a256 planemo upload for repository https://github.com/Marie59/champ_blocs commit 0d86db7d42b608c386a54500064f5f9c9d7019a4 ecology parents: diff changeset	1506 v1_split_ <- as.data.frame(matrix(unlist(split_), ncol = 4, byrow = TRUE))
89f977a3a256 planemo upload for repository https://github.com/Marie59/champ_blocs commit 0d86db7d42b608c386a54500064f5f9c9d7019a4 ecology parents: diff changeset	1507 split_ <- strsplit(df_$V2, "_")
89f977a3a256 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))
89f977a3a256 planemo upload for repository https://github.com/Marie59/champ_blocs commit 0d86db7d42b608c386a54500064f5f9c9d7019a4 ecology parents: diff changeset	1509
89f977a3a256 planemo upload for repository https://github.com/Marie59/champ_blocs commit 0d86db7d42b608c386a54500064f5f9c9d7019a4 ecology parents: diff changeset	1510 df_ <- dplyr::bind_cols(df_, v1_split_)
89f977a3a256 planemo upload for repository https://github.com/Marie59/champ_blocs commit 0d86db7d42b608c386a54500064f5f9c9d7019a4 ecology parents: diff changeset	1511 df_ <- dplyr::bind_cols(df_, v2_split_)
89f977a3a256 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)
89f977a3a256 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_))
89f977a3a256 planemo upload for repository https://github.com/Marie59/champ_blocs commit 0d86db7d42b608c386a54500064f5f9c9d7019a4 ecology parents: diff changeset	1514
89f977a3a256 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.")
89f977a3a256 planemo upload for repository https://github.com/Marie59/champ_blocs commit 0d86db7d42b608c386a54500064f5f9c9d7019a4 ecology parents: diff changeset	1516
89f977a3a256 planemo upload for repository https://github.com/Marie59/champ_blocs commit 0d86db7d42b608c386a54500064f5f9c9d7019a4 ecology parents: diff changeset	1517 rm(split_, v1_split_, v2_split_)
89f977a3a256 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)
89f977a3a256 planemo upload for repository https://github.com/Marie59/champ_blocs commit 0d86db7d42b608c386a54500064f5f9c9d7019a4 ecology parents: diff changeset	1519
89f977a3a256 planemo upload for repository https://github.com/Marie59/champ_blocs commit 0d86db7d42b608c386a54500064f5f9c9d7019a4 ecology parents: diff changeset	1520 matri_list[[x]] <- df_red_
89f977a3a256 planemo upload for repository https://github.com/Marie59/champ_blocs commit 0d86db7d42b608c386a54500064f5f9c9d7019a4 ecology parents: diff changeset	1521 matri_list <<- matri_list
89f977a3a256 planemo upload for repository https://github.com/Marie59/champ_blocs commit 0d86db7d42b608c386a54500064f5f9c9d7019a4 ecology parents: diff changeset	1522
89f977a3a256 planemo upload for repository https://github.com/Marie59/champ_blocs commit 0d86db7d42b608c386a54500064f5f9c9d7019a4 ecology parents: diff changeset	1523 rm(df_red_, qecbnato0_x, x)
89f977a3a256 planemo upload for repository https://github.com/Marie59/champ_blocs commit 0d86db7d42b608c386a54500064f5f9c9d7019a4 ecology parents: diff changeset	1524
89f977a3a256 planemo upload for repository https://github.com/Marie59/champ_blocs commit 0d86db7d42b608c386a54500064f5f9c9d7019a4 ecology parents: diff changeset	1525 }
89f977a3a256 planemo upload for repository https://github.com/Marie59/champ_blocs commit 0d86db7d42b608c386a54500064f5f9c9d7019a4 ecology parents: diff changeset	1526
89f977a3a256 planemo upload for repository https://github.com/Marie59/champ_blocs commit 0d86db7d42b608c386a54500064f5f9c9d7019a4 ecology parents: diff changeset	1527 matri_df <- do.call("rbind", matri_list)
89f977a3a256 planemo upload for repository https://github.com/Marie59/champ_blocs commit 0d86db7d42b608c386a54500064f5f9c9d7019a4 ecology parents: diff changeset	1528
89f977a3a256 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")
89f977a3a256 planemo upload for repository https://github.com/Marie59/champ_blocs commit 0d86db7d42b608c386a54500064f5f9c9d7019a4 ecology parents: diff changeset	1530
89f977a3a256 planemo upload for repository https://github.com/Marie59/champ_blocs commit 0d86db7d42b608c386a54500064f5f9c9d7019a4 ecology parents: diff changeset	1531 matri_df <<- matri_df
89f977a3a256 planemo upload for repository https://github.com/Marie59/champ_blocs commit 0d86db7d42b608c386a54500064f5f9c9d7019a4 ecology parents: diff changeset	1532
89f977a3a256 planemo upload for repository https://github.com/Marie59/champ_blocs commit 0d86db7d42b608c386a54500064f5f9c9d7019a4 ecology parents: diff changeset	1533 hist(matri_df$dist.)
89f977a3a256 planemo upload for repository https://github.com/Marie59/champ_blocs commit 0d86db7d42b608c386a54500064f5f9c9d7019a4 ecology parents: diff changeset	1534
89f977a3a256 planemo upload for repository https://github.com/Marie59/champ_blocs commit 0d86db7d42b608c386a54500064f5f9c9d7019a4 ecology parents: diff changeset	1535 }
89f977a3a256 planemo upload for repository https://github.com/Marie59/champ_blocs commit 0d86db7d42b608c386a54500064f5f9c9d7019a4 ecology parents: diff changeset	1536
89f977a3a256 planemo upload for repository https://github.com/Marie59/champ_blocs commit 0d86db7d42b608c386a54500064f5f9c9d7019a4 ecology parents: diff changeset	1537 data_ <- dplyr::filter(qecbnato0, Type.Bloc == "Bloc mobile")
89f977a3a256 planemo upload for repository https://github.com/Marie59/champ_blocs commit 0d86db7d42b608c386a54500064f5f9c9d7019a4 ecology parents: diff changeset	1538 matri_list <- vector("list", length(unique(data_$site_year_month_day)))
89f977a3a256 planemo upload for repository https://github.com/Marie59/champ_blocs commit 0d86db7d42b608c386a54500064f5f9c9d7019a4 ecology parents: diff changeset	1539
89f977a3a256 planemo upload for repository https://github.com/Marie59/champ_blocs commit 0d86db7d42b608c386a54500064f5f9c9d7019a4 ecology parents: diff changeset	1540 matri_fct_bmm(data = data_, conca = c(bret_egmp_basq_qecb, egmp_basq_qecb))
89f977a3a256 planemo upload for repository https://github.com/Marie59/champ_blocs commit 0d86db7d42b608c386a54500064f5f9c9d7019a4 ecology parents: diff changeset	1541 hist(matri_df$dist., main = c(paste("Histo. of Bray (0-adjusted) dist. dissimilarity measures"), paste(" (sqrt transfo) - BMfs vs BMfi -")))
89f977a3a256 planemo upload for repository https://github.com/Marie59/champ_blocs commit 0d86db7d42b608c386a54500064f5f9c9d7019a4 ecology parents: diff changeset	1542
89f977a3a256 planemo upload for repository https://github.com/Marie59/champ_blocs commit 0d86db7d42b608c386a54500064f5f9c9d7019a4 ecology parents: diff changeset	1543 matri_full_bm_bf_fi <- matri_df
89f977a3a256 planemo upload for repository https://github.com/Marie59/champ_blocs commit 0d86db7d42b608c386a54500064f5f9c9d7019a4 ecology parents: diff changeset	1544
89f977a3a256 planemo upload for repository https://github.com/Marie59/champ_blocs commit 0d86db7d42b608c386a54500064f5f9c9d7019a4 ecology parents: diff changeset	1545 rm(data_, matri_df, matri_list)
89f977a3a256 planemo upload for repository https://github.com/Marie59/champ_blocs commit 0d86db7d42b608c386a54500064f5f9c9d7019a4 ecology parents: diff changeset	1546
89f977a3a256 planemo upload for repository https://github.com/Marie59/champ_blocs commit 0d86db7d42b608c386a54500064f5f9c9d7019a4 ecology parents: diff changeset	1547
89f977a3a256 planemo upload for repository https://github.com/Marie59/champ_blocs commit 0d86db7d42b608c386a54500064f5f9c9d7019a4 ecology parents: diff changeset	1548 #############################################################
89f977a3a256 planemo upload for repository https://github.com/Marie59/champ_blocs commit 0d86db7d42b608c386a54500064f5f9c9d7019a4 ecology parents: diff changeset	1549 # #
89f977a3a256 planemo upload for repository https://github.com/Marie59/champ_blocs commit 0d86db7d42b608c386a54500064f5f9c9d7019a4 ecology parents: diff changeset	1550 # Plot dissimilarity #
89f977a3a256 planemo upload for repository https://github.com/Marie59/champ_blocs commit 0d86db7d42b608c386a54500064f5f9c9d7019a4 ecology parents: diff changeset	1551 # #
89f977a3a256 planemo upload for repository https://github.com/Marie59/champ_blocs commit 0d86db7d42b608c386a54500064f5f9c9d7019a4 ecology parents: diff changeset	1552 #############################################################
89f977a3a256 planemo upload for repository https://github.com/Marie59/champ_blocs commit 0d86db7d42b608c386a54500064f5f9c9d7019a4 ecology parents: diff changeset	1553 ## plot
89f977a3a256 planemo upload for repository https://github.com/Marie59/champ_blocs commit 0d86db7d42b608c386a54500064f5f9c9d7019a4 ecology parents: diff changeset	1554
89f977a3a256 planemo upload for repository https://github.com/Marie59/champ_blocs commit 0d86db7d42b608c386a54500064f5f9c9d7019a4 ecology parents: diff changeset	1555 # activate line
89f977a3a256 planemo upload for repository https://github.com/Marie59/champ_blocs commit 0d86db7d42b608c386a54500064f5f9c9d7019a4 ecology parents: diff changeset	1556
89f977a3a256 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)
89f977a3a256 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$Site)
89f977a3a256 planemo upload for repository https://github.com/Marie59/champ_blocs commit 0d86db7d42b608c386a54500064f5f9c9d7019a4 ecology parents: diff changeset	1559 matri_full_bm_bf_fs <- subset(matri_full_bm_bf_fs, select = - c(departement))
89f977a3a256 planemo upload for repository https://github.com/Marie59/champ_blocs commit 0d86db7d42b608c386a54500064f5f9c9d7019a4 ecology parents: diff changeset	1560
89f977a3a256 planemo upload for repository https://github.com/Marie59/champ_blocs commit 0d86db7d42b608c386a54500064f5f9c9d7019a4 ecology parents: diff changeset	1561 matri_full_bm_bf_fs <- tibble::add_column(matri_full_bm_bf_fs, Date = as.Date(paste0(matri_full_bm_bf_fs$Year, "-", matri_full_bm_bf_fs$Month, "-", matri_full_bm_bf_fs$Day), origin = "1970-01-01"), .after = "Site")
89f977a3a256 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)
89f977a3a256 planemo upload for repository https://github.com/Marie59/champ_blocs commit 0d86db7d42b608c386a54500064f5f9c9d7019a4 ecology parents: diff changeset	1563
89f977a3a256 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)
89f977a3a256 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$Site)
89f977a3a256 planemo upload for repository https://github.com/Marie59/champ_blocs commit 0d86db7d42b608c386a54500064f5f9c9d7019a4 ecology parents: diff changeset	1566 matri_full_bm_bf_fi <- subset(matri_full_bm_bf_fi, select = - c(departement))
89f977a3a256 planemo upload for repository https://github.com/Marie59/champ_blocs commit 0d86db7d42b608c386a54500064f5f9c9d7019a4 ecology parents: diff changeset	1567 matri_full_bm_bf_fi <- tibble::add_column(matri_full_bm_bf_fi, Date = as.Date(paste0(matri_full_bm_bf_fi$Year, "-", matri_full_bm_bf_fi$Month, "-", matri_full_bm_bf_fi$Day), origin = "1970-01-01"), .after = "Site")
89f977a3a256 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)
89f977a3a256 planemo upload for repository https://github.com/Marie59/champ_blocs commit 0d86db7d42b608c386a54500064f5f9c9d7019a4 ecology parents: diff changeset	1569
89f977a3a256 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"
89f977a3a256 planemo upload for repository https://github.com/Marie59/champ_blocs commit 0d86db7d42b608c386a54500064f5f9c9d7019a4 ecology parents: diff changeset	1571
89f977a3a256 planemo upload for repository https://github.com/Marie59/champ_blocs commit 0d86db7d42b608c386a54500064f5f9c9d7019a4 ecology parents: diff changeset	1572
89f977a3a256 planemo upload for repository https://github.com/Marie59/champ_blocs commit 0d86db7d42b608c386a54500064f5f9c9d7019a4 ecology parents: diff changeset	1573 bf_fs_plot <- ggplot2::ggplot(matri_full_bm_bf_fs, ggplot2::aes(x = Site, y = dist.)) +
89f977a3a256 planemo upload for repository https://github.com/Marie59/champ_blocs commit 0d86db7d42b608c386a54500064f5f9c9d7019a4 ecology parents: diff changeset	1574 ggplot2::geom_boxplot() +
89f977a3a256 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)) +
89f977a3a256 planemo upload for repository https://github.com/Marie59/champ_blocs commit 0d86db7d42b608c386a54500064f5f9c9d7019a4 ecology parents: diff changeset	1576 ggplot2::xlab("") +
89f977a3a256 planemo upload for repository https://github.com/Marie59/champ_blocs commit 0d86db7d42b608c386a54500064f5f9c9d7019a4 ecology parents: diff changeset	1577 ggplot2::ylab("distance diss. BM.BF_FS") +
89f977a3a256 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))
89f977a3a256 planemo upload for repository https://github.com/Marie59/champ_blocs commit 0d86db7d42b608c386a54500064f5f9c9d7019a4 ecology parents: diff changeset	1579
89f977a3a256 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)
89f977a3a256 planemo upload for repository https://github.com/Marie59/champ_blocs commit 0d86db7d42b608c386a54500064f5f9c9d7019a4 ecology parents: diff changeset	1581
89f977a3a256 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.)) +
89f977a3a256 planemo upload for repository https://github.com/Marie59/champ_blocs commit 0d86db7d42b608c386a54500064f5f9c9d7019a4 ecology parents: diff changeset	1583 ggplot2::geom_boxplot() +
89f977a3a256 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)) +
89f977a3a256 planemo upload for repository https://github.com/Marie59/champ_blocs commit 0d86db7d42b608c386a54500064f5f9c9d7019a4 ecology parents: diff changeset	1585 ggplot2::xlab("") +
89f977a3a256 planemo upload for repository https://github.com/Marie59/champ_blocs commit 0d86db7d42b608c386a54500064f5f9c9d7019a4 ecology parents: diff changeset	1586 ggplot2::ylab("distance diss. BM_FS.FI") +
89f977a3a256 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))
89f977a3a256 planemo upload for repository https://github.com/Marie59/champ_blocs commit 0d86db7d42b608c386a54500064f5f9c9d7019a4 ecology parents: diff changeset	1588
89f977a3a256 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)
89f977a3a256 planemo upload for repository https://github.com/Marie59/champ_blocs commit 0d86db7d42b608c386a54500064f5f9c9d7019a4 ecology parents: diff changeset	1590
89f977a3a256 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).
89f977a3a256 planemo upload for repository https://github.com/Marie59/champ_blocs commit 0d86db7d42b608c386a54500064f5f9c9d7019a4 ecology parents: diff changeset	1592 matri_full_bm_bf_fs$Quadrat <- NA
89f977a3a256 planemo upload for repository https://github.com/Marie59/champ_blocs commit 0d86db7d42b608c386a54500064f5f9c9d7019a4 ecology parents: diff changeset	1593 for (i in c(1:seq_len(nrow(matri_full_bm_bf_fs)))) {
89f977a3a256 planemo upload for repository https://github.com/Marie59/champ_blocs commit 0d86db7d42b608c386a54500064f5f9c9d7019a4 ecology parents: diff changeset	1594 ifelse(matri_full_bm_bf_fs$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])
89f977a3a256 planemo upload for repository https://github.com/Marie59/champ_blocs commit 0d86db7d42b608c386a54500064f5f9c9d7019a4 ecology parents: diff changeset	1595 }
89f977a3a256 planemo upload for repository https://github.com/Marie59/champ_blocs commit 0d86db7d42b608c386a54500064f5f9c9d7019a4 ecology parents: diff changeset	1596 matri_full_bm_bf_fs$Numéro.Bloc <- NA
89f977a3a256 planemo upload for repository https://github.com/Marie59/champ_blocs commit 0d86db7d42b608c386a54500064f5f9c9d7019a4 ecology parents: diff changeset	1597 for (i in c(1:seq_len(nrow(matri_full_bm_bf_fs)))) {
89f977a3a256 planemo upload for repository https://github.com/Marie59/champ_blocs commit 0d86db7d42b608c386a54500064f5f9c9d7019a4 ecology parents: diff changeset	1598 ifelse(matri_full_bm_bf_fs$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])
89f977a3a256 planemo upload for repository https://github.com/Marie59/champ_blocs commit 0d86db7d42b608c386a54500064f5f9c9d7019a4 ecology parents: diff changeset	1599 }
89f977a3a256 planemo upload for repository https://github.com/Marie59/champ_blocs commit 0d86db7d42b608c386a54500064f5f9c9d7019a4 ecology parents: diff changeset	1600
89f977a3a256 planemo upload for repository https://github.com/Marie59/champ_blocs commit 0d86db7d42b608c386a54500064f5f9c9d7019a4 ecology parents: diff changeset	1601 matri_full_bm_bf_fs <- tibble::add_column(matri_full_bm_bf_fs, site_year_month_day.q_BMnb = paste0(matri_full_bm_bf_fs$site_year_month_day, "_", matri_full_bm_bf_fs$Quadrat, "_", matri_full_bm_bf_fs$Numéro.Bloc), .after = "site_year_month_day")
89f977a3a256 planemo upload for repository https://github.com/Marie59/champ_blocs commit 0d86db7d42b608c386a54500064f5f9c9d7019a4 ecology parents: diff changeset	1602 matri_full_bm_bf_fi <- tibble::add_column(matri_full_bm_bf_fi, site_year_month_day.q_BMnb = paste0(matri_full_bm_bf_fi$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")
89f977a3a256 planemo upload for repository https://github.com/Marie59/champ_blocs commit 0d86db7d42b608c386a54500064f5f9c9d7019a4 ecology parents: diff changeset	1603
89f977a3a256 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 = "_")
89f977a3a256 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)
89f977a3a256 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 = "_")
89f977a3a256 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)
89f977a3a256 planemo upload for repository https://github.com/Marie59/champ_blocs commit 0d86db7d42b608c386a54500064f5f9c9d7019a4 ecology parents: diff changeset	1608
89f977a3a256 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.")])
89f977a3a256 planemo upload for repository https://github.com/Marie59/champ_blocs commit 0d86db7d42b608c386a54500064f5f9c9d7019a4 ecology parents: diff changeset	1610
89f977a3a256 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)
89f977a3a256 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$Site)
89f977a3a256 planemo upload for repository https://github.com/Marie59/champ_blocs commit 0d86db7d42b608c386a54500064f5f9c9d7019a4 ecology parents: diff changeset	1613 matri_full <- subset(matri_full, select = - c(departement))
89f977a3a256 planemo upload for repository https://github.com/Marie59/champ_blocs commit 0d86db7d42b608c386a54500064f5f9c9d7019a4 ecology parents: diff changeset	1614 matri_full <- tibble::add_column(matri_full, Date = as.Date(paste0(matri_full$Year, "-", matri_full$Month, "-", matri_full$Day), origin = "1970-01-01"), .after = "Site")
89f977a3a256 planemo upload for repository https://github.com/Marie59/champ_blocs commit 0d86db7d42b608c386a54500064f5f9c9d7019a4 ecology parents: diff changeset	1615
89f977a3a256 planemo upload for repository https://github.com/Marie59/champ_blocs commit 0d86db7d42b608c386a54500064f5f9c9d7019a4 ecology parents: diff changeset	1616 # Name for report/plot
89f977a3a256 planemo upload for repository https://github.com/Marie59/champ_blocs commit 0d86db7d42b608c386a54500064f5f9c9d7019a4 ecology parents: diff changeset	1617
89f977a3a256 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$Site, .after = "Site")
89f977a3a256 planemo upload for repository https://github.com/Marie59/champ_blocs commit 0d86db7d42b608c386a54500064f5f9c9d7019a4 ecology parents: diff changeset	1619
89f977a3a256 planemo upload for repository https://github.com/Marie59/champ_blocs commit 0d86db7d42b608c386a54500064f5f9c9d7019a4 ecology parents: diff changeset	1620 matri_full$Site_bis <- ifelse(matri_full$Site == "GDMO_Locmariaquer", "Locmariaquer", matri_full$Site_bis)
89f977a3a256 planemo upload for repository https://github.com/Marie59/champ_blocs commit 0d86db7d42b608c386a54500064f5f9c9d7019a4 ecology parents: diff changeset	1621 matri_full$Site_bis <- ifelse(matri_full$Site == "GDMO_BegLann", "Beg Lann", matri_full$Site_bis)
89f977a3a256 planemo upload for repository https://github.com/Marie59/champ_blocs commit 0d86db7d42b608c386a54500064f5f9c9d7019a4 ecology parents: diff changeset	1622 matri_full$Site_bis <- ifelse(matri_full$Site == "FOUR_PlateauFour", "Plateau du Four", matri_full$Site_bis)
89f977a3a256 planemo upload for repository https://github.com/Marie59/champ_blocs commit 0d86db7d42b608c386a54500064f5f9c9d7019a4 ecology parents: diff changeset	1623 matri_full$Site_bis <- ifelse(matri_full$Site == "EGMP_GroinCou", "Groin du Cou", matri_full$Site_bis)
89f977a3a256 planemo upload for repository https://github.com/Marie59/champ_blocs commit 0d86db7d42b608c386a54500064f5f9c9d7019a4 ecology parents: diff changeset	1624 matri_full$Site_bis <- ifelse(matri_full$Site == "EGMP_PasEmsembert", "Le Pas d'Emsembert", matri_full$Site_bis)
89f977a3a256 planemo upload for repository https://github.com/Marie59/champ_blocs commit 0d86db7d42b608c386a54500064f5f9c9d7019a4 ecology parents: diff changeset	1625 matri_full$Site_bis <- ifelse(matri_full$Site == "EGMP_BreeBains", "La Brée-les-Bains", matri_full$Site_bis)
89f977a3a256 planemo upload for repository https://github.com/Marie59/champ_blocs commit 0d86db7d42b608c386a54500064f5f9c9d7019a4 ecology parents: diff changeset	1626 matri_full$Site_bis <- ifelse(matri_full$Site == "EGMP_PerreAntiochat", "Le Perré d'Antiochat", matri_full$Site_bis)
89f977a3a256 planemo upload for repository https://github.com/Marie59/champ_blocs commit 0d86db7d42b608c386a54500064f5f9c9d7019a4 ecology parents: diff changeset	1627 matri_full$Site_bis <- ifelse(matri_full$Site == "EGMP_Chassiron", "Chassiron", matri_full$Site_bis)
89f977a3a256 planemo upload for repository https://github.com/Marie59/champ_blocs commit 0d86db7d42b608c386a54500064f5f9c9d7019a4 ecology parents: diff changeset	1628 matri_full$Site_bis <- ifelse(matri_full$Site == "BASQ_FlotsBleusZP", "Les Flots Bleus / zone pêcheurs", matri_full$Site_bis)
89f977a3a256 planemo upload for repository https://github.com/Marie59/champ_blocs commit 0d86db7d42b608c386a54500064f5f9c9d7019a4 ecology parents: diff changeset	1629 matri_full$Site_bis <- ifelse(matri_full$Site == "BASQ_FlotsBleusZF", "Les Flots Bleus / zone familles", matri_full$Site_bis)
89f977a3a256 planemo upload for repository https://github.com/Marie59/champ_blocs commit 0d86db7d42b608c386a54500064f5f9c9d7019a4 ecology parents: diff changeset	1630 matri_full$Site_bis <- ifelse(matri_full$Site == "GONB_IlotStMichel", "Îlot Saint-Michel", matri_full$Site_bis)
89f977a3a256 planemo upload for repository https://github.com/Marie59/champ_blocs commit 0d86db7d42b608c386a54500064f5f9c9d7019a4 ecology parents: diff changeset	1631 matri_full$Site_bis <- ifelse(matri_full$Site == "FINS_Quemenes", "Quéménès", matri_full$Site_bis)
89f977a3a256 planemo upload for repository https://github.com/Marie59/champ_blocs commit 0d86db7d42b608c386a54500064f5f9c9d7019a4 ecology parents: diff changeset	1632 matri_full$Site_bis <- ifelse(matri_full$Site == "FINS_SeinGoulenez", "Île de Sein - Goulenez", matri_full$Site_bis)
89f977a3a256 planemo upload for repository https://github.com/Marie59/champ_blocs commit 0d86db7d42b608c386a54500064f5f9c9d7019a4 ecology parents: diff changeset	1633 matri_full$Site_bis <- ifelse(matri_full$Site == "FINS_SeinKilaourou", "Île de Sein - Kilaourou", matri_full$Site_bis)
89f977a3a256 planemo upload for repository https://github.com/Marie59/champ_blocs commit 0d86db7d42b608c386a54500064f5f9c9d7019a4 ecology parents: diff changeset	1634 matri_full$Site_bis <- ifelse(matri_full$Site == "ARMO_Verdelet", "Îlot du Verdelet", matri_full$Site_bis)
89f977a3a256 planemo upload for repository https://github.com/Marie59/champ_blocs commit 0d86db7d42b608c386a54500064f5f9c9d7019a4 ecology parents: diff changeset	1635 matri_full$Site_bis <- ifelse(matri_full$Site == "ARMO_Piegu", "Piégu", matri_full$Site_bis)
89f977a3a256 planemo upload for repository https://github.com/Marie59/champ_blocs commit 0d86db7d42b608c386a54500064f5f9c9d7019a4 ecology parents: diff changeset	1636 matri_full$Site_bis <- ifelse(matri_full$Site == "ARMO_Bilfot", "Pointe de Bilfot", matri_full$Site_bis)
89f977a3a256 planemo upload for repository https://github.com/Marie59/champ_blocs commit 0d86db7d42b608c386a54500064f5f9c9d7019a4 ecology parents: diff changeset	1637 matri_full$Site_bis <- ifelse(matri_full$Site == "ARMO_IlePlate", "Île Plate", matri_full$Site_bis)
89f977a3a256 planemo upload for repository https://github.com/Marie59/champ_blocs commit 0d86db7d42b608c386a54500064f5f9c9d7019a4 ecology parents: diff changeset	1638 matri_full$Site_bis <- ifelse(matri_full$Site == "PDMO_Perharidy", "Perharidy", matri_full$Site_bis)
89f977a3a256 planemo upload for repository https://github.com/Marie59/champ_blocs commit 0d86db7d42b608c386a54500064f5f9c9d7019a4 ecology parents: diff changeset	1639 matri_full$Site_bis <- ifelse(matri_full$Site == "BRES_Keraliou", "Keraliou", matri_full$Site_bis)
89f977a3a256 planemo upload for repository https://github.com/Marie59/champ_blocs commit 0d86db7d42b608c386a54500064f5f9c9d7019a4 ecology parents: diff changeset	1640 matri_full$Site_bis <- ifelse(matri_full$Site == "FINS_Mousterlin", "Pointe de Mousterlin", matri_full$Site_bis)
89f977a3a256 planemo upload for repository https://github.com/Marie59/champ_blocs commit 0d86db7d42b608c386a54500064f5f9c9d7019a4 ecology parents: diff changeset	1641 matri_full$Site_bis <- ifelse(matri_full$Site == "FINS_StNicolasGlenan", "Saint-Nicolas des Glénan", matri_full$Site_bis)
89f977a3a256 planemo upload for repository https://github.com/Marie59/champ_blocs commit 0d86db7d42b608c386a54500064f5f9c9d7019a4 ecology parents: diff changeset	1642 matri_full$Site_bis <- ifelse(matri_full$Site == "FINS_AnseRoz", "Pointe de l'Anse du Roz", matri_full$Site_bis)
89f977a3a256 planemo upload for repository https://github.com/Marie59/champ_blocs commit 0d86db7d42b608c386a54500064f5f9c9d7019a4 ecology parents: diff changeset	1643
89f977a3a256 planemo upload for repository https://github.com/Marie59/champ_blocs commit 0d86db7d42b608c386a54500064f5f9c9d7019a4 ecology parents: diff changeset	1644 saveRDS(matri_full, "matri_full.RDS")
89f977a3a256 planemo upload for repository https://github.com/Marie59/champ_blocs commit 0d86db7d42b608c386a54500064f5f9c9d7019a4 ecology parents: diff changeset	1645
89f977a3a256 planemo upload for repository https://github.com/Marie59/champ_blocs commit 0d86db7d42b608c386a54500064f5f9c9d7019a4 ecology parents: diff changeset	1646 #############################################################
89f977a3a256 planemo upload for repository https://github.com/Marie59/champ_blocs commit 0d86db7d42b608c386a54500064f5f9c9d7019a4 ecology parents: diff changeset	1647 # #
89f977a3a256 planemo upload for repository https://github.com/Marie59/champ_blocs commit 0d86db7d42b608c386a54500064f5f9c9d7019a4 ecology parents: diff changeset	1648 # Plot the dissimilarity per site #
89f977a3a256 planemo upload for repository https://github.com/Marie59/champ_blocs commit 0d86db7d42b608c386a54500064f5f9c9d7019a4 ecology parents: diff changeset	1649 # #
89f977a3a256 planemo upload for repository https://github.com/Marie59/champ_blocs commit 0d86db7d42b608c386a54500064f5f9c9d7019a4 ecology parents: diff changeset	1650 #############################################################
89f977a3a256 planemo upload for repository https://github.com/Marie59/champ_blocs commit 0d86db7d42b608c386a54500064f5f9c9d7019a4 ecology parents: diff changeset	1651 ## plot dissimilarity coefficient
89f977a3a256 planemo upload for repository https://github.com/Marie59/champ_blocs commit 0d86db7d42b608c386a54500064f5f9c9d7019a4 ecology parents: diff changeset	1652
89f977a3a256 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)
89f977a3a256 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)
89f977a3a256 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)
89f977a3a256 planemo upload for repository https://github.com/Marie59/champ_blocs commit 0d86db7d42b608c386a54500064f5f9c9d7019a4 ecology parents: diff changeset	1656
89f977a3a256 planemo upload for repository https://github.com/Marie59/champ_blocs commit 0d86db7d42b608c386a54500064f5f9c9d7019a4 ecology parents: diff changeset	1657
89f977a3a256 planemo upload for repository https://github.com/Marie59/champ_blocs commit 0d86db7d42b608c386a54500064f5f9c9d7019a4 ecology parents: diff changeset	1658 ## BM_FS.FI_dist => mobile boulder upper vs lower faces
89f977a3a256 planemo upload for repository https://github.com/Marie59/champ_blocs commit 0d86db7d42b608c386a54500064f5f9c9d7019a4 ecology parents: diff changeset	1659
89f977a3a256 planemo upload for repository https://github.com/Marie59/champ_blocs commit 0d86db7d42b608c386a54500064f5f9c9d7019a4 ecology parents: diff changeset	1660 # Stats
89f977a3a256 planemo upload for repository https://github.com/Marie59/champ_blocs commit 0d86db7d42b608c386a54500064f5f9c9d7019a4 ecology parents: diff changeset	1661
89f977a3a256 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.)))
89f977a3a256 planemo upload for repository https://github.com/Marie59/champ_blocs commit 0d86db7d42b608c386a54500064f5f9c9d7019a4 ecology parents: diff changeset	1663
89f977a3a256 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)
89f977a3a256 planemo upload for repository https://github.com/Marie59/champ_blocs commit 0d86db7d42b608c386a54500064f5f9c9d7019a4 ecology parents: diff changeset	1665
89f977a3a256 planemo upload for repository https://github.com/Marie59/champ_blocs commit 0d86db7d42b608c386a54500064f5f9c9d7019a4 ecology parents: diff changeset	1666 # Quality scale based on quartiles
89f977a3a256 planemo upload for repository https://github.com/Marie59/champ_blocs commit 0d86db7d42b608c386a54500064f5f9c9d7019a4 ecology parents: diff changeset	1667
89f977a3a256 planemo upload for repository https://github.com/Marie59/champ_blocs commit 0d86db7d42b608c386a54500064f5f9c9d7019a4 ecology parents: diff changeset	1668 if (choice == "N") {
89f977a3a256 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$BM_FS.FI_dist., 0.25, na.rm = TRUE))["BM_FS.FI_dist."])), digits = 3)
89f977a3a256 planemo upload for repository https://github.com/Marie59/champ_blocs commit 0d86db7d42b608c386a54500064f5f9c9d7019a4 ecology parents: diff changeset	1670 two <- round(mean(unlist(dplyr::filter(matri_full, BM_FS.FI_dist. > quantile(matri_full$BM_FS.FI_dist., 0.25, na.rm = TRUE) & BM_FS.FI_dist. <= quantile(matri_full$BM_FS.FI_dist., 0.5, na.rm = TRUE))["BM_FS.FI_dist."])), digits = 3)
89f977a3a256 planemo upload for repository https://github.com/Marie59/champ_blocs commit 0d86db7d42b608c386a54500064f5f9c9d7019a4 ecology parents: diff changeset	1671 three <- round(mean(unlist(dplyr::filter(matri_full, BM_FS.FI_dist. > quantile(matri_full$BM_FS.FI_dist., 0.5, na.rm = TRUE) & BM_FS.FI_dist. <= quantile(matri_full$BM_FS.FI_dist., 0.75, na.rm = TRUE))["BM_FS.FI_dist."])), digits = 3)
89f977a3a256 planemo upload for repository https://github.com/Marie59/champ_blocs commit 0d86db7d42b608c386a54500064f5f9c9d7019a4 ecology parents: diff changeset	1672 four <- round(mean(unlist(dplyr::filter(matri_full, BM_FS.FI_dist. > quantile(matri_full$BM_FS.FI_dist., 0.75, na.rm = TRUE))["BM_FS.FI_dist."])), digits = 3)
89f977a3a256 planemo upload for repository https://github.com/Marie59/champ_blocs commit 0d86db7d42b608c386a54500064f5f9c9d7019a4 ecology parents: diff changeset	1673 }else {
89f977a3a256 planemo upload for repository https://github.com/Marie59/champ_blocs commit 0d86db7d42b608c386a54500064f5f9c9d7019a4 ecology parents: diff changeset	1674 one <- 0.47
89f977a3a256 planemo upload for repository https://github.com/Marie59/champ_blocs commit 0d86db7d42b608c386a54500064f5f9c9d7019a4 ecology parents: diff changeset	1675 two <- 0.7
89f977a3a256 planemo upload for repository https://github.com/Marie59/champ_blocs commit 0d86db7d42b608c386a54500064f5f9c9d7019a4 ecology parents: diff changeset	1676 three <- 0.83
89f977a3a256 planemo upload for repository https://github.com/Marie59/champ_blocs commit 0d86db7d42b608c386a54500064f5f9c9d7019a4 ecology parents: diff changeset	1677 four <- 0.98
89f977a3a256 planemo upload for repository https://github.com/Marie59/champ_blocs commit 0d86db7d42b608c386a54500064f5f9c9d7019a4 ecology parents: diff changeset	1678 }
89f977a3a256 planemo upload for repository https://github.com/Marie59/champ_blocs commit 0d86db7d42b608c386a54500064f5f9c9d7019a4 ecology parents: diff changeset	1679
89f977a3a256 planemo upload for repository https://github.com/Marie59/champ_blocs commit 0d86db7d42b608c386a54500064f5f9c9d7019a4 ecology parents: diff changeset	1680 val_xmax <- as.Date(paste0(as.character(choice_date + 1), "-01-01"), origin = "1970-01-01")
89f977a3a256 planemo upload for repository https://github.com/Marie59/champ_blocs commit 0d86db7d42b608c386a54500064f5f9c9d7019a4 ecology parents: diff changeset	1681
89f977a3a256 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$Site)))) {
89f977a3a256 planemo upload for repository https://github.com/Marie59/champ_blocs commit 0d86db7d42b608c386a54500064f5f9c9d7019a4 ecology parents: diff changeset	1683
89f977a3a256 planemo upload for repository https://github.com/Marie59/champ_blocs commit 0d86db7d42b608c386a54500064f5f9c9d7019a4 ecology parents: diff changeset	1684 df1 <- dplyr::filter(bm_fs_fi_dist_stat, bm_fs_fi_dist_stat$Site == unique(bm_fs_fi_dist_stat$Site)[i])
89f977a3a256 planemo upload for repository https://github.com/Marie59/champ_blocs commit 0d86db7d42b608c386a54500064f5f9c9d7019a4 ecology parents: diff changeset	1685
89f977a3a256 planemo upload for repository https://github.com/Marie59/champ_blocs commit 0d86db7d42b608c386a54500064f5f9c9d7019a4 ecology parents: diff changeset	1686 bm_fs_fi_plot <- ggplot2::ggplot() +
89f977a3a256 planemo upload for repository https://github.com/Marie59/champ_blocs commit 0d86db7d42b608c386a54500064f5f9c9d7019a4 ecology parents: diff changeset	1687 ggplot2::geom_point(ggplot2::aes(x = bm_fs_fi_dist_stat$Date, y = bm_fs_fi_dist_stat$BM_FS.FI_dist.med), col = "grey") +
89f977a3a256 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) +
89f977a3a256 planemo upload for repository https://github.com/Marie59/champ_blocs commit 0d86db7d42b608c386a54500064f5f9c9d7019a4 ecology parents: diff changeset	1689 ggplot2::geom_rect(ggplot2::aes(xmin = as.Date("2013-01-01", origin = "1970-01-01"), xmax = val_xmax, ymin = one, ymax = two, fill = "green"), alpha = 0.3) +
89f977a3a256 planemo upload for repository https://github.com/Marie59/champ_blocs commit 0d86db7d42b608c386a54500064f5f9c9d7019a4 ecology parents: diff changeset	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) +
89f977a3a256 planemo upload for repository https://github.com/Marie59/champ_blocs commit 0d86db7d42b608c386a54500064f5f9c9d7019a4 ecology parents: diff changeset	1691 ggplot2::geom_rect(ggplot2::aes(xmin = as.Date("2013-01-01", origin = "1970-01-01"), xmax = val_xmax, ymin = three, ymax = four, fill = "orange"), alpha = 0.3) +
89f977a3a256 planemo upload for repository https://github.com/Marie59/champ_blocs commit 0d86db7d42b608c386a54500064f5f9c9d7019a4 ecology parents: diff changeset	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) +
89f977a3a256 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")) +
89f977a3a256 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$BM_FS.FI_dist.max), col = "black") +
89f977a3a256 planemo upload for repository https://github.com/Marie59/champ_blocs commit 0d86db7d42b608c386a54500064f5f9c9d7019a4 ecology parents: diff changeset	1695 ggplot2::xlab("Date") +
89f977a3a256 planemo upload for repository https://github.com/Marie59/champ_blocs commit 0d86db7d42b608c386a54500064f5f9c9d7019a4 ecology parents: diff changeset	1696 ggplot2::ylab("Coef dissim BM FS-FI") +
89f977a3a256 planemo upload for repository https://github.com/Marie59/champ_blocs commit 0d86db7d42b608c386a54500064f5f9c9d7019a4 ecology parents: diff changeset	1697 ggplot2::ggtitle(unique(df1$Site_bis)) +
89f977a3a256 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")
89f977a3a256 planemo upload for repository https://github.com/Marie59/champ_blocs commit 0d86db7d42b608c386a54500064f5f9c9d7019a4 ecology parents: diff changeset	1699
89f977a3a256 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)
89f977a3a256 planemo upload for repository https://github.com/Marie59/champ_blocs commit 0d86db7d42b608c386a54500064f5f9c9d7019a4 ecology parents: diff changeset	1701
89f977a3a256 planemo upload for repository https://github.com/Marie59/champ_blocs commit 0d86db7d42b608c386a54500064f5f9c9d7019a4 ecology parents: diff changeset	1702 }
89f977a3a256 planemo upload for repository https://github.com/Marie59/champ_blocs commit 0d86db7d42b608c386a54500064f5f9c9d7019a4 ecology parents: diff changeset	1703
89f977a3a256 planemo upload for repository https://github.com/Marie59/champ_blocs commit 0d86db7d42b608c386a54500064f5f9c9d7019a4 ecology parents: diff changeset	1704 rm(df1, four, i, one, three, two, xmax_, xmin_, ymax_, ymin_)
89f977a3a256 planemo upload for repository https://github.com/Marie59/champ_blocs commit 0d86db7d42b608c386a54500064f5f9c9d7019a4 ecology parents: diff changeset	1705
89f977a3a256 planemo upload for repository https://github.com/Marie59/champ_blocs commit 0d86db7d42b608c386a54500064f5f9c9d7019a4 ecology parents: diff changeset	1706
89f977a3a256 planemo upload for repository https://github.com/Marie59/champ_blocs commit 0d86db7d42b608c386a54500064f5f9c9d7019a4 ecology parents: diff changeset	1707 ## BM.BF_FS_dist => mobile boulder vs fixed boulder upper faces
89f977a3a256 planemo upload for repository https://github.com/Marie59/champ_blocs commit 0d86db7d42b608c386a54500064f5f9c9d7019a4 ecology parents: diff changeset	1708
89f977a3a256 planemo upload for repository https://github.com/Marie59/champ_blocs commit 0d86db7d42b608c386a54500064f5f9c9d7019a4 ecology parents: diff changeset	1709 # Stats
89f977a3a256 planemo upload for repository https://github.com/Marie59/champ_blocs commit 0d86db7d42b608c386a54500064f5f9c9d7019a4 ecology parents: diff changeset	1710
89f977a3a256 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.)))
89f977a3a256 planemo upload for repository https://github.com/Marie59/champ_blocs commit 0d86db7d42b608c386a54500064f5f9c9d7019a4 ecology parents: diff changeset	1712
89f977a3a256 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)
89f977a3a256 planemo upload for repository https://github.com/Marie59/champ_blocs commit 0d86db7d42b608c386a54500064f5f9c9d7019a4 ecology parents: diff changeset	1714
89f977a3a256 planemo upload for repository https://github.com/Marie59/champ_blocs commit 0d86db7d42b608c386a54500064f5f9c9d7019a4 ecology parents: diff changeset	1715 # Quality scale based on quartiles
89f977a3a256 planemo upload for repository https://github.com/Marie59/champ_blocs commit 0d86db7d42b608c386a54500064f5f9c9d7019a4 ecology parents: diff changeset	1716
89f977a3a256 planemo upload for repository https://github.com/Marie59/champ_blocs commit 0d86db7d42b608c386a54500064f5f9c9d7019a4 ecology parents: diff changeset	1717 if (choice == "N") {
89f977a3a256 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)
89f977a3a256 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)
89f977a3a256 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)
89f977a3a256 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$BM.BF_FS_dist., 0.75, na.rm = TRUE))["BM.BF_FS_dist."])), digits = 3)
89f977a3a256 planemo upload for repository https://github.com/Marie59/champ_blocs commit 0d86db7d42b608c386a54500064f5f9c9d7019a4 ecology parents: diff changeset	1722
89f977a3a256 planemo upload for repository https://github.com/Marie59/champ_blocs commit 0d86db7d42b608c386a54500064f5f9c9d7019a4 ecology parents: diff changeset	1723 }else {
89f977a3a256 planemo upload for repository https://github.com/Marie59/champ_blocs commit 0d86db7d42b608c386a54500064f5f9c9d7019a4 ecology parents: diff changeset	1724 one <- 0.19
89f977a3a256 planemo upload for repository https://github.com/Marie59/champ_blocs commit 0d86db7d42b608c386a54500064f5f9c9d7019a4 ecology parents: diff changeset	1725 two <- 0.32
89f977a3a256 planemo upload for repository https://github.com/Marie59/champ_blocs commit 0d86db7d42b608c386a54500064f5f9c9d7019a4 ecology parents: diff changeset	1726 three <- 0.455
89f977a3a256 planemo upload for repository https://github.com/Marie59/champ_blocs commit 0d86db7d42b608c386a54500064f5f9c9d7019a4 ecology parents: diff changeset	1727 four <- 0.735
89f977a3a256 planemo upload for repository https://github.com/Marie59/champ_blocs commit 0d86db7d42b608c386a54500064f5f9c9d7019a4 ecology parents: diff changeset	1728 }
89f977a3a256 planemo upload for repository https://github.com/Marie59/champ_blocs commit 0d86db7d42b608c386a54500064f5f9c9d7019a4 ecology parents: diff changeset	1729 # Plot
89f977a3a256 planemo upload for repository https://github.com/Marie59/champ_blocs commit 0d86db7d42b608c386a54500064f5f9c9d7019a4 ecology parents: diff changeset	1730
89f977a3a256 planemo upload for repository https://github.com/Marie59/champ_blocs commit 0d86db7d42b608c386a54500064f5f9c9d7019a4 ecology parents: diff changeset	1731 for (i in c(1:length(unique(bm_bf_fs_dist_stat$Site)))) {
89f977a3a256 planemo upload for repository https://github.com/Marie59/champ_blocs commit 0d86db7d42b608c386a54500064f5f9c9d7019a4 ecology parents: diff changeset	1732
89f977a3a256 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])
89f977a3a256 planemo upload for repository https://github.com/Marie59/champ_blocs commit 0d86db7d42b608c386a54500064f5f9c9d7019a4 ecology parents: diff changeset	1734
89f977a3a256 planemo upload for repository https://github.com/Marie59/champ_blocs commit 0d86db7d42b608c386a54500064f5f9c9d7019a4 ecology parents: diff changeset	1735 bm_bf_fs_plot <- ggplot2::ggplot() +
89f977a3a256 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") +
89f977a3a256 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) +
89f977a3a256 planemo upload for repository https://github.com/Marie59/champ_blocs commit 0d86db7d42b608c386a54500064f5f9c9d7019a4 ecology parents: diff changeset	1738 ggplot2::geom_rect(ggplot2::aes(xmin = as.Date("2013-01-01", origin = "1970-01-01"), xmax = val_xmax, ymin = one, ymax = two, fill = "orange"), alpha = 0.3) +
89f977a3a256 planemo upload for repository https://github.com/Marie59/champ_blocs commit 0d86db7d42b608c386a54500064f5f9c9d7019a4 ecology parents: diff changeset	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) +
89f977a3a256 planemo upload for repository https://github.com/Marie59/champ_blocs commit 0d86db7d42b608c386a54500064f5f9c9d7019a4 ecology parents: diff changeset	1740 ggplot2::geom_rect(ggplot2::aes(xmin = as.Date("2013-01-01", origin = "1970-01-01"), xmax = val_xmax, ymin = three, ymax = four, fill = "green"), alpha = 0.3) +
89f977a3a256 planemo upload for repository https://github.com/Marie59/champ_blocs commit 0d86db7d42b608c386a54500064f5f9c9d7019a4 ecology parents: diff changeset	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) +
89f977a3a256 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")) +
89f977a3a256 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") +
89f977a3a256 planemo upload for repository https://github.com/Marie59/champ_blocs commit 0d86db7d42b608c386a54500064f5f9c9d7019a4 ecology parents: diff changeset	1744 ggplot2::xlab("Date") +
89f977a3a256 planemo upload for repository https://github.com/Marie59/champ_blocs commit 0d86db7d42b608c386a54500064f5f9c9d7019a4 ecology parents: diff changeset	1745 ggplot2::ylab("Coef dissim BM-BF FS") +
89f977a3a256 planemo upload for repository https://github.com/Marie59/champ_blocs commit 0d86db7d42b608c386a54500064f5f9c9d7019a4 ecology parents: diff changeset	1746 ggplot2::ggtitle(unique(df1$Site_bis)) +
89f977a3a256 planemo upload for repository https://github.com/Marie59/champ_blocs commit 0d86db7d42b608c386a54500064f5f9c9d7019a4 ecology parents: diff changeset	1747 ggplot2::theme(axis.text.x = ggplot2::element_text(angle = 90, vjust = 0.5, hjust = 1), legend.position = "none")
89f977a3a256 planemo upload for repository https://github.com/Marie59/champ_blocs commit 0d86db7d42b608c386a54500064f5f9c9d7019a4 ecology parents: diff changeset	1748
89f977a3a256 planemo upload for repository https://github.com/Marie59/champ_blocs commit 0d86db7d42b608c386a54500064f5f9c9d7019a4 ecology parents: diff changeset	1749 ggplot2::ggsave(paste0("bm_bf_", df1$Site, ".png"), device = "png", bm_bf_fs_plot, height = 3, width = 3.5)
89f977a3a256 planemo upload for repository https://github.com/Marie59/champ_blocs commit 0d86db7d42b608c386a54500064f5f9c9d7019a4 ecology parents: diff changeset	1750
89f977a3a256 planemo upload for repository https://github.com/Marie59/champ_blocs commit 0d86db7d42b608c386a54500064f5f9c9d7019a4 ecology parents: diff changeset	1751 }
89f977a3a256 planemo upload for repository https://github.com/Marie59/champ_blocs commit 0d86db7d42b608c386a54500064f5f9c9d7019a4 ecology parents: diff changeset	1752
89f977a3a256 planemo upload for repository https://github.com/Marie59/champ_blocs commit 0d86db7d42b608c386a54500064f5f9c9d7019a4 ecology parents: diff changeset	1753 rm(df1, four, i, one, three, two, xmax_, xmin_, ymax_, ymin_)

Mercurial > repos > ecology > cb_ivr

annotate cb_dissimilarity.r @ 0:89f977a3a256 draft