Mercurial > repos > ecology > ecology_homogeneity_normality
comparison graph_stat_presence_abs.r @ 1:3df8937fd6fd draft default tip
"planemo upload for repository https://github.com/Marie59/Data_explo_tools commit 60627aba07951226c8fd6bb3115be4bd118edd4e"
| author | ecology |
|---|---|
| date | Fri, 13 Aug 2021 18:16:46 +0000 |
| parents | 9f679060051a |
| children |
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| 0:9f679060051a | 1:3df8937fd6fd |
|---|---|
| 18 hr <- args[2] | 18 hr <- args[2] |
| 19 var <- as.numeric(args[3]) | 19 var <- as.numeric(args[3]) |
| 20 spe <- as.numeric(args[4]) | 20 spe <- as.numeric(args[4]) |
| 21 loc <- as.numeric(args[5]) | 21 loc <- as.numeric(args[5]) |
| 22 time <- as.numeric(args[6]) | 22 time <- as.numeric(args[6]) |
| 23 source(args[7]) | |
| 23 } | 24 } |
| 24 | 25 |
| 25 if (hr == "false") { | 26 if (hr == "false") { |
| 26 hr <- FALSE | 27 hr <- FALSE |
| 27 }else{ | 28 }else{ |
| 35 colspe <- colnames(data)[spe] | 36 colspe <- colnames(data)[spe] |
| 36 colloc <- colnames(data)[loc] | 37 colloc <- colnames(data)[loc] |
| 37 coltime <- colnames(data)[time] | 38 coltime <- colnames(data)[time] |
| 38 | 39 |
| 39 data <- data[grep("^$", data[, spe], invert = TRUE), ] | 40 data <- data[grep("^$", data[, spe], invert = TRUE), ] |
| 40 time <- as.integer(substring(data[, time], first = 1, last = 4)) | |
| 41 | 41 |
| 42 #####Your analysis | 42 #####Your analysis |
| 43 | 43 |
| 44 ####Median and data dispersion#### | 44 ####Median and data dispersion#### |
| 45 | 45 |
| 73 | 73 |
| 74 | 74 |
| 75 #### Zero problem in data #### | 75 #### Zero problem in data #### |
| 76 | 76 |
| 77 #Put data in form | 77 #Put data in form |
| 78 make_table_analyse <- function(data, var, spe, var2, var3) { | |
| 79 tab <- reshape(data | |
| 80 , v.names = var | |
| 81 , idvar = c(var2, var3) | |
| 82 , timevar = spe | |
| 83 , direction = "wide") | |
| 84 tab[is.na(tab)] <- 0 ###### remplace les na par des 0 / replace NAs by 0 | |
| 85 | 78 |
| 86 colnames(tab) <- sub(var, "", colnames(tab))### remplace le premier pattern "abond." par le second "" / replace the column names "abond." by "" | |
| 87 return(tab) | |
| 88 } | |
| 89 data_num <- make_table_analyse(data, colvar, colspe, colloc, coltime) | 79 data_num <- make_table_analyse(data, colvar, colspe, colloc, coltime) |
| 90 nb_spe <- length(unique(data[, spe])) | 80 nb_spe <- length(unique(data[, spe])) |
| 91 nb_col <- ncol(data_num) - nb_spe + 1 | 81 nb_col <- ncol(data_num) - nb_spe + 1 |
| 92 data_num <- data_num[, nb_col:ncol(data_num)] | 82 data_num <- data_num[, nb_col:ncol(data_num)] |
| 93 | 83 |