diff FunctExeCalcPresAbsGalaxy.r @ 0:c9dfe4e20a45 draft

"planemo upload for repository https://github.com/ColineRoyaux/PAMPA-Galaxy commit 07f1028cc764f920b1e6419c151f04ab4e3600fa"

--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/FunctExeCalcPresAbsGalaxy.r	Tue Jul 21 05:59:49 2020 -0400
@@ -0,0 +1,75 @@
+#Rscript 
+
+#####################################################################################################################
+#####################################################################################################################
+############################ Calculate presence absence table from observation data #################################
+#####################################################################################################################
+#####################################################################################################################
+
+###################### Packages
+suppressMessages(library(tidyr))
+
+###################### Load arguments and declaring variables
+
+args = commandArgs(trailingOnly=TRUE)
+#options(encoding = "UTF-8")
+
+if (length(args) < 2) {
+    stop("At least one argument must be supplied, an input dataset file (.tabular).", call.=FALSE) #si pas d'arguments -> affiche erreur et quitte / if no args -> error and exit1
+
+} else {
+    Importdata<-args[1] ###### Nom du fichier importé avec son extension / file name imported with the file type ".filetype"  
+    source(args[2]) ###### Import functions
+
+}
+#### Data must be a dataframe with at least 3 variables : unitobs representing location and year ("observation.unit"), species code ("species.code") and abundance ("number")
+
+
+#Import des données / Import data 
+obs<- read.table(Importdata,sep="\t",dec=".",header=TRUE,encoding="UTF-8") #
+obs[obs == -999] <- NA 
+factors <- fact.det.f(Obs=obs)
+ObsType <- def.typeobs.f(Obs=obs)
+obs <- create.unitobs(data=obs)
+
+vars_data<-c("observation.unit","species.code","number")
+err_msg_data<-"The input dataset doesn't have the right format. It need to have at least the following 3 variables :\n- observation.unit (or point and year)\n- species.code\n- number\n"
+check_file(obs,err_msg_data,vars_data,3)
+
+
+####################################################################################################
+#################### Create presence/absence table ## Function : calc.presAbs.f ####################
+####################################################################################################
+
+calc.presAbs.f <- function(Data,
+                           nbName="number")
+{
+    ## Purpose: Compute presence absence 
+    ## ----------------------------------------------------------------------
+    ## Arguments: Data : temporary metrics table
+    ##            nbName : name of abundance column
+    ##
+    ## Output: presence absence vector
+    ## ----------------------------------------------------------------------
+    ## Author: Yves Reecht, Date: 20 déc. 2011, 12:04 modified by Coline ROYAUX 04 june 2020
+
+    ## Presence - absence :
+    presAbs <- integer(nrow(Data))
+    presAbs[Data[ , nbName] > 0] <- as.integer(1) 
+    presAbs[Data[ , nbName] == 0] <- as.integer(0) 
+
+    return(presAbs)
+}
+
+
+################# Analysis
+
+res <- calc.numbers.f(obs, ObsType=ObsType , factors=factors, nbName="number")
+res$pres.abs <- calc.presAbs.f(res, nbName="number")
+res <- create.year.point(res)
+
+#Save dataframe in a tabular format
+filenamePresAbs <- "TabPresAbs.tabular"
+write.table(res, filenamePresAbs, row.names=FALSE, sep="\t", dec=".",fileEncoding="UTF-8")
+cat(paste("\nWrite table with presence/absence. \n--> \"",filenamePresAbs,"\"\n",sep=""))
+