Mercurial > repos > ecology > pampa_presabs

annotate FunctExeCalcPresAbsGalaxy.r @ 0:c9dfe4e20a45 draft

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"planemo upload for repository https://github.com/ColineRoyaux/PAMPA-Galaxy commit 07f1028cc764f920b1e6419c151f04ab4e3600fa"
author ecology
date Tue, 21 Jul 2020 05:59:49 -0400
parents
children 8d8aec182fb1
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c9dfe4e20a45 "planemo upload for repository https://github.com/ColineRoyaux/PAMPA-Galaxy commit 07f1028cc764f920b1e6419c151f04ab4e3600fa"
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1 #Rscript
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3 #####################################################################################################################
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4 #####################################################################################################################
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5 ############################ Calculate presence absence table from observation data #################################
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6 #####################################################################################################################
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7 #####################################################################################################################
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9 ###################### Packages
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10 suppressMessages(library(tidyr))
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12 ###################### Load arguments and declaring variables
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14 args = commandArgs(trailingOnly=TRUE)
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15 #options(encoding = "UTF-8")
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17 if (length(args) < 2) {
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18 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
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20 } else {
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21 Importdata<-args[1] ###### Nom du fichier importé avec son extension / file name imported with the file type ".filetype"
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22 source(args[2]) ###### Import functions
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24 }
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25 #### Data must be a dataframe with at least 3 variables : unitobs representing location and year ("observation.unit"), species code ("species.code") and abundance ("number")
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28 #Import des données / Import data
c9dfe4e20a45 "planemo upload for repository https://github.com/ColineRoyaux/PAMPA-Galaxy commit 07f1028cc764f920b1e6419c151f04ab4e3600fa"
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29 obs<- read.table(Importdata,sep="\t",dec=".",header=TRUE,encoding="UTF-8") #
c9dfe4e20a45 "planemo upload for repository https://github.com/ColineRoyaux/PAMPA-Galaxy commit 07f1028cc764f920b1e6419c151f04ab4e3600fa"
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30 obs[obs == -999] <- NA
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31 factors <- fact.det.f(Obs=obs)
c9dfe4e20a45 "planemo upload for repository https://github.com/ColineRoyaux/PAMPA-Galaxy commit 07f1028cc764f920b1e6419c151f04ab4e3600fa"
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32 ObsType <- def.typeobs.f(Obs=obs)
c9dfe4e20a45 "planemo upload for repository https://github.com/ColineRoyaux/PAMPA-Galaxy commit 07f1028cc764f920b1e6419c151f04ab4e3600fa"
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33 obs <- create.unitobs(data=obs)
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35 vars_data<-c("observation.unit","species.code","number")
c9dfe4e20a45 "planemo upload for repository https://github.com/ColineRoyaux/PAMPA-Galaxy commit 07f1028cc764f920b1e6419c151f04ab4e3600fa"
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36 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"
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37 check_file(obs,err_msg_data,vars_data,3)
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40 ####################################################################################################
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41 #################### Create presence/absence table ## Function : calc.presAbs.f ####################
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42 ####################################################################################################
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44 calc.presAbs.f <- function(Data,
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45 nbName="number")
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46 {
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47 ## Purpose: Compute presence absence
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48 ## ----------------------------------------------------------------------
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49 ## Arguments: Data : temporary metrics table
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50 ## nbName : name of abundance column
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51 ##
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52 ## Output: presence absence vector
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53 ## ----------------------------------------------------------------------
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54 ## Author: Yves Reecht, Date: 20 déc. 2011, 12:04 modified by Coline ROYAUX 04 june 2020
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56 ## Presence - absence :
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57 presAbs <- integer(nrow(Data))
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58 presAbs[Data[ , nbName] > 0] <- as.integer(1)
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59 presAbs[Data[ , nbName] == 0] <- as.integer(0)
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61 return(presAbs)
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62 }
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65 ################# Analysis
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67 res <- calc.numbers.f(obs, ObsType=ObsType , factors=factors, nbName="number")
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68 res$pres.abs <- calc.presAbs.f(res, nbName="number")
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69 res <- create.year.point(res)
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71 #Save dataframe in a tabular format
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72 filenamePresAbs <- "TabPresAbs.tabular"
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73 write.table(res, filenamePresAbs, row.names=FALSE, sep="\t", dec=".",fileEncoding="UTF-8")
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74 cat(paste("\nWrite table with presence/absence. \n--> \"",filenamePresAbs,"\"\n",sep=""))
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