Mercurial > repos > ecology > stoc_mainglm

annotate ExeMainGlmGalaxy.r @ 1:68692ec51b47 draft default tip

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"planemo upload for repository https://github.com/Alanamosse/Galaxy-E/tree/stoctool/tools/stoc commit d49a4da1ffac1f33a15fdb7ae98827d0034a7879"
author ecology
date Mon, 11 May 2020 21:14:37 +0000
parents 37cb73b98f67
children
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37cb73b98f67 "planemo upload for repository https://github.com/Alanamosse/Galaxy-E/tree/stoctool/tools/stoc commit f82f897ab22464de40c878e17616333855814e25"
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1 #!/usr/bin/env Rscript
37cb73b98f67 "planemo upload for repository https://github.com/Alanamosse/Galaxy-E/tree/stoctool/tools/stoc commit f82f897ab22464de40c878e17616333855814e25"
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37cb73b98f67 "planemo upload for repository https://github.com/Alanamosse/Galaxy-E/tree/stoctool/tools/stoc commit f82f897ab22464de40c878e17616333855814e25"
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3 ######################################################################################################################################
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4 ############## COMMAND LINE TO CALCULATE AND PLOT EVOLUTION OF SPECIES POPULATION function:main.glm ##############################
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5 ######################################################################################################################################
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37cb73b98f67 "planemo upload for repository https://github.com/Alanamosse/Galaxy-E/tree/stoctool/tools/stoc commit f82f897ab22464de40c878e17616333855814e25"
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7 #### Based on Romain Lorrillière R script
37cb73b98f67 "planemo upload for repository https://github.com/Alanamosse/Galaxy-E/tree/stoctool/tools/stoc commit f82f897ab22464de40c878e17616333855814e25"
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8 #### Modified by Alan Amosse and Benjamin Yguel for integrating within Galaxy-E
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37cb73b98f67 "planemo upload for repository https://github.com/Alanamosse/Galaxy-E/tree/stoctool/tools/stoc commit f82f897ab22464de40c878e17616333855814e25"
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10 #suppressMessages(library(lme4))
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11 suppressMessages(library(ggplot2))
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12 suppressMessages(library(speedglm))
37cb73b98f67 "planemo upload for repository https://github.com/Alanamosse/Galaxy-E/tree/stoctool/tools/stoc commit f82f897ab22464de40c878e17616333855814e25"
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13 suppressMessages(library(arm))
37cb73b98f67 "planemo upload for repository https://github.com/Alanamosse/Galaxy-E/tree/stoctool/tools/stoc commit f82f897ab22464de40c878e17616333855814e25"
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14 #suppressMessages(library(reshape))
37cb73b98f67 "planemo upload for repository https://github.com/Alanamosse/Galaxy-E/tree/stoctool/tools/stoc commit f82f897ab22464de40c878e17616333855814e25"
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15 suppressMessages(library(data.table))
37cb73b98f67 "planemo upload for repository https://github.com/Alanamosse/Galaxy-E/tree/stoctool/tools/stoc commit f82f897ab22464de40c878e17616333855814e25"
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16 suppressMessages(library(reshape2))
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19 ###########
37cb73b98f67 "planemo upload for repository https://github.com/Alanamosse/Galaxy-E/tree/stoctool/tools/stoc commit f82f897ab22464de40c878e17616333855814e25"
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20 #delcaration des arguments et variables/ declaring some variables and load arguments
37cb73b98f67 "planemo upload for repository https://github.com/Alanamosse/Galaxy-E/tree/stoctool/tools/stoc commit f82f897ab22464de40c878e17616333855814e25"
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22 args = commandArgs(trailingOnly=TRUE)
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23 options(encoding = "UTF-8")
37cb73b98f67 "planemo upload for repository https://github.com/Alanamosse/Galaxy-E/tree/stoctool/tools/stoc commit f82f897ab22464de40c878e17616333855814e25"
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24 source(args[6],encoding="UTF-8")### chargement des fonctions / load the functions
37cb73b98f67 "planemo upload for repository https://github.com/Alanamosse/Galaxy-E/tree/stoctool/tools/stoc commit f82f897ab22464de40c878e17616333855814e25"
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26 if ( (length(args)<8) || (length(args)>9)) {
37cb73b98f67 "planemo upload for repository https://github.com/Alanamosse/Galaxy-E/tree/stoctool/tools/stoc commit f82f897ab22464de40c878e17616333855814e25"
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27 stop("At least 5 arguments must be supplied :\n- An input dataset filtered (.tabular). May come from the filter rare species tool.\n- A species detail table (.tabular)\n- An id to fix output repository name.\n- A list of species to exclude, can be empty.\n- TRUE/FALSE to perform the glm with confidence intervals calculations.\n\n", call.=FALSE) #si pas d'arguments -> affiche erreur et quitte / if no args -> error and exit1
37cb73b98f67 "planemo upload for repository https://github.com/Alanamosse/Galaxy-E/tree/stoctool/tools/stoc commit f82f897ab22464de40c878e17616333855814e25"
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28 } else {
37cb73b98f67 "planemo upload for repository https://github.com/Alanamosse/Galaxy-E/tree/stoctool/tools/stoc commit f82f897ab22464de40c878e17616333855814e25"
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29 Datafilteredfortrendanalysis<-args[1] ###### Nom du fichier avec extension ".typedefichier", peut provenir de la fonction "FiltreEspeceRare" / file name without the file type ".filetype", may result from the function "FiltreEspeceRare"
37cb73b98f67 "planemo upload for repository https://github.com/Alanamosse/Galaxy-E/tree/stoctool/tools/stoc commit f82f897ab22464de40c878e17616333855814e25"
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30 tabSpecies<-args[2] ###### Nom du fichier avec extension ".typedefichier", fichier mis à disposition dans Galaxy-E avec specialisation à l'habitat des especes et si espece considérée comme indicatrice / file name without the file type ".filetype", file available in Galaxy-E containing habitat specialization for each species and whether or not they are considered as indicator
37cb73b98f67 "planemo upload for repository https://github.com/Alanamosse/Galaxy-E/tree/stoctool/tools/stoc commit f82f897ab22464de40c878e17616333855814e25"
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31 id<-args[3] ##### nom du dossier de sortie des resultats / name of the output folder
37cb73b98f67 "planemo upload for repository https://github.com/Alanamosse/Galaxy-E/tree/stoctool/tools/stoc commit f82f897ab22464de40c878e17616333855814e25"
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32 spExclude <- strsplit(args [4],",")[[1]] ##### liste d'espece qu on veut exclure de l analyse / list of species that will be excluded
37cb73b98f67 "planemo upload for repository https://github.com/Alanamosse/Galaxy-E/tree/stoctool/tools/stoc commit f82f897ab22464de40c878e17616333855814e25"
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33 AssessIC <-args [5] ########## TRUE ou FALSE réalise glm "standard" avec calcul d'intervalle de confiance ou speedglm sans IC bien plus rapide / TRUE or FALSE perform a "standard" glm with confidance interval or speedglm without CI much more fast
37cb73b98f67 "planemo upload for repository https://github.com/Alanamosse/Galaxy-E/tree/stoctool/tools/stoc commit f82f897ab22464de40c878e17616333855814e25"
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34 }
37cb73b98f67 "planemo upload for repository https://github.com/Alanamosse/Galaxy-E/tree/stoctool/tools/stoc commit f82f897ab22464de40c878e17616333855814e25"
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36 ## creation d'un dossier pour y mettre les resultats / create folder for the output of the analyses
37cb73b98f67 "planemo upload for repository https://github.com/Alanamosse/Galaxy-E/tree/stoctool/tools/stoc commit f82f897ab22464de40c878e17616333855814e25"
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38 dir.create(paste("Output/",id,sep=""),recursive=TRUE,showWarnings=FALSE)
37cb73b98f67 "planemo upload for repository https://github.com/Alanamosse/Galaxy-E/tree/stoctool/tools/stoc commit f82f897ab22464de40c878e17616333855814e25"
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39 #cat(paste("Create Output/",id,"\n",sep=""))
37cb73b98f67 "planemo upload for repository https://github.com/Alanamosse/Galaxy-E/tree/stoctool/tools/stoc commit f82f897ab22464de40c878e17616333855814e25"
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40 dir.create(paste("Output/",id,"/Incertain/",sep=""),recursive=TRUE,showWarnings=FALSE)
37cb73b98f67 "planemo upload for repository https://github.com/Alanamosse/Galaxy-E/tree/stoctool/tools/stoc commit f82f897ab22464de40c878e17616333855814e25"
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41 #cat(paste("Create Output/",id,"Incertain/\n",sep=""))
37cb73b98f67 "planemo upload for repository https://github.com/Alanamosse/Galaxy-E/tree/stoctool/tools/stoc commit f82f897ab22464de40c878e17616333855814e25"
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44 #Import des données / Import data
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45 tabCLEAN <- fread(Datafilteredfortrendanalysis,sep="\t",dec=".",header=TRUE,encoding="UTF-8") #### charge le fichier de données d abondance / load abundance of species
37cb73b98f67 "planemo upload for repository https://github.com/Alanamosse/Galaxy-E/tree/stoctool/tools/stoc commit f82f897ab22464de40c878e17616333855814e25"
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46 tabsp <- fread(tabSpecies,sep="\t",dec=".",header=TRUE,encoding="UTF-8") #### charge le fichier de donnees sur nom latin, vernaculaire et abbreviation, espece indicatrice ou non / load the file with information on species specialization and if species are indicators
37cb73b98f67 "planemo upload for repository https://github.com/Alanamosse/Galaxy-E/tree/stoctool/tools/stoc commit f82f897ab22464de40c878e17616333855814e25"
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48 vars_tabCLEAN<-c("carre","annee","espece","abond")
37cb73b98f67 "planemo upload for repository https://github.com/Alanamosse/Galaxy-E/tree/stoctool/tools/stoc commit f82f897ab22464de40c878e17616333855814e25"
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49 err_msg_tabCLEAN<-"The input dataset filtered doesn't have the right format. It need to have the following 4 variables :\n- carre\n- annee\n- espece\n- abond\n"
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51 vars_tabsp<-c("espece","nom","nomscientific","indicateur","specialisation")
37cb73b98f67 "planemo upload for repository https://github.com/Alanamosse/Galaxy-E/tree/stoctool/tools/stoc commit f82f897ab22464de40c878e17616333855814e25"
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52 err_msg_tabsp<-"\nThe species dataset filtered doesn't have the right format. It need to have the following 4 variables :\n- espece\n- nom\n- nomscientific\n- indicateur\n- specialisation\n"
37cb73b98f67 "planemo upload for repository https://github.com/Alanamosse/Galaxy-E/tree/stoctool/tools/stoc commit f82f897ab22464de40c878e17616333855814e25"
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54 check_file(tabCLEAN,err_msg_tabCLEAN,vars_tabCLEAN,4)
37cb73b98f67 "planemo upload for repository https://github.com/Alanamosse/Galaxy-E/tree/stoctool/tools/stoc commit f82f897ab22464de40c878e17616333855814e25"
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55 check_file(tabsp,err_msg_tabsp,vars_tabsp,5)
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59 firstYear <- min(tabCLEAN$annee) #### Recupère 1ere annee des donnees / retrieve the first year of the dataset
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60 lastYear <- max(tabCLEAN$annee) #### Récupère la dernière annee des donnees / retrieve the last year of the dataset
37cb73b98f67 "planemo upload for repository https://github.com/Alanamosse/Galaxy-E/tree/stoctool/tools/stoc commit f82f897ab22464de40c878e17616333855814e25"
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61 annees <- firstYear:lastYear ##### !!!! une autre variable s'appelle annee donc peut être à modif en "periode" ? ### argument de la fonction mais DECLARER DANS LA FONCTION AUSSI donc un des 2 à supprimer
37cb73b98f67 "planemo upload for repository https://github.com/Alanamosse/Galaxy-E/tree/stoctool/tools/stoc commit f82f897ab22464de40c878e17616333855814e25"
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62 spsFiltre=unique(tabCLEAN$espece) #### Recupère la liste des especes du tabCLEAN qui ont été sélectionnée et qui ont passé le filtre / retrieve species name that were selected and then filtered before
37cb73b98f67 "planemo upload for repository https://github.com/Alanamosse/Galaxy-E/tree/stoctool/tools/stoc commit f82f897ab22464de40c878e17616333855814e25"
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63 #cat("\n\nspsFiltre\n")
37cb73b98f67 "planemo upload for repository https://github.com/Alanamosse/Galaxy-E/tree/stoctool/tools/stoc commit f82f897ab22464de40c878e17616333855814e25"
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64 tabsp=subset (tabsp, (espece %in% spsFiltre)) #### liste des espèces exclu par le filtre ou manuellement / List of species excluded manually or by the filter from the analyses
37cb73b98f67 "planemo upload for repository https://github.com/Alanamosse/Galaxy-E/tree/stoctool/tools/stoc commit f82f897ab22464de40c878e17616333855814e25"
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65 #cat("\n\ntabsp\n")
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66 sp=as.character(tabsp$espece) ##### liste des espece en code ou abbreviation gardées pour les analyses ### arg de la fonction DECLARE AUSSI APRES DS FONCTION / list of the code or abbreviation of the species kept for the analyses
37cb73b98f67 "planemo upload for repository https://github.com/Alanamosse/Galaxy-E/tree/stoctool/tools/stoc commit f82f897ab22464de40c878e17616333855814e25"
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67 #cat("\n\nsp\n")
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68 if(length(spExclude)!=0) {
37cb73b98f67 "planemo upload for repository https://github.com/Alanamosse/Galaxy-E/tree/stoctool/tools/stoc commit f82f897ab22464de40c878e17616333855814e25"
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69 tabCLEAN <- subset(tabCLEAN,!(espece %in% spExclude))
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70 tabsp <- subset(tabsp, !(espece %in% spExclude))
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72 cat("\n\nEspèces exclues de l'analyse :\n")
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73 cat(spExclude)
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74 cat("\n")
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75 }
37cb73b98f67 "planemo upload for repository https://github.com/Alanamosse/Galaxy-E/tree/stoctool/tools/stoc commit f82f897ab22464de40c878e17616333855814e25"
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76 if(length(tabCLEAN$espece)==0){
37cb73b98f67 "planemo upload for repository https://github.com/Alanamosse/Galaxy-E/tree/stoctool/tools/stoc commit f82f897ab22464de40c878e17616333855814e25"
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77 stop("There is no species left for the analyse.", call.=FALSE) #si pas plus d'espèce après filtre / if no more species after filter
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78 }
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79 #cat("\n\ntabsp\n")
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82 ##################
37cb73b98f67 "planemo upload for repository https://github.com/Alanamosse/Galaxy-E/tree/stoctool/tools/stoc commit f82f897ab22464de40c878e17616333855814e25"
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83 ### Do your analysis
37cb73b98f67 "planemo upload for repository https://github.com/Alanamosse/Galaxy-E/tree/stoctool/tools/stoc commit f82f897ab22464de40c878e17616333855814e25"
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37cb73b98f67 "planemo upload for repository https://github.com/Alanamosse/Galaxy-E/tree/stoctool/tools/stoc commit f82f897ab22464de40c878e17616333855814e25"
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85 main.glm(donneesAll=tabCLEAN,tabsp=tabsp,id=id,assessIC=AssessIC)
37cb73b98f67 "planemo upload for repository https://github.com/Alanamosse/Galaxy-E/tree/stoctool/tools/stoc commit f82f897ab22464de40c878e17616333855814e25"
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37cb73b98f67 "planemo upload for repository https://github.com/Alanamosse/Galaxy-E/tree/stoctool/tools/stoc commit f82f897ab22464de40c878e17616333855814e25"
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37cb73b98f67 "planemo upload for repository https://github.com/Alanamosse/Galaxy-E/tree/stoctool/tools/stoc commit f82f897ab22464de40c878e17616333855814e25"
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37cb73b98f67 "planemo upload for repository https://github.com/Alanamosse/Galaxy-E/tree/stoctool/tools/stoc commit f82f897ab22464de40c878e17616333855814e25"
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37cb73b98f67 "planemo upload for repository https://github.com/Alanamosse/Galaxy-E/tree/stoctool/tools/stoc commit f82f897ab22464de40c878e17616333855814e25"
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90