Mercurial > repos > ecology > pampa_glmsp

annotate FunctExeCalcGLMSpGalaxy.r @ 0:0778efa9eb2e draft

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"planemo upload for repository https://github.com/ColineRoyaux/PAMPA-Galaxy commit 07f1028cc764f920b1e6419c151f04ab4e3600fa"
author ecology
date Tue, 21 Jul 2020 06:00:51 -0400
parents
children 6c14021f678e
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0778efa9eb2e "planemo upload for repository https://github.com/ColineRoyaux/PAMPA-Galaxy commit 07f1028cc764f920b1e6419c151f04ab4e3600fa"
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1 #Rscript
0778efa9eb2e "planemo upload for repository https://github.com/ColineRoyaux/PAMPA-Galaxy commit 07f1028cc764f920b1e6419c151f04ab4e3600fa"
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0778efa9eb2e "planemo upload for repository https://github.com/ColineRoyaux/PAMPA-Galaxy commit 07f1028cc764f920b1e6419c151f04ab4e3600fa"
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3 #####################################################################################################################
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4 #####################################################################################################################
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5 ################################# Compute a Generalized Linear Model from your data #################################
0778efa9eb2e "planemo upload for repository https://github.com/ColineRoyaux/PAMPA-Galaxy commit 07f1028cc764f920b1e6419c151f04ab4e3600fa"
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6 #####################################################################################################################
0778efa9eb2e "planemo upload for repository https://github.com/ColineRoyaux/PAMPA-Galaxy commit 07f1028cc764f920b1e6419c151f04ab4e3600fa"
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7 #####################################################################################################################
0778efa9eb2e "planemo upload for repository https://github.com/ColineRoyaux/PAMPA-Galaxy commit 07f1028cc764f920b1e6419c151f04ab4e3600fa"
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9 ###################### Packages
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10 #suppressMessages(library(MASS))
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11 suppressMessages(library(multcomp))
0778efa9eb2e "planemo upload for repository https://github.com/ColineRoyaux/PAMPA-Galaxy commit 07f1028cc764f920b1e6419c151f04ab4e3600fa"
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12 suppressMessages(library(glmmTMB)) ###Version: 0.2.3
0778efa9eb2e "planemo upload for repository https://github.com/ColineRoyaux/PAMPA-Galaxy commit 07f1028cc764f920b1e6419c151f04ab4e3600fa"
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13 suppressMessages(library(gap))
0778efa9eb2e "planemo upload for repository https://github.com/ColineRoyaux/PAMPA-Galaxy commit 07f1028cc764f920b1e6419c151f04ab4e3600fa"
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15 ###################### Load arguments and declaring variables
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0778efa9eb2e "planemo upload for repository https://github.com/ColineRoyaux/PAMPA-Galaxy commit 07f1028cc764f920b1e6419c151f04ab4e3600fa"
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17 args = commandArgs(trailingOnly=TRUE)
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18 #options(encoding = "UTF-8")
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20 if (length(args) < 10) {
0778efa9eb2e "planemo upload for repository https://github.com/ColineRoyaux/PAMPA-Galaxy commit 07f1028cc764f920b1e6419c151f04ab4e3600fa"
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21 stop("At least 4 arguments must be supplied : \n- two input dataset files (.tabular) : metrics table and unitobs table \n- Interest variable field from metrics table \n- Response variable from unitobs table.", call.=FALSE) #si pas d'arguments -> affiche erreur et quitte / if no args -> error and exit1
0778efa9eb2e "planemo upload for repository https://github.com/ColineRoyaux/PAMPA-Galaxy commit 07f1028cc764f920b1e6419c151f04ab4e3600fa"
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23 } else {
0778efa9eb2e "planemo upload for repository https://github.com/ColineRoyaux/PAMPA-Galaxy commit 07f1028cc764f920b1e6419c151f04ab4e3600fa"
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24 Importdata <- args[1] ###### file name : metrics table
0778efa9eb2e "planemo upload for repository https://github.com/ColineRoyaux/PAMPA-Galaxy commit 07f1028cc764f920b1e6419c151f04ab4e3600fa"
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25 ImportUnitobs <- args[2] ###### file name : unitobs informations
0778efa9eb2e "planemo upload for repository https://github.com/ColineRoyaux/PAMPA-Galaxy commit 07f1028cc764f920b1e6419c151f04ab4e3600fa"
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26 colmetric <- as.numeric(args[3]) ###### Selected interest metric for GLM
0778efa9eb2e "planemo upload for repository https://github.com/ColineRoyaux/PAMPA-Galaxy commit 07f1028cc764f920b1e6419c151f04ab4e3600fa"
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27 listFact <- strsplit(args [4],",")[[1]] ###### Selected response factors for GLM
0778efa9eb2e "planemo upload for repository https://github.com/ColineRoyaux/PAMPA-Galaxy commit 07f1028cc764f920b1e6419c151f04ab4e3600fa"
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28 listRand <- strsplit(args [5],",")[[1]] ###### Selected randomized response factors for GLM
0778efa9eb2e "planemo upload for repository https://github.com/ColineRoyaux/PAMPA-Galaxy commit 07f1028cc764f920b1e6419c151f04ab4e3600fa"
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29 colFactAna <- args[6] ####### (optional) Selected splitting factors for GLMs
0778efa9eb2e "planemo upload for repository https://github.com/ColineRoyaux/PAMPA-Galaxy commit 07f1028cc764f920b1e6419c151f04ab4e3600fa"
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30 Distrib <- args[7] ###### (optional) Selected distribution for GLM
0778efa9eb2e "planemo upload for repository https://github.com/ColineRoyaux/PAMPA-Galaxy commit 07f1028cc764f920b1e6419c151f04ab4e3600fa"
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31 log <- args[8] ###### (Optional) Log on interest metric ?
0778efa9eb2e "planemo upload for repository https://github.com/ColineRoyaux/PAMPA-Galaxy commit 07f1028cc764f920b1e6419c151f04ab4e3600fa"
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32 aggreg <- args[9] ###### Aggregation level of the data table
0778efa9eb2e "planemo upload for repository https://github.com/ColineRoyaux/PAMPA-Galaxy commit 07f1028cc764f920b1e6419c151f04ab4e3600fa"
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33 source(args[10]) ###### Import functions
0778efa9eb2e "planemo upload for repository https://github.com/ColineRoyaux/PAMPA-Galaxy commit 07f1028cc764f920b1e6419c151f04ab4e3600fa"
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35 }
0778efa9eb2e "planemo upload for repository https://github.com/ColineRoyaux/PAMPA-Galaxy commit 07f1028cc764f920b1e6419c151f04ab4e3600fa"
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36 #### Data must be a dataframe with at least 3 variables : unitobs representing location and year ("observation.unit"), species code ("species.code") and abundance ("number")
0778efa9eb2e "planemo upload for repository https://github.com/ColineRoyaux/PAMPA-Galaxy commit 07f1028cc764f920b1e6419c151f04ab4e3600fa"
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38
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39 #Import des données / Import data
0778efa9eb2e "planemo upload for repository https://github.com/ColineRoyaux/PAMPA-Galaxy commit 07f1028cc764f920b1e6419c151f04ab4e3600fa"
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40 obs<- read.table(Importdata,sep="\t",dec=".",header=TRUE,encoding="UTF-8") #
0778efa9eb2e "planemo upload for repository https://github.com/ColineRoyaux/PAMPA-Galaxy commit 07f1028cc764f920b1e6419c151f04ab4e3600fa"
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41 obs[obs == -999] <- NA
0778efa9eb2e "planemo upload for repository https://github.com/ColineRoyaux/PAMPA-Galaxy commit 07f1028cc764f920b1e6419c151f04ab4e3600fa"
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42 metric <- colnames(obs)[colmetric]
0778efa9eb2e "planemo upload for repository https://github.com/ColineRoyaux/PAMPA-Galaxy commit 07f1028cc764f920b1e6419c151f04ab4e3600fa"
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43 tabUnitobs <- read.table(ImportUnitobs,sep="\t",dec=".",header=TRUE,encoding="UTF-8")
0778efa9eb2e "planemo upload for repository https://github.com/ColineRoyaux/PAMPA-Galaxy commit 07f1028cc764f920b1e6419c151f04ab4e3600fa"
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44 tabUnitobs[tabUnitobs == -999] <- NA
0778efa9eb2e "planemo upload for repository https://github.com/ColineRoyaux/PAMPA-Galaxy commit 07f1028cc764f920b1e6419c151f04ab4e3600fa"
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46 vars_data1<- c("species.code")
0778efa9eb2e "planemo upload for repository https://github.com/ColineRoyaux/PAMPA-Galaxy commit 07f1028cc764f920b1e6419c151f04ab4e3600fa"
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47 err_msg_data1<-"The input metrics dataset doesn't have the right format. It needs to have at least the following 3 variables :\n- species.code \n- observation.unit (or year and site)\n- numeric or integer metric\n"
0778efa9eb2e "planemo upload for repository https://github.com/ColineRoyaux/PAMPA-Galaxy commit 07f1028cc764f920b1e6419c151f04ab4e3600fa"
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48 check_file(obs,err_msg_data1,vars_data1,3)
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49
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50 vars_data2 <- c(listFact,listRand)
0778efa9eb2e "planemo upload for repository https://github.com/ColineRoyaux/PAMPA-Galaxy commit 07f1028cc764f920b1e6419c151f04ab4e3600fa"
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51 vars_data2 <- vars_data2[vars_data2 != "None"]
0778efa9eb2e "planemo upload for repository https://github.com/ColineRoyaux/PAMPA-Galaxy commit 07f1028cc764f920b1e6419c151f04ab4e3600fa"
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52 err_msg_data2<-"The input unitobs dataset doesn't have the right format. It needs to have at least the following 2 variables :\n- observation.unit (or year and site)\n- factors used in GLM (habitat, year and/or site)\n"
0778efa9eb2e "planemo upload for repository https://github.com/ColineRoyaux/PAMPA-Galaxy commit 07f1028cc764f920b1e6419c151f04ab4e3600fa"
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53 check_file(tabUnitobs,err_msg_data2,vars_data2,2)
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54
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55
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56 if (colFactAna != "None")
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57 {
0778efa9eb2e "planemo upload for repository https://github.com/ColineRoyaux/PAMPA-Galaxy commit 07f1028cc764f920b1e6419c151f04ab4e3600fa"
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58 FactAna <- colFactAna
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59 if (class(obs[FactAna]) == "numeric" || FactAna == "observation.unit"){stop("Wrong chosen separation factor : Analysis can't be separated by observation unit or numeric factor")}
0778efa9eb2e "planemo upload for repository https://github.com/ColineRoyaux/PAMPA-Galaxy commit 07f1028cc764f920b1e6419c151f04ab4e3600fa"
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60 }else{
0778efa9eb2e "planemo upload for repository https://github.com/ColineRoyaux/PAMPA-Galaxy commit 07f1028cc764f920b1e6419c151f04ab4e3600fa"
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61 FactAna <- colFactAna
0778efa9eb2e "planemo upload for repository https://github.com/ColineRoyaux/PAMPA-Galaxy commit 07f1028cc764f920b1e6419c151f04ab4e3600fa"
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62 }
0778efa9eb2e "planemo upload for repository https://github.com/ColineRoyaux/PAMPA-Galaxy commit 07f1028cc764f920b1e6419c151f04ab4e3600fa"
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63
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64
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65 #factors <- fact.det.f(Obs=obs)
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66
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67 ####################################################################################################
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68 ########## Computing Generalized Linear Model ## Function : modeleLineaireWP2.unitobs.f ############
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69 ####################################################################################################
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70
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71 modeleLineaireWP2.species.f <- function(metrique, listFact, listRand, FactAna, Distrib, log=FALSE, tabMetrics, tableMetrique, tabUnitobs, unitobs="observation.unit", outresiduals = FALSE, nbName="number")
0778efa9eb2e "planemo upload for repository https://github.com/ColineRoyaux/PAMPA-Galaxy commit 07f1028cc764f920b1e6419c151f04ab4e3600fa"
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72 {
0778efa9eb2e "planemo upload for repository https://github.com/ColineRoyaux/PAMPA-Galaxy commit 07f1028cc764f920b1e6419c151f04ab4e3600fa"
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73 ## Purpose: Gestions des différentes étapes des modèles linéaires.
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74 ## ----------------------------------------------------------------------
0778efa9eb2e "planemo upload for repository https://github.com/ColineRoyaux/PAMPA-Galaxy commit 07f1028cc764f920b1e6419c151f04ab4e3600fa"
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75 ## Arguments: metrique : la métrique choisie.
0778efa9eb2e "planemo upload for repository https://github.com/ColineRoyaux/PAMPA-Galaxy commit 07f1028cc764f920b1e6419c151f04ab4e3600fa"
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76 ## factAna : le facteur de séparation des graphiques.
0778efa9eb2e "planemo upload for repository https://github.com/ColineRoyaux/PAMPA-Galaxy commit 07f1028cc764f920b1e6419c151f04ab4e3600fa"
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77 ## factAnaSel : la sélection de modalités pour ce dernier
0778efa9eb2e "planemo upload for repository https://github.com/ColineRoyaux/PAMPA-Galaxy commit 07f1028cc764f920b1e6419c151f04ab4e3600fa"
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78 ## listFact : liste du (des) facteur(s) de regroupement
0778efa9eb2e "planemo upload for repository https://github.com/ColineRoyaux/PAMPA-Galaxy commit 07f1028cc764f920b1e6419c151f04ab4e3600fa"
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79 ## listFactSel : liste des modalités sélectionnées pour ce(s)
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80 ## dernier(s)
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81 ## tabMetrics : table de métriques.
0778efa9eb2e "planemo upload for repository https://github.com/ColineRoyaux/PAMPA-Galaxy commit 07f1028cc764f920b1e6419c151f04ab4e3600fa"
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82 ## tableMetrique : nom de la table de métriques.
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83 ## dataEnv : environnement de stockage des données.
0778efa9eb2e "planemo upload for repository https://github.com/ColineRoyaux/PAMPA-Galaxy commit 07f1028cc764f920b1e6419c151f04ab4e3600fa"
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84 ## baseEnv : environnement de l'interface.
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85 ## ----------------------------------------------------------------------
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86 ## Author: Yves Reecht, Date: 18 août 2010, 15:59
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87
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88 tmpData <- tabMetrics
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89
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90 if (listRand[1] != "None")
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91 {
0778efa9eb2e "planemo upload for repository https://github.com/ColineRoyaux/PAMPA-Galaxy commit 07f1028cc764f920b1e6419c151f04ab4e3600fa"
ecology
parents:
diff changeset
92 if (all(is.element(listFact,listRand)) || listFact[1] == "None")
0778efa9eb2e "planemo upload for repository https://github.com/ColineRoyaux/PAMPA-Galaxy commit 07f1028cc764f920b1e6419c151f04ab4e3600fa"
ecology
parents:
diff changeset
93 {
0778efa9eb2e "planemo upload for repository https://github.com/ColineRoyaux/PAMPA-Galaxy commit 07f1028cc764f920b1e6419c151f04ab4e3600fa"
ecology
parents:
diff changeset
94 RespFact <- paste("(1|",paste(listRand,collapse=") + (1|"),")")
0778efa9eb2e "planemo upload for repository https://github.com/ColineRoyaux/PAMPA-Galaxy commit 07f1028cc764f920b1e6419c151f04ab4e3600fa"
ecology
parents:
diff changeset
95 listF <- NULL
0778efa9eb2e "planemo upload for repository https://github.com/ColineRoyaux/PAMPA-Galaxy commit 07f1028cc764f920b1e6419c151f04ab4e3600fa"
ecology
parents:
diff changeset
96 listFact <- listRand
0778efa9eb2e "planemo upload for repository https://github.com/ColineRoyaux/PAMPA-Galaxy commit 07f1028cc764f920b1e6419c151f04ab4e3600fa"
ecology
parents:
diff changeset
97 }else{
0778efa9eb2e "planemo upload for repository https://github.com/ColineRoyaux/PAMPA-Galaxy commit 07f1028cc764f920b1e6419c151f04ab4e3600fa"
ecology
parents:
diff changeset
98 listF <- listFact[!is.element(listFact,listRand)]
0778efa9eb2e "planemo upload for repository https://github.com/ColineRoyaux/PAMPA-Galaxy commit 07f1028cc764f920b1e6419c151f04ab4e3600fa"
ecology
parents:
diff changeset
99 RespFact <- paste(paste(listF, collapse=" + ")," + (1|",paste(listRand,collapse=") + (1|"),")")
0778efa9eb2e "planemo upload for repository https://github.com/ColineRoyaux/PAMPA-Galaxy commit 07f1028cc764f920b1e6419c151f04ab4e3600fa"
ecology
parents:
diff changeset
100 listFact <- c(listF,listRand)
0778efa9eb2e "planemo upload for repository https://github.com/ColineRoyaux/PAMPA-Galaxy commit 07f1028cc764f920b1e6419c151f04ab4e3600fa"
ecology
parents:
diff changeset
101 }
0778efa9eb2e "planemo upload for repository https://github.com/ColineRoyaux/PAMPA-Galaxy commit 07f1028cc764f920b1e6419c151f04ab4e3600fa"
ecology
parents:
diff changeset
102 }else{
0778efa9eb2e "planemo upload for repository https://github.com/ColineRoyaux/PAMPA-Galaxy commit 07f1028cc764f920b1e6419c151f04ab4e3600fa"
ecology
parents:
diff changeset
103 listF <- listFact
0778efa9eb2e "planemo upload for repository https://github.com/ColineRoyaux/PAMPA-Galaxy commit 07f1028cc764f920b1e6419c151f04ab4e3600fa"
ecology
parents:
diff changeset
104 RespFact <- paste(listFact, collapse=" + ")
0778efa9eb2e "planemo upload for repository https://github.com/ColineRoyaux/PAMPA-Galaxy commit 07f1028cc764f920b1e6419c151f04ab4e3600fa"
ecology
parents:
diff changeset
105 }
0778efa9eb2e "planemo upload for repository https://github.com/ColineRoyaux/PAMPA-Galaxy commit 07f1028cc764f920b1e6419c151f04ab4e3600fa"
ecology
parents:
diff changeset
106 ##Creating model's expression :
0778efa9eb2e "planemo upload for repository https://github.com/ColineRoyaux/PAMPA-Galaxy commit 07f1028cc764f920b1e6419c151f04ab4e3600fa"
ecology
parents:
diff changeset
107 #if (log == FALSE) {
0778efa9eb2e "planemo upload for repository https://github.com/ColineRoyaux/PAMPA-Galaxy commit 07f1028cc764f920b1e6419c151f04ab4e3600fa"
ecology
parents:
diff changeset
108 exprML <- eval(parse(text=paste(metrique, "~", RespFact)))
0778efa9eb2e "planemo upload for repository https://github.com/ColineRoyaux/PAMPA-Galaxy commit 07f1028cc764f920b1e6419c151f04ab4e3600fa"
ecology
parents:
diff changeset
109 #}else{
0778efa9eb2e "planemo upload for repository https://github.com/ColineRoyaux/PAMPA-Galaxy commit 07f1028cc764f920b1e6419c151f04ab4e3600fa"
ecology
parents:
diff changeset
110 # exprML <- eval(parse(text=paste("log(",metrique,")", "~", RespFact)))
0778efa9eb2e "planemo upload for repository https://github.com/ColineRoyaux/PAMPA-Galaxy commit 07f1028cc764f920b1e6419c151f04ab4e3600fa"
ecology
parents:
diff changeset
111 #}
0778efa9eb2e "planemo upload for repository https://github.com/ColineRoyaux/PAMPA-Galaxy commit 07f1028cc764f920b1e6419c151f04ab4e3600fa"
ecology
parents:
diff changeset
112
0778efa9eb2e "planemo upload for repository https://github.com/ColineRoyaux/PAMPA-Galaxy commit 07f1028cc764f920b1e6419c151f04ab4e3600fa"
ecology
parents:
diff changeset
113 ##Creating analysis table :
0778efa9eb2e "planemo upload for repository https://github.com/ColineRoyaux/PAMPA-Galaxy commit 07f1028cc764f920b1e6419c151f04ab4e3600fa"
ecology
parents:
diff changeset
114 listFactTab <- c(listFact,FactAna)
0778efa9eb2e "planemo upload for repository https://github.com/ColineRoyaux/PAMPA-Galaxy commit 07f1028cc764f920b1e6419c151f04ab4e3600fa"
ecology
parents:
diff changeset
115 listFactTab <- listFactTab[listFactTab != "None"]
0778efa9eb2e "planemo upload for repository https://github.com/ColineRoyaux/PAMPA-Galaxy commit 07f1028cc764f920b1e6419c151f04ab4e3600fa"
ecology
parents:
diff changeset
116
0778efa9eb2e "planemo upload for repository https://github.com/ColineRoyaux/PAMPA-Galaxy commit 07f1028cc764f920b1e6419c151f04ab4e3600fa"
ecology
parents:
diff changeset
117 if (all(is.na(match(tmpData[,unitobs],tabUnitobs[,unitobs])))) {stop("Observation units doesn't match in the two input tables")}
0778efa9eb2e "planemo upload for repository https://github.com/ColineRoyaux/PAMPA-Galaxy commit 07f1028cc764f920b1e6419c151f04ab4e3600fa"
ecology
parents:
diff changeset
118
0778efa9eb2e "planemo upload for repository https://github.com/ColineRoyaux/PAMPA-Galaxy commit 07f1028cc764f920b1e6419c151f04ab4e3600fa"
ecology
parents:
diff changeset
119 if(is.element("species.code",colnames(tmpData)))
0778efa9eb2e "planemo upload for repository https://github.com/ColineRoyaux/PAMPA-Galaxy commit 07f1028cc764f920b1e6419c151f04ab4e3600fa"
ecology
parents:
diff changeset
120 {
0778efa9eb2e "planemo upload for repository https://github.com/ColineRoyaux/PAMPA-Galaxy commit 07f1028cc764f920b1e6419c151f04ab4e3600fa"
ecology
parents:
diff changeset
121 col <- c(unitobs,metrique,FactAna)
0778efa9eb2e "planemo upload for repository https://github.com/ColineRoyaux/PAMPA-Galaxy commit 07f1028cc764f920b1e6419c151f04ab4e3600fa"
ecology
parents:
diff changeset
122 tmpData <- cbind(tmpData[,col], tabUnitobs[match(tmpData[,unitobs],tabUnitobs[,unitobs]),listFact])
0778efa9eb2e "planemo upload for repository https://github.com/ColineRoyaux/PAMPA-Galaxy commit 07f1028cc764f920b1e6419c151f04ab4e3600fa"
ecology
parents:
diff changeset
123 colnames(tmpData) <- c(col,listFact)
0778efa9eb2e "planemo upload for repository https://github.com/ColineRoyaux/PAMPA-Galaxy commit 07f1028cc764f920b1e6419c151f04ab4e3600fa"
ecology
parents:
diff changeset
124
0778efa9eb2e "planemo upload for repository https://github.com/ColineRoyaux/PAMPA-Galaxy commit 07f1028cc764f920b1e6419c151f04ab4e3600fa"
ecology
parents:
diff changeset
125 for (i in listFactTab) {
0778efa9eb2e "planemo upload for repository https://github.com/ColineRoyaux/PAMPA-Galaxy commit 07f1028cc764f920b1e6419c151f04ab4e3600fa"
ecology
parents:
diff changeset
126 tmpData[,i] <- as.factor(tmpData[,i])
0778efa9eb2e "planemo upload for repository https://github.com/ColineRoyaux/PAMPA-Galaxy commit 07f1028cc764f920b1e6419c151f04ab4e3600fa"
ecology
parents:
diff changeset
127 }
0778efa9eb2e "planemo upload for repository https://github.com/ColineRoyaux/PAMPA-Galaxy commit 07f1028cc764f920b1e6419c151f04ab4e3600fa"
ecology
parents:
diff changeset
128 }else{
0778efa9eb2e "planemo upload for repository https://github.com/ColineRoyaux/PAMPA-Galaxy commit 07f1028cc764f920b1e6419c151f04ab4e3600fa"
ecology
parents:
diff changeset
129 stop("Warning : wrong data frame, data frame should be aggregated by observation unit (year and site) and species")
0778efa9eb2e "planemo upload for repository https://github.com/ColineRoyaux/PAMPA-Galaxy commit 07f1028cc764f920b1e6419c151f04ab4e3600fa"
ecology
parents:
diff changeset
130 }
0778efa9eb2e "planemo upload for repository https://github.com/ColineRoyaux/PAMPA-Galaxy commit 07f1028cc764f920b1e6419c151f04ab4e3600fa"
ecology
parents:
diff changeset
131
0778efa9eb2e "planemo upload for repository https://github.com/ColineRoyaux/PAMPA-Galaxy commit 07f1028cc764f920b1e6419c151f04ab4e3600fa"
ecology
parents:
diff changeset
132 ## Suppression des 'levels' non utilisés :
0778efa9eb2e "planemo upload for repository https://github.com/ColineRoyaux/PAMPA-Galaxy commit 07f1028cc764f920b1e6419c151f04ab4e3600fa"
ecology
parents:
diff changeset
133 tmpData <- dropLevels.f(tmpData)
0778efa9eb2e "planemo upload for repository https://github.com/ColineRoyaux/PAMPA-Galaxy commit 07f1028cc764f920b1e6419c151f04ab4e3600fa"
ecology
parents:
diff changeset
134
0778efa9eb2e "planemo upload for repository https://github.com/ColineRoyaux/PAMPA-Galaxy commit 07f1028cc764f920b1e6419c151f04ab4e3600fa"
ecology
parents:
diff changeset
135 ## Aide au choix du type d'analyse :
0778efa9eb2e "planemo upload for repository https://github.com/ColineRoyaux/PAMPA-Galaxy commit 07f1028cc764f920b1e6419c151f04ab4e3600fa"
ecology
parents:
diff changeset
136 if (Distrib == "None")
0778efa9eb2e "planemo upload for repository https://github.com/ColineRoyaux/PAMPA-Galaxy commit 07f1028cc764f920b1e6419c151f04ab4e3600fa"
ecology
parents:
diff changeset
137 {
0778efa9eb2e "planemo upload for repository https://github.com/ColineRoyaux/PAMPA-Galaxy commit 07f1028cc764f920b1e6419c151f04ab4e3600fa"
ecology
parents:
diff changeset
138 if (metrique == "pres.abs")
0778efa9eb2e "planemo upload for repository https://github.com/ColineRoyaux/PAMPA-Galaxy commit 07f1028cc764f920b1e6419c151f04ab4e3600fa"
ecology
parents:
diff changeset
139 {
0778efa9eb2e "planemo upload for repository https://github.com/ColineRoyaux/PAMPA-Galaxy commit 07f1028cc764f920b1e6419c151f04ab4e3600fa"
ecology
parents:
diff changeset
140 loiChoisie <- "binomial"
0778efa9eb2e "planemo upload for repository https://github.com/ColineRoyaux/PAMPA-Galaxy commit 07f1028cc764f920b1e6419c151f04ab4e3600fa"
ecology
parents:
diff changeset
141 }else{
0778efa9eb2e "planemo upload for repository https://github.com/ColineRoyaux/PAMPA-Galaxy commit 07f1028cc764f920b1e6419c151f04ab4e3600fa"
ecology
parents:
diff changeset
142 switch(class(tmpData[,metrique]),
0778efa9eb2e "planemo upload for repository https://github.com/ColineRoyaux/PAMPA-Galaxy commit 07f1028cc764f920b1e6419c151f04ab4e3600fa"
ecology
parents:
diff changeset
143 "integer"={loiChoisie <- "poisson"},
0778efa9eb2e "planemo upload for repository https://github.com/ColineRoyaux/PAMPA-Galaxy commit 07f1028cc764f920b1e6419c151f04ab4e3600fa"
ecology
parents:
diff changeset
144 "numeric"={loiChoisie <- "gaussian"},
0778efa9eb2e "planemo upload for repository https://github.com/ColineRoyaux/PAMPA-Galaxy commit 07f1028cc764f920b1e6419c151f04ab4e3600fa"
ecology
parents:
diff changeset
145 stop("Selected metric class doesn't fit, you should select an integer or a numeric variable"))
0778efa9eb2e "planemo upload for repository https://github.com/ColineRoyaux/PAMPA-Galaxy commit 07f1028cc764f920b1e6419c151f04ab4e3600fa"
ecology
parents:
diff changeset
146 }
0778efa9eb2e "planemo upload for repository https://github.com/ColineRoyaux/PAMPA-Galaxy commit 07f1028cc764f920b1e6419c151f04ab4e3600fa"
ecology
parents:
diff changeset
147 }else{
0778efa9eb2e "planemo upload for repository https://github.com/ColineRoyaux/PAMPA-Galaxy commit 07f1028cc764f920b1e6419c151f04ab4e3600fa"
ecology
parents:
diff changeset
148 loiChoisie <- Distrib
0778efa9eb2e "planemo upload for repository https://github.com/ColineRoyaux/PAMPA-Galaxy commit 07f1028cc764f920b1e6419c151f04ab4e3600fa"
ecology
parents:
diff changeset
149 }
0778efa9eb2e "planemo upload for repository https://github.com/ColineRoyaux/PAMPA-Galaxy commit 07f1028cc764f920b1e6419c151f04ab4e3600fa"
ecology
parents:
diff changeset
150
0778efa9eb2e "planemo upload for repository https://github.com/ColineRoyaux/PAMPA-Galaxy commit 07f1028cc764f920b1e6419c151f04ab4e3600fa"
ecology
parents:
diff changeset
151 ##Create results table :
0778efa9eb2e "planemo upload for repository https://github.com/ColineRoyaux/PAMPA-Galaxy commit 07f1028cc764f920b1e6419c151f04ab4e3600fa"
ecology
parents:
diff changeset
152 lev <- unlist(lapply(listF,FUN=function(x){levels(tmpData[,x])}))
0778efa9eb2e "planemo upload for repository https://github.com/ColineRoyaux/PAMPA-Galaxy commit 07f1028cc764f920b1e6419c151f04ab4e3600fa"
ecology
parents:
diff changeset
153
0778efa9eb2e "planemo upload for repository https://github.com/ColineRoyaux/PAMPA-Galaxy commit 07f1028cc764f920b1e6419c151f04ab4e3600fa"
ecology
parents:
diff changeset
154 if (listRand[1] != "None") ## if random effects
0778efa9eb2e "planemo upload for repository https://github.com/ColineRoyaux/PAMPA-Galaxy commit 07f1028cc764f920b1e6419c151f04ab4e3600fa"
ecology
parents:
diff changeset
155 {
0778efa9eb2e "planemo upload for repository https://github.com/ColineRoyaux/PAMPA-Galaxy commit 07f1028cc764f920b1e6419c151f04ab4e3600fa"
ecology
parents:
diff changeset
156 TabSum <- data.frame(species=levels(tmpData[,FactAna]),AIC=NA,BIC=NA,logLik=NA, deviance=NA,df.resid=NA)
0778efa9eb2e "planemo upload for repository https://github.com/ColineRoyaux/PAMPA-Galaxy commit 07f1028cc764f920b1e6419c151f04ab4e3600fa"
ecology
parents:
diff changeset
157 colrand <- unlist(lapply(listRand,
0778efa9eb2e "planemo upload for repository https://github.com/ColineRoyaux/PAMPA-Galaxy commit 07f1028cc764f920b1e6419c151f04ab4e3600fa"
ecology
parents:
diff changeset
158 FUN=function(x){lapply(c("Std.Dev","NbObservation","NbLevels"),
0778efa9eb2e "planemo upload for repository https://github.com/ColineRoyaux/PAMPA-Galaxy commit 07f1028cc764f920b1e6419c151f04ab4e3600fa"
ecology
parents:
diff changeset
159 FUN=function(y){paste(x,y,collapse = ":")
0778efa9eb2e "planemo upload for repository https://github.com/ColineRoyaux/PAMPA-Galaxy commit 07f1028cc764f920b1e6419c151f04ab4e3600fa"
ecology
parents:
diff changeset
160 })
0778efa9eb2e "planemo upload for repository https://github.com/ColineRoyaux/PAMPA-Galaxy commit 07f1028cc764f920b1e6419c151f04ab4e3600fa"
ecology
parents:
diff changeset
161 }))
0778efa9eb2e "planemo upload for repository https://github.com/ColineRoyaux/PAMPA-Galaxy commit 07f1028cc764f920b1e6419c151f04ab4e3600fa"
ecology
parents:
diff changeset
162 TabSum[,colrand] <- NA
0778efa9eb2e "planemo upload for repository https://github.com/ColineRoyaux/PAMPA-Galaxy commit 07f1028cc764f920b1e6419c151f04ab4e3600fa"
ecology
parents:
diff changeset
163
0778efa9eb2e "planemo upload for repository https://github.com/ColineRoyaux/PAMPA-Galaxy commit 07f1028cc764f920b1e6419c151f04ab4e3600fa"
ecology
parents:
diff changeset
164 if (! is.null(lev)) ## if fixed effects + random effects
0778efa9eb2e "planemo upload for repository https://github.com/ColineRoyaux/PAMPA-Galaxy commit 07f1028cc764f920b1e6419c151f04ab4e3600fa"
ecology
parents:
diff changeset
165 {
0778efa9eb2e "planemo upload for repository https://github.com/ColineRoyaux/PAMPA-Galaxy commit 07f1028cc764f920b1e6419c151f04ab4e3600fa"
ecology
parents:
diff changeset
166 colcoef <- unlist(lapply(c("(Intercept)",lev),
0778efa9eb2e "planemo upload for repository https://github.com/ColineRoyaux/PAMPA-Galaxy commit 07f1028cc764f920b1e6419c151f04ab4e3600fa"
ecology
parents:
diff changeset
167 FUN=function(x){lapply(c("Estimate","Std.Err","Zvalue","Pvalue","signif"),
0778efa9eb2e "planemo upload for repository https://github.com/ColineRoyaux/PAMPA-Galaxy commit 07f1028cc764f920b1e6419c151f04ab4e3600fa"
ecology
parents:
diff changeset
168 FUN=function(y){paste(x,y,collapse = ":")
0778efa9eb2e "planemo upload for repository https://github.com/ColineRoyaux/PAMPA-Galaxy commit 07f1028cc764f920b1e6419c151f04ab4e3600fa"
ecology
parents:
diff changeset
169 })
0778efa9eb2e "planemo upload for repository https://github.com/ColineRoyaux/PAMPA-Galaxy commit 07f1028cc764f920b1e6419c151f04ab4e3600fa"
ecology
parents:
diff changeset
170 }))
0778efa9eb2e "planemo upload for repository https://github.com/ColineRoyaux/PAMPA-Galaxy commit 07f1028cc764f920b1e6419c151f04ab4e3600fa"
ecology
parents:
diff changeset
171 }else{ ## if no fixed effects
0778efa9eb2e "planemo upload for repository https://github.com/ColineRoyaux/PAMPA-Galaxy commit 07f1028cc764f920b1e6419c151f04ab4e3600fa"
ecology
parents:
diff changeset
172 colcoef <- NULL
0778efa9eb2e "planemo upload for repository https://github.com/ColineRoyaux/PAMPA-Galaxy commit 07f1028cc764f920b1e6419c151f04ab4e3600fa"
ecology
parents:
diff changeset
173 }
0778efa9eb2e "planemo upload for repository https://github.com/ColineRoyaux/PAMPA-Galaxy commit 07f1028cc764f920b1e6419c151f04ab4e3600fa"
ecology
parents:
diff changeset
174
0778efa9eb2e "planemo upload for repository https://github.com/ColineRoyaux/PAMPA-Galaxy commit 07f1028cc764f920b1e6419c151f04ab4e3600fa"
ecology
parents:
diff changeset
175 }else{ ## if no random effects
0778efa9eb2e "planemo upload for repository https://github.com/ColineRoyaux/PAMPA-Galaxy commit 07f1028cc764f920b1e6419c151f04ab4e3600fa"
ecology
parents:
diff changeset
176 TabSum <- data.frame(species=levels(tmpData[,FactAna]),AIC=NA,Resid.deviance=NA,df.resid=NA,Null.deviance=NA,df.null=NA)
0778efa9eb2e "planemo upload for repository https://github.com/ColineRoyaux/PAMPA-Galaxy commit 07f1028cc764f920b1e6419c151f04ab4e3600fa"
ecology
parents:
diff changeset
177
0778efa9eb2e "planemo upload for repository https://github.com/ColineRoyaux/PAMPA-Galaxy commit 07f1028cc764f920b1e6419c151f04ab4e3600fa"
ecology
parents:
diff changeset
178 switch(loiChoisie,
0778efa9eb2e "planemo upload for repository https://github.com/ColineRoyaux/PAMPA-Galaxy commit 07f1028cc764f920b1e6419c151f04ab4e3600fa"
ecology
parents:
diff changeset
179 "gaussian"={colcoef <- unlist(lapply(c("(Intercept)",lev),
0778efa9eb2e "planemo upload for repository https://github.com/ColineRoyaux/PAMPA-Galaxy commit 07f1028cc764f920b1e6419c151f04ab4e3600fa"
ecology
parents:
diff changeset
180 FUN=function(x){lapply(c("Estimate","Std.Err","Tvalue","Pvalue","signif"),
0778efa9eb2e "planemo upload for repository https://github.com/ColineRoyaux/PAMPA-Galaxy commit 07f1028cc764f920b1e6419c151f04ab4e3600fa"
ecology
parents:
diff changeset
181 FUN=function(y){paste(x,y,collapse = ":")
0778efa9eb2e "planemo upload for repository https://github.com/ColineRoyaux/PAMPA-Galaxy commit 07f1028cc764f920b1e6419c151f04ab4e3600fa"
ecology
parents:
diff changeset
182 })
0778efa9eb2e "planemo upload for repository https://github.com/ColineRoyaux/PAMPA-Galaxy commit 07f1028cc764f920b1e6419c151f04ab4e3600fa"
ecology
parents:
diff changeset
183 }))},
0778efa9eb2e "planemo upload for repository https://github.com/ColineRoyaux/PAMPA-Galaxy commit 07f1028cc764f920b1e6419c151f04ab4e3600fa"
ecology
parents:
diff changeset
184 "quasipoisson"={colcoef <- unlist(lapply(c("(Intercept)",lev),
0778efa9eb2e "planemo upload for repository https://github.com/ColineRoyaux/PAMPA-Galaxy commit 07f1028cc764f920b1e6419c151f04ab4e3600fa"
ecology
parents:
diff changeset
185 FUN=function(x){lapply(c("Estimate","Std.Err","Tvalue","Pvalue","signif"),
0778efa9eb2e "planemo upload for repository https://github.com/ColineRoyaux/PAMPA-Galaxy commit 07f1028cc764f920b1e6419c151f04ab4e3600fa"
ecology
parents:
diff changeset
186 FUN=function(y){paste(x,y,collapse = ":")
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187 })
0778efa9eb2e "planemo upload for repository https://github.com/ColineRoyaux/PAMPA-Galaxy commit 07f1028cc764f920b1e6419c151f04ab4e3600fa"
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188 }))},
0778efa9eb2e "planemo upload for repository https://github.com/ColineRoyaux/PAMPA-Galaxy commit 07f1028cc764f920b1e6419c151f04ab4e3600fa"
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189 colcoef <- unlist(lapply(c("(Intercept)",lev),
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190 FUN=function(x){lapply(c("Estimate","Std.Err","Zvalue","Pvalue","signif"),
0778efa9eb2e "planemo upload for repository https://github.com/ColineRoyaux/PAMPA-Galaxy commit 07f1028cc764f920b1e6419c151f04ab4e3600fa"
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191 FUN=function(y){paste(x,y,collapse = ":")
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192 })
0778efa9eb2e "planemo upload for repository https://github.com/ColineRoyaux/PAMPA-Galaxy commit 07f1028cc764f920b1e6419c151f04ab4e3600fa"
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193 })))
0778efa9eb2e "planemo upload for repository https://github.com/ColineRoyaux/PAMPA-Galaxy commit 07f1028cc764f920b1e6419c151f04ab4e3600fa"
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194
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195 }
0778efa9eb2e "planemo upload for repository https://github.com/ColineRoyaux/PAMPA-Galaxy commit 07f1028cc764f920b1e6419c151f04ab4e3600fa"
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196
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197 TabSum[,colcoef] <- NA
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198
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199 ### creating rate table
0778efa9eb2e "planemo upload for repository https://github.com/ColineRoyaux/PAMPA-Galaxy commit 07f1028cc764f920b1e6419c151f04ab4e3600fa"
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200 TabRate <- data.frame(species=levels(tmpData[,FactAna]), complete_plan=NA, balanced_plan=NA, NA_proportion_OK=NA, no_residual_dispersion=NA, uniform_residuals=NA, outliers_proportion_OK=NA, no_zero_inflation=NA, observation_factor_ratio_OK=NA, enough_levels_random_effect=NA, rate=NA)
0778efa9eb2e "planemo upload for repository https://github.com/ColineRoyaux/PAMPA-Galaxy commit 07f1028cc764f920b1e6419c151f04ab4e3600fa"
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201
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202 ## Compute Model(s) :
0778efa9eb2e "planemo upload for repository https://github.com/ColineRoyaux/PAMPA-Galaxy commit 07f1028cc764f920b1e6419c151f04ab4e3600fa"
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203
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204 for (sp in levels(tmpData[,FactAna]))
0778efa9eb2e "planemo upload for repository https://github.com/ColineRoyaux/PAMPA-Galaxy commit 07f1028cc764f920b1e6419c151f04ab4e3600fa"
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205 {
0778efa9eb2e "planemo upload for repository https://github.com/ColineRoyaux/PAMPA-Galaxy commit 07f1028cc764f920b1e6419c151f04ab4e3600fa"
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206 cutData <- tmpData[grep(sp,tmpData[,FactAna]),]
0778efa9eb2e "planemo upload for repository https://github.com/ColineRoyaux/PAMPA-Galaxy commit 07f1028cc764f920b1e6419c151f04ab4e3600fa"
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207 cutData <- dropLevels.f(cutData)
0778efa9eb2e "planemo upload for repository https://github.com/ColineRoyaux/PAMPA-Galaxy commit 07f1028cc764f920b1e6419c151f04ab4e3600fa"
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208
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209 res <-""
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210
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211 if (listRand[1] != "None")
0778efa9eb2e "planemo upload for repository https://github.com/ColineRoyaux/PAMPA-Galaxy commit 07f1028cc764f920b1e6419c151f04ab4e3600fa"
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212 {
0778efa9eb2e "planemo upload for repository https://github.com/ColineRoyaux/PAMPA-Galaxy commit 07f1028cc764f920b1e6419c151f04ab4e3600fa"
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213 res <- tryCatch(glmmTMB(exprML,family=loiChoisie, data=cutData), error=function(e){})
0778efa9eb2e "planemo upload for repository https://github.com/ColineRoyaux/PAMPA-Galaxy commit 07f1028cc764f920b1e6419c151f04ab4e3600fa"
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214 }else{
0778efa9eb2e "planemo upload for repository https://github.com/ColineRoyaux/PAMPA-Galaxy commit 07f1028cc764f920b1e6419c151f04ab4e3600fa"
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215 res <- tryCatch(glm(exprML,data=cutData,family=loiChoisie), error=function(e){})
0778efa9eb2e "planemo upload for repository https://github.com/ColineRoyaux/PAMPA-Galaxy commit 07f1028cc764f920b1e6419c151f04ab4e3600fa"
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216 }
0778efa9eb2e "planemo upload for repository https://github.com/ColineRoyaux/PAMPA-Galaxy commit 07f1028cc764f920b1e6419c151f04ab4e3600fa"
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217
0778efa9eb2e "planemo upload for repository https://github.com/ColineRoyaux/PAMPA-Galaxy commit 07f1028cc764f920b1e6419c151f04ab4e3600fa"
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218 ## Écriture des résultats formatés dans un fichier :
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219 if (! is.null(res))
0778efa9eb2e "planemo upload for repository https://github.com/ColineRoyaux/PAMPA-Galaxy commit 07f1028cc764f920b1e6419c151f04ab4e3600fa"
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220 {
0778efa9eb2e "planemo upload for repository https://github.com/ColineRoyaux/PAMPA-Galaxy commit 07f1028cc764f920b1e6419c151f04ab4e3600fa"
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221 TabSum <- sortiesLM.f(objLM=res, TabSum=TabSum, factAna=factAna, cut=sp, colAna="species", lev=lev, Data=cutData, metrique=metrique, type="espece", listFact=listFact)
0778efa9eb2e "planemo upload for repository https://github.com/ColineRoyaux/PAMPA-Galaxy commit 07f1028cc764f920b1e6419c151f04ab4e3600fa"
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222
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223 TabRate[TabRate[,"species"]==sp,c(2:11)] <- noteGLM.f(data=cutData, objLM=res, metric=metrique, listFact=listFact, details=TRUE)
0778efa9eb2e "planemo upload for repository https://github.com/ColineRoyaux/PAMPA-Galaxy commit 07f1028cc764f920b1e6419c151f04ab4e3600fa"
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224
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225 }else{
0778efa9eb2e "planemo upload for repository https://github.com/ColineRoyaux/PAMPA-Galaxy commit 07f1028cc764f920b1e6419c151f04ab4e3600fa"
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226 cat("\nCannot compute GLM for species",sp,"Check if one or more factor(s) have only one level, or try with another distribution for the model in advanced settings \n\n")
0778efa9eb2e "planemo upload for repository https://github.com/ColineRoyaux/PAMPA-Galaxy commit 07f1028cc764f920b1e6419c151f04ab4e3600fa"
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227 }
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228
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229 }
0778efa9eb2e "planemo upload for repository https://github.com/ColineRoyaux/PAMPA-Galaxy commit 07f1028cc764f920b1e6419c151f04ab4e3600fa"
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230 noteGLMs.f(tabRate=TabRate,exprML=exprML,objLM=res,file_out=TRUE)
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231
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232 ## simple statistics and infos :
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ecology
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233 filename <- "GLMSummaryFull.txt"
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234
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235 ## Save data on model :
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236
0778efa9eb2e "planemo upload for repository https://github.com/ColineRoyaux/PAMPA-Galaxy commit 07f1028cc764f920b1e6419c151f04ab4e3600fa"
ecology
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diff changeset
237 infoStats.f(filename=filename, Data=tmpData, agregLevel=aggreg, type="stat",
0778efa9eb2e "planemo upload for repository https://github.com/ColineRoyaux/PAMPA-Galaxy commit 07f1028cc764f920b1e6419c151f04ab4e3600fa"
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diff changeset
238 metrique=metrique, factGraph=factAna, #factGraphSel=modSel,
0778efa9eb2e "planemo upload for repository https://github.com/ColineRoyaux/PAMPA-Galaxy commit 07f1028cc764f920b1e6419c151f04ab4e3600fa"
ecology
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239 listFact=listFact)#, listFactSel=listFactSel)
0778efa9eb2e "planemo upload for repository https://github.com/ColineRoyaux/PAMPA-Galaxy commit 07f1028cc764f920b1e6419c151f04ab4e3600fa"
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240
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ecology
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241 return(TabSum)
0778efa9eb2e "planemo upload for repository https://github.com/ColineRoyaux/PAMPA-Galaxy commit 07f1028cc764f920b1e6419c151f04ab4e3600fa"
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242 }
0778efa9eb2e "planemo upload for repository https://github.com/ColineRoyaux/PAMPA-Galaxy commit 07f1028cc764f920b1e6419c151f04ab4e3600fa"
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243
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ecology
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244 ################# Analysis
0778efa9eb2e "planemo upload for repository https://github.com/ColineRoyaux/PAMPA-Galaxy commit 07f1028cc764f920b1e6419c151f04ab4e3600fa"
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245
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ecology
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diff changeset
246 Tab <- modeleLineaireWP2.species.f(metrique=metric, listFact=listFact, listRand=listRand, FactAna=FactAna, Distrib=Distrib, tabMetrics=obs, tableMetrique=aggreg, tabUnitobs=tabUnitobs, outresiduals=SupprOutlay, nbName="number")
0778efa9eb2e "planemo upload for repository https://github.com/ColineRoyaux/PAMPA-Galaxy commit 07f1028cc764f920b1e6419c151f04ab4e3600fa"
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247
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ecology
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diff changeset
248 write.table(Tab,"GLMSummary.tabular", row.names=FALSE, sep="\t", dec=".",fileEncoding="UTF-8")
0778efa9eb2e "planemo upload for repository https://github.com/ColineRoyaux/PAMPA-Galaxy commit 07f1028cc764f920b1e6419c151f04ab4e3600fa"
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diff changeset
249