| Next changeset 1:5c244408661f (2020-05-11) |
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Commit message:
"planemo upload for repository https://github.com/Alanamosse/Galaxy-E/tree/stoctool/tools/stoc commit f82f897ab22464de40c878e17616333855814e25" |
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added:
FunctExeTemporalAnalysisofIndicatorTrait.r FunctTrendSTOCGalaxy.r coordCarreSTOCfaux.tabular species_indicateur_fonctionnel.tabular stoceps_macros.xml tabSpecies.csv temp_analysis_indic.xml |
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| diff -r 000000000000 -r 916b49d725ba FunctExeTemporalAnalysisofIndicatorTrait.r --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/FunctExeTemporalAnalysisofIndicatorTrait.r Thu Apr 02 03:35:29 2020 -0400 |
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| b'@@ -0,0 +1,328 @@\n+#!/usr/bin/env Rscript\n+\n+########################################################################################################################################################################\n+############## FUNCTION TO CALCULATE AND PLOT VARIATION IN TIME OF INDICATOR OR MEAN TRAIT VALUE OF COMMUNITIES function:csi_cti_ctri ##############################\n+########################################################################################################################################################################\n+\n+#### Based on Romain Lorrilli\xc3\xa8re R script\n+#### Modified by Alan Amosse and Benjamin Yguel for integrating within Galaxy-E\n+### made with R version 3.5.1\n+\n+\n+suppressMessages(library(RODBC)) ##Version: 1.3-15\n+suppressMessages(library(reshape)) ##Version: 0.8.8\n+suppressMessages(library(data.table)) ##Version: 1.12.0\n+suppressMessages(library(rgdal)) ##Version: 1.3-4\n+suppressMessages(library(lubridate)) ##Version: 1.7.4\n+#suppressMessages(library(RPostgreSQL)) ##Version: 0.6-2\n+suppressMessages(library(doBy)) ##Version: 4.6-2\n+suppressMessages(library(arm)) ##Version: 1.10-1\n+suppressMessages(library(ggplot2)) ##Version: 3.1.0\n+suppressMessages(library(scales)) ##Version: 1.0.0\n+suppressMessages(library(mgcv)) ##Version: 1.8-24\n+#suppressMessages(library(visreg)) ##Version: 2.5-0\n+suppressMessages(library(plyr)) ##Version: 1.8.4\n+#suppressMessages(library(lme4)) ##Version: 1.1-18-1\n+#suppressMessages(library(lmerTest)) ##Version: 3.1-0\n+suppressMessages(library(glmmTMB)) ###Version: 0.2.3\n+\n+\n+###########\n+#delcaration des arguments et variables/ declaring some variables and load arguments\n+\n+args = commandArgs(trailingOnly=TRUE)\n+#for( i in 1:length(args)){print(args[i])}\n+if (length(args)<12) {\n+ stop("At least 12 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- A species ssi/sti table.\\n- A table with plots coordinates.\\n- table with csi calculated before 2001.\\n\\n", call.=FALSE) #si pas d\'arguments -> affiche erreur et quitte / if no args -> error and exit1\n+} else {\n+ Datafiltered<-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" \n+ tabSpecies<-args[2] ###### Nom du fichier avec extension ".typedefichier", fichier mis \xc3\xa0 disposition dans Galaxy-E avec specialisation \xc3\xa0 l\'habitat des especes et si espece consid\xc3\xa9r\xc3\xa9e 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 \n+ tabtrait<-args[3] ##### Nom du fichier avec extension ".typedefichier", fichier mis \xc3\xa0 disposition dans Galaxy-E avec degre de specialisation de l espece et affinite thermique /file name without the file type ".filetype", file available in Galaxy-E containing specilalization degree as well as thermic preferences\n+ coordCarre<-args[4] #### Nom du fichier avec extension ".typedefichier", fichier mis \xc3\xa0 disposition dans Galaxy-E avec les coordonnees gps des carres /file name without the file type ".filetype", file available in Galaxy-E containing gps coordinates of the plots\n+ Var <- args[5] #### Nom du trait dans fichier de traits "nomdutrait" exemple: "ssi" pour l\'indice de specialisation par sps / Name of the trait in the file containing trait data \n+ indicator <- args[6] #### Nom de l\'indicateur ou du trait par communaut\xc3\xa9 ex pour ssi c\'est csi calcul\xc3\xa9 au niveau communaut\xc3\xa9 / Name of the indicator or the trait per community ex: for the ssi, it is the csi measured at the community level \n+ methode <- args[7] #### Methode d\'analyse de l\'evolution du trait ou de l\'indicateur, lmer pour mod\xc3\xa8loe mixte seul ou gam pour generalized additive model / name of the models '..b' are used, while varianceProf converts from the standard-deviation to the variance scale\n+ MODconfint <- confint (md.f) #### plus rapide de ne pas passer par la fonction profile et pas indispensable fonctionne aussi directement sur modele mixte md.f / more rapid using both function profile and confint but works also directly on output of the model \n+ se.sup <- MODconfint[2:nban,2]#### [2:nban+2,2] version pour sortie lmer()\n+ se.inf <- MODconfint[2:nban,1]#### [2:nban+2,2] version pour sortie lmer()\n+ if (ic) {\n+ ggdata$se.sup <- se.sup \n+ ggdata$se.inf <- se.inf\n+ } else{\n+ ggdata$se.sup <- "not assessed"\n+ ggdata$se.inf <- "not assessed"\n+ }\n+ coefdata.f$se.inf <- ggdata$se.inf\n+ coefdata.f$se.sup <- ggdata$se.sup\n+ #gg <<- ggplot(ggdata,aes(x=year,y=estimate))+ geom_ribbon(ymin=ggdata$se.infR,ymax=ggdata$se.supR,alpha=.25)+geom_errorbar(ymin=ggdata$se.infR,ymax=ggdata$se.supR,width=0,alpha=.25)+ geom_point() + geom_line() + ylim(min(ggdata$se.infR),max(ggdata$se.supR)) + labs(x="Years",y=paste(indic," variation",sep="")) ##### AVEC INTERVAL ROMAIN\n+ gg <- ggplot(ggdata,aes(x=year,y=estimate))+ geom_point() + geom_line() + labs(x="Years",y=paste(indicator," variation",sep="")) #####+ ylim(min(ggdata$se.inf),max(ggdata$se.sup))\n+ gg <- gg + geom_line(size=1.5,colour=couleur)+ geom_point(size=3,colour=couleur) + geom_point(size=1.5,colour="white")\n+ if (ic)\t{\n+ gg <- gg + geom_ribbon(aes(ymin=ggdata$se.inf,ymax=ggdata$se.sup),alpha=.25,fill = couleur) + geom_errorbar(ymin=ggdata$se.inf,ymax=ggdata$se.sup,width=0,alpha=.25)\n+ }\n+ ggfile <- paste("Output/",indicator,"_glmmTMB_",id,".png",sep="")\n+ ggsave(ggfile,gg)\n+\n+ ############ Estimation de la tendance sur la periode \xc3\xa9tudi\xc3\xa9e / Trends estimation on the time period studied\n+ #cat("\\nEstimation de la tendance lmer(",indicator,"~ year+(1|id_plot)\\n",sep="")\n+ cat("\\nEstimation de la tendance glmmTMB(",indicator,"~ year+(1|id_plot)\\n",sep="")\n+ #md.c <- lmer(indic~ year+(1|id_plot),data=dd)##### effet aleatoire li\xc3\xa9s aux carr\xc3\xa9s sur l\'ordonn\xc3\xa9e \xc3\xa0 l\'origine / random effects of plots on intercept ### version lmer\n+ md.c <- glmmTMB(indic~ year+(1|id_plot),data=dd)\n+ smd.c<-summary(md.c)\n+ # coefdata.c <- as.data.frame(smd.c$coefficients) #### pour la version lmer\n+ coefdata.c <- as.data.frame(smd.c$coefficients$cond)[2,]\n+ #profc=profile(md.c) ######### Ajout des intervalles de confiances / addition of the confidence intervals\n+ if (ic) {\n+ MODconfint=confint(md.c) ### plus rapide de ne pas passer par profile\n+ se.inf=MODconfint[2,1]### [4,1] pour la version lmer\n+ se.sup=MODconfint[2,2]### [4,2] pour la version lmer\n+ } else{\n+ se.inf <- "not assessed"\n+ se.sup <- "not assessed"\n+ }\n+ coefdata.c <- data.frame(model = "Linear trend", variable = rownames(coefdata.c),coefdata.c,se.inf,se.sup)\n+ coefdata <- rbind(coefdata.c,coefdata.f)\n+ write.table(coefdata,paste("Output/GlmmTMB_coefficient_",indicator,id,".tabular",sep=""),row.names=FALSE,sep="\\t")\n+ write.table(ggdata,paste("Output/ggdata_",indicator,id,".tabular",sep=""),row.names=FALSE,sep="\\t")\n+ smd.file <- paste("Output/summary_lmer_",indicator,"_",id,".txt",sep="")\n+ #####################\n+ }\n+}\n+\n+\n+\n+\n+\n+################## \n+### Do your analysis\n+\n+csi_cti_ctri(tabCLEAN=tabCLEAN,coordCarre=coordCarre,spTrait=spTrait,dd=NULL,Var=Var,indicator=indicator,ic=ic,plot_smooth = plot_smooth,methode=methode)#,init_1989 = FALSE) ##### exemple pour l\'indicateur csi sans csi d\xc3\xa9j\xc3\xa0 calcul\xc3\xa9 donc \xc3\xa0 partir du ssi avec interval de confiance et utilisant modele mixte / example for the csi index which is not already calculated from the ssi with confidence interval using the mixte model \n+\n' |
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| diff -r 000000000000 -r 916b49d725ba FunctTrendSTOCGalaxy.r --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/FunctTrendSTOCGalaxy.r Thu Apr 02 03:35:29 2020 -0400 |
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| b'@@ -0,0 +1,776 @@\n+#!/usr/bin/env Rscript\n+\n+\n+##################################################################################################################################\n+############## FUNCTION TO CALCULATE AND PLOT EVOLUTION OF SPECIES POPULATION function:main.glm ##############################\n+##################################################################################################################################\n+\n+#### Based on Romain Lorrilli\xc3\xa8re R script\n+#### Modified by Alan Amosse and Benjamin Yguel for integrating within Galaxy-E\n+\n+##### workes with the R version 3.5.1 (2018-07-02)\n+##### Package used with the version:\n+#suppressMessages(library(lme4)) version 1.1.18.1\n+#suppressMessages(library(ggplot2)) version 3.0.0\n+#suppressMessages(library(speedglm)) version 0.3.2\n+#suppressMessages(library(arm)) version 1.10.1\n+#suppressMessages(library(reshape)) version 0.8.8\n+#suppressMessages(library(data.table)) version 1.12.0\n+#suppressMessages(library(reshape2)) version 1.4.3\n+\n+\n+\n+######################################### debut de la fonction makeTableAnalyse / stard of the function makeTableAnalyse\n+## mise en colonne des especes et rajout de zero mais sur la base des carr\xc3\xa9s selectionn\xc3\xa9 sans l\'import / Species are placed in separated columns and addition of zero on plots where at least one selected species is present \n+\n+makeTableAnalyse <- function(data) {\n+ tab <- reshape(data\n+ ,v.names="abond"\n+ ,idvar=c("carre","annee") \n+ ,timevar="espece"\n+ ,direction="wide")\n+ tab[is.na(tab)] <- 0 ###### remplace les na par des 0 / replace NAs by 0 \n+\n+ colnames(tab) <- sub("abond.","",colnames(tab))### remplace le premier pattern "abond." par le second "" / replace the column names "abond." by ""\n+ return(tab)\n+}\n+\n+######################################### fin de la fonction makeTableAnalyse / end of the function makeTableAnalyse\n+\n+\n+\n+\n+\n+############################################# les fonctions qui filtrent les donn\xc3\xa9es pas suffisantes pour analyses fiables / The filtering functions removing species with not enough data to perform accurate analyses\n+\n+filter_absent_species<-function(tab){\n+##################### Filtre les esp\xc3\xa8ces jamais pr\xc3\xa9sentes (abondance=0) / Filter of species with 0 abundance\n+################################################################################# PARTIE POTENTIELLEMENT ISOLABLE ET INSERABLE AVANT LA BOUCLE = permet de gagner du temps sur la boucle car supprime sps pas vu, donc pas repris par la boucle\n+ \n+ ## Fait la somme des abondances totales par esp\xc3\xa8ce / calculate the sum of all abundance per species\n+ if(ncol(tab)==3) {\n+\ttabSum <- sum(tab[,3])## cas d\'une seule especes (probl\xc3\xa8me de format et manip un peu differente) / when selecting only one species, use a different method\n+\tnames(tabSum) <- colnames(tab)[3]\n+ } else { ## cas de plusieurs esp\xc3\xa8ce/ when selecting more than one species\n+ tabSum <- colSums(tab[,-(1:2)])\n+ }\n+ ## colNull= espece(s) toujours absente /species with 0 total abundance\n+ colNull <- names(which(tabSum==0))\n+ ## colconserve= espece(s) au moins presente 1 fois/ species at least with 1 presence\n+ colConserve <- names(which(tabSum>0))\n+ ## Affichage des esp\xc3\xa8ces rejetees / show species eliminated for the analyses\n+ if(length(colNull)>0){\n+ cat("\\n",length(colNull)," Species removed from the analysis, abundance is always 0.\\n\\n",sep="") #Esp\xc3\xa8ces enlev\xc3\xa9es de l\'analyse car abondance toujours \xc3\xa9gale a 0\\n\\n",sep="")\n+ #tabNull <- data.frame(Code_espece = colNull, nom_espece = tabsp[colNull,"nom"])\n+ #cat("\\n\\n",sep="")\n+ tab <- tab[,c("carre","annee",colConserve)]\n+ }\n+################################################################################ FIN DE LA PARTIE ISOLABLE\n+ return(tab) \n+}\n+\n+\n+\n+\n+###################### Filtre les especes trop ra'..b' ggplot2 / plots with ggplot2\n+ titre <- paste("Variation de l\'indicateur groupe de specialisation",sep="")\n+\n+ vecCouleur <- setNames(groupeCouleur,groupeNom)\n+ #browser()\n+ p <- ggplot(data = da, mapping = aes(x = annee, y = abondance_relative, colour=groupe,fill=groupe))\n+ p <- p + geom_hline(aes(yintercept = 1), colour="white", alpha=1,size=1.2) \n+ if(ICfigureGroupeSp)\n+ p <- p + geom_ribbon(mapping=aes(ymin=IC_inferieur,ymax=IC_superieur),linetype=2,alpha=.1,size=0.1) \n+ p <- p + geom_line(size=1.5)\n+ p <- p + ylab("") + xlab("Annee")+ ggtitle(titre) \n+ if(!is.null(groupeNom)) p <- p + scale_colour_manual(values=vecCouleur, name = "" )+\n+ scale_x_continuous(breaks=unique(da$annee))\n+ if(!is.null(groupeNom)) p <- p + scale_fill_manual(values=vecCouleur, name="")\n+ p <- p + theme(panel.grid.minor=element_blank(), panel.grid.major.y=element_blank()) \n+ ggsave(nameFileSpepng, p,width=17,height=10,units="cm")\n+\n+ # cat(" <==",nameFileSpepng,"\\n")\n+ \n+ ## calul pour chaque groupe une pente de regression d\'evolution des abondances sur la periode \xc3\xa9tudi\xc3\xa9e / calculating for each group the regression slope for the abundance evolution on the studied period\n+ vecSpe <- unique(da$groupe)\n+ datasum <- data.frame(groupe=NULL,tendance=NULL,pourcentage_variation=NULL)\n+ for(spe in 1:4){\n+ # print(spe)\n+ subtab <- subset(da,groupe==vecSpe[spe])\n+ if(nrow(subtab)>1) {\n+ sumlm <- summary(lm(abondance_relative~annee,data=subtab)) ##### recup\xc3\xa8re les resultats du mod\xc3\xa8le lin\xc3\xa9aire / retrieve the results of the linear model\n+ subdatasum <- data.frame(groupe=vecSpe[spe],\n+ tendance=round(sumlm$coefficients[2,1],3),\n+ pourcentage_variation=round(sumlm$coefficients[2,1]*(nrow(subtab)-1)*100,3)) #### assemble les resultats pour en faire une sortie / bring together the results for an output file\n+ datasum <- rbind(datasum,subdatasum)\n+ \n+ }\n+ \n+ }\n+ datasum <- merge(datasum,tIncert,by="groupe") #### \n+ datasum <- data.frame(id,datasum)\n+ #datasum$cat_tendance_EBCC <- affectCatEBCC(trend,pVal,ICinf,ICsup\n+ namefilesum <- paste("Output/",id,"/tendancesGlobalesGroupes_",id,\n+ ".tabular",sep="" )\n+ write.table(datasum,file=namefilesum,row.names=FALSE,quote=FALSE,sep="\\t",dec=".",fileEncoding="UTF-8")\n+ cat("-->",namefilesum,"\\n")\n+}\n+\n+################################################################################################################## fin de la fonction analyseGroupe / end of the function analyseGroupe\n+\n+\n+\n+\n+\n+\n+\n+################################################################################################################### debut de la fonction check_file / start of the function check_file\n+# Fonction pour verifier les donn\xc3\xa9es d\'entr\xc3\xa9e / General function to check integrity of input file. Will check numbers and contents of variables(colnames). \n+#return an error message and exit if mismatch detected\n+#Faut rentrer le nom du jeu de donn\xc3\xa9es, le nbre et le nom des variables / Enter dataset name, expected number and names of variables. + an exit error message to guide user.\n+\n+check_file<-function(dataset,err_msg,vars,nb_vars){\n+ if(ncol(dataset)!=nb_vars){ #Verifiction de la pr\xc3\xa9sence du bon nb de colonnes, si c\'est pas le cas= message d\'erreur / checking for right number of columns in the file if not = error message\n+ cat("\\nerr nb var\\n") \n+ stop(err_msg, call.=FALSE)\n+ }\n+\n+ for(i in vars){\n+ if(!(i %in% names(dataset))){\n+ stop(err_msg,call.=FALSE)\n+ }\n+ }\n+}\n+\n+#####################################################################################################################\n+\n' |
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| diff -r 000000000000 -r 916b49d725ba coordCarreSTOCfaux.tabular --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/coordCarreSTOCfaux.tabular Thu Apr 02 03:35:29 2020 -0400 |
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| b'@@ -0,0 +1,2789 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|
| b |
| diff -r 000000000000 -r 916b49d725ba species_indicateur_fonctionnel.tabular --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/species_indicateur_fonctionnel.tabular Thu Apr 02 03:35:29 2020 -0400 |
| b |
| b'@@ -0,0 +1,442 @@\n+"pk_species"\t"ssi"\t"ssi_old"\t"ssi_2007"\t"sti"\t"sti_europe"\t"thermal_niche_mean"\t"thermal_niche_range"\t"thermal_niche_max"\t"thermal_niche_min"\t"stri"\t"exp_stri"\t"trophic_vegetation"\t"trophic_invertebrate"\t"trophic_vertebrate"\n+"_ANTVIR"\t""\t""\t""\t""\t"15.6536"\t""\t""\t""\t""\t""\t""\t""\t""\t""\n+"_EMBRUS"\t""\t""\t""\t""\t"6.33549"\t""\t""\t""\t""\t""\t""\t""\t""\t""\n+"ACCGEN"\t"1.86088"\t""\t""\t""\t"11.8008"\t""\t""\t""\t""\t"3"\t"20.09"\t""\t""\t""\n+"ACCNIS"\t"0.614413"\t"0.787363"\t"0.620015"\t"13.8629"\t"11.9163"\t"12.3454"\t"15.773"\t"20.0974"\t"4.3244"\t"3"\t"20.09"\t0\t0\t100\n+"ACRAGR"\t""\t""\t""\t""\t"15.605"\t""\t""\t""\t""\t""\t""\t""\t""\t""\n+"ACRARU"\t""\t""\t""\t""\t"13.8794"\t""\t""\t""\t""\t""\t""\t""\t""\t""\n+"ACRDUM"\t""\t""\t""\t""\t"9.51237"\t""\t""\t""\t""\t""\t""\t""\t""\t""\n+"ACRMEL"\t""\t""\t""\t""\t"16.574"\t""\t""\t""\t""\t""\t""\t""\t""\t""\n+"ACRPAL"\t""\t""\t""\t""\t"12.3618"\t""\t""\t""\t""\t""\t""\t""\t""\t""\n+"ACRRIS"\t"1.70476"\t""\t""\t""\t"12.2481"\t""\t""\t""\t""\t"2"\t"7.39"\t""\t""\t""\n+"ACRSCH"\t"2.50428"\t""\t""\t""\t"11.3914"\t""\t""\t""\t""\t"1.95"\t"7.03"\t""\t""\t""\n+"ACRSCI"\t"2.08314"\t""\t""\t""\t"13.1524"\t""\t""\t""\t""\t"1.95"\t"7.03"\t""\t""\t""\n+"ACTHYP"\t""\t""\t""\t""\t"11.2048"\t""\t""\t""\t""\t""\t""\t""\t""\t""\n+"AEGCAU"\t"0.585681"\t"0.62316"\t"0.438564"\t"14.4881"\t"12.6608"\t"12.9783"\t"13.3142"\t"19.328"\t"6.01376"\t"1.95"\t"7.03"\t5\t95\t0\n+"AEGFUN"\t""\t""\t""\t""\t"9.10055"\t""\t""\t""\t""\t""\t""\t""\t""\t""\n+"AEGMON"\t""\t""\t""\t""\t"16.1423"\t""\t""\t""\t""\t""\t""\t""\t""\t""\n+"AIXGAL"\t""\t""\t""\t""\t"12.0189"\t""\t""\t""\t""\t""\t""\t""\t""\t""\n+"AIXSPO"\t""\t""\t""\t""\t"12.3348"\t""\t""\t""\t""\t""\t""\t""\t""\t""\n+"ALAARV"\t"1.18758"\t"1.1554"\t"0.921955"\t"14.1497"\t"12.1983"\t"12.508"\t"15.4477"\t"19.7438"\t"4.29613"\t"1.25"\t"3.49"\t75\t25\t0\n+"ALCATT"\t"2.18545"\t""\t""\t""\t"13.5319"\t""\t""\t""\t""\t"2.81"\t"16.61"\t""\t""\t""\n+"ALCTOR"\t""\t""\t""\t""\t"8.98323"\t""\t""\t""\t""\t""\t""\t""\t""\t""\n+"ALEBAR"\t""\t""\t""\t""\t"17.9565"\t""\t""\t""\t""\t""\t""\t""\t""\t""\n+"ALECHU"\t""\t""\t""\t""\t"16.2056"\t""\t""\t""\t""\t""\t""\t""\t""\t""\n+"ALEGRA"\t""\t""\t""\t""\t"13.1661"\t""\t""\t""\t""\t""\t""\t""\t""\t""\n+"ALERUF"\t"1.10584"\t"1.0973"\t"0.92039"\t"16.0692"\t"14.8075"\t"15.2367"\t"11.2723"\t"20.5323"\t"9.26"\t"1.1"\t"3"\t90\t10\t0\n+"ALLALL"\t""\t""\t""\t""\t"-8.26474"\t""\t""\t""\t""\t""\t""\t""\t""\t""\n+"ALOAEG"\t""\t""\t""\t""\t"12.3931"\t""\t""\t""\t""\t""\t""\t""\t""\t""\n+"ANAACU"\t""\t""\t""\t""\t"8.52735"\t""\t""\t""\t""\t""\t""\t""\t""\t""\n+"ANACLY"\t""\t""\t""\t""\t"11.7556"\t""\t""\t""\t""\t""\t""\t""\t""\t""\n+"ANACRE"\t""\t""\t""\t""\t"10.0713"\t""\t""\t""\t""\t""\t""\t""\t""\t""\n+"ANAPEN"\t""\t""\t""\t""\t"6.68293"\t""\t""\t""\t""\t""\t""\t""\t""\t""\n+"ANAPLA"\t""\t""\t""\t""\t"11.8111"\t""\t""\t""\t""\t""\t""\t""\t""\t""\n+"ANAQUE"\t""\t""\t""\t""\t"12.3896"\t""\t""\t""\t""\t""\t""\t""\t""\t""\n+"ANASTR"\t""\t""\t""\t""\t"12.5159"\t""\t""\t""\t""\t""\t""\t""\t""\t""\n+"ANSALB"\t""\t""\t""\t""\t"1.40206"\t""\t""\t""\t""\t""\t""\t""\t""\t""\n+"ANSANS"\t""\t""\t""\t""\t"11.1956"\t""\t""\t""\t""\t""\t""\t""\t""\t""\n+"ANSBRA"\t""\t""\t""\t""\t"3.35896"\t""\t""\t""\t""\t""\t""\t""\t""\t""\n+"ANSERY"\t""\t""\t""\t""\t"2.03545"\t""\t""\t""\t""\t""\t""\t""\t""\t""\n+"ANSFAB"\t""\t""\t""\t""\t"4.29454"\t""\t""\t""\t""\t""\t""\t""\t""\t""\n+"ANTCAM"\t"2.42803"\t"1.99574"\t"1.50106"\t"16.3834"\t"14.429"\t"15.7224"\t"11.5149"\t"21.4068"\t"9.89193"\t"1.95"\t"7.03"\t5\t95\t0\n+"ANTCER"\t""\t""\t""\t""\t"3.13445"\t""\t""\t""\t""\t""\t""\t""\t""\t""\n+"ANTHOD"\t""\t""\t""\t""\t"4.92396"\t""\t""\t""\t""\t""\t""\t""\t""\t""\n+"ANTPRA"\t"1.37755"\t"1.37459"\t"1.26191"\t"11.8267"\t"9.94877"\t"9.85028"\t"13.4452"\t"15.2037"\t"1.75849"\t"1.75"\t"5.75"\t25\t75\t0\n+"ANTSPI"\t""\t""\t""\t""\t"11.6825"\t""\t""\t""\t""\t""\t""\t""\t""\t""\n+"ANTSPISPI"\t""\t""\t""\t""\t"11.6825"\t""\t""\t""\t""\t""\t""\t""\t""\t""\n+"ANTTRI"\t"0.729307"\t"0.910273"\t"0.705309"\t"13.2523"\t"11.2439"\t"11.6459"\t"13.9098"\t"17.9549"\t"4.04508"\t"1.95"\t"7.03"\t5\t95\t0\n+"APUAPU"\t"1.27125"\t"1.29827"\t"1.24046"\t"14.3837"\t"12.447"\t"13.2293"\t"16.075"\t"21.2854"\t"5.21042"\t"2"\t"7.39"\t0\t100\t0\n+"APUCAF"\t""\t""\t""\t""\t"19.268"\t""\t""\t""\t""\t""\t""\t""\t""\t""\n+"APUMEL"\t""\t""\t""\t""\t"14.7488"\t""\t""\t""\t""\t""\t""\t""\t""\t""\n+"APUPAL"\t""\t""\t""\t""\t"17.4132"\t""\t""\t""\t""\t""\t""\t""\t""\t""\n+"AQUCHR"\t""\t""\t""\t""\t"10.7378"\t""\t""\t""\t""\t""\t""\t""\t""\t""\n+"AQUCLA"\t""\t""\t""\t""\t"12.2126"\t""\t""\t""\t""\t""\t""\t""\t""\t""\n+"AQUPOM"\t""\t""\t""\t""\t"12.6813"\t""\t""\t""\t""\t""\t""\t""\t""\t""\n+"ARDCIN"\t""\t""\t""\t""\t"12.6944"\t""\t""\t""\t""\t""\t""\t""\t""\t""\n+"ARDP'..b'"\t""\t""\t""\t""\t""\t""\n+"STRTUR"\t"0.451923"\t"0.400338"\t"0.379551"\t"15.7236"\t"13.7662"\t"15.5491"\t"21.8016"\t"29.5579"\t"7.75632"\t"1"\t"2.72"\t100\t0\t0\n+"STRURA"\t""\t""\t""\t""\t"9.2298"\t""\t""\t""\t""\t""\t""\t""\t""\t""\n+"STUROS"\t""\t""\t""\t""\t"15.8791"\t""\t""\t""\t""\t""\t""\t""\t""\t""\n+"STUUNI"\t""\t""\t""\t""\t"16.5557"\t""\t""\t""\t""\t""\t""\t""\t""\t""\n+"STUVUL"\t"0.678736"\t"0.570593"\t"0.530414"\t"13.7636"\t"11.8028"\t"12.3572"\t"14.9439"\t"19.2662"\t"4.32237"\t"1.5"\t"4.48"\t50\t50\t0\n+"SULBAS"\t""\t""\t""\t""\t"8.73326"\t""\t""\t""\t""\t""\t""\t""\t""\t""\n+"SYLATR"\t"0.291053"\t"0.316278"\t"0.235556"\t"14.5232"\t"12.6192"\t"13.1921"\t"13.8615"\t"20.0016"\t"6.14015"\t"1.6"\t"4.95"\t40\t60\t0\n+"SYLBOR"\t"0.679919"\t"0.693892"\t"0.449187"\t"13.299"\t"11.3163"\t"12.0225"\t"13.1888"\t"17.7172"\t"4.52839"\t"1.6"\t"4.95"\t40\t60\t0\n+"SYLCAN"\t"1.77527"\t"1.33114"\t"1.24176"\t"18.0076"\t"16.4215"\t"17.3734"\t"12.0385"\t"22.1208"\t"10.0823"\t"1.8"\t"6.05"\t20\t80\t0\n+"SYLCOM"\t"0.624932"\t"0.653973"\t"0.556872"\t"14.5746"\t"12.6536"\t"13.3891"\t"13.5529"\t"20.3339"\t"6.78104"\t"1.6"\t"4.95"\t40\t60\t0\n+"SYLCON"\t""\t""\t""\t""\t"16.9718"\t""\t""\t""\t""\t""\t""\t""\t""\t""\n+"SYLCUR"\t"0.91895"\t"1.01449"\t"0.773661"\t"13.6456"\t"11.6399"\t"12.3091"\t"13.3496"\t"18.5634"\t"5.21378"\t"1.8"\t"6.05"\t20\t80\t0\n+"SYLHOR"\t"2.04495"\t"1.35"\t"0.966924"\t"17.7918"\t"16.2234"\t"17.5009"\t"12.0605"\t"21.8019"\t"9.74135"\t"1.7"\t"5.47"\t30\t70\t0\n+"SYLMEL"\t"1.61695"\t"0.755948"\t"0.596166"\t"18.4332"\t"16.9658"\t"18.3292"\t"12.0397"\t"23.0259"\t"10.9863"\t"1.7"\t"5.47"\t30\t70\t0\n+"SYLNIS"\t""\t""\t""\t""\t"12.8776"\t""\t""\t""\t""\t""\t""\t""\t""\t""\n+"SYLRUE"\t""\t""\t""\t""\t"19.113"\t""\t""\t""\t""\t""\t""\t""\t""\t""\n+"SYLSAR"\t""\t""\t""\t""\t"17.5973"\t""\t""\t""\t""\t""\t""\t""\t""\t""\n+"SYLUND"\t"2.66103"\t"2.06494"\t"1.46052"\t"17.1553"\t"15.8211"\t"16.7325"\t"10.1522"\t"21.0617"\t"10.9095"\t"1.9"\t"6.69"\t10\t90\t0\n+"SYRREE"\t""\t""\t""\t""\t"13.4773"\t""\t""\t""\t""\t""\t""\t""\t""\t""\n+"TACRUF"\t""\t""\t""\t""\t"13.4634"\t""\t""\t""\t""\t""\t""\t""\t""\t""\n+"TADFER"\t""\t""\t""\t""\t"15.5742"\t""\t""\t""\t""\t""\t""\t""\t""\t""\n+"TADTAD"\t""\t""\t""\t""\t"12.0434"\t""\t""\t""\t""\t""\t""\t""\t""\t""\n+"TARCYA"\t""\t""\t""\t""\t"6.56761"\t""\t""\t""\t""\t""\t""\t""\t""\t""\n+"TETRAX"\t""\t""\t""\t""\t"16.1633"\t""\t""\t""\t""\t""\t""\t""\t""\t""\n+"TETRIX"\t""\t""\t""\t""\t"8.99648"\t""\t""\t""\t""\t""\t""\t""\t""\t""\n+"TETURO"\t""\t""\t""\t""\t"8.73708"\t""\t""\t""\t""\t""\t""\t""\t""\t""\n+"TICMUR"\t""\t""\t""\t""\t"11.0821"\t""\t""\t""\t""\t""\t""\t""\t""\t""\n+"TRICIN"\t""\t""\t""\t""\t"10.598"\t""\t""\t""\t""\t""\t""\t""\t""\t""\n+"TRIERY"\t""\t""\t""\t""\t"4.77171"\t""\t""\t""\t""\t""\t""\t""\t""\t""\n+"TRIGLA"\t""\t""\t""\t""\t"7.67062"\t""\t""\t""\t""\t""\t""\t""\t""\t""\n+"TRINEB"\t""\t""\t""\t""\t"6.45053"\t""\t""\t""\t""\t""\t""\t""\t""\t""\n+"TRIOCH"\t""\t""\t""\t""\t"9.87852"\t""\t""\t""\t""\t""\t""\t""\t""\t""\n+"TRISTA"\t""\t""\t""\t""\t"13.0028"\t""\t""\t""\t""\t""\t""\t""\t""\t""\n+"TRITOT"\t""\t""\t""\t""\t"11.0359"\t""\t""\t""\t""\t""\t""\t""\t""\t""\n+"TROTRO"\t"0.430257"\t"0.371592"\t"0.34744"\t"14.0432"\t"12.2368"\t"12.9074"\t"15.9244"\t"20.6657"\t"4.74128"\t"2"\t"7.39"\t0\t100\t0\n+"TURILI"\t""\t""\t""\t""\t"8.25096"\t""\t""\t""\t""\t""\t""\t""\t""\t""\n+"TURMER"\t"0.237414"\t"0.233557"\t"0.193482"\t"14.4463"\t"12.5843"\t"13.7146"\t"16.3924"\t"21.7949"\t"5.40248"\t"1.6"\t"4.95"\t40\t60\t0\n+"TURPHI"\t"0.45115"\t"0.401706"\t"0.375644"\t"13.3325"\t"11.3957"\t"11.6012"\t"14.214"\t"17.9786"\t"3.76458"\t"1.57"\t"4.81"\t43\t57\t0\n+"TURPIL"\t"1.49239"\t"1.38586"\t"0.892988"\t"12.1874"\t"10.0287"\t"10.5189"\t"13.5309"\t"16.2458"\t"2.71486"\t"1.6"\t"4.95"\t40\t60\t0\n+"TURRUF"\t""\t""\t""\t""\t"4.03574"\t""\t""\t""\t""\t""\t""\t""\t""\t""\n+"TURSYL"\t""\t""\t""\t""\t"20.7412"\t""\t""\t""\t""\t""\t""\t""\t""\t""\n+"TURTOR"\t"2.24162"\t""\t""\t""\t"9.03076"\t""\t""\t""\t""\t"1.7"\t"5.47"\t""\t""\t""\n+"TURVIS"\t"0.529272"\t"0.517882"\t"0.506435"\t"13.8021"\t"11.9147"\t"12.4433"\t"14.7843"\t"19.8083"\t"5.02401"\t"1.55"\t"4.71"\t45\t55\t0\n+"TYTALB"\t""\t""\t""\t""\t"13.9906"\t""\t""\t""\t""\t""\t""\t""\t""\t""\n+"UPUEPO"\t"0.544659"\t"0.606751"\t"0.386247"\t"16.2542"\t"14.1794"\t"15.9169"\t"15.3301"\t"24.5791"\t"9.24903"\t"2"\t"7.39"\t0\t100\t0\n+"URIAAL"\t""\t""\t""\t""\t"9.58898"\t""\t""\t""\t""\t""\t""\t""\t""\t""\n+"URILOM"\t""\t""\t""\t""\t"1.03554"\t""\t""\t""\t""\t""\t""\t""\t""\t""\n+"VANVAN"\t"2.20961"\t"2.22758"\t"2.01969"\t"13.5008"\t"11.5326"\t"11.9405"\t"14.1509"\t"18.5567"\t"4.40578"\t"1.9"\t"6.69"\t10\t90\t0\n+"XENCIN"\t""\t""\t""\t""\t"10.598"\t""\t""\t""\t""\t""\t""\t""\t""\t""\n' |
| b |
| diff -r 000000000000 -r 916b49d725ba stoceps_macros.xml --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/stoceps_macros.xml Thu Apr 02 03:35:29 2020 -0400 |
| [ |
| @@ -0,0 +1,73 @@ +<macros> + <token name="@VERSION@">0.0.1</token> + <xml name="reshape_requirements"> + <requirements> + <requirement type="package" version="0.8.8">r-reshape</requirement> + <requirement type="package" version="1.12.0">r-data.table</requirement> + </requirements> + </xml> + <xml name="reshape2_requirements"> + <requirements> + <requirement type="package" version="1.4.3">r-reshape2</requirement> + </requirements> + </xml> + <xml name="mainglm_requirements"> + <requirements> + <requirement type="package" version="3.0.0">r-ggplot2</requirement> + <requirement type="package" version="0.3_2">r-speedglm</requirement> + <requirement type="package" version="1.10_1">r-arm</requirement> + <requirement type="package" version="1.12.0">r-data.table</requirement> + <requirement type="package" version="1.4.3">r-reshape2</requirement> + </requirements> + </xml> + <xml name="temp_indic_requirements"> + <requirements> + <requirement type="package" version="1.3_15">r-rodbc</requirement> + <requirement type="package" version="0.8.8">r-reshape</requirement> + <requirement type="package" version="1.12.0">r-data.table</requirement> + <requirement type="package" version="1.4_3">r-rgdal</requirement> + <requirement type="package" version="1.7.4">r-lubridate</requirement> + <requirement type="package" version="4.6_2">r-doby</requirement> + <requirement type="package" version="1.10_1">r-arm</requirement> + <requirement type="package" version="3.1.0">r-ggplot2</requirement> + <requirement type="package" version="1.0.0">r-scales</requirement> + <requirement type="package" version="1.8_24">r-mgcv</requirement> + <requirement type="package" version="1.8.4">r-plyr</requirement> + <requirement type="package" version="0.3_2">r-speedglm</requirement> + <requirement type="package" version="3.1_0">r-lmertest</requirement> + <requirement type="package" version="0.2.3">r-glmmtmb</requirement> + </requirements> + </xml> + <xml name="stoceps_input_filtered"> + <param name="input" type="data" format="tabular" label="Stoc filtered input" help="Input Stoc count file, shaped and filtered with the 'preprocess population data' and 'filter species' tools." /> + </xml> + <xml name="stoceps_advanced_params_select"> + <param name="advanced" type="select" label="Specify advanced parameters"> + <option value="simple" selected="true">No, use program defaults.</option> + <option value="advanced">Yes, see full parameter list.</option> + </param> + <when value="simple"> + </when> + </xml> + <xml name="stoceps_compute_ic"> + <param name="compute_ic" type="boolean" truevalue="TRUE" falsevalue="FALSE" checked="yes" label="Compute confidence intervals"/> + </xml> + <xml name="stoceps_filter_glmmtmb"> + <filter> settings['advanced'] == 'advanced'</filter> + <filter> settings['method'] == 'glmmtmb'</filter> + </xml> + <xml name="stoceps_filter_gam"> + <filter> settings['method'] == 'gam'</filter> + </xml> + <xml name="stoceps_bibref"> + <citations> + <citation type="bibtex"> + @unpublished{stocepsromain, + title={Vigie-Nature STOC unpublished scripts}, + author={Lorrilliere, R}, + url={http://www.vigienature.fr/sites/vigienature/files/atoms/files/analysestoceps_0.zip} + } + </citation> + </citations> + </xml> +</macros> |
| b |
| diff -r 000000000000 -r 916b49d725ba tabSpecies.csv --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/tabSpecies.csv Thu Apr 02 03:35:29 2020 -0400 |
| b |
| b'@@ -0,0 +1,325 @@\n+"espece"\t"nom"\t"nomscientific"\t"indicateur"\t"specialisation"\n+"ACCGEN"\t"Autour des palombes"\t"Accipiter gentilis"\tFALSE\t""\n+"ACCNIS"\t"Epervier d\'Europe"\t"Accipiter nisus"\tFALSE\t""\n+"ACRARU"\t"Rousserolle turdo\xc3\xafde"\t"Acrocephalus arundinaceus"\tFALSE\t""\n+"ACRMEL"\t"Lusciniole \xc3\xa0 moustaches"\t"Acrocephalus melanopogon"\tFALSE\t""\n+"ACRPAL"\t"Phragmite aquatique"\t"Acrocephalus paludicola"\tFALSE\t""\n+"ACRRIS"\t"Rousserolle verderolle"\t"Acrocephalus palustris"\tFALSE\t""\n+"ACRSCH"\t"Phragmite des joncs"\t"Acrocephalus schoenobaenus"\tFALSE\t""\n+"ACRSCI"\t"Rousserolle effarvatte"\t"Acrocephalus scirpaceus"\tFALSE\t""\n+"ACTHYP"\t"Chevalier guignette"\t"Actitis hypoleucos"\tFALSE\t""\n+"AEGCAU"\t"M\xc3\xa9sange \xc3\xa0 longue queue"\t"Aegithalos caudatus"\tFALSE\t""\n+"AEGFUN"\t"Chouette de Tengmalm"\t"Aegolius funereus"\tFALSE\t""\n+"AIXGAL"\t"Canard mandarin"\t"Aix galericulata"\tFALSE\t""\n+"AIXSPO"\t"Canard carolin"\t"Aix sponsa"\tFALSE\t""\n+"ALAARV"\t"Alouette des champs"\t"Alauda arvensis"\tTRUE\t"milieux agricoles"\n+"ALCATT"\t"Martin-p\xc3\xaacheur d\'Europe"\t"Alcedo atthis"\tFALSE\t""\n+"ALCTOR"\t"Pingouin torda"\t"Alca torda"\tFALSE\t""\n+"ALEGRA"\t"Perdrix bartavelle"\t"Alectoris graeca"\tFALSE\t""\n+"ALERUF"\t"Perdrix rouge"\t"Alectoris rufa"\tTRUE\t"milieux agricoles"\n+"ALLALL"\t"Mergule nain"\t"Alle alle"\tFALSE\t""\n+"ALOAEG"\t"Ouette d\'Egypte"\t"Alopochen aegyptiaca"\tFALSE\t""\n+"ANAACU"\t"Canard pilet"\t"Anas acuta"\tFALSE\t""\n+"ANACLY"\t"Canard souchet"\t"Anas clypeata"\tFALSE\t""\n+"ANACRE"\t"Sarcelle d\'hiver"\t"Anas crecca"\tFALSE\t""\n+"ANAPEN"\t"Canard siffleur"\t"Anas penelope"\tFALSE\t""\n+"ANAPLA"\t"Canard colvert"\t"Anas platyrhynchos"\tFALSE\t""\n+"ANAQUE"\t"Sarcelle d\'\xc3\xa9t\xc3\xa9"\t"Anas querquedula"\tFALSE\t""\n+"ANASTR"\t"Canard chipeau"\t"Anas strepera"\tFALSE\t""\n+"ANSANS"\t"Oie cendr\xc3\xa9e"\t"Anser anser"\tFALSE\t""\n+"ANSIND"\t"Oie \xc3\xa0 t\xc3\xaate barr\xc3\xa9e"\t"Anser indicus"\tFALSE\t""\n+"ANTCAM"\t"Pipit rousseline"\t"Anthus campestris"\tTRUE\t"milieux agricoles"\n+"ANTCER"\t"Pipit \xc3\xa0 gorge rousse"\t"Anthus cervinus"\tFALSE\t""\n+"ANTPET"\t"Pipit maritime"\t"Anthus petrosus"\tFALSE\t""\n+"ANTPRA"\t"Pipit farlouse"\t"Anthus pratensis"\tTRUE\t"milieux agricoles"\n+"ANTRIC"\t"Pipit de Richard"\t"Anthus richardi"\tFALSE\t""\n+"ANTSPI"\t"Pipit spioncelle"\t"Anthus spinoletta"\tFALSE\t""\n+"ANTTRI"\t"Pipit des arbres"\t"Anthus trivialis"\tFALSE\t""\n+"APUAPU"\t"Martinet noir"\t"Apus apus"\tTRUE\t"milieux b\xc3\xa2tis"\n+"APUMEL"\t"Martinet \xc3\xa0 ventre blanc"\t"Apus melba"\tFALSE\t""\n+"APUPAL"\t"Martinet p\xc3\xa2le"\t"Apus pallidus"\tFALSE\t""\n+"AQUCHR"\t"Aigle royal"\t"Aquila chrysaetos"\tFALSE\t""\n+"ARDCIN"\t"H\xc3\xa9ron cendr\xc3\xa9"\t"Ardea cinerea"\tFALSE\t""\n+"ARDPUR"\t"H\xc3\xa9ron pourpr\xc3\xa9"\t"Ardea purpurea"\tFALSE\t""\n+"ARDRAL"\t"Crabier chevelu"\t"Ardeola ralloides"\tFALSE\t""\n+"AREINT"\t"Tournepierre \xc3\xa0 collier"\t"Arenaria interpres"\tFALSE\t""\n+"ASIFLA"\t"Hibou des marais"\t"Asio flammeus"\tFALSE\t""\n+"ASIOTU"\t"Hibou moyen-duc"\t"Asio otus"\tFALSE\t""\n+"ATHNOC"\t"Chev\xc3\xaache d\'Ath\xc3\xa9na"\t"Athene noctua"\tFALSE\t""\n+"AYTAFF"\t"Fuligule \xc3\xa0 t\xc3\xaate noire"\t"Aythya affinis"\tFALSE\t""\n+"AYTFER"\t"Fuligule milouin"\t"Aythya ferina"\tFALSE\t""\n+"AYTFUL"\t"Fuligule morillon"\t"Aythya fuligula"\tFALSE\t""\n+"AYTMAR"\t"Fuligule milouinan"\t"Aythya marila"\tFALSE\t""\n+"BOMGAR"\t"Jaseur bor\xc3\xa9al"\t"Bombycilla garrulus"\tFALSE\t""\n+"BONBON"\t"G\xc3\xa9linotte des bois"\t"Bonasa bonasia"\tFALSE\t""\n+"BOTSTE"\t"Butor \xc3\xa9toil\xc3\xa9"\t"Botaurus stellaris"\tFALSE\t""\n+"BRABER"\t"Bernache cravant"\t"Branta bernicla"\tFALSE\t""\n+"BRACAN"\t"Bernache du Canada"\t"Branta canadensis"\tFALSE\t""\n+"BRALEU"\t"Bernache nonnette"\t"Branta leucopsis"\tFALSE\t""\n+"BUBBUB"\t"Grand-duc d\'Europe"\t"Bubo bubo"\tFALSE\t""\n+"BUBIBI"\t"H\xc3\xa9ron garde-boeufs"\t"Bubulcus ibis"\tFALSE\t""\n+"BUROED"\t"Oedicn\xc3\xa8me criard"\t"Burhinus oedicnemus"\tFALSE\t""\n+"BUTBUT"\t"Buse variable"\t"Buteo buteo"\tTRUE\t"milieux agricoles"\n+"CALACU"\t"B\xc3\xa9casseau \xc3\xa0 queue pointue"\t"Calidris acuminata"\tFALSE\t""\n+"CALALB"\t"B\xc3\xa9casseau sanderling"\t"Calidris alba"\tFALSE\t""\n+"CALALP"\t"B\xc3\xa9casseau variable"\t"Calidris alpina"\tFALSE\t""\n+"CALBRA"\t"Alouette calandrelle"\t"Calandrella brachydactyla"\tFALSE\t""\n+"CALCAN"\t"B\xc3\xa9casseau maub\xc3\xa8che"\t"Calidris canutus"\tFALSE\t""\n+"CALMIN"\t"B\xc3\xa9'..b'Bouvreuil pivoine"\t"Pyrrhula pyrrhula"\tTRUE\t"milieux forestiers"\n+"PYRRAX"\t"Crave \xc3\xa0 bec rouge"\t"Pyrrhocorax pyrrhocorax"\tFALSE\t""\n+"RALAQU"\t"R\xc3\xa2le d\'eau"\t"Rallus aquaticus"\tFALSE\t""\n+"RECAVO"\t"Avocette \xc3\xa9l\xc3\xa9gante"\t"Recurvirostra avosetta"\tFALSE\t""\n+"REGIGN"\t"Roitelet \xc3\xa0 triple bandeau"\t"Regulus ignicapilla"\tTRUE\t"milieux forestiers"\n+"REGREG"\t"Roitelet hupp\xc3\xa9"\t"Regulus regulus"\tTRUE\t"milieux forestiers"\n+"RIPRIP"\t"Hirondelle de rivage"\t"Riparia riparia"\tFALSE\t""\n+"SAXRUB"\t"Tarier des pr\xc3\xa9s"\t"Saxicola rubetra"\tTRUE\t"milieux agricoles"\n+"SAXTOR"\t"Tarier p\xc3\xa2tre"\t"Saxicola rubicola"\tTRUE\t"milieux agricoles"\n+"SCORUS"\t"B\xc3\xa9casse des bois"\t"Scolopax rusticola"\tFALSE\t""\n+"SERCIT"\t"Venturon montagnard"\t"Serinus citrinella"\tFALSE\t""\n+"SERCOR"\t"Venturon corse"\t"Serinus corsicanus"\tFALSE\t""\n+"SERSER"\t"Serin cini"\t"Serinus serinus"\tTRUE\t"milieux b\xc3\xa2tis"\n+"SITEUR"\t"Sittelle torchepot"\t"Sitta europaea"\tTRUE\t"milieux forestiers"\n+"SITWHI"\t"Sittelle corse"\t"Sitta whiteheadi"\tFALSE\t""\n+"STEALB"\t"Sterne naine"\t"Sternula albifrons"\tFALSE\t""\n+"STEHIR"\t"Sterne pierregarin"\t"Sterna hirundo"\tFALSE\t""\n+"STESAN"\t"Sterne caugek"\t"Thalasseus sandvicensis"\tFALSE\t""\n+"STRALU"\t"Chouette hulotte"\t"Strix aluco"\tFALSE\t""\n+"STRDEC"\t"Tourterelle turque"\t"Streptopelia decaocto"\tTRUE\t"milieux b\xc3\xa2tis"\n+"STRORI"\t"Tourterelle orientale"\t"Streptopelia orientalis"\tFALSE\t""\n+"STRSEN"\t"Tourterelle maill\xc3\xa9e"\t"Streptopelia senegalensis"\tFALSE\t""\n+"STRTUR"\t"Tourterelle des bois"\t"Streptopelia turtur"\tFALSE\t""\n+"STUROS"\t"\xc3\x89tourneau roselin"\t"Sturnus roseus"\tFALSE\t""\n+"STUUNI"\t"\xc3\x89tourneau unicolore"\t"Sturnus unicolor"\tFALSE\t""\n+"STUVUL"\t"\xc3\x89tourneau sansonnet"\t"Sturnus vulgaris"\tFALSE\t""\n+"SURULU"\t"Chouette \xc3\xa9pervi\xc3\xa8re"\t"Surnia ulula"\tFALSE\t""\n+"SYLATR"\t"Fauvette \xc3\xa0 t\xc3\xaate noire"\t"Sylvia atricapilla"\tTRUE\t"generaliste"\n+"SYLBOR"\t"Fauvette des jardins"\t"Sylvia borin"\tFALSE\t""\n+"SYLCAN"\t"Fauvette passerinette"\t"Sylvia cantillans"\tFALSE\t""\n+"SYLCOM"\t"Fauvette grisette"\t"Sylvia communis"\tTRUE\t"milieux agricoles"\n+"SYLCON"\t"Fauvette \xc3\xa0 lunettes"\t"Sylvia conspicillata"\tFALSE\t""\n+"SYLCUR"\t"Fauvette babillarde"\t"Sylvia curruca"\tFALSE\t""\n+"SYLHOR"\t"Fauvette orph\xc3\xa9e"\t"Sylvia hortensis"\tFALSE\t""\n+"SYLMEL"\t"Fauvette m\xc3\xa9lanoc\xc3\xa9phale"\t"Sylvia melanocephala"\tTRUE\t"milieux forestiers"\n+"SYLNIS"\t"Fauvette \xc3\xa9pervi\xc3\xa8re"\t"Sylvia nisoria"\tFALSE\t""\n+"SYLSAR"\t"Fauvette sarde"\t"Sylvia sarda"\tFALSE\t""\n+"SYLUND"\t"Fauvette pitchou"\t"Sylvia undata"\tFALSE\t""\n+"SYRREE"\t"Faisan v\xc3\xa9n\xc3\xa9r\xc3\xa9"\t"Syrmaticus reevesii"\tFALSE\t""\n+"TACRUF"\t"Gr\xc3\xa8be castagneux"\t"Tachybaptus ruficollis"\tFALSE\t""\n+"TADFER"\t"Tadorne casarca"\t"Tadorna ferruginea"\tFALSE\t""\n+"TADTAD"\t"Tadorne de Belon"\t"Tadorna tadorna"\tFALSE\t""\n+"TETRAX"\t"Outarde canepeti\xc3\xa8re"\t"Tetrax tetrax"\tFALSE\t""\n+"TETRIX"\t"T\xc3\xa9tras lyre"\t"Tetrao tetrix"\tFALSE\t""\n+"TETURO"\t"Grand T\xc3\xa9tras"\t"Tetrao urogallus"\tFALSE\t""\n+"THRAET"\t"Ibis sacr\xc3\xa9"\t"Threskiornis aethiopicus"\tFALSE\t""\n+"TICMUR"\t"Tichodrome \xc3\xa9chelette"\t"Tichodroma muraria"\tFALSE\t""\n+"TRIERY"\t"Chevalier arlequin"\t"Tringa erythropus"\tFALSE\t""\n+"TRIGLA"\t"Chevalier sylvain"\t"Tringa glareola"\tFALSE\t""\n+"TRINEB"\t"Chevalier aboyeur"\t"Tringa nebularia"\tFALSE\t""\n+"TRIOCH"\t"Chevalier culblanc"\t"Tringa ochropus"\tFALSE\t""\n+"TRITOT"\t"Chevalier gambette"\t"Tringa totanus"\tFALSE\t""\n+"TROTRO"\t"Troglodyte mignon"\t"Troglodytes troglodytes"\tTRUE\t"milieux forestiers"\n+"TURILI"\t"Grive mauvis"\t"Turdus iliacus"\tFALSE\t""\n+"TURMER"\t"Merle noir"\t"Turdus merula"\tTRUE\t"generaliste"\n+"TURPHI"\t"Grive musicienne"\t"Turdus philomelos"\tTRUE\t"milieux forestiers"\n+"TURPIL"\t"Grive litorne"\t"Turdus pilaris"\tFALSE\t""\n+"TURRUF"\t"Grive \xc3\xa0 gorge noire ou rousse"\t"Turdus ruficollis"\tFALSE\t""\n+"TURTOR"\t"Merle \xc3\xa0 plastron"\t"Turdus torquatus"\tFALSE\t""\n+"TURVIS"\t"Grive draine"\t"Turdus viscivorus"\tTRUE\t"milieux forestiers"\n+"TYTALB"\t"Effraie des clochers"\t"Tyto alba"\tFALSE\t""\n+"UPUEPO"\t"Huppe fasci\xc3\xa9e"\t"Upupa epops"\tTRUE\t"milieux agricoles"\n+"VANVAN"\t"Vanneau hupp\xc3\xa9"\t"Vanellus vanellus"\tTRUE\t"milieux agricoles"\n+"ZOODAU"\t"Grive dor\xc3\xa9e"\t"Zoothera dauma"\tFALSE\t""\n' |
| b |
| diff -r 000000000000 -r 916b49d725ba temp_analysis_indic.xml --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/temp_analysis_indic.xml Thu Apr 02 03:35:29 2020 -0400 |
| [ |
| b'@@ -0,0 +1,209 @@\n+<tool id="stoceps_trend_indic" name="Temporal trend indicator" version="@VERSION@">\n+ <description>using GlmmTMB or GAM models</description>\n+ <macros>\n+ <import>stoceps_macros.xml</import>\n+ </macros>\n+ <expand macro="temp_indic_requirements"/>\n+ <command detect_errors="exit_code"><![CDATA[\n+ Rscript \n+ \'$__tool_directory__/FunctExeTemporalAnalysisofIndicatorTrait.r\' \n+ \'$input\'\n+ \'$inputtabSpecies\'\n+ \'$inputspeciesindic\'\n+ \'$inputcoord\'\n+ #if $index==\'csi\' \n+ \'ssi\'\n+ \'csi\'\n+ #elif $index==\'cti\'\n+ \'sti\'\n+ \'cti\'\n+ #else\n+ \'stri\'\n+ \'ctri\'\n+ #end if\n+ #if $settings.advanced==\'advanced\' \n+ $settings.method \'\' \'idindicatortrait\'\n+ $settings.smooth_plot\n+ $settings.compute_ic\n+ #else\n+ \'gam\' \'\' \'idindicatortrait\'\n+ \'TRUE\'\n+ \'TRUE\'\n+ #end if\n+ \'$__tool_directory__/FunctTrendSTOCGalaxy.r\' \n+ ]]>\n+ </command>\n+ <inputs>\n+ <expand macro="stoceps_input_filtered"/>\n+ <param name="inputcoord" type="data" format="tabular" label="Coordinates of sites" help="Input localization tabular file, with 3 columns (site ID, latitude, longitude)." />\n+ <param name="inputtabSpecies" type="data" format="tabular" label="Species file" help="Input species tabular file, with 5 columns (species ID, species name, species scientific name, specialization status)." />\n+ <param name="inputspeciesindic" type="data" format="tabular" label="indicators info file" help="Input indicator info tabular file, with a `species ID` column and at least one index column (named `ssi` or `sti` or `stri`)." />\n+ <param name="index" type="select" help="Available index" label="Chose the index you want to compute">\n+ <option selected="true" value="csi">CSI</option>\n+ <option value="cti">CTI</option>\n+ <option value="ctri">CTRI</option>\n+ </param>\n+ <conditional name="settings">\n+ <expand macro="stoceps_advanced_params_select"/>\n+ <when value="advanced">\n+ <param name="smooth_plot" type="boolean" truevalue="TRUE" falsevalue="FALSE" checked="yes" label="Smooth visualization."/>\n+ <param name="method" type="select" help="Available methods are GlmmTMB and Gam" label="Chose the model method">\n+ <option selected="true" value="glmmtmb">GlmmTMB</option>\n+ <option value="gam">Gam</option>\n+ </param>\n+ <expand macro="stoceps_compute_ic"/>\n+ </when>\n+ </conditional>\n+ </inputs>\n+ <outputs>\n+ <data name="output_tab_gammcomplet" from_work_dir="Output/csi_gammCOMPLET_France.tabular" format="tabular" label="GAM - Temp trends all data - on ${on_string}">\n+ <expand macro="stoceps_filter_gam"/>\n+ </data>\n+ <data name="output_tab_gam_annee" from_work_dir="Output/csi_gammParannee_France.tabular" format="tabular" label="GAM - Temp trends per year - on ${on_string}">\n+ <expand macro="stoceps_filter_gam"/>\n+ </data>\n+ <data name="output_plot_carre" from_work_dir="Output/figcsi_carre_France.png" format="png" label="GAM - Temp trends plot on ${on_string}">\n+ <expand macro="stoceps_filter_gam"/>\n+ </data>\n+ <data name="output_plot__gam_csiplot" from_work_dir="Output/figcsi_plotFrance.png" format="png" label="GAM - Temp trends plot on ${on_string}">\n+ <expand macro="stoceps_filter_gam"/>\n+ </data>\n+ <data name="output_tab_gam_smoothed" from_work_dir="Output/csi_gammsmoothFrance.tabular" format="tabular" label="GAM - Temp trends smoothed data on ${on_string}">\n+ <expand macro="stoceps_filter_gam"/>\n+ </data>\n+ \n+ <data name="output_plot_glmmtb_csiplot" '..b' name="output_plot_carre">\n+ <assert_contents>\n+ <has_text text="PNG"/>\n+ </assert_contents>\n+ </output>\n+ <output name="output_plot__gam_csiplot">\n+ <assert_contents>\n+ <has_text text="PNG"/>\n+ </assert_contents>\n+ </output>\n+ </test>\n+ <test>\n+ <param name="input" value="Datafilteredfortrendanalysis.tabular"/>\n+ <param name="inputcoord" value="coordCarreSTOCfaux.tabular"/>\n+ <param name="inputspeciesindic" value="species_indicateur_fonctionnel.tabular"/>\n+ <param name="inputtabSpecies" value="tabSpecies.csv"/>\n+ <param name="advanced" value="advanced"/>\n+ <param name="smooth_plot" value="FALSE"/>\n+ <param name="method" value="glmmtmb"/>\n+ <param name="compute_ic" value="TRUE"/>\n+ <output name="output_plot_glmmtb_csiplot">\n+ <assert_contents>\n+ <has_text text="PNG"/>\n+ </assert_contents>\n+ </output>\n+ <output name="output_tab_glmmtb_annee">\n+ <assert_contents>\n+ <has_n_lines n="18"/>\n+ <has_size value="1400" delta="50"/>\n+ </assert_contents>\n+ </output>\n+ <output name="output_tab_glmmtb_gammcomplet">\n+ <assert_contents>\n+ <has_n_lines n="19"/>\n+ <has_size value="2900" delta="100"/>\n+ </assert_contents>\n+ </output>\n+ </test>\n+ </tests>\n+ <help><![CDATA[\n+=================================================\n+STOC Temporal population trend indicator\n+=================================================\n+\n+**What it does**\n+\n+Compute and plot time variation of indicator or mean trait values of communities.\n+\n+CSI Temporal analysis indicator\n+This script computes the indicator csi, cti and ctri per year and site, wich also correspond to a community weighted mean (CWM), and analyse its temporal evolution trend and create graphical vizualisation.\n+As indicator you can thus use also a trait.\n+\n+|\n+\n+**Input description**\n+\n+A tabular file with count data including one column for the abundance, one column indicating the species, one indicating the site and one indicating the year\n+that could be extracted from the STOC on demand: romain.lorrilliere@mnhn.fr \n+\n+IMPORTANT: The tabular file with the count data should not include zero count because this will biais the estimation of the weighted mean.\n+In the same line, the species trait data should be complete or you should remove the species without trait value from your count data file. \n+\n+One tabular species file, with a `species ID` column and species names.\n+\n+One tabular file with trait data including at least one column with the species name or ID (the one used in the count data file) and one column with the trait value for each species (named `ssi` or `sti` or `stri`). For the CSI indicator notably (community specialization index), this should be the ssi (species specialization index). \n+\n+One tabular file with coordinates in latitude and longitude (one column for each) including also the site ID (the one used in the count data file) \n+\n+|\n+\n+**Output**\n+\n+Gam method ::\n+\n+ - Two tabulars that details computed indicator per year and globaly and one optional and additional table with the smoothed data.\n+\n+ - One plot that show trends across years and one optional and additional plot with the smooth method.\n+\n+|\n+\n+GlmmTMB method ::\n+\n+ - Two tabulars that details computed indicator per year and globaly.\n+\n+ - A plot that show trends across years.\n+\n+\n+|\n+\n+**Source**\n+\n+UnPublished script available at http://www.vigienature.fr/sites/vigienature/files/atoms/files/analysestoceps_0.zip\n+and the first version written by Romain Lorrilliere\n+\n+ ]]></help>\n+ <expand macro="stoceps_bibref" />\n+</tool>\n' |