Mercurial > repos > ecology > stoc_mainglm_group
changeset 2:8f953c35c787 draft default tip
"planemo upload for repository https://github.com/Alanamosse/Galaxy-E/tree/stoctool/tools/stoc commit d49a4da1ffac1f33a15fdb7ae98827d0034a7879"
| author | ecology |
|---|---|
| date | Mon, 11 May 2020 17:34:04 -0400 |
| parents | e3e173ae01b0 |
| children | |
| files | FunctTrendSTOCGalaxy.r mainglm_group.xml stoceps_macros.xml |
| diffstat | 3 files changed, 6 insertions(+), 7 deletions(-) [+] |
line wrap: on
line diff
--- a/FunctTrendSTOCGalaxy.r Tue Apr 07 17:46:10 2020 -0400 +++ b/FunctTrendSTOCGalaxy.r Mon May 11 17:34:04 2020 -0400 @@ -62,7 +62,7 @@ if(length(colNull)>0){ cat("\n",length(colNull)," Species removed from the analysis, abundance is always 0.\n\n",sep="") #Espèces enlevées de l'analyse car abondance toujours égale a 0\n\n",sep="") #tabNull <- data.frame(Code_espece = colNull, nom_espece = tabsp[colNull,"nom"]) - #cat("\n\n",sep="") + cat("Removed absent species : \n-",paste(colNull,collapse="\n-"),sep="") tab <- tab[,c("carre","annee",colConserve)] } ################################################################################ FIN DE LA PARTIE ISOLABLE @@ -119,7 +119,7 @@ cat("\n",length(colSupr)," Rare species removed from the analysis.\n\n",sep="") #tabSupr <- subset(tabsp,espece %in% colSupr ,select=c("espece","nom")) #tabSupr <- tabSupr[order(tabSupr$espece),] - #cat("\n\n",sep="") + cat("Removed rare species : \n-",paste(colSupr,collapse="\n-"),sep="") } if(length(colConserve)==0) {
--- a/mainglm_group.xml Tue Apr 07 17:46:10 2020 -0400 +++ b/mainglm_group.xml Mon May 11 17:34:04 2020 -0400 @@ -91,7 +91,7 @@ -Compute and plot trends of species population by specialization group, using a glm model. +Compute and plot trends of species population by specialization group, using a glm model. The same model than glm per species is used but results are aggregated by specialization group. |
--- a/stoceps_macros.xml Tue Apr 07 17:46:10 2020 -0400 +++ b/stoceps_macros.xml Mon May 11 17:34:04 2020 -0400 @@ -1,5 +1,5 @@ <macros> - <token name="@VERSION@">0.0.1</token> + <token name="@VERSION@">0.0.2</token> <xml name="reshape_requirements"> <requirements> <requirement type="package" version="0.8.8">r-reshape</requirement> @@ -53,11 +53,10 @@ <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> + <filter> method['model'] == 'glmmtmb'</filter> </xml> <xml name="stoceps_filter_gam"> - <filter> settings['method'] == 'gam'</filter> + <filter> method['model'] == 'gam'</filter> </xml> <xml name="stoceps_bibref"> <citations>