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"planemo upload for repository https://github.com/Alanamosse/Galaxy-E/tree/stoctool/tools/stoc commit d49a4da1ffac1f33a15fdb7ae98827d0034a7879"
author ecology
date Mon, 11 May 2020 17:18:16 -0400
parents df3ce23d0d23
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0:df3ce23d0d23 1:a961be0a964f
1 <tool id="stoceps_glm" name="Estimate temporal population evolution" version="@VERSION@"> 1 <tool id="stoceps_glm" name="Estimate temporal population variation" version="@VERSION@">
2 <description>by species</description> 2 <description>by species</description>
3 <macros> 3 <macros>
4 <import>stoceps_macros.xml</import> 4 <import>stoceps_macros.xml</import>
5 </macros> 5 </macros>
6 <expand macro="mainglm_requirements"/> 6 <expand macro="mainglm_requirements"/>
92 </output_collection> 92 </output_collection>
93 </test> 93 </test>
94 </tests> 94 </tests>
95 <help><![CDATA[ 95 <help><![CDATA[
96 ================================================= 96 =================================================
97 STOC Estimate species population evolution 97 STOC Estimate species population variation
98 ================================================= 98 =================================================
99 99
100 **What it does** 100 **What it does**
101 101
102 Compute and plot evolution of species population, using a glm model. 102 Compute and plot trends of species population, using a glm model of formula : abundance ~ site + year. Testing the effect of site and year on abundance with quasipoisson distribution.
103 103
104 | 104 |
105 105
106 **Input description** 106 **Input description**
107 107
140 **Source** 140 **Source**
141 141
142 UnPublished script available at http://www.vigienature.fr/sites/vigienature/files/atoms/files/analysestoceps_0.zip 142 UnPublished script available at http://www.vigienature.fr/sites/vigienature/files/atoms/files/analysestoceps_0.zip
143 the first version written by Romain Lorrilliere 143 the first version written by Romain Lorrilliere
144 144
145 Original script information:
146
147 Estimate temporal evolution of population per species - ExeMainGlmGalaxy.r
148 This script analyse the temporal evolution of species population and create graphical vizualisation.
149
150 Script needs the followings inputs :
151 - stoc or community data filtered with at least 4 columns: year, site, species, and abundance with 0. Corresponding to "observed" or predicted 0 abundance. May come from the tools "Preprocess population data for evolution trend analyzes" (ExemakeTableAnalyseGalaxy.r) followed by "Filter species with rare and low abundances" (ExeFilteringRareLowabundSPGalaxy.r).
152 - species details file with name and indicator status file with at least 2 columns: the species name or species ID (found in the community data or in stoc data) and his status as indicator species
153 - file that stocks functions : "FunctTrendSTOCGalaxy.r"
154
155
156 Arguments are :
157 - spExclude: list of species (using the the species name or ID) that you want to exclude
158 - assessIC : compute and show confidence interval in plots (TRUE / FALSE)
159 - analysis custom id
160
161
162 How to execute, eg :
163 # all files are available in github repo
164 #Exec id=mainglm, return IC on plot, no species excluded
165 $ Rscript ExeMainGlmGalaxy.r' Datafilteredfortrendanalysis.tabular tabSpecies.csv 'mainglm' '' 'TRUE' FunctTrendSTOCGalaxy.r
166
167
168 Outputs are created in an Output repo :
169 GLM gives 1 graph per species and 2 tables:
170 - nameofspecies_id.png (one plot per species)
171 - tendanceGlobalEspece_id.tabular
172 - variationsAnnuellesEspece_id.tabular
173
174
175 R library needed
176 r-lme4 version 1.1.18.1
177 r-ggplot2 version 3.0.0
178 r-speedglm version 0.3.2
179 r-arm version 1.10.1
180 r-reshape version 0.8.8
181 r-data.table version 1.12.0
182 r-reshape2 version 1.4.3
183 ]]></help> 145 ]]></help>
184 <expand macro="stoceps_bibref" /> 146 <expand macro="stoceps_bibref" />
185 </tool> 147 </tool>