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comparison glmmpql_en.xml @ 0:5b126f770671 draft

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author mnhn65mo
date Fri, 03 Aug 2018 08:28:22 -0400
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1 <tool id="glmmpql" name="Expected temporal trend" version="0.1">
2 <description>of species abundance</description>
3 <requirements>
4 <requirement type="package" version="3.1_131">r-nlme</requirement>
5 <requirement type="package" version="7.3_48">r-mass</requirement>
6 <requirement type="package" version="0.9.10">xorg-libxrender</requirement>
7 <requirement type="package" version="1.2.2">xorg-libsm</requirement>
8 </requirements>
9 <command detect_errors="exit_code"><![CDATA[
10 Rscript '$__tool_directory__/glmmpql.R' '$input1' '$output' '$output2' ]]>
11 </command>
12 <inputs>
13 <param format="tabular" name="input1" type="data" label="Tabular file generated by the ab_index tool"/>
14 </inputs>
15 <outputs>
16 <data format="png" name="output" from_work_dir="output-plot.png" />
17 <data format="tabular" name="output2" from_work_dir="output-glmmpql" />
18 </outputs>
19 <tests>
20 <test>
21 <param name="input1" value="data_index.tabular"/>
22 <param name="output" value="glmmpql-plot.png"/>
23 <output name="output2" value="glmmpql.tabular"/>
24 </test>
25 </tests>
26 <help><![CDATA[
27
28 .. class:: infomark
29
30 ==========================
31 Temporal trends of species abundance
32 ==========================
33
34 This tool is an implementation of the glmmpql function from `RegionalGAM package: https://github.com/RetoSchmucki/regionalGAM/
35 This function computes a collated index for each year and estimates the temporal trend.
36 ]]></help>
37 <citations>
38 <citation type="doi">10.1111/1365-2664.12561</citation>
39 </citations>
40 </tool>