view ab_index_en.xml @ 0:5b126f770671 draft

author mnhn65mo
date Fri, 03 Aug 2018 08:28:22 -0400
children b8fa05dbcff4
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<tool id="ab_index" name="Abundance index" version="0.1">
    <description>computation across species, sites and years</description>
        <requirement type="package" version="3.4">r</requirement>
    <command detect_errors="exit_code"><![CDATA[
        Rscript '$__tool_directory__/ab_index.R' '$__tool_directory__/dennis_gam_initial_functions.R' '$input1' '$input2' '$output' ]]>
        <param format="tabular,csv" name="input1" type="data" label="Count file" help="The file must contain the SPECIES, SITE, YEAR, MONTH, DAY and COUNT columns. CSV file separator ',' or tab."/>
        <param format="tabular" name="input2" type="data" label="Flight curve output"/>
        <data format="tabular" name="output" from_work_dir="data.index" />
        <test> <!-- FAILED -->
            <param name="input1" value="gatekeeper_CM"/>
            <param name="input2" value="flight_curve_result.tabular"/>
            <output name="output" value="data_index.tabular"/>

.. class:: infomark 

Compute abundance index

This tool is an implementation of the abundance_index function from `RegionalGAM package:

This function compute the Abundance Index across sites and years from your dataset and the regional flight curve.

        <citation type="doi">10.1111/1365-2664.12561</citation>