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Test Diversity Example with only note widget
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‎Code Examples/Extensions Examples/sr/Diversity Example.nlogox‎

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<?xml version="1.0" encoding="utf-8"?>
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<model version="NetLogo 7.0.0" snapToGrid="false">
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<code><![CDATA[;; Diversity example of R-extension
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;;
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;;
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;; by Jan C. Thiele
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;; University of Goettingen, Germany
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;; Department Ecoinformatics, Biometrics and Forest Growth
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;; Buesgenweg 4
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;; 37077 Goettingen
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;; Germany
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;;
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;; Contact: jthiele@gwdg.de
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;;
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;; Copyright: 2011, J.C. Thiele
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;; Converted to run with the SimpleR-Extension
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extensions [sr]
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;; one patch equals a plot of 1 ha
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;; at each plot the number of trees will be counted
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;; trees are individuals/turtles
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breed [beeches beech]
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breed [birches birch]
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breed [hornbeams hornbeam]
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breed [oaks oak]
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breed [maples maple]
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breed [ashs ash]
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breed [poplars poplar]
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patches-own
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[
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beechcount
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birchcount
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hornbeamcount
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oakcount
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maplecount
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ashcount
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poplarcount
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speccount
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shannon
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simpson
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pielou
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]
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to setup
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clear-all
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;; reset the R-workspace
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sr:setup
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;; create the forest
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set-default-shape turtles "tree"
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create-beeches random 100
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[
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set xcor random-xcor
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set ycor random-ycor
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]
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create-birches random 100
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[
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set xcor random-xcor
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set ycor random-ycor
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]
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create-hornbeams random 100
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[
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set xcor random-xcor
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set ycor random-ycor
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]
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create-oaks random 100
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[
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set xcor random-xcor
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set ycor random-ycor
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]
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create-maples random 100
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[
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set xcor random-xcor
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set ycor random-ycor
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]
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create-ashs random 100
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[
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set xcor random-xcor
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set ycor random-ycor
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]
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create-poplars random 100
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[
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set xcor random-xcor
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set ycor random-ycor
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]
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let insp one-of patches with [count beeches-here > 0]
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;;inspect insp
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reset-ticks
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end
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to calc-diversity
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;; calculate the number of individuals of each species for each patch
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ask patches
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[
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set beechcount count beeches-here
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set birchcount count birches-here
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set hornbeamcount count hornbeams-here
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set oakcount count oaks-here
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set maplecount count maples-here
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set ashcount count ashs-here
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set poplarcount count poplars-here
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]
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;; assign a new data.frame with patch-variables (the patches will be asigned in lines from upper left to lower right)
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(sr:set-agent-data-frame "dfpatches" patches "pxcor" "pycor" "beechcount" "birchcount" "hornbeamcount" "oakcount" "maplecount" "ashcount" "poplarcount")
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;; create a data.frame without the coordinates
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sr:run "df <- dfpatches[,3:7]"
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;; load R-library vegan (must be installed!)
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sr:run "library(vegan)"
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;; calculate diversity
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sr:run "spec <- specnumber(df)"
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sr:run "shan <- diversity(df, 'shannon')"
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;; Pielou's evenness (J), if spec = 0, value of pielou will be NaN:
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sr:run "pielou <- shan/log(spec)"
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sr:run "simp <- diversity(df, 'simpson')"
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;; the following section is a little bit complicated
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;; it's done to save the calculated diversity values in the corresponding patch-variables
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;; to get just the diversity values as a list, call: print sr:runresult "shan"
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;; create lists with the coordinates
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let xlist sr:runresult "dfpatches$pxcor"
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let ylist sr:runresult "dfpatches$pycor"
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let xylist (map [ [?1 ?2] -> list ?1 ?2 ] xlist ylist)
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;; save the diversity value into the corresponding patch-variables
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let counter 1
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foreach xylist
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[ ?1 ->
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ask patch (item 0 ?1) (item 1 ?1)
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[
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set speccount (sr:runresult (word "spec[" counter "]"))
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set shannon (sr:runresult (word "shan[" counter "]"))
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set simpson (sr:runresult (word "simp[" counter "]"))
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set pielou (sr:runresult (word "pielou[" counter "]"))
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]
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set counter counter + 1
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]
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set-histogram-num-bars 20
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set-current-plot "pielou"
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histogram filter is-number? [pielou] of patches
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set-current-plot "speccount"
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histogram filter is-number? [speccount] of patches
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set-current-plot "shannon"
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histogram filter is-number? [shannon] of patches
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set-current-plot "simpson"
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histogram filter is-number? [simpson] of patches
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end
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to display-results
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set-current-plot "pielou"
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set-histogram-num-bars 25
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set-plot-pen-mode 1
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histogram filter is-number? [pielou] of patches
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set-current-plot "speccount"
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set-plot-pen-mode 1
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set-plot-x-range min filter is-number? [speccount] of patches max filter is-number? [speccount] of patches
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set-histogram-num-bars (max filter is-number? [speccount] of patches) - (min filter is-number? [speccount] of patches)
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histogram filter is-number? [speccount] of patches
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set-current-plot "shannon"
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set-plot-pen-mode 1
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set-histogram-num-bars 25
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histogram filter is-number? [shannon] of patches
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set-current-plot "simpson"
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set-plot-pen-mode 1
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set-histogram-num-bars 25
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histogram filter is-number? [simpson] of patches
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end
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; Public Domain:
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; To the extent possible under law, Uri Wilensky has waived all
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; copyright and related or neighboring rights to this model.]]></code>
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<code></code>
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<widgets>
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<view x="340" wrappingAllowedX="false" y="15" frameRate="30.0" minPycor="0" height="334" showTickCounter="true" patchSize="30.0" fontSize="10" wrappingAllowedY="false" width="334" tickCounterLabel="ticks" maxPycor="10" updateMode="1" maxPxcor="10" minPxcor="0"></view>
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<plot x="123" autoPlotX="true" yMax="10.0" autoPlotY="true" yAxis="count" y="218" xMin="0.0" height="150" legend="false" xMax="1.0" yMin="0.0" width="200" xAxis="shannon" display="shannon">
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<setup> set-histogram-num-bars 10</setup>
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<update></update>
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<pen interval="1.0" mode="0" display="default" color="-16777216" legend="true">
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<setup></setup>
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<update> histogram filter is-number? [shannon] of patches</update>
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</pen>
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</plot>
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<plot x="123" autoPlotX="true" yMax="10.0" autoPlotY="true" yAxis="count" y="372" xMin="0.0" height="150" legend="false" xMax="1.0" yMin="0.0" width="200" xAxis="simpson" display="simpson">
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<setup> set-histogram-num-bars 20</setup>
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<update></update>
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<pen interval="1.0" mode="0" display="default" color="-16777216" legend="true">
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<setup></setup>
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<update> histogram filter is-number? [simpson] of patches</update>
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</pen>
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</plot>
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<plot x="123" autoPlotX="true" yMax="1.0" autoPlotY="true" yAxis="count" y="64" xMin="0.0" height="150" legend="false" xMax="1.0" yMin="0.0" width="200" xAxis="pielou" display="pielou">
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<setup>set-histogram-num-bars 30</setup>
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<update></update>
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<pen interval="1.0" mode="0" display="default" color="-16777216" legend="true">
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<setup></setup>
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<update>histogram filter is-number? [pielou] of patches </update>
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</pen>
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</plot>
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<plot x="330" autoPlotX="true" yMax="10.0" autoPlotY="true" yAxis="count" y="372" xMin="0.0" height="150" legend="false" xMax="1.0" yMin="0.0" width="200" xAxis="speccount" display="speccount">
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<setup> set-histogram-num-bars 20</setup>
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<update></update>
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<pen interval="1.0" mode="0" display="default" color="-16777216" legend="true">
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<setup></setup>
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<update> histogram filter is-number? [speccount] of patches</update>
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</pen>
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</plot>
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<note x="26" y="19" backgroundDark="0" fontSize="17" width="304" markdown="false" height="34" textColorDark="-1" textColorLight="-2674135" backgroundLight="0">R-Package "vegan" has to be installed</note>
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<button x="28" y="64" height="35" disableUntilTicks="false" forever="false" kind="Observer" width="63">setup</button>
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<button x="27" y="105" height="35" disableUntilTicks="true" forever="false" kind="Observer" width="64" display="run">calc-diversity
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display-results</button>
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</widgets>
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<info><![CDATA[## WHAT IS IT?
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@@ -961,5 +739,5 @@ For more examples of the Simple R Extension, see the other example models in the
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</indicator>
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</shape>
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</linkShapes>
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<previewCommands>setup calc-diversity</previewCommands>
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<previewCommands>print "whee"</previewCommands>
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</model>

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