| Focus 2.1 settings: Focusconfig.xml Example |
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The settings for Focus are controlled through the focusconfig.xml file; these may be changed by opening the file in a text editor such as WordPad. Upon doing so you are presented with code similar to that below:
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<!-- This is the configuration file for the FOCUS-2.0 program. Please refer to the user guide for parameter settings -->
<?xml version="1.0" encoding="UTF-8"?>
<Focus>
<Configuration>
<Number_Of_Iterations>1000</Number_Of_Iterations>
<Maximum_Plots_Per_Iteration>10
</Maximum_Plots_Per_Iteration>
<Report_Zero_Regressions>no</Report_Zero_Regressions>
<DuplicateSamples>
<Allow>no</Allow>
<Retrials>100</Retrials>
</DuplicateSamples>
<FunctionalStability>
<Enable>yes</Enable>
<Maximum_Order>5</Maximum_Order>
<Percentage_Of_Runs>50</Percentage_Of_Runs>
</FunctionalStability>
<Statistics>yes</Statistics>
<WritePlots>yes</WritePlots>
</Configuration>
<PlotSet>
<Type>Plot-Buffer</Type>
<InputFiles>
Plot-to-plot distances<Plot_Distances>
Distance_Matrix.csv</Plot_Distances>
Species response matrix<Predictor_Variables>
Predictor_Context_Variables.csv</Predictor_Variables>
Habitat at diff scales <Response_Variables>Response_Variables.csv
</Response_Variables>
</InputFiles>
<OutputFiles>
<BaseName>TestRun</BaseName>
<TimeStamp>no</TimeStamp>
</OutputFiles>
<Constraints>
<Distance>
<Value>20</Value>
List of spatial scales to use in analyses
<Value>40</Value>
<Value>60</Value>
</Distance>
<Multiplier>2</Multiplier>
<SampleType>outside</SampleType>
</Constraints>
</PlotSet>
</Focus>
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The text in blue indicates what some of the inputs are. User inputs are shown in red. Note that input files should be in csv format, and be located within the same directory as the Focus program. For more details on all the settings available and what they do please refer to the pdf User Guide. For more detailed background information please refer to the paper in BioScience by Holland, Bert and Fahrig.
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