Supplement 1. R and WinBUGS code for fitting the model of species occurrence and detection and example data sets.

<h2>File List</h2><blockquote> <p><a href="breedingBirdData.txt">breedingBirdData.txt</a><br> <a href="butterflyData.txt">butterflyData.txt</a><br> <a href="ExampleSession.txt">ExampleSession.txt</a><br> <a href="MultiSpeciesSiteOcc.R">MultiSpeciesSiteOcc.R</a><br> <a href="MultiSpeciesSiteOccModel.txt">MultiSpeciesSiteOccModel.txt</a><br> <a href="CumNumSpeciesPresent.R">CumNumSpeciesPresent.R</a></p> <p> </p> </blockquote><h2>Description</h2><blockquote> <p>“breedingBirdData.txt” is an example data set in ASCII comma-delimited format. Each row corresponds to data for a single species observed in the avian survey. The 50 columns correspond to 50 sample locations.</p> <p>“butterflyData.txt” is an example data set in ASCII comma-delimited format. Each row corresponds to data for a single species observed in the butterfly survey. The 20 columns correspond to 20 sample locations.</p> <p>“ExampleSession.txt” illustrates an example session in R where the butterfly data are read into memory and then analyzed using the R and WinBUGS code.</p> <p>“MultiSpeciesSiteOcc.R” defines an R function for fitting the model of species occurrence and detection to data. This function specifies a Gibbs sampler wherein 55000 random draws are computed for each of 4 different Markov chains. These computations may require nontrivial execution times. For example, analysis of the avian data required about 4 hours using a computer equipped with a 3.20 GHz Pentium 4 processor. Analysis of the butterfly data required about 1.5 hours.</p> <p>“MultiSpeciesSiteOccModel.txt” contains WinBUGS code for specifying the model of species occurrence and detection.</p> <p>“CumNumSpeciesPresent.R” defines an R function for computing a sample of the posterior-predictive distribution of a species-accumulation curve whose abscissa ranges from 1 to nsites sites.</p>