Robert M. Dorazio, J. Andrew Royle, Bo Söderström, and Anders Glimskär. 2006. Estimating species richness and accumulation by modeling species occurrence and detectability. Ecology 87:842–854.

Supplement

R and WinBUGS code for fitting the model of species occurrence and detection and example data sets.
Ecological Archives E087-050-S1.

Copyright

Authors
File list (downloads)
Description

Author(s)

Robert M. Dorazio
USGS -- Florida Integrated Science Center
Department of Statistics
University of Florida
P.O. Box 110339
Gainesville, Florida 32611-0339
bdorazio@usgs.gov

J. Andrew Royle
USGS -- Patuxent Wildlife Research Center
12100 Beech Forest Road
Laural, Maryland 20708
aroyle@usgs.gov

Bo Soderstrom
Department of Conservation Biology
Swedish UNiversity of Agricultural Sciences
P. O. Box 7002
750 07 Uppsala, Sweden
bo.soderstrom@nvb.slu.se

Anders Glimskar
Department of Conservation Biology
Swedish UNiversity of Agricultural Sciences
P. O. Box 7002
750 07 Uppsala, Sweden
anders.glimskar@nvb.slu.se

File list

breedingBirdData.txt
butterflyData.txt
ExampleSession.txt
MultiSpeciesSiteOcc.R
MultiSpeciesSiteOccModel.txt
CumNumSpeciesPresent.R

Description

“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.

“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.

“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.

“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.

“MultiSpeciesSiteOccModel.txt” contains WinBUGS code for specifying the model of species occurrence and detection.

“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.