Lance B. McNew and Colleen M. Handel. 2015. Evaluating species richness: Biased ecological inference results from spatial heterogeneity in detection probabilities. Ecological Applications 25:16691680. http://dx.doi.org/10.1890/14-1248.1


Supplement

R code for (1) simulating 400 data sets of bird occurrence across three temporal replicates within a closed period at 50 survey sites for a community of 40 species of birds when species detection probabilities declined with the site covariate and averaged ~0.65 (scenario 3 in text) and (2) analyzing these data sets to evaluate four estimators of local species richness: raw species counts (nave richness), second order jackknife, Chao, and multi-species occupancy model.
Ecological Archives A025-102-S1.

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Author(s)

Lance B. McNew
Montana State University
Department of Animal and Range Sciences
Bozeman, MT, USA
E-mail: lance.mcnew@montana.edu

Colleen M. Handel
U.S. Geological Survey
Alaska Science Center
Anchorage, AK, USA
E-mail: cmhandel@usgs.gov


File list

Rscript_birds.R (MD5: 979c3596c47192f566cd9c65cfcce1d4)

Description

Rscript_birds.R: R code for (1) simulating 400 data sets of bird occurrence across three temporal replicates within a closed period at 50 survey sites for a community of 40 species of birds when species detection probabilities declined with the site covariate and averaged ~0.65 (scenario 3 in text) and (2) analyzing these data sets to evaluate four estimators of local species richness: raw species counts (naïve richness), second order jackknife, Chao, and multi-species occupancy model.

R code yields simulation and analyses of a single detection scenario (3) described in the manuscript.