Software, source code, and data files for the analysis of site occupancy rates of anuran species.
Ecological Archives E083-041-S1.
Darryl I. MacKenzie
Department of Statistics
North Carolina State University
Proteus Research & Consulting Ltd.
PO Box 5193
software.zip -- contains software and FORTRAN source code**
data.zip -- contains data files for the anuran examples
**the random number generator and simplex algorithm are NOT included due to copyright restrictions. See below.
Below is a description of the zip files.
software.zip contains 9 files:
monitoring.exe is a compiled program that can be used to estimate the fraction of sites occupied by a species. Only simplistic models can be fit using this program. A more advanced, Windows-based program is currently under developement and should be available for download from the following sites from January 2002: http://www.proteus.co.nz or http://www.mbr-pwrc.usgs.gov/software .
Only the following models can be fit using monitoring.exe:
The logistic model is used for all covariates. Output contains estimates of model parameters, estimated total number of sites occupied and associated standard error. The standard error is estimated using the non-parametric bootstrap.
- constant presence and detection probabilities
- constant presence probability, time specific detection probabilities
- constant presence probability, detection probabilities function of time specific covariate
- presence probability function of site specific covariate, constant detection probabilities
- presence probability function of site specific covariate, time specific detection probabilities
- presence probability function of site specific covariate, detection probabilities function of time specific covariate
The *.for files contain the FORTRAN source code for monitoring.exe with the exception of 3 Numerical Recipes (http://www.nr.com ) algorithms that cannot be distibuted here due to copyright restrictions. The required NR algorithms are:
- ran1 - a random number generator
- amoeba - a downhill simplex algorithm used to maximize the likelihood
- amoebatry - used by amoeba
data.zip contains 7 files:
The 6 data files contain the anuran data in the correct format for monitoring.exe.
AmToad.txt and SpPeep.txt contain the detection/nondetection data for American toads and spring peepers respectively. The values are defined as:ATPonds.txt and SPPonds.txt contain the covariate indicating whether the monitored sites were distinct bodies of water (= 1.0) or otherwise (= 0.0).1 = species detected
0 = species not detected
- = missing value, no sampling was conducted.
ATTemp.txt and SPTemp.txt contain air temperature data for the sites at the time of sampling, which can be used as a detection probability covariate. Note '0.0' may denote a temperature of zero, or be a placeholder for occasions when no sampling occurred.
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