Darryl I. MacKenzie, James D. Nichols, Gideon B. Lachman, Sam Droege, J. Andrew Royle, and Catherine A. Langtimm. 2002. Estimating site occupancy rates when detection probabilities are less than one. Ecology 83:2248-2255.


Supplement

Software, source code, and data files for the analysis of site occupancy rates of anuran species.
Ecological Archives
E083-041-S1
.

Copyright


Authors
File list
Description
Download files


Author

Darryl I. MacKenzie
Department of Statistics
North Carolina State University

Present Address:
Proteus Research & Consulting Ltd.
PO Box 5193
Dunedin
NEW ZEALAND
Darryl@proteus.co.nz


File list

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.


Description

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.

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:

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:
1 = species detected
0 = species not detected
- = missing value, no sampling was conducted.
ATPonds.txt and SPPonds.txt contain the covariate indicating whether the monitored sites were distinct bodies of water (= 1.0) or otherwise (= 0.0).

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.


ESA Publications | Ecological Archives | Permissions | Citation | Contacts