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SODA: A software tool to assist in the design of single-season occupancy studies
SODA is a tool developed to assist in the design of single-season occupancy studies. It provides automated searches for suitable designs and can evaluate the properties of specified designs. A key feature of SODA is that it uses simulation to investigate the small sample properties of maximum likelihood estimators, rather than relying on asymptotic approximations. The methodology is described in Ref [1] below.
SODA is written in Matlab and is currently available only for Microsoft Windows. For R users, we have provided a separate R function that simulates the basic single species occupancy model with given parameter values, assuming a given number of sampling sites and visits per site, and displays the results in tabular form and graphically. Comments at the start of the function explain usage. This function can be used to compare different designs 'manually', to mimic the automatic searches in the Matlab version.
SODA was written by Gurutzeta Guillera-Arroita, as part of her PhD in the Statistics group at Kent, supervised by Byron Morgan and myself.
Downloading the software
For the Matlab version, you should start by reading the user guide. The files that you need to download depend on whether or not you have Matlab on your machine.
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If you have Matlab installed on your machine
The files you need are in this zip file.
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If you DO NOT have Matlab installed on your machine
The files you need are in this zip file. However, you will also need to download and install the Matlab Compiler Runtime (MCR) tool, unless you already have the correct version (7.10) installed on your machine. Be warned that this is a VERY LARGE file (150Mb). Please consult these detailed instructions about what you need to do. For general information about this tool see the Matlab webpage.
Reference
[1] Guillera-Arroita, G., Ridout, M.S. and Morgan, B.J.T. (2010) Occupancy studies with imperfect detection: considerations for study design. Methods in Ecology and Evolution, 1, 131-139. [Paper]
