Species-Presence exercise

This exercise is designed to show how to run programs PRESENCE to compute species presence and detectability estimates from 'presence-absence' data.

Input data consists of 'detection-histories' of individuals at survey sites.

Run program PRESENCE

The program is designed to look like program MARK (with the hope that it will not take long to learn how to use).

A dialog box will appear asking for a title, filename, number of sites,etc. Click the 'Input Data Form' button.

You're now presented with a 'Results Browser' window where a summary of each model will be saved.

Run first model

A summary window should appear showing the AIC value and number of parameters estimated for that model. Click 'OK' to make the program save the results to the Results Browser window.

View the estimates from this model

To run our second model, click 'Run/Analysis:single-season' from the menu-bar.

When the 'Setup Numerical Estimation Run' window appears, select '1-group, survey-specific P', then click 'OK to Run' to run this pre-defined model. A summary window should appear showing the AIC value and number of parameters estimated for that model. Click 'OK' to make the program save the results to the Results Browser window.

To view the estimates from this model, click on the model name with the right mouse button, then click 'view model output' using the left mouse button.

Now, let's run the last model using the design-matrix. Click 'Run/Analysis:Single-season', and click the 'Custom model' option. By default, occupancy (psi) is a constant, and detection is constant. To make detection probabilities survey-specific, click the 'Detection' tab, then click 'Initial/Full Identity'. Next, go back to the 'Setup Numerical Estimation Run' window and enter 'psi,p(t)' for the model name and click 'OK to run'.