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.
Click 'File/New Project' to start a new analysis. A dialog box will appear asking for a title, filename, number of sites,etc. Click the 'Input Data Form' button.
Now, start your spreadsheet program, and load the sample data file named 'Blue_Ridge_pg99.csv'. Select all cells ('Cntl-A'), and copy to the clipboard ('Edit'/'Copy').
Next, return to program PRESENCE and click in the first cell of the input data form (site 1, 1-1). Go to the 'Edit' menu, and click 'Paste', 'paste values'.
Save the input by clikcing 'File/Save as' and name the file 'Blue_Ridge_pg99.pao'. Close the Input Data Form window by clicking the X in the upper right corner or clicking 'File/Close'.
Next, click the 'Click to select file' button on the 'Enter Specifications' window. When the dialog box appears, select the file just created (Blue_Ridge_pg99.pao) and click 'Open'. Click in the 'Title' box and enter 'single-season example from page 99'. Click 'OK'.
You're now presented with a 'Results Browser' window where a summary of each model will be saved. To run our first model, click 'Run/Analysis:single-season' from the menu-bar.
When the 'Setup Numerical Estimation Run' window appears, click 'OK to Run' to run the default 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 '1 group, Constant P' with the right mouse button, then click 'view model output' using the left mouse button.
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'.