Species-Presence exercise 3 - Multi-season example

This exercise is designed to show how to run programs PRESENCE to compute species presence, detectability, extinction and colonization estimates from 'presence-absence' data which includes covariates.

Input data consists of 'detection-histories' of individuals at survey sites, a site covariate, and two sample covariates.

Running the program

Start program PRESENCE.

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 'Click to select file' button and find the file named 'housefinch.pao' in the sample_data folder, then click 'OK'.

You can view the data by clicking 'View/Data' from the menus. After viewing, close the data window, and click in the 'Title' box and enter 'Multi-season example (housefinch) from page 201'. 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:multi-season' from the menu-bar.

When the 'Setup Numerical Estimation Run' window appears, a design matrix window will appear. By default, a model with one parameter for occupancy (psi) will appear in the occupancy tab, and one parameter (column) will appear for all 5 p's. Also, one parameter will be estimated for extinction (eps), and one parameter for colonization(gam). Before running this model, change the name to 'psi(.),eps(.),gam(.),p(.)'. Click 'OK to Run' to run this model.

After the analysis is complete, click 'yes' to append the output to the results browser.

Next, let's run a model from the book. The top ('best') model {psi(d),gam(yr*d),eps(d),p(yr*d+f)}, has psi as a function of the 'distance-band' covariate, so we'll add a column to the occupancy design matrix (Edit/Add column), and put the covariate name in the last column (Init/*1000_Bands).

Colonization is a function of year times distance-band, so click the 'colonization' tab and add 9 more columns (Edit/Add Columns). To get the year effects, click 'Init/Full Identity' and to add the distance-band effects, click 'Init/*1000_bands'. Duplicate this value in the 2nd set of 5 columns in the matrix.

Next, click the 'extinction' tab and add 1 column and change the 2nd column to '*1000_bands'. Next, click the 'Detection' tab and add 12 more columns. Click 'Init/Seasonal effects' to get the year part of the model {p(yr*d+f)}. In the first row, 6th column, type '1000_Bands', then hit control-c. Then, click 'Edit/Copy down' and enter '49' to copy this value 49 more times. In the 51st row, click in the 7th column and hit control-v (to paste). Click 'Edit/copy down' and enter 49. Repeat this for columns 8-10. Go back to the top and click in the last column of the first row and click 'Init/*f'.

Go back to the 'Setup Numerical estimation run' window and change the model name to 'psi(d),gam(yr*d),eps(d),p(yr*d+f)' and click 'OK to run'. This will take a while (minutes) to run.