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).
- Click menu 'File'
- Click menu item 'New Project'
A dialog box will appear asking for a title, filename, number of sites,etc.
Click the 'Input Data Form' button.
- Start spreadsheet program
- load the sample data file named 'Blue_Ridge_pg99.csv'
- Select all cells ('Cntl-A')
- copy to the clipboard ('Cntl-C' or use edit menu)
- return to program PRESENCE and click in the first cell of the input
data form (site 1, 1-1)
- Click menu 'Edit'
- Click menu item 'Paste'
- Click menu item 'paste values'
- Save the input
- click menu 'File'
- click menu item 'Save as'
- name the file 'Blue_Ridge_pg99.pao'
- click 'Save' in the dialog box
- Close the Input Data Form window by clicking the X in the upper right corner or
clicking 'File/Close'
- 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' button
You're now presented with a 'Results Browser' window where a summary of each
model will be saved.
Run first model
- click menu 'Run'
- click menu item 'Run Analysis:single-season'
- 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.
View the estimates from this model
- Click on the model name '1 group, Constant P' with the right mouse button
- 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'.