In-class Exercise Lab 9:

Program DISTANCE

For this exercise, we will use 'SnowshoeHare_DistanceData.xls' which can be found at S:\Courses\WLF448\Distance\.

Data Entry

1. Open program DISTANCE 5.0.  Click Start - UI Software - Programs - Analytical - Distance 5.0.

    2.    Start a new project (in the "File" drop-down menu).

    3.    Name your project and select a directory on your network drive or other media.

    4.    The "Project Setup Wizard" should appear.  Read the directions carefully and follow the step by step instructions for entering data.

    5.    Check the box next to "Analyze a survey that has been completed".  Click "Next".  Read the next screen and click "Next" again.

    6.    Note the options available to you for different transect types, etc. Choose "Line transect" by clicking on the appropriate survey type.  Choose "Single observer".  Choose "Perpendicular distance".  Choose "Single object".  We will estimate observations as single objects.  Selecting clusters would invoke a routine to estimate cluster size based on distances and related cluster sizes from your data set and inevitably multiply the average cluster size by the density estimate for groups to get the population density estimate.  Click "Next".

    7.    Enter the units in which distances (meters), transects (kilometers), and areas (km²) are measured.

    8.  Next you should see the ‘Multipliers’ screen.  Leave this screen the way it is, however, note that you can change the sampling fraction (currently 1), indicating that the entire line or point was sampled.  A smaller value would indicate only a portion of the line or point was sampled or could be seen.  You also may correct for g(0) being less than 1 or for indirect surveys where single animals may leave multiple marks of their presence.

Using the Import Data Wizard (as an alternative to manually entering data into DISTANCE):

1. Save SnowshoeHare_DistanceData.xls as a comma-delimited text file.  You will need to follow several steps to make this happen.  In excel save as a CSV file (comma delimited).  Then open this file in notepad, check formatting (something to get in the hang of for all datafiles in txt format), and save as a .txt file.  This is the file you will import using the data wizard.

2. Under 'Tools', select 'Import Data Wizard'.  Read the instructions and click "Next".

3. Select the appropriate drive and select 'rabbitfile.txt'.  (whatever you named your datafile)

4. The 'Data Destination' screen will appear.  Click "Next".

5. Select comma delimited data, do not import first row, and click "Next". 

6. Read the directions at the top of the screen BEFORE you begin. Identify the appropriate data file structure by clicking in the column headers and identifying the appropriate 'data layer', 'field name', and 'field type' for each column.  Click the box for columns in the same order as they appear on screen.  You will have manually enter field names for several layers.  You should end with a table similar to this:

   Layer Name:	Region	Region	Line Transect	Line Transect	Observation
   Field Name:	Stratum	Area	TransectNum	LineLength	Perp Distance
   Field Type:	Text	Decimal	Text	Decimal	Decimal

7. Click "Next", then click "Finish".

Data Analysis

1. DISTANCE is designed for interactive modeling of your data, you can run multiple models (i.e. different shapes for detectability functions) and compare the results using information criterion (i.e. AIC). To create, manage, and compare analyses we will use the ‘Analyses Browser." This is the 5th tab on the project browser window.  Click the ‘Show details of selected analysis’ button (3rd to the left of 'Analysis' to begin.

    2.  Select  the 'Properties' of the 'Data Filter’ and observe the options under each tab.

Data Selection: This allows you to work with only portions of your data set. We will use the entire data set.

Intervals: This allows you to transform your data set into intervals for analysis. This is appropriate for ocular distance estimates at large distances when realistically you could only estimate distances into intervals.

Truncation: This allows you to specify your sighting width by truncating at the largest observation distance, discarding a given percentage of the largest distances, or by discarding observations beyond a specified distance.

At the bottom of the screen you can change the name of the data filter to something meaningful to your analysis.

    3.  Then select Ok.

    4.  Select 'Properties' of ‘Model Definition’ and observe the options under each tab.

Estimate: We will do an analysis without stratification. If you want to stratify (as you will for the homework), make sure in Quantities to Estimate’ you check the boxes under 'Stratum' to get separate estimates for each stratum.

Detection Function: Click the (+) sign twice to add 2 more models

    Model 1: Uniform key with a simple polynomial series expansion.
    Model 2: Exponential key with a simple polynomial series expansion.
    Model 3: Half-normal key with a simple polynomial series expansion.

Select among models using AICc

    5. At the bottom of the screen, name the model you created

    6. Select Ok.

    7. Name your analysis.

    8. Select Run.

    9. The ‘Results’ screen should appear (we will go through the results), if this screen does not automatically appear, find it by clicking on "Analysis Details".

Options summary
Model Fitting
By detection function
Model selection
Parameter Estimates—based on selected model
Detection Probability Plot
Probability Density Function Plot
Chi-square goodness-of-fit test
Density Estimates
Estimation Summary

If you are going to use a word-processing program to view and edit your output (which I recommend), change the font type and font size to a Courier font of size ~8pt. This will help keep numbers in tables aligned.

Revised: 18 October 2011