In-class Exercise:

Scenario

We will meet for lecture and walk to the Old Arboretum as a group on Monday, September 24, 2007.  Attendance is required and is necessary in order to complete the Distance sampling Lab.  During your lab session this week, we will use the Windows version of Program DISTANCE 4.1 to analyze line-transect and point-count data you collect during the arboretum exercise. These analyses will form the core of the 1st half of your homework assignment. 

Procedure overview

Upon arriving at the arboretum, we will split the class into 2 groups of approximately equal size.  You will notice that transect and point stations have been established for you in advance.  You will also notice that colored birds have been placed to represent different foraging guilds.  We will gather data on ground- and arboreal-foragers.  

Before beginning data collection, you will practice making ocular estimates of distance -- This will aid you in collecting accurate data.  When it is your turn, you will collect and record your own data while walking two 100m transect through the Arboretum study area.  You will also collect and record data from 2 point count stations (within 25m radius around your point).  Keep these data in original or spreadsheet form (transect or point count no., ground or foliage guild, distance to each bird detected). You will need your data in order to successfully complete the lab homework AND you will be required to hand in a copy of your data in the Appendix section of your exercise.  

Data collection

Pay close attention to the data collection demonstration.  Data collected at each bird sighting should include: 1)transect or station no., 2)an ocular estimate of the perpendicular distance (meters) from the transect to the bird or the radial distance to the bird from plot center and 3)location of the bird (i.e., ground bird or arboreal bird).  We will run through analysis procedures for your line transect and point count data during our In-Class lab session.  You will write up these analyses for the first half of your homework assignment.  The second half of the assignment will give you the opportunity to find and assess an actual case study from the literature in which distance sampling methods were employed.

Program Distance

 Your Data Set

Data Entry

1. Open program DISTANCE 4.1 under class software from the Programs menu.

    2. Start a new project (In the file drop-down menu).

    3. Name your project and select the appropriate directory (directory of your choice).

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

    5. Choose either line transect or point transect by clicking on the appropriate survey type. (You will enter both, but separately).

            a.     If you did a line transect then choose perpendicular distance.

    6. 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.

    7. Leave the ‘sampling fraction’ at 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.

    8. Enter the units that you measured your distances in (meters) and the units that you want your results to be presented in (meters).

    9. Enter the area units of your study area (square meters). Use 500m² for the line transect and 1962.5m² for the point count plot.

   10. Next you should see the ‘multipliers’ screen where you can correct for g(0) being less than 1 or for indirect surveys where single animals may leave multiple marks of their presence. Leave this screen the way it is and go on to the next one.

   11. Next you can select to use the ‘Data Entry Wizard’ or read the data from a file or return to DISTANCE. Use the ‘Data Entry Wizard’, and select FINISH.

   12. The ‘data entry wizard’ should open. Read the description carefully.

   13. Enter an appropriate label for your data in the ‘Study Area’ category, then click next.

   14. Create 2 rows corresponding to the 2 available stratum. Do this by clicking in the "Region" label cell to activate the tool bar and then clicking on ‘Insert New Record Before Current’ twice to create 2 rows. Label the 2 stratum appropriately (ground, arboreal) and put 500 in the area column indicating that each stratum area was 500 square meters. Select Next.

   15. Create the appropriate number of rows for the survey within each stratum. How many lines did you walk, or points did  you sample? Click on a cell to activate the tool bars to create additional records. Click on ‘Insert New Record Before Current’ to create a new line within a given stratum. Appropriately label each row of data and enter the corresponding length of each line (100 meters) under line length for line transect data. For point counts enter a 1 for survey effort, indicating that the entire point (360 degrees) was sampled. Click on Next.

    16.  Enter the appropriate distances for each line. One distance is entered for each ‘ID’ line. Thus, you need to build the appropriate number of observations cells for each point or line of your survey and duplicate this within each stratum. Click on the blank ‘ID’ box of the first line under ‘Observation Layer’. Click on ‘Insert New Record Before the Current’ to start creating observation lines. Continue to select this option until you have created an equivalent number of lines to the number of observations in your data set for the corresponding line, by stratum. Then enter the distance for each observation under the ‘Distance’ column. Follow this procedure for all additional lines and strata.

    17.  Select Next, read the following screen and then select Finish.

    18.  Now you have entered your data.

 

Data Analysis

1. DISTANCE is designed for interactive modeling of your data, you can run multiple models and compare the results using information criterion. To create, manage, and compare analyses we will use the ‘Analysis Browser.’ Click the ‘New Analysis’ button to begin.

    2.  Select ‘New 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 ‘New Model Definition’ and observe the options under each tab.

Estimate: Select ‘No stratification,’ and under ‘Quantities to Estimate’ make sure quantities are only checked in the global category. This estimates across strata instead of within strata.

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

    Model 1: Half-normal key with a cosine series expansion.
    Model 2: Uniform key with a simple polynomial series expansion.
    Model 3: Hazard-rate key with a hermite polynomial series expansion.

Select among models using AIC

    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 (T.A. will go through the results with you), 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

How good was your estimate? Think about potential problems with survey design and possible biases.

Data Entry

1. Start a new project and save it in the appropriate directory.
2. You should now be in the ‘Project Setup Wizard.’
3. Select line transect with perpendicular distances and single objects.
4. Select meters for all distances and area in square meters.
5. Do not use any multipliers.
6. Select ‘Proceed to Data Import Wizard’ and then select Finish.
7. Select the appropriate drive and select the file fkbird.txt.
8. Read the introductory screen and select next.
9. Select semicolon delimited data and click on next.
10. . 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 data layer and appropriate data type for each column. Select Next.
11. . Select ‘Append to Existing Data’ and click on Finish.
12. . Under view select ‘Data Explorer’ to view the data set.

 

Stratified Analysis Procedure

13. . Under view select ‘Analysis Browser.’
14. . Select ‘New Analysis.’
15. . Edit the ‘Data Filter.’
16. . Select ‘Intervals,’ create 5 intervals with cutpoints at 2, 5, 10, 15, and 20 meters. The "zero" cutpoint should start at "0", representing the line.
17. . Select ‘Truncation.’ Make sure it is set to discard all observations beyond 20 meters.
18. . Name the data filter.
19. . Select Ok.
20. . Create ‘New Model Definitions’ .
21. . By clicking on the "Detection Function" tab, create your model definitions.

    Model 1: half-normal key function with a cosine series expansion.
    Model 2: Uniform key function with a simple polynomial series expansion.
    Model 3: Hazard-rate key function with a hermite polynomial series expansion.

    22. In the ‘Estimate’ section select ‘Use Stratum Layer by Region’ and check the box under ‘Stratum’ in the ‘Level of Resolution of Estimates’ table. This will estimate density within strata.

Change the global density estimate to "Sum" of stratum estimates since strata represented different birds within the same area. Hint: you may want to use mean for the problem set when you are estimating bird densities across the town and combining estimates from 2 different areas. Think about what a sum or a mean would indicate for your estimate.

Name the Model and then select Ok.

• Name the analysis and select Ok.

23. View the results, observe the differences between this and the first analysis.

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 and also helps keep the histograms somewhat legible. Note: depending on what program you are using, you may have to highlight the text before selecting a new font type and size.

Return to Lab Notes

Revised: 18 September 2008