Chapter 19 Prevalence Estimator Data Export

19.1 What is the Prevalence Estimator Data Export?

The Prevalence Estimator Data Export summarizes sample data from the CWD Data Warehouse for use in the external SpeedGoat Estimator Tool. The SpeedGoat Estimator is an independent online tool used to estimate the underlying prevalence of CWD after sampling has occurred and no positive cases were detected.

19.2 What Questions Does it Answer?

Question 1. Can I use the CWD Data Warehouse with the SpeedGoat Estimation Tool? Yes. The Prevalence Estimator Data Export allows you to download data from the CWD Warehouse Data for immediate upload into the SpeedGoat Estimator tool. This way, managers using the CWD Data Warehouse do not need to reprocess their surveillance data to use another helpful CWD tool.

Question 2. When do I use the SpeedGoat Estimator Tool? The SpeedGoat Estimator tool is used after sampling has occurred when no positive cases were found to estimate the maximum possible prevalence of CWD in the age/sex segment of interest.

19.3 Output Details

19.3.1 Outputs in the CWD Data Warehouse:

The SpeedGoat_data.xlsx file, which is necessary for immediate upload into the external SpeedGoat Estimator tool.

19.3.2 Outputs in the Estimator Tool of the SpeedGoat software:

The upper bound of the credible interval, which indicates that the user can be 95% confident that the true prevalence of CWD is at or below that bound. The computation of that bound hinges on the sampling effort in your data and no CWD-confirmed results.

19.4 Abbreviated Tutorial

  1. Run the Prevalence Estimator Data Export to summarize and format sample data from the CWD Data Warehouse.
  2. If the selected data does not satisfy at least one prior in the SpeedGoat tool, then the execution log will tell you that the tool did not produce a file.
  3. If the selected data satisfies at least one prior in the SpeedGoat tool, then the Warehouse will produce a file called SpeedGoatOutputMatrix.xlsx.
  4. Whenever the tool produces the SpeedGoatOutputMatrix.xlsx file, download the file from the attachments column of the model execution page of the CWD Data Warehouse.
  5. Use your internet browser to access the external SpeedGoat software located at http://public.spdgt.com/app/wtsurv.
  6. Upload the SpeedGoatOutputMatrix.xlsx file using the batch estimation command in the SpeedGoat software.
  7. In the model setting section of the SpeedGoat Estimator tool, specify the species reflected in your data.
  8. Deploy the SpeedGoat Estimation tool.

19.5 Parameters Needed to Execute the Model

  • Model type: Select ‘Prevalence Estimator Data Export’ from the drop-down list.

  • Reference name: Label the run.

  • (Optional) Applicable season-year: Label the season-year of the run to assist in documentation.

  • (Optional) Notes: Enter any remarks about the run.

  • Species: Select the species of interest for estimation.

  • Season-year: Select the season-year to be used in the estimation. Please note that underlying prevalence can be estimated for only one season at a time.

19.6 Additional Details on the Theory

Heisey DM, Jennelle CS, Russell RE, Walsh DP. 2014. Using Auxiliary Information to Improve Wildlife Disease Surveillance When Infected Animals Are Not Detected: A Bayesian Approach. PLoS ONE 9(3): e89843. https://doi.org/10.1371/journal.pone.0089843