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adopting for new surveys

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Jin Gao edited this page Mar 9, 2016 · 5 revisions

The geostatistical index standardization model, and the software to implement it on this GitHub repository, are designed to be (relatively) easy to adapt for other fishery surveys in other regions (besides the U.S. West Coast shelf-slope bottom trawl survey, for which it was originally designed).

However, there are several necessary steps to adapt this tool to a new survey:

  1. Please read the glossary to understand the terminology used in the software and wiki.

  2. Obtain necessary data. Please read Data for new regions for details

  3. Figure out how to modify "Data_Fn" to generate the tagged-list of data inputs for TMB.

*Variables ending in "_i" (i.e., a_i, b_i, v_i, s_i, and t_i) are necessary for every observation i in your survey.

*Variables involving "_x" (i.e., a_xl, X_xj) are necessary for each polygon that is used to encompass the domain of your survey. One way to calculate these values is to make a high-resolution grid covering your survey domain, i.e., replacing extrapolation_data with a similar grid built for your region. This grid is then pre-processed to calculate a_xl as shown in the West Coast example West Coast example using Data_Set="Canary"

  1. Given that you've correctly run "Data_Fn" with new inputs from your survey, the rest of the code run similar to the West Coast example. Please report any exceptions on the Wiki tool tracker.

  2. After running, please check model diagnostics following recommendations in the West Coast best-practices guide

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