SC: Conditional Age-At-Length ISS

The following describes the workflow to obtain conditional-age-at length (CAAL) input sample size (ISS) for data provided by AFSC bottom trawl surveys. Please see the ‘Getting started’ vignette for installing and loading the surveyISS package, as well as querying data. To obtain CAAL ISS you will follow the same steps outlined in the ‘Getting started’ vignette from Step 1 through Step 4, here we provide instructions on how to run the CAAL function to obtain ISS that would be conducted in Step 5.

The primary difference when running the surveyISS::srvy_iss_caal() as compared to the surveyISS::srvy_iss() function is fewer arguments that need to be defined (as length frequency data is not being expanded to population numbers at length). To obtain standard, 1 cm length bin CAAL ISS, the following is provided as an example for GOA stocks:

surveyISS::srvy_iss_caal(iters = 10, 
                         specimen_data = data$specimen, 
                         cpue_data = data$cpue, 
                         yrs = 1990,
                         boot_hauls = TRUE, 
                         boot_ages = TRUE,
                         al_var = TRUE, 
                         al_var_ann = TRUE, 
                         age_err = TRUE,
                         region = 'goa', 
                         save = 'test')

As with the other functions included in the surveyISS package there are several additional arguments that can be included, and we refer you to the package R documentation for the surveyISS::srvy_iss_caal() function. The output of the surveyISS::srvy_iss_caal() function is in many ways similar to the output provided by the standard surveyISS::srvy_iss() function, with several nuanced differences. First, there will only be one output file for CAAL ISS, and will be denoted by caal at the end of the file name. The start of the file name will be whatever you have defined the save argument in the function. And second, within the CAAL ISS output file there will be an additional column named length that will denote for which length bin the computed ISS is provided. All the other columns will be the same as the surveyISS::srvy_iss() function (including the sex category identification and descriptions), and note that the nss and nhl columns denote the sample size and number of sampled hauls for that year-species_code-sex-length bin combination.