sample_wtatage: Sample empirical weight-at-age data and write to file for use...
In ss3sim: Fisheries Stock Assessment Simulation Testing with Stock Synthesis

Description Usage Arguments Value Which arguments to specifiy in case files Author(s) See Also

Take a data.SS_new file containing expected values and sample from true ages to get realistic proportions for the number of fish in each age bin, then use the mean size-at-age and CV for growth to generate random samples of size, which are then converted to weight and averaged to get mean weight-at-age values. Missing ages and years are filled according to a specified function. These matrices are then written to file for the EM. By calling this function, ss3sim will turn on the empirical weight-at-age function (set maturity option to 5) automatically. See ss3sim_base for more details on how that is implemented. If used with run_ss3sim the case file should be named wtatage.

1 2	sample_wtatage(wta_file_in, outfile, dat_list, ctl_file_in, years, fill_fnc = fill_across, fleets, cv_wtatage = NULL)

`wta_file_in`	The file to read weight-at-age from. Specifically to get the age-0 weight-at-age. This is typically `wtatage.ss_new`.
`outfile`	A character string specifying the file name to use when writing the information to the disk. The string must include the proper file extension. No file is written using the default value of `NULL`, which leads to increased speed because writing the file takes time and computing resources.
`dat_list`	An SS data list object as read in from `SS_readdat` in the r4ss package. Make sure you select option `section=2`.
`ctl_file_in`	A path to the control file, output from an OM, containing the OM parameters for growth and weight/length relationship. These values are used to determine the uncertainty about weight for fish sampled in each age bin. Commonly `control.ss_new`
`years`	*A list the same length as `fleets` giving the years as numeric vectors. If no fleet collected samples, keep the value to `years=NULL`.
`fill_fnc`	*A function to fill in missing values (ages and years). The resulting weight-at-age file will have values for all years and ages.One function is `fill_across`.
`fleets`	*A vector of integers specifying which fleets to include. The order of the fleets pertains to the input order of other arguments. An entry of `fleets=NULL` leads to zero samples for any fleet.
`cv_wtatage`	A user specified CV for growth. Default is `NULL`.

A modified .wtatage.ss file if !is.null(outfile). A list object containing the modified .wtatage.ss file is returned invisibly.

All function argument descriptions that start with an asterisk (*) will be passed through the case files to run_ss3sim. If one of these arguments is not specified in a case file, then a value of NULL will be passed, which may or may not be an appropriate value. Other arguments will be ignored if specified.

Cole Monnahan, Allan Hicks, Peter Kuriyama

fill_across

Other sampling functions: clean_data, sample_agecomp, sample_calcomp, sample_index, sample_lcomp, sample_mlacomp