sample_calcomp {ss3sim}

Sample conditional age-at-length (CAL) data and write to file for use by the EM.

Description

Sample conditional age-at-length (CAL) data and write to file for use by the EM.

Usage

sample_calcomp(dat_list, outfile = NULL, fleets = c(1, 2), years,
  Nsamp)

Arguments

dat_list

An SS data list object as read in from SS_readdat in the r4ss package. Make sure you select option section=2.

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.

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.

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.

Nsamp

*A numeric list of the same length as fleets. Either single values or vectors of the same length as the number of years can be passed through. Single values are repeated for all years. If no fleet collected samples, keep the value to Nsamp=NULL.

Details

Take a data.SS_new file containing expected values and sample from true lengths, using length comp sample sizes, to get realistic sample sizes for age bins given a length. Only the multinomial distribution is currently implemented. xIf no fish are sampled then that row is discarded. A value of NULL for fleets indicates to delete the data so the EM If used with run_ss3sim the case file should be named calcomp.

Value

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

Which arguments to specifiy in case files

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.

Note

This function is only reliable when using multinomial length compositions for the matching fleet. The real-valued length compositions resulting from the Dirichlet distribution cause difficulties in the sampling code. See the vignette for more.

Author(s)

Cole Monnahan, Kotaro Ono

See Also

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