sample_index: Sample the biomass with observation error
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 Examples

This function creates an index of abundance sampled from the expected available biomass for given fleets in given years. Let B_y be the biomass from the operating model for year y. Then the sampled value is calculated as: B_y*exp(rnorm(1, 0, sds_obs)-sds_obs^2/2). The second term adjusts the random samples so that their expected value is B_y (i.e. the log-normal bias correction). If used with run_ss3sim the case file should be named index. A suggested (default) case letter is D for data.

1 2	sample_index(dat_list, outfile = NULL, fleets, years, sds_obs, make_plot = FALSE)

`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`.
`sds_obs`	*A list the same length as `fleets`. The list should contain either single values or numeric vectors of the same length as the number of years which represent the standard deviation of the observation error. Single values are repeated for all years.
`make_plot`	A logical switch for whether to make a crude plot showing the results. Useful for testing and exploring the function.

A modified .dat file if !is.null(outfile). A list object containing the modified .dat 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, Kotaro Ono

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

## Not run: 
# Find the example data location:
d <- system.file("extdata", package = "ss3sim")
f_in <- file.path(d, "example-om", "ss3_expected_values.dat")
dat_list <- r4ss::SS_readdat(f_in, version = NULL, verbose = FALSE)
# Note the initial expected values for the index data:
dat_list$CPUE # Only has expected values for fleet 2 in every other year from
# 76 to 100, so can only sample from fleet 2 during every other year between
# 76 and 100
sam_yrs <- seq(76, 100, by = 2)
ex1 <- sample_index(dat_list,
                   outfile = NULL,
                   fleets = 2,
                   years = list(sam_yrs),
                   sds_obs=list(seq(.001, .1,
                     length.out = length(sam_yrs))))
ex1$CPUE
# could sample from less years, but not more:
ex2 <- sample_index(dat_list,
                    outfile = NULL,
                    fleets = 2,
                    years = list(sam_yrs[c(-1, -2)]),
                    sds_obs=list(seq(.001, .1,
                      length.out = length(sam_yrs[c(-1, -2)]))))
ex2$CPUE
# Also, sd can be fixed across years:
ex3 <- sample_index(dat_list,
                    outfile = NULL,
                    fleets = 2,
                    years = list(sam_yrs),
                    sds_obs=list(0.01))
ex3$CPUE
# If fleet 1 also had expected values in the index that you wanted to sample:
# ex4 <- sample_index(dat_list,
#                     outfile = NULL,
#                     fleets = c(1,2),
#                     years = list(sam_yrs, sam_yrs),
#                     sds_obs=list(0.01, 0.01))

## End(Not run)