change_data: Change the data that is available as output from an SS...
In ss3sim: Fisheries Stock Assessment Simulation Testing with Stock Synthesis

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

change_data alters the data structure for a data list as read in by SS_readdat, for use in preparing the data file for an SS operating model. Original data is removed and dummy data is added, as specified, to the SS .dat file. This causes SS to produce expected values (OM "truth") when the operating model is run, from which data can be sampled. For each data type altered, change_data will add data for the fleets and years given; potentially adding many rows of redundant data. Currently, .dat files with multiple sexes cannot be manipulated with change_data. calculate_data_units is used internally in ss3sim_base to create a superset of fleets and years from sample arguments, and clean_data to strip out unused data after change_data is called (see examples below). change_data is called internally automatically, but can also be used by an ss3sim user to manipulate data as a case, or to prepare a new OM for use in a simulation. See the vignette for more details.

change_data(dat_list, outfile = NULL, fleets, years, types,
  age_bins = NULL, len_bins = NULL, pop_binwidth = NULL,
  pop_minimum_size = NULL, pop_maximum_size = NULL,
  lcomp_constant = NULL, tail_compression = NULL, nsex = 1)

`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 numeric vector of fleets
`years`	A numeric vector of years
`types`	A vector that can take combinations of the following entries: `"index"`, `"len"`, `"age"`, `"cal"`, `"mla"`. `types` controls what data structures the function acts on, with `"index"` changing indices/CPUE, `"len"` augmenting the length composition data, `"age"` augmenting the age composition, `"cal"` augmenting the conditional age at length, and `"mla"` augmenting the mean length at age data.
`age_bins`	*A numeric vector of age bins to use. If left as `NULL` then the age bin structure will be taken from the OM.
`len_bins`	*A numeric vector of length bins to use. If left as `NULL` then the length bin structure will be taken from the OM. For conditional age-at-length (CAAL) data, the last value provided to `len_bins` will be used for Lbin_lo and -1 will be used for Lbin_hi for the largest length bin category, i.e., row of CAAL data.
`pop_binwidth`	*Population length bin width. Note that this value must be smaller than the bin width specified in length composition data `len_bins` or SS will fail (see notes in the SS manual).
`pop_minimum_size`	*Population minimum length bin value.
`pop_maximum_size`	*Population maximum length bin value.
`lcomp_constant`	*A new robustification constant for length composition data to be used. Must be a numeric value, as a proportion. For example 0.1 means 10 percent. See the SS manual for further information. A `NULL` value indicates no action resulting in using the current value, and a value of 0 will throw an error since that leads to an error when zeroes exist in the data. Instead use a very small value like `1e-07`.
`tail_compression`	*A new tail compression value to be used in SS. Must be a numeric value, as a proportion. For example 0.1 means 10 percent. See the SS manual for further information. A `NULL` value indicates no action, a negative value indicates to SS to ignore it (not use that feature).
`nsex`	An integer value of 1 or 2 specifying the number of sexes in the model. If 1, then females are the only included sex. This information can be found in the data file for a given model and dictates how the composition data are structured.

The robustification constant is added to both the observed and expected proportions of length composition data, before being normalized internally. It is designed to help stabilize the model, but is unclear how and when to use it for optimal effect. The same value is used for all length data.

An invisible data list, and a file is written to the disk if an entry other than NULL is provided for outfile.

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, Ian Taylor, Sean Anderson, Kelli Johnson

sample_lcomp, sample_agecomp

Other change functions: change_em_binning, change_e, change_f_par, change_f, change_o, change_retro, change_tv

d <- system.file("extdata", package = "ss3sim")
fleets <- 1:2
years <- c(5, 10, 15)
types <- c("len", "age")
file_in <- r4ss::SS_readdat(file.path(d, "models", "cod-om", "codOM.dat"),
  version = NULL, verbose = FALSE)

# Basic test with just length data, default bins:
out <- change_data(file_in, outfile = NULL, types = "len",
  years = years, fleets = fleets)
print(out$lbin_vector)
print(out$lencomp)

# Change the length bins:
out <- change_data(file_in, outfile = NULL, types = "len",
  years = years, fleets = fleets, len_bins = 3:6)
out$lbin_vector
out$lencomp

# Change the population length bins:
out <- change_data(file_in, outfile = NULL, types = "len",
  years = years, fleets = fleets, pop_binwidth = 1, pop_minimum_size = 5,
  pop_maximum_size = 210)
out$binwidth
out$maximum_size
out$minimum_size