run_LIME: run LIME model - simulation mode
In merrillrudd/LIME: Length-based Integrated Mixed Effects (LIME) assessment method

Description Usage Arguments Value Author(s)

run_LIME run length-based integrated mixed-effects model with generated data

run_LIME(
  modpath,
  input,
  data_avail,
  Fpen = 1,
  SigRpen = 1,
  SigRprior = c(0.737, 0.3),
  LFdist = 1,
  C_type = 0,
  est_more = FALSE,
  fix_more = FALSE,
  est_F_ft = TRUE,
  f_startval_ft = NULL,
  rdev_startval_t = NULL,
  est_selex_f = TRUE,
  vals_selex_ft = -1,
  est_rdev_t = TRUE,
  newtonsteps = 3,
  F_up = 10,
  S50_up = NULL,
  derive_quants = FALSE,
  itervec = NULL,
  simulation = FALSE,
  rewrite = TRUE,
  mirror = NULL,
  est_totalF = FALSE,
  prop_f = 1
)

`modpath`	model directory
`input`	tagged list of LIME inputs. Output from create_inputs.
`data_avail`	types of data included, must at least include LCX where X is the number of years of length composition data. May also include "Catch" or "Index" separated by underscore. For example, "LC10", "Catch_LC1", "Index_Catch_LC20".
`Fpen`	penalty on fishing mortality 0= off, 1=on
`SigRpen`	penalty on sigmaR, 0=off, 1=on
`SigRprior`	vector with prior info for sigmaR penalty, first term is the mean and second term is the standard deviation
`LFdist`	likelihood distribution for length composition data, default=0 for multinomial, alternate=1 for dirichlet-multinomial
`C_type`	default=0, NO catch data available. Copt=1 means the catch is in numbers, Copt2 means the catch is in weight.
`est_more`	list of variance parameters to estimate, must match parameter names: log_sigma_R, log_sigma_C, log_sigma_I, log_CV_L, log_sigma_F
`fix_more`	default=FALSE - parameters are fixed depending on the data available. Can also list vector of parameter names to fix at their starting values (use param_adjust and val_adjust to set these adjustments)
`est_F_ft`	default=TRUE, otherwise 0 for off and 1 for on in matrix that matches fleets in rows and years in columns
`f_startval_ft`	default=NULL and F starting values are at 0 for all years. Can also specify vector of F starting values for all years to be modeled (can start at truth for debugging).
`rdev_startval_t`	default=NULL and Recruitment deviation starting values are at 0 for all years. Can also specify vector of recruitment deviation starting values for all years to be modeled (can start at truth for debugging)
`est_selex_f`	default=TRUE to estimate selectivity parameters, can set to FALSE for all or multiple fleets
`vals_selex_ft`	input selectivity-at-length (columns) by fleet (rows) - negative values in the first column indicate to estimate selectivity
`est_rdev_t`	default=TRUE to estimate recruitment deviations, or specify vector with 0 to turn off deviations in a specific year and 1 to keep them on
`newtonsteps`	number of extra newton steps to take after optimization; FALSE to turn off
`F_up`	upper bound of fishing mortality estimate; default=10
`S50_up`	upper bound of length at 50 percent selectivity; default=NULL
`derive_quants`	if TRUE, derive MSY-related reference points, default=FALSE
`itervec`	number of datasets to generate in a simulation study. default=NULL for real stock assessment application.
`simulation`	is this a simulation? default FALSE means you are using real data (can set itervec=NULL)
`rewrite`	default=TRUE; if results already exist in the directory, should we rewrite them? TRUE or FALSE
`mirror`	vector of parameter names to mirror between fleets
`est_totalF`	TRUE estimate total F instead of by fleet
`prop_f`	proportion of catch from each fleet