format_input: TMB input formatting
In merrillrudd/LIME: Length-based Integrated Mixed Effects (LIME) assessment method

Description Usage Arguments Value Author(s)

format_input Formats data, parameters, random effects, and mapped parameters for TMB input

format_input(
  input,
  data_avail,
  Fpen,
  SigRpen,
  SigRprior,
  LFdist,
  C_type,
  est_more,
  fix_more,
  est_F_ft,
  f_startval_ft,
  rdev_startval_t,
  est_selex_f,
  vals_selex_ft,
  est_rdev_t,
  mirror,
  est_totalF,
  prop_f
)

`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
`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
`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