create_lh_list: Create new life history list
In merrillrudd/LIME: Length-based Integrated Mixed Effects (LIME) assessment method

Description Usage Arguments Value Author(s)

create_lh_list Creates list of life history information

create_lh_list(
  vbk,
  linf,
  lwa,
  lwb,
  S50,
  M50,
  S95 = NULL,
  M95 = NULL,
  Sslope = NULL,
  Mslope = NULL,
  selex_input = "length",
  maturity_input = "length",
  selex_type = "logistic",
  dome_sd = NULL,
  binwidth = 1,
  t0 = -0.01,
  CVlen = 0.1,
  SigmaC = 0.001,
  SigmaI = 0.001,
  SigmaR = 0.737,
  SigmaF = 0.2,
  R0 = 1,
  h = 1,
  qcoef = 1e-05,
  M = NULL,
  AgeMax = NULL,
  Fequil = 0.5,
  Frate = 0.2,
  start_ages = 0,
  rho = 0,
  theta = 1,
  nseasons = 1,
  nfleets = 1
)

`vbk`	von Bertalanffy k Brody growth coefficient
`linf`	von Bertalanffy Linf asymptotic length
`lwa`	length-weight scaling parameter
`lwb`	length-weight allometric parameter
`S50`	starting value for age or length at 50 percent selectivity (will be estimated in LIME method) – can be vector for multiple fleets
`M50`	age or length at 50 percent maturity
`S95`	default=NULL for one-parameter logistic model; starting value for age or length at 95 percent selectivity – can be vector for multiple fleets
`M95`	default=NULL for one-parameter logistic model; age or length at 50 percent maturity
`Sslope`	default=NULL, option to specify slope of logistic curve for length-at-selectivity – can be vector for multiple fleets
`Mslope`	default=NULL option to specify slope of logistic curve for length-at-maturity
`selex_input`	specify whether argument S50 is an age or a length (default length)
`maturity_input`	specify whether argument M50 is an age or a length (default length)
`selex_type`	default="logistic" for 1-parameter logistic selex, alternate="dome" for dome-shaped selectivity and must specify dome-params LV and RV. – can be vector for multiple fleets
`dome_sd`	standard deviation of normal distribution to the right side of the fully selected age/length – can be vector for multiple fleets
`binwidth`	width of length bins (default = 1)
`t0`	theoretical age at length=0 (default = -0.01); avoid fixing to zero due to some issues with the first age/length bin
`CVlen`	CV of the growth curve (default = 0.1)
`SigmaC`	standard deviation - observation error of catch data (default = 0.2)
`SigmaI`	standard deviation - observation error of index data (default = 0.2)
`SigmaR`	standard deviation - process error for recruitment time series (default = 0.6 – starting value, will be estimated)
`SigmaF`	standard deviation - process error for fishing mortality time series (default = 0.3) – can be vector for multiple fleets
`R0`	equilibrium recruitment (default = 1); when no information on scale is available, will estimate relative deviations around equilibrium 1
`h`	steepness parameter (default = 1)
`qcoef`	starting value for catchability coefficient (when index data is available, default = 1e-5) – can be vector for multiple fleets
`M`	value for natural mortality if there has been a study (default = NULL, calculated internally from vbk)
`AgeMax`	option to specify maximum age; default=NULL will calculate as the age at which 1 percent of individuals are left in the unfished condition
`Fequil`	equilibrium fishing mortality rate (used for simulation; default=0.2) – can be vector for multiple fleets
`Frate`	parameter used to simulate fishing moratality time series (default=NULL) – can be vector for multiple fleets
`start_ages`	age to start (either 0 or 1; default = 0)
`rho`	first-order autocorrelation in recruitment residuals parameter, default=0 (recruitment not autocorrelated)
`theta`	dirichlet-multinomial parameter related to effective sample size. default to 10, will not be used if length frequency distribution LFdist is set to multinomial (0). Only used if distribution is dirichlet-multinomial (LFdist=1)
`nseasons`	specify number of sub-time periods per year; default=1 (instantaneous sampling)
`nfleets`	specify number of fleets - fleet-specific parameters can be length nfleets, or shared by specifying only one number