barrierALK: Barrier ALK, fit a barrier ALK model to age-growth data to...

In jgbabyn/barrierALK: Age-Length Keys with physical barriers

Description

Fit smooth age-length keys with the possibility of incorporating spatial error terms represented by approximations of Guassian Fields using SPDEs

Usage

barrierALK(
  formula,
  minAge,
  maxAge,
  lengthVar = "length",
  equalSlopes = FALSE,
  data = NULL,
  silent = TRUE,
  runSA = TRUE,
  control = NULL,
  ...,
  optMethod = "nlminb",
  cores = parallel::detectCores(),
  lambda = 0,
  penalty.matrix = NULL,
  penalize.hyper = FALSE,
  starting.param = NULL,
  scale = FALSE,
  edf.calc = TRUE
)

Arguments

formula	formula for the barrier alk fit
lengthVar	the name of the length variable in the data
equalSlopes	TRUE or FALSE for equal slopes assumption, or formla specifiying which are
data	optionally data frame containing data
silent	whether to run the trace from TMB
runSA	Apply Symbolic Analysis from TMB package in effort to up model
control	control options for optimr optimizer
optMethod	the optimizer within optimr to use
lambda	the value or vector for penalization factors, default is 0, no penalization
penalty.matrix	manually set the penalty matrix to use
penalize.hyper	penalize the hyper parameters for the gf approximations?
starting.param	named list to replace default starting parameter values with

jgbabyn/barrierALK documentation built on Dec. 20, 2021, 11:09 p.m.