Fit retrospective peels and add them to the fitted model object

Function to add fitted retrospective peels to fitted model returned by fit_wham. Calls retro. to fit the model peeling off 1, 2, ..., n.peels years of data. This is just a wrapper for retro that instead of returning just the list of peels, returns the fitted model with the peels.

do_retro_peels(
  model,
  n.peels = 7,
  ran = NULL,
  use.mle = TRUE,
  do.sdrep = FALSE,
  n.newton = 0,
  MakeADFun.silent = FALSE,
  retro.silent = FALSE,
  save.input = FALSE,
  do.brps = FALSE,
  check.version = TRUE
)

Arguments

model

Optimized TMB model, output from fit_tmb.

n.peels

Integer, number of peels to use in retrospective analysis. Default = 7.

ran

Character, specifies which parameters to treat as random effects. Default = "model$input$random".

use.mle

T/F, use MLEs from full model fit as initial values for each peel? If not, the initial values from full model input are used. Default = TRUE.

do.sdrep

T/F, calculate standard deviations of model parameters for each peel? Default = FALSE.

n.newton

integer, number of additional Newton steps after optimization for each peel. Default = 0.

MakeADFun.silent

T/F, Passed to silent argument of TMB::MakeADFun. Default = FALSE.

retro.silent

T/F, Passed to argument of internal fit_peel function. Determines whether peel number is printed to screen. Default = FALSE.

save.input

T/F, should modified input list be saved for every peel? Necessary to project from a peel but increases model object size. Default = FALSE.

do.brps

T/F, calculate and report biological reference points

check.version

T/F, whether to verify the wham package commit and version for the fitted model are the same as the currently used package.

Value

peels, a list of length n.peels, where entry i is a model fit by peeling off i years of data.

See also

fit_wham, retro, fit_peel