Run sraplus

The main function for taking an object created by format_driors and fitting a model using sraplus

fit_sraplus(
  driors,
  include_fit = TRUE,
  seed = 42,
  plim = 0.05,
  model_name = "sraplus_tmb",
  randos = "log_proc_errors",
  draws = 1e+05,
  n_keep = 2000,
  engine = "sir",
  cores = 4,
  chains = 1,
  cleanup = FALSE,
  max_treedepth = 10,
  adapt_delta = 0.8,
  estimate_shape = FALSE,
  estimate_qslope = FALSE,
  estimate_q = TRUE,
  estimate_proc_error = TRUE,
  estimate_initial_state = TRUE,
  estimate_k = TRUE,
  estimate_f = FALSE,
  learn_rate = 0.001,
  analytical_q = FALSE,
  use_baranov = TRUE,
  include_m = FALSE,
  ci = 0.89,
  try_again = FALSE,
  eps = 1e-06,
  max_time = Inf,
  eval.max = 200,
  iter.max = 150,
  rel.tol = 1e-10,
  loopnum = 1,
  newtonsteps = 1,
  tune_prior_predictive = TRUE,
  index_fit_tuner = "sir",
  refresh = 250,
  log_bias_correct = TRUE,
  workers = workers,
  thin_draws = FALSE,
  thin_rate = 0.5,
  ...
)

Arguments

driors	a list of driors passed from sraplus::format_driors
include_fit	logical indicating whether to return the fitted object
seed	seed for model runs
plim	cutoff (in units of B/K) for hockey stick PT function
model_name	the name of the sraplus TMB version to be run, defaults to "sraplus_tmb"
randos	random effects when passing to TMB
draws	the number of SIR samples to run
n_keep	the number of SIR samples to keep
engine	one of 'sir','stan', or 'tmb'
cores	number of cores for stan fits
chains	number of chains for stan fits
cleanup	logical indicating whether to remove the compiled TMB model after running
max_treedepth	max_treedepth for models fit using stan
adapt_delta	adap_delta for models fit using stan
estimate_shape	logical indicating whether to estimate the shape parameter of the Pella-Tomlinson model. If FALSE shape parameter is held at the initial value, either default or supplied
estimate_qslope	logical indicating whether to estimate a slope parameter for q in CPUE fitting. If FALSE q_slope is held at the initial value, either default or supplied. if TRUE, estimate_proc_error should be set to FALSE
estimate_proc_error	logical indicating whether to estimate process errors. If FALSE process errors are not included in the model
ci	confidence/credible interval range for summaries
...

Value

a fitted sraplus object