add_upr: Add column containing upper limit for censored poisson

In pbs-assess/gfsynopsis: Data Synopsis Reports for PBS Groundfish

Add column containing upper limit for censored poisson

Description

Add column containing upper limit for censored poisson

Usage

add_upr(
  dat,
  prop_removed_col,
  n_catch_col,
  n_hooks_col,
  pstar_col = "pstar",
  pstar = NULL
)

Arguments

dat	A data frame from prep_stitch_dat().
prop_removed_col	Name of the column containing the proportion of baits removed in each fishing event from any species. I.e., the proportion of hooks returning without bait for any reason.
n_catch_col	Name of the column containing the observed catch counts on each fishing event of the target species.
n_hooks_col	Name of the column containing the number of hooks retrieved on each fishing event.
pstar_col	Name of the column containing a single value between ⁠0 <= pstar <= 1⁠ specifying the breakdown point of observed catch counts as a result of hook competition. See get_pstar(), ⁠[sdmTMB::censored_poisson()]⁠
pstar	Optional. If pstar_col is not specified, pstar can be provided as a single value between 0 <= pstar <= 1' default = NULL.

Value

dat with a new column upr containing numeric vector of upper bound catch counts of the target species to improve convergence of the censored method. See the documentation in ⁠[sdmTMB::get_censored_upper()]⁠

pbs-assess/gfsynopsis documentation built on March 26, 2024, 7:30 p.m.