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Stratified estimator for Ms.GSI

Source: R/stra_est.R
stratified_estimator_msgsi.Rd

Combine the stock group estimates of multiple mixtures (i.e., strata) weighted by harvest numbers or fishing efforts. Summary can be done by extracting the stock-specific total catch/harvest output from the model runs or by multiplying harvest (provided as input) by stock proportions. Reporting groups can stay in the same format or be reorganized by combining old reporting groups or reorganizing collections. See vignette for details.

Usage

stratified_estimator_msgsi(
  mdl_out = NULL,
  path = NULL,
  mixvec,
  new_pop_info = NULL,
  new_pop_by = "repunit",
  naive = FALSE,
  catchvec = NULL,
  cv = NULL
)

Arguments

mdl_out

Optional. Ms.GSI output object name for combining group proportions and harvest of a single mixture.

path

Where to find output from each mixture as a folder.

mixvec

Character vector of mixture sillies that are used to locate the folders where output .csv files lives, if mdl_out is not provided.

new_pop_info

Population information for the new grouping. A tibble with columns repunit and new_repunit. repunit is the names of the original reporting groups. Can include a column for collection if reorganizing using collections.

new_pop_by

Option to reorganize the reporting groups by "repunit" or "collection". Default is "repunit".

naive

TRUE if you want the summary done by the old way (stock-specific harvets = harvest * stock proportion), or you are using fishing effort instead of catch number.

catchvec

If naive = TRUE, manually input harvest or fishing effort means with the same order as mixvec.

cv

If naive = TRUE, manually input harvest or fishing effort cv's with the same order as mixvec.

Value

A tibble of proportions and harvest numbers by reporting group for combined mixtures/strata.

Examples

if (FALSE) { # \dontrun{
new_groups <- mdl_out$summ_comb %>% dplyr::select(group) %>%
 dplyr::mutate(new_repunit = c(rep("broad", 9), rep("regional", 3))) %>%
 dplyr::rename(repunit = group)

stratified_estimator_msgsi(path = "test", mixvec = c("m1", "m2", "m3"), new_pop_info = new_groups)
} # }