bootstrap_index_fun_run: Computes Regional and Coastwide Bootstrapped Relative...

In pbs-assess/hookCompetition: An R package for estimating relative abundance indices from longline data using a censored likelihood approach

Computes Regional and Coastwide Bootstrapped Relative Abundance Indices See the vignette for details

Description

Computes Regional and Coastwide Bootstrapped Relative Abundance Indices See the vignette for details

Usage

bootstrap_index_fun_run(
  species,
  survey_boundaries,
  ICR_adjust = F,
  data,
  R = 1000,
  return = F,
  ncpus = 1,
  type = "perc",
  plot = T,
  preserve_inter_regional_differences = F
)

Arguments

species	a character of the species (linked to the variables 'N_it' in the dataframe)
survey_boundaries	a sf polygons object containing the survey boundary definitions
ICR_adjust	if FALSE/TRUE it computes a CPUE-based/instantaneous catch rate-adjusted index
data	a sf points object containing the IPHC data
R	specifies the number of bootstrap samples desired
return	when TRUE it returns the indices
ncpus	specifies the number of cores to use in parallel
type	specifies the type of bootstrap intervals to use (default percentile)
plot	when TRUE it returns the plot.
preserve_inter_regional_differences	if TRUE estimated inter-regional differences in mean abundance are shown at a cost of higher variance. Does not affect coastwide index.

pbs-assess/hookCompetition documentation built on April 27, 2023, 12:47 p.m.