read_Data_hookcomp: Loads the IPHC catch count data for a species. It returns a...

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

Loads the IPHC catch count data for a species. It returns a list containing two entries: Reduced_data_sp is a SpatialPointsDataFrame containing all the set-level catch counts of the species specified (e.g. stored as a variable name 'N_it_yelloweye'). survey_boundaries are the survey boundaries projected into the same CRS as the Reduced_data_sp object.

Description

Loads the IPHC catch count data for a species. It returns a list containing two entries: Reduced_data_sp is a SpatialPointsDataFrame containing all the set-level catch counts of the species specified (e.g. stored as a variable name 'N_it_yelloweye'). survey_boundaries are the survey boundaries projected into the same CRS as the Reduced_data_sp object.

Usage

read_Data_hookcomp(
  species_vec = "yelloweye rockfish",
  at_PBS = F,
  simple_species_vec = "yelloweye",
  data_wd = "./",
  min_dist = 50,
  min_dist_to_boundary = 0,
  years_all_vec = c(1995, 1996, 2003:2012, 2014:2019),
  years_20_vec = c(1997:2002, 2013, 2020),
  survey_boundaries = NULL
)

Arguments

species_vec	is a character vector of the one or more species desired for modelling
at_PBS	is a logical flag determining if the user has access to the gf data. If FALSE, yelloweye rockfish must be the specified species.
simple_species_vec	is a character vector containing the desired shortened names of the species
data_wd	is a character vector stating the working directory where the rds files will be saved
min_dist	is a numeric stating the minimum distance (km) required for a temporary IPHC station to be from a permanent IPHC station to be included
min_dist_to_boundary	is a numeric stating the minimum distance (km) required for an IPHC station to be from the survey boundary
years_all_vec	is a numeric vector stating the years all hooks were enumerated
years_20_vec	is a numeric vector stating the years only 20 hooks were enumerated
survey_boundaries	is a sf polygons object containing user-specified survey boundaries for indices to be computed in. If NULL QCS, WCHG, WCVI, HS used. The data.frame *must* contain a factor variable 'Region' with levels equal to the names of the regions

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