calc_iphc_ser_all: Calculate Series A, B, C and D from the IPHC data

In pbs-assess/gfiphc: Data Extraction and Analysis for Groundfish Data from the IPHC Longline Survey in BC

Calculate Series A, B, C and D from the IPHC data

Description

Calculate all four series for as many years as possible, including bootstrapped values. Series with no data are treated slightly different to each other (ser_C ends up as an empty tibble, which may cause problems down the road). Default is to only use standard stations.

Usage

calc_iphc_ser_all(set_counts, lat_cut_off = 50.6, only_standard = TRUE)

Arguments

set_counts	species-specific set-level counts from tidy_iphc_survey() or other.
lat_cut_off	cut off below which sets are excluded for Series A and B, default is that used in YYR 2014 assessment.
only_standard	only use the standard stations (default is TRUE); for first synopsis report all stations were indadvertently used for 2018 (see Issue 14).

Details

The four series are:

Series A: first 20 hooks from each skate, only north of WCVI

Series B: all hooks from each skate, only north of WCVI

Series C: all hooks from each skate, full coast

Series D: first 20 hooks from each skate, full coast

Value

list containing four tibbles, one for each survey (ser_A, ser_B, ser_C and ser_D). Each tibble has one row for each set in each year, with columns year, station, lat, lon, E_it (effective skate number), N_it (number of fish caught of the given species), C_it (catch rate of given species, as numbers per effective skate), E_it20, N_it20 and C_it20 are the same but considering the first 20 hooks of each skate only, usable (whether the set should be used, based on IPHC codes; note that some should not be used for geospatial analysis but are included here).

Examples

## Not run: 
yelloweye <- tidy_iphc_survey(
 get_iphc_hooks("yelloweye rockfish"),
 get_iphc_skates_info(),
 get_iphc_sets_info()
)
calc_iphc_ser_all(yelloweye)

## End(Not run)

pbs-assess/gfiphc documentation built on July 4, 2023, 1:13 p.m.