make_survdat_occu: make SURVDAT tidy occupancy dataset

View source: R/nefsc_groundfish_access.R

make_survdat_occuR Documentation

make SURVDAT tidy occupancy dataset

Description

make a tidy occupancy dataset from the cleaned SURVDAT dataset, where each row represents a unique tow - species - occupancy record for every species in species_keep. In creating this occupancy dataset, we take the total biomass or abundance across sex/sizes and impute "absence" observations, such that there is a record for every species in 'species_keep' at every unique tow.

Usage

make_survdat_occu(survdat_clean, species_keep)

Arguments

survdat_clean

Survdat data, after usual preparations are completed. These include removal of old strata, labeling of areas of interest, and inclusion of the annual effort in each.

species_keep

Vector of character species names or vector of numeric species codes to filter SURVDAT['comname'] (if character), or SURVDAT['svspp'] (if numeric)

Value

tidy occupancy dataframe containing one row for every unique tow-species

Examples

# not run
# make_survdat_occu(survdat_clean = survdat_clean, species_keep = c("atlantic cod", "offshore hake"))

gulfofmaine/gmRi documentation built on Jan. 26, 2025, 5:12 a.m.