canada_extract_samples_from_db: Extract the Canadian biological sample data

In pacific-hake/hake-assessment: Stock Assessment for Pacific Hake

Extract the Canadian biological sample data

Description

Extract the Canadian biological sample data from the GFBIOSQL database The data frame returned will be raw and unfiltered

Usage

canada_extract_samples_from_db(
  dr = "/srv/hake/other/samples",
  ret_df = FALSE,
  overwrite = FALSE,
  unsorted_only = FALSE,
  species_code = 225
)

Arguments

dr	The directory to save the samples RDS file in
ret_df	Logical. If TRUE, return the data frame from the function and do not write a csv file. If FALSE, write the csv file and return nothing
overwrite	Logical. Overwrite the RDS file for sample data if it exists
unsorted_only	Only include unsorted samples. For hake in Canada, this needs to be FALSE or some years will show no ages at all. See gfdata::get_commercial_samples() for additional information
species_code	The DFO Groundfish database species code; default: 225 (hake)

Value

If ret_df is TRUE, return the sample data frame. If ret_df is FALSE, return nothing, write an RDS file instead

pacific-hake/hake-assessment documentation built on July 21, 2024, 8:19 a.m.