Pull data from databases for Pacific Hake

Extraction of

  • catch data,

  • weight measurements,

  • length measurements,

  • age reads, and

  • management quantities from NORPAC and PacFIN databases for the Pacific Hake assessment. Other, additional, databases may be added in the future through the database = argument.

pull_database(
  database = c("NORPAC", "PacFIN"),
  startyear = list(NORPAC = 2008, PacFIN = c(1980, 2008)),
  endyear = hakedata_year(),
  passwordfile = "password.txt",
  savedir = hakedata_wd()
)

Arguments

database

A vector of character strings indicating which databases you want to pull information from. Options include c("NORPAC", "PacFIN"), one or both (the default) can be specified. Note that case matters here.

startyear

An ordered list the same length as database with at least one integer entry per list item specifying the first year that you want data for. If only a single value per database is provided, then then the year will be recycled for catch and composition information. Otherwise, the first entry is the start year for catches and the second is the start year for the biological data. Names of the list must match entries in database or be NULL.

endyear

An integer value specifying the final year of data to include in the extraction. The default uses hakedata_year() to determine the terminal year.

passwordfile

A file path directing R to a file that contains a password for each database listed in database. Each password should be on its own line. The default case would place your NORPAC password on the first line and the second line would be your PacFIN password without quotes. If this argument is NULL, users will be prompted for their passwords. Passwords are needed because the databases store confidential data.

savedir

A full path to a directory where you want files saved. The default is to save them in a folder found using hakedata_wd(), which returns a path specific to the personal preferences of JTC members.

Value

An environment or list with several objects pulled from the NORPAC and PacFIN databases. Several Rdat files are saved to the disk in the extractedData folder, one file for each object and a summary file.

Details

pull_database() includes several steps, outlined below, and leads to many files being saved to your computer. Originally, files were NOT overwritten. In 2022, Kelli F. Johnson changed the code to not save previous downloads to save on disk space, reduce the storing of redundant information, and simplify the code base that needed maintenance.

  • Find the folder where the data should be saved with hakedata_wd().

  • Extract data from NORPAC.

    • Catch data

    • Weight and age data

    • Squash table of ages (that also includes lengths)

    • Foreign ages

    • Species list

  • Extract data from PacFIN.

    • Catch data

    • Age, length, and weight data from bds table

    • At-sea data

    • Management quantities such as allowable catch limits (ACL) for the Pacific Fisheries Management Council, i.e., U.S. quantities of interest.

  • Save each object to the disk in the "extractedData" directory in hakedata_wd().

Author

Kelli F. Johnson

Examples

if (FALSE) {
# An environment with objects is returned
dataenv <- pull_database()
# Access individual objects using `get()`
head(get("ncatch", envir = dataenv))
# Access individual objects pretending the environment is a list
dataenv[["ncatch"]][1:5, ]
}