gmri_survdat_prep: Tidy the Survdat Dataset

In gulfofmaine/gmRi: Utility Functions for GMRI Research Team

Tidy the Survdat Dataset

Description

Processing function to tidy/prepare the "survdat" groundfish survey dataset received from the Northeast Fisheries Science Center. This function performs all common steps done when preparing the data for any analyses that rely on abundance or biomass by species and the details of where/when they were caught.

This function will by default load the most up-to-date version of the dataset that has been received from the NEFSC using survdat = NULL. Optionally, users may provide a dataframe from the environment to be prepared using the same steps.

The processing steps performed by this function include:

- loading a specific survdat dataset: "most recent" loads the most current and complete dataset. "bigelow" returns data sampled only by the RV bigelow, in its raw form, with no adjustments to catch that transform numbers to be more consistent with the RV albatross. "bio" loads the biological dataset, which contains additional details that require follow-up lab procedures like age information

- Flag and create any columns that are missing or inconsistent with how the dataset has been sent over time. Messages will appear in the terminal to accompany any columns created or modified

- Perform column formatting: length and biomass are renamed to be unit specific length_cm & biomass_kg. Survey stratum numbers are pulled from the longer stratum field, these are used to match up to the fields of the shapefiles for them. comname values are converted to be all lowercase. The id field is formatted to not read as scientific, svspp is treated as a string.

- Perform row filtering: eliminate stratum that are no longer sampled or sampled inconsistently (values less than 01010 or greater than 01760 removed, in addition to 1310, 1320, 1330, 1350, 1410, 1420, & 1490). Any rows without abundance or biomass information are dropped. Select species codes are also removed (0, 285-299, 305, 306, 307, 316, 323, 910-915, 955-961, 978, 979, 980, 998)

- Perform spatial filters: Data is kept for all strata within these major regional definitions: "Georges Bank" = 13-23, "Gulf of Maine" = 24-40, "Southern New England" 01-12, "Mid-Atlantic Bight" = 61-76.

- Perform numlen (numbers at length) adjustment: numlen is not adjusted to correct for the change in survey vessels and gear that happened in 2008. These values consequently are not equal to the overall abundance of a species, nor total biomass of a species which are systematically adjusted to adjust for the gear change.

Because of this and also some instances of bad data, there are cases where more/less fishes are measured than initially tallied* in the abundance field. This section ensures that the numlen totals for a station & species are equal to abundance column (which has been adjusted already for the gear change.)

- Remove any duplicate records: One final step is the verification that any duplicated records are removed.

Usage

gmri_survdat_prep(
  survdat = NULL,
  survdat_source = "most recent",
  box_location = "root|cloudstorage"
)

Arguments

survdat	optional starting dataframe in the R environment to run through size spectra build.
survdat_source	String indicating which survdat file to load from box
box_location	String indicating value to pass to 'boxpath_switch'

Value

Returns a dataframe filtered and tidy-ed for size spectrum analysis.

Examples

# not run
# gmri_survdat_prep(survdat_source = "most recent")

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