README.md

In cfree14/wcfish: West Coast fisheries data

wcfish: U.S. West Coast fisheries data

Installation

The "wcfish" R package can be installed from GitHub with:

# Run if you don't already have devtools installed
install.packages("devtools")

# Run once devtools is successfully installed
devtools::install_github("cfree14/wcfish", force=T)
library(wcfish)

Alternatively, you can download the datasets included in this package as Excel files from the Dryad open-access data repository here: https://datadryad.org/stash/dataset/doi:10.25349/D9M907

Datasets

The package includes the following West Coast fisheries datasets (listed below):

Coastwide datasets - West Coast commercial fisheries species: ?taxa - West Coast commercial fishing ports: ?ports - West Coast commercial fishing blocks shapefile: ?blocks

California (CDFW) spatial datasets - California marine protected areas (MPAs) shapefile: ?mpas_ca

California (CDFW) fisheries datasets - Annual commercial landings by source and species: ?cdfw_waters - Annual commercial landings by port and species: ?cdfw_ports - Annual number of licensed commercial fishers by area of residence: ?cdfw_n_comm_fishers - Annual number of registered commercial fishing vessels by length class: ?cdfw_n_comm_vessels_length - Annual number of registered commercial fishing vessels by port complex: ?cdfw_n_comm_vessels_port - Annual number of registered commercial fishing vessels: ?cdfw_n_comm_vessels - Annual CPFV landings by species: ?cdfw_cpfv - Annual CPFV landings by port complex and species: ?cdfw_cpfv_port - Annual CPFV participation and effort by port complex and species: ?cdfw_cpfv_effort - Annual kelp harvest by bed type: ?cdfw_kelp - Annual kelp harvest overall: ?cdfw_kelp_tots

PACFIN datasets - Species meta-data: ?pacfin_species - Ports and port complexes meta-data: ?pacfin_ports - Annual commercial landings by state (CA/OR/WA) and species: ?pacfin_all1 - Annual commercial landings by state (CA/OR/WA), gear, and species: ?pacfin_all2 - Annual commercial landings by state (CA/OR/WA), port complex, and species: ?pacfin_all5 - Monthly commercial landings by state (CA/OR/WA) and species: ?pacfin_all6 - Monthly commercial Dungeness crab landings by state (CA/OR/WA) and port complex: ?pacfin_crab2

RECFIN datasets - Annual recreational mortality by state, water area, mode, trip type, and species: ?recfin_cte2 - Annual recreational mortality by state, mode, and species: ?recfin_cte3 - Weekly salmon mortality in OR and WA by sub-areas, trip type, and species: ?recfin_cte5 - Monthly salmon landings in CA by water area, mode, and species: ?recfin_cte7

Other West Coast fisheries datasets - Monthly commercial landings in CA by port complex and species from the SWFCC: ?swfsc - Annual commercial landings in CA by port complex, gear type, and species from the CALCOM: ?calcom

A dataset can be accessed and inspected as in the following example:

# See dataset metadata by typing a question mark and the dataset name
?wcfish::blocks

# Store the dataset in an object of your own choosing as follows:
blocks_sf <- wcfish::blocks

Functions

The package implements miscellaneous functions including functions to:

• Check spelling of common names: ?check_names
• Reverse the format of common names (e.g., "Crab, Dungeness" to "Dungeness crab"): ?reverse_names
• Convert common names to a common format (i.e., all to "regular" or "reverse" formats): ?convert_names
• Harmonize common names and scientific names: ?harmonize_names
• Extract the CDFW block id associated with a list of GPS coordinates:?block_from_gps

Vignette

A vignette illustrating the use of the wcfish R package is available here: https://chrismfree.com/wp-content/uploads/wcfish-vignette.html

Citation

Free CM, Vargas Poulsen C, Bellquist LF, Wassermann SN, Oken KL (2022) The CALFISH database: a century of California’s non-confidential fisheries landings and participation data. Ecological Informatics 69: 101599. https://doi.org/10.1016/j.ecoinf.2022.101599

cfree14/wcfish documentation built on July 20, 2024, 7:50 p.m.