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