The goal of species.shifts is to consolidate a variety of federal data
sets commonly used by the Gulf of Maine Research
Institute in Portland, Maine. Many of the data
sets support collaborations with the New England, Mid-Atlantic, and
South Atlantic Fisheries Management Councils. This package pulls,
cleans, and analyzes these data sets from a pre-existing data
repository. Many of these data sets are confidential and/or require an
explicit data request from the relevant bodies. Given data acquisition,
it is recommended to store all data in a central repository for ease of
access within the R functions.
There are a set of functions within this package to pull, clean, and
plot federal fisheries data. Any pull_() function will read in and
clean the data from the corresponding data set.
species_list() contains a list of species that are of interest to the
Mid-Atlantic Fisheries Management Council. It
contains how these species are named in each particular data set and a
clean_name, which is the same across all data sets. If species need to
be added or removed before subsequent analyses, please amend this
function as needed.
All functions that begin with map_() or plot_() will filter to the
species of interest, so long as they are included in the species list.
The pull_() function for that particular data set will need to be run
prior to any plotting function.
In development: indicators() will analyze and return a specific set
of species distribution shift indicators for a particular species or set
of species.
All three groups of functions will ultimately yield the materials needed to generate a summary report, describing the patterns of distribution as described across the federal fishery dependent and independent data sets.
NOAA Fisheries Vessel Trip Reports
NEFSC Spring-Fall Bottom Trawl Survey
GARFO Dealer Reported Landings
NOAA Fisheries Marine Recreational Information Program
You can install the development version from GitHub with:
pak::pak("carlylovas/species.shifts")Accessing and cleaning federal fisheries data
Plotting federal fisheries data