species.shifts: Northeast US Species Distribution Change
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.
Work flow
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.
Featured Data Sets
NOAA Fisheries Vessel Trip Reports
NEFSC Spring-Fall Bottom Trawl Survey
Installation
You can install the development version from GitHub with:
devtools::install_github("https://github.com/carlylovas/species.shifts")