README.Rmd

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output: github_document
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## species.shifts: Northeast US Species Distribution Change 
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The goal of `species.shifts` is to consolidate a variety of federal data sets commonly used by the [**Gulf of Maine Research Institute**](https://www.gmri.org/) 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.

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## 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](https://www.mafmc.org/). 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.

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  <img src="man/figures/package_data_flow.svg">
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## Featured Data Sets

[NOAA Fisheries Vessel Trip Reports](https://www.fisheries.noaa.gov/inport/item/11489)

[NEFSC Observer at Sea](https://www.fisheries.noaa.gov/inport/item/24111)

[NEFSC Spring-Fall Bottom Trawl Survey](https://www.fisheries.noaa.gov/inport/item/22557)

[GARFO Permits Data](https://apps-garfo.fisheries.noaa.gov/permits/)

[GARFO Dealer Reported Landings](https://www.fisheries.noaa.gov/contact/greater-atlantic-regional-fisheries-office)

[NOAA Fisheries Marine Recreational Information Program](https://www.fisheries.noaa.gov/insight/marine-recreational-information-program)

## Installation

You can install the development version from [GitHub](www.github.com) with:

``` r
pak::pak("carlylovas/species.shifts")
```

## Vignettes

[Accessing and cleaning federal fisheries data](https://carlylovas.github.io/species.shifts/articles/data_cleaning_functions.html)

[Plotting federal fisheries data](https://carlylovas.github.io/species.shifts/articles/plotting_functions.html)

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