In BigelowLab/mpatools: mpatools - for analysis of marine protected areas

knitr::opts_chunk$set(echo = TRUE)

Tools for working with Marine Protected Areas to compute species diversity metrics using OBIS data.

Requirements

• R v4+

• rlang

• dplyr

• readr

• rappsdir

• wdpar

• sf

• vegan

• robis

Installation

remotes::install_github("BigelowLab/mpatools")

Usage

Polygons for MPAs

We use the wdpar R package to fetch MPAs by country (or 'global' for the complete dataset.) By default, we store the files you download in the path returned by rappdirs::user_data_dir("wdpar") in GeoPackage format. Once you have downloaded a dataset you can simply read the file from disk using read_mpa("name"). Below, we use the list_mpa() function to determine if we already have the Cuba dataset.

library(rappdirs)
library(sf)
library(mpatools)
country <- "Cuba"
if (has_mpa(country)){
  mpa <- read_mpa(name = country)
} else {
  mpa <- fetch_mpa(name = country)
}
# 
plot(sf::st_geometry(mpa))

OBIS occurrence data

Once you have MPA polygons in hand, it is easy to request OBIS records that fall within the polygons. We use the robis R package to fetch occurrence data. By default we store files you downlaod in the path returned by rappdirs::user_data_dir("robis") in GeoPackage. Once you have downloaded format you can simply read the file from disk using read_obis().

if (has_obis(country)){
  obis <- read_obis(name = country, form = "sf")
} else {
  obis <- fetch_obis_country(name = country)
}
head(obis)

We actually find occurrences that fall within the convex hull of a set of polygons, but you can enforce a stricter policy using the policy argument for fetch_obis(). See ?fetch_obis.

plot(sf::st_geometry(mpa))
plot(sf::st_geometry(obis), col = 'orange', pch = 16, add = TRUE)

Where are MPAs and OBIS data stored?

We use rappsdir R package to manage the stirage location. We store data here rappdirs::user_data_dir("wdpar") and here rappdirs::user_data_dir("robis"). This is a very effective way to store data per user. But if you want to store data at a system-wide location you can do that using the ubiquitous path argument.

BigelowLab/mpatools documentation built on Jan. 20, 2022, 3:46 p.m.