path-global-health / pathtools

R package for cross-portfolio code and resources

PATHtools

The goal of PATHtools is to provide a common set of miscellanous R functions and assets that could be used by any R-based analytical work. This will allow us to share common resources, which will prevent duplicate coding and version-control issues.

This is a public repository, which means that there will never be private or protected data and/or code contained within this package.

Installation

The PATHtools package is hosted on Github and constantly under development. You can install the package like so:

install.packages("devtools")
devtools::install_github("PATH-Global-Health/PATHtools")

Examples

library(PATHtools)

# Shapefiles --------------------
# Check for available shapefiles
available_shapefile(country = "Senegal")
available_shapefile(admin_level = 2)

# Load shapefile
shp <- load_shapefile(country = "Nigeria", admin_level = 1)
plot(shp)

# Save GeoJSON file locally
load_shapefile(country = "Nigeria", admin_level = 1, download = TRUE)

Contributing

Requesting features

You can suggest new ideas or requests for features by opening an issue on Github. Please provide as much description and examples as possible, and link to external sources (if possible). We will use Issue to discuss developing new features, and document progress.

Providing new functions

Before starting a new contribution, please check the existing issues and open a new issue if needed. You can add new code to the package by creating a new fork and submitting a pull request (PR). Please reference the issue your PR is addressing, and run devtools::check() before submission.

pathtools's Issues

rgdal archived, updated installation instructions needed

rgdal was recently archived. Instructions for installing rgdal prior to PATHtools is needed.

Create README

Develop README which describes package purpose, installation, contributing, and licensing.

The `surface` argument of `getRaster()` is deprecated as of malariaAtlas 1.6.0.

Error in getRasterDatasetIdFromSurface(availableRasters, individual_surface) :
Surface with title Global friction surface enumerating land-based travel speed with access to motorized transport for a nominal year 2019 not found. Please use the dataset_id parameter instead anyway. As thes surface parameter will be removed in next version.
In addition: Warning message:
The surface argument of getRaster() is deprecated as of malariaAtlas 1.6.0.
ℹ The argument 'surface' has been deprecated. It will be removed in the next version. Please
use dataset_id to specify the raster instead.
ℹ The deprecated feature was likely used in the PATHtools package.

Create PATH palette objects

Use for plots, may also want to create ggplot-specific function (e.g., scale_fill_path())

Voronoi tesselations from points

Probably will be multiple functions depending on the feature set we aim to cover. I do think that we will want sf-focused output (at least as an option) since sp is in the process of depreciation.

Some features to consider:

• Input type (data.frame, sf/sp object)
• Bounding shapefile (options to restrict within polygons/fields from reference shapefile)

Function(s) for loading shapefiles from PATH geometries

Probably need individual functions for:

• Listing available files
• Downloading files (specify the location and file type?)
• Loading directly into R

Function to check which rainfall rasters are available

Need to write a function that looks in this repo https://data.chc.ucsb.edu/products/CHIRPS-2.0/global_daily/cogs/p05/ and check when the earliest and most recent surfaces are available.