ehulland/travel-time-health-facilities-vhf-outbreak-preparedness-africa

Toolkit of functions to assess and visualize time to travel to health facilities from areas of outbreak potential # Travel time to health facilities in areas of outbreak potential: maps for guiding local preparedness and response - 2019 This repo contains the codes used to generate the raster files used to create the maps in the manuscript "Travel time to health facilities in areas of outbreak potential: maps for guiding local preparedness and response". ## The repo contains 2 files: ### 1) Travel_Time_Functions.R This file generates the functions needed to produce the rasters used in the manuscript. Each of the functions is described subsequently: `binary_threshold` : Converts a raster with continuous values into dichotomous presence (1) or absence (0) based on a user-defined threshold `only_country` : Takes two rasters (or the same raster, twice) as inputs, and masks out values of the first raster to NA where the values are Inf in the second `mask_lake` : Requires a country, directory, and shapefile of lakes (usually >100km) cropped to the country of interest, and returns a shapefile with the lakes cropped out in the directory provided `generate_tt` : Requires a specified country and directory as well as a database of health facilities with latitude (named Latitude, numeric) and longitude (named Longitude, numeric), at minimum (but could contain other columns), and a raster file at 5x5-km resolution with binary classification of presence / absence of one or more pathogens. Can use `binary_threshold` to produce the binary classification, and may want to consider using `mask_lake` to produce a shapefile with lakes removed for calculating travel times (function will search for this file if it exists, but will not throw an error if it doesn't). This function returns raster *pathogen_access_raster* (5x5-km resolution) of travel times to the most accessible health facility from any grid-cell at risk for the pathogen specified. Examples of plots made with *pathogen_access_raster* from the manuscript include the following raw and percentile ranked travel times to health faci …