Data set details

Data set description: Malaria data in different locations
Source: Malaria Atlas Project
Details on the retrieved data: Parasite rate (PR) survey data and vector occurrence data in Zimbabwe and India.
Spatial and temporal resolution: Malaria data at country level (with information on specific sites).

Downloading and visualising malaria data with malariaAtlas

This tutorial shows how to use the malariaAtlas package to download, visualize and manipulate global malaria data hosted by the Malaria Atlas Project. These data can be explored and downloaded interactively at data explorer.

The malariaAtlas package enables users to download three types of data:

  • parasite rate (PR) survey data (Plasmodium falciparum and Plasmodium vivax)
  • vector occurrence data
  • administrative boundary shapefiles to visualise data
  • rasters covering a range of modelled outputs related to malaria research such as predicted malaria parasite prevalence

Installation of malariaAtlas package

The malariaAtlas package can be installed from CRAN and loaded as follows:

install.packages("malariaAtlas")
library(malariaAtlas)

Checking available data

The malariaAtlas package provides users with a convenient API to interact with the publicly available malaria data hosted by the Malaria Atlas Project. The listData() function helps retrieve a list of all the available data which can be downloaded, and is a wrapper for listPoints(), listRaster() and listShp(). We can find all countries that have PR survey points data with listData(datatype = "pr points"), and all countries with vector occurrence data with listData(datatype = "vector points"). We can also see raster data available with listData(datatype = "raster"), and shapefiles available with listData(datatype = "shape").

The isAvailable_pr() function can be used to check whether a specified country or location has PR survey points. Similarly, isAvailable_vec() checks whether a specified country or location has vector occurrence data. For example, we can check whether Zimbabwe has PR survey points and India has vector occurrence data as follows:

isAvailable_pr(country = "Zimbabwe")
isAvailable_vec(country = "India")

Dowloading and visualising data

PR survey data

The getPR() function downloads all the publicly available PR points for a country (or countries) and returns it as a dataframe. The species argument is a string specifying the Plasmodium species and can be Pf, Pv or BOTH.

ZM_PR_data <- getPR(country = "Zimbabwe", species = "BOTH")

autoplot() can be used to quickly and easily visualise the downloaded PR survey points.

autoplot(ZM_PR_data)
## OGR data source with driver: ESRI Shapefile 
## Source: "C:\Users\dilin\AppData\Local\Temp\RtmpshUMYV\shp\shp320c102f39c3\mapadmin_0_2018.shp", layer: "mapadmin_0_2018"
## with 1 features
## It has 8 fields

Vector data

The getVecOcc() function downloads all publicly available vector points for a country (or countries) and returns it as a dataframe. The species argument is a string specifying the Anopheles species for finding the vector occurrences points, the options are Anopheles.... or ALL.

IN_VEC_data <- getVecOcc(country = "India", species = "ALL")