# An R Interface to Open-Access Malaria Data, Hosted by the 'Malaria Atlas Project'

## Documentation for package ‘malariaAtlas’ version 1.7.0

- DESCRIPTION file
- User guides, package vignettes and other documentation
- Package NEWS
- Package README

## Help Pages

malariaAtlas-package | An R interface to open-access malaria data, hosted by the Malaria Atlas Project.
as.MAPraster | Convert Raster objects into MAPraster objects
as.MAPshp | Convert SpatialPolygon objects into MAPshp objects
as.pr.points | Convert data.frames to pr.points objects.
as.vectorpoints | Convert data.frames to vector.points objects.
autoplot.default | Default autoplot method
autoplot.MAPraster | Quickly visualise Rasters downloaded from MAP
autoplot.MAPshp | Create a basic plot to visualise downloaded shapefiles
autoplot.pr.points | Create a basic plot showing locations of downloaded PR points
autoplot.sf | Create a basic plot to visualise downloaded shapefiles
autoplot.SpatRaster | Quickly visualise Rasters downloaded from MAP
autoplot.SpatRasterCollection | Quickly visualise Rasters downloaded from MAP
autoplot.vector.points | Create a basic plot showing locations of downloaded Vector points
autoplot_MAPraster | Quickly visualise Rasters downloaded from MAP
convertPrevalence | convert prevalences from one age range to another
download_rst | Download rasters from the MAP geoserver to a specifed location. If file already exists it will read it instead.
extractRaster | Extract pixel values from MAP rasters using point coordinates.
fillDHSCoordinates | Add DHS locations to malaria data
getMaskBand | Get mask band for masked raster.
getPR | Download PR points from the MAP database
getRaster | Download Rasters produced by the Malaria Atlas Project
getShp | Download MAPadmin2013 Administrative Boundary Shapefiles from the MAP geoserver
getSpBbox | Return sp style bbox
getVecOcc | Download Vector Occurrence points from the MAP database 'getVecOcc' downloads all publicly available vector occurrence points for a specified country (or countries) and returns this as a dataframe. 'country' and 'ISO' refer to countries and a lower-level administrative regions such as French Guiana.
isAvailable | Available data to download from the MAP geoserver.
isAvailable_pr | Check whether PR points are available for a given location
isAvailable_vec | Check whether Vector Occurrence points are available for a given location
isMaskedRaster | Returns true if second band of raster is a mask
listData | Deprecated function. Please instead use listPRPointCountries for pr points, listVecOccPointCountries for vector points, listRaster for raster and listShp for shape.
listPoints | Deprecated function. Please instead use listPRPointCountries for pr points, and listVecOccPointCountries for vector points
listPRPointCountries | List countries where there is pr point data available
listPRPointVersions | List all dataset versions from the Web Feature Services provided by the Malaria Atlas Project within the Parasite Rate workspace.
listRaster | List all MAP Rasters available to download.
listShp | List administrative units for which shapefiles are stored on the MAP geoserver.
listShpVersions | List all versions of admin unit shapes from the Web Feature Services provided by the Malaria Atlas Project within the Admin Units workspace.
listSpecies | list all species which have occurrence data within the MAP database.
listVecOccPointCountries | List countries where there is vector occurrence point data available
listVecOccPointVersions | List all dataset versions from the Web Feature Services provided by the Malaria Atlas Project within the Vector Occurrence workspace.
makeSpatRasterAutoplot | Create a single (sub) plot for a SpatRaster
malariaAtlas | An R interface to open-access malaria data, hosted by the Malaria Atlas Project.