Table 2.
Outline of malariaAtlas functions
| Category | Function name | Purpose | Data type | R object class |
|---|---|---|---|---|
| ‘List’ available data | listData | Wrapper for below functions, returning a data.frame outlining data availability | – | data.frame |
| listPoints | Return a data.frame listing countries with parasite rate survey points | Point data | data.frame | |
| listShp | Return a data.frame listing administrative units with shapefiles available to download | Shapefile | data.frame | |
| listRaster | Return a data.frame listing rasters available to download | Raster | data.frame | |
| ‘Get’ available data | getPR | Download parasite rate survey data for specified location(s) and species | Point data | data.frame; pr.points a |
| getShp | Download shapefiles for specified location(s) and administrative level(s) | Shapefile | SpatialPolygon(s); data.frame; mapShp a | |
| getRaster | Download specified rasters for specified location(s) and year(s) | Raster | RasterLayer; RasterBrick; RasterStack; data.frame; mapRaster a | |
| ‘Autoplot’ downloaded data | autoplot.pr.points | Quickly visualise parasite rate survey locations and raw PR values for data downloaded using malariaAtlas | Point data | gg |
| autoplot.mapShp | Quickly visualise shapefiles downloaded using malariaAtlas | Shapefile | gg | |
| autoplot.mapRaster | Quickly visualise rasters downloaded using malariaAtlas | Raster | gg/list | |
| Utility functions | extractRaster | Extract values from specified rasters at specified point locations (lat/long) | Point data | data.frame |
| convertPrevalence b | Convert parasite rate from a given age-range to another | Prevalence | numeric | |
| as.mapShp | Convert SpatialPolygon or SpatialPolygons objects to mapShpa objects | Shapefile | mapShpa; data.frame | |
| as.mapRaster | Convert objects of RasterLayer; RasterBrick; RasterStack classes or a list of RasterBrick/RasterStacks to mapRastera objects | Raster | mapRastera; data.frame |
a malariaAtlas specific object class defined for purposes of quick visualisation using autoplot (pr.points; mapShp; and mapRaster) or in-built optional conversion of Spatial* classes to data.frame formats (mapShp; mapRaster)
b See the ageStand R package on GitHub [43] or malariaAtlas help files for additional information on convertPrevalence