malariaAtlas

An R interface to open-access malaria data, hosted by the Malaria Atlas Project.

Overview

This package allows you to download parasite rate data (Plasmodium falciparum and P. vivax) and modelled raster outputs from the Malaria Atlas Project.

Available Data:

The data can be explored at https://map.ox.ac.uk/explorer/#/explorer.

list* Functions

listData() retrieves a list of available data to download.

Use:

listData(datatype = "points") OR listPoints() to see for which countries PR survey point data can be downloaded.
use listData(datatype = "rasters") OR listRaster() to see rasters available to download.
use listData(datatype = "shape") OR listShp() to see shapefiles available to download.

listData(datatype = "points")

listData(datatype = "raster")

listData(datatype = "shape")

is_available

isAvailable confirms whether or not PR survey point data is available to download for a specified country.

Check whether PR data is available for Madagascar:

isAvailable(country = "Madagascar")

## Confirming availability of PR data for: Madagascar...

## Data is available for Madagascar.

Check whether PR data is available for the United States of America

isAvailable(ISO = "USA")

## Confirming availability of PR data for: USA...

## Error in isAvailable(ISO = "USA"): Specified location not found, see below comments: 
##  
## Data not found for 'USA', did you mean UGA OR SAU?

Downloading & Visualising Data:

get* functions & autoplot methods

Parasite Rate Survey Points

getPR() downloads all publicly available PR data points for a specified country and plasmodium species (Pf, Pv or BOTH) and returns this as a dataframe with the following format:

MDG_pr_data <- getPR(country = "Madagascar", species = "both")

## Observations: 905
## Variables: 29
## $ dhs_id                    <fct> , , , , , , , , , , , , , , , , , , ...
## $ site_id                   <int> 16586, 2683, 8008, 8689, 16899, 2167...
## $ site_name                 <fct> Tsarahasina, Manalalondo, Andafiatsi...
## $ latitude                  <dbl> -19.74900, -19.25900, -19.38400, -16...
## $ longitude                 <dbl> 46.79900, 47.11300, 47.66600, 49.683...
## $ rural_urban               <fct> , , , rural, , , , rural, , , , , , ...
## $ country                   <fct> Madagascar, Madagascar, Madagascar, ...
## $ country_id                <fct> MDG, MDG, MDG, MDG, MDG, MDG, MDG, M...
## $ continent_id              <fct> Africa, Africa, Africa, Africa, Afri...
## $ month_start               <int> NA, NA, NA, 11, NA, NA, 1, 11, NA, 3...
## $ year_start                <int> NA, NA, NA, 1989, NA, NA, 1987, 1989...
## $ month_end                 <int> NA, NA, NA, 11, NA, NA, 1, 12, NA, 3...
## $ year_end                  <int> NA, NA, NA, 1989, NA, NA, 1987, 1989...
## $ lower_age                 <dbl> NA, NA, NA, 5, NA, NA, 0, 5, NA, 0, ...
## $ upper_age                 <int> NA, NA, NA, 15, NA, NA, 99, 15, NA, ...
## $ examined                  <int> NA, NA, NA, 165, NA, NA, 50, 258, NA...
## $ pf_pos                    <dbl> NA, NA, NA, 144.000, NA, NA, 0.075, ...
## $ pf_pr                     <dbl> NA, NA, NA, 0.87272727, NA, NA, 0.00...
## $ pv_pos                    <int> NA, NA, NA, 10, NA, NA, NA, 2, NA, N...
## $ pv_pr                     <dbl> NA, NA, NA, 0.06060606, NA, NA, NA, ...
## $ method                    <fct> , , , Microscopy, , , Microscopy, Mi...
## $ rdt_type                  <fct> , , , , , , , , , , , , , , , , , , ...
## $ pcr_type                  <lgl> NA, NA, NA, NA, NA, NA, NA, NA, NA, ...
## $ malaria_metrics_available <fct> false, false, false, true, false, fa...
## $ location_available        <fct> true, true, true, true, true, true, ...
## $ permissions_info          <fct> No permission to release data, No pe...
## $ citation1                 <fct> Jambou, R., Ranaivo, L., Raharimalal...
## $ citation2                 <fct> Jambou, R. (2008) personal communica...
## $ citation3                 <lgl> NA, NA, NA, NA, NA, NA, NA, NA, NA, ...

autoplot.pr.points configures autoplot method to enable quick mapping of the locations of downloaded PR points.

autoplot(MDG_pr_data)

N.B. Facet-wrapped option is also available for species stratification.

autoplot(MDG_pr_data,
         facet = TRUE,
         map_title = "Example MAP of PR point locations,\nstratified by species")

Shapefiles

getShp() downloads a shapefile for a specified country (or countries) and returns this as either a spatialPolygon or data.frame object.

MDG_shp <- getShp(ISO = "MDG", admin_level = "both")

## OGR data source with driver: ESRI Shapefile 
## Source: "/tmp/RtmpT5GXYN/shp/admin0_map_2013.shp", layer: "admin0_map_2013"
## with 1 features
## It has 8 fields
## OGR data source with driver: ESRI Shapefile 
## Source: "/tmp/RtmpT5GXYN/shp/admin1_map_2013.shp", layer: "admin1_map_2013"
## with 22 features
## It has 5 fields

## Formal class 'SpatialPolygonsDataFrame' [package "sp"] with 5 slots
##   ..@ data       :'data.frame':  23 obs. of  6 variables:
##   .. ..$ NAME         : Factor w/ 23 levels "Madagascar","Alaotra Mangoro",..: 1 2 3 4 5 6 7 8 9 10 ...
##   .. ..$ COUNTRY_ID   : Factor w/ 1 level "MDG": 1 1 1 1 1 1 1 1 1 1 ...
##   .. ..$ GAUL_CODE    : int [1:23] 150 41750 41751 41752 41753 41754 41755 41756 41757 41758 ...
##   .. ..$ ADMN_LEVEL   : Factor w/ 2 levels "0","1": 1 2 2 2 2 2 2 2 2 2 ...
##   .. ..$ PARENT_ID    : int [1:23] 0 150 150 150 150 150 150 150 150 150 ...
##   .. ..$ country_level: chr [1:23] "MDG_0" "MDG_1" "MDG_1" "MDG_1" ...
##   ..@ polygons   :List of 23
##   .. ..$ :Formal class 'Polygons' [package "sp"] with 5 slots
##   .. ..$ :Formal class 'Polygons' [package "sp"] with 5 slots
##   .. ..$ :Formal class 'Polygons' [package "sp"] with 5 slots
##   .. ..$ :Formal class 'Polygons' [package "sp"] with 5 slots
##   .. ..$ :Formal class 'Polygons' [package "sp"] with 5 slots
##   .. ..$ :Formal class 'Polygons' [package "sp"] with 5 slots
##   .. ..$ :Formal class 'Polygons' [package "sp"] with 5 slots
##   .. ..$ :Formal class 'Polygons' [package "sp"] with 5 slots
##   .. ..$ :Formal class 'Polygons' [package "sp"] with 5 slots
##   .. ..$ :Formal class 'Polygons' [package "sp"] with 5 slots
##   .. ..$ :Formal class 'Polygons' [package "sp"] with 5 slots
##   .. ..$ :Formal class 'Polygons' [package "sp"] with 5 slots
##   .. ..$ :Formal class 'Polygons' [package "sp"] with 5 slots
##   .. ..$ :Formal class 'Polygons' [package "sp"] with 5 slots
##   .. ..$ :Formal class 'Polygons' [package "sp"] with 5 slots
##   .. ..$ :Formal class 'Polygons' [package "sp"] with 5 slots
##   .. ..$ :Formal class 'Polygons' [package "sp"] with 5 slots
##   .. ..$ :Formal class 'Polygons' [package "sp"] with 5 slots
##   .. ..$ :Formal class 'Polygons' [package "sp"] with 5 slots
##   .. ..$ :Formal class 'Polygons' [package "sp"] with 5 slots
##   .. ..$ :Formal class 'Polygons' [package "sp"] with 5 slots
##   .. ..$ :Formal class 'Polygons' [package "sp"] with 5 slots
##   .. ..$ :Formal class 'Polygons' [package "sp"] with 5 slots
##   ..@ plotOrder  : int [1:23] 1 8 21 19 18 7 12 11 2 5 ...
##   ..@ bbox       : num [1:2, 1:2] 43.2 -25.6 50.5 -11.9
##   .. ..- attr(*, "dimnames")=List of 2
##   ..@ proj4string:Formal class 'CRS' [package "sp"] with 1 slot

autoplot.MAPshp configures autoplot method to enable quick mapping of downloaded shapefiles.

MDG_shp <- as.MAPshp(MDG_shp)
autoplot(MDG_shp)

N.B. Facet-wrapped option is also available for species stratification.

autoplot(MDG_shp,
         facet = TRUE,
         map_title = "Example of facetted shapefiles.")

Modelled Rasters

getRaster()downloads publicly available MAP rasters for a specific surface & year, clipped to a given bounding box or shapefile

MDG_shp <- getShp(ISO = "MDG", admin_level = "admin0")
MDG_PfPR2_10 <- getRaster(surface = "PfPR2-10", shp = MDG_shp, year = 2013)

N.B. to use downloaded rasters and shapefiles directly with autoplot, use as.MAPraster() and as.MAPshp() to convert these to data.frames. Alternatively autoplot_MAPraster() will work directly with RasterLayer, RasterStack or RasterBrick objects downloaded with getRaster().

autoplot.MAPraster&autoplot_MAPrasterconfigures autoplot method to enable quick mapping of downloaded rasters.

MDG_PfPR2_10_df <- as.MAPraster(MDG_PfPR2_10)
MDG_shp_df <- as.MAPshp(MDG_shp)
p <- autoplot(MDG_PfPR2_10_df, shp_df = MDG_shp_df)

Combined visualisation

By using the above tools along with ggplot, simple comparison figures can be easily produced.

MDG_shp <- getShp(ISO = "MDG", admin_level = "admin0")
MDG_shp_df <- as.MAPshp(MDG_shp)
MDG_PfPR2_10 <- getRaster(surface = "PfPR2-10", shp = MDG_shp, year = 2013)
MDG_PfPR2_10_df <- as.MAPraster(MDG_PfPR2_10)

p <- autoplot(MDG_PfPR2_10_df, shp_df = MDG_shp_df, printed = FALSE)

pr <- getPR(country = c("Madagascar"), species = "Pf")
p[[1]] +
geom_point(data = pr[pr$year_start==2013,], aes(longitude, latitude, fill = pf_pos / examined, size = examined), shape = 21)+
scale_size_continuous(name = "Survey Size")+
 scale_fill_distiller(name = "PfPR", palette = "RdYlBu")+
 ggtitle("Raw PfPR Survey points\n + Modelled PfPR 2-10 in Madagascar in 2013")

spgriffin / malariaAtlas