Basic malariaAtlas usage.

Dan Pfeffer, Tim Lucas

2018-04-09

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 interactively explored at https://map.ox.ac.uk/explorer/#/explorer. This is also useful for finding information on the raster data available and checking the extents of different rasters (some are Africa only for example).

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.

library(malariaAtlas)
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...
## PR points are 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: 1,793
## Variables: 28
## $ dhs_id                    <fct> , , , , , , , , , , , , , , , , , , ...
## $ site_id                   <int> 6221, 6021, 15070, 15795, 7374, 1309...
## $ site_name                 <fct> Andranomasina, Andasibe, Ambohimarin...
## $ latitude                  <dbl> -18.7170, -19.8340, -18.7340, -19.76...
## $ longitude                 <dbl> 47.4660, 47.8500, 47.2520, 46.6870, ...
## $ rural_urban               <fct> , , , , , , , , , , rural, , , , , r...
## $ 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> 1, 3, 1, 7, 4, 1, 1, 7, 4, 7, 11, 4,...
## $ year_start                <int> 1987, 1987, 1987, 1995, 1986, 1987, ...
## $ month_end                 <int> 1, 3, 1, 8, 6, 1, 1, 8, 4, 8, 11, 6,...
## $ year_end                  <int> 1987, 1987, 1987, 1995, 1986, 1987, ...
## $ lower_age                 <dbl> 0, 0, 0, 2, 7, 0, 0, 2, 6, 2, 2, 7, ...
## $ upper_age                 <int> 99, 99, 99, 9, 22, 99, 99, 9, 12, 9,...
## $ examined                  <int> 50, 246, 50, 50, 119, 50, 50, 50, 20...
## $ positive                  <dbl> 0.075, 126.000, 0.025, 0.060, 37.000...
## $ pr                        <dbl> 0.0015, 0.5122, 0.0005, 0.0012, 0.31...
## $ species                   <chr> "P. falciparum", "P. falciparum", "P...
## $ method                    <fct> Microscopy, Microscopy, Microscopy, ...
## $ rdt_type                  <fct> , , , , , , , , , , , , , , , , , , ...
## $ pcr_type                  <lgl> NA, NA, NA, NA, NA, NA, NA, NA, NA, ...
## $ malaria_metrics_available <fct> true, true, true, true, true, true, ...
## $ location_available        <fct> true, true, true, true, true, true, ...
## $ permissions_info          <fct> , , , , , , , , , , , , , , , , , , ...
## $ citation1                 <fct> Lepers, J.P., Ramanamirija, J.A., An...
## $ citation2                 <fct> , , , , , , , , , , , , , , , , , , ...
## $ citation3                 <lgl> NA, NA, NA, NA, NA, NA, NA, NA, NA, ...

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

autoplot(MDG_pr_data)

Furthermore, being ggplot2 plots, these plots can easily be added to or modified.

p <- autoplot(MDG_pr_data, printed = FALSE)
p + 
  scale_fill_gradientn(colours = rev(palettetown::pokepal('charmeleon', spread = 3))) +
  theme_minimal()

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/RtmpIUxmWU/shp/mapadmin_0_2013.shp", layer: "mapadmin_0_2013"
## with 1 features
## It has 9 fields
## OGR data source with driver: ESRI Shapefile 
## Source: "/tmp/RtmpIUxmWU/shp/mapadmin_1_2013.shp", layer: "mapadmin_1_2013"
## with 22 features
## It has 6 fields
## Formal class 'SpatialPolygonsDataFrame' [package "sp"] with 5 slots
##   ..@ data       :'data.frame':  23 obs. of  7 variables:
##   .. ..$ gid          : int [1:23] 138 2790 2791 2792 2793 2794 2795 2796 2797 2798 ...
##   .. ..$ 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)

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 = "Plasmodium falciparum PR2-10", 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 and autoplot_MAPraster are autoplot methods 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 = "Plasmodium falciparum PR2-10", 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 = positive / 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")