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malariaAtlas

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

The gitlab version of the malariaAtlas package has some additional bugfixes over the stable CRAN package. If you have any issues, try installing the latest github version. See below for instructions.

Overview

This package allows you to download parasite rate data (Plasmodium falciparum and P. vivax), survey occurrence data of the 41 dominant malaria vector species, and modelled raster outputs from the Malaria Atlas Project.

More details and example analyses can be found in the [published paper)[(https://malariajournal.biomedcentral.com/articles/10.1186/s12936-018-2500-5).

Available Data:

The data can be explored at https://data.malariaatlas.org/maps.

List Versions Functions

The list version functions are used to list the available versions of different datasets, and all return a data.frame with a single column for version. These versions can be passed to functions such as listShp, listSpecies, listPRPointCountries, listVecOccPointCountries, getPR, getVecOcc and getShp.

Use:

  • listPRPointVerions() to see the available versions for PR point data, which can then be used in listPRPointCountries and getPR.

  • listVecOccPointVersions() to see the available versions for vector occurrence data, which can then be used in listSpecies, listVecOccPointCountries and getVecOcc.

  • listShpVersions() to see the available versions for admin unit shape data, which can then be used in listShp and getShp.

listPRPointVersions()
listVecOccPointVersions()
listShpVersions()

List Countries and Species Functions

To list the countries where there is available data for PR points or vector occurrence points, use:

  • listPRPointCountries() for PR points
  • listVecOccPointCountries() for vector occurrence points

To list the species available for vector point data use listSpecies()

All three of these functions can optionally take a version parameter (which can be found with the list versions functions). If you choose not to provide a version, the most recent version of the relevant dataset will be selected by default.

listPRPointCountries(version = "202206")
listVecOccPointCountries(version = "201201")
listSpecies(version = "201201")

List Administrative Units

To list administrative units for which shapefiles are stored on the MAP geoserver, use listShp(). Similar to the list countries and species functions, this function can optionally take a version.

listShp(version = "202206")

List Raster Function

listRaster() gets minimal information on all available rasters. It returns a data.frame with several columns for each raster such as dataset_id, title, abstract, min_raster_year and max_raster_year. The dataset_id can then be used in getRaster and extractRaster.

listRaster()

Is Available Functions

isAvailable_pr confirms whether or not PR survey point data is available to download for a specified country, ISO3 code or continent.

Check whether PR data is available for Madagascar:

isAvailable_pr(country = "Madagascar")

Check whether PR data is available for the United States of America by ISO code:

isAvailable_pr(ISO = "USA")

Check whether PR data is available for Asia:

isAvailable_pr(continent = "Asia")

isAvailable_vec confirms whether or not vector survey point data is available to download for a specified country, ISO3 code or continent.

Check whether vector data is available for Myanmar:

isAvailable_vec(country = "Myanmar")

Check whether vector data is available for multiple countries:

isAvailable_vec(country = c("Nigeria", "Ethiopia"))

You can also pass these functions a dataset version. If you don't they will default to using the most recent version.

isAvailable_pr(country = "Madagascar", version = "202206")

Downloading & Visualising Data:

get* functions & autoplot methods

Parasite Rate Survey Points

getPR() downloads all publicly available PR data points for a specified location (country, ISO, continent or extent) 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")
## Rows: 395
## Columns: 28
## $ dhs_id                    <chr> NA, NA, NA, NA, NA, NA, NA, NA, NA, NA, NA, NA, NA, NA, NA, NA, NA, NA, NA, NA, NA, NA, NA, NA, NA, NA, N…
## $ site_id                   <int> 8689, 6221, 18093, 6021, 15070, 15795, 7374, 13099, 9849, 11961, 21475, 11572, 15943, 7930, 13748, 16323,…
## $ site_name                 <chr> "Vodivohitra", "Andranomasina", "Ankazobe", "Andasibe", "Ambohimarina", "Antohobe", "Ambohimazava", "Anke…
## $ latitude                  <dbl> -16.21700, -18.71700, -18.31600, -19.83400, -18.73400, -19.76990, -25.03230, -18.70100, -18.71920, -19.36…
## $ longitude                 <dbl> 49.68300, 47.46600, 47.11800, 47.85000, 47.25200, 46.68700, 46.99600, 47.16600, 47.49050, 48.16667, 47.46…
## $ rural_urban               <chr> "RURAL", "UNKNOWN", "RURAL", "UNKNOWN", "UNKNOWN", "UNKNOWN", "UNKNOWN", "UNKNOWN", "UNKNOWN", "UNKNOWN",…
## $ country                   <chr> "Madagascar", "Madagascar", "Madagascar", "Madagascar", "Madagascar", "Madagascar", "Madagascar", "Madaga…
## $ country_id                <chr> "MDG", "MDG", "MDG", "MDG", "MDG", "MDG", "MDG", "MDG", "MDG", "MDG", "MDG", "MDG", "MDG", "MDG", "MDG", …
## $ continent_id              <chr> "Africa", "Africa", "Africa", "Africa", "Africa", "Africa", "Africa", "Africa", "Africa", "Africa", "Afri…
## $ month_start               <int> 11, 1, 11, 3, 1, 7, 4, 1, 1, 2, 7, 11, 4, 7, 11, 4, 9, 7, 7, 3, 7, 7, 7, 11, 3, 4, 6, 3, 11, 11, 7, 7, 7,…
## $ year_start                <int> 1989, 1987, 1989, 1987, 1987, 1995, 1986, 1987, 1987, 2003, 1995, 1989, 1986, 1995, 1997, 1986, 1991, 199…
## $ month_end                 <int> 11, 1, 12, 3, 1, 8, 6, 1, 1, 2, 8, 12, 4, 8, 11, 6, 9, 8, 8, 6, 7, 7, 7, 12, 3, 6, 6, 6, 11, 11, 7, 8, 8,…
## $ year_end                  <int> 1989, 1987, 1989, 1987, 1987, 1995, 1986, 1987, 1987, 2003, 1995, 1989, 1986, 1995, 1997, 1986, 1991, 199…
## $ lower_age                 <dbl> 5, 0, 5, 0, 0, 2, 7, 0, 0, 0, 2, 5, 6, 2, 2, 7, 0, 2, 2, 0, 2, 0, 0, 5, 0, 7, 0, 0, 6, 5, 0, 2, 2, 2, 13,…
## $ upper_age                 <int> 15, 99, 15, 99, 99, 9, 22, 99, 99, 99, 9, 15, 12, 9, 9, 22, 99, 9, 9, 5, 9, 99, 99, 15, 99, 22, 99, 5, 12…
## $ examined                  <int> 165, 50, 258, 246, 50, 50, 119, 50, 50, 210, 50, 340, 20, 50, 61, 156, 104, 50, 50, 147, 147, 944, 541, 9…
## $ positive                  <dbl> 144.0, 7.5, 139.0, 126.0, 2.5, 6.0, 37.0, 13.5, 4.5, 34.0, 11.5, 255.0, 8.0, 7.0, 3.0, 97.0, 24.0, 33.0, …
## $ pr                        <dbl> 0.87272727, 0.15000000, 0.53875969, 0.51219512, 0.05000000, 0.12000000, 0.31092437, 0.27000000, 0.0900000…
## $ species                   <chr> "P. falciparum", "P. falciparum", "P. falciparum", "P. falciparum", "P. falciparum", "P. falciparum", "P.…
## $ method                    <chr> "Microscopy", "Microscopy", "Microscopy", "Microscopy", "Microscopy", "Microscopy", "Microscopy", "Micros…
## $ rdt_type                  <chr> NA, NA, NA, NA, NA, NA, NA, NA, NA, NA, NA, NA, NA, NA, NA, NA, NA, NA, NA, NA, NA, NA, NA, NA, NA, NA, N…
## $ pcr_type                  <chr> NA, NA, NA, NA, NA, NA, NA, NA, NA, NA, NA, NA, NA, NA, NA, NA, NA, NA, NA, NA, NA, NA, NA, NA, NA, NA, N…
## $ malaria_metrics_available <lgl> TRUE, TRUE, TRUE, TRUE, TRUE, TRUE, TRUE, TRUE, TRUE, TRUE, TRUE, TRUE, TRUE, TRUE, TRUE, TRUE, TRUE, TRU…
## $ location_available        <lgl> TRUE, TRUE, TRUE, TRUE, TRUE, TRUE, TRUE, TRUE, TRUE, TRUE, TRUE, TRUE, TRUE, TRUE, TRUE, TRUE, TRUE, TRU…
## $ permissions_info          <chr> NA, NA, NA, NA, NA, NA, NA, NA, NA, NA, NA, NA, NA, NA, NA, NA, NA, NA, NA, NA, NA, NA, NA, NA, NA, NA, N…
## $ citation1                 <chr> "Lepers, J.P. (1989). <i>Rapport sur la situation du paludisme dans la région de Mananara Nord.</i> . Ant…
## $ citation2                 <chr> NA, NA, NA, NA, NA, NA, NA, NA, NA, NA, NA, NA, NA, NA, NA, NA, NA, NA, NA, NA, NA, NA, NA, NA, NA, NA, N…
## $ citation3                 <chr> NA, NA, NA, NA, NA, NA, NA, NA, NA, NA, NA, NA, NA, NA, NA, NA, NA, NA, NA, NA, NA, NA, NA, NA, NA, NA, N…
Africa_pvpr_data <- getPR(continent = "Africa", species = "Pv")
Extent_pfpr_data <- getPR(extent = rbind(c(-2.460181, 13.581921), c(-3.867188, 34.277344)), species = "Pf")

You can also pass this function a dataset version. If you don't it will default to using the most recent version.

MDG_pr_data_202206 <- getPR(country = "Madagascar", species = "both", version = "202206")

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

autoplot(MDG_pr_data)

A version without facetting is also available.

autoplot(MDG_pr_data,
         facet = FALSE)

Vector Survey Points

getVecOcc() downloads all publicly available Vector survey points for a specified location (country, ISO, continent or extent) and species (options for which can be found with listSpecies) and returns this as a dataframe with the following format:

MMR_vec_data <- getVecOcc(country = "Myanmar")
## Rows: 2,866
## Columns: 25
## $ id             <int> 1945, 1946, 1951, 1952, 790, 781, 772, 791, 773, 783, 774, 776, 777, 792, 778, 779, 780, 1953, 784, 785, 786, 788, 7…
## $ site_id        <int> 30243, 30243, 30243, 30243, 1000000072, 1000000071, 1000000071, 1000000072, 1000000071, 1000000071, 1000000071, 1000…
## $ latitude       <dbl> 16.2570, 16.2570, 16.2570, 16.2570, 17.3500, 17.3800, 17.3800, 17.3500, 17.3800, 17.3800, 17.3800, 17.3800, 17.3800,…
## $ longitude      <dbl> 97.7250, 97.7250, 97.7250, 97.7250, 96.0410, 96.0370, 96.0370, 96.0410, 96.0370, 96.0370, 96.0370, 96.0370, 96.0370,…
## $ country        <chr> "Myanmar", "Myanmar", "Myanmar", "Myanmar", "Myanmar", "Myanmar", "Myanmar", "Myanmar", "Myanmar", "Myanmar", "Myanm…
## $ country_id     <chr> "MMR", "MMR", "MMR", "MMR", "MMR", "MMR", "MMR", "MMR", "MMR", "MMR", "MMR", "MMR", "MMR", "MMR", "MMR", "MMR", "MMR…
## $ continent_id   <chr> "Asia", "Asia", "Asia", "Asia", "Asia", "Asia", "Asia", "Asia", "Asia", "Asia", "Asia", "Asia", "Asia", "Asia", "Asi…
## $ month_start    <int> 2, 3, 8, 9, 5, 5, 5, 5, 5, 5, 5, 5, 5, 5, 5, 5, 5, 10, 5, 5, 5, 5, 5, 5, 5, 5, 5, 5, 5, 5, 5, 5, 5, 5, 5, 5, 5, 5, 5…
## $ year_start     <int> 1998, 1998, 1998, 1998, 1998, 1998, 1998, 1998, 1998, 1998, 1998, 1998, 1998, 1998, 1998, 1998, 1998, 1998, 1998, 19…
## $ month_end      <int> 2, 3, 8, 9, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 10, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3…
## $ year_end       <int> 1998, 1998, 1998, 1998, 2000, 2000, 2000, 2000, 2000, 2000, 2000, 2000, 2000, 2000, 2000, 2000, 2000, 1998, 2000, 20…
## $ anopheline_id  <int> 17, 17, 17, 17, 50, 49, 17, 51, 11, 4, 15, 1, 35, 30, 50, 51, 30, 17, 17, 11, 15, 1, 35, 49, 4, 17, 11, 15, 1, 35, 5…
## $ species        <chr> "Anopheles dirus species complex", "Anopheles dirus species complex", "Anopheles dirus species complex", "Anopheles …
## $ species_plain  <chr> "Anopheles dirus", "Anopheles dirus", "Anopheles dirus", "Anopheles dirus", "Anopheles stephensi", "Anopheles sinens…
## $ id_method1     <chr> "unknown", "unknown", "unknown", "unknown", "morphology", "morphology", "morphology", "morphology", "morphology", "m…
## $ id_method2     <chr> NA, NA, NA, NA, NA, NA, NA, NA, NA, NA, NA, NA, NA, NA, NA, NA, NA, NA, NA, NA, NA, NA, NA, NA, NA, NA, NA, NA, NA, …
## $ sample_method1 <chr> "man biting", "man biting", "man biting", "man biting", "man biting indoors", "man biting indoors", "man biting indo…
## $ sample_method2 <chr> "animal baited net trap", "animal baited net trap", "animal baited net trap", "animal baited net trap", "man biting …
## $ sample_method3 <chr> NA, NA, NA, NA, "animal baited net trap", "animal baited net trap", "animal baited net trap", "animal baited net tra…
## $ sample_method4 <chr> NA, NA, NA, NA, "house resting inside", "house resting inside", "house resting inside", "house resting inside", "hou…
## $ assi           <chr> "", "", "", "", "", "", "", "", "", "", "", "", "", "", "", "", "", "", "", "", "", "", "", "", "", "", "", "", "", …
## $ citation       <chr> "Oo, T.T., Storch, V. and Becker, N. (2003).  <b><i>Anopheles</i> <i>dirus</i> and its role in malaria transmission …
## $ time_start     <date> 1998-02-01, 1998-03-01, 1998-08-01, 1998-09-01, 1998-05-01, 1998-05-01, 1998-05-01, 1998-05-01, 1998-05-01, 1998-05…
## $ time_end       <date> 1998-02-01, 1998-03-01, 1998-08-01, 1998-09-01, 2000-03-01, 2000-03-01, 2000-03-01, 2000-03-01, 2000-03-01, 2000-03…
## $ geometry       <POINT [°]> POINT (97.725 16.257), POINT (97.725 16.257), POINT (97.725 16.257), POINT (97.725 16.257), POINT (96.041 17.3…

You can also pass this function a dataset version. If you don't it will default to using the most recent version.

MMR_vec_data_201201 <- getVecOcc(country = "Myanmar", version = "201201")

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

autoplot(MMR_vec_data)

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

autoplot(MMR_vec_data,
         facet = TRUE)

Shapefiles

getShp() downloads a shapefile for a specified country (or countries) and returns this as a simple feature object.

MDG_shp <- getShp(ISO = "MDG", admin_level = c("admin0", "admin1"))
## Rows: 23
## Columns: 17
## $ iso           <chr> "MDG", "MDG", "MDG", "MDG", "MDG", "MDG", "MDG", "MDG", "MDG", "MDG", "MDG", "MDG", "MDG", "MDG", "MDG", "MDG", "MDG"…
## $ admn_level    <int> 0, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1
## $ name_0        <chr> "Madagascar", "Madagascar", "Madagascar", "Madagascar", "Madagascar", "Madagascar", "Madagascar", "Madagascar", "Mada…
## $ id_0          <int> 10000910, 10000910, 10000910, 10000910, 10000910, 10000910, 10000910, 10000910, 10000910, 10000910, 10000910, 1000091…
## $ type_0        <chr> "Country", "Country", "Country", "Country", "Country", "Country", "Country", "Country", "Country", "Country", "Countr…
## $ name_1        <chr> NA, "Alaotra Mangoro", "Amoron I Mania", "Analamanga", "Analanjirofo", "Androy", "Anosy", "Atsimo Andrefana", "Atsimo…
## $ id_1          <int> NA, 10022998, 10022989, 10022983, 10022999, 10023001, 10023002, 10023003, 10022990, 10023000, 10022994, 10022995, 100…
## $ type_1        <chr> NA, "Region", "Region", "Region", "Region", "Region", "Region", "Region", "Region", "Region", "Region", "Region", "Re…
## $ name_2        <lgl> NA, NA, NA, NA, NA, NA, NA, NA, NA, NA, NA, NA, NA, NA, NA, NA, NA, NA, NA, NA, NA, NA, NA
## $ id_2          <lgl> NA, NA, NA, NA, NA, NA, NA, NA, NA, NA, NA, NA, NA, NA, NA, NA, NA, NA, NA, NA, NA, NA, NA
## $ type_2        <lgl> NA, NA, NA, NA, NA, NA, NA, NA, NA, NA, NA, NA, NA, NA, NA, NA, NA, NA, NA, NA, NA, NA, NA
## $ name_3        <lgl> NA, NA, NA, NA, NA, NA, NA, NA, NA, NA, NA, NA, NA, NA, NA, NA, NA, NA, NA, NA, NA, NA, NA
## $ id_3          <lgl> NA, NA, NA, NA, NA, NA, NA, NA, NA, NA, NA, NA, NA, NA, NA, NA, NA, NA, NA, NA, NA, NA, NA
## $ type_3        <lgl> NA, NA, NA, NA, NA, NA, NA, NA, NA, NA, NA, NA, NA, NA, NA, NA, NA, NA, NA, NA, NA, NA, NA
## $ source        <chr> "Madagascar NMCP 2016", "Madagascar NMCP 2016", "Madagascar NMCP 2016", "Madagascar NMCP 2016", "Madagascar NMCP 2016…
## $ country_level <chr> "MDG_0", "MDG_1", "MDG_1", "MDG_1", "MDG_1", "MDG_1", "MDG_1", "MDG_1", "MDG_1", "MDG_1", "MDG_1", "MDG_1", "MDG_1", …
## $ geometry      <MULTIPOLYGON [°]> MULTIPOLYGON (((44.2278 -25..., MULTIPOLYGON (((48.2394 -16..., MULTIPOLYGON (((45.7685 -19..., MULTIPOLYGON (((46.74…

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

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 dataset_id & year, clipped to a given bounding box or shapefile

MDG_shp <- getShp(ISO = "MDG", admin_level = "admin0")
MDG_PfPR2_10 <- getRaster(dataset_id = "Explorer__2020_Global_PfPR", shp = MDG_shp, year = 2013)

autoplot.SpatRaster & autoplot.SpatRasterCollection configures autoplot method to enable quick mapping of downloaded rasters.

p <- autoplot(MDG_PfPR2_10, shp_df = MDG_shp)

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_PfPR2_10 <- getRaster(dataset_id = "Explorer__2020_Global_PfPR", shp = MDG_shp, year = 2013)

p <- autoplot(MDG_PfPR2_10, shp_df = MDG_shp, 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")

Similarly for vector survey data

MMR_shp <- getShp(ISO = "MMR", admin_level = "admin0")
MMR_An_dirus <- getRaster(dataset_id = "Explorer__2010_Anopheles_dirus_complex", shp = MMR_shp)

p <- autoplot(MMR_An_dirus, shp_df = MMR_shp, printed = FALSE)

vec <- getVecOcc(country = c("Myanmar"), species = "Anopheles dirus")
p[[1]] +
geom_point(data = vec, aes(longitude, latitude, colour = species))+
  scale_colour_manual(values = "black", name = "Vector survey locations")+
 scale_fill_distiller(name = "Predicted distribution of An. dirus complex", palette = "PuBuGn", direction = 1)+
 ggtitle("Vector Survey points\n + The predicted distribution of An. dirus complex")

Installation

Latest stable version from CRAN

Just install using install.packages("malariaAtlas") or using the package manager in RStudio.

Latest version from github

While this version is not as well-tested, it may include additional bugfixes not in the stable CRAN version. Install the devtools package and then install using devtools::install_github('malaria-atlas-project/malariaAtlas')

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Version

Install

install.packages('malariaAtlas')

Monthly Downloads

498

Version

1.6.3

License

MIT + file LICENSE

Issues

16

Pull Requests

0

Stars

45

Forks

22

Maintainer

Mauricio van den Berg

Last Published

August 26th, 2024

Functions in malariaAtlas (1.6.3)

build_cql_filter

Builds a cql filter to be used with getFeatures, that will filter based on the given list of values.
extractRaster

Extract pixel values from MAP rasters using point coordinates.
fillDHSCoordinates

Add DHS locations to malaria data
download_rst

Download rasters from the MAP geoserver to a specifed location. If file already exists it will read it instead.
getLongitudeColumn

Returns the best longitude column name in df data.frame, if one exists.
extractLayerValues

Returns a data.frame of the extracted raster values with columns for layerName, year, value, long and lat.
fetchCountriesGivenDatasetId

Get the list of available countries for a given dataset_id in the Explorer workspace,
convert_to_date_with_trycatch

Tries to convert character into a Date object. If this fails, the program will be stopped and an error message shown to the user
getLatitudeColumn

Returns the best latitude column name in df data.frame, if one exists.
callGetFeaturesWithFilters

Calls getFeatures on the given type with the given filters, where they are not NULL.
getLatestVersionForAdminData

Get the latest version of admin boundary data
getSpBbox

Return sp style bbox
getPR

Download PR points from the MAP database
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.
getRaster

Download Rasters produced by the Malaria Atlas Project
getShp

Download MAPadmin2013 Administrative Boundary Shapefiles from the MAP geoserver
getMinAndMaxYear

Gets the minimum and maximum year for the time dimension values of a WMS Layer.
isMaskedRaster

Returns true if second band of raster is a mask
isAvailable

Available data to download from the MAP geoserver.
get_name_from_wfs_feature_type_id

Get the name from a wfs feature type id.
get_wcs_client_from_raster_id

Get the WCS client for a raster ID.
isAvailable_vec

Check whether Vector Occurrence points are available for a given location
isAvailable_pr

Check whether PR points are available for a given location
listPRPointVersions

List all dataset versions from the Web Feature Services provided by the Malaria Atlas Project within the Parasite Rate workspace.
get_wcs_clients

WCS clients lazily created or from cache
get_workspace_and_version_from_wfs_feature_type_id

Get the workspace and version from a wfs feature type id.
get_wfs_clients

WFS clients lazily created or from cache
getRasterDatasetIdFromSurface

Gets the rasters dataset id, given a surface (title). If more than one rasters have that surface/title, then the one with the most recent version is selected. If there are no matches, the program will stop with a relevant message.
get_workspace_and_version_from_coverage_id

Get the workspace and version from a raster id.
get_wms_clients

WMS clients lazily created or from cache
getPropertiesForAdminLevel

Gets the property string to provide to getFeatures input propertyName, given an admin level.
listShpVersions

List all versions of admin unit shapes from the Web Feature Services provided by the Malaria Atlas Project within the Admin Units workspace.
listShp

List administrative units for which shapefiles are stored on the MAP geoserver.
listPRPointCountries

List countries where there is pr point data available
listData

Deprecated function. Please instead use listPRPointCountries for pr points, listVecOccPointCountries for vector points, listRaster for raster and listShp for shape.
listVecOccPointCountries

List countries where there is vector occurrence point data available
listRaster

List all MAP Rasters available to download.
malariaAtlas

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

Deprecated function. Please instead use listPRPointCountries for pr points, and listVecOccPointCountries for vector points
listSpecies

list all species which have occurrence data within the MAP database.
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
get_wcs_coverage_summary_from_raster_id

Get the WCS coverage summary for a raster ID.
listFeatureTypeDatasetsFromWorkspace

List all datasets from the Web Feature Services provided by the Malaria Atlas Project within the given workspace.
as.pr.points

Convert data.frames to pr.points objects.
as.MAPraster

Convert Raster objects into MAPraster objects
autoplot.SpatRaster

Quickly visualise Rasters downloaded from MAP
autoplot.pr.points

Create a basic plot showing locations of downloaded PR points
autoplot.MAPraster

Quickly visualise Rasters downloaded from MAP
autoplot.default

Default autoplot method
autoplot.SpatRasterCollection

Quickly visualise Rasters downloaded from MAP
as.MAPshp

Convert SpatialPolygon objects into MAPshp objects
autoplot.MAPshp

Create a basic plot to visualise downloaded shapefiles
as.vectorpoints

Convert data.frames to vector.points objects.
clean_mosquito_names

Function to clean up a bunch of mess in the mosquito names.
autoplot.sf

Create a basic plot to visualise downloaded shapefiles
autoplot.vector.points

Create a basic plot showing locations of downloaded Vector points
autoplot_MAPraster

Quickly visualise Rasters downloaded from MAP
build_cql_bbox_filter

Builds a CQL filter to be used with getFeatures, that will filter based on the given bounding box.
build_cql_time_filter

Builds a cql filter to be used with getFeatures, that will filter based on the time range provided by start_date and end_date.
build_bbox_filter

Builds a filter to be used with getFeatures, that will filter based on the given bounding box.
convertPrevalence

convert prevalences from one age range to another
combine_cql_filters

Builds a cql filter from a list of cql sub filters