Package: malariaAtlas 1.6.1.9999

Mauricio van den Berg

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

A suite of tools to allow you to download all publicly available parasite rate survey points, mosquito occurrence points and raster surfaces from the 'Malaria Atlas Project' <https://malariaatlas.org/> servers as well as utility functions for plotting the downloaded data.

Authors:Mauricio van den Berg [aut, cre], Sarah Connor [aut], Daniel Pfeffer [aut], Tim Lucas [aut], Daniel May [aut], Suzanne Keddie [aut], Jen Rozier [aut], Oliver Watson [aut], Harry Gibson [aut], Nick Golding [ctb], David Smith [ctb]

malariaAtlas_1.6.1.9999.tar.gz
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malariaAtlas.pdf |malariaAtlas.html✨
malariaAtlas/json (API)
NEWS

# Install 'malariaAtlas' in R:
install.packages('malariaAtlas', repos = c('https://malaria-atlas-project.r-universe.dev', 'https://cloud.r-project.org'))

Peer review:

Bug tracker:https://github.com/malaria-atlas-project/malariaatlas/issues

On CRAN:

databasemalariaopendataraster

25 exports 42 stars 3.67 score 88 dependencies 3 dependents 3 mentions 114 scripts 603 downloads

Last updated 2 months agofrom:76223bc0c2. Checks:OK: 7. Indexed: yes.

TargetResultDate
Doc / VignettesOKSep 13 2024
R-4.5-winOKSep 13 2024
R-4.5-linuxOKSep 13 2024
R-4.4-winOKSep 13 2024
R-4.4-macOKSep 13 2024
R-4.3-winOKSep 13 2024
R-4.3-macOKSep 13 2024

Exports:as.MAPrasteras.MAPshpas.pr.pointsas.vectorpointsautoplot_MAPrasterconvertPrevalenceextractRasterfillDHSCoordinatesgetPRgetRastergetShpgetVecOccisAvailableisAvailable_prisAvailable_veclistDatalistPointslistPRPointCountrieslistPRPointVersionslistRasterlistShplistShpVersionslistSpecieslistVecOccPointCountrieslistVecOccPointVersions

Dependencies:askpassassertthatbitbit64classclassIntclicliprcodetoolscolorspacecpp11crayoncurldata.tableDBIdigestdplyre1071fansifarverfilelockfuturefuture.applygenericsgeometaggnewscaleggplot2globalsgluegridExtragtablehmshttrisobandjsonliteKernSmoothkeyringlabelinglatticelifecyclelistenvlubridatemagrittrMASSMatrixmgcvmimemunsellnlmeopensslows4RparallellypillarpkgconfigprettyunitsprogressproxypurrrR6rappdirsRColorBrewerRcppreadrrlangs2scalessfsodiumstringistringrsysterratibbletidyrtidyselecttidyterratimechangetzdbunitsutf8vctrsviridisLitevroomwithrwkXMLxml2yaml

Basic malariaAtlas usage.

Dan Pfeffer, Tim Lucas

Rendered fromoverview.Rmdusingknitr::rmarkdownon Sep 13 2024.

Last update: 2023-10-02
Started: 2018-04-04

Readme and manuals

Help Manual

Help pageTopics
Convert Raster objects into MAPraster objectsas.MAPraster
Convert SpatialPolygon objects into MAPshp objectsas.MAPshp
Convert data.frames to pr.points objects.as.pr.points
Convert data.frames to vector.points objects.as.vectorpoints
Quickly visualise Rasters downloaded from MAPautoplot_MAPraster
Quickly visualise Rasters downloaded from MAPautoplot.MAPraster
Create a basic plot to visualise downloaded shapefilesautoplot.MAPshp
Create a basic plot showing locations of downloaded PR pointsautoplot.pr.points
Create a basic plot to visualise downloaded shapefilesautoplot.sf
Quickly visualise Rasters downloaded from MAPautoplot.SpatRaster
Quickly visualise Rasters downloaded from MAPautoplot.SpatRasterCollection
Create a basic plot showing locations of downloaded Vector pointsautoplot.vector.points
convert prevalences from one age range to anotherconvertPrevalence
Download rasters from the MAP geoserver to a specifed location. If file already exists it will read it instead.download_rst
Extract pixel values from MAP rasters using point coordinates.extractRaster
Add DHS locations to malaria datafillDHSCoordinates
Download PR points from the MAP databasegetPR
Download Rasters produced by the Malaria Atlas ProjectgetRaster
Download MAPadmin2013 Administrative Boundary Shapefiles from the MAP geoservergetShp
Return sp style bboxgetSpBbox
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.getVecOcc
Available data to download from the MAP geoserver.isAvailable
Check whether PR points are available for a given locationisAvailable_pr
Check whether Vector Occurrence points are available for a given locationisAvailable_vec
Returns true if second band of raster is a maskisMaskedRaster
Deprecated function. Please instead use listPRPointCountries for pr points, listVecOccPointCountries for vector points, listRaster for raster and listShp for shape.listData
Deprecated function. Please instead use listPRPointCountries for pr points, and listVecOccPointCountries for vector pointslistPoints
List countries where there is pr point data availablelistPRPointCountries
List all dataset versions from the Web Feature Services provided by the Malaria Atlas Project within the Parasite Rate workspace.listPRPointVersions
List all MAP Rasters available to download.listRaster
List administrative units for which shapefiles are stored on the MAP geoserver.listShp
List all versions of admin unit shapes from the Web Feature Services provided by the Malaria Atlas Project within the Admin Units workspace.listShpVersions
list all species which have occurrence data within the MAP database.listSpecies
List countries where there is vector occurrence point data availablelistVecOccPointCountries
List all dataset versions from the Web Feature Services provided by the Malaria Atlas Project within the Vector Occurrence workspace.listVecOccPointVersions
Create a single (sub) plot for a SpatRastermakeSpatRasterAutoplot
An R interface to open-access malaria data, hosted by the Malaria Atlas Project.malariaAtlas