Package: malariaAtlas 1.7.0.9999

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], 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_1.7.0.9999.tar.gz
malariaAtlas_1.7.0.9999.zip(r-4.7)malariaAtlas_1.7.0.9999.zip(r-4.6)malariaAtlas_1.7.0.9999.zip(r-4.5)
malariaAtlas_1.7.0.9999.tgz(r-4.6-any)malariaAtlas_1.7.0.9999.tgz(r-4.5-any)
malariaAtlas_1.7.0.9999.tar.gz(r-4.7-any)malariaAtlas_1.7.0.9999.tar.gz(r-4.6-any)
malariaAtlas_1.7.0.9999.tgz(r-4.6-emscripten)
manual.pdf |manual.html✨
DESCRIPTION |NEWS
card.svg |card.png
malariaAtlas/json (API)

# Install 'malariaAtlas' in R:

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

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

On CRAN:

database malaria opendata raster

9.37 score 52 stars 3 packages 185 scripts 1.0k downloads 3 mentions 25 exports 79 dependencies

Last updated from:36cc777947. Checks:9 OK. Indexed: yes.

Target	Result	Time
linux-devel-x86_64	OK	199
source / vignettes	OK	340
linux-release-x86_64	OK	210
macos-release-arm64	OK	232
macos-oldrel-arm64	OK	252
windows-devel	OK	141
windows-release	OK	140
windows-oldrel	OK	122
wasm-release	OK	139

Exports:as.MAPraster as.MAPshp as.pr.points as.vectorpoints autoplot_MAPraster convertPrevalence extractRaster fillDHSCoordinates getPR getRaster getShp getVecOcc isAvailable isAvailable_pr isAvailable_vec listData listPoints listPRPointCountries listPRPointVersions listRaster listShp listShpVersions listSpecies listVecOccPointCountries listVecOccPointVersions

Dependencies:askpass bit bit64 class classInt cli clipr codetools cpp11 crayon curl data.table DBI digest dplyr e1071 farver filelock future future.apply generics geometa ggnewscale ggplot2 globals glue gridExtra gtable hms httr isoband jsonlite KernSmooth keyring labeling lifecycle listenv lubridate magrittr MASS mime openssl ows4R parallelly pillar pkgconfig prettyunits progress proxy purrr R6 RColorBrewer Rcpp readr rlang s2 S7 scales sf stringi stringr sys terra tibble tidyr tidyselect tidyterra timechange tzdb units utf8 vctrs viridisLite vroom withr wk XML xml2 yaml

Basic malariaAtlas usage.

Rendered fromoverview.Rmdusingknitr::rmarkdown

Last update: 2024-08-23
Started: 2018-04-04

Citation

Development and contributors

Readme and manuals

Help Manual

Help page	Topics
Convert Raster objects into MAPraster objects	as.MAPraster
Convert SpatialPolygon objects into MAPshp objects	as.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 MAP	autoplot_MAPraster
Default autoplot method	autoplot.default
Quickly visualise Rasters downloaded from MAP	autoplot.MAPraster
Create a basic plot to visualise downloaded shapefiles	autoplot.MAPshp
Create a basic plot showing locations of downloaded PR points	autoplot.pr.points
Create a basic plot to visualise downloaded shapefiles	autoplot.sf
Quickly visualise Rasters downloaded from MAP	autoplot.SpatRaster
Quickly visualise Rasters downloaded from MAP	autoplot.SpatRasterCollection
Create a basic plot showing locations of downloaded Vector points	autoplot.vector.points
convert prevalences from one age range to another	convertPrevalence
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 data	fillDHSCoordinates
Get mask band for masked raster.	getMaskBand
Download PR points from the MAP database	getPR
Download Rasters produced by the Malaria Atlas Project	getRaster
Download MAPadmin2013 Administrative Boundary Shapefiles from the MAP geoserver	getShp
Return sp style bbox	getSpBbox
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 location	isAvailable_pr
Check whether Vector Occurrence points are available for a given location	isAvailable_vec
Returns true if second band of raster is a mask	isMaskedRaster
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 points	listPoints
List countries where there is pr point data available	listPRPointCountries
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 available	listVecOccPointCountries
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 SpatRaster	makeSpatRasterAutoplot
An R interface to open-access malaria data, hosted by the Malaria Atlas Project.	malariaAtlas-package malariaAtlas