Package ‘malariaAtlas’

October 27, 2023

Title An R Interface to Open-Access Malaria Data, Hosted by the
'Malaria Atlas Project'
Version 1.5.1
Description 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:
//[Link]/> servers as well as utility functions for plotting
the downloaded data.
License MIT + file LICENSE
Encoding UTF-8
Imports xml2, gridExtra, httr, dplyr, tidyr, methods, stats, utils,
rlang, sf, lifecycle, terra, tidyterra, ows4R, [Link],
lubridate, jsonlite, stringr
Depends ggplot2
RoxygenNote 7.2.3
Suggests testthat, knitr, rmarkdown, palettetown, magrittr, tibble,
rdhs (>= 0.8.0)
URL [Link]
BugReports [Link]
VignetteBuilder knitr
NeedsCompilation no
Author Mauricio van den Berg [aut, cre],
Sarah Connor [aut],
Daniel Pfeffer [aut] (<[Link]
Tim Lucas [aut] (<[Link]
Daniel May [aut] (<[Link]
Suzanne Keddie [aut] (<[Link]
Jen Rozier [aut] (<[Link]
Oliver Watson [aut] (<[Link]
Harry Gibson [aut] (<[Link]
Nick Golding [ctb],
David Smith [ctb]

1
2 R topics documented:

Maintainer Mauricio van den Berg <[Link]@[Link]>

Repository CRAN
Date/Publication 2023-10-27 [Link] UTC

R topics documented:
[Link] . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 3
[Link] . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 4
[Link] . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 5
[Link] . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 6
[Link] . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 6
[Link] . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 8
[Link] . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 9
[Link] . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 10
[Link] . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 11
[Link] . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 13
[Link] . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 14
autoplot_MAPraster . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 15
convertPrevalence . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 17
extractRaster . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 18
fillDHSCoordinates . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 19
getPR . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 21
getRaster . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 23
getShp . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 24
getSpBbox . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 26
getVecOcc . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 27
isAvailable . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 28
isAvailable_pr . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 30
isAvailable_vec . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 31
listData . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 32
listPoints . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 33
listPRPointCountries . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 33
listPRPointVersions . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 34
listRaster . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 34
listShp . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 35
listShpVersions . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 36
listSpecies . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 37
listVecOccPointCountries . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 37
listVecOccPointVersions . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 38
makeSpatRasterAutoplot . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 39
malariaAtlas . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 40

Index 41
[Link] 3

[Link] Convert Raster objects into MAPraster objects

Description
[Link] converts a RasterLayer or RasterStack object into a ’MAPraster’ object ([Link])
for easy plotting with ggplot.

Usage
[Link](raster_object)

Arguments
raster_object RasterLayer or Rasterstack object to convert into a MAPraster.

Value
[Link] returns a MAPraster object ([Link]) containing the below columns.

1. x - x coordinates of raster pixels

2. y - y coordinates of raster pixels
3. z - value of raster pixels
4. raster_name - name of raster for which values are stored in z

See Also
getRaster:
to download rasters directly from MAP.
[Link]:
to convert RasterLayer/RasterStack objects into a ’MAPraster’ object ([Link]) for easy plotting
with ggplot.
[Link]:
to quickly visualise MAPraster objects created using [Link].

Examples
# Download PfPR2-10 Raster for Madagascar in 2015 and visualise this on a map.
## Not run:
MDG_shp <- getShp(ISO = "MDG", admin_level = "admin0")
MDG_PfPR2_10 <- getRaster(surface = "Plasmodium falciparum PR2-10", shp = MDG_shp, year = 2015)
MDG_PfPR2_10 <- [Link](MDG_PfPR2_10)
autoplot(MDG_PfPR2_10)
## End(Not run)

#Download global raster of G6PD deficiency from Howes et al 2012 and visualise this on a map.
4 [Link]

## Not run:
G6PDd_global <- getRaster(surface = "G6PD Deficiency Allele Frequency")
G6PDd_global <- [Link](G6PDd_global)
autoplot(G6PDd_global)
## End(Not run)

[Link] Convert SpatialPolygon objects into MAPshp objects

Description

[Link] converts a SpatialPolygon or SpatialPolygonsDataframe object downloaded using get-

Shp into a ’MAPshp object ([Link]) for easy plotting with ggplot.

Usage

[Link](object)

Arguments

object SpatialPolygon or SpatialPolygonsDataframe object to convert into a ’MAP-

shp’.

Value

[Link] returns a MAPshp object ([Link]) containing the below columns.

1. country_id ISO-3 code of given administrative unit (or the ISO code of parent unit for
administrative-level 1 units).
2. gaul_code GAUL code of given administrative unit.
3. admn_level administrative level of the given administrative unit - either 0 (national) or 1
(first-level division)
4. parent_id GAUL code of parent administrative unit of a given polygon (for admin0 polygons,
PARENT_ID = 0).
5. country_level composite country_id_admn_level field.

See Also

[Link]
to download rasters directly from MAP.
[Link] 5

Examples
#Download shapefiles for Madagascar and visualise these on a map.

## Not run:
MDG_shp <- getShp(ISO = "MDG", admin_level = "admin0")
MDG_shp <- [Link](MDG_shp)
autoplot(MDG_shp)

## End(Not run)

[Link] Convert [Link] to [Link] objects.

Description

Will create empty columns for any missing columns expected in a [Link] [Link]. This func-
tion is particularly useful for use with packages like dplyr that strip objects of their classes.

Usage

[Link](x)

Arguments

x A [Link]

Examples
#Download PfPR data for Nigeria and Cameroon and map the locations of these points using autoplot
## Not run:
library(dplyr)
NGA_CMR_PR <- getPR(country = c("Nigeria", "Cameroon"), species = "Pf")

# Filter the data frame then readd [Link] class so that autoplot can be used.
NGA_CMR_PR %>%
filter(year_start > 2010) %>%
[Link] %>%
autoplot

## End(Not run)
6 [Link]

[Link] Convert [Link] to [Link] objects.

Description
Will create empty columns for any missing columns expected in a [Link] [Link]. This
function is particularly useful for use with packages like dplyr that strip objects of their classes.

Usage
[Link](x)

Arguments
x A [Link]

Examples
## Not run:
library(dplyr)
Brazil_vec <- getVecOcc(country = "Brazil")

# Filter [Link] then readd vector points class so autoplot can be used.
Brazil_vec %>%
filter(sample_method1 == 'larval collection') %>%
[Link] %>%
autoplot

## End(Not run)

[Link] Quickly visualise Rasters downloaded from MAP

Description
[Link] creates a map of all rasters in a MAPraster object and displays these in a
grid.

Usage
## S3 method for class 'MAPraster'
autoplot(
object,
...,
shp_df = NULL,
legend_title = "",
[Link] 7

plot_titles = TRUE,
fill_scale_transform = "identity",
fill_colour_palette = "RdYlBu",
printed = TRUE
)

Arguments
object MAPraster object to be visualised.
... Other arguments passed to specific methods
shp_df Shapefile(s) ([Link]) to plot with downloaded raster.
legend_title String used as title for all colour scale legends.
plot_titles Plot name of raster object as header for each individual raster plot?
fill_scale_transform
String givning a transformation for the fill aesthetic. See the trans argument in
continuous_scale for possible values.
fill_colour_palette
String referring to a colorbrewer palette to be used for raster colour scale.
printed Logical vector indicating whether to print maps of supplied rasters.

Value
[Link] returns a list of plots (gg objects) for each supplied raster.

See Also
getRaster:
to download rasters directly from MAP.
[Link]:
to convert RasterLayer/RasterStack objects into a ’MAPraster’ object ([Link]) for easy plotting
with ggplot.
[Link]:
to quickly visualise MAPraster objects created using [Link].

Examples
## Not run:
# Download PfPR2-10 Raster (Bhatt et al 2015) and raw survey points
# for Madagascar in 2013 and visualise these together on a map.

# Download madagascar shapefile to use for raster download.

MDG_shp <- getShp(ISO = "MDG", admin_level = "admin0")

# Download PfPR2-10 Raster for 2013 & plot this

MDG_PfPR2_10 <- getRaster(surface = "Plasmodium falciparum PR2-10",
shp = MDG_shp, year = 2013)
p <- autoplot(MDG_PfPR2_10, shp_df = MDG_shp)
8 [Link]

# Download raw PfPR survey points & plot these over the top of the raster
pr <- getPR(country = c("Madagascar"), species = "Pf")

# Download global raster of G6PD deficiency (Howes et al 2012) and visualise this on a map.
G6PDd_global <- getRaster(surface = "G6PD Deficiency Allele Frequency")
autoplot(G6PDd_global)

## End(Not run)

[Link] Create a basic plot to visualise downloaded shapefiles

Description
[Link] creates a map of shapefiles downloaded using getShp.

Usage
## S3 method for class 'MAPshp'
autoplot(object, ..., map_title = NULL, facet = FALSE, printed = TRUE)

Arguments
object A MAPshp object downloaded using getShp with format = "df" specified.
... Other arguments passed to specific methods
map_title Custom title used for the plot.
facet If TRUE, splits map into a separate facet for each administrative level.
printed Should the plot print to graphics device.

Value
[Link] returns a map (gg object) of the supplied MAPShp dataframe.

Examples
## Not run:
MDG_shp <- getShp(ISO = "MDG", admin_level = "admin0")
autoplot([Link](MDG_shp))

## End(Not run)
[Link] 9

[Link] Create a basic plot showing locations of downloaded PR points

Description
[Link] creates a map of PR points downloaded from MAP.

Usage
## S3 method for class '[Link]'
autoplot(
object,
...,
shp_df = NULL,
admin_level = "admin0",
map_title = "PR Survey Locations",
fill_legend_title = "Raw PR",
fill_scale_transform = "identity",
facet = NULL,
hide_confidential = FALSE,
printed = TRUE
)

Arguments
object a [Link] object downloaded using getPR
... Other arguments passed to specific methods
shp_df Shapefile(s) ([Link]) to plot with downloaded points. (If not specified auto-
matically uses getShp() for all countries included in [Link] object).
admin_level the administrative level used for plotting administrative boundaries; either "admin0";
"admin1" OR "both"
map_title custom title used for the plot
fill_legend_title
Add a title to the legend.
fill_scale_transform
String givning a transformation for the fill aesthetic. See the trans argument in
continuous_scale for possible values.
facet if TRUE, splits map into a separate facet for each malaria species; by default
FALSE if only one species is present in object, TRUE if both P. falciparum and
P. vivax data are present in object.
hide_confidential
if TRUE, removes confidential points from the map
printed Should the plot be printed to the graphics device.
10 [Link]

Value
[Link] returns a plots (gg object) for the supplied [Link] dataframe.

Examples
## Not run:
PfPR_surveys_NGA <- getPR(country = c("Nigeria"), species = "Pf")
autoplot(PfPR_surveys_NGA)

# Download PfPR2-10 Raster (Bhatt et al. 2015) and raw survey points for Madagascar in
# 2013 and visualise these together on a map.

# Download madagascar shapefile to use for raster download.

MDG_shp <- getShp(ISO = "MDG", admin_level = "admin0")

# Download PfPR2-10 Raster for 2013 & plot this

MDG_PfPR2_10 <- getRaster(surface = "Plasmodium falciparum PR2-10", shp = MDG_shp, year = 2013)
p <- autoplot(MDG_PfPR2_10)

# Download raw PfPR survey points & plot these over the top of the raster
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")

## End(Not run)

[Link] Create a basic plot to visualise downloaded shapefiles

Description
[Link] creates a map of shapefiles downloaded using getShp.

Usage
## S3 method for class 'sf'
autoplot(object, ..., map_title = NULL, facet = FALSE, printed = TRUE)

Arguments
object A sf object downloaded using getShp.
... Other arguments passed to specific methods
[Link] 11

map_title Custom title used for the plot.

facet If TRUE, splits map into a separate facet for each administrative level.
printed Should the plot print to graphics device.

Value
[Link] returns a map of the supplied sf object

Examples
## Not run:
MDG_shp <- getShp(ISO = "MDG", admin_level = "admin0")
autoplot(MDG_shp)

## End(Not run)

[Link] Quickly visualise Rasters downloaded from MAP

Description
[Link] creates a map of all rasters in a SpatRaster object and displays these in a
grid.

Usage
## S3 method for class 'SpatRaster'
autoplot(
object,
...,
shp_df = NULL,
legend_title = "",
plot_titles = TRUE,
fill_scale_transform = "identity",
fill_colour_palette = "RdYlBu",
printed = TRUE
)

Arguments
object SpatRaster object to be visualised.
... Other arguments passed to specific methods
shp_df Shapefile(s) ([Link]) to plot with downloaded raster.
legend_title String used as title for all colour scale legends.
plot_titles Plot name of raster object as header for each individual raster plot?
12 [Link]

fill_scale_transform
String givning a transformation for the fill aesthetic. See the trans argument in
continuous_scale for possible values.
fill_colour_palette
String referring to a colorbrewer palette to be used for raster colour scale.
printed Logical vector indicating whether to print maps of supplied rasters.

Value

[Link] returns a list of plots (gg objects) for each supplied raster.

See Also

getRaster:
to download rasters directly from MAP.

Examples
## Not run:
# Download PfPR2-10 Raster (Bhatt et al 2015) and raw survey points
# for Madagascar in 2013 and visualise these together on a map.

# Download madagascar shapefile to use for raster download.

MDG_shp <- getShp(ISO = "MDG", admin_level = "admin0")

# Download PfPR2-10 Raster for 2013 & plot this

MDG_PfPR2_10 <- getRaster(surface = "Plasmodium falciparum PR2-10",
shp = MDG_shp, year = 2013)
p <- autoplot(MDG_PfPR2_10, shp_df = MDG_shp)

# Download raw PfPR survey points & plot these over the top of the raster
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")

# Download global raster of G6PD deficiency (Howes et al 2012) and visualise this on a map.
G6PDd_global <- getRaster(surface = "G6PD Deficiency Allele Frequency")
autoplot(G6PDd_global)

## End(Not run)
[Link] 13

[Link]
Quickly visualise Rasters downloaded from MAP

Description
[Link] creates a map of all rasters in a [Link]
object and displays these in a grid.

Usage
## S3 method for class 'SpatRasterCollection'
autoplot(
object,
...,
shp_df = NULL,
legend_title = "",
plot_titles = TRUE,
fill_scale_transform = "identity",
fill_colour_palette = "RdYlBu",
printed = TRUE
)

Arguments
object SpatRasterCollection object to be visualised.
... Other arguments passed to specific methods
shp_df Shapefile(s) ([Link]) to plot with downloaded raster.
legend_title String used as title for all colour scale legends.
plot_titles Plot name of raster object as header for each individual raster plot?
fill_scale_transform
String givning a transformation for the fill aesthetic. See the trans argument in
continuous_scale for possible values.
fill_colour_palette
String referring to a colorbrewer palette to be used for raster colour scale.
printed Logical vector indicating whether to print maps of supplied rasters.

Value
[Link] returns a list of plots (gg objects) for each supplied raster.
gg object
14 [Link]

[Link]
Create a basic plot showing locations of downloaded Vector points

Description
[Link] creates a map of Vector points downloaded from MAP.

Usage
## S3 method for class '[Link]'
autoplot(
object,
...,
shp_df = NULL,
admin_level = "admin0",
map_title = "Vector Survey Locations",
fill_legend_title = "Raw Vetor Occurrences",
fill_scale_transform = "identity",
facet = NULL,
printed = TRUE
)

Arguments
object a [Link] object downloaded using getVecOcc
... Other arguments passed to specific methods
shp_df Shapefile(s) ([Link]) to plot with downloaded points. (If not specified auto-
matically uses getShp() for all countries included in [Link] object).
admin_level the administrative level used for plotting administrative boundaries; either "admin0";
"admin1" OR "both"
map_title custom title used for the plot
fill_legend_title
Add a title to the legend.
fill_scale_transform
String givning a transformation for the fill aesthetic. See the trans argument in
continuous_scale for possible values.
facet if TRUE, splits map into a separate facet for each malaria species; by default
FALSE.
printed Should the plot be printed to the graphics device.

Value
[Link] returns a plots (gg object) for the supplied [Link] dataframe.
autoplot_MAPraster 15

Examples
## Not run:
Vector_surveys_NGA_NG <- getVecOcc(country = c("Nigeria", "Niger"))
autoplot(Vector_surveys_NGA_NG)

# Download the predicted distribution of An. dirus species complex Raster and
# vector points for Myanmar and visualise these together on a map.

# Download Myanmar shapefile to use for raster download.

MMR_shp <- getShp(ISO = "MMR", admin_level = "admin0")

# Download An. dirus predicted distribution Raster & plot this

MMR_An_dirus <- getRaster(surface = "Anopheles dirus species complex", shp = MMR_shp)
p <- autoplot(MMR_An_dirus, shp_df = MMR_shp, printed = FALSE)

# Download raw occurrence points & plot these over the top of the raster
species <- getVecOcc(country = "Myanmar", species = "Anopheles dirus")
# p[[1]] +
# geom_point(data = species,
# aes(longitude,
# latitude,
# colour = species))+
# scale_colour_manual(values = "black", name = "Vector suvery 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")

## End(Not run)

autoplot_MAPraster Quickly visualise Rasters downloaded from MAP

Description
autoplot_MAPraster is a wrapper for [Link] that calls [Link] to allow
automatic map creation for RasterLayer/RasterStack objects downloaded from MAP.

Usage
autoplot_MAPraster(object, ...)

Arguments
object RasterLayer/RasterStack object to be visualised.
... other optional arguments to [Link] (e.g. shp_df, legend_title, page_title...)
16 autoplot_MAPraster

Value

autoplot_MAPraster returns a list of plots (gg objects) for each supplied raster.

See Also

getRaster:
to download rasters directly from MAP.
[Link]:
to convert RasterLayer/RasterStack objects into a ’MAPraster’ object ([Link]) for easy plotting
with ggplot.
[Link]:
to quickly visualise MAPraster objects created using [Link].

Examples

## Not run:
#Download PfPR2-10 Raster (Bhatt et al 2015) and raw survey points for Madagascar in
# 2013 and visualise these together on a map.

# Download madagascar shapefile to use for raster download.

MDG_shp <- getShp(ISO = "MDG", admin_level = "admin0")

# Download PfPR2-10 Raster for 2013 & plot this

MDG_PfPR2_10 <- getRaster(surface = "Plasmodium falciparum PR2-10", shp = MDG_shp, year = 2013)
# p <- autoplot_MAPraster(MDG_PfPR2_10)

# Download raw PfPR survey points & plot these over the top of the raster
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")
## End(Not run)

# Download global raster of G6PD deficiency (Howes et al 2012) and visualise this on a map.
## Not run:
G6PDd_global <- getRaster(surface = "G6PD Deficiency Allele Frequency")
#autoplot_MAPraster(G6PDd_global)

## End(Not run)
convertPrevalence 17

convertPrevalence convert prevalences from one age range to another

Description
convert prevalences from one age range to another

Usage
convertPrevalence(
prevalence,
age_min_in,
age_max_in,
age_min_out = rep(2, length(prevalence)),
age_max_out = rep(9, length(prevalence)),
parameters = "Pf_Smith2007",
sample_weights = NULL
)

Arguments
prevalence Vector of prevalence values
age_min_in Vector of minimum ages sampled
age_max_in Vector maximum ages sampled.
age_min_out Length 1 numeric or vector of same length as prevalence given the required age
range upper bound
age_max_out Length 1 numeric or vector of same length as prevalence given the required age
range lower bound
parameters Specifies the set of parameters to use in the model. This can either be "Pf_Smith2007"
to use the parameters for *Plasmodium falciparum* defined in that paper, "Pv_Gething2012"
for the *P. vivax* parameters used in that paper, or a user-specified vector givng
the values of parameters ‘b‘, ‘s‘, ‘c‘ and ‘alpha‘, in that order. If specified,
sample_weights Must be a vector of length 85 giving the sample weights for each age category
(the proportion of the population in that age category) . If ‘NULL‘, The sample
weights used in Smith et al. 2007 are used.

References
Smith, D. L. et al. Standardizing estimates of the Plasmodium falciparum parasite rate. Malaria
Journal 6, 131 (2007).
Gething, Peter W., et al. "A long neglected world malaria map: Plasmodium vivax endemicity in
2010." PLoS neglected tropical diseases 6.9 (2012): e1814.
Code written by Nick Golding and Dave Smith
18 extractRaster

Examples
# Convert from prevalence 2 to 5 to prevalence 2 to 10
pr2_10 <- convertPrevalence(0.1, 2, 5, 2, 10)

# Convert many surveys all to 2 to 10.

pr <- runif(20, 0.1, 0.15)
min_in <- sample(1:5, 20, replace = TRUE)
max_in <- rep(8, 20)
min_out <- rep(2, 20)
max_out <- rep(10, 20)
pr_standardised <- convertPrevalence(pr, min_in, max_in,
min_out, max_out)

plot(pr_standardised, pr)

extractRaster Extract pixel values from MAP rasters using point coordinates.

Description
extractRaster extracts pixel values from MAP rasters at user-specified point locations (without
downloading the entire raster).

Usage
extractRaster(
df,
csv_path = NULL,
surface = NULL,
year = NULL,
dataset_id = NULL
)

Arguments
df [Link] containing coordinates of input point locations, must contain columns
named ’latitude’/’lat’/’x’ AND ’longitude’/’long’/’y’)
csv_path (optional) user-specified path to which extractRaster coordinates and results are
stored.
surface deprecated argument. Please remove it from your code.
year for time-varying rasters: if downloading a single surface for one or more years,
year should be a vector specifying the desired year(s). if downloading more
than one surface, use a list the same length as surface, providing the desired
year-range for each time-varying surface in surface or NA for static rasters.
dataset_id A character string specifying the dataset ID(s) of one or more rasters. These
dataset ids can be found in the [Link] returned by listRaster, in the dataset_id
column e.g. c(’Malaria__202206_Global_Pf_Mortality_Count’, ’Malaria__202206_Global_Pf_Parasite_
fillDHSCoordinates 19

Value
extractRaster returns the input dataframe (df), with the following columns appended, providing
values for each raster, location and year.

1. layerName dataset id corresponding to extracted raster values for a given row, check listRaster
for raster metadata.
2. year the year for which raster values were extracted (time-varying rasters only; static rasters
do not have this column).
3. value the raster value for the pixel in which a given point location falls.

See Also
autoplot method for quick mapping of PR point locations ([Link]).

Examples
#Download PfPR data for Nigeria and Cameroon and map the locations of these points using autoplot
## Not run:
# Get some data and remove rows with NAs in location or examined or positive columns.
NGA_CMR_PR <- getPR(country = c("Nigeria", "Cameroon"), species = "Pf")
complete <- [Link](NGA_CMR_PR[, c(4, 5, 16, 17)])
NGA_CMR_PR <- NGA_CMR_PR[complete, ]

# Extract PfPR data at those locations.

data <- extractRaster(df = NGA_CMR_PR[, c('latitude', 'longitude')],
dataset_id = 'Malaria__202206_Global_Pf_Parasite_Rate',
year=2020)

# Some rasters are stored with NA encoded as -9999

data$value[data$value == -9999] <- NA

# We can quickly plot a summary

plot((NGA_CMR_PR$positive / NGA_CMR_PR$examined) ~ data$value)

## End(Not run)

fillDHSCoordinates Add DHS locations to malaria data

Description
We cannot directly share DHS data. We can share coordinates, but not the data values. This function
attempts to fill the data gaps directly from the DHS server using the package rdhs. To use the
function you will need to setup an account on the DHS website and request any datasets you wish
to use (including requesting the GPS data). Confirmation can take a few days. Once this has been
verified, you should be able to use this function.
20 fillDHSCoordinates

Usage
fillDHSCoordinates(
data,
email = NULL,
project = NULL,
cache_path = NULL,
config_path = NULL,
global = TRUE,
verbose_download = FALSE,
verbose_setup = TRUE,
data_frame = NULL,
timeout = 30,
password_prompt = FALSE,
prompt = TRUE
)

Arguments
data Data to add DHS coordinates to
email Character for email used to login to the DHS website.
project Character for the name of the DHS project from which datasets should be down-
loaded.
cache_path Character for directory path where datasets and API calls will be cached. If left
bank, a suitable directory will be created within your user cache directory for
your operating system (permission granting).
config_path Character for where the config file should be saved. For a global configuration,
‘config_path‘ must be ’~/.[Link]’. For a local configuration, ‘config_path‘
must be ’[Link]’. If left bank, the config file will be stored within your user
cache directory for your operating system (permission granting).
global Logical for the config_path to be interpreted as a global config path or a local
one. Default = TRUE.
verbose_download
Logical for dataset download progress bars to be shown. Default = FALSE.
verbose_setup Logical for rdhs setup and messages to be printed. Default = TRUE.
data_frame Function with which to convert API calls into. If left blank data_frame objects
are returned. Must be passed as a character. Examples could be: [Link]::[Link]
tibble::[Link]
timeout Numeric for how long in seconds to wait for the DHS API to respond. Default
= 30.
password_prompt
Logical whether user is asked to type their password, even if they have previ-
ously set it. Default = FALSE. Set to TRUE if you have mistyped your password
when using set_rdhs_config.
prompt Logical for whether the user should be prompted for permission to write to files.
This should not need be
getPR 21

Details
This function requires the package rdhs which is currently only suggested by the package (not a
dependency). So you will need to install it.
Note that the project has to be the exact name in your DHS project.

Author(s)
OJ Watson

Examples
## Not run:
pf <- malariaAtlas::getPR("all",species = "pf")
pf <- fillDHSCoordinates(pf,
email = "pretend_email@[Link]",
project = "pretend project name")

## End(Not run)

getPR Download PR points from the MAP database

Description
getPR downloads all publicly available PR points for a specified country (or countries) and returns
this as a dataframe.

Usage
getPR(
country = NULL,
ISO = NULL,
continent = NULL,
species = NULL,
extent = NULL,
start_date = NULL,
end_date = NULL,
version = NULL
)

Arguments
country string containing name of desired country, e.g. c("Country1", "Country2",
...) OR = "ALL". (Use one of country OR ISO OR continent, not combined)
ISO string containing ISO3 code for desired country, e.g. c("XXX", "YYY", ...)
OR = "ALL". (Use one of country OR ISO OR continent, not combined)
22 getPR

continent string containing continent (one of "Africa", "Americas", "Asia", "Oceania")

for desired data, e.g. c("continent1", "continent2", ...). (Use one of
country OR ISO OR continent, not combined)
species string specifying the Plasmodium species for which to find PR points, options
include: "Pf" OR "Pv" OR "BOTH"
extent an object specifying spatial extent within which PR data is desired, as returned
by sf::st_bbox() - the first column has the minimum, the second the maximum
values; rows 1 & 2 represent the x & y dimensions respectively (matrix(c("xmin",
"ymin","xmax", "ymax"), nrow = 2, ncol = 2, dimnames = list(c("x", "y"),
c("min", "max"))))
start_date string object representing the lower date to filter the PR data by (inclusive) e.g.
’2020-01-01’
end_date string object representing the upper date to filter the PR data by (exclusive) e.g.
’2020-01-01’
version (optional) The PR dataset version to return. If not provided, will just use the
most recent version of PR data. (To see available version options, use listPR-
PointVersions)

Details
country and ISO refer to countries and a lower-level administrative regions such as Mayotte and
French Guiana. While we cannot direectly distribute DHS coordinates, we can distribute the
number of examined and positive. If the coordinates are needed they can be downloaded from
[Link], via the rdhs package or using malariaAtlas:fillDHSCoordinates().

Value
getPR returns a dataframe containing the below columns, in which each row represents a distinct
data point/ study site.

1. dhs_id The dhs survey id if appropriate.

2. site_id Unique site identifier
3. site_name Name of site.

See Also
autoplot method for quick mapping of PR point locations ([Link]).

Examples
#Download PfPR data for Nigeria and Cameroon and map the locations of these points using autoplot
## Not run:
NGA_CMR_PR <- getPR(country = c("Nigeria", "Cameroon"), species = "Pf")
autoplot(NGA_CMR_PR)

#Download PfPR data for Madagascar and map the locations of these points using autoplot
Madagascar_pr <- getPR(ISO = "MDG", species = "Pv")
autoplot(Madagascar_pr)
getRaster 23

getPR(country = "ALL", species = "BOTH")

## End(Not run)

getRaster Download Rasters produced by the Malaria Atlas Project

Description
getRaster downloads publicly available MAP rasters for a specific surface & year, clipped to a
provided bounding box or shapefile.

Usage
getRaster(
dataset_id = NULL,
surface = NULL,
shp = NULL,
extent = NULL,
file_path = NULL,
year = NULL,
vector_year = NULL
)

Arguments
dataset_id A character string specifying the dataset ID(s) of one or more rasters. These
dataset ids can be found in the [Link] returned by listRaster, in the dataset_id
column e.g. c(’Malaria__202206_Global_Pf_Mortality_Count’, ’Malaria__202206_Global_Pf_Parasite_
surface deprecated argument. Please remove it from your code.
shp SpatialPolygon(s) object of a shapefile to use when clipping downloaded rasters.
(use either shp OR extent; if neither is specified global raster is returned).
extent 2x2 matrix specifying the spatial extent within which raster data is desired, as
returned by sf::st_bbox() - the first column has the minimum, the second the
maximum values; rows 1 & 2 represent the x & y dimensions respectively
(matrix(c("xmin", "ymin","xmax", "ymax"), nrow = 2, ncol = 2, dimnames =
list(c("x", "y"), c("min", "max")))) (use either shp OR extent; if neither is
specified global raster is returned).
file_path string specifying the directory to which raster files will be downloaded, if you
want to download them. If none given, rasters will not be saved to files.
year default = rep(NA, length(dataset_id)) (use NA for static rasters); for time-
varying rasters: if downloading a single surface for one or more years, year
should be a string specifying the desired year(s). if downloading more than one
surface, use a list the same length as dataset_id, providing the desired year-
range for each time-varying surface in dataset_id or NA for static rasters.
24 getShp

vector_year deprecated argument. Please remove it from your code.

Value
getRaster returns a SpatRaster for the specified extent. Or a SpatRasterCollection if the two rasters
are incompatible in terms of projection/extent/resolution

See Also
autoplot_MAPraster
to quickly visualise rasters downloded using getRaster.
[Link]
to convert RasterLayer/RasterStack objects into a ’MAPraster’ object ([Link]) for easy plotting
with ggplot.
[Link]
to quickly visualise MAPraster objects created using [Link].

Examples
# Download PfPR2-10 Raster for Madagascar and visualise this immediately.
## Not run:
MDG_shp <- getShp(ISO = "MDG", admin_level = "admin0")
MDG_PfPR2_10 <- getRaster(dataset_id = "Malaria__202206_Global_Pf_Parasite_Rate", shp = MDG_shp)
autoplot(MDG_PfPR2_10)

## End(Not run)

getShp Download MAPadmin2013 Administrative Boundary Shapefiles from

the MAP geoserver

Description
getShp downloads a shapefile for a specified country (or countries) and returns this as either a
spatialPolygon or [Link] object.

Usage
getShp(
country = NULL,
ISO = NULL,
extent = NULL,
admin_level = c("admin0"),
format = NULL,
long = NULL,
lat = NULL,
getShp 25

version = NULL
)

Arguments
country string containing name of desired country, e.g. c("Country1", "Country2",
...) OR = "ALL" (use either ISO OR country)
ISO string containing ISO3 code for desired country, e.g. c("XXX", "YYY", ...)
OR = "ALL" (use either ISO OR country)
extent 2x2 matrix specifying the spatial extent within which polygons are desired,
as returned by sp::bbox() - the first column has the minimum, the second the
maximum values; rows 1 & 2 represent the x & y dimensions respectively
(matrix(c("xmin", "ymin","xmax", "ymax"), nrow = 2, ncol = 2, dimnames =
list(c("x", "y"), c("min", "max")))).
admin_level string specifying the administrative level for which shapefile are desired (only
"admin0","admin1","admin2","admin3", or "all" accepted). N.B. Not all admin-
istrative levels are available for all countries. Use listShp to check which shape-
files are available. If an administrative level is requested that is not available,
the closest available administrative level shapefiles will be returned.
format deprecated argument. Please remove it from your code.
long longitude of a point location falling within the desired shapefile.
lat latitude of a point location falling within the desired shapefile.
version The admin unit dataset version to return. Is NULL by default, and if left NULL
will just use the most recent version of admin unit data.

Value
getShp returns a sf object for requested administrative unit polygons. The following attribute fields
are included:

1. iso ISO-3 code of given administrative unit (or the ISO code of parent unit for administrative-
level 1 units).
2. admn_level administrative level of the given administrative unit - either 0 (national), 1 (first-
level division), 2 (second-level division), 3 (third-level division).
3. name_0 name of admin0 parent of a given administrative unit (or just shapefile name for ad-
min0 units)
4. id_0 id code of admin0 parent of the current shapefile (or just shapefile id for admin0 units)
5. type_0 if applicable, type of administrative unit or admin0 parent
6. name_1 name of admin1 parent of a given administrative unit (or just shapefile name for ad-
min1 units); NA for admin0 units
7. id_1 id code of admin1 parent of the current shapefile (or just shapefile id for admin1 units);
NA for admin0 units
8. type_1 if applicable, type of administrative unit or admin1 parent
9. name_2 name of admin2 parent of a given administrative unit (or just shapefile name for ad-
min2 units); NA for admin0, admin1 units
26 getSpBbox

10. id_2 id code of admin2 parent of the current shapefile (or just shapefile id for admin2 units);
NA for admin0, admin1 units
11. type_2 if applicable, type of administrative unit or admin2 parent
12. name_3 name of admin3 parent of a given administrative unit (or just shapefile name for ad-
min3 units); NA for admin0, admin1, admin2 units
13. id_3 id code of admin3 parent of the current shapefile (or just shapefile id for admin3 units);
NA for admin0, admin1, admin2 units
14. type_3 if applicable, type of administrative unit
15. source source of administrative boundaries
16. geometry geometry of administrative boundaries
17. country_level composite iso_admn_level field.

See Also
autoplot method for quick mapping of PR point locations ([Link]).

Examples
#Download PfPR data & associated shapefiles for Nigeria and Cameroon
## Not run:
NGA_CMR_PR <- getPR(country = c("Nigeria", "Cameroon"), species = "Pf")
NGA_CMR_shp <- getShp(country = c("Nigeria", "Cameroon"))

#Download PfPR data & associated shapefiles for Chad

Chad_PR <- getPR(ISO = "TCD", species = "both")
Chad_shp <- getShp(ISO = "TCD")

#' #Download PfPR data & associated shapefiles defined by extent for Madagascar
MDG_PR <- getPR(country = "Madagascar", species = "Pv")

## End(Not run)

getSpBbox Return sp style bbox

Description
Return sp style bbox

Usage
getSpBbox(sfBboxOrShp)

Arguments
sfBboxOrShp sf shapefile or result of sf::st_bbox(sf_shp)
getVecOcc 27

Value
bbox in sp style. A 2x2 matrix - the first column has the minimum, the second the maximum
values; rows 1 & 2 represent the x & y dimensions respectively (matrix(c("xmin", "ymin","xmax",
"ymax"), nrow = 2, ncol = 2, dimnames = list(c("x", "y"), c("min", "max"))))

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.

Description
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.

Usage
getVecOcc(
country = NULL,
ISO = NULL,
continent = NULL,
species = "all",
extent = NULL,
start_date = NULL,
end_date = NULL,
version = NULL
)

Arguments
country string containing name of desired country, e.g. c("Country1", "Country2",
...) OR = "ALL". (Use one of country OR ISO OR continent, not combined)
ISO string containing ISO3 code for desired country, e.g. c("XXX", "YYY", ...)
OR = "ALL". (Use one of country OR ISO OR continent, not combined)
continent string containing continent (one of "Africa", "Americas", "Asia", "Oceania")
for desired data, e.g. c("continent1", "continent2", ...). (Use one of
country OR ISO OR continent, not combined)
species string specifying the Anopheles species for which to find vector occurrence
points, options include: "Anopheles...." OR "ALL"
extent an object specifying spatial extent within which PR data is desired, as returned
by sf::st_bbox(). - the first column has the minimum, the second the maxi-
mum values; rows 1 & 2 represent the x & y dimensions respectively (ma-
trix(c("xmin", "ymin","xmax", "ymax"), nrow = 2, ncol = 2, dimnames = list(c("x",
"y"), c("min", "max"))))
28 isAvailable

start_date string object representing the lower date to filter the vector occurrence data by
(inclusive)
end_date string object representing the upper date to filter the vector occurrence data by
(exclusive)
version (optional) The vector points dataset version to use. If not provided, will just use
the most recent version of vector points data. (To see available version options,
use listVecOccPointVersions)

Value
getVecOcc returns a dataframe containing the below columns, in which each row represents a
distinct data point/ study site.

1. COLUMNNAME description of contents

2. COLUMNNAME description of contents
3. COLUMNNAME description of contents

See Also
autoplot method for quick mapping of Vector occurrence point locations ([Link]).

Examples
# Download vector occurrence data for Brazil and map the locations using [Link]
## Not run:
Brazil_vec <- getVecOcc(country = "Brazil")
autoplot(Brazil_vec)

# Download vector data for Madagascar and map the locations using autoplot
Madagascar_vec <- getVecOcc(ISO = "MDG", species = "All")
autoplot(Madagascar_vec)

# Subset by extent.
extent_vec <- getVecOcc(extent = matrix(c(100,13,110,18), nrow = 2), species = 'all')

## End(Not run)

isAvailable Available data to download from the MAP geoserver.

Description
isAvaiable is a wrapper for isAvailable_pr and isAvailable_vec, listing data (PR survey point
location data and vector occurrence locations available to download from the MAP geoserver.
isAvailable 29

Usage

isAvailable(
sourcedata = NULL,
full_results = FALSE,
country = NULL,
ISO = NULL,
continent = NULL,
...
)

Arguments

sourcedata One of ’pr points’ or ’vector points’

full_results Should the list be printed to the console?
country string containing name of desired country, e.g. c("Country1", "Country2",
...) OR = "ALL" (use one of country OR ISO OR continent, not combined)
ISO string containing ISO3 code for desired country, e.g. c("XXX", "YYY", ...)
OR = "ALL" (use one of country OR ISO OR continent, not combined)
continent string containing continent for desired data, e.g. c("continent1", "continent2",
...) (use one of country OR ISO OR continent, not combined)
... passed on to isAvailable_vec and isAvailable_pr

Value

isAvailable returns a [Link] detailing the administrative units for which shapefiles are stored
on the MAP geoserver.

See Also

link{isAvailable_pr} isAvailable_vec

Examples

## Not run:
available_pr_locations <- isAvailable_pr(ISO = 'IDN')
available_vector_locations <- isAvailable_vec(ISO = 'IDN')

## End(Not run)
30 isAvailable_pr

isAvailable_pr Check whether PR points are available for a given location

Description
isAvailable_pr checks whether the MAP database contains PR points for the specified coun-
try/location.

Usage
isAvailable_pr(
sourcedata = NULL,
country = NULL,
ISO = NULL,
continent = NULL,
full_results = FALSE,
version = NULL
)

Arguments
sourcedata deprecated argument. Please remove it from your code.
country string containing name of desired country, e.g. c("Country1", "Country2",
...) (use one of country OR ISO OR continent, not combined)
ISO string containing ISO3 code for desired country, e.g. c("XXX", "YYY", ...)
(use one of country OR ISO OR continent, not combined)
continent string containing name of continent for desired data, e.g. c("Continent1",
"Continent2", ...)(use one of country OR ISO OR continent, not com-
bined)
full_results By default this is FALSE meaning the function only gives a message outlining
whether specified country is available, if full_results == TRUE, the function
returns a named list outlining data availability.
version (optional) The PR dataset version to use. If not provided, will just use the most
recent version of PR data. (To see available version options, use listPRPointVer-
sions)

Value
isAvailable_pr returns a named list of input locations with information regarding data availability.
if full_results == TRUE, a named list is returned with the following elements:

1. location - specified input locations

2. is_available- 1 or 0; indicating whether data is available for this location
3. possible_match- agrep-matched country names indicating potential mispellings of countries
where is_available == 0; NA if data is available for this location.
isAvailable_vec 31

Examples
## Not run:
isAvailable_pr(country = "Suriname")
x <- isAvailable_pr(ISO = "NGA", full_results = TRUE)
x <- isAvailable_pr(continent = "Oceania", full_results = TRUE)

## End(Not run)

isAvailable_vec Check whether Vector Occurrence points are available for a given lo-
cation

Description
isAvailable_vec checks whether the MAP database contains Vector Occurrence points for the
specified country/location.

Usage
isAvailable_vec(
sourcedata = NULL,
country = NULL,
ISO = NULL,
continent = NULL,
full_results = FALSE,
version = NULL
)

Arguments
sourcedata deprecated argument. Please remove it from your code.
country string containing name of desired country, e.g. c("Country1", "Country2",
...) (use one of country OR ISO OR continent, not combined)
ISO string containing ISO3 code for desired country, e.g. c("XXX", "YYY", ...)
(use one of country OR ISO OR continent, not combined)
continent string containing name of continent for desired data, e.g. c("Continent1",
"Continent2", ...)(use one of country OR ISO OR continent, not com-
bined)
full_results By default this is FALSE meaning the function only gives a message outlining
whether specified country is available, if full_results == TRUE, the function
returns a named list outlining data availability.
version (optional) The vector points dataset version to use. If not provided, will just use
the most recent version of vector points data. (To see available version options,
use listVecOccPointVersions)
32 listData

Value

isAvailable_Vec returns a named list of input locations with information regarding data availabil-
ity.
if full_results == TRUE, a named list is returned with the following elements:

1. location - specified input locations

2. is_available- 1 or 0; indicating whether data is available for this location
3. possible_match- agrep-matched country names indicating potential mispellings of countries
where is_available == 0; NA if data is available for this location.

Examples
## Not run:
isAvailable_vec(country = "Suriname")
x <- isAvailable_vec(ISO = "NGA", full_results = TRUE)
x <- isAvailable_vec(continent = "Oceania", full_results = TRUE)

## End(Not run)

listData Deprecated function. Please instead use listPRPointCountries for

pr points, listVecOccPointCountries for vector points, listRaster for
raster and listShp for shape.

Description

listData deprecated function Please remove it from your code.

Usage

listData(datatype, printed = TRUE, ...)

Arguments

datatype "pr points", "vector points" "raster", or "shape"

printed whether to pretty print the output in console
... passed on to listPRPointCountries, listVecOccPointCountries, listShp
listPoints 33

listPoints Deprecated function. Please instead use listPRPointCountries for pr

points, and listVecOccPointCountries for vector points

Description
listPoints deprecated function Please remove it from your code.

Usage
listPoints(printed = TRUE, sourcedata, version = NULL)

Arguments
printed whether to pretty print the output in console
sourcedata "pr points" or "vector points"
version (optional) The PR dataset version to use If not provided, will just use the most
recent version of PR data. (To see available version options, use listPRPointVer-
sions)

listPRPointCountries List countries where there is pr point data available

Description
listPRPointCountries

Usage
listPRPointCountries(printed = TRUE, version = NULL)

Arguments
printed Should the list be printed to the console?
version (optional) The PR dataset version to use If not provided, will just use the most
recent version of PR data. (To see available version options, use listPRPointVer-
sions)

Value
listPRPointCountries returns a [Link] detailing the countries for which PR points are pub-
licly available.
34 listRaster

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

Description
listPRPointVersions lists available versions of parasite rate point data from the Web Feature
Services provided by the Malaria Atlas Project.

Usage
listPRPointVersions(printed = TRUE)

Arguments
printed Should the list be printed to the console?

Value
A [Link] with column ’version’ The version can then be provided to other functions to fetch the
data within that dataset. e.g. in getPR

Examples
## Not run:
prDatasets <- listPRPointVersions()

## End(Not run)

listRaster List all MAP Rasters available to download.

Description
listRaster lists all rasters available to download from the Malaria Atlas Project database.

Usage
listRaster(printed = TRUE)

Arguments
printed Should the list be printed to the console?
listShp 35

Value
listRaster returns a [Link] detailing the following information for each raster available to
download from the Malaria Atlas Project database.

1. dataset_id the unique dataset ID of the raster, which can the be used in functions such as
getRaster and extractRaster
2. raster_code unique identifier for each raster
3. title abbreviated title for each raster, used as surface argument in getRaster()
4. title_extended extended title for each raster, detailing raster content
5. abstract full description of each raster, outlining raster creation methods, raster content and
more.
6. citation citation of peer-reviewed article in which each raster has been published
7. pub_year year in which raster was published, used as pub_year argument in getRaster() to
updated raster versions from their predecessor(s).
8. min_raster_year earliest year for which each raster is available
9. max_raster_year latest year for which each raster is available

Examples
## Not run:
available_rasters <- listRaster()

## End(Not run)

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

Description
listShp lists all administrative units for which shapefiles are stored on the MAP geoserver.

Usage
listShp(printed = TRUE, admin_level = c("admin0", "admin1"), version = NULL)

Arguments
printed Should the list be printed to the console?
admin_level Specifies which administrative unit level for which to return available poly-
gon shapefiles. A string vector including one or more of"admin0", "admin1",
"admin2" OR "admin3". Default: c("admin0", "admin1")
version The admin unit dataset version to return. Is NULL by default, and if left NULL
will just use the most recent version of admin unit data.
36 listShpVersions

Value

listShp returns a [Link] detailing the administrative units for which shapefiles are stored on
the MAP geoserver.

Examples
## Not run:
available_admin_units <- listShp()
available_admin_units <- listShp(admin_level = c('admin2','admin3'), version = '202206')

## End(Not run)

listShpVersions List all versions of admin unit shapes from the Web Feature Ser-
vices provided by the Malaria Atlas Project within the Admin Units
workspace.

Description

listShpVersions lists available versions of Admin Unit shapefiles from the Web Feature Services
provided by the Malaria Atlas Project.

Usage

listShpVersions(printed = TRUE)

Arguments

printed Should the list be printed to the console?

Value

A [Link] with column ’version’. The version can then be provided to other functions to fetch
the data within that dataset. e.g. in getShp

Examples
## Not run:
vecOccDatasets <- listShpVersions()

## End(Not run)
listSpecies 37

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

Description
listSpecies lists all species occurrence data available to download from the Malaria Atlas Project
database.

Usage
listSpecies(printed = TRUE, version = NULL)

Arguments
printed should the list be printed to the database.
version (optional) The vector dataset version to use If not provided, will just use the
most recent version of vector dataset data. (To see available version options, use
listVecOccPointVersions)

Value
listSpecies returns a [Link] detailing the following information for each species available to
download from the Malaria Atlas Project database.

1. species string detailing species

Examples
## Not run:
available_species <- listSpecies()

## End(Not run)

listVecOccPointCountries
List countries where there is vector occurrence point data available

Description
listVecOccPointCountries

Usage
listVecOccPointCountries(printed = TRUE, version = NULL)
38 listVecOccPointVersions

Arguments

printed Should the list be printed to the console?

version (optional) The vector occurrence dataset version to use If not provided, will just
use the most recent version of vector occurrence data. (To see available version
options, use listVecOccPointVersions)

Value

listVecOccPointCountries returns a [Link] detailing the countries for which vector occur-
rence points are publicly available.

listVecOccPointVersions
List all dataset versions from the Web Feature Services provided by the
Malaria Atlas Project within the Vector Occurrence workspace.

Description

listVecOccPointVersions lists available versions of all the feature datasets in the Vector Occur-
rence workspace from the Web Feature Services provided by the Malaria Atlas Project.

Usage

listVecOccPointVersions(printed = TRUE)

Arguments

printed Should the list be printed to the console?

Value

A [Link] with column ’version’. The version can then be provided to other functions to fetch
the data within that dataset. e.g. in getVecOcc

Examples
## Not run:
vecOccDatasets <- listVecOccPointVersions()

## End(Not run)
makeSpatRasterAutoplot 39

makeSpatRasterAutoplot
Create a single (sub) plot for a SpatRaster

Description

Create a single (sub) plot for a SpatRaster

Usage

makeSpatRasterAutoplot(
spatraster,
rastername,
shp_df,
legend_title,
fill_scale_transform,
fill_colour_palette,
plot_titles
)

Arguments

spatraster SpatRaster object containing a single layer

rastername raster name, to include in title
shp_df sf shapefile
legend_title title for legend
fill_scale_transform
scale
fill_colour_palette
palette
plot_titles bool, whether to include title

Value

ggplot object
40 malariaAtlas

malariaAtlas An R interface to open-access malaria data, hosted by the Malaria

Atlas Project.

Description
malariaAtlas provides a suite of tools to allow you to download all publicly available PR points
for a specified country (or ALL countries) as a dataframe within R.

malariaAtlas functions
1. listAll - lists all countries for which there are publicly visible PR datapoints in the MAP
database.
2. is_available - checks whether the MAP database contains PR points for the specified coun-
try/countries.
3. getPR - downloads all publicly available PR points for a specified country (or countries) and
returns this as a dataframe.
Index

[Link], 3, 3, 7, 15, 16, 24 makeSpatRasterAutoplot, 39

[Link], 4 malariaAtlas, 40
[Link], 5
[Link], 6
[Link], 3, 6, 7, 15, 16, 24
[Link], 4, 8
[Link], 9, 19, 22, 26
[Link], 10
[Link], 11
[Link], 13
[Link], 14, 28
autoplot_MAPraster, 15, 24

continuous_scale, 7, 9, 12–14
convertPrevalence, 17

extractRaster, 18

fillDHSCoordinates, 19

getPR, 9, 21
getRaster, 3, 7, 12, 16, 23, 24
getShp, 8, 10, 24
getSpBbox, 26
getVecOcc, 14, 27

isAvailable, 28
isAvailable_pr, 30
isAvailable_vec, 29, 31

listData, 32
listPoints, 33
listPRPointCountries, 33
listPRPointVersions, 34
listRaster, 19, 34
listShp, 35
listShpVersions, 36
listSpecies, 37
listVecOccPointCountries, 37
listVecOccPointVersions, 38

41