Package 'cart'

Title: Malaria Cartographic Information
Description: Extract population, prevalence and vector cartographic information for use with malarisimulation.
Authors: Pete Winskill [aut, cre]
Maintainer: Pete Winskill <[email protected]>
License: MIT + file LICENSE
Version: 0.1.0
Built: 2024-12-08 04:32:36 UTC
Source: https://github.com/mrc-ide/cart

Help Index

Get population raster.

Description

Downloads the unconstrained individual countries 2000-2020 UN adjusted (1km resolution) from the WorldPop server.

Usage

get_pop(iso3c, year)

Arguments

iso3c

Country iso3c code
year

Year of prevalence outputs

Value

Population raster

Get prevalence rasters.

Description

Downloads the specified malaria atlas project prevalence rasters.

Usage

get_prev(prevalence_rasters, year, pop)

Arguments

prevalence_rasters

List of prevalence rasters. See listRaster for available rasters. Default is for both falciparum and vivax.
year

Year of prevalence outputs
pop

Population raster

Value

A List of prevalence rasters.

Get spatial limits rasters.

Description

Downloads the specified malaria atlas project spatial limits of transmission rasters.

Usage

get_spatial_limits(spatial_limits_rasters, pop)

Arguments

spatial_limits_rasters

List of spatial distribution limits rasters. Default is for both falciparum and vivax. See listRaster for available rasters.
pop

Population raster

Value

A List of spatial limits rasters.

Get vector species.

Description

Downloads the specified malaria atlas project vector species rasters.

Usage

get_vectors(vector_rasters, year, pop)

Arguments

vector_rasters

List of vector species rasters. See listRaster for available rasters. Specified rasters must have an extent >= to the extent of the country specified. Please note the different definitions of vector species metrics - especially relative abundance vs probability of occurrence.
year

Year of prevalence outputs
pop

Population raster

Value

A List of vector species rasters.

Pull cartographic information

Description

Pull cartographic information

Usage

pull_cart(
  iso3c,
  year,
  vector_rasters = list(funestus = "Anopheles funestus", arabiensis =
    "Anopheles arabiensis Patton, 1905", gambiae = "Anopheles gambiae Giles, 1902"),
  prevalence_rasters = list(pfpr = "Plasmodium falciparum PR2 - 10 version 2020", pvpr
    = "Plasmodium vivax PR1-99 version 2020"),
  spatial_limits_rasters = list(pf_limits = "Plasmodium falciparum Spatial Limits",
    pv_limits = "Plasmodium vivax Spatial Limits")
)

Arguments

iso3c

Country iso3c code
year

Year of prevalence outputs
vector_rasters

List of vector species rasters. See listRaster for available rasters. Specified rasters must have an extent >= to the extent of the country specified. Please note the different definitions of vector species metrics - especially relative abundance vs probability of occurrence.
prevalence_rasters

List of prevalence rasters. See listRaster for available rasters. Default is for both falciparum and vivax.
spatial_limits_rasters

List of spatial distribution limits rasters. Default is for both falciparum and vivax. See listRaster for available rasters.

Value

A raster stack

Extract information from rasters

Description

Extract information from rasters

Usage

unpack_cart(iso3c_sf, stack)

Arguments

iso3c_sf

A simple feature shape file to extract for
stack

The raster stack from pull_cart

Value

Tibble with list columns of raw extracted values