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malariaAtlas: an R interface to global malariometric data hosted by the Malaria Atlas Project

Title: malariaAtlas: an R interface to global malariometric data hosted by the Malaria Atlas Project
Authors: Pfeffer, DA
Lucas, TCD
May, D
Harris, J
Rozier, J
Twohig, KA
Dalrymple, U
Guerra, CA
Moyes, CL
Thorn, M
Nguyen, M
Bhatt, S
Cameron, E
Weiss, DJ
Howes, RE
Battle, KE
Gibson, HS
Gething, PW
Item Type: Journal Article
Abstract: Background The Malaria Atlas Project (MAP) has worked to assemble and maintain a global open-access database of spatial malariometric data for over a decade. This data spans various formats and topics, including: geo-located surveys of malaria parasite rate; global administrative boundary shapefiles; and global and regional rasters representing the distribution of malaria and associated illnesses, blood disorders, and intervention coverage. MAP has recently released malariaAtlas, an R package providing a direct interface to MAP’s routinely-updated malariometric databases and research outputs. Methods and results The current paper reviews the functionality available in malariaAtlas and highlights its utility for spatial epidemiological analysis of malaria. malariaAtlas enables users to freely download, visualise and analyse global malariometric data within R. Currently available data types include: malaria parasite rate and vector occurrence point data; subnational administrative boundary shapefiles; and a large suite of rasters covering a diverse range of metrics related to malaria research. malariaAtlas is here used in two mock analyses to illustrate how this data may be incorporated into a standard R workflow for spatial analysis. Conclusions malariaAtlas is the first open-access R-interface to malariometric data, providing a new and reproducible means of accessing such data within a freely available and commonly used statistical software environment. In this way, the malariaAtlas package aims to contribute to the environment of data-sharing within the malaria research community.
Issue Date: 5-Oct-2018
Date of Acceptance: 29-Sep-2018
URI: http://hdl.handle.net/10044/1/64861
DOI: https://dx.doi.org/10.1186/s12936-018-2500-5
ISSN: 1475-2875
Publisher: BioMed Central
Journal / Book Title: Malaria Journal
Volume: 17
Issue: 1
Copyright Statement: © 2018 The Author(s). This article is distributed under the terms of the Creative Commons Attribution 4.0 International License (http://creativecommons.org/licenses/by/4.0/), which permits unrestricted use, distribution, and reproduction in any medium, provided you give appropriate credit to the original author(s) and the source, provide a link to the Creative Commons license, and indicate if changes were made. The Creative Commons Public Domain Dedication waiver (http://creativecommons.org/publicdomain/zero/1.0/) applies to the data made available in this article, unless otherwise stated.
Sponsor/Funder: Medical Research Council (MRC)
Bill & Melinda Gates Foundation
Funder's Grant Number: MR/K010174/1B
1606H5002/JH6
Keywords: Science & Technology
Life Sciences & Biomedicine
Infectious Diseases
Parasitology
Tropical Medicine
Malaria
Open-access
Malariometric data
Parasite rate
R package
PLASMODIUM-FALCIPARUM
GEOGRAPHICAL DISTRIBUTIONS
AFRICA
MORTALITY
AREAS
MAP
Animal Distribution
Animals
Anopheles
Databases, Factual
Humans
Incidence
Mosquito Vectors
Prevalence
Software
1108 Medical Microbiology
Publication Status: Published
Article Number: 352
Online Publication Date: 2018-10-05
Appears in Collections:Faculty of Medicine
Epidemiology, Public Health and Primary Care



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