PrevMap:An R Package for Prevalence Mapping

Giorgi, Emanuele and Diggle, Peter John (2017) PrevMap:An R Package for Prevalence Mapping. Journal of Statistical Software, 78 (8). ISSN 1548-7660

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Abstract

In this paper we introduce a new R package, PrevMap, for the analysis of spatially referenced prevalence data, including both classical maximum likelihood and Bayesian approaches to parameter estimation and plug-in or Bayesian prediction. More specifically, the new package implements fitting of geostatistical models for binomial data, based on two distinct approaches. The first approach uses a generalized linear mixed model with logistic link function, binomial error distribution and a Gaussian spatial process as a stochastic component in the linear predictor. A simpler, but approximate, alternative approach consists of fitting a linear Gaussian model to empirical-logit-transformed data. The package also includes implementations of convolution-based low-rank approximations to the Gaussian spatial process to enable computationally efficient analysis of large spatial datasets. We illustrate the use of the package through the analysis of Loa loa prevalence data from Cameroon and Nigeria. We illustrate the use of the low rank approximation using a simulated geostatistical dataset.

Item Type: Journal Article
Journal or Publication Title: Journal of Statistical Software
Uncontrolled Keywords: /dk/atira/pure/subjectarea/asjc/1800/1804
Subjects:
Departments: Faculty of Health and Medicine > Medicine
ID Code: 86666
Deposited By: ep_importer_pure
Deposited On: 12 Jun 2017 12:16
Refereed?: Yes
Published?: Published
Last Modified: 13 Nov 2019 07:14
URI: https://eprints.lancs.ac.uk/id/eprint/86666

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