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PrevMap: An R Package for Prevalence Mapping

Research output: Contribution to Journal/MagazineJournal articlepeer-review

<mark>Journal publication date</mark>9/06/2017
<mark>Journal</mark>Journal of Statistical Software
Issue number8
Number of pages29
Pages (from-to)1-29
Publication StatusPublished
<mark>Original language</mark>English


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.