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anatembea

anatembea is a tool for AnteNatal Assessment of Temporal malaria Epidemiology using Mechanistic models, Bayesian Estimation, and Analysis, an open-source R package, which translates monthly malaria prevalence collected at first antenatal clinic visit (ANC1) into seasonal patterns in malaria transmission and clinical cases. Our framework is underpinned by an established mechanistic model of malaria dynamics, providing the basis for simulating data-informed hypothetical scenarios to evaluate the likely impact of alternative intervention approaches.

For more information, see the published article in The Lancet Microbe: https://www.sciencedirect.com/science/article/pii/S2666524726000704

Installation

You can install the development version of anatembea from GitHub with:

# install.packages("devtools")
devtools::install_github("mrc-ide/anatembea")
library(anatembea)

Reproducibility for accepted ANC pMCMC manuscript

The current package continues to develop beyond the published analysis. The exact package state used for that work remains preserved at the v1.0-paper tag.

The analyses were run with R 4.4 using this frozen package state. To install the paper version, use:

remotes::install_github("mrc-ide/anatembea@v1.0-paper")

Key package versions used in the manuscript workflow included:

  • odin 1.5.11
  • dust 0.15.3
  • mcstate 0.9.22

Analysis scripts and workflow are available at: https://github.com/jt-hicks/anc_pmcmc_pub

Usage

For an example implementation, check out the vignette at https://mrc-ide.github.io/anatembea/articles/anatembea_intro.html