Source code and data for Towards estimating true cholera burden: a systematic review and meta-analysis of Vibrio cholerae positivity
Kirsten E. Wiens, Hanmeng Xu, Kaiyue Zou, John Mwaba, Justin Lessler, Espoir B. Malembaka, Maya N. Demby, Godfrey Bwire, Firdausi Qadri, Elizabeth C. Lee, Andrew S. Azman
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Find data extracted from studies in the systematic review in data/extracted_data.
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Download shapefile from the links below and save in folder data/shapefiles.
- Global admin 0 shapefile with iso3 codes: https://www.naturalearthdata.com/downloads/50m-cultural-vectors/50m-admin-0-countries-2/
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If running latent class analysis to generate new sensitivity/specificity estimates by test type with the JAGS program, use "launch_rstan_models.R". Instructions and JAGS settings are at the top of the script.
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If running running generalized linear model to generate new cholera positivity rate estimates with the Stan program, also use "launch_rstan_models.R". Settings for Stan models are set at the top of that script.
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Use "main.Rmd" to run analyses that correspond to figures and tables in manuscript.
| File | Description |
|---|---|
| latent_class_cd_meta.jags | Latent class analysis program with conditional dependence adapted from code provided in Wang et al. (2020) |
| launch_rstan_models.R | Script to prep data and run JAGS and/or Stan models with different settings indicated at top of script |
| main.Rmd | Notebook that runs manuscript analyses and creates tables/figures using previously-generated positivity rate estimates |
| meta_analysis_re.stan | Stan program for estimating postivity rate accounting for test performance and covariates |
| meta_analysis_re_unadj.stan | Stan program for estimating postivity rate without adjustments for test performance |
| meta_analysis_re_sa.stan | Stan program for estimating postivity rate accounting for test performance and covariates, with the prior on the global intercept shifted |
| utils.R | Helper functions used in R scripts and Rmd notebooks |