├── Epi_VivIDEpi_one_ring_to_rule_them_all.Rmd
├── R # Helper functions
├── README.md
├── Spatial_VivIDEpi_one_ring_to_rule_them_all.Rmd
├── VivIDRiskFactorAnalysis.Rproj
├── analyses
├── internal_datamap_files # internal files for "lifting over" covariates
├── model_datamaps # "Lift overs" for Epi models
The Rmarkdown files Epi_VivIDEpi_one_ring_to_rule_them_all.Rmd and Spatial_VivIDEpi_one_ring_to_rule_them_all.Rmd knit together the various pieces of the epidemiologic and spatial analyses, respectively. The analysis folder contains the individual scripts, which follow a conventional numbering system for order in which they are to be run.
Due to data privacy considerations relating to the Demographic Health Survey, the molecular PCR results generated and analyzed during the current study are available from the corresponding author upon reasonable request. All other epidemiological data is publicly available, although the corresponding author can provide intermediary files upon reasonable request.