This is a repository containing minimal datasets, code, and results for the manuscript:
Perez-Saez, J., Lessler, J., Lee, E.C., Luquero, F.J., Malembaka, E.B., Finger, F., Langa, J.P., Yennan, S., Zaitchik, B. and Azman, A.S., 2022. The seasonality of cholera in sub-Saharan Africa: a statistical modelling study, The Lancet Global Health. https://doi.org/10.1016/S2214-109X(22)00007-9.
The repository is structured as follows in its current state in the main branch:
1 .
2 ¦--analysis
3 ¦ ¦--01_data_preparation -- (not on this repo).
4 ¦ ¦--02_modeling
5 ¦ ¦ ¦--01_run_model_prior.R --- Runs the seasonality model with priors only
6 ¦ ¦ ¦--02_run_model.R --- Runs the seasonality model
7 ¦ ¦ ¦--03_generate_simulations.R --- Generates simulated outputs from model fits
8 ¦ ¦ °--configs --- Configs used for model running
9 ¦ ¦ ¦--cases ---- Cases as thershold for cholera presence
10 ¦ ¦ ¦--default_config.yml ---- Annotated example config
11 ¦ ¦ ¦--mean_annual_incidence ---- Mean annual incidence as threshold
12 ¦ ¦ °--occurrence ---- Occurrence as thershold
13 ¦ ¦--03_postprocessing
14 ¦ ¦ ¦--01_extract_prior_results_config.R --- Extracts outputs from prior model fits
15 ¦ ¦ ¦--02_extract_fitting_results_config.R --- Extracts outputs from model fits
16 ¦ ¦ ¦--03_compute_seasonality_index.R --- Computes the seasonality index
17 ¦ ¦ °--04_postprocess_outputs.R --- Postprocesses outputs for reporting
18 ¦ ¦--04_clustering
19 ¦ ¦ ¦--01_compute_grouping.R --- Runs clustering model
20 ¦ ¦ °--02_extract_clustering_results.R --- Extracts clustering outputs
21 ¦ ¦--05_outputs
22 ¦ ¦ ¦--01_final_stats.R --- Makes statistics statements used in manuscript
23 ¦ ¦ °--02_final_plots.R --- Makes all figures in manuscript
24 ¦ ¦--distribution_utils.R -- Helper functions for preparing this repo
25 ¦ ¦--make_output_metadata.R -- Script to make output metadata
26 ¦ ¦--make_repo_tree.R -- Script to make the repo tree
27 ¦ ¦--modeling_utils.R -- Helper functions for seasonality models
28 ¦ ¦--nbgraph_utils.R -- Helper functions for spatial adjacency
29 ¦ ¦--plotting_utils.R -- Helper functions for plotting
30 ¦ ¦--postprocessing_utils.R -- Helper functions for postprocessing
31 ¦ ¦--simulation_utils.R -- Helper functions for simulations
32 ¦ ¦--stan -- All stan code
33 ¦ °--utils.R -- Misc helper functions
34 ¦--figures
35 ¦ °--pub_figures -- Figures in main text and supplement
36 ¦--generated_data
37 ¦ ¦--best_seasonality_estimates_schema.json -- Final seasonality estimates metadata
38 ¦ ¦--best_seasonality_estimates.csv -- Final seasonality estimates
39 ¦ ¦--data_mapping -- Formatted data for stan
40 ¦ ¦--geodata -- Geographic data used in the analysis
41 ¦ ¦--model_outputs -- Modeling outputs used to reproduce figures and tables
42 ¦ ¦--postprocessing -- Postprocessed data to reproduce figures and tables
43 ¦ °--run_data -- Data used to run the models
44 ¦ ¦--all_run_data_mean_annual_incidence.csv --- Compilation of all run data for the main analysis
45 ¦ °--all_run_data_schema.json --- Metadata of the run data
46 °--manuscript
47 °--supplement
48 ¦--refs.bib --- References used in the supplement
49 ¦--supplement_cholera_seasonality.pdf --- Supplementary material pdf
50 °--supplement_cholera_seasonality.Rmd --- RMD to produce supplementary material pdf The content of the main branch consists of:
figures/pub_figures)generated_data/run_data/all_run_data_mean_annual_incidence.csv)generated_data/best_seasonality_estiamtes.csv)manuscript/supplement).Details on project implementation are given in the notebook in notebooks/project_details.html. This file is currently empty and will be updated soon.
All data and outputs necessary to replicate the results are available in branch for_replication. A separate branch was created because it requires checking out a large number of files. To access the branch run:
git checkout for_replication