petedodd/tippi

Cost-effectiveness analysis of interventions to improve diagnosis and preventive therapy for paediatric tuberculosis in 9 sub-Saharan African countries: A modelling study # tippi ## License This work is licensed under a Creative Commons Attribution 4.0 International License creativecommons.org ## Structure & analysis order The repo is structured as: ``` . ├── dataprep │   ├── graphs │   └── outdata ├── inference │   ├── data │   ├── graphs │   └── outdata └── model ├── data ├── graphs ├── indata └── outdata ``` Analyses should be run in this order: - *dataprep* : preparation of pre/post data for inference. Also contains some utility functions. - *inference* : statistical analyses of pre/post data - can all be run and post-processed using the bash script. - *model* : the main modelling analysis - *modeldata.R* : prepares effect estimates from the inference analysis and makes parts of Table 1 - *modeloutcomes.R* : main results for each sensitivity scenario - *runmodel.sh* : bash script to run all modelling analyses at once (on multicore machine with plenty memory) *resultsupload.R* in the top level parses and uploads results to googlesheets for inclusion in the article. The uploads require authetication (authors only). ### Required packages ### The following R packages are required: - inference: rstanarm - plotting: ggplot2, scales, ggpubr, ggthemes - modelling: HEdtree, discly (install using `devtools::install_github('petedodd/packagename')` ) - data manipulation: data.table - utilities: glue, here, - data I/O: googlesheets4, readxl