OJWatson/kenya_non_falciparum

Analysis of non-falciparum malaria in Kenya ## Research compendium for non-falciparum in Kenya This is a working R compendium (think R package but for reproducible analysis). The analysis directory contains R scripts used to generate the results. ### Installation git clone github.com cd kenya_non_falciparum open kenya_non_falciparum.Rproj devtools::install_deps() ### Overview The structure within analysis is as follows: | |──R/ # R functions used throughout analysis | |──analysis/ | ├── 00_<>.R # analysis scripts | ├── data/ │ ├── DO-NOT-EDIT-ANY-FILES-IN-HERE-BY-HAND │ ├── raw/ # data obtained from elsewhere │ └── derived/ # data generated during the analysis | ├── plots/ # plots generated by analysis | ├── tables/ # table generated by analysis ### Compendium DOI: The files at the URL above will generate the results as found in the publication. The files hosted at github.com are the development versions and may have changed since the report was published ### Overview of contents This repository is our research compendium for our analysis of . The compendium contains all data, code, and text associated with the publication. The `R` files in the `analysis` directory contain details of how all the analyses reported in the paper were conducted, as well as instructions on how to rerun the analysis to reproduce the results. The `data/` directory in the `analysis/` directory contains all the raw and derived data generated. ### The R package This repository is organized as an R package. There are only a few R functions exported in this package - the majority of the R code is in the analysis directory. The R package structure is here to help manage dependencies, to take advantage of continuous integration, and so we can keep file and data management simple. To download the package source as you see it on GitHub, for offline browsing, use this line a …