SWMadagascar

The goal of SWMadagascar is to develop an end-to-end data processing pipeline for the SW-Madagascar cohort study, from raw data ingestion to final reporting of up to date datasets from the SW Madagascar cohort.

The package is built using the {fusen} package, which allows building R packages from Rmarkdown files. This makes it easy to maintain both code and documentation in a single file.

The pipeline is based on the {targets} package, which provides a robust framework for defining and executing data analysis pipelines in R.

Installation

You can install the development version of SWMadagascar like so:

# FILL THIS IN! HOW CAN PEOPLE INSTALL YOUR DEV PACKAGE?

Example

This is a basic example which shows you how to solve a common problem:

library(SWMadagascar)
## basic example code

What is special about using README.Rmd instead of just README.md? You can include R chunks like so:

summary(cars)
#>      speed           dist       
#>  Min.   : 4.0   Min.   :  2.00  
#>  1st Qu.:12.0   1st Qu.: 26.00  
#>  Median :15.0   Median : 36.00  
#>  Mean   :15.4   Mean   : 42.98  
#>  3rd Qu.:19.0   3rd Qu.: 56.00  
#>  Max.   :25.0   Max.   :120.00

You’ll still need to render README.Rmd regularly, to keep README.md up-to-date. devtools::build_readme() is handy for this.

You can also embed plots, for example:

In that case, don’t forget to commit and push the resulting figure files, so they display on GitHub and CRAN.