lintermanlab/Hill_RTS-s_immune_development_code

Supporting code for Hill et al. "Immune system development varies according to age, location and anemia in African children" # Hill RTS-s immune development code Supporting code for Hill et al. "Immune system development varies according to age, location and anemia in African children" 2020. ## Introduction This code outlines the analyses behind various figures in the paper. This is a github mirror of an RStudio project. The relevant data is supplied in the folder `/data` Html output is provided in the folder `/html`. Knitting the provided Rmarkdown files (.Rmd) here will re-generate these html files in the project directory. The contents of `/html` are difficult to view on github.com (it does not render the html) - the RStudio viewer will render these so you can compare your local results to our own. R packages are managed by the packrat package manager, so the end-user can install this repository on their local machine on a 'fresh' version of R/Rstudio. Source code packages are included, which should work on Windows/OSX/Unix. We have tested OSX and Unix. Use `packrat::status()` and `packrat::restore()` before trying to run the .Rmd files. ## Workflow [for novices] 1. Install RStudio rstudio.com - tested with Rstudio 1.2.5019 and R 3.6.1 2. Install git, either via: i. git-scm.com ii. or, **if you do not have administrator rights**, via `conda` (which does not require admin rights to install) - follow miniconda2 installation guide for your OS eg conda.io - you can use alternative versions of conda. Be aware that sup code D will need to be alternately configured so that R can 'see' your installation of python and reticulate library. - for OS X 10.14.6 (testing machine), python2 is default so miniconda2 used. - to add git to your environment, run `conda install git` in Terminal (or its equivalent in your OS) 3. Follow RStudio's guide to pull this project from GitHub into a new project. 4. Install the included packages, by running the following in RStudio console: …