The BayesPharma website package contains a collection of R tools for analyzing pharmacology data using Bayesian statistics.

Package Development Workflows

Basic Workflow

The basic workflow follows the package development practices described in the R Packages book

1. Check out the repository using password-protected SSH keys

git clone https://github.com/maomlab/BayesPharma.git
cd BayesPharma

2. Build the package

make clean
make deps
make build
make install

4. The edit and re-load from during development

devtools::document()
devtools::load_all()

Build the manuscript and vignettes

The manuscript is a multi-part Quarto document in vignettes_src/manuscript

Building the manuscript and vignettes requires pandoc, which is available through Rstudio. But if you are not using Rstudio you please follow the instructions here.

1. We have used Paperpile to organize the references, to update

make update_references

2. To build the manuscript

make manuscript

To build the sections into the website

3. Build the website

make build_site

To see the site locally, navigate to BayesPharma/docs/index.html

Package testing and deployment

1. Run all the tests

make test