README.md

In maomlab/BayesPharma: Tools for Bayesian Analysis of Non-Linear Pharmacology Models

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

```{shell clone-repo} git clone https://github.com/maomlab/BayesPharma.git cd BayesPharma

2) Build the package

```{shell install-package}
make clean
make deps
make build
make install

4) The edit and re-load from during development

```{r edit-and-run} 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](https://pandoc.org/installing.html).

1) We have used Paperpile to organize the references, to update
```{shell update-references}
make update_references

2) To build the manuscript

```{shell build-manuscript} make manuscript

To build the sections into the website

3) Build the website
```{shell build-site}
make build_site

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

Package testing and deployment

1) Run all the tests

{shell test-package} make test

maomlab/BayesPharma documentation built on Aug. 24, 2024, 8:45 a.m.