https://github.com/insightsengineering/biomarker-catalog
Biomarker Analysis Templates of Tables And Graphs 📊
https://github.com/insightsengineering/biomarker-catalog
Last synced: 7 months ago
JSON representation
Biomarker Analysis Templates of Tables And Graphs 📊
- Host: GitHub
- URL: https://github.com/insightsengineering/biomarker-catalog
- Owner: insightsengineering
- Created: 2023-03-21T16:00:25.000Z (about 3 years ago)
- Default Branch: main
- Last Pushed: 2025-02-12T17:27:31.000Z (over 1 year ago)
- Last Synced: 2025-02-12T18:35:03.264Z (over 1 year ago)
- Language: SCSS
- Homepage: https://insightsengineering.github.io/biomarker-catalog/
- Size: 94.7 MB
- Stars: 9
- Watchers: 9
- Forks: 2
- Open Issues: 3
-
Metadata Files:
- Readme: README.md
Awesome Lists containing this project
README
# Biomarker Analysis Catalog
Catalog for tables and graphs produced by Statistical Engineering products.
## Architecture
This repository follows a very straightforward architecture.
```mermaid
sequenceDiagram
autonumber
Author->>Repo: Creates content + pushes updates
Repo->>GitHub Actions: Triggers builds
GitHub Actions->>GitHub Pages: Publishes the catalog
Analyst->>GitHub Pages: Refers to catalog
```
## Technology
- Dependency management: [`staged.dependencies`](https://openpharma.github.io/staged.dependencies/) for installing dependencies
- Building and rendering: [`Quarto`](https://quarto.org/)
- Publishing: [`GitHub Actions`](https://docs.github.com/en/actions)
- Hosting: [`GitHub Pages`](https://pages.github.com/)
## Development
This repository is based on the [Quarto books](https://quarto.org/docs/books/) framework.
As a pre-requsite, you need to [install Quarto](https://quarto.org/docs/get-started/) and also [install and configure staged.dependencies](https://github.com/openpharma/staged.dependencies#usage).
You can install dependencies simply by running the following in an R session:
```R
# Assuming:
# 1. Your current working directory is the same as the project directory
# 2. You have set up your GITHUB_PAT environment variable
options(
staged.dependencies.token_mapping = c(
"https://github.com" = "GITHUB_PAT"
)
)
library(staged.dependencies)
x <- dependency_table(project = ".", verbose = 1)
install_deps(x, verbose = 1, install_project = FALSE)
```
Then, install this "package" (because it's not really a package, but it emulates a package as it has a `DESCRIPTION` file from which metadata is inferred):
```shell
R CMD INSTALL .
```
You'll see that files under [tables](tables) and [graphs](graphs) are in a `.qmd` file format, which translates to a **q**uarto **m**ark**d**own format. Note that the format is _almost exactly_ the same as Rmarkdown, with some minor differences, so you would write content within those files exactly as you would write Rmarkdown.
If you are adding a new table or graph in the form a a new `qmd` file, then you will also need to update the index in the [_quarto.yml](_quarto.yml) file with the new file name.