insightsengineering/biomarker-catalog

Biomarker Analysis Templates of Tables And Graphs 📊

Biomarker Analysis Catalog

Catalog for tables and graphs produced by Statistical Engineering products.

Architecture

This repository follows a very straightforward architecture.

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

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Technology

• Dependency management: staged.dependencies for installing dependencies
• Building and rendering: Quarto
• Publishing: GitHub Actions
• Hosting: GitHub Pages

Development

This repository is based on the Quarto books framework.

As a pre-requsite, you need to install Quarto and also install and configure staged.dependencies.

You can install dependencies simply by running the following in an R session:

# 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):

R CMD INSTALL .

You'll see that files under tables and graphs are in a .qmd file format, which translates to a quarto markdown 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 file with the new file name.