lbstproj

lbstproj provides a lightweight set of tools for the L-Biostat group to create, maintain, and use standardized statistical analysis projects in R. It enforces a consistent folder structure, keeps every figure and table registered in a central Table of Tables (TOT), and makes it easy to generate reproducible Quarto reports.

Installation

Currently the package is not available on CRAN, so it needs to be installed from github.

# install.packages("remotes")
remotes::install_github("L-Biostat/lbstproj")

Overview

Step	What you do	Key function(s)
1. Create	Set up a new project	create_project()
2. Register	Fill in the table of tables (TOT), then import	import_tot()
3. Generate scripts	Create template R scripts from the TOT	create_from_tot()
4. Analyse	Write your code, then run all scripts	run_all_figures(), run_all_tables()
5. Report	Assemble and render a Quarto report	create_report(), run_report()
6. Archive	Move the rendered report to results/reports/	archive_report()

Quick start

library(lbstproj)

# 1 - Scaffold a new project
create_project(path = ".", title = "My project", author = "Jane Doe")

# 2 - Fill in data/tot/table_of_tables.xlsx, then import it
import_tot()

# 3 - Generate R script stubs for every TOT entry
create_from_tot(dry_run = FALSE)

# 4 - Fill in the scripts, then run them all
run_all_files("data")
run_all_figures()
run_all_tables()

# 5 - Assemble and render the report
create_report(output_type = "html")
run_report()
archive_report()

Project structure

create_project() produces the following layout:

my-project/
|-- data/
   |-- raw/          # Raw input files (never modified)
   |-- processed/    # Cleaned datasets (.rds)
   |-- tables/       # Saved gt tables (.rds)
   |-- figures/      # Saved ggplot objects (.rds)
   \-- tot/          # table_of_tables.xlsx + cached tot.rds
|-- R/
   |-- data/         # Data preparation scripts
   |-- figures/      # Figure scripts
   |-- tables/       # Table scripts
   \-- functions/    # Shared helper functions
|-- results/
   |-- figures/      # Final PNG / PDF figures
   |-- tables/       # Word tables (.docx)
   \-- reports/      # Archived reports
|-- report/           # Quarto report
\-- docs/             # Meeting notes, costing documents

Learn more

See the Get Started vignette for a full walkthrough using a simulated oncology trial dataset.