Example Project

This project automates data cleaning, analysis, and report generation for a LaTeX manuscript using R. The run_all.R script orchestrates the workflow, ensuring that tables and figures are updated before compiling the manuscript.

Project Structure

├── LICENSE               # License for the project
├── README.md             # Project overview and instructions
├── example_project.Rproj # RStudio project file
├── manuscript/
│   ├── manuscript.tex    # LaTeX manuscript source
│   └── manuscript.pdf    # Compiled PDF output
├── outputs/              # Generated output files
│   ├── figures/          # Figures used in the manuscript
│   │   └── fig_1.png     # Example figure
│   ├── logs/             # Logs from table generation or other processes
│   │   └── log.txt       # Example log file
│   └── tables/           # Tables used in the manuscript
│       ├── table_1.log
│       └── table_1.tex
├── renv/                 # renv environment for dependency management
│   ├── activate.R
├── renv.lock             # Snapshot of package versions
├── run_all.R             # Main script to run the entire workflow
└── src/                  # R scripts for various tasks
    ├── clean.R           # Data cleaning scripts
    ├── figures.R         # Figure generation scripts
    └── tables.R          # Table generation scripts

Workflow

1. Data Processing: The src/ directory contains R scripts (clean.R, figures.R, tables.R) for data preparation, analysis, and visualizations.

2. Automated Run Script: run_all.R sequentially runs all scripts, generates updated tables and figures in outputs/, and compiles the LaTeX manuscript located in manuscript/.

3. Output: After running run_all.R, the latest manuscript PDF (manuscript.pdf) reflects the most recent data, figures, and tables.

Environment Management

This project uses the renv package to manage R package dependencies. To set up the environment, run:

renv::restore()

Compiling the Manuscript

The manuscript is compiled automatically by run_all.R using tinytex::latexmk(). Ensure that TinyTeX or a LaTeX distribution is installed.

Usage

Run the entire workflow by executing run_all.R:

source("run_all.R")