tidy_bib

Tidy_bib automates the preprocessing of .bib files exported from databases like Web of Science and Scopus, preparing the data for analysis in biblioshiny or for enrichment via APIs (Crossref, OpenAlex, ROR).

https://github.com/danielbrazil303/tidy_bib

Repository

Tidy_bib automates the preprocessing of .bib files exported from databases like Web of Science and Scopus, preparing the data for analysis in biblioshiny or for enrichment via APIs (Crossref, OpenAlex, ROR).

README.Rmd

---
output: github_document
---

# 📚 Tidy\_bib

> A modular and reproducible pipeline for cleaning and organizing bibliographic data using R.

---

## 🎯 Purpose

`Tidy_bib` automates the preprocessing of `.bib` files exported from databases like **Web of Science** and **Scopus**, preparing the data for analysis in `biblioshiny` or for enrichment via APIs (Crossref, OpenAlex, ROR).

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## 🗂️ Project Structure

```text
Tidy_bib/
├── R/               # Function scripts (e.g., safe_convert2df.R)
├── data/            # Raw files (.bib)
├── output/          # Cleaned data, spreadsheets, logs
├── tests/           # Unit tests with testthat
├── docs/            # Additional documentation or generated reports
├── run_pipeline.R   # Main execution script
├── config.yaml      # Configuration file
├── README.Rmd       # This file
├── .gitignore       # Files to ignore in version control
└── renv/            # Dependency management
```

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## ⚙️ How to Run the Pipeline

### 1. Install required packages:

```r
install.packages(c("bibliometrix", "yaml", "here", "fs", "dplyr"))
```

### 2. Run the pipeline:

```r
source("R/convert_bib_files_to_df.R")
source("R/safe_convert2df.R")
source("run_pipeline.R")

initialize_pipeline("config.yaml")
```

---

## 🧪 Testing

This project uses `testthat`. To run the tests:

```r
devtools::test()
```

---

## 👥 Contributing

1. Fork the repository
2. Create a branch: `git checkout -b new-feature`
3. Commit your changes: `git commit -m "feat: add new feature"`
4. Push to your branch: `git push origin new-feature`
5. Open a pull request

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## 🔒 License

This project is licensed under the MIT License. See the `LICENSE` file for details.

---

## 📌 Citation

If you use this project, please cite as:

```
Arraes, D. (2025). Tidy_bib: A modular bibliographic cleaning pipeline in R. https://github.com/danielbrazil303/Tidy_bib
```

Owner

Citation (CITATION.cff)

cff-version: 1.2.0
message: "If you use this project, please cite it as below."
title: "Tidy_bib: A modular bibliographic cleaning pipeline in R"
version: "0.1.0"
authors:
  - family-names: Arraes
    given-names: Daniel
    email: dan.arraes@uece.br
    affiliation: Universidade Estadual do Ceará (UECE)
    orcid: "https://orcid.org/0000-0003-0697-2268" 
date-released: 2025-07-30
license: MIT
repository-code: https://github.com/danielbrazil303/Tidy_bib

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