ro-crate-r/README.Rmd at main · ResearchObject/ro-crate-r · GitHub

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---
output: github_document
---

<!-- README.md is generated from README.Rmd. Please edit that file -->

```{r, include = FALSE}
knitr::opts_chunk$set(
  collapse = TRUE,
  comment = "#>",
  fig.path = "man/figures/README-",
  out.width = "100%"
)
```

# rocrateR: Tools for Creating and Manipulating RO-Crates <img src="man/figures/logo.png" alt="logo" align="right" height=200px style="float:right; height:200px;"/>

<!-- badges: start -->
[![CRAN status](https://www.r-pkg.org/badges/version/rocrateR)](https://CRAN.R-project.org/package=rocrateR)
[![R-CMD-check](https://github.com/ResearchObject/ro-crate-r/actions/workflows/R-CMD-check.yaml/badge.svg)](https://github.com/ResearchObject/ro-crate-r/actions/workflows/R-CMD-check.yaml)
[![Codecov test coverage](https://codecov.io/gh/ResearchObject/ro-crate-r/graph/badge.svg)](https://app.codecov.io/gh/ResearchObject/ro-crate-r)
![Lifecycle: experimental](https://img.shields.io/badge/lifecycle-experimental-orange)
<!-- badges: end -->

`{rocrateR}` provides a native R interface for creating, manipulating, validating and packaging RO-Crates.
RO-Crate is a lightweight approach to packaging research data with structured metadata using JSON-LD.

## Installation

You can install the released version of `{rocrateR}` from [CRAN](https://cran.r-project.org/package=rocrateR) with:

``` r
install.packages("rocrateR")
```

And the development version from [GitHub](https://github.com/ResearchObject/ro-crate-r/) with:

``` r
# install.packages("pak")
pak::pak("ResearchObject/ro-crate-r@dev")
```

## Quick Start

```{r, eval = FALSE}
# create a crate
crate <- rocrateR::rocrate()

crate <- crate |>
  # add a dataset entity
  rocrateR::add_dataset("iris.csv", iris) |>
  # add workflow entity
  rocrateR::add_workflow(
    file_id = "analysis.R",
    name = "Data analysis pipeline",
    content = c(
      "data <- read.csv('iris.csv')",
      "summary(data)"
    )
  ) |>
  # add software entity
  rocrateR::add_software("R", version = R.version.string)

# write to disk
path_to_rocrate_bag <- rocrateR::bag_rocrate(crate, path = "./my_roc")

path_to_rocrate_bag_contents <- path_to_rocrate_bag |>
    rocrateR::unbag_rocrate(output = "ROC")
```


```{r, echo = FALSE}
# create a crate
crate <- rocrateR::rocrate()

crate <- crate |>
  # add a dataset entity
  rocrateR::add_dataset("iris.csv", iris) |>
  # add workflow entity
  rocrateR::add_workflow(
    file_id = "analysis.R",
    name = "Data analysis pipeline",
    content = c(
      "data <- read.csv('iris.csv')",
      "summary(data)"
    )
  ) |>
  # add software entity
  rocrateR::add_software("R", version = R.version.string)

# write to disk
tmp_dir <- "./my_roc"
dir.create(tmp_dir, showWarnings = FALSE, recursive = TRUE)
suppressMessages(
  path_to_rocrate_bag <- rocrateR::bag_rocrate(crate, path = tmp_dir)
)
# extract files in temporary directory
suppressMessages(
  path_to_rocrate_bag_contents <- path_to_rocrate_bag |>
    rocrateR::unbag_rocrate(output = file.path(tmp_dir, "ROC"))
)

# create tree with the files
withr::with_dir(
  dirname(path_to_rocrate_bag_contents),
  fs::dir_tree(basename(path_to_rocrate_bag_contents))
)
unlink(tmp_dir, recursive = TRUE)
```


## What You Can Do

* 📦 Create RO-Crates from projects or folders
* 📄 Add datasets, software, workflows, notebooks, authors
* ✏️ Edit and enrich metadata
* 🔍 Inspect crate contents
* ✅ Validate structure and metadata
* 🧳 Create RO-Crate Bags for preservation

## Typical Workflow

```{r, eval = FALSE}
roc_bag_path <- rocrateR::crate_project() |>
  rocrateR::add_author("Alice Smith") |>
  rocrateR::add_dataset("data/raw.csv") |>
  rocrateR::add_software("analysis.R") |>
  rocrateR::bag_rocrate(path = ".")
```

## Validation

```{r, eval = FALSE}
rocrateR::validate_rocrate(roc_bag_path)
```


## Learn More

For further details, see the following vignette:

```{r, eval = FALSE}
vignette("getting-started-with-rocrateR")
```

## Why rocrateR?

- Native R interface to RO-Crate
- No external system dependencies
- Supports BagIt packaging (RFC 8493)
- Structural validation tools
- Designed for reproducible research workflows