osfr

osfr: An R Interface to the Open Science Framework - Published in JOSS (2020)

https://github.com/ropensci/osfr

Keywords

Repository

R interface to the Open Science Framework (OSF)

README.Rmd

---
output: github_document
---



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

Sys.unsetenv(c("OSF_SERVER", "OSF_PAT"))
```

# osfr 


[![CRAN status](https://www.r-pkg.org/badges/version/osfr)](https://CRAN.R-project.org/package=osfr)
[![R-CMD-check](https://github.com/ropensci/osfr/actions/workflows/R-CMD-check.yaml/badge.svg)](https://github.com/ropensci/osfr/actions/workflows/R-CMD-check.yaml)
[![Coverage status](https://codecov.io/gh/ropensci/osfr/branch/master/graph/badge.svg)](https://codecov.io/github/ropensci/osfr?branch=master)
[![](https://badges.ropensci.org/279_status.svg)](https://github.com/ropensci/software-review/issues/279)
[![JOSS](https://joss.theoj.org/papers/10.21105/joss.02071/status.svg)](https://doi.org/10.21105/joss.02071)
[![DOI](https://zenodo.org/badge/42329785.svg)](https://zenodo.org/badge/latestdoi/42329785)


## Overview

osfr provides a suite of functions for interacting with the Open Science Framework ([OSF][osf]).

**What is OSF?**

*OSF is a free and [open source][osf-gh] project management repository designed to support researchers across their entire project lifecycle. The service includes unlimited cloud storage and file version history, providing a centralized location for all your research materials that can be kept private, shared with select collaborators, or made publicly available with citable DOIs.*

## Installation

You can install the current release of osfr from CRAN (*recommended*):

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

Or the development version from GitHub with the *remotes* package:

``` r
# install.packages("remotes")
remotes::install_github("ropensci/osfr")
```

## Usage Examples

*Note: You need to [setup an OSF personal access token (PAT)][auth] to use osfr to manage projects or upload files.*

### Accessing Open Research Materials

Many researchers use OSF to archive and share their work. You can use osfr to explore publicly accessible projects and download the associated files---all you need to get started is the project's URL or GUID (global unique identifier).

Every user, project, component, and file on OSF is assigned a GUID that is embedded in the corresponding entity's URL. For example, you can access the main OSF project for the *Cancer Reproducibility Project* at . The GUID for this project is `e81xl`.

We can then use osfr to *retrieve* this project and load it into R by providing the GUID:

```{r message=FALSE}
library(osfr)

cr_project <- osf_retrieve_node("e81xl")
cr_project
```

This returns an `osf_tbl` object with a single row representing the retrieved project. Let's list the files that have been uploaded to this project.

```{r}
osf_ls_files(cr_project)
```

This returns another `osf_tbl` with 1 row for each of the files and directories in the project. We can examine any of these files directly on OSF with `osf_open()`, which opens the corresponding file's view in your default browser.

This project contains 2 ***components***: *Replication Studies* and *Data collection and publishing guidelines*. We can list these components with osfr using `osf_ls_nodes()`.

```{r}
osf_ls_nodes(cr_project)
```

osfr is compatible with the [pipe operator][magrittr] and [dplyr][], providing a powerful set of tools for working with `osf_tbl`s. Here, we're listing the sub-components nested within the *Replication Studies* component, filtering for a specific study ([*Study 19*](https://osf.io/7zqxp/)) and then listing the files uploaded to that study's component.

```{r message=FALSE}
library(dplyr)

cr_project %>%
  osf_ls_nodes() %>%
  filter(name == "Replication Studies") %>%
  osf_ls_nodes(pattern = "Study 19") %>%
  osf_ls_files()
```

We could continue this pattern of exploration and even download local copies of project files using `osf_download()`. Or, if you come across a publication that  directly references a file's OSF URL, you could quickly download it to your project directory by providing the URL or simply the GUID:

```{r}
osf_retrieve_file("https://osf.io/btgx3/") %>%
  osf_download()
```


### Managing Projects

You can use osfr to [create projects][osf-create], [add sub-components][osf-create] or [directories][osf-mkdir], and [upload files][osf-upload]. See [Getting Started][getting-started] to learn more about building projects with osfr, but here is a quick example in which we:

1. Create a new project called *Motor Trend Car Road Tests*
2. Create a sub-component called *Car Data*
3. Create a directory named *rawdata*
4. Upload a file (`mtcars.csv`) to the new directory
5. Open the uploaded file on OSF

```{r eval=FALSE}
# create an external data file
write.csv(mtcars, "mtcars.csv")

osf_create_project(title = "Motor Trend Car Road Tests") %>%
  osf_create_component("Car Data") %>%
  osf_mkdir("rawdata") %>%
  osf_upload("mtcars.csv") %>%
  osf_open()
```

![Screenshot of the uploaded file on OSF](man/figures/screen-shot.png)

## Details on `osf_tbls`

There are 3 main types of OSF entities that osfr can work with:

1. **nodes:** both [projects][help-proj] and [components][help-comp] (i.e., sub-projects) are referred to as nodes
2. **files:** this includes both files *and* folders stored on OSF
3. **users:** individuals with OSF accounts

osfr represents these entities within `osf_tbl`s---specialized data frames built on the tibble class that provide useful information about the entities like their `name` and unique `id` for users, and API data in the `meta` column that's necessary for osfr's internal functions. Otherwise, they're just `data.frames` and can be manipulated using standard functions from base R or dplyr.

## Acknowledgments

OSF is developed by the [Center for Open Science][cos] in Charlottesville, VA.

The original version of osfr was developed by [Chris Chartgerink][chris] and further developed by [Brian Richards][brian] and [Ryan Hafen][ryan]. The current version was developed by [Aaron Wolen][aaron] and is *heavily* inspired by [Jennifer Bryan][jenny] and [Lucy D'Agostino McGowan][lucy]'s excellent [googledrive][] package. Seriously, we borrowed a lot of great ideas from them. Other important resources include [http testing](https://books.ropensci.org/http-testing/) by Scott Chamberlain and [R Packages](https://r-pkgs.org) by Hadley Wickham. Development was also greatly facilitated by OSF's excellent [API documentation][osf-api].

Big thanks to Rusty Speidel for designing our logo and [Tim Errington][tim] for his feedback during development.

## Contributing

Check out the [Contributing Guidelines][contrib] to get started with osfr development and note that by contributing to this project, you agree to abide by the terms outlined in the [Contributor Code of Conduct][coc].

```{r cleanup, include=FALSE}
unlink("Study_19_Figure_1.pdf")
```

[![ropensci_footer](https://ropensci.org/public_images/ropensci_footer.png)](https://ropensci.org)


[osf]: https://osf.io "Open Science Framework"
[cos]: https://www.cos.io "Center for Open Science"
[osf-gh]: https://github.com/CenterForOpenScience/osf.io "OSF's GitHub Repository"
[osf-api]: https://developer.osf.io "OSF API Documentation"
[help]: https://help.osf.io "OSF Support"
[help-proj]: https://help.osf.io/article/383-creating-a-project "OSF: Create a Project"
[help-comp]: https://help.osf.io/article/253-create-components "OSF: Create a Component"
[magrittr]: https://magrittr.tidyverse.org
[dplyr]: https://dplyr.tidyverse.org
[googledrive]: https://googledrive.tidyverse.org
[tibble]: https://tibble.tidyverse.org

[chris]: https://github.com/chartgerink
[brian]: https://github.com/bgrich
[ryan]: https://github.com/hafen
[aaron]: https://github.com/aaronwolen
[jenny]: https://github.com/jennybc
[lucy]: https://github.com/lucymcgowan
[tim]: https://github.com/timerrington

[getting-started]: https://docs.ropensci.org/osfr/articles/getting_started
[auth]: https://docs.ropensci.org/osfr/articles/auth

[osf-create]: https://docs.ropensci.org/osfr/reference/osf_create
[osf-mkdir]: https://docs.ropensci.org/osfr/reference/osf_mkdir
[osf-upload]: https://docs.ropensci.org/osfr/reference/osf_upload

[contrib]: https://github.com/ropensci/osfr/blob/master/.github/CONTRIBUTING.md
[coc]: https://github.com/ropensci/osfr/blob/master/.github/CODE_OF_CONDUCT.md

Owner

JOSS Publication

osfr: An R Interface to the Open Science Framework

Published

February 06, 2020

DOI

10.21105/joss.02071

Volume 5, Issue 46, Page 2071

Authors

Aaron R. Wolen
Transplant Research Institute, Department of Surgery, University of Tennessee Health Science Center

Chris H.j. Hartgerink
Liberate Science GmbH

Ryan Hafen
Department of Statistics, Purdue University

Brian G. Richards
Merkle Group Inc.

Courtney K. Soderberg
Center for Open Science

Timothy P. York
Data Science Lab, Department of Human and Molecular Genetics, Virginia Commonwealth University

Editor

Kristen Thyng

Tags

open science reproducible research project management

View PDF Review Thread Software Archive

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