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README.Rmd
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README.Rmd
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---
output: github_document
---
<!-- README.md is generated from README.Rmd. Please edit that file -->
```{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 <a href="https://docs.ropensci.org/osfr/"><img src="man/figures/logo.png" align="right" height="139" /></a>
<!-- badges: start -->
[](https://CRAN.R-project.org/package=osfr)
[](https://github.com/ropensci/osfr/actions/workflows/R-CMD-check.yaml)
[](https://codecov.io/github/ropensci/osfr?branch=master)
[](https://github.com/ropensci/software-review/issues/279)
[](https://doi.org/10.21105/joss.02071)
[](https://zenodo.org/badge/latestdoi/42329785)
<!-- badges: end -->
## 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 <https://osf.io/e81xl/>. 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()
```
## 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")
```
[](https://ropensci.org)
<!-- links -->
[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