RStudio#Reproducible analyses with vignettes

A strength of RStudio is its support for reproducible analysesReproducibility is key in science. In The Logic of Scientific Discovery, Karl Popper wrote, "non-reproducible single occurrences are of no significance to science." But a theory is "falsified only if we discover a reproducible effect which refutes the theory". Popper (1968, p. 86). However, reproducibility is not easy to obtain. In a 2016 survey of over 1,500 scientists, 52% agreed that there was "a significant crisis" in the reproducibility of scientific results. Another 38% said there was "a slight crisis"; 7% "didn't know", and only 3% said there was no crisis. Worse, "more than 70% of researchers had tried and failed to reproduce another scientist's experiments, and more than half had failed to reproduce their own experiments (emphasis added). See Baker (2016). with R Markdown vignettes. These allow users to mix text with code in R, Python, Julia, shell scripts, SQL, Stan, JavaScript, C, C++, Fortran, and others,Xie et al. (2023, esp. sec. 2.7). similar to Jupyter Notebooks. R Markdown can be used to create dynamic reports that are automatically updated when new data become available. These reports can also be exported in various formats, including HTML, PDF, Microsoft Word, and LaTeX, with templates specific to the requirements of many scientific journals.Xie, Allaire, and Grolemund (2023).

R Markdown vignettes and Jupyter notebooks make the data analysis completely reproducible. R Markdown vignettes have been included as appendices with tutorials on Wikiversity.e.g., v:US Gross Domestic Product (GDP) per capita and v:Forecasting nuclear proliferation, accessed 5 January 2024. Many more examples are included in Xie, Dervieux, and Riederer (2023).

In 2022, Posit announced an R Markdown-like publishing system called Quarto. In addition to combining results of R, code and results using Python, Julia, Observable JavaScript, and Jupyter notebooks can also be used in Quarto documents. Compared to the file extension .Rmd that R Markdown has, Quarto documents have the file extension .qmd.{{Cite web |last=Machlis |first=Sharon |date=2022-07-28 |title=What is Quarto? RStudio rolls out next-generation R Markdown |url=https://www.infoworld.com/article/3666743/what-is-quarto-rstudio-quietly-rolls-out-next-generation-r-markdown.html |access-date=2024-05-17 |website=InfoWorld |language=en}}

One difference between R Markdown files and Quarto documents is defining options in code chunks. In R Markdown, they would be inline within the curly brackets.

```{r chunk_name, echo=FALSE, warning=FALSE}

print(42)

```

In contrast, Quarto documents define the chunk options below the curly brackets, prefixed using a pound character and vertical pipe (or "hash-pipe").

```{r}

#| label: chunk_name

#| echo: false

#| warning: false

print(42)

```

The RStudio integrated development environment (IDE) is available with the GNU Affero General Public License version 3. The AGPL v3 is an open source license that guarantees the freedom to share the code.

RStudio Desktop and RStudio Server are both available in free and fee-based (commercial) editions. OS support depends on the format/edition of the IDE. Prepackaged distributions of RStudio Desktop are available for Windows, macOS, and Linux. RStudio Server and Server Pro run on Debian, Ubuntu, Red Hat Linux, CentOS, openSUSE and SLES.{{cite web|url=https://www.rstudio.com/products/RStudio/|title=RStudio|work=rstudio.com|access-date=2 December 2016|archive-date=30 October 2015|archive-url=https://web.archive.org/web/20151030120222/https://www.rstudio.com/products/rstudio/|url-status=live}}

The RStudio IDE is partly written in the C++ programming language and uses the Qt framework for its graphical user interface.{{cite book|title = Getting Started with RStudio|last = Verzani|first = John|date = 23 September 2011|publisher = O'Reilly Media, Inc|isbn = 9781449309039|page = 4}} The bigger percentage of the code is written in Java. JavaScript is also used.{{Cite web|url=https://github.com/rstudio/rstudio|title=rstudio/rstudio|website=GitHub|language=en|access-date=2018-09-13|archive-date=2018-06-10|archive-url=https://web.archive.org/web/20180610233904/https://github.com/rstudio/rstudio|url-status=live}}

Work on the RStudio IDE started around December 2010,{{cite web |url=https://github.com/rstudio/rstudio/commit/484cb884c28913c19822c42b0cd099ee22832211 |title=portable download of java dependencies · rstudio/rstudio@484cb88 · GitHub |publisher=Github.com |date=2010-12-07 |access-date=2015-05-01 |archive-date=2019-04-05 |archive-url=https://web.archive.org/web/20190405131717/https://github.com/rstudio/rstudio/commit/484cb884c28913c19822c42b0cd099ee22832211 |url-status=live }} and the first public beta version (v0.92) was officially announced in February 2011.{{cite web |url=http://blog.rstudio.org/2011/02/28/rstudio-new-open-source-ide-for-r/ |title=RStudio, new open-source IDE for R | RStudio Blog |date=28 February 2011 |publisher=Blog.rstudio.org |access-date=2015-05-01 |archive-date=2015-01-24 |archive-url=https://web.archive.org/web/20150124101406/http://blog.rstudio.org/2011/02/28/rstudio-new-open-source-ide-for-r/ |url-status=live }} Version 1.0 was released on 1 November 2016.{{cite web|title=Announcing RStudio v1.0!|url=https://blog.rstudio.org/2016/11/01/announcing-rstudio-v1-0/|website=RStudio Blog|date=1 November 2016|access-date=1 November 2016|archive-date=30 June 2017|archive-url=https://web.archive.org/web/20170630032325/https://blog.rstudio.org/2016/11/01/announcing-rstudio-v1-0/|url-status=live}} Version 1.1 was released on 9 October 2017.{{cite web|title=RStudio v1.1 Released|url=https://blog.rstudio.com/2017/10/09/rstudio-v1.1-released/|website=RStudio Blog|date=9 October 2017|access-date=23 December 2017|archive-date=28 October 2021|archive-url=https://web.archive.org/web/20211028093407/https://blog.rstudio.com/2017/10/09/rstudio-v1.1-released/|url-status=dead}}

The RStudio IDE provides a mechanism for executing R functions interactively from within the IDE through the Addins menu.{{Cite web|url=https://rstudio.github.io/rstudioaddins/|title=RStudio Addins|website=RStudio|access-date=2018-09-16|archive-date=2018-09-10|archive-url=https://web.archive.org/web/20180910094946/http://rstudio.github.io/rstudioaddins/|url-status=live}} This enables packages to include graphical user interfaces (GUIs) for increased accessibility. Popular R packages that use this feature include:

• bookdown – a knitr extension to create books
• colourpicker – a graphical tool to pick colours for plots
• datasets.load – a graphical tool to search and load datasets
• googleAuthR – Authenticate with Google APIs

The RStudio IDE is developed by Posit, PBC, a public-benefit corporation{{cite web|url = https://posit.co/about/pbc-report/|title = Posit Benefit Corporation Annual Report|access-date = 2023-01-19|archive-date = 2023-01-19|archive-url = https://web.archive.org/web/20230119135242/https://posit.co/about/pbc-report/|url-status = live}} founded by J. J. Allaire,{{cite web |url=https://posit.co/about/ |title=About |publisher=Posit.co |access-date=2015-12-15 |archive-date=2022-11-02 |archive-url=https://web.archive.org/web/20221102162102/https://posit.co/about/ |url-status=live }} creator of the programming language ColdFusion. Posit has no formal connection to the R Foundation, a not-for-profit organization located in Vienna, Austria,{{cite web |url=https://www.r-project.org/foundation/Rfoundation-statutes.pdf |title="Statutes of "The R Foundation for Statistical Computing"" |work=The R Foundation |access-date=2019-08-12 |archive-date=2020-04-03 |archive-url=https://web.archive.org/web/20200403234736/https://www.r-project.org/foundation/Rfoundation-statutes.pdf |url-status=live }} which is responsible for overseeing development of the R environment for statistical computing. Posit was formerly known as RStudio Inc. In July 2022, it announced that it changed its name to Posit, to signify its broadening exploration towards other programming languages such as Python.{{cite web |url=https://posit.co/blog/rstudio-is-becoming-posit/ |title=RStudio is becoming Posit |date=27 July 2022 |publisher=Posit.co |access-date=2022-07-28 |archive-date=2022-11-02 |archive-url=https://web.archive.org/web/20221102164456/https://posit.co/blog/rstudio-is-becoming-posit/ |url-status=live }}

{{Portal|Free and open-source software}}

• R interfaces
• Comparison of integrated development environments

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== Notes ==

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• {{Official website}}

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{{Integrated development environments}}

Category:Free R (programming language) software

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Category:Science software for Linux

Category:Software using the GNU Affero General Public License