integrated development environments (IDEs)

If all you want to do is done in R, your best choice of IDE is probably Rstudio. For all other purposes, you will have to look around and try what works for you.

Microsoft Visual Studio Code

VS Code offers a lot of plugins for all common languages, plus lots of useful plugins for other stuff (and all for free). It has extensive documentation, but the best way to get started is probably to simply download VS code and jump right in. Several people in our group currently use it, with the possibility to work on a remote project on a server via ssh a very useful and heavily used feature.

VS Code has a very lively Extension Marketplace that provides lots of useful plugins. However, as extension can potentially execute malicious code on your machine, please do at least a basic check whether extensions are safe to install.

Here are some that have proven very useful to us:

  • The Remote - SSH extension enables you to log onto a server via an ssh connection. You can then open a project folder and browse and edit files, while you can also open a Terminal / shell to run commands.
  • The snakemake extension gives you syntax highlighting for Snakefiles.
  • The Rainbow CSV extension gives you systematic per-column colors in comma-separated and tab-separated value files.
  • The Edit CSV extension allows you to edit .csv and .tsv files in a tabular view, so that you can create and delete columns and rows, and copy-paste things.

In addition, VS Code will often offer you to install plugins for filetypes you open, or for languages that you use. Explore.

Positron

Positron is a free, next-generation, multi-language integrated development environment (IDE) built on Code OSS, the same base as Microsoft Visual Studio Code. It was designed specifically for data science by Posit PBC (formerly RStudio) and offers native support for Python and R, making it easy to switch between different versions of these languages. From a user perspective, it is basically a mixup between the user interfaces of Rstudio and VS Code, so migration should be relatively easy of you are familiar with either, or both. The docs even offer migration guides for Rstudio (Workbench) and VS Code.

Positron supports Quarto documents and integrates jupyter notebooks, scripts, consoles, and interactive outputs into a unified workspace (rather than an R project), has its own data explorer, AI assistant (Positron assistant), and supports VSCode extensions. Further, Positron provides essential data analysis workflow functionality via built in extensions, for example remote ssh sessions and git version control.

There's also a Posit video with a quick tour of Positron, if this is your prefered mode of learning.

Positron uses Open VSX, an open-source marketplace for VS Code extensions. As such, you can mostly choose from the same extensions as for VS Code, so have a look at the VS Code recommendations above. But please note that Open VSX is only starting to implement security checks for extensions, so the checks suggested for credibility of extensions for VS Code are even more import for this marketplace. Hopefully, it will have much more extensive marketplace protections in the near future.

Note that Positron comes with a number of vetted and builtin VS Code extensions, which you can list by searching for @builtin in the extensions Extensions tab of the left sidebar (blocks symbol). Among them, is the Open Remote - SSH plugin, equivalent to the Remote - SSH extension mentioned above, so there's no need to install that yourself.

In addition, there are a couple of useful extension functionalities that Positron does not have built in (yet):

Jet Brains

Jet Brains develops a suite of IDEs for different languages (just use the language filter on the right) and offers a free version for academic purposes.