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Posts with the rstats category can also be found at RBloggers, R Weekly and DataCamp Community.

By Amy Peterson Using Git Git is a version control system that allows you to track changes made to files while working on a project, either independently or in collaboration with others. It provides a way to save many different components of a project in progress, including the source code, but also the figures and data that the code produces. The importance of understanding and using Git lies in its ability to maintain an organized record of a project, also referred to as a repository or repo, as it evolves.

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By Steve Semick. What do you do when you want to use results from the literature to anchor your own analysis? When these results are in the form of an easily accessible table, such as a .csv file or .xlsx file, then it is simple enough to download them and incorporate them into your research. Often times, however, published findings are not so easy to handle. Today, we’ll go through a practical scenario on scraping an html table from a Nature Genetics article into R and wrangling the data into a useful format.

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By L. Collado-Torres. If you are working at LIBD or with large data, it’s very likely that it won’t fit in your laptop and that you’ll be using the terminal to interact with a high performance computing cluster (like JHPCE) or server. Some small edits to your bash configuration file can make your terminal experience much more enjoyable and hopefully boost your productivity. The edits described below work for any OS.

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By L. Collado-Torres. For the past 6-7 years I have been using TextMate 2 as my text editor which I’ve found useful for R code, bash, Markdown, etc. You could also look into Sublime Text or use RStudio (post about this setup coming soon). Sometimes students are interested in this setup, which is what I’ll document here. Though I want to highlight that you can get a very similar setup using other tools.

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In this blog post Leonardo Collado-Torres explains how to contribute posts to the LIBD rstats club. While some parameters are specific to this blog, you could also use this for creating your own community blog. Install necessary tools We first need to get the appropriate tools installed in our computer. 1. R Lets start by installing the latest version of R. At the time of writing this post, that would be R 3.

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Contact

If you have questions about the LIBD rstats club, please get in touch with L. Collado-Torres.

Code of conduct

The LIBD rstats club is committed to providing a welcoming and harassment-free experience for everyone, regardless of gender, gender identity and expression, age, sexual orientation, disability, physical appearance, body size, race, ethnicity, religion (or lack thereof), or technology choices. We do not tolerate harassment of website participants in any form. Sexual language and imagery is not appropriate for any venue related to this website, including blog posts, talks, workshops, parties, Twitter and other online media. Website participants violating these rules may be sanctioned or expelled from the website at the discretion of the LIBD rstats club members.

This code of conduct applies to all participants, including LIBD rstats club members and applies to all modes of interaction, both in-person and online, including LieberInstitute GitHub project repos, the LIBD rstats club comments section, Slack channels and Twitter.

LIBD rstats club participants agree to:

  • Be considerate in speech and actions, and actively seek to acknowledge and respect the boundaries of fellow participants.
  • Refrain from demeaning, discriminatory, or harassing behavior and speech. Harassment includes, but is not limited to: deliberate intimidation; stalking; unwanted photography or recording; sustained or willful disruption of talks or other events; inappropriate physical contact; use of sexual or discriminatory imagery, comments, or jokes; and unwelcome sexual attention. If you feel that someone has harassed you or otherwise treated you inappropriately, please alert any LIBD rstats club member.
  • Take care of each other. Alert a LIBD rstats club member if you notice a dangerous situation, someone in distress, or violations of this code of conduct, even if they seem inconsequential.

If any participant engages in harassing behavior, the LIBD rstats club organizers may take any lawful action we deem appropriate, including but not limited to warning the offender or asking the offender to leave the website. (If you feel you have been unfairly accused of violating this code of conduct, you should contact the LIBD rstats club organizers with a concise description of your grievance.)

The above text has been modified from the rOpenSci 2018 unconference code of conduct, which in turn states that parts of the text are licensed CC BY-SA 4.0. Credit to SRCCON. Also inspired by the Ada Initiative’s “how to design a code of conduct for your community.”