For our July 13th 2018 LIBD rstats club meeting we decided to check as much as we could the useR!2018 conference. Here’s what we were able to figure out about it in about an hour. Hopefully our quick notes will help other rstats enthusiasts, users and developers get a glimpse of the conference. Although there’s bound to me more videos and material about the conference coming out in the following days.
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.
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.
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.
Welcome to the LIBD rstats club!
A few months ago Carrie Wright and Leonardo Collado-Torres started an R + Journal club where we have been meeting every other week to talk about R packages and discuss journal articles in our field. Some examples of what we covered are tidyverse (Wickham, 2017), BiocStyle (Oleś, Morgan, and Huber, 2017) and rmarkdown (Allaire, Xie, McPherson, Luraschi, et al., 2018) presentations. We are now taking the R portion of the club to the next level.