Welcome to the LIBD rstats club!
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.
Like we say in the about section, we are researchers at LIBD that frequently use R and other tools. The R community has been growing a lot in recent years and it’s not easy to keep ourselves updated on all the recent developments. We also work in a dynamic environment where new people join LIBD frequently as students, post-docs and staff.
In the LIBD rstats club we plan to write blog posts about R packages we are interested in or are just learning how to use, how to do guides, and occasionally our own open-source software. For our how to do guides, the idea is that if two people asks us how to do \(X\), then it’s probably a good time to write a blog post. Similar to David Robinson’s advice:
When you’ve written the same code 3 times, write a function
— David Robinson (@drob) November 9, 2017
When you’ve given the same in-person advice 3 times, write a blog post
We are doing this to help each other at LIBD, to help future new colleagues and students, and the community at large. We also hope to receive feedback from the community (that complies with our code of conduct) that will be beneficial to everyone reading the posts. Maybe you know of an alternative way to do the same task we describe.
Thank you for tuning in! Follow us via RSS (allows email subscriptions) or Twitter.
Founding members: Leonardo Collado-Torres, Carrie Wright and Emily E. Burke.
PS This is not a course or boot camp site to get started using R, for that there are other resources available.
Details
Anyone at LIBD is welcome to participate and contribute blog posts: we will add you to the members section. Just remember that your blog posts have to comply with the confidentiality agreement we signed. We also welcome anonymous posts, though signing them can be useful for exposure and CV building, although not necessary.
Acknowledgments
This blog post was made possible thanks to:
References
[1] J. Allaire, Y. Xie, J. McPherson, J. Luraschi, et al. rmarkdown: Dynamic Documents for R. R package version 1.9. 2018. URL: https://CRAN.R-project.org/package=rmarkdown.
[2] C. Boettiger. knitcitations: Citations for ‘Knitr’ Markdown Files. R package version 1.0.8. 2017. URL: https://CRAN.R-project.org/package=knitcitations.
[3] A. Oleś, M. Morgan and W. Huber. BiocStyle: Standard styles for vignettes and other Bioconductor documents. R package version 2.6.1. 2017. URL: https://github.com/Bioconductor/BiocStyle.
[4] H. Wickham. tidyverse: Easily Install and Load the ‘Tidyverse’. R package version 1.2.1. 2017. URL: https://CRAN.R-project.org/package=tidyverse.
[5] H. Wickham, J. Hester and W. Chang. devtools: Tools to Make Developing R Packages Easier. R package version 1.13.5. 2018. URL: https://CRAN.R-project.org/package=devtools.
[6] Y. Xie, A. P. Hill and A. Thomas. blogdown: Creating Websites with R Markdown. ISBN 978-0815363729. Boca Raton, Florida: Chapman and Hall/CRC, 2017. URL: https://github.com/rstudio/blogdown.
Reproducibility
## Session info ----------------------------------------------------------------------------------------------------------## setting value
## version R version 3.4.3 (2017-11-30)
## system x86_64, darwin15.6.0
## ui X11
## language (EN)
## collate en_US.UTF-8
## tz America/New_York
## date 2018-03-08## Packages --------------------------------------------------------------------------------------------------------------## package * version date source
## backports 1.1.2 2017-12-13 CRAN (R 3.4.3)
## base * 3.4.3 2017-12-07 local
## bibtex 0.4.2 2017-06-30 CRAN (R 3.4.1)
## BiocStyle * 2.6.1 2017-11-30 Bioconductor
## blogdown 0.5.9 2018-03-08 Github (rstudio/blogdown@dc1f41c)
## bookdown 0.7 2018-02-18 cran (@0.7)
## colorout * 1.2-0 2018-02-19 Github (jalvesaq/colorout@2f01173)
## compiler 3.4.3 2017-12-07 local
## datasets * 3.4.3 2017-12-07 local
## devtools * 1.13.5 2018-02-18 CRAN (R 3.4.3)
## digest 0.6.15 2018-01-28 CRAN (R 3.4.3)
## evaluate 0.10.1 2017-06-24 CRAN (R 3.4.1)
## graphics * 3.4.3 2017-12-07 local
## grDevices * 3.4.3 2017-12-07 local
## htmltools 0.3.6 2017-04-28 CRAN (R 3.4.0)
## httr 1.3.1 2017-08-20 CRAN (R 3.4.1)
## jsonlite 1.5 2017-06-01 CRAN (R 3.4.0)
## knitcitations * 1.0.8 2017-07-04 CRAN (R 3.4.1)
## knitr 1.20 2018-02-20 cran (@1.20)
## lubridate 1.7.3 2018-02-27 CRAN (R 3.4.3)
## magrittr 1.5 2014-11-22 CRAN (R 3.4.0)
## memoise 1.1.0 2017-04-21 CRAN (R 3.4.0)
## methods * 3.4.3 2017-12-07 local
## plyr 1.8.4 2016-06-08 CRAN (R 3.4.0)
## R6 2.2.2 2017-06-17 CRAN (R 3.4.0)
## Rcpp 0.12.15 2018-01-20 CRAN (R 3.4.3)
## RefManageR 0.14.20 2017-08-17 CRAN (R 3.4.1)
## rmarkdown 1.9 2018-03-01 cran (@1.9)
## rprojroot 1.3-2 2018-01-03 CRAN (R 3.4.3)
## stats * 3.4.3 2017-12-07 local
## stringi 1.1.6 2017-11-17 CRAN (R 3.4.2)
## stringr 1.3.0 2018-02-19 cran (@1.3.0)
## tools 3.4.3 2017-12-07 local
## utils * 3.4.3 2017-12-07 local
## withr 2.1.1 2017-12-19 CRAN (R 3.4.3)
## xfun 0.1 2018-01-22 CRAN (R 3.4.3)
## xml2 1.2.0 2018-01-24 CRAN (R 3.4.3)
## yaml 2.1.17 2018-02-27 cran (@2.1.17)