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In a recent blog post I wrote about having a template for blogdown posts. I wanted to know if it was possible to do this and make my life (and others hopefully) easier for writing new blog posts that are ready to go with the features I frequently re-use.
In my case, I like using BiocStyle (Oleś, Morgan, and Huber, 2017) for functions such as CRANpkg(), Biocpkg() and Githubpkg(). I also like using knitcitations (Boettiger, 2017) for citing with citep() packages or papers; I use citation() and bib_metadata() to get the necessary information, respectively. Furthermore, I prefer devtools::session_info() (Wickham, Hester, and Chang, 2018) over sessionInfo() since it provides information of where you got the package, which becomes specially relevant when using packages from GitHub. Finally, I like thanking the creators of the tools I use, which in this case is blogdown (Xie, Hill, and Thomas, 2017).
I also like reminding myself how to do some common tasks. Basically, the equivalent of the new R Markdown file you get when using RStudio. In my case, I want to remind myself of the YAML options I frequently use (toc, fig height and width) or how to add screenshots.
My first post on this topic is actually rather messy. That’s because at that time:
- I didn’t know about hugo archetypes which are template files,
- I hadn’t even thought of making the Insert Image addin.
I went down the rabbit hole of archetypes and blogdown, reported an issue resulated to this topic that was in the way of using archetypes for .Rmd posts. After some encouragement by Yihui Xie, I ended up fixing this issues in my first pull request ever to an RStudio package. The PR also added the Archetype option to the New Post RStudio addin (which I used right now ^^).
Creating my blogdown archetype (template)
To make my archetype (template) for blog posts I looked at the GitHub repo for the theme I’m using. It contains an archetypes directory with several files. I just looked at the one called post.md (check it here) and copied it from themes/hugo-academic/archetypes/post.md to archetypes/post.md. Next I added my favorite R code below the last +++ mark. You can check out the final version here. Below I display the version at the time of writing this blog post (I’m using a .txt extension otherwise the embedded gist doesn’t look good, but you want it to end in .md).
I couldn’t get the archetype to respect some of the YAML that blogdown adds, but well, that’s a single copy-paste I have to do now (if I actually decide to use the custom YAML options which are only for .Rmd posts).
I encourage you to make your own blogdown archetype (template). At least it should remind you to include reproducibility information which matters whenever any R code is involved.
Acknowledgements
This blog post was made possible thanks to:
- BiocStyle (Oleś, Morgan, and Huber, 2017)
- blogdown (Xie, Hill, and Thomas, 2017)
- devtools (Wickham, Hester, and Chang, 2018)
- knitcitations (Boettiger, 2017)
Yihui Xie also talked about my first PR in his blog.
References
[1] C. Boettiger. knitcitations: Citations for ‘Knitr’ Markdown Files. R package version 1.0.8. 2017. URL: https://CRAN.R-project.org/package=knitcitations.
[2] 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.
[3] 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.
[4] 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 2018-03-10 ## 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)
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