And the fun is back with blogdown and R Markdown!

This was the big last project I needed to finish before 2018 kicks the door. Now that the semester ended (and students and secretary have gone and phone does not ring during two weeks), I was able to have some fun during several good hours prior to the holidays to work on my to do list - and the new lab website was at the top priority. I did it - finally moved my Lab website from WordPress to blogdown framework. It happened just about the time blogdown book was released and Academic theme for Hugo was updated with lots of new stuff.

I became aware of blogdown earlier this year and, whenever possible, I spent some time testing it. It is not because I needed all that time (beyond becoming busier as new Editor in Chief and chair of a graduate program in 2017) to install blogdown, setup a theme and start writing content; the first two can be done within a few minutes. The book is the key reference but I found this excellent visual guide to make it up and running by one of the authors.

I should add that it is not that simple to implement a new website engines when you already have one up and running for many years and you are not a newbie in website development. Essentially, I procrastinated because I needed to:

  • Gain knowledge about how static site generators like Hugo work;
  • Choose and customize a theme - the hardest one for me and
  • Structure the new website and migrate content.

This move would be a logic step for someone who became a keen learner and follower of #rstats tidyverse. I was very interested in producing data analysis reports using R Markdown websites as well as flexdashboard technologies during the last year (check this and this example of research compendium in my GitHub).

You may be wondering which are the benefits from leaving behind the leading state-of-the-art CMS like WordPress which I have used for many years. There are several pages or posts discussing this issue, but such decisions are quite personal and here are mine:

  1. Using RStudio as my sole working environment I was becoming more efficient and productive for most everything I needed during my daily teaching and quantitative researching activities: analyzing data, producing teaching notes, building static and interactive graphs, deploying a template for html-based reproducible research compendium and writing manuscripts. The website was the only one missing in the list.

  2. I was getting quite frustrated with the constant updates of WP engine and themes and the need to worry about security issues. In my case, it was even more difficult due to restrictions imposed by the University. For example, I could not log in without the University proxy and install anything from a machine which was not the one from my office - and plugins could be installed only via FTP, not the admin interface. The fun has gone and, as a result, my Lab website was almost abandoned during entire 2017, compared to previous years when I was more actively posting and updating content.

Fair note: I do believe WP is a great and easy to use tool for institutional websites where you have (and needed to train) other people that regularly use the admin interface for posting news or updating contents (e.g. my Department website). The downside is that maintenance will be needed and you will be the one around to do it. I am suggesting other colleagues from Departments and Graduate Programs to use University-maintained Wordpress websites so that staff may take care of these things!

And the fun is back with Blogdown! I used to do web-designing for fun in the earlier world wide web times, which further turned into a freelance job since the late 1990s when I was finishing my Masters in Agricultural sciences - I was using my skills to earn something developing webpages for departments and graduate programs. During all these years as web designer, I can see three phases, usually linked to my professional activities.

During phase I (late 1990 to early 2000), I started using text editors and further the award winning First Page 2000 software for hand-coding html. I witnessed the rise (and fall) of several web technologies, and many of them I have used in my projects (SHTML, DHTML, JavaScript, PHP) while I have completely skipped others (e.g. all WYSIWYG editors such as Dreamweaver and Flash) that looked like a black box for me. During every new project I was improving my skills and testing new stuff (besides supplementing stipend!). Hence, I used to know all those tricks about coding in HTML+CSS and associated technologies. I tweeted about this early experience.

During Phase II (mid 2000), I was beginning my career as a young faculty and thought that I could use previous experience to build web-based professional projects, such as database of plant diseases, which were requiring more complex environments and programming skills. Then, I discovered the PHP-based CMS (Content management system) world and have tested a dozen of them (CMSMadesimple, XOOPS, EZ Publish etc.) until I found WordPress (WP) by the late 2000s, which I used to build the Del Ponte Lab website at both my previous University and here at UFV during four years (screen below).

It was a phase of adaptation to a new, more complex, data-base driven dynamic-page environment where my knowledge on html+CSS was not a big advantage, except that I could see the code in the WYSIWIG WP editor and tweak CSS files. Take into account the huge amount of time for a young faculty to invest on developing teaching materials for new courses, writing grant proposals and keeping up with publications. It was a tough time, but I survived :).

The Phase III began when I accepted the offer to move my Lab to UFV (Campus photo above) during early 2014 and took the responsibility to offer a data analysis course for graduate students, besides the plant disease epidemiology course I was offering since 2007. Until then, I was not good at all in statistics (still am not, but learning!) and was a mediocre user of base R especially programming which is not something I like - always had greater ability with data visualization though.

As a plant disease epidemiologist, it just sounded mandatory to enhance my skills in data analysis and modeling for my new teaching responsibility and research ambitions. I took the decision that I would only use R/R Studio and abandon completely other statistical environments (I have used SAS before, but I was quite mediocre too). In this regard, it has been a pleasure to work together and learn from awesome colleagues as Adam Sparks who is an active #rstats programmer and package developer in our field. During these last four years I discovered and immersed in a new universe: R Studio, R Markdown, ggplot2 and the early developments of the tidyverse. What an exciting new universe! what an amazing feeling to be skilled at a minimum in programming to do stuff you need! The fun and simplicity was back and several of my latent skills would be of more value and definitely improve in this new environment. I was amazed by the fact that data analysis and production of beautiful plots and html reports could be done from a single environment where I can also output reports to Word or PDF files. I still need to use MS Word for my editorial duties (final checking accepted manuscripts prior to sending to typesetting), but as Zhian Kamvar said, when I asked about having MS Word, there is one upside :)

An important note here: by late 2012 I have seen beautiful Latex outputs (thanks to collaborative work with Denis A. Shah), but then R Markdown was on the rise and I think it was a great benefit for me to start as a fresh R Markdown user much more interested in html than PDF for print. This post discusses these two technologies.

And here is the website using the Academic website framework for Hugo static website generator.I have seen this theme before and I did not pick it at first. I just found that its new version had more flexibility and interesting features. Because I do not like to use pure standard templates, I was able to tweak it just a little to look like a lab/group website and not a personal one. Many people in academia are using the Academic theme thanks to continuing efforts by the developer George Cushen and Yihui Xie who promoted this theme in the book.

The migration has not been completed yet and will follow during the next weeks. I was able to upload it to a GitHub repository and publish at Netlify in less than five minutes. I just followed the excellent advice in the Blogdown book.


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