UQRUG 40
meeting
Overview: Using quarto and revealjs to create presentations with R markdown.
Questions: learning about knitr, combining shiny with quarto, fixing OneDrive breaking R, cmdstanr, brms
Questions: learning about knitr, combining shiny with quarto, fixing OneDrive breaking R, cmdstanr, brms
2023-07-26: UQRUG 40
R Overview of the Month
Nick will be providing an overview on creating HTML based presentations in R with Quarto and reveal.js
Find more details and the slides here: https://uqrug.netlify.app/posts/2023-07-26-july-q-pres/
Attendees
Add your name, where you’re from, and why you’re here:
| Name | Where are you from? | What brings you here? |
|---|---|---|
| Nicholas Wiggins | Library | Here to help! |
| Mikesh Patel | QCMHR | Learning R |
| Raul Riesco | ACE | Learning/helping |
| Ryan | SOE | Learning |
| Luke Gaiter | Library | Here to help! |
| Rene Erhardt | PACE | learning |
| Trinh Huynh | USC | learning |
| Danelle Kenny | CHSR | checking in and trying new things |
| Pia Wohland | SENV | Checking in |
| Jaimee Wheelhouse | Very new to R | |
| Graeme Mattison | TPCH | Learning R! |
| Fran Powell | SVS | Need some help |
| Jocelyn Hume | UQCCR | Still learning |
| David Green | UQ RCC | learning/helping … R on HPC and Shiny |
| Anne-Claire Bouton | SOE | Learning |
| Windy | SENV | Still learning |
| Valentina Urrutia Guada | Library | Here to help! |
| Gerry Katai | new to R learning |
Questions
Q1 - Learning more about knitr - Trinh Huynh
I haven’t worked with R markdown and I would like to learn from beginning- Trinh Huynh
Answers
- Take a look at this episode of the R for Reproducible Science workshop:
- The library offers introductory training modules, as well as advanced. You can look for the upcomming sessions in this website:
- After doing that training, you’re more than welcome to bring questions that you have to UQRUG
Q2 - knit Shiny/plotly objects to local html - Mikesh
Solutions for saving Rmarkdown files with shiny objects locally (no server)? Want to allow someone without R installed on their computer, access the interactive html file. maybe todays session?…
Answers
- Nick - I haven’t tried combining shiny and quarto, as Shiny will always need that Shiny server running, so I try to stick to HTML related dependencies.
- If you want to have a quarto website or presentation, you can easily publish them to a variety of free sites such as GitHub Pages, Netlify, or Quarto Pub:
- @Mikesh When you are thinking about this data access question again, please reach out to me via rcc-support@uq.edu.au
Q3 - How to get cmdstanr working - Fran
When I run cmdstan R, I get a make error.
cmdstanr:::get_cmdstan_flags('STANCFLAGS')
Error in `(function (command = NULL, args = character(), error_on_status = TRUE, …`:
! System command 'make' failed
---
Exit status: 2
Stderr:
make: *** /c/Users/uqfpowe1/OneDrive: Is a directory. Stop.
---Answers
- We spent a while working on this one. Eventually David, Valentina, Nick, and Fran managed to get it working.
- The issue appears to be that cmdstanr is for some reason pointing at the OneDrive, rather than the local C: drive
- We tried changing the standard working directory, but this did not work
- We also pulled everything off of OneDrive that was associated with R and cmdstanr, but it still wasn’t working
- David got us to open the makefile command file inside the cmdstanr installation folder and we found that it was hard coded to run from the $HOME directory.
- This is apparently different to the working directory. We found that we could check what this was with the following code:
Sys.getenv("HOME")
- We were able to change this with the following code:
Sys.setenv(HOME="C:/Users/MyName/Documents")
- We then had the code working.