#AcademicChatter Hello, fellow academic chatters. I'm an experimental scientist. And I regularly have the problem of how to organize acquired data by different participants to a same experiment. I'd like to have some feedback of how other people do this. Not necessarily specific computer programmes (such as digital labbooks), but rather how-tos based on robust, basic things, such as text and csv files, folder structures etc. I'm often battling with the workflow which is including handwritten measurements, their digital counterparts, metadata for the measurements, codes for samples, all of these done by different people, but all will have to end in one final dataset, where I would like to be able to trace data back to the paper files, and their metadata. And all of this with not too much additional effort by everybody ;-) Have done this usually with some shared server space, but usually it ends up as something a bit difficult to get through. I'm now rather thinking about a system involving perhaps something based on #MarkDown or even #RMarkdown or #knitr etc. Any feedback much welcome 😁
#ReproducibleResearch

Performing some quick statistical analyses in classic #RStats and neatly “knitting” them into a PDF using #RMarkdown, #knitr, and #MacTeX #texLaTeX.

Call me old-fashioned, but I really enjoy this workflow. 

#OpenSource #FOSS #statistics

Switching from #rmarkdown and #rdatatable to #quarto and #polars is a bit cumbersome. I just want to compile a document with tables to pdf.

If I print a polars table, I get the data type with it. If I convert it to pandas df, I get an index. If I set_tbl_hide_column_data_types, my strings get quotes. Is there no #knitr kable equivalent in #Python /Quarto?

Dear #rstats experts, do you see the culprit in this problem and how it can be avoided/fixed?

I get an unclosed sink() after I

- set a time limit
- run #knitr with timeout in chunk
- open a new plot afterwards

Details on SO, tagging @yihui

https://stackoverflow.com/questions/79594532

Unclosed sink from knitr after setTimeLimit

Overview: I'm running knitr on a large number of R/Markdown files (actually R/exams exercises to be more specific), some of which take too long to complete. Hence I want to set a time limit for this

Stack Overflow
Any way in #knitr #rstats to do arbitrary (i.e., regex) string replacement in the output - e.g., there's a known account id you don't want showing up in the output

I posted a new introduction to surface #gifti and volume #NIfTI #fMRI data at https://mvpa.blogspot.com/2025/01/intro-to-working-with-volume-and.html.

The material is mostly general, with all examples using #baseR #rstats code; it's accompanied by a major update to my gifti #knitr tutorial.

I hope these will be useful to folks getting started with #neuroimaging datasets, as well as anyone looking for example scripts for reading, plotting, and manipulating (human fMRI) brain data files.

intro to working with volume and surface brain data

When preparing to update my surface (gifti) tutorial knitr , I realized that some of the confusion I was trying to address wasn't due to the...

Why call it #knitr and #R #Markdown when they could have called it R-TeX? 🦖

Holy cow is #Rmarkdown #RStats #knitr inferior to #Jupyter. 😠

- WHY does it need to rerun EVERYTHING for hours when making a HTML/PDF?
- WHY is the apparent solution (caching) so weird? No clear instructions, only blog posts with broken formatting everywhere.
- WHY don't you at least see where it hangs during the process? No indication which line is currently executed?
- WHY does making a PDF silently fail after hours?

[/rant]

@lwpembleton it was gradual for me. Grad school used it for stats classes and my advisor suggested to rewrite a standalone population genetics program in R. He then suggested to make it into a package and sent me to one of Hadley Wickham’s trainings (pre-RStudio). I then found out about #knitr and stated making websites in R and was hooked.
#TidyTuesday @ShinyConf How are packages linked to @Posit's {shiny}. For linked packages, the most popular imports are #dplyr & #ggplot2. Most common suggestions are #testthat, @rmarkdown and #knitr.
Data: #ShinyConf2024, @tracykteal & @jonthegeek
Code🔗https://tinyurl.com/tidy-shny
Tools: #rstats #ggplot2 #treemapify
projects_presentations/projects/tidy_shiny_packages.R at main · Aditya-Dahiya/projects_presentations

Presentations, Data Viz & More. Contribute to Aditya-Dahiya/projects_presentations development by creating an account on GitHub.

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