#knitr — Public Fediverse posts

#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. :awesome:

#OpenSource #FOSS #statistics

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.

Major thanks to @tannguyen for spotting and reporting a bug in my niftiPlottingFunctions.R plot.volume() function!

The code at https://osf.io/k8u2c is updated; see https://mvpa.blogspot.com/2023/03/bugfix-for-niftiplottingfunctionsr.html for info and examples.

(This #baseR #rstats function is for plotting #fMRI #nifti images in #knitr documents.)

... it is painful to find out there was a bug, but so much better to fix it than to continue its propagation! I am grateful to @tannguyen and hope anyone else seeing something odd lets me know.

Can anyone help me setting figure options in :python: when calling it via #knitr in :rstats: using #reticulate? #rstats

I'm probably overlooking something obvious because I don't know enough about #python

Details:

https://stackoverflow.com/questions/75590659/set-figure-options-for-python-with-knitr

A methods paper of mine is now at https://doi.org/10.3389/fnimg.2023.1070274 . This little #NewNeuroPaper demonstrates human task #fMRI quality control, as part of the FMRI Open QC Project (which I hope to discuss at #OHBM and elsewhere as it wraps up).

Its supplemental (https://doi.org/10.17605/OSF.IO/HT543) may be of interest to #rstats folks, particularly if looking for examples of #baseR #knitr #graphics and/or scripts aiming to minimize dependencies and maximize long-term usability.

@ERDonnachie @tgtads @datamaps

I can't resist a #tidyverse vs. #baseR #rstats thread. 😅

It is totally possible to work without tidyverse, and base R graphics can be incredibly flexible. If you'd like some examples, just this morning I uploaded yet another set of all-base #knitr supplemental files (https://osf.io/ht543), with very pretty (and highly useful) graphics, if I say so myself. (Tidyverse can be ok, but it's not at all required.)

#introduction

I'm a staff scientist at Washington U in St Louis (#WashU #wustl #Missouri, USA), mostly working with human task fMRI datasets. I'm a big fan of #baseR and #knitr #rstats, #QC, and very extensive #supplementary materials. I insist on looking at data early and often; some #tutorials and examples on my blog. (#GotBrains?)

I'm a #FirstGen college grad, #IowaStateU; BS in #forestry. I also occasionally share cats, #knitting, and #crochet. Promoting abortion rights, not book bans.