Nicola Romanò @nicolaromano@qoto.org

BBC's Visual and Data Journalism Cookbook for R Graphics and their {bbplot} #RStats 📦are useful resources for making publication-quality graphics in
#R

https://bbc.github.io/rcookbook/

#ggplot2 #DataViz

Hey, every fucking company these days, when you send me that email telling me that I have a new document to view, that I have to access by clicking on a link, then entering my credentials, then waiting for you to text me a code that I have to type in before having to hit through your terrible menu to find where you hid the messages... then looking again because that messages page wasn't the type of message the email was talking about...

Could you, I dunno... maybe mention what the fuck the document is fucking about in the god damned mother fucking email!!?!!??!

Hello World :)

I am pleased to present you a small project that I have been working on these last weeks:

MARL (Mastodon Archive Reader Lite) is a small web app that allows you to explore in detail the content of your Mastodon posts archive, including attached files (images, videos, sounds), and with different search options.

https://github.com/s427/MARL

🙏 Boosts welcome! 🙏

(More info in the post below 👇)

#Mastodon #archive

The problem of fake science papers when trying to write a systematic review https://www.science.org/content/article/systematic-reviews-aim-extract-broad-conclusions-many-studies-are-peril

#surveycomparison #representationbias
New #R-package out now!
"sampcompR" provides functions to easily compare surveys against benchmark surveys (e.g. for bias estimation) on a univariate, bivariate, and multivariate level.

By Björn Rohr & Barbara Felderer

https://bjoernrohr.github.io/sampcompR/

Confidence intervals and p-values can be either calculated with normal, parametric methods or as bootstrap confidence intervals and p-values and additionally adjusted for multiple testing.

@tehstu I don't know how to get Microsoft to fix that, but I *do* know my solution to that whole fiasco last year... was to load Linux and never looking back since.

A few weeks ago I asked everyone for some examples of fictional maths teachers 👩‍🏫✖️➗

Earlier this week we released a @sci_burst episode all about maths anxiety & maths teachers in #popculture, touching on some of your suggestions!

✨ Link in replies ✨

#maths #science #scicomm #podcast

How a misinterpretation of a BMJ publication from 1996 caused (and yes, I do mean caused) the explosion in rates of peanut allergy.

In a nutshell: for decades the guidance issued in the USA and UK was the opposite of what it should have been and left a generation with preventable, life-threatening allergies.

https://news.harvard.edu/gazette/story/2024/10/excerpt-from-blind-spots-by-marty-makary/

@pyconasia @mariatta
I was told that being a woman is just being a bride.
But I was rebellious and I went to study.

#PyCon #Python #PyConAPAC #PyLadies

A question about data management during (bioinformatics) analysis:

do you use any of:

- git annex
- DataLad
- something else? (git LFS...)

Why?

I see several hurdles with directly using git-annex, such as the need to unlock files before modifying them (useful for raw data, inconvenient for intermediate data).

#Reproducibility

Which scientific publishers/journals are worst affected by fraudulent or dubious research papers, and which have done least to clean up their portfolio?
A science-integrity startup called Argos says it has answers.
There are quite a few integrity tools now that look for red flags in papers, but this is the first to go public with what it's finding across journals and publishers.
Here's my exclusive look at their figures.
https://www.nature.com/articles/d41586-024-03427-w

“tinytable is a small but powerful R package to draw beautiful tables in a variety of formats: HTML, LaTeX, Word, PDF, PNG, Markdown, and Typst. The user interface is minimalist and easy to learn, while giving users access to powerful frameworks to create endlessly customizable tables.” - @vincentab

https://vincentarelbundock.github.io/tinytable/

{tinytable} #rstats 📦 @rstats

[New paper]: Two subtle problems with over-representation analysis.
ORA is a type of enrichment analysis that analyses over-represented functional categories in gene lists. These tools have accumulated ~190k citations, but they have subtly different behaviours. Here we unpack the differences and investigate two subtle problems in some implementations, which may have negatively impacted those 190k research papers.
https://doi.org/10.1093/bioadv/vbae159
#genomics #bioinformatics

I’m a software developer with a bunch of industry experience. I’m also a comp sci professor, and whenever a CS alum working in industry comes to talk to the students, I always like to ask, “What do you wish you’d taken more of in college?”

Almost without exception, they answer, “Writing.”

One of them said, “I do more writing at Google now than I did when I was in college.”

I am therefore begging, begging you to listen to @stephstephking: https://mstdn.social/@stephstephking/113336270193370876

Six tips for going public with your lab’s software: https://www.nature.com/articles/d41586-024-03344-y
1) make time for maintenance
2) simplify installation
3) add a GUI or good CLI
4) good documentation
5) use github/git
6) automated testing

Any other tips people have? #SoftwareEngineering #opensource #openscience

#academicchatter I read a published paper on the other day and noticed a panel in the figure is clearly duplicated but by mistake, I knew this because the authors uploaded the raw data as table and the table has a complete set of numbers that doesn't match the figure panel. Importantly the correct data didnot change the conclusion. This
#openscience approach either enforced by publishers or volunteered by authors maintained the trust I have with the finding they reported.

"My paper was proved wrong. After a sleepless night, here’s what I did next"

column by @oaggimenez describing how to gracefully react when mistakes are discovered in ones published papers.

https://www.nature.com/articles/d41586-024-02870-z