Dr. Robert M Flight

@rmflight
1.2K Followers
632 Following
18.9K Posts

Research parasite* @universityofky. Interested in #openscience, #rstats, bioinformatics, #datavis he/him

*One who uses others data to conduct research, both publicly available data, and those from direct collaborations.

#fedi22

GitHubhttps://github.com/rmflight
Websitehttps://rmflight.github.io

I'm analyzing Medicare data -- my first real experience with a large dataset, where the number of observations of interest to me is in the millions. We have repeated measures/clusters to worry about, each ranging from 2 to 10 observations, give or take.

I'm struggling with performance issues in pretty much every approach I take to this dataset. One outcome of interest is a proportion. zoib is painfully slow, even when I take a (stratified) random sample of 2% of rows -- in an hour it's only 4% done fitting my null model. Boundary values (0,1) are common in the data, ruling out "transform and just do lmer."

What general tools are available for modeling bigger datasets in R? Because of data privacy agreements I'm required to do all of the computing on-prem, so unfortunately I don't know that I can take advantage of high throughput computing on other servers, if it were even workable in this case.

#rstats #lme4 #zoib

If you are someone who has ever thought running a bunch of samples through recount3 on your own hardware is a good idea, and you are horrid at writing shell scripts to manage it all, I've created a little #RStats package that helps with:

- running samples through recount-pump and unify;
- copying unify outputs into a directory that recount3 will see and load;
- checking your fq.gz files to make sure they aren't bad before running pump.

https://moseleybioinformaticslab.github.io/rc3helpers/

#Bioinformatics #RNASeq

recount3 Directory Helpers

Simple functions for creating a custom recount3 directory.

I really can't tell you how much joy it gave me yesterday to pick out these two t-shirts while shopping at the giant conglomerate box store yesterday.
Hey geeks! We're ordering extra blank mugs for the upcoming Mother's Day, but if you want one of our statistical parent mugs, please get your order in. https://smbc-store.myshopify.com/products/good-parent-mug
finally, Wendell Berry's standards for technological innovation--truly as relevant now as they were in 1987 #othernetworks

[blog] A Better R Programming Experience Thanks to Tree-sitter

Did you know that thnaks to Tree-sitter's support for R help you get

✨ reformatting through Air and linting through Jarl;

✨ auto-completion or help on hover in the Positron IDE;

✨ better search for R on GitHub;
✨ and more!

By @maelle, edited by @etiennebacher, @davis, @steffilazerte

https://ropensci.org/blog/2026/04/02/tree-sitter-overview/

#RStats

A Better R Programming Experience Thanks to Tree-sitter

Modern tooling for parsing, searching, formatting, editing R code, just like for other programming languages.

After getting in a "fender-bender" from the ridiculous icy streets we had back on Mar 17, I finally got the van in for an estimate for repairs. Now I know why I see so many just driving around with broken cars.

$7.5K to replace rear hatch, a radar module, and related. 😳

We are just under the limit to total our 2014 van. If I knew I could find a similar vehicle at a good price, I'd definitely consider totaling. Thankful we aren't the ones liable, that we have the insurance. But yikes.

Actually, let me try something different than just asking for money for TDOV:

If you have any possible leads or hiring power for a job that hires for WFH customer/tech support out of Washington state PLEASE message or DM me and if you don't please share this.

When your friends ask
how we will get through
the coming crisis
tell them:
“the same way we got through
the pandemic,
by taking care of each other,”
and when they reply
that we have not
actually gotten through
the pandemic,
calmly and firmly tell them:
exactly.