#reticulate — Public Fediverse posts

When editors of Q1-Journals leave the editing business to AI.

#BMCGenomics sending out a paper for review based on three, one per species, complete plastomes "[revealing] #Phylogenetic conflict [and] #reticulate evolution in #Quercus section Cerris subsection Campylolepides: Evidence from chloroplast genomes and its biogeographic implications (researchers from Shanghai Institute of Technology)
Key pic attached
#FightTheFog
1/2

Balanced #DecisionMaking (single-blind #PeerReview) @ Plant Diversity
https://www.sciencedirect.com/journal/plant-diversity

Rev. 1: "... resolve the complex #reticulate evolutionary history of the Hoya-Dischidia lineage ... is ambitious and addresses an interesting evolutionary question, there are several fundamental flaws..."

Rev. 2: "... ambitious, the dataset is substantial, and the topic is suitable for Plant Diversity...a valuable piece of research with a strong methodological core."

Verdict: Reject

For a change, a proper #milestone. 1000 reads on RG for the #Reticulate origin of modern plane trees (#Platanus, Platanaceae): A nuclear marker puzzle

https://www.researchgate.net/profile/Guido-Grimm/achievement/6929624c0df56f392494b91f

It's profoundly comforting to see that one's work is still raising interest after more than a decade, especially, something that at the time of publication was harshly attacked by "expert #reviewers" –anonymously of course (#FightTheFog). And ignored by the botanical High Priests beyond the Big Pond 😎😎😎

Took a while, but finally out:

Pruning the Tree: Comparing #OTUs and #ASVs in High-Throughput Sequencing of 5S-IGS Nuclear Ribosomal DNA in #Phylogenetic Studies

How to reduced 100ks of reads down to the 100 really needed, a comparison between #Mothur and #dada2 pipelines using our nigh-#reticulate #beech dataset as test subject

https://doi.org/10.1002/ece3.72242

Na #PythonCerrado2025, tivemos ontem um excelente tutorial do Lucas Marcondes Pavelski https://github.com/lucasmpavelski.

Aprendemos sobre #R, #tidyverse, #reticulate, várias ferramentas essenciais como #ggplot2 e #dplyr, vendo na prática como aplicá-las. Foco na ponte #Python <-> R.

Tudo novidade pra mim, vieram várias ideias interessantes de análises e plots.

#PythonCerrado

The unfiltered paper, with all the major deficits outlined by Kong's/New Phyt's #PeerReview experts still in it, is now online on bioRvix.

Worth et al. Whole #chloroplast #Genomes reveal a complex genetic legacy of #LostLineages, past radiations and #SecondaryContacts in the dominant temperate deciduous tree genus #Fagus

https://doi.org/10.1101/2025.06.03.653586

Being not limited, we moved a few more figures from the supplement to the main text 😎

https://figshare.com/projects/Supplement_to_Worth_et_al_2025_Reticulate_history_of_beech/251480

#PhyloNetworks #reticulate #evolution

A classic, my first paper on #beech #genetics getting a RG-#milestone: 1000 reads for "The #evolutionary history of #Fagus in western Eurasia: Genes, morphology and the #fossil record" RG added #reticulate #evolution, suppressed #speciation, could say that.

http://dx.doi.org/10.1007/s006060200044

Low impact? Enduring research still (obviously) worth a read over 20 yrs later 😎

PS Still happy with it. But wouldn't just use a tree anymore for #phylogenetics

Overall, I am quite impressed with the responses! With minimal prompt engineering, document cleaning! It was able to return accurate responses, and even separated different conditions and provided appropriate treatment options. It was also able to return the correct response for tricky questions that our RAG was not able to. It definitely has potential! #rstats #reticulate #gemini #llm https://www.kenkoonwong.com/blog/gemini/

The PyWhy Causal-learn Discord community is fantastic! The package documentation is equally impressive, making experiential learning both fun and informative. Truly, it’s another exceptional tool for causal discovery at our fingertips! ❤️
#causallearn #pywhy #rstats #Python #reticulate
https://www.kenkoonwong.com/blog/causal-learn/

I got Python working to run LangChain document loaders in VSCode on both my Mac and Windows machines - plus in RStudio with {reticulate}! 🎉 I feel like I ought to go buy a lottery ticket 😀

#python #LangChain #reticulate #RStudio

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

R and Python sitting in a tree — R. E. T. I. C. U. LATE.

Our hackathon goal was to showcase how easy it is to work as a part of cross-language team of Python and R to deliver on end-to-end data science project.

This article deep dives into my journey of using #Reticulate in R to call API function calls written by Riesling in Python with the goal of getting relevant data into R data frames which we could then visualize using GGPlot2.

#R4DS #Python #RStats

https://medium.com/data-science-at-microsoft/collaborating-between-python-and-r-using-reticulate-25246b367957

This time I did it all in #python but then pulled the #pandas dataframe into #rstats via #reticulate for plotting

How to access an #api for first time users. Riesling and I wanted to analyze data related to our hobby as part of msft hackathon. Here’s the first article in an upcomig series of analyzing Ravelry knitting projects data using #rstats and #python . Next up in series - Using #Reticulate to combine their powers!
https://medium.com/data-science-at-microsoft/how-to-access-an-api-for-first-time-api-users-879002f5f58d?source=friends_link&sk=c2763957800727392111bfe47da08fb3

#reticulate is a great package to work with #python in #rstats. Here is a very simple example of how to use it in #RKWard.

RKWard supports syntax highlighting for several languages, including Python. However, this is not done automatically, but must be selected by the user (blue arrow).

The best love story to share on Valentine's Day in #rstats and #python community: http://bit.ly/2HpTVZW #ValentinesDay2020 #DataScience @rstudio #reticulate