Paired Ends Wrapped: Top 10 Posts From 2025
R + AI, uv, RAG+Zotero, Quarto books, Codex in Positron, Positron assistant & copilot, academia to biotech, RAG in R with ragnar, genome engineering biodiversity conservation, returning to UVA SDS
I wrote 105 posts here in 2025. Here’s a look back at the 10 most viewed last year.
The Modern R Stack for Production AI
There was a time in late 2023 to early 2024 when I and probably many others in the R community felt like R was falling woefully behind Python in tooling for development using AI and LLMs. This is no longer the case. The R community, and Posit in particular, have been on an absolute tear bringing new packages online to take advantage of all the capabilit…
Build a local RAG application with Open WebUI to chat with your Zotero library
In a previous post I demonstrated how to set up a local LLM that you can run through either a command line interface (Ollama) or a graphical user interface (Open WebUI and others), and quickly demonstrated how to “chat with your documents” with a local model using LMStudio.
Writing a book with Quarto
In the spirit of learning in public, I wanted an excuse to dive into Quarto to learn more about publishing formats beyond simple PDF and HTML documents.
Using OpenAI Codex in Positron
Last month I wrote about agentic coding in Positron using Positron assistant, which uses the Claude API on the back end.
Positron Assistant: GitHub Copilot and Claude-Powered Agentic Coding in R
I have a little hobby project I’m working on and I wanted to use the opportunity to fully make the switch to Positron from RStudio. I used Positron here and there when it first came out, but now that it’s out of beta and has a more complete feature set (like
Moving from academia to biotech
I originally wrote and published this essay at The Connected Ideas Project, an excellent newsletter by my good friend and colleague Alexander Titus. If you’re not reading TCIP you’re missing out.
Tidy RAG in R with ragnar
Note: After I wrote this post last week, the Tidyverse team released ragnar 0.2.0 on July 12. Everything here should still work, but take a look at the release notes to learn about some nice new features that aren’t covered here.
Genome engineering in biodiversity conservation and restoration
I’m thrilled to share the publication of our new paper published today in Nature Reviews Biodiversity:
Returning to Academia: UVA Data Science
I started my academic career in biomedical research as faculty in the University of Virginia (UVA) School of Medicine. After eight years I jumped to industry & government consulting to tackle problems in public health and biosecurity for a few years before joining