Starting a blog!
Published:
I figured it would be fun to keep a record of all the projects I’m working on in a blog format, so I’ve set up the blog page on my website! You’ll be able to access this page at any time by going to ahl27.com/blog!
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Converting vectors to dendrograms in R
6 minute read
Published:
I do really like R’s dendrogram object, but it can be really clunky to work with them. I recently implemented random forests from scratch, and the decision trees within were stored as two vectors. However, it would be really nice to be able to plot these decision trees to visualize their contents. This got me thinking–is it possible to convert vectors of values into dendrogram objects in R if we know the vectors are ordered in a known tree traversal? In other languages this would be fairly simple, but the nested list structure of dendrogram objects (and their other attributes) makes it a little trickier in R.
Automated R Testing and Coverage on GitHub (without Codecov!)
4 minute read
Published:
I’ve recently been working on adding some unit testing to Biostrings as part of working I’m doing for a grant awarded by R’s Infrastructure Steering Committee. As part of implementing unit tests, I wanted to add an automatic workflow that would evaluate the current tests on any future pull requests, so that (1) we could be sure contributed code isn’t breaking any additional functionality (2) we can be sure that contributed code is adequately tested.
Clustering without RAM
12 minute read
Published:
Update: This project has progressed pretty far from this inital sketch. This post describes my first pass at this problem–the final version is quite a bit different. I’ll write another post soon to incorporate those thoughts (will be linked here when done). Original post is below.
Writing a Random Forest from Scratch
24 minute read
Published:
I’ve recently had to implement random forests from scratch in R. This is a much longer post than I normally make, since I’m going to go through all the details of actually implementing one of these models. By “from scratch”, I mean a complete Random Forest prediction model, written in R, with no packages aside from those provided in a base installation.