Joshua Batson
Joshua Batson
Hello, Running on a Mac, clean install today (required upgrading libpng, libjpeg, libtiff by hand for some reason). When I run the demo from the README, I get poor performance:...
Hello! Thanks for the excellent repo, I found it by following up on the Color [return-to-work model](https://www.color.com/wp-content/uploads/2020/08/FINAL-v7-Color-Return-to-On-Site-Testing_v7C_072320.pdf), which was useful for thinking through the impact of different testing regimes on...
https://github.com/nextstrain/ncov/blob/24f5256be44b61eb4b0e6ca2789205c49010e2e1/scripts/calculate_delta_frequency.py#L142 The logistic growth model fit is based on KDE estimates of variant frequency. In time intervals where there are not very many samples, these estimates can be rather poor,...
**Context** I cannot find or click on the purple branch because they are thin in a dense region.  **Description** There are two ways I can think of to solve...
Hello! I believe you shared with me some code for exporting a baltic tree as a Nextstrain JSON. I expect it would be widely useful at this point. `exportJSON` perhaps?
If sometimes happens that there is a huge increase in loss in a single step. Increasing the penalty changes the objective function, but it may also be possible that the...
Are the factors ordered in some way? For classical PCA, PCs are canonically defined and ordered by variance explained. I noticed from a small experiment that the loadings appear to...