Skip to content
New issue

Have a question about this project? Sign up for a free GitHub account to open an issue and contact its maintainers and the community.

By clicking “Sign up for GitHub”, you agree to our terms of service and privacy statement. We’ll occasionally send you account related emails.

Already on GitHub? Sign in to your account

Flag potential lineages for new Nextstrain clades #71

Open
joverlee521 opened this issue Nov 6, 2023 · 1 comment
Open

Flag potential lineages for new Nextstrain clades #71

joverlee521 opened this issue Nov 6, 2023 · 1 comment
Labels
enhancement New feature or request

Comments

@joverlee521
Copy link
Contributor

Context

Requested by @trvrb in today's forecasting-automation meeting:

Separately, I’m still running Mathematica version of fitting linear regression to logit-transformed frequencies to demarcate our >0.05 per day growth in frequency threshold

  • Could we write a small script to scan forecast-ncov results for this threshold? It really should be clade-in-question vs “other” however.
  • Should be able to convert relative growth advantage to per-day growth rate (site: delta in models)
  • Multiply Pango lineage frequency by relative fitness will give mean fitness
  • Per day relative fitness is in the model already
@joverlee521 joverlee521 added the enhancement New feature or request label Nov 6, 2023
@corneliusroemer
Copy link
Member

How would this work for regions for which we have no countries included, e.g. South America/Africa? Using this flaggin strategy would increase clade bias towards high income/sequencing countries. See #64

Sign up for free to join this conversation on GitHub. Already have an account? Sign in to comment
Labels
enhancement New feature or request
Projects
None yet
Development

No branches or pull requests

2 participants