Generic framework for the coalescent simulation of pathogen trees within host trees in R
active 2023-08-31 → 2026-08-07 (UTC)
Activity over time
Daily event counts in the loaded window
Line chart, 1073 days from 2023-08-31 to 2026-08-07. Pushes: 52 total, peak 3 in a day. Pull requests: 2 total, peak 1 in a day. Issues: 19 total, peak 3 in a day. Comments: 18 total, peak 2 in a day. Stars: 1 total, peak 1 in a day.
- Pushes
- Pull requests
- Issues
- Comments
- Stars
Stars, PRs, issues and forks are under-captured in the later part of this window. GH Archive progressively stopped capturing non-push events during 2026 — −95% or worse by the end of the window. Every series here except Pushes fades for that reason, so a decline above reflects the archive, not this repository. Pushes stay reliable throughout, so read them, and the contributor counts derived from them, as the real signal. Data health has the measurements.
Top contributors
Pushes, PRs, issues, reviews and comments — stars and forks excluded, so this is contribution rather than popularity
| Contributor | Contributions | Pushes | PRs | Comments |
|---|---|---|---|---|
| ArtPoon | 81 | 42 | 2 | 18 |
| WongDWai | 8 | 8 | 0 | 0 |
| VVZ-info | 2 | 2 | 0 | 0 |
| hugocastelan | 1 | 0 | 0 | 0 |
Recent activity
Latest issues, pull requests and releases
- Issue#168ArtPoon2026-08-07 17:05Superinfection needs unit testing
- Issue#152ArtPoon2026-03-14 14:47Update README.Rmd
- ReleaseArtPoon2026-03-13 18:49Version 1.0
- Pull request#169ArtPoon2026-03-13 18:45
- Issue comment#152ArtPoon2026-03-12 02:50Update README.Rmd
- Issue#166ArtPoon2026-03-12 02:48Error in sim.inner.tree
- Issue comment#161ArtPoon2026-03-05 22:21Pass compartment labels to outer and inner trees
- Issue#163ArtPoon2026-03-05 20:18Biased sampling events in outer tree
- Issue#160ArtPoon2026-03-04 22:51Contemporaneous sampling
- Issue#162ArtPoon2026-03-04 22:24Model with migration among demes has difficulty coalescing to root host
- Issue comment#162ArtPoon2026-03-04 22:19Model with migration among demes has difficulty coalescing to root host
- Issue comment#162ArtPoon2026-03-04 22:11Model with migration among demes has difficulty coalescing to root host
- Issue#162ArtPoon2026-03-04 20:47Model with migration among demes has difficulty coalescing to root host
- Issue comment#159ArtPoon2026-02-27 17:52Error simulating inner tree
- Issue comment#157ArtPoon2026-02-17 14:59as.phylo.OuterTree is broken
- Issue#156ArtPoon2026-02-12 23:06plot.OuterTree missing samples
- Issue comment#154ArtPoon2026-02-12 22:43Error generating transmission tree from outer simulation
- Issue comment#154ArtPoon2026-02-12 21:39Error generating transmission tree from outer simulation
- Issue comment#154ArtPoon2026-02-10 20:49Error generating transmission tree from outer simulation
- Issue#154ArtPoon2026-02-10 18:10Error generating transmission tree from outer simulation
- Issue#153ArtPoon2026-02-06 21:51OuterTree is not producing a valid phylo object
- Issue#153ArtPoon2026-02-06 21:41OuterTree is not producing a valid phylo object
- Issue#126ArtPoon2026-02-06 15:49Instead of fixing bottleneck size for CompartmentType, draw from distribution
- Issue comment#126ArtPoon2026-02-06 15:49Instead of fixing bottleneck size for CompartmentType, draw from distribution
- Issue#127ArtPoon2026-02-05 22:16invalid 'type' (list) of argument
Totals cover only the window loaded into ClickHouse and count events, not GitHub's lifetime totals — 1 stars here means stars gained during the window, not the repo's star count.