lineagefreq
Lineage Frequency Dynamics from Genomic Surveillance Counts
Models pathogen lineage frequency dynamics from genomic surveillance count data. Provides a unified interface for multinomial logistic regression, hierarchical partial-pooling models, and the Piantham approximation for relative reproduction number estimation. Features include rolling-origin backtesting, standardized forecast scoring, lineage collapsing, emergence detection, and sequencing power analysis. Designed for real-time public health surveillance of any variant-resolved pathogen. Methods described in Abousamra, Figgins, and Bedford (2024) <doi:10.1371/journal.pcbi.1012443>.
Versions across snapshots
| Version | Repository | File | Size |
|---|---|---|---|
0.2.0 |
rolling linux/jammy R-4.5 | lineagefreq_0.2.0.tar.gz |
1.9 MiB |
0.2.0 |
rolling linux/noble R-4.5 | lineagefreq_0.2.0.tar.gz |
1.9 MiB |
0.2.0 |
rolling source/ R- | lineagefreq_0.2.0.tar.gz |
1.8 MiB |
0.2.0 |
latest linux/jammy R-4.5 | lineagefreq_0.2.0.tar.gz |
1.9 MiB |
0.2.0 |
latest linux/noble R-4.5 | lineagefreq_0.2.0.tar.gz |
1.9 MiB |
0.2.0 |
latest source/ R- | lineagefreq_0.2.0.tar.gz |
1.8 MiB |
0.2.0 |
2026-04-26 source/ R- | lineagefreq_0.2.0.tar.gz |
1.8 MiB |
0.2.0 |
2026-04-23 source/ R- | lineagefreq_0.2.0.tar.gz |
1.8 MiB |
0.2.0 |
2026-04-09 windows/windows R-4.5 | lineagefreq_0.2.0.zip |
1.9 MiB |