lineagefreq-package: lineagefreq: Lineage Frequency Dynamics from Genomic...

In lineagefreq: Lineage Frequency Dynamics from Genomic Surveillance Counts

lineagefreq: Lineage Frequency Dynamics from Genomic Surveillance Counts

Description

Models pathogen lineage frequency dynamics from genomic surveillance count data. Provides a unified fit_model() interface with multiple engines (MLR, hierarchical MLR, Piantham), rolling-origin backtesting via backtest(), standardized scoring via score_forecasts(), emergence detection, and sequencing power analysis.

Quick start

x <- lfq_data(my_counts, lineage = lineage, date = date, count = n)
fit <- fit_model(x, engine = "mlr")
growth_advantage(fit, generation_time = 5)

Author(s)

Maintainer: Cuiwei Gao [e-mail] [copyright holder]

See Also

Useful links:

• https://github.com/CuiweiG/lineagefreq

• Report bugs at https://github.com/CuiweiG/lineagefreq/issues

lineagefreq documentation built on April 3, 2026, 9:09 a.m.