Lineage Frequency Dynamics from Genomic Surveillance Counts R package lineagefreq version 0.2.0 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>. Software Depends: R (>= 4.1.0) Imports: cli (>= 3.4.0), dplyr (>= 1.1.0), grDevices, ggplot2 (>= 3.4.0), MASS, numDeriv, rlang (>= 1.1.0), stats, tibble (>= 3.1.0), tidyr (>= 1.3.0) Suggests: broom, cmdstanr, covr, knitr, posterior, rmarkdown, testthat (>= 3.0.0), withr Cuiwei Gao <48gaocuiwei@gmail.com> Comprehensive R Archive Network (CRAN) Cuiwei Gao [aut, cre, cph] MIT + file LICENSE (https://CRAN.R-project.org/package=lineagefreq/LICENSE) 2026-04-03 application/tgz https://CRAN.R-project.org/package=lineagefreq doi:10.32614/CRAN.package.lineagefreq en-US