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>.

Version:	0.2.0
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
Published:	2026-04-03
DOI:	10.32614/CRAN.package.lineagefreq
Author:	Cuiwei Gao [aut, cre, cph]
Maintainer:	Cuiwei Gao <48gaocuiwei at gmail.com>
BugReports:	https://github.com/CuiweiG/lineagefreq/issues
License:	MIT + file LICENSE
URL:	https://github.com/CuiweiG/lineagefreq
NeedsCompilation:	no
Additional_repositories:	https://mc-stan.org/r-packages/
Language:	en-US
Citation:	lineagefreq citation info
Materials:	README, NEWS
CRAN checks:	lineagefreq results

Documentation:

Reference manual:	lineagefreq.html , lineagefreq.pdf
Vignettes:	Getting started with lineagefreq (source, R code) Comparing modeling engines (source, R code) Analyzing real CDC surveillance data (source, R code) Surveillance workflow (source, R code)

Downloads:

Package source:	lineagefreq_0.2.0.tar.gz
Windows binaries:	r-devel: lineagefreq_0.2.0.zip, r-release: not available, r-oldrel: not available
macOS binaries:	r-release (arm64): lineagefreq_0.2.0.tgz, r-oldrel (arm64): not available, r-release (x86_64): not available, r-oldrel (x86_64): not available

Linking:

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