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lineagefreq  

Lineage Frequency Dynamics from Genomic Surveillance Counts
View on CRAN: Click here


Download and install lineagefreq package within the R console
Install from CRAN:
install.packages("lineagefreq")

Install from Github:
library("remotes")
install_github("cran/lineagefreq")

Install by package version:
library("remotes")
install_version("lineagefreq", "0.2.0")



Attach the package and use:
library("lineagefreq")
Maintained by
Cuiwei Gao
[Scholar Profile | Author Map]
All associated links for this package
First Published: 2026-04-03
Latest Update: 2026-04-03
Description:
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>.
How to cite:
Cuiwei Gao (2026). lineagefreq: Lineage Frequency Dynamics from Genomic Surveillance Counts. R package version 0.2.0, https://cran.r-project.org/web/packages/lineagefreq. Accessed 07 Aug. 2026.
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Complete documentation for lineagefreq
Functions, R codes and Examples using the lineagefreq R package
Full lineagefreq package functions and examples
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