Package: lineagefreq
Title: Lineage Frequency Dynamics from Genomic Surveillance Counts
Version: 0.2.0
Authors@R: 
    person("Cuiwei", "Gao", , "48gaocuiwei@gmail.com",
    role = c("aut", "cre", "cph"))
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>.
License: MIT + file LICENSE
URL: https://github.com/CuiweiG/lineagefreq
BugReports: https://github.com/CuiweiG/lineagefreq/issues
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
Additional_repositories: https://mc-stan.org/r-packages/
VignetteBuilder: knitr
Config/testthat/edition: 3
Language: en-US
Encoding: UTF-8
LazyData: true
RoxygenNote: 7.3.3
NeedsCompilation: no
Packaged: 2026-03-30 15:43:33 UTC; openclaw
Author: Cuiwei Gao [aut, cre, cph]
Maintainer: Cuiwei Gao <48gaocuiwei@gmail.com>
Repository: CRAN
Date/Publication: 2026-04-03 08:00:08 UTC
Built: R 4.6.0; ; 2026-06-04 04:09:57 UTC; windows
