Package: lineagefreq
Title: Lineage Frequency Dynamics from Genomic Surveillance Counts
Version: 0.6.0
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, Compositional
        Adaptive Prediction Sets (CAPS) for horizon-aware calibrated
        forecasting, 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,
        https://cuiweig.github.io/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, scales,
        testthat (>= 3.0.0), withr
Additional_repositories: https://stan-dev.r-universe.dev
VignetteBuilder: knitr
Config/testthat/edition: 3
Language: en-US
Encoding: UTF-8
LazyData: true
Roxygen: list(markdown = TRUE)
RoxygenNote: 7.3.3
Config/pak/sysreqs: libicu-dev
Repository: https://cuiweig.r-universe.dev
Date/Publication: 2026-04-19 04:22:42 UTC
RemoteUrl: https://github.com/cuiweig/lineagefreq
RemoteRef: HEAD
RemoteSha: a08fca034b66ac388d6c4cf4937becd531c82833
NeedsCompilation: no
Packaged: 2026-06-18 10:49:44 UTC; root
Author: Cuiwei Gao [aut, cre, cph]
Maintainer: Cuiwei Gao <48gaocuiwei@gmail.com>