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 (may not be active yet) |
| 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 |
| 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) |
| Package source: | lineagefreq_0.2.0.tar.gz |
| Windows binaries: | r-devel: not available, 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 |
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