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# CITATION file created with {cffr} R package
# See also: https://docs.ropensci.org/cffr/
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cff-version: 1.2.0
message: 'To cite package "lineagefreq" in publications use:'
type: software
license: MIT
title: 'lineagefreq: Lineage Frequency Dynamics from Genomic Surveillance Counts'
version: 0.6.0
identifiers:
- type: doi
  value: 10.32614/CRAN.package.lineagefreq
abstract: 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) <https://doi.org/10.1371/journal.pcbi.1012443>.
authors:
- family-names: Gao
  given-names: Cuiwei
  email: 48gaocuiwei@gmail.com
preferred-citation:
  type: manual
  title: 'lineagefreq: Modelling Pathogen Lineage Frequency Dynamics and Forecasting
    Variant Replacement from Genomic Surveillance Data'
  authors:
  - family-names: Gao
    given-names: Cuiwei
    email: 48gaocuiwei@gmail.com
  year: '2026'
  notes: R package version 0.5.1
  url: https://CRAN.R-project.org/package=lineagefreq
repository: https://cuiweig.r-universe.dev
repository-code: https://github.com/CuiweiG/lineagefreq
commit: a08fca034b66ac388d6c4cf4937becd531c82833
url: https://cuiweig.github.io/lineagefreq
date-released: '2026-04-19'
contact:
- family-names: Gao
  given-names: Cuiwei
  email: 48gaocuiwei@gmail.com