summarize_emerging: Summarize emerging lineages

In lineagefreq: Lineage Frequency Dynamics from Genomic Surveillance Counts

Summarize emerging lineages

Description

Tests whether each lineage's frequency is significantly increasing over time using a binomial GLM. Useful for early warning of lineages that may warrant enhanced surveillance.

Usage

summarize_emerging(data, threshold = 0.01, min_obs = 3L, p_adjust = "holm")

Arguments

data	An lfq_data object.
threshold	Minimum current frequency to test. Default 0.01.
min_obs	Minimum time points observed. Default 3.
p_adjust	P-value adjustment method. Default "holm".

Value

A tibble with columns: lineage, first_seen, last_seen, n_timepoints, current_freq, growth_rate, p_value, p_adjusted, significant, direction.

Examples

sim <- simulate_dynamics(
  n_lineages = 4,
  advantages = c(emerging = 1.5, stable = 1.0, declining = 0.7),
  n_timepoints = 12, seed = 42)
summarize_emerging(sim)

lineagefreq documentation built on April 3, 2026, 9:09 a.m.