collapse_lineages: Collapse rare lineages into an aggregate group

In lineagefreq: Lineage Frequency Dynamics from Genomic Surveillance Counts

Collapse rare lineages into an aggregate group

Description

Merges lineages that never exceed a frequency or count threshold into a single group (default "Other"). Useful for reducing noise from dozens of low-frequency lineages.

Usage

collapse_lineages(
  x,
  min_freq = 0.01,
  min_count = 10L,
  other_label = "Other",
  mapping = NULL
)

Arguments

x	An lfq_data object.
min_freq	Minimum peak frequency a lineage must reach at any time point to be kept. Default 0.01 (1%).
min_count	Minimum total count across all time points to be kept. Default 10.
other_label	Label for the collapsed group. Default "Other".
mapping	Optional named character vector for custom grouping. Names = original lineage names, values = group names. If provided, min_freq and min_count are ignored.

Value

An lfq_data object with rare lineages merged.

Examples

sim <- simulate_dynamics(n_lineages = 6,
  advantages = c(A = 1.3, B = 1.1, C = 0.95, D = 0.5, E = 0.3),
  n_timepoints = 12, seed = 1)
collapsed <- collapse_lineages(sim, min_freq = 0.05)
attr(collapsed, "lineages")

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