filter_sparse: Filter sparse time points and lineages

In lineagefreq: Lineage Frequency Dynamics from Genomic Surveillance Counts

Filter sparse time points and lineages

Description

Removes time points with very low total counts and lineages observed at too few time points.

Usage

filter_sparse(x, min_total = 10L, min_timepoints = 3L)

Arguments

x	An lfq_data object.
min_total	Minimum total sequences per time point. Default 10.
min_timepoints	Minimum number of time points a lineage must appear to be retained. Default 3.

Value

An lfq_data object with sparse entries removed.

Examples

sim <- simulate_dynamics(n_lineages = 3,
  advantages = c("A" = 1.2, "B" = 0.8), seed = 1)
filtered <- filter_sparse(sim, min_total = 100)

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