cluster_sequences: Cluster sequences from a distance object

In gp3sequences: Transparent Analysis of Ordered Categorical Sequences

Cluster sequences from a distance object

Description

Cluster sequences from a distance object

Usage

cluster_sequences(
  distance,
  k,
  method = c("hierarchical", "pam", "clara"),
  linkage = "average",
  seed = 1L,
  ...
)

Arguments

distance	A dist object or square matrix.
k	Number of clusters.
method	"hierarchical", "pam", or "clara".
linkage	Hierarchical linkage method.
seed	Reproducibility seed for optional stochastic methods.
...	Additional arguments passed to the selected clustering function.

Value

A list of class gp3_sequence_clustering containing assignments, model object, medoid identifiers where available, and settings.

Examples

sequences <- data.frame(
  sequence_id = rep(c("s1", "s2", "s3", "s4"), each = 4L),
  sequence_order = rep(1:4, times = 4L),
  state = c("A", "B", "C", "D", "A", "B", "C", "C",
            "D", "C", "B", "A", "D", "C", "A", "A"),
  group = rep(c("g1", "g2"), each = 8L),
  stringsAsFactors = FALSE
)
distance <- compute_sequence_distance(sequences)
cluster_sequences(distance, k = 2L)

gp3sequences documentation built on Aug. 23, 2026, 5:10 p.m.