summarise_sequence_transitions: Summarise Adjacent Sequence Transitions

In gp3sequences: Transparent Analysis of Ordered Categorical Sequences

Summarise Adjacent Sequence Transitions

Description

Counts transitions between adjacent ordered states for each sequence and across the complete data set.

Usage

summarise_sequence_transitions(
  data,
  sequence_id_col,
  order_col,
  state_col,
  metadata_cols = NULL,
  expected_states = NULL,
  include_self = TRUE
)

Arguments

data	A data frame containing ordered state observations.
sequence_id_col	Name of the sequence identifier column.
order_col	Name of the numeric sequence-order column.
state_col	Name of the categorical state column.
metadata_cols	Optional character vector naming columns that should remain constant within each sequence.
expected_states	Optional vector of known or permitted state values.
include_self	Logical value indicating whether transitions from a state to the same state should be included.

Details

A transition is defined only between adjacent rows after deterministic ordering by sequence identifier, sequence order, and original row. Sequences with one state contribute no transitions.

Value

A named list containing:

• by_sequence: transition counts, proportions within each sequence, and conditional proportions within each origin state;

• overall: transition counts, sequence coverage, global proportions, and conditional origin-state proportions;

• audit, status, mapping, and the resolved include_self setting.

Examples

sequences <- data.frame(
  id = c("s1", "s1", "s1", "s2", "s2"),
  position = c(1, 2, 3, 1, 2),
  state = c("A", "B", "C", "A", "C")
)

transitions <- summarise_sequence_transitions(
  sequences,
  sequence_id_col = "id",
  order_col = "position",
  state_col = "state"
)

transitions$by_sequence
transitions$overall

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