function compute_connected_sets

deeptime.markov.compute_connected_sets(count_matrix, connectivity_threshold: float = 0, directed=True)

Computes the connected sets of a count matrix C.

Parameters:

• count_matrix ((N, N) np.ndarray) – count matrix

• connectivity_threshold (float, optional, default=0) – Minimum count required to be included in the connected set computation.

• directed (boolean) – True: Seek connected sets in the directed graph. False: Seek connected sets in the undirected graph.

Returns:

• A list of arrays, each array representing a connected set by enumerating the respective states. The list is in

• descending order by size of connected set.