def expand(self, order=0, include_path: bool = False) -> List[Path]:
"""Converts the path in subpaths of length oder."""
paths = []
for path in self.paths.values():
expanded = []
if order == 0:
for uid in path.as_nodes:
expanded.append(
Path.from_nodes([path.nodes[uid]],
**path.attributes.to_dict()))
elif 0 < order < len(path):
for subpath in window(path.as_edges, size=order):
edges = [path.edges[uid] for uid in subpath]
expanded.append(
Path.from_edges(edges, **path.attributes.to_dict()))
elif order == len(path) and include_path:
expanded.append(path)
else:
pass
# add sub path if exist
if expanded:
paths.append(expanded)
return paths
def generate(self, order: int = 1) -> HigherOrderNetwork:
"""Generate a null model."""
# TODO: Add null model for order 1
if order == 0:
return HigherOrderNetwork(self.network, order=0)
if order == 1:
return HigherOrderNetwork(self.network, order=1)
# some information for debugging
log.debug('start generate null model')
a = datetime.datetime.now()
# generate all possible paths
possible_paths = self.possible_paths(order=order)
# get observed paths
observed = self.network.subpaths.counter(min_length=order - 1,
max_length=order - 1)
# get transition matrix of the underlying network
transition_matrix = self.network.transition_matrix(
weight=config['attributes']['frequency'])
# get the ordered node uids of the underlying network as a list
nodes = list(self.network.nodes)
# generate hon with possible paths
hon = HigherOrderNetwork(order=order)
for path in possible_paths:
# generate "empty" higher order nodes
v = HigherOrderNode()
w = HigherOrderNode()
# add first order edges to the higher oder nodes
for v_uid, w_uid in zip(path[:-1], path[1:]):
v.add_edge(self.network.edges[v_uid])
w.add_edge(self.network.edges[w_uid])
# generate the expected frequencies of all possible paths
uid = self.network.separator['path'].join(path[:-1])
frequency = 0
if uid in observed:
frequency = observed[uid] * transition_matrix[
nodes.index(w.as_nodes[-2]),
nodes.index(w.as_nodes[-1])]
# add higher order nodes to the hon
# TODO: use automatically hon separator
e = Edge(v, w, separator=hon.separator['hon'])
hon.add_path(Path.from_edges([e], frequency=frequency))
# hon.add_edge(Edge(v, w, separator=hon.separator['hon']),
# frequency=frequency)
# some information for debugging
b = datetime.datetime.now()
log.debug('end generate null model:' +
' {} seconds'.format((b - a).total_seconds()))
# safe hon in class and order
hon.network = self.network
self.hon = hon
self.order = order
# return null model
return hon