phylox.networkproperties.properties

Functions

`b2_balance`(network[, connect_roots])	returns the B_2 balance of the network
`blob_properties`(network)	finds a list of all blobs of the network and their properties.
`count_reducible_pairs`(network)	finds the number of reducible pairs in the network split up by number of cherries and number of reticulated cherries.
`level`(network)	returns the level of the network

phylox.networkproperties.properties.count_reducible_pairs(network)

finds the number of reducible pairs in the network split up by number of cherries and number of reticulated cherries.

Parameters:: network – a phylogenetic network.
Returns:: a dictionary with the number of reducible pairs in the network keys are “cherries” and “reticulate_cherries”
Example:

>>> from phylox import DiNetwork
>>> from phylox.networkproperties.properties import count_reducible_pairs
>>> network = DiNetwork(
...     edges=[(-1,0),(0,1),(1,2),(1,3),(2,3),(2,4),(3,5),(0,6),(6,7),(6,8)],
... )
>>> counts = count_reducible_pairs(network)
>>> counts["cherries"] == 1 and counts["reticulate_cherries"] == 1
True

phylox.networkproperties.properties.blob_properties(network)

finds a list of all blobs of the network and their properties. Each blob is a pair (blob_size, blob_level) where blob_size is the number of nodes in the blob and blob_level is the number of reticulations in the blob.

Parameters:: network – a phylogenetic network.
Returns:: a list of pairs (blob_size, blob_level)
Example:

>>> from phylox import DiNetwork
>>> from phylox.networkproperties.properties import blob_properties
>>> network = DiNetwork(
...     edges=[(1,2),(2,3),(2,4),(3,4),(3,5),(4,6),(6,7),(6,8),(7,8),(7,9),(8,10)],
... )
>>> blob_properties(network)
[(3, 1), (3, 1)]

>>> network = DiNetwork(
...     edges=[(0,1),(1,2),(1,3),(2,4),(3,5),(2,5),(3,4),(4,6),(5,7)],
... )
>>> blob_properties(network)
[(5, 2)]

phylox.networkproperties.properties.level(network)

returns the level of the network

Parameters:: network – a phylogenetic network.
Returns:: the level of the network
Example:

>>> from phylox import DiNetwork
>>> from phylox.networkproperties.properties import level
>>> network = DiNetwork(
...     edges=[(1,2),(2,3),(2,4),(3,4),(3,5),(4,6),(6,7),(6,8),(7,8),(7,9),(8,10)],
... )
>>> level(network)
1

>>> network = DiNetwork(
...     edges=[(0,1),(1,2),(1,3),(2,4),(3,5),(2,5),(3,4),(4,6),(5,7)],
... )
>>> level(network)
2

phylox.networkproperties.properties.b2_balance(network, connect_roots=False)

returns the B_2 balance of the network

Parameters:

network – a phylogenetic network.
connect_roots – if True, connects all roots to a new root.

Returns:

the B_2 balance of the network

Example:

>>> from phylox import DiNetwork
>>> from phylox.networkproperties.properties import b2_balance
>>> network = DiNetwork(
...     edges=[(0, 1), (1, 2), (1, 3), (2, 4), (2, 5), (3, 6), (3, 7)],
... )
>>> b2_balance(network) == 2
True