## Functions | |

def | ped_to_graph |

def | find_ancestors |

def | find_ancestors_g |

def | find_descendants |

def | immediate_family |

def | count_offspring |

def | offspring_influence |

def | most_influential_offspring |

def | get_founder_descendants |

def | get_node_degrees |

def | get_node_degree_histograms |

def | mean_geodesic |

def | graph_density |

def | dyad_census |

def | mean_degree_centrality |

def | mean_value |

def | get_closeness_centrality |

def | get_clustering_coefficient |

def | get_betweenness_centrality |

def | get_node_betweenness |

def PyPedal::pyp_network::count_offspring | ( | pedgraph, |
||

anid | ||||

) |

count_offspring() returns the number of offspring of an animal.

**Parameters:**-
*pedgraph*An instance of a networkx DiGraph. *anid*The animal for whom offspring are to be counted.

**Returns:**- Count of offspring. integer
count_offspring() returns the number of offspring of an animal.

Definition at line 181 of file pyp_network.py.

def PyPedal::pyp_network::dyad_census | ( | pg, |
||

debug = `0` , |
||||

debuglog = `0` | ||||

) |

dyad_census() calculates the number of null, asymmetric, and mutual edges between all pairs of nodes in a directed graph.

**Parameters:**-
*pg*An instance of a NetworkX DiGraph. *debug*Flag to turn debugging messages on (1) or off (0). *debuglog*Flag to turn debugging messages to the logfile on (1) or off (0).

**Returns:**- A dictionary of counts. dictionary
dyad_census() calculates the number of null, asymmetric, and mutual edges between all pairs of nodes in a directed graph.

Definition at line 412 of file pyp_network.py.

def PyPedal::pyp_network::find_ancestors | ( | pedgraph, |
||

anid, |
||||

_ancestors = `[]` | ||||

) |

find_ancestors() identifies the ancestors of an animal and returns them in a list.

**Parameters:**-
*pedgraph*An instance of a networkx DiGraph. *anid*The animal for whom ancestors are to be found. *_ancestors*The list of ancestors already found.

**Returns:**- List of ancestors of anid. list
find_ancestors() identifies the ancestors of an animal and returns them in a list.

Definition at line 92 of file pyp_network.py.

def PyPedal::pyp_network::find_ancestors_g | ( | pedgraph, |
||

anid, |
||||

_ancestors = `{}` , |
||||

gens = `3` | ||||

) |

find_ancestors_g() identifies the ancestors of an animal going back a user-specified number of generations and returns them in a list.

**Parameters:**-
*pedgraph*An instance of a networkx DiGraph. *anid*The animal for whom ancestors are to be found. *_ancestors*The list of ancestors already found.

**Returns:**- List of ancestors of anid. list
find_ancestors_g() identifies the ancestors of an animal and returns them in a list.

Definition at line 116 of file pyp_network.py.

def PyPedal::pyp_network::find_descendants | ( | pedgraph, |
||

anid, |
||||

_descendants = `[]` | ||||

) |

find_descendants() identifies the descendants of an animal and returns them in a list.

**Parameters:**-
*pedgraph*An instance of a networkx DiGraph. *anid*The animal for whom descendants are to be found. *_descendants*The list of descendants already found.

**Returns:**- List of descendants of anid. list
find_descendants() identifies the descendants of an animal and returns them in a list.

Definition at line 144 of file pyp_network.py.

def PyPedal::pyp_network::get_betweenness_centrality | ( | pg |
) |

get_betweenness_centrality(pg) returns a dictionary of the betweenness centrality of each node in the graph.

**Parameters:**-
*pg*An instance of a NetworkX DiGraph.

**Returns:**- A dictionary of closeness centralities. dictionary
get_betweenness_centrality(pg) returns a dictionary of the betweenness centrality of each node in the graph.

Definition at line 554 of file pyp_network.py.

def PyPedal::pyp_network::get_closeness_centrality | ( | pg |
) |

get_closeness_centrality(pg) returns a dictionary of the closeness centrality (1/(average distance to all nodes from n)) for each node in the graph.

**Parameters:**-
*pg*An instance of a NetworkX DiGraph.

**Returns:**- A dictionary of closeness centralities. dictionary
get_closeness_centrality(pg) returns a dictionary of the close- ness centrality (1/(average distance to all nodes from n)) for each node in the graph.

Definition at line 513 of file pyp_network.py.

def PyPedal::pyp_network::get_clustering_coefficient | ( | pg |
) |

get_clustering_coefficient(pg) returns a dictionary of the clustering coefficient of each node in the graph based on the definition of Watts and Strogatz (1998).

**Parameters:**-
*pg*An instance of a NetworkX DiGraph.

**Returns:**- A dictionary of clustering coefficients. dictionary
get_clustering_coefficient(pg) returns a dictionary of the clustering coefficient of each node in the graph based on the definition of Watts and Strogatz (1998).

Definition at line 534 of file pyp_network.py.

def PyPedal::pyp_network::get_founder_descendants | ( | pedgraph |
) |

get_founder_descendants() returns a dictionary containing a list of descendants of each founder in the pedigree.

**Parameters:**-
*pedgraph*An instance of a NetworkX DiGraph.

**Returns:**- A dictionary containing a list of descendants for each founder in the graph. dictionary
get_founder_descendants() returns a dictionary containing a list of descendants of each founder in the pedigree.

Definition at line 270 of file pyp_network.py.

def PyPedal::pyp_network::get_node_betweenness | ( | pg |
) |

get_node_betweenness(pg) returns a dictionary of the number of shortest paths that go through each node in the graph.

**Parameters:**-
*pg*An instance of a NetworkX DiGraph.

**Returns:**- A dictionary of node betweennesses. dictionary
get_node_betweenness(pg) returns a dictionary of the number of shortest paths that go through each node in the graph.

Definition at line 573 of file pyp_network.py.

def PyPedal::pyp_network::get_node_degree_histograms | ( | node_degrees |
) |

get_node_degree_histograms() returns a dictionary containing histograms of the number of vertices (nodes) in pg with a given number of incoming, outgoing, or total edges.

**Parameters:**-
*node_degrees*A dictionary of dictionaries of in, out, and total node degrees.

**Returns:**- A dictionary of dictionaries containing in, out, and total degree histograms. dictionary
get_node_degree_histograms() returns a dictionary containing histograms of the number of vertices (nodes) in pg with a given number of incoming, outgoing, or total edges.

Definition at line 321 of file pyp_network.py.

def PyPedal::pyp_network::get_node_degrees | ( | pg |
) |

get_node_degrees() returns a dictionary containing the number of vertices (nodes) in pg with a given number of incoming, outgoing, or total edges.

**Parameters:**-
*pg*An instance of a NetworkX DiGraph.

**Returns:**- A dictionary of dictionaries containing in, out, and total node degrees. dictionary
get_node_degrees() returns a dictionary containing the number of vertices (nodes) in pg with a given number of incoming, outgoing, or total edges.

Definition at line 295 of file pyp_network.py.

def PyPedal::pyp_network::graph_density | ( | pg |
) |

graph_density() calculates the density of a digraph, which is the ratio of edges in the gaph to the maximum possible number of edges.

**Parameters:**-
*pg*An instance of a NetworkX DiGraph.

**Returns:**- The density of the pedigree represented in pg. float
graph_density() calculates the density of a digraph, which is the ratio of edges in the gaph to the maximum possible number of edges.

Definition at line 389 of file pyp_network.py.

def PyPedal::pyp_network::immediate_family | ( | pedgraph, |
||

anid | ||||

) |

immediate_family() returns parents and offspring of an animal.

**Parameters:**-
*pedgraph*An instance of a networkx DiGraph. *anid*The animal for whom immediate family are to be found.

**Returns:**- List of immediate family members of anid. list
immediate_family() returns parents and offspring of an animal.

Definition at line 165 of file pyp_network.py.

def PyPedal::pyp_network::mean_degree_centrality | ( | pg, |
||

normalize = `0` | ||||

) |

mean_degree_centrality(pg) calculates mean in- and out-degree centralities for directed graphs and simple degree-centralities for undirected graphs. If the normalize flag is set, each node's centralities are weighted by the number of edges in the (di)graph.

**Parameters:**-
*pg*An instance of a NetworkX DiGraph. *normalize*Flag to turn normalization on (1) or off (0).

**Returns:**- A dictionary of mean degree centralities. dictionary
mean_degree_centrality(pg) calculates mean in- and out-degree centralities for directed graphs and simple degree-centralities for undirected graphs. If the normalize flag is set, each node's centralities are weighted by the number of edges in the (di)graph.

Definition at line 455 of file pyp_network.py.

def PyPedal::pyp_network::mean_geodesic | ( | pg, |
||

debug = `0` | ||||

) |

mean_geodesic() calculates the mean geodesic (shortest) distance between two vertices in a network.

**Parameters:**-
*pg*An instance of a NetworkX DiGraph. *debug*Flag to turn debugging messages on (1) or off (0).

**Returns:**- The mean geodesic for the pedigree represented in pg. float
mean_geodesic() calculates the mean geodesic (shortest) distance between two vertices in a network.

Definition at line 355 of file pyp_network.py.

def PyPedal::pyp_network::mean_value | ( | mydict |
) |

mean_value() calculates the mean from all values in a dictionary.

**Parameters:**-
*mydict*A dictionary whose values are integers or reals.

**Returns:**- The mean of values in mydict. float
mean_value() calculates the mean from all values in a dictionary.

Definition at line 494 of file pyp_network.py.

def PyPedal::pyp_network::most_influential_offspring | ( | pedgraph, |
||

anid, |
||||

resolve = `'all'` | ||||

) |

most_influential_offspring() returns the most influential offspring of an animal as measured by their number of offspring.

**Parameters:**-
*pedgraph*An instance of a networkx DiGraph. *anid*The animal for whom the most influential offspring is to be found. *resolve*Indicates how ties should be handled ('first'|'last'|'all').

**Returns:**- The most influential offspring of anid. dictionary
most_influential_offspring() returns the most influential offspring of an animal as measured by their number of offspring.

Definition at line 219 of file pyp_network.py.

def PyPedal::pyp_network::offspring_influence | ( | pedgraph, |
||

anid | ||||

) |

offspring_influence() returns the number of grand-children by each child of a given animal.

**Parameters:**-
*pedgraph*An instance of a networkx DiGraph. *anid*The animal for whom grand-progeny are to be counted.

**Returns:**- A dictionary of counts of progeny per child. dictionary
offspring_influence() returns the number of grand-children by each child of a given animal.

Definition at line 197 of file pyp_network.py.

def PyPedal::pyp_network::ped_to_graph | ( | pedobj, |
||

oid = `0` | ||||

) |

ped_to_graph() Takes a PyPedal pedigree object and returns a networkx XDiGraph object.

**Parameters:**-
*pedobj*A PyPedal pedigree object. *oid*Flag indicating if original (1) or renumbered (0) IDs should be used.

**Returns:**- DiGraph object graph
ped_to_graph() Takes a PyPedal pedigree object and returns a networkx XDiGraph object.

Definition at line 57 of file pyp_network.py.

Generated on Fri Mar 28 14:34:59 2008 for PyPedal by 1.5.3