-*
Copyright 2020 Carlos Amendola, Luis David Garcia Puente, Roser Homs Pons,
Olga Kuznetsova, Harshit J Motwani.
You may redistribute this file under the terms of the GNU General Public
License as published by the Free Software Foundation, either version 2 of
the License, or any later version.
*-
newPackage(
"StatGraphs",
Version => "0.1",
Date => "3 August 2020",
Authors => {{Name=> "Carlos Amendola",
Email=> "carlos.amendola@tum.de",
HomePage=>"http://www.carlos-amendola.com/"},
{Name => "Luis David Garcia Puente",
Email => "lgarcia@shsu.edu",
HomePage => "http://www.shsu.edu/~ldg005"},
{Name=> "Roser Homs Pons",
Email=> "roser.homs@tum.de",
HomePage=>"https://personal-homepages.mis.mpg.de/homspons/index.html"},
{Name=> "Olga Kuznetsova",
Email=> "kuznetsova.olga@gmail.com",
HomePage=>"https://okuznetsova.com"},
{Name=> "Harshit J Motwani",
Email=> "harshitmotwani2015@gmail.com",
HomePage=> "https://sites.google.com/view/harshitjmotwani/home"}},
Headline => "Graphs specific for algebraic statistics",
Keywords => {"Algebraic Statistics", "Graph Theory"},
DebuggingMode => false,
PackageExports => {"Graphs"}
)
export {
"Bigraph",
"bigraph",
"MixedGraph",
"mixedGraph",
"collateVertices",
"partitionLMG",
"isLoopless",
"undirectedGraph"
}
if Graphs.Options.Version < "0.3.3" then error "StatGraphs requires Graphs version 0.3.3 or later"
Bigraph = new Type of Graph
bigraph = method(TypicalValue =>Bigraph, Options => {Singletons => null, EntryMode => "auto"})
bigraph HashTable := opts -> g -> new Bigraph from graph(g, opts)
bigraph List := opts -> L -> new Bigraph from graph(L, opts)
bigraph (List, List):= opts -> (V,L) -> new Bigraph from graph(V,L, opts)
bigraph (List, Matrix) := opts -> (V,A) -> new Bigraph from graph(V,A, opts)
bigraph Matrix := opts -> A -> new Bigraph from graph(A, opts)
MixedGraph = new Type of HashTable
mixedGraph = method(TypicalValue =>MixedGraph)
mixedGraph (Graph, Digraph, Bigraph) := (g,d,b) -> (
C := new MutableHashTable;
C#cache = new CacheTable from {};
h := new MutableHashTable;
h#Graph = g;
h#Digraph = d;
h#Bigraph = b;
C#graph = new HashTable from h;
new MixedGraph from C)
mixedGraph Graph := g -> mixedGraph(g,digraph {}, bigraph {})
mixedGraph Digraph := d -> mixedGraph(graph {},d, bigraph {})
mixedGraph Bigraph := b -> mixedGraph(graph {},digraph {}, b)
mixedGraph (Digraph, Bigraph) := (d,b) -> mixedGraph(graph {},d,b)
mixedGraph (Bigraph, Digraph) := (b,d) -> mixedGraph(graph {},d,b)
mixedGraph (Graph, Digraph) := (g,d) -> mixedGraph(g,d,bigraph {})
mixedGraph (Digraph, Graph) := (d,g) -> mixedGraph(g,d,bigraph {})
mixedGraph (Graph, Bigraph) := (g,b) -> mixedGraph(g,digraph {},b)
mixedGraph (Bigraph, Graph) := (b,g) -> mixedGraph(g,digraph {},b)
mixedGraph (Digraph, Bigraph, Graph) := (d,b,g) -> mixedGraph(g,d,b)
mixedGraph (Bigraph, Graph, Digraph) := (b,g,d) -> mixedGraph(g,d,b)
mixedGraph (Graph, Bigraph, Digraph) := (g,b,d) -> mixedGraph(g,d,b)
mixedGraph (Bigraph, Digraph, Graph) := (b,d,g) -> mixedGraph(g,d,b)
mixedGraph (Digraph, Graph, Bigraph) := (d,g,b) -> mixedGraph(g,d,b)
net MixedGraph := g -> horizontalJoin flatten (
net class g,
"{",
stack (horizontalJoin \ sort apply(pairs (g#graph),(k,v) -> (net k, " => ", net v))),
"}"
)
toString MixedGraph := g -> concatenate(
"new ", toString class g#graph,
if parent g#graph =!= Nothing then (" of ", toString parent g),
" from {",
if #g#graph > 0 then demark(", ", apply(pairs g#graph, (k,v) -> toString k | " => " | toString v)) else "",
"}"
)
graph MixedGraph := opts -> g -> g#graph --used to transform the MixedGraph into a hashtable
undirectedGraph = method(TypicalValue =>Graph)
undirectedGraph MixedGraph := g -> g#graph#Graph
digraph MixedGraph := opts -> g -> g#graph#Digraph
bigraph MixedGraph := opts -> g -> g#graph#Bigraph
vertices MixedGraph := G -> toList sum(apply(keys(G#graph),i->set keys(graph (G#graph)#i)))
vertexSet MixedGraph := G -> vertices G
descendents (MixedGraph, Thing) := (G,v) -> descendents(digraph collateVertices G, v)
descendants (MixedGraph, Thing) := (G,v) -> descendants(digraph collateVertices G, v)
nondescendents (MixedGraph, Thing) := (G,v) -> nondescendents(digraph collateVertices G, v)
nondescendants (MixedGraph, Thing) := (G,v) -> nondescendants(digraph collateVertices G, v)
parents (MixedGraph, Thing) := (G,v) -> parents(digraph collateVertices G, v)
foreFathers (MixedGraph, Thing) := (G,v) -> foreFathers(digraph collateVertices G, v)
children (MixedGraph, Thing) := (G,v) -> children(digraph collateVertices G, v)
neighbors (MixedGraph, Thing) := (G,v) -> neighbors(undirectedGraph collateVertices G, v)
nonneighbors (MixedGraph, Thing) := (G,v) -> nonneighbors(undirectedGraph collateVertices G, v)
collateVertices = method(TypicalValue =>MixedGraph)
collateVertices MixedGraph := g -> (
v := vertices g;
hh := new MutableHashTable;
G := graph g;
-- Graph
x := graph G#Graph;
scan(v,j->if x#?j then hh#j=x#j else hh#j={});
gg := graph(new HashTable from hh);
-- Digraph
x = graph G#Digraph;
scan(v,j->if x#?j then hh#j=x#j else hh#j={});
dd := digraph(new HashTable from hh);
-- Bigraph
x = graph G#Bigraph;
scan(v,j->if x#?j then hh#j=x#j else hh#j={});
bb := bigraph(new HashTable from hh);
mixedGraph(gg,dd,bb))
graphComponents = {}
graphFunctions ={graph,bigraph,digraph}
indexLabelGraph MixedGraph := MixedGraph => G -> (
V := vertices G;
h := hashTable apply(#V, i -> V_i => i);
U := G#graph#Graph;
B := G#graph#Bigraph;
D := G#graph#Digraph;
inputG:=new MutableHashTable;
inputG#graphComponents={U,B,D};
inputG#graphFunctions={graph,bigraph,digraph};
inputG=new HashTable from inputG;
G=mixedGraph toSequence(
for i to #inputG#graphComponents-1 list (
E := apply(toList \ edges inputG#graphComponents_i, e -> {h#(e_0), h#(e_1)});
inputG#graphFunctions_i(flatten E, E,EntryMode => "edges")
)
)
);
-- Makes a partition U\cup W of the vertices V of a loopless mixed graph (inputted as a MixedGraph)
-- such that U contains all the vertices adjacent to undirected edges,
-- W contains all the vertices adjacent to bidirected edges
-- and there are no directed edges from W to U
-- and all vertices in U have lower value than those in W.
partitionLMG = method(TypicalValue =>Sequence)
partitionLMG MixedGraph := g -> (
--check it's a loopless graph
if isLoopless(g)==false then error ("The expected input is a loopless mixed graph.");
--retrieve graph, bigraph and digraph
G:= g#graph#Graph;
B:= g#graph#Bigraph;
D:= g#graph#Digraph;
--check there are no directed cycles
if isCyclic g then error ("The expected input is a loopless mixed graph without directed cycles.");
--naive partition (vertices only adjacent to directed edges are not considered)
U:=vertices G;
W:=vertices B;
--check there are no common vertices for undirected and bidirected edges
if not (set U * set W===set {}) then
error("Vertices cannot be adjacent to bidirected and undirected edges simultaneously.");
--check that vertices in U (undir) have lower value than vertices in W (bidir):
if max U > min W then error ("Vertex ordering issues: vertices adjacent to undirected edges should have lower value than vertices adjacent to bidirected edges");
--check there are no directed edges from set U to set W
for e in edges D do (if (member(e_0,set W) and member(e_1,set U))
then error("Directed edges cannot go from vertices adjacent to a bidirected edge to vertices adjacent to an undirected edge"));
--check directed edges always go from lower value to higher value
for e in edges D do (
if e_0 > e_1 then error ("Vertex ordering issues: directed edges must go from low to high");
);
--check whether there are remaining vertices (only adjacent to directed edges)
V:=set vertices g-set W-set U;
if V===set{} then return (U,W);
--place remaining vertices in either U or W depending on their value
for v in toList V do (if v < max U then U=append(U,v) else W=append(W,v););
sort U,sort W
)
--Check whether a graph is loopless in each type of edges
isLoopless = method(TypicalValue =>Boolean)
isLoopless MixedGraph := Boolean => g -> (
--retrieve graph, digraph and bigraph
G:= g#graph#Graph;
B:= g#graph#Bigraph;
D:= g#graph#Digraph;
--check there are no loops and no repetitions
isSimple(G) and isSimple(underlyingGraph D) and isSimple(B)
)
isLoopless Graph := Boolean => g -> (
isSimple(g)
)
isLoopless Bigraph := Boolean => g -> (
isSimple(g)
)
isLoopless Digraph := Boolean => g -> (
isSimple(underlyingGraph g)
)
-- Internal function to check whether a MixedGraph contains multiple edges
hasMultipleEdges = g -> (
--retrieve graph, digraph and bigraph
G:= g#graph#Graph;
B:= g#graph#Bigraph;
D:= g#graph#Digraph;
--retrieve underlying undirected edges
edG:=edges G;
edD:=edges underlyingGraph D;
edB:=edges B;
--build list of underlying edges with and without repetitions
d:=join(edG,edD,edB);
e:=unique(d);
--check there are no repetitions
not #d==#e
)
-- Check whether a MixedGraph is simple
isSimple MixedGraph := Boolean => G -> (
isLoopless G and not hasMultipleEdges G
)
-- Check whether a MixedGraph is cyclic, i.e., does not contain any directed cycles
isCyclic MixedGraph := Boolean => g -> (
G:=indexLabelGraph g;
flag:= isCyclic digraph G;
if flag then flag else(
U:= graph(sort vertices G#graph#Graph,edges G#graph#Graph);
B:= bigraph(sort vertices G#graph#Bigraph,edges G#graph#Bigraph);
D:= digraph(vertices G,edges G#graph#Digraph);
compU:=connectedComponents U;
compB:=connectedComponents B;
vertOnlyDir:=vertices D - set vertices U - set vertices B;
allComp:=flatten {connectedComponents U,connectedComponents B, pack(vertOnlyDir,1)};
n:=# compU + # compB + #vertOnlyDir;
adjMG:=mutableMatrix(ZZ,n,n);
-- form the adjacency matrix of the graph of chain components
for i from 0 to n - 1 do
(
for j from 0 to n - 1 do
(if not submatrix(adjacencyMatrix D, toList(set(allComp_i)*set(vertices D)), toList(set(allComp_j)*set(vertices D)))==0 then adjMG_(i,j)=1 else adjMG_(i,j)=0
));
adjMG=matrix adjMG;
isCyclic (digraph adjMG)))
--******************************************--
-- DOCUMENTATION --
--******************************************--
beginDocumentation()
doc ///
Key
StatGraphs
Headline
a package for graphs used in statistical models
Description
Text
This package contains the types of graphs that are used in algebraic
statistics: @TO Bigraph@ and @TO MixedGraph@.
A bigraph is graph with bidirected edges and no multiple edges.
A mixed graph is a graph with undirected, directed and bidirected edges.
This is an example of a bigraph on 4 vertices. It is created using the method @TO bigraph@.
Example
G = bigraph {{3,4},{1,2},{2,4}}
Text
Next is an example of a mixed graph on 4 vertices with undirected, directed and bidirected edges. It is created using
the method @TO mixedGraph@.
Example
G = mixedGraph(graph{{1,2}},digraph {{1,3},{2,3}},bigraph {{3,4}})
Text
One can extract key information about mixed graphs using:
@TO (undirectedGraph,MixedGraph)@,
@TO (bigraph,MixedGraph)@,
@TO (digraph,MixedGraph)@,
@TO (vertices,MixedGraph)@,
or convert a mixed graph into a more convenient form using:
@TO (collateVertices,MixedGraph)@,
@TO (indexLabelGraph,MixedGraph)@.
There are several methods that allow to check the properties of mixed graphs:
@TO (isCyclic,MixedGraph)@,
@TO (isLoopless,MixedGraph)@,
@TO (isSimple,MixedGraph)@.
One can also study the properties of vertices using:
@TO (children, MixedGraph, Thing)@,
@TO (parents, MixedGraph, Thing)@,
@TO (descendants, MixedGraph, Thing)@,
@TO (nondescendants, MixedGraph, Thing)@,
@TO (forefathers, MixedGraph, Thing)@,
@TO (neighbors, MixedGraph, Thing)@,
@TO (nonneighbors, MixedGraph, Thing)@.
This package allows to construct loopless mixed graphs (LMG) as introduced in
Kayvan Sadeghi and Steffen Lauritzen, {\em Markov properties for mixed graphs},
Bernoulli 20.2 (2014): 676-696 and to check whether a mixedGraph is an LMG using
@TO partitionLMG@.
Caveat
StatGraphs requires @TO Graphs@ version 0.3.3 or later.
SeeAlso
Graphs
///
--------------------------------
-- Documentation
--------------------------------
--------------------------------------------
-- Documentation Bigraph
--------------------------------------------
doc ///
Key
Bigraph
Headline
a graph with bidirected edges and no multiple edges
Description
Text
Bigraph is a simple graph that has bidirected edges.
To create a bigraph, use @TO bigraph@.
SeeAlso
bigraph
///
--------------------------------------------
-- Documentation bigraph
--------------------------------------------
doc ///
Key
bigraph
(bigraph, HashTable)
(bigraph, List)
(bigraph, List, List)
(bigraph, List, Matrix)
(bigraph, Matrix)
Headline
create a bigraph
Usage
G= bigraph(H)
G= bigraph(L)
G= bigraph(V,L)
G= bigraph(V,A)
G= bigraph(A)
Inputs
H:HashTable
hashtable of edges
L:List
list of edges
V:List
list of vertices
A:Matrix
adjacency matrix
Outputs
:Bigraph
Description
Text
This is a constructor of a simple graph of class @TO Bigraph@. One can use the same input types
as in @TO graph@.
Example
G = bigraph {{3,4},{1,2},{2,4}}
SeeAlso
Bigraph
///
--------------------------------------------
-- Optional arguments for bigraph
--------------------------------------------
doc ///
Key
[bigraph,EntryMode]
Headline
optional input, accepts 'auto', 'edges', or 'neighbors'
Description
Text
The options for EntryMode are 'auto'(the default), 'neighbors' and 'edges'.
If 'edges' is selected, then the input should contain a list of lists and
the inner lists correspond to pairs of vertices incident to a given edge.
If 'neighbors' is selected, then the input should contain a list of lists and
in the inner lists, the 0th entry is a vertex and the 1st entry is the list of
its neighbors.
The default 'auto' option distinguished between the other two options automatically.
Example
graph ({{a,{b,c,d,e}}, {b,{d,e}}, {e,{a}}},EntryMode=>"neighbors")
graph ({{a,{b,c,d,e}}, {b,{d,e}}, {e,{a}}},EntryMode=>"auto")
graph ({{a,b}, {b,d}, {c,d},EntryMode=>"edges"})
graph ({{a,b}, {b,d}, {c,d},EntryMode=>"auto"})
SeeAlso
bigraph
[graph,EntryMode]
graph
///
doc ///
Key
[bigraph,Singletons]
Headline
optional input, accepts the list of isolated vertices in a bigraph
Description
Example
bigraph({{1,2},{2,3},{3,4}}, Singletons => {5,6,7})
SeeAlso
bigraph
[bigraph,Singletons]
graph
///
--------------------------------------------
-- Documentation MixedGraph
--------------------------------------------
doc ///
Key
MixedGraph
Headline
a graph that has undirected, directed and bidirected edges
Description
Text
MixedGraph is a graph that has undirected, directed and bidirected edges.
To create a mixed graph, use @TO mixedGraph@. Each type of subgraph (undirected,
directed and bidirected) does not have multiple edges and can
appear at most once.
SeeAlso
mixedGraph
collateVertices
///
--------------------------------------------
-- Documentation mixedGraph
--------------------------------------------
doc ///
Key
mixedGraph
(mixedGraph, Graph, Digraph, Bigraph)
(mixedGraph, Graph,Bigraph,Digraph)
(mixedGraph, Digraph,Graph,Bigraph)
(mixedGraph, Digraph,Bigraph,Graph)
(mixedGraph, Bigraph,Graph,Digraph)
(mixedGraph, Bigraph,Digraph,Graph)
(mixedGraph, Graph, Digraph)
(mixedGraph, Digraph,Graph)
(mixedGraph, Digraph, Bigraph)
(mixedGraph, Bigraph,Digraph)
(mixedGraph, Graph, Bigraph)
(mixedGraph, Bigraph, Graph)
(mixedGraph, Graph)
(mixedGraph, Digraph)
(mixedGraph, Bigraph)
Headline
create a mixed graph from a combination of undirected graph, digraph and bigraph
Usage
G= mixedGraph(U, D, B)
G= mixedGraph G
G= mixedGraph D
G= mixedGraph B
G= mixedGraph(G, D)
G= mixedGraph(G, B)
G= mixedGraph(D, B)
Inputs
U:Graph
component that contains all undirected edges of the graph
D:Digraph
component that contains all directed edges of the graph
B:Bigraph
component that contains all bidirected edges of the graph
Outputs
:MixedGraph
Description
Text
This is a constructor of graphs of class @TO MixedGraph@ from a combination of subgraphs of classes @TO Graph@,
@TO Digraph@ and @TO Bigraph@. One can also input any subset
and any permutation of the arguments. Each type of subgraph can appear at most once.
Note that this constructor does not check the input satisfies the properties of loopless mixed graphs from
Sadeghi and Lauritzen, 2020 <@HREF"https://arxiv.org/pdf/1109.5909.pdf"@>.
Example
G = mixedGraph(graph{{1,2}},digraph {{1,3},{2,3}},bigraph {{3,4}})
SeeAlso
MixedGraph
///
--------------------------------------------
-- Operations on MixedGraph
--------------------------------------------
--------------------------------------------
-- Documentation bigraph(MixedGraph)
--------------------------------------------
doc ///
Key
(bigraph, MixedGraph)
Headline
extract the bigraph component of a mixed graph
Usage
B=bigraph G
Inputs
G:MixedGraph
Outputs
:Bigraph
Description
Text
This method extracts the largest component of class @TO Bigraph@ of a mixed graph.
Example
G= mixedGraph(graph{{a,b},{b,c}},digraph {{a,d},{c,e},{f,g}},bigraph {{d,e}})
bigraph G
SeeAlso
MixedGraph
(digraph, MixedGraph)
(graph, MixedGraph)
(undirectedGraph, MixedGraph)
///
--------------------------------------------
-- Documentation digraph(MixedGraph)
--------------------------------------------
doc ///
Key
(digraph, MixedGraph)
Headline
extract the digraph component of a mixed graph
Usage
D=digraph G
Inputs
G:MixedGraph
Outputs
:Digraph
Description
Text
This method extracts the largest component of class @TO Digraph@ of a mixed graph.
Example
G= mixedGraph(graph{{a,b},{b,c}},digraph {{a,d},{c,e},{f,g}},bigraph {{d,e}})
digraph G
SeeAlso
MixedGraph
(bigraph, MixedGraph)
(graph, MixedGraph)
(undirectedGraph, MixedGraph)
///
--------------------------------------------
-- Documentation undirectedGraph(MixedGraph)
--------------------------------------------
doc ///
Key
undirectedGraph
(undirectedGraph, MixedGraph)
Headline
extract the undirected graph component of a mixed graph
Usage
U=undirectedGraph G
Inputs
G:MixedGraph
Outputs
:Graph
Description
Text
This method extracts the largest component of class @TO Graph@ of a mixed graph.
Example
G= mixedGraph(graph{{a,b},{b,c}},digraph {{a,d},{c,e},{f,g}},bigraph {{d,e}})
undirectedGraph G
SeeAlso
MixedGraph
(bigraph, MixedGraph)
(digraph, MixedGraph)
(graph, MixedGraph)
///
--------------------------------------------
-- Documentation graph(MixedGraph)
--------------------------------------------
doc ///
Key
(graph, MixedGraph)
Headline
convert mixed graph to a hash table
Usage
U=graph G
Inputs
G:MixedGraph
Outputs
:HashTable
Description
Text
This method creates a hash table whose key-value pairs correspond to the
components of G.
Example
G= mixedGraph(graph{{a,b},{b,c}},digraph {{a,d},{c,e},{f,g}},bigraph {{d,e}})
graph G
keys (graph G)
(graph G)#Bigraph === bigraph G
SeeAlso
MixedGraph
(bigraph, MixedGraph)
(digraph, MixedGraph)
(undirectedGraph, MixedGraph)
///
--------------------------------------------
-- Documentation collateVertices
--------------------------------------------
doc ///
Key
collateVertices
(collateVertices, MixedGraph)
Headline
convert a mixed graph into a new mixed graph where each component subgraph has the same set of vertices
Usage
collateVertices(G)
Inputs
G:MixedGraph
Outputs
:MixedGraph
Description
Text
Let G=mixedGraph(U,D,B) and denote the vertices of U by V1,
the vertices of D by V2 and the vertices of B by V3.
Then the method collateVertices(G) outputs a mixedGraph with same
edges as before but with V1 \cup V2 \cup V3 as the vertices of U,D
and B.
Example
U = graph{{1,2},{2,3},{3,4},{1,4},{1,5}}
D = digraph{{2,1},{3,1},{7,8}}
B = bigraph{{1,5}}
G = mixedGraph(U,D,B)
collateVertices G
///
--------------------------------------------
-- Documentation isSimple(MixedGraph)
--------------------------------------------
doc ///
Key
(isSimple, MixedGraph)
Headline
check whether a mixed graph is simple
Usage
isSimple(G)
Inputs
G:MixedGraph
Outputs
:Boolean
Description
Text
This method checks whether a graph is simple: does not contain
loops or multiple edges.
Note that since @TO graph@, @TO digraph@ and @TO bigraph@ do not
allow multiple edges, a graph of class @TO MixedGraph@ can only have multiple edges
of different types.
In the following example, there are no loops or multiple edges.
Example
U = graph{{1,2},{2,3},{3,4}}
D = digraph{{2,5}}
B = bigraph{{5,6}}
G = mixedGraph(U,D,B)
isSimple G
Text
This example contains multiple edges on vertices 1 and 2.
Example
U = graph{{1,2},{2,3},{3,4}}
D = digraph{{1,2},{2,5}}
B = bigraph{{5,6}}
G = mixedGraph(U,D,B)
isSimple G
Text
This example contains a loop.
Example
U = graph{{1,2},{2,3},{3,4}}
D = digraph{{2,5}}
B = bigraph{{5,6},{5,5}}
G = mixedGraph(U,D,B)
isSimple G
///
--------------------------------------------
-- Documentation indexLabelGraph
--------------------------------------------
doc ///
Key
(indexLabelGraph, MixedGraph)
Headline
relabel the vertices of a mixed graph according to their indices, indexed from 0
Usage
G=indexLabelGraph G
Inputs
G:MixedGraph
Outputs
:MixedGraph
Description
Text
This method relabels the vertices of a graph of class @TO MixedGraph@ according to their indices.
The method indexes from 0 to the number of vertices minus one.
This is an adaptation of the method @TO indexLabelGraph@.
Example
G= mixedGraph(graph{{a,b},{b,c}},digraph {{a,d},{c,e},{f,g}},bigraph {{d,e}})
indexLabelGraph G
SeeAlso
MixedGraph
indexLabelGraph
///
--------------------------------------------
-- Documentation isLoopless
--------------------------------------------
doc ///
Key
isLoopless
(isLoopless, MixedGraph)
(isLoopless, Graph)
(isLoopless, Bigraph)
(isLoopless, Digraph)
Headline
check whether a graph contains a loop
Usage
isLoopless(G)
Inputs
G:
graph of class @TO MixedGraph@, @TO Graph@, @TO Digraph@ or @TO Bigraph@
Outputs
:Boolean
Description
Text
This method checks whether a graph contains a loop.
If the input is a @TO Graph@ or a @TO Bigraph@, then this is equivalent to
@TO isSimple@.
If the input is a @TO Digraph@, then this is equivalent to checking whether
the @TO underlyingGraph@ @TO isSimple@.
If the input is a @TO MixedGraph@, then this checks whether the undirected,
directed and bidirected subgraphs separately contain loops.
Example
U = graph{{1,2},{2,3},{3,4}}
D = digraph{{2,5}}
B = bigraph{{5,6}}
G = mixedGraph(U,D,B)
isLoopless G
Example
U = graph{{1,1}}
isLoopless U
///
--------------------------------------------
-- Documentation (isCyclic, MixedGraph)
--------------------------------------------
doc ///
Key
(isCyclic, MixedGraph)
Headline
check whether a mixed graph contains a directed cycle
Usage
isCyclic(G)
Inputs
G:MixedGraph
Outputs
:Boolean
Description
Text
This method checks whether a @TO MixedGraph@ is cyclic, i.e. contains
a directed cycle or a cycle on directed edges.
A directed cycle is a cycle in the @TO Digraph@ constructed from a
mixed graph G by identifying all connected components on bidirected and undirected edges.
Such a connected component contains either bidirected edges only or
undirected edges only.
In the following example, there are no directed cycles.
Example
U = graph{{1,2},{2,3},{3,4},{1,4},{1,5}}
D = digraph{{2,1},{3,1},{7,8}}
B = bigraph{{1,5}}
G = mixedGraph(U,D,B)
isCyclic G
Text
In the next example, there are no cycles inside the digraph of the
mixed graph, but there is a directed cycle after you identify the
vertices {1,2} and {3,4}.
Example
U = graph{{1,2},{3,4}}
D = digraph{{1,3},{4,2}}
G = mixedGraph(U,D)
isCyclic G
Text
This is a similar example as before, but now the vertices {1,2} are
connected by an undirected edge and {3,4} by a bidirected edge.
Example
U = graph{{1,2}}
B = bigraph{{3,4}}
D = digraph{{1,3},{4,2}}
G = mixedGraph(U,D,B)
isCyclic G
Text
In the following example, there is a cycle on the directed edges
that is inside a connected undirected component.
Example
G = mixedGraph(graph{{1,2}},digraph {{1,2},{2,1}})
isCyclic G
///
--------------------------------------------
-- Documentation partitionLMG
--------------------------------------------
doc ///
Key
partitionLMG
(partitionLMG, MixedGraph)
Headline
partition the vertices of a loopless mixed graph into adjacent to undirected edges and adjacent to bidirected edges
Usage
partitionLMG(G)
Inputs
G:MixedGraph
Outputs
:Sequence
(U,W) where U are vertices adjacent to undirected edges and W are vertices adjacent to bidirected edges
Description
Text
This function makes a partition $U\cup W$ of the vertices V of a loopless mixed graph such that:
- if $i-j$ in $G$ then $i,j\in U$,
- if $i\leftarrow \rightarrow j$ in $G$ then $i,j\in W$
- there is no directed edge $i\to j$ in $G$ such that $i\in W$ and $j\in U$.
These conditions are equivalent to those introduced in Seth Sullivant, Kelli Talaska, and Jan Draisma,
{\em Trek separation for Gaussian graphical models}, The Annals of Statistics
38.3 (2010): 1665-1685.
For technical purposes we assume, without loss of generality, that vertices in the LMG are ordered such that:
1. all vertices in U come before vertices in W,
2. if there is a directed edge from $i$ to $j$, then $i bigraph ({d, e}, {{d, e}}), Graph =>
graph ({a, b, c}, {{a, b}, {c, b}}), Digraph => digraph ({a, d, c, e, f, g}, {{a, d}, {c, e}, {f, g}})})
///
--------------------------------------------
-- Tests for collateVertices
--------------------------------------------
TEST ///
U = graph{{1,2},{2,3},{3,4},{1,4},{1,5}}
D = digraph{{2,1},{3,1},{7,8}}
B = bigraph{{1,5}}
G1 = mixedGraph(U,D,B)
G2 = collateVertices G1
assert(vertices bigraph G2 === vertices G1)
///
TEST ///
U = graph{{1,2},{2,3},{3,4},{1,4},{1,5}}
D = digraph{{2,1},{3,1},{7,8}}
B = bigraph{{1,5}}
G1 = mixedGraph(U,D,B)
G2 = collateVertices G1
assert(edges bigraph G2 === edges B)
///
--------------------------------------------
-- Tests for isSimple(MixedGraph)
--------------------------------------------
TEST ///
U = graph{{1,2},{2,3},{3,4}}
D = digraph{{2,5}}
B = bigraph{{5,6}}
G = mixedGraph(U,D,B)
assert (isSimple G)
///
TEST ///
U = graph{{1,2},{2,3},{3,4}}
D = digraph{{1,2},{2,5}}
B = bigraph{{5,6}}
G = mixedGraph(U,D,B)
assert (not isSimple G)
///
--------------------------------------------
-- Tests for indexLabelGraph
--------------------------------------------
TEST ///
G1 = mixedGraph(graph{{a,b},{b,c}},digraph {{a,d},{c,e},{f,g}},bigraph {{d,e}})
G2 = indexLabelGraph G1
assert(graph G2 === new HashTable from {Bigraph => bigraph ({1, 2}, {{1, 2}}), Graph =>
graph ({5, 6, 0}, {{5, 6}, {0, 6}}), Digraph => digraph ({5, 1, 0, 2,
3, 4}, {{5, 1}, {0, 2}, {3, 4}})})
///
--------------------------------------------
-- Tests for isLoopless
--------------------------------------------
TEST ///
U = graph{{1,2},{2,3},{3,4}}
D = digraph{{2,5}}
B = bigraph{{5,6}}
G = mixedGraph(U,D,B)
assert(isLoopless G)
///
TEST ///
U = graph{{1,1}}
assert (not isLoopless U)
///
--------------------------------------------
-- Tests for isCyclic(Mixed Graph)
--------------------------------------------
TEST ///
U = graph{{1,2},{2,3},{3,4},{1,4},{1,5}}
D = digraph{{2,1},{3,1},{7,8}}
B = bigraph{{1,5}}
G = mixedGraph(U,D,B)
assert(not isCyclic G)
///
TEST ///
U = graph{{1,2},{3,4}}
D = digraph{{1,3},{4,2}}
G = mixedGraph(U,D)
assert(isCyclic G)
///
TEST ///
U = graph{{1,2}}
B = bigraph{{3,4}}
D = digraph{{1,3},{4,2}}
G = mixedGraph(U,D,B)
assert(isCyclic G)
///
TEST ///
U = graph{{1,2}}
D = digraph{{1,2},{2,1}}
G = mixedGraph(U,D)
assert(isCyclic G)
///
--------------------------------------------
-- Tests for partititionLMG
--------------------------------------------
TEST ///
U = graph{{1,2},{2,3},{3,4},{1,4},{1,5}}
D = digraph{{2,1},{3,1},{7,8}}
B = bigraph{{1,5}}
G = mixedGraph(U,D,B)
assert(try partitionLMG G then false else true)
///
TEST ///
U = graph{{1,2},{3,4}}
D = digraph{{1,3},{4,2}}
G = mixedGraph(U,D)
assert(try partitionLMG G then false else true)
///
TEST ///
U = graph{{1,2}}
B = bigraph{{3,4}}
D = digraph{{1,3},{4,2}}
G = mixedGraph(U,D,B)
assert(try partitionLMG G then false else true)
///
TEST ///
U = graph{{1,2},{2,3},{1,3}}
D = digraph{{4,1},{3,7}}
B = bigraph{{4,5},{5,6},{7,8}}
G = mixedGraph(U,D,B)
assert(try partitionLMG G then false else true)
///
TEST ///
U = graph{{1,2},{2,3},{1,3}}
D = digraph{{1,4},{3,7}}
B = bigraph{{4,5},{5,6},{7,8}}
G = mixedGraph(U,D,B)
assert(partitionLMG G === ({1, 2, 3}, {4, 5, 6, 7, 8}))
///
TEST ///
U = graph{{1,2},{2,3},{1,3}}
D = digraph{{1,4},{3,7},{8,9}}
B = bigraph{{4,5},{5,6},{7,9}}
G = mixedGraph(U,D,B)
assert(partitionLMG G === ({1, 2, 3}, {4, 5, 6, 7, 8, 9}))
///
TEST ///
U = graph{{2,3},{3,4},{4,2}}
D = digraph{{1,2},{2,5},{4,9}}
B = bigraph{{5,6},{6,7},{8,9}}
G = mixedGraph(U,D,B)
assert(partitionLMG G === ({1, 2, 3, 4}, {5, 6, 7, 8, 9}))
///
--------------------------------------------
-- Operations on vertices of a MixedGraph
--------------------------------------------
--------------------------------------------
-- Tests for children
--------------------------------------------
TEST ///
G = mixedGraph(graph{{3,1}},digraph {{1,2},{2,3}},bigraph {{3,4},{2,4}})
assert(children (G,1)===set{2})
assert(children (G,2)===set{3})
assert(children (G,3)===set{})
///
--------------------------------------------
-- Tests for parents
--------------------------------------------
TEST ///
G = mixedGraph(graph{{3,1}},digraph {{1,2},{2,3}},bigraph {{3,4},{2,4}})
assert(parents (G,1)===set{})
assert(parents (G,2)===set{1})
assert(parents (G,3)===set{2})
///
--------------------------------------------
-- Tests for descendants
--------------------------------------------
TEST ///
G = mixedGraph(graph{{3,1}},digraph {{1,2},{2,3}},bigraph {{3,4},{2,4}})
assert(descendants (G,1)===set{1,2,3})
assert(descendants (G,2)===set{2,3})
assert(descendants (G,3)===set{3})
///
--------------------------------------------
-- Tests for nondescendants
--------------------------------------------
TEST ///
G = mixedGraph(graph{{3,1}},digraph {{1,2},{2,3}},bigraph {{3,4},{2,4}})
assert(nondescendents (G,1)===set{4})
assert(nondescendents (G,2)===set{1,4})
assert(nondescendents (G,3)===set{1,2,4})
///
--------------------------------------------
-- Tests for foreFathers
--------------------------------------------
TEST ///
G = mixedGraph(graph{{3,1}},digraph {{1,2},{2,3}},bigraph {{3,4},{2,4}})
assert(foreFathers (G,1)===set{1})
assert(foreFathers (G,2)===set{1,2})
assert(foreFathers (G,3)===set{1,2,3})
///
--------------------------------------------
-- Tests for neighbors
--------------------------------------------
TEST ///
G = mixedGraph(graph{{3,1}},digraph {{1,2},{2,3}},bigraph {{3,4},{2,4}})
assert(neighbors (G,1)===set{3})
assert(neighbors (G,2)===set{})
///
--------------------------------------------
-- Tests for nonneighbors
--------------------------------------------
TEST ///
G = mixedGraph(graph{{3,1}},digraph {{1,2},{2,3}},bigraph {{3,4},{2,4}})
assert(nonneighbors (G,1)===set{2,4})
assert(nonneighbors (G,2)===set{1,3,4})
///
--------------------------------------------
-- Tests for vertices and vertexSet
--------------------------------------------
TEST ///
G = mixedGraph(graph{{3,1}},digraph {{1,2},{2,3}},bigraph {{3,4}})
assert(vertices G=== {1,2,3,4})
assert(vertexSet G=== {1,2,3,4})
///
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