Add graph references
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Abdelrahman Said
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<?xml version="1.0"?>
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<!DOCTYPE refentry PUBLIC "-//OASIS//DTD DocBook XML V4.3//EN"
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"http://www.oasis-open.org/docbook/xml/4.3/docbookx.dtd" [
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]>
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<!-- Do not edit this file directly. Edit glossary.md and re-generate this file using pandoc. -->
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<chapter id="igraph-Glossary">
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<title>Glossary</title>
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<para>
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This glossary defines common terms used throughout the igraph
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documentation.
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</para>
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<itemizedlist spacing="compact">
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<listitem>
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<para>
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<emphasis role="strong">attribute</emphasis>: A piece of data
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associated with a vertex, an edge, or the graph itself. The
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igraph C library currently supports numeric, string and Boolean
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attribute values, and provides a means for implementing
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attribute handlers that support custom types.
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</para>
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</listitem>
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<listitem>
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<para>
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<emphasis role="strong">adjacent</emphasis>: Two vertices are
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called <emphasis role="strong">adjacent</emphasis> if there is
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an edge connecting them. This term describes a vertex-to-vertex
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relation.
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</para>
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</listitem>
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<listitem>
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<para>
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<emphasis role="strong">adjacency list</emphasis>: A data
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structure that associates a list of neighbours (i.e. adjacent
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vertices) to each vertex.
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</para>
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</listitem>
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<listitem>
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<para>
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<emphasis role="strong">adjacency matrix</emphasis>: A
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representation of a graph as a square matrix.
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<literal>A_ij</literal> gives the number of edge endpoints
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connecting from the <literal>i</literal>th vertex to the
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<literal>j</literal>th vertex. Conventionally, the diagonal of
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the adjacency matrix of an undirected graph contains
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<emphasis>twice</emphasis> the number of self-loops. All igraph
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functions follow this convention unless noted otherwise.
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</para>
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</listitem>
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<listitem>
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<para>
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<emphasis role="strong">biadjacency matrix</emphasis>: Analogous
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to the adjacency matrix, but used for bipartite graphs. Element
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<literal>B_ij</literal> gives the number of edges from the
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<literal>i</literal>th vertex of the first group to the
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<literal>j</literal>th vertex of the second group.
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</para>
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</listitem>
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<listitem>
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<para>
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<emphasis role="strong">bipartite graph</emphasis>: A graph
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whose vertices can be partitioned into two groups in such a way
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that connections are present only between members of different
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groups.
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</para>
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</listitem>
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<listitem>
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<para>
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<emphasis role="strong">complete graph</emphasis>: Also called
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<emphasis role="strong">full graph</emphasis> within the context
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of igraph, a graph in which all pairs of vertices are connected
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to each other.
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</para>
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</listitem>
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<listitem>
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<para>
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<emphasis role="strong">connected graph</emphasis>: A connected
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graph consists of a single component, in which any vertex is
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reachable from any other. In igraph, the null graph is not
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considered connected, as it has not one, but zero components.
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</para>
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</listitem>
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<listitem>
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<para>
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<emphasis role="strong">edge</emphasis>: A
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<emphasis role="strong">connection</emphasis> between two
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vertices, also called a <emphasis role="strong">link</emphasis>.
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In igraph, edges are referred to by integer indices called
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<emphasis role="strong">edge IDs</emphasis>.
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</para>
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</listitem>
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<listitem>
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<para>
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<emphasis role="strong">finalizer stack</emphasis>: A global
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stack used internally by igraph to keep track of currently
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allocated objects and their destructors, so that they can be
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automatically destroyed in case of an error.
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</para>
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</listitem>
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<listitem>
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<para>
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<emphasis role="strong">game</emphasis>: Within igraph, this
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term is used for stochastic graph generators, i.e. functions
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that sample from random graph models.
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</para>
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</listitem>
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<listitem>
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<para>
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<emphasis role="strong">graph</emphasis> or
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<emphasis role="strong">network</emphasis>: A set of vertices
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with connections between them. In igraph, graphs may carry
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associated data in the form of vertex, edge or graph attributes.
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</para>
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</listitem>
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<listitem>
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<para>
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<emphasis role="strong">incident</emphasis>: An edge is called
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<emphasis role="strong">incident</emphasis> to the vertices that
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are its endpoints. This term describes a vertex-to-edge
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relation.
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</para>
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</listitem>
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<listitem>
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<para>
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<emphasis role="strong">incidence list</emphasis>: A data
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structure that associates a list of incident edges to each
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vertex.
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</para>
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</listitem>
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<listitem>
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<para>
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<emphasis role="strong">incidence matrix</emphasis>: A matrix
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describing the incidence relation between vertices (rows) and
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edges (columns).
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</para>
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</listitem>
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<listitem>
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<para>
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<emphasis role="strong">membership vector</emphasis>: Membership
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vectors are a means of encoding a partitioning of items, usually
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vertices, into several groups. The <literal>i</literal>th
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element of the vector gives an integer identifier of the group
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the <literal>i</literal>th vertex belongs to. Membership vectors
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are typically used to describe a vertex clustering obtained
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through community detection, or by identifying the connected
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components of a graph.
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</para>
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</listitem>
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<listitem>
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<para>
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<emphasis role="strong">multi-edges</emphasis> or
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<emphasis role="strong">parallel edges</emphasis>: More than one
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edge connecting the same two vertices. In a directed graph,
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<literal>a -> b, a -> b</literal> are considered parallel
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edges, but <literal>a -> b, a <- b</literal> are not.
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</para>
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</listitem>
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<listitem>
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<para>
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<emphasis role="strong">null graph</emphasis>: A graph with no
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vertices (and no edges).
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</para>
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</listitem>
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<listitem>
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<para>
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<emphasis role="strong">self-loop</emphasis>,
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<emphasis role="strong">self-edge</emphasis>, or simply
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<emphasis role="strong">loop</emphasis>: An edge that connects a
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vertex to itself.
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</para>
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</listitem>
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<listitem>
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<para>
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<emphasis role="strong">simple graph</emphasis>: A graph that
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does not have self-loops or multi-edges.
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</para>
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</listitem>
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<listitem>
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<para>
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<emphasis role="strong">singleton graph</emphasis>: A graph
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having a single vertex. This term usually refers to a single
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vertex with no edges, but note that self-loops may in principle
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be present.
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</para>
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</listitem>
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<listitem>
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<para>
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<emphasis role="strong">vertex</emphasis>: Graphs consist of
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vertices, also called <emphasis role="strong">nodes</emphasis>,
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that are connected to each other. In igraph, vertices are
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referred to by integer indices called
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<emphasis role="strong">vertex IDs</emphasis>.
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</para>
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</listitem>
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</itemizedlist>
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</chapter>
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