Index
A
- ARF layout / The ARF layout
- assortative on income
- about / Clustering and homophily
- attraction strength / Force Atlas
- Attractive and Repulsive Forces (ARF)
- about / ARF
- Attractive and Repulsive Forces (ARF) layout
- about / The ARF layout, Layout strengths and weaknesses
- Neighbor attraction force / The ARF layout
- General attraction force / The ARF layout
- Repulsive force / The ARF layout
- Precision force / The ARF layout
- testing / Testing the ARF layout
- attribute-based DNA
- about / Attribute-based DNA
- data, preparing / Preparing the data
- dynamic attribute networks, implementing / Implementing and viewing dynamic attribute networks
- dynamic attribute networks, viewing / Implementing and viewing dynamic attribute networks
- attributes filter
- about / Attributes
- Equal function / Attributes
- Inter Edges / Attributes
- Intra Edges / Attributes
- Non-null condition / Attributes
- Partition filter / Attributes
- Partition Count filter / Attributes
- Range filter condition / Attributes
- average path length, network measures / Average path length
- average path length, network statistics / Average path length
B
- Barabasi-Albert scale free model / Using Gephi generators
- betweenness centrality / Centrality, Betweenness centrality, Betweenness centrality, Betweenness centrality
- bibliography / Bibliography
- bipartite graph / The Multipartite layout
- brush function / Modifying the graph
C
- Center for Computational Analysis of Social and Organizational Systems (CASOS)
- URL / Web resources
- Center for Network Science (CNS)
- URL / Web resources
- centrality / Centrality
- centrality measures, graph statistics
- about / Centrality measures
- degree centrality (undirected graphs) / Degree centrality (undirected graphs)
- in-degree centrality (directed graphs) / In-degree centrality (directed graphs)
- out-degree centrality (directed graphs) / Out-degree centrality (directed graphs)
- closeness centrality / Closeness centrality
- eigenvector centrality / Eigenvector centrality
- betweenness centrality / Betweenness centrality
- centrality statistics
- degree centrality / Degree centrality
- closeness centrality / Closeness centrality
- eigenvector centrality / Eigenvector centrality
- betweenness centrality / Betweenness centrality
- centrality statistics, interpreting
- about / Interpreting centrality statistics
- degree centrality / Degree centrality
- in-degree centrality / In-degree centrality
- out-degree centrality / Out-degree centrality
- closeness centrality / Closeness centrality
- eigenvector centrality / Eigenvector centrality
- betweenness centrality / Betweenness centrality
- Chinese Whispers algorithm
- about / Chinese Whispers
- Chinese Whispers plugin
- circular layout / The Circular layout
- Circular layout
- about / Circular layouts, The Circular layout
- Concentric layout / The Concentric layout
- Dual Circle layout / The Dual Circle layout
- closeness centrality / Closeness centrality, Closeness centrality, Closeness centrality
- cluster analysis
- about / Clustering
- clustering / Clustering – Chinese Whispers
- about / Clustering and homophily, Clustering
- clustering and neighborhood measures, graph statistics
- about / Clustering and neighborhood measures
- clustering coefficient / Clustering coefficient
- number of triangles / Number of triangles
- modularity / Modularity
- link communities / Link Communities
- neighborhood overlap and embeddedness / Neighborhood overlap and embeddedness
- clustering coefficient, clustering and neighborhood measures / Clustering coefficient
- clustering statistics
- about / Clustering statistics
- clustering coefficient / Clustering coefficient
- number of triangles / Number of triangles
- modularity / Modularity
- link communities / Link Communities
- embeddedness / Embeddedness
- clustering statistics, interpreting
- about / Interpreting clustering statistics
- clustering coefficients, interpreting / Interpreting clustering coefficients
- number of triangles / Number of triangles
- modularity statistic / Modularity
- link communities statistic / Link Communities
- embeddedness / Embeddedness
- CmapTools
- URL / Contagion
- community detection / Partitioning and clustering options
- complex filters
- about / Working with complex filters
- multiple filter conditions, applying / Applying multiple filter conditions
- subfilters, using / Using subfilters
- Mask, working with / Working with Mask and Intersection conditions
- INTERSECTION filter / Working with Mask and Intersection conditions
- UNION operator / Working with the UNION operator
- Concentric layout
- about / The Concentric layout, Layout strengths and weaknesses
- testing / The Concentric layout
- concentric layout / The Concentric layout
- connected components, network measures / Connected components
- connected graph / Components
- connections / A network graph analysis primer
- connectivity / Connectivity
- contagion / Paths and connectivity
- about / Contagion
- SIR model / The SIR model
- contagion network
- viewing / Viewing a contagion network
- CSV files / CSV files
- CSV import, data laboratory / CSV import
- cycles / Cycles
D
- data
- formatting, for Gephi / Formatting the data for Gephi
- importing, into Gephi / Importing data into Gephi
- data laboratory
- about / Data laboratory, Data laboratory
- manual entry / Manual entry
- CSV import / CSV import
- Excel import / Excel import
- MySQL import / MySQL import
- Graph file import / Graph file import
- helper / Data laboratory helper
- data sources
- identifying / Identifying the data sources
- about / Data sources
- degree centrality / Centrality, Degree centrality, Degree centrality
- degree centrality (undirected graphs) / Degree centrality (undirected graphs)
- Degree Range filter / Topology
- density / Density
- diameter, network measures / Diameter
- diffusion / Diffusion
- diffusion network
- viewing / Viewing network diffusion
- Directed Acyclic Graphs (DAG) layout / DAG layout
- about / Layout strengths and weaknesses
- DL files / DL files
- DNA
- uses / When to use DNA
- types / When to use DNA
- topology-based DNA / Topology-based DNA
- Dual Circle layout
- dynamic attribute networks
- dynamic filtering / Primary filtering functions in Gephi
- dynamic GEXF files
- creating / Creating dynamic GEXF files
- URL / Creating dynamic GEXF files
- dynamic network, topology-based DNA
- generating / Generating a dynamic network
- implementing / Implementing and viewing a dynamic network
- viewing / Implementing and viewing a dynamic network
E
- eccentricity, network measures / Eccentricity
- eccentricity, network statistics / Eccentricity
- edge betweenness, network statistics / Edge betweenness
- edge betweenness statistic, , network measures / Edge betweenness
- Edge Cut / The OpenOrd algorithm
- edge pencil tool / Modifying the graph
- edges
- filtering / Filtering edges
- edges filter
- Edge Weight filter / Edges
- Ego Network function / Topology
- eigenvector centrality / Centrality, Eigenvector centrality, Eigenvector centrality, Eigenvector centrality
- embeddedness, clustering statistics / Embeddedness
- Equal filter
- using / Using the Equal filter
- regex function, applying / Applying the regex function
- Equal function / Attributes
- erdos number, network measures / Erdos number
- Erdos Number Project
- Excel import, data laboratory / Excel import
- expansion / Markov clustering
- exports
- about / Exports
- Sigmajs Exporter / Sigma.js Exporter
- Seadragon Web Export / Seadragon Web Export
- Graph Streaming plugin / Graph Streaming
- ExportToEarth / ExportToEarth
- ExportToEarth / ExportToEarth
F
- filtering
- about / The filtering theory
- functions / Primary filtering functions in Gephi
- primary filtering / Primary filtering functions in Gephi
- simple filters / Using simple filters
- Equal filter / Using the Equal filter
- complex filters / Working with complex filters
- filtering tab / The filtering tab
- force-based layouts
- attraction / Force-based layouts
- replusion / Force-based layouts
- gravity / Force-based layouts
- Force Atlas 2 layout
- Force Atlas 3D layout
- about / Force Atlas 3D
- Force Atlas layout
- friends of friends' network / Working with the Topology filters
- Fruchterman-Reingold algorithm
- Fruchterman Reingold algorithm
- about / Layout strengths and weaknesses
- Fruchterman Reingold layout
- about / The Fruchterman-Reingold layout
G
- GDF files / GDF files
- generators
- about / Generator – the Complex Generators plugin
- using / Using Gephi generators
- geodesic path / Paths
- geographic layouts
- about / Geographic layouts
- Geo layout / The Geo layout
- Maps of Countries layout / The Maps of Countries layout
- Geo layout
- Gephi
- overview / Overviewing Gephi
- existing networks / Using Gephi to understand existing networks
- wiki, URL / Using Gephi to understand existing networks
- projects, creating / Creating new Gephi projects
- Gephi wiki
- URL / Data sources
- Giant Component filter / Topology
- Give color to nodes (Tools) / Give color to nodes – tools
- graph
- applications / Graph applications
- collaboration / Collaboration graphs
- Who-Talks-to-Whom graphs / Who-talks-to-whom graphs
- information linkages / Information linkages
- technological networks / Technological networks
- natural world networks / Natural-world networks
- analyzing / Analyzing the graph, Analyzing the graph
- modifying / Modifying the graph, Modifying the graph
- exporting / Exporting the graph
- graph aesthetics
- about / Graph aesthetics
- example / Working example of graph aesthetics
- graph density, network measures / Graph density
- graph density, network statistics / Graph density
- Graph Exchange XML Format (GEXF) files
- URL / GEXF files
- graph file exporters
- about / Overview of the available tools, Graph file exporters
- CSV files / CSV files
- DL files / DL files
- GDF files / GDF files
- Graph Exchange XML Format (GEXF) files / GEXF files
- Graph Modeling Language (GML) files / GML files
- GraphML files / GraphML files
- NET files / NET files
- VNA files / VNA files
- graphing needs, Miles Davis network example
- about / Assessing your graphing needs, Actual example – the Miles Davis network
- analysis goal / Analysis goal
- dataset parameters / Dataset parameters
- network density / Network density
- network behaviors / Network behaviors
- network display / Network display
- temporal elements / Temporal elements
- interactivity / Interactivity
- GraphML files
- about / GraphML files
- URL / GraphML files
- Graph Modeling Language (GML) files / GML files
- graph statistics
- about / Overview of graph statistics
- network measures / Network measures
- centrality measures / Centrality measures
- clustering and neighborhood measures / Clustering and neighborhood measures
- interpreting / Interpreting graph statistics
- network measures, interpreting / Interpreting network measures
- centrality statistics, interpreting / Interpreting centrality statistics
- clustering statistics, interpreting / Interpreting clustering statistics
- used, for filtering / Filtering using graph statistics
- graph statistics, interpreting
- about / Interpreting graph statistics
- graph window
- about / Graph window
- GUESS
- URL / GDF files
H
- hairball effect / The Hiveplot layout
- hive plot layout / The Hiveplot layout
- Hiveplot layout
- homophily / Homophily
- about / Clustering and homophily, Homophily
- identifying / Identifying homophily
- Hyperlink-Induced Topic Search (HITS) function, , network measures / HITS
I
- image exporters
- about / Overview of the available tools, Image exporters
- PNG export / PNG export
- SVG export / SVG export
- Image Preview tool
- URL / PDF export
- import processes
- about / Import processes
- in-degree centrality / In-degree centrality
- in-degree centrality (directed graphs) / In-degree centrality (directed graphs)
- In Degree Range filter / Topology
- inflation / Markov clustering
- initial graph layout
- viewing / Viewing the initial graph layout
- Inkscape
- PDF file, editing / Editing a PDF file in Inkscape
- Inter Edges / Attributes
- INTERSECTION filter / Working with Mask and Intersection conditions
- INTERSECTION operator / Operator
- intervals, topology-based DNA
- creating, in existing project / Creating time intervals in an existing project
- Intra Edges / Attributes
- Isometric layout
K
- KONECT
- URL / Data sources
L
- Layered layout
- layered layout / The Layered layout
- layout
- about / Layout
- multipartite layout / The Multipartite layout
- hive plot layout / The Hiveplot layout
- concentric layout / The Concentric layout
- OpenOrd layout / The OpenOrd layout
- circular layout / The Circular layout
- layered layout / The Layered layout
- ARF layout / The ARF layout, The ARF layout
- selecting / Selecting a layout
- types / Overviewing the layout types
- force-based layouts / Force-based layouts
- Force Atlas layout / Force Atlas
- Force Atlas 2 layout / Force Atlas 2
- Force Atlas 3D layout / Force Atlas 3D
- Fruchterman-Reingold algorithm / The Fruchterman-Reingold algorithm
- OpenOrd algorithm / The OpenOrd algorithm
- Yifan Hu algorithm / The Yifan Hu algorithm
- Yifan Hu Proportional layout / The Yifan Hu Proportional layout
- Yifan Hu Multilevel approach / The Yifan Hu multilevel approach
- tree layouts / Tree layouts
- Circular layouts / Circular layouts
- Circular layout / The Circular layout
- radial layouts / Radial layouts
- geographic layouts / Geographic layouts
- additional / Additional layouts
- Isometric layout / The Isometric layout
- Multipartite layout / The Multipartite layout
- Layered layout / The Layered layout
- Network Splitter 3D / Network Splitter 3D
- additional layout tools / Additional layout tools
- strengths / Layout strengths and weaknesses
- weaknesses / Layout strengths and weaknesses
- testing / Testing layouts
- ARF layout, testing / Testing the ARF layout
- Concentric layout / The Concentric layout
- Radial Axis layout, testing / Testing the Radial Axis layout
- selection, criteria / Layout selection criteria
- layouts tab / The layouts tab
- link communities, clustering and neighborhood measures / Link Communities
- link communities statistic, clustering statistics / Link Communities
- links / A network graph analysis primer
- Loxa Web Site Export / Loxa Web Site Export, Loxa Web Site Export
M
- Maps of Countries layout / The Maps of Countries layout
- about / Layout strengths and weaknesses
- Markov approach
- about / Markov clustering
- Markov Clustering plugin
- Marvel Social network / Using Gephi to understand existing networks
- MASK (Edges) operator / Operator
- modularity, clustering and neighborhood measures / Modularity
- modularity statistic, clustering statistics / Modularity
- multipartite layout / The Multipartite layout
- Multipartite layout
- MySQL import, data laboratory / MySQL import
N
- neighborhood overlap and embeddedness, clustering and neighborhood measures / Neighborhood overlap and embeddedness
- Neighbors Network filter / Topology
- NET files / NET files
- NetLogo
- URL / Web resources
- network
- diffusion / Contagion and diffusion
- contagion / Contagion and diffusion
- growth / Network growth
- growth patterns / Network growth patterns
- contagion network, viewing / Viewing a contagion network
- diffusion, viewing / Viewing network diffusion
- clustering / Network clustering
- network analysis
- network diameter, network statistics / Network diameter
- network graph
- analysis primer / A network graph analysis primer
- paths and connectivity / Paths and connectivity
- paths / Paths
- cycles / Cycles
- connectivity / Connectivity
- structure / Network structure
- process flow, proposed / A proposed process flow
- idea or topic, identifying / Identifying an idea or topic
- final output, determining / Determining the final output
- data sources, identifying / Identifying the data sources
- data, formatting for Gephi / Formatting the data for Gephi
- data, importing into Gephi / Importing data into Gephi
- initial graph layout, viewing / Viewing the initial graph layout
- layout, selecting / Selecting a layout
- analyzing / Analyzing the graph
- modifying / Modifying the graph
- exporting / Exporting the graph
- example graph, creating / Creating an example graph
- network graph, example graph
- topic, identifying / Identifying the topic
- data source, finding / Finding the data source
- data, formatting for Gephi / Formatting the data for Gephi
- data, importing / Importing the data
- initial network, viewing / Viewing the initial network
- appropriate layout, selecting / Selecting an appropriate layout
- Force Atlas layout / The Force Atlas layout
- Fruchterman Reingold layout / The Fruchterman-Reingold layout
- Radial Axis layout / The Radial Axis layout
- Yifan hu layout / The Yifan Hu layout
- network graph, structure
- about / Network structure
- centrality / Centrality
- components / Components
- giant component / Giant components and clustering
- clustering / Giant components and clustering
- Homophily / Homophily
- density / Density
- behaviors / Network behaviors
- network measures, graph statistics
- about / Network measures
- diameter / Diameter
- eccentricity / Eccentricity
- graph density / Graph density
- average path length / Average path length
- connected components / Connected components
- erdos number / Erdos number
- Hyperlink-Induced Topic Search (HITS) function / HITS
- edge betweenness / Edge betweenness
- network measures, interpreting
- about / Interpreting network measures
- diameter / Interpreting network measures
- eccentricity / Interpreting network measures
- graph density statistic / Interpreting network measures
- average path length / Interpreting network measures
- HITS / Interpreting network measures
- Network Splitter 3D layout
- network statistics
- about / Network statistics
- network diameter / Network diameter
- eccentricity / Eccentricity
- graph density / Graph density
- average path length / Average path length
- edge betweenness / Edge betweenness
- centrality statistics / Centrality statistics
- node pencil tool / Modifying the graph
- Non-null condition / Attributes
- NOT (Edges) operator / Operator
- NOT (Nodes) operator / Operator
- number of triangles, clustering and neighborhood measures / Number of triangles
- number of triangles, clustering statistics / Number of triangles
- Num Iterations / The OpenOrd algorithm
- Num Threads / The OpenOrd algorithm
O
- OpenOrd algorithm
- about / The OpenOrd algorithm
- OpenOrd layout / The OpenOrd layout
- about / Layout strengths and weaknesses
- operator
- out-degree centrality / Out-degree centrality
- out-degree centrality (directed graphs) / Out-degree centrality (directed graphs)
- Out Degree Range filter / Topology
P
- painter function / Modifying the graph
- Pajek program
- URL / NET files
- Partition Count filter / Attributes
- Partition filter / Attributes
- using / Using the Partition filter
- partitioning / Partitioning
- partitioning and clustering, examples
- about / Partitioning and clustering examples, Partitioning
- Ranking tab / Working with the Ranking tab
- color and size options, using / Using color and size options
- manual graph segmentation / Manual graph segmentation
- Chinese Whispers plugin, using / Using the Chinese Whispers plugin
- Markov Clustering plugin, using / Using the Markov Clustering plugin
- partitioning and clustering, options
- about / Partitioning and clustering options
- Partition tab / The Partition tab
- Ranking tab / The Ranking tab
- manual settings / Manual settings
- Chinese Whispers algorithm / Chinese Whispers
- Markov clustering / Markov clustering
- Partition tab
- about / The Partition tab
- paths / Paths
- PDF export
- about / PDF export
- PDF file, editing in Inkscape / Editing a PDF file in Inkscape
- plugins
- about / Essential plugins
- clustering / Clustering – Chinese Whispers
- data laboratory / Data laboratory
- data laboratory, helper / Data laboratory helper
- exports / Exports
- generators / Generator – the Complex Generators plugin
- layout / Layout
- additional / Additional plugins
- Link communities (Metrics) / Link Communities – metrics
- Give color to nodes (Tools) / Give color to nodes – tools
- PNG export
- about / PNG export
- preview window
- about / Preview window
- PNG option / Preview window
- SVG option / Preview window
- PDF option / Preview window
- primary filtering
- about / Primary filtering functions in Gephi
- attributes / Primary filtering functions in Gephi, Attributes
- edges / Primary filtering functions in Gephi, Edges
- operator / Primary filtering functions in Gephi, Operator
- topology / Primary filtering functions in Gephi, Topology
- primary windows
- about / Primary windows
- data laboratory / Data laboratory
- graph window / Graph window
- preview window / Preview window
- project, high school network
- about / Project 2 – high school network with dynamic edges
- network in Gephi, exploring / Using Gephi to explore the network
- creating, as PDF / Creating the project as a PDF
- project, Newman NetScience dataset
- about / Project 1 – Newman NetScience dataset
- network in Gephi, exploring / Exploring the network in Gephi
- project, deploying to Web / Deploying the project to the Web
- projects
- creating / Creating new Gephi projects
- Newman NetScience dataset / Project 1 – Newman NetScience dataset
- high school network, with dynamic edges / Project 2 – high school network with dynamic edges
R
- Radial Axis layout
- radial layout
- about / Radial layouts
- Hiveplot layout / The Hiveplot layout
- Radial Axis layout / The Radial Axis layout
- Range filter / Attributes
- Ranking tab
- about / The Ranking tab
- working with / Working with the Ranking tab
- RDF
- regex function
- applying / Applying the regex function
- Regular Expression (regex) / Using Gephi to understand existing networks
- repulsion strength / Force Atlas
S
- Seadragon / Seadragon
- Seadragon Web Export / Seadragon Web Export, Seadragon Web Export
- secondary windows (tabs)
- about / Secondary windows – tabs
- filtering tab / The filtering tab
- statistics tab / The statistics tab
- layouts tab / The layouts tab
- Self-Loop filter / Edges
- semantic filtering / Primary filtering functions in Gephi
- SigmaExporter / Sigma.js Exporter, SigmaExporter
- Sigmajs Exporter / Sigma.js Exporter
- simple filters
- about / Using simple filters
- Equal filter, using / Using the Equal filter
- regex function, applying / Applying the regex function
- edges, filtering / Filtering edges
- Partition filter, using / Using the Partition filter
- topology filters / Working with the Topology filters
- simple path / Paths
- SIR model (Susceptible, Infectious, and Removed)
- about / The SIR model
- SIRS model / The SIRS model
- SIS model / The SIS model
- six degrees of separation / Analyzing the graph
- sizer function / Modifying the graph
- small world networks / Using Gephi generators
- Social Network Analysis (SNA) / Graph applications
- Stanford Large Network Dataset Collection
- Stanford Network Analysis Project (SNAP)
- URL / Data sources
- statistical measures, application
- about / Application of statistical measures
- basic statistical applications / Basic statistical applications
- graph statistics, used, for filtering / Filtering using graph statistics
- statistics tab / The statistics tab
- subfilters, complex filters
- using / Using subfilters
- SVG export / SVG export
- SVG file, editing with Inkscape / Editing an SVG file with Inkscape
T
- ties / A network graph analysis primer
- time intervals, topology-based DNA
- about / Understanding time intervals
- adding, to new project / Adding time intervals to a new project
- timelines, topology-based DNA
- about / Working with timelines
- working with / Working with timelines
- applying / Applying the timeline
- as filters / Timelines as filters
- topology
- topology, primary filtering
- about / Topology
- topology-based DNA
- about / Topology-based DNA
- dynamic network, generating / Generating a dynamic network
- time intervals / Understanding time intervals
- timelines / Working with timelines
- data, preparing / Preparing and importing data for DNA
- data, importing / Preparing and importing data for DNA
- dynamic network, implementing / Implementing and viewing a dynamic network
- dynamic network, viewing / Implementing and viewing a dynamic network
- time intervals, creating in existing project / Creating time intervals in an existing project
- time intervals, adding to new project / Adding time intervals to a new project
- existing GEXF file, using / Using an existing GEXF file
- multiple timeframes, adding / Adding multiple timeframes
- timelines, working with / Working with timelines
- timelines, applying / Applying the timeline
- timelines, as filters / Timelines as filters
- topology filters, simple filters / Working with the Topology filters
- tree layouts
- about / Tree layouts
- Directed Acyclic Graphs (DAG) layout / DAG layout
U
- UCINET program
- URL / DL files
- UNION operator / Operator, Working with the UNION operator
V
- VNA files / VNA files
W
- Watts-Strogatz small world Alpha model / Using Gephi generators
- web exporters
- about / Overview of the available tools, Web exporters
- Seadragon Web Export / Web exporters, Seadragon Web Export
- Sigmajs Exporter / Web exporters
- Loxa Web Site Export / Web exporters, Loxa Web Site Export
- SigmaExporter / Sigma.js Exporter
- web graph
- exporting / Exporting a web graph
- Seadragon / Seadragon
- SigmaExporter / SigmaExporter
- Loxa Web Site Export / Loxa Web Site Export
- web sources
- about / Web resources
- Who-Talks-to-Whom graphs / Who-talks-to-whom graphs
Y
- Yifan Hu algorithm
- Yifan hu layout
- about / The Yifan Hu layout
- Yifan Hu Multilevel approach
- Yifan Hu Proportional layout