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# (PART) Additional Material{-}
# Table of Contents Quick Reference{- #TableOfContents}
{width=100%}
The purpose of this section is to provide a quick index of topics covered in this document so that you can easily identify and work on specific things. Use the cross-reference links below to find what you are looking for.
## Welcome{-}
[Welcome](#Welcome)
* [How Should I Use this Online Companion?](#HowTo)
* [Reproducibility](#Repro)
* [Computational Archaeology Discord Community](#Discord)
* [New to R and R Studio?](#NewToR)
* [Contribute to the Project](#Contributing)
* [Help Build the Community](#Community)
* [Acknowledgements](#Acknowledgements)
## PART II: GETTING STARTED{-}
## Section 1: Getting Started with R{-}
[Getting Started with R](#GettingStarted)
* [Download and Install R](#InstallR)
+ [Windows](#Windows)
+ [MacOC](#MacOS)
+ [Linux](#Linux)
* [Download and Install R-Studio](#InstallRStudio)
* [Run R-Studio](#RunRStudio)
* [R and R-Studio Basics](#RBasics)
+ [Organization of R-Studio](#Org)
+ [Mathematical Operations](#Math)
+ [Creating Variables/Objects](#Variables)
+ [Logical Operators](#Logical)
+ [Vectors](#Vectors)
+ [Using Basic R Functions](#Functions)
+ [Tabular Data](#Tabular)
+ [Data Types in R](#DataTypes)
+ [Object Types in R](#ObjectTypes)
- [Vectors](#Vec)
- [Matrices](#Mat)
- [Data Frames](#DF)
- [Lists](#List)
* [The Workspace Tab](#WorkspaceTab)
+ [Setting the Working Directory](#Directory)
+ [Working with your first R script](#FirstScript)
* [Installing and Using Packages](#InstallPackages)
* [Working with External Files](#WorkingWithFiles)
* [Plotting Data](#Plotting)
* [Warnings and Messages in R](#Warnings)
* [More Advanced R Features](#AdvancedR)
+ [Conditional Statements](#Conditionsls)
+ [Loops](#Loops)
+ [Custom Functions](#CustomFunctions)
* [Test Your Skills](#TestYourSkills)
## PART II: WORK WHILE YOU READ{-}
## Section 2: Data and Workspace Setup{-}
[Data and Workspace Setup](#DataAndWorkspace)
* [Data Sets](#DataSets)
+ [Just Give Me Everything](#Everything)
+ [Roman Road Networks](#RomanRoads)
+ [Southwest Social Networks Project Ceramic Similarity Networks](#SWSN)
+ [Cibola Region Technological Similarity Networks](#Cibola)
+ [Himalayan Visibility Networks](#Himalaya)
+ [Archaeological Publication Networks](#ArchPubs)
+ [Iron Age Sites in Southern Spain](#Guadalquivir)
* [Importing Data in R](#Importing)
* [Required/Suggested R Packages](#PrimaryPackages)
+ [Should I Just Install Everything](#ShouldIInstall)
* [R Environment](#Environment)
* [Suggested Workspace Setup](#WorkspaceSetup)
## Section 3: Network Data in R{-}
[Network Data in R](#NetworkData)
* [Network Data Formats](#NetworkDataFormats)
+ [Edge list](#Edgelist)
+ [Adjacency list](#AdjacencyList)
+ [Adjacency matrix](#AdjacencyMatrix)
+ [Incidence matrix](#IncidenceMatrix)
+ [Node and edge attribute data](#NodeAttributes)
* [Network Types](#TypesOfNetworks)
+ [Simple networks](#SimpleNetworks)
+ [Directed networks](#Directed Networks)
+ [Signed, Categorized, and Weighted Networks](#WeightedNetworks)
+ [Two-mode networks](#TwoMode)
+ [Similarity networks](#SimilarityNetworks)
- [Brainerd-Robinson similarity](#BrainerdRobinson)
- [Morisita's Index](#Morisita)
- [$\chi^{2}$ Distance](#ChiSquare)
- [Jaccard Similarity](#Jaccard)
- [Creating network objects from similarity matrices](#NetFromSim)
+ [Ego networks](#EgoNetworks)
+ [Multilayer networks](#Multinet)
* [Converting among network object types](#ConvertingNetworkFormats)
## Section 4: Exploratory Network Analysis{-}
[Exploratory Network Analysis](#Exploratory)
* [Example Network Objects](#ExampleNetworkObjects)
* [Calculating Network Metrics in R](#CalcMetric)
* [Network Centrality](#Centrality)
+ [Degree Centrality](#Degree)
+ [Betweenness Centrality](#Betweenness)
+ [Eigenvector Centraoity](#Eigenvector)
+ [Page Rank](#PageRank)
+ [Closeness Centrality](#Closeness)
+ [Hubs and Authorities](#HubsAndAuthorities)
* [Triads and Clustering](#TriadsAndClustering)
+ [Triads](#Triads)
+ [Triad Census](#Triads)
+ [Transitivity](#Transitivity)
* [Walks, Paths, and Distance](#WalksPathsDistance)
+ [Distance](#Distance)
+ [Shortest Paths](#ShortestPaths)
+ [Network Diameter](#Diameter)
* [Components and Bridges](#ComponentsAndBridges)
+ [Identifying Components](#IdentifyingComponents)
+ [Cutpoints](#Cutpoints)
+ [Bridges](#Bridges)
* [Cliques and Communities](#CliquesAndCommunities)
+ [Cliques](#Cliques)
+ [K-Cores](#KCores)
+ [Cluster Detection Agloritms](#ClusterDetection)
- [Girvan-Newman Clustering](#GirvanNewman)
- [Walktrap Algorithm](#Walktrap)
- [Louvain Modularity](#Louvain)
- [Calculating Modularity of Partitions](#Modularity)
- [Finding Edges Between Communities](#FindingEdgesBetween)
* [Case Study: Roman Roads in the Iberian Peninsula](#ExploratoryRomanRoads)
## Section 5: Quantifying Uncertainty{-}
[Quantifying Uncertainty](#Uncertainty)
* [R Scripts for Conducting Uncertainty Analysis](#UncertaintyScripts)
* [A General Approach to Uncertainty](#UncertaintyGeneral)
* [Nodes Missing at Random](#NodesAtRandom)
* [Edges Missing at Random](#EdgesAtRandom)
* [Assessing Individual Nodes/Edges Missing at Random](#IndNodesAtRandom)
* [Nodes/Edges Missing Due To Biased Sampling](#MissingBiased)
* [Resampling with Incidence Matrices](#SimIncidence)
* [Edge Probability Modeling](#EdgeProbability)
+ [Edge Probability and Similarity Networks](#EdgeProbSim)
* [Uncertainty Due to Small or Variable Sample Sizes](#SampleSize)
## Section 6: Network Visualization{-}
[Network Visualization](#NetworkVisualization)
* [Data and R Setup](#VizDatasets)
* [Visualizing Networks in R](#VisInR)
+ [`network` package](#networkpackage)
+ [`igraph` package](#igraphpackage)
+ [`ggraph` package](#ggraphpackage)
* [Network Visualization Options](#NetVizOptions)
+ [Graph Layouts](#GraphLayouts)
- [Manual Layouts](#ManualLayouts)
- [Geographic Layouts](#GeographicLayouts)
- [Shape-based and Algorithmic Layouts](#AlgorithmicLayouts)
+ [Node and Edge Options](#NodeEdgeOptions)
- [Nodes](#NodeOptions)
- [Edges](#EdgeOptions)
- [Labels](#LabelOptions)
+ [Be Kind To the Color Blind](#Colorblind)
+ [Communities and Groups](#ViZCommunities)
* [Replicating the Book Figures](#ReplicatingBookFigures)
+ [Figure 6.1 - Manual Layout](#Figure_6_1)
+ [Figure 6.2 - Examples of Common Network Plot Formats](#Figure_6_2)
+ [Figure 6.3 - Examples of Rare Network Plot Formats](#Figure_6_3)
+ [Figure 6.4 - Simple Network with Clusters](#Figure_6_4)
+ [Figure 6.5 - Interactive Layout](#Figure_6_5)
+ [Figure 6.6 - Absolute Geographic Layout](#Figure_6_6)
+ [Figure 6.7 - Distorted Geographic Layout](#Figure_6_7)
+ [Figure 6.8 - Graph Layout Algorithms](#Figure_6_8)
+ [Figure 6.9 - Heirarchical Graph Layouts](#Figure_6_9)
+ [Figure 6.10 - Be Kind To the Color Blind](#Figure_6_10)
+ [Figure 6.11 - Node Symbol and Color Schemes](#Figure_6_11)
+ [Figure 6.12 - Image for Node, Example 1](#Figure_6_12)
+ [Figure 6.13 - Image for Node, Example 2](#Figure_6_13)
+ [Figure 6.14 - Edge Thickness and Color](#Figure_6_14)
+ [Figure 6.15 - Edge Direction](#Figure_6_15)
+ [Figure 6.16 - Edge Binarization](#Figure_6_16)
+ [Figure 6.17 - Edge Bundling](#Figure_6_17)
+ [Figure 6.18 - Group-in-a-box Layout](#Figure_6_18)
+ [Figure 6.19 - Weighted Adjacency Matrix](#Figure_6_19)
+ [Figure 6.20 - Nodetrix Diagram Interactive Plot](#Figure_6_20)
+ [Figure 6.21 - Temporal Change, The Filmstrip Approach](#Figure_6_21)
+ [Figure 6.22 - Temporal Change, Similtaneous Display](#Figure_6_22)
+ [Figure 6.23 - Timelines and Time Prisms](#Figure_6_23)
+ [Figure 6.24 - Animation](#Figure_6_24)
+ [Figure 6.25 - Interactive Networks](#Figure_6_25)
+ [Figure 6.26 - Case Study, SWSN Example 1](#Figure_6_26)
+ [Figure 6.27 - Case Study, SWSN Example 2](#Figure_6_27)
## Section 7: Spatial Networks{-}
[Spatial Networks](#SpatialNetworks)
* [Working with Geographic Data in R](#GeoData)
* [Example Data](#ExampleData)
* [Planar Networks and Trees](#PlanarTrees)
+ [Evaluating Planarity](#EvaluatingPlanarity)
+ [Defining Trees](#DefiningTress)
* [Spatial Network Models](#SpatialNetworkModels)
+ [Relative Neighborhood Networks](#RelativeNeighborhoods)
+ [Gabrial Graphs](#GabrialGraphs)
+ [Beta Skeletons](#BetaSkeletons)
+ [Minimum Spanning Trees](#MinSpanningTrees)
+ [Delaunay Triangulation](#DelaunayTri)
+ [K-Nearest Neighbors](#KNN)
+ [Max Distance Networks](#MaxDist)
* [Case Studies: Spatial Networks and Networks in Space](#SpaceCaseStudies)
+ [Proximity of Iron Age Sites in Southern Spain](#IronAgeSpain)
+ [Networks in Space in the U.S. Southwest](#SpaceSW)
## PART III: GOING BEYOND THE BOOK{-}
## Section 8: Exponential Random Graph Models{-}
[Exponential Random Graph Models](#ERGM)
* [ERGMs in R](#ERGMsInR)
* [Cranborne Chase Visibility Network Example](#CranborneChase)
+ [Assessments of Network Properties](#NetProperties)
+ [Fitting Models with `ergm`](#FitModels)
+ [Building a Model Based on Theory](#ModelTheory)
+ [Assessing Goodness-of-Fit](#GOF)
+ [Asessing Models and MCMC Diagnostics](#Diagnostics)
* [Simulating Networks from ERGMs](#SimERGMs)
* [Additinoal Info on ERGM Terms](#ERGMterms)
+ [Avoiding Model Degeneracy](#Degeneracy)
## Section 9: Spatial Interaction Models{-}
[Spatial Interaction Models](#SpatialInteraction)
* [Simple Gravity Models](#GravityModel)
+ [Parameterizing the Gravity Model](#ParameterizingGravity)
* [The Rihll and Wilson "Retail" Model](#RihllWilson)
+ [Parameterizing the Retail Model](#ParameterizingRetail)
* [Truncated Power Functions](#TruncatedPower)
* [Other Spatial Interaction Models](#OtherModels)
## Section 10: Affiliation Data and Co-Association{-}
[Affiliation Data and Co-Association](#Affiliation)
* [Analyzing Two-Mode Networks](#AnalyzingTwoMode)
+ [Using Traditional Network Metrics](#TraditionalMetrics)
+ [Using Two-Mode Specific Network Metrics](#TwoModeMetrics)
+ [Projecting Two-Mode Networks Before Analysis](#ProjectingTwoMode)
* [Correspondence Analysis](#CorrespondenceAnalysis)
+ [Network Visuals Using Correspondence Analysis](#CAViz)
* [Measuring Co-Association](#MeasuringCoassociation)
+ [Alternative Methods for Visualizing Co-associations](#COViz)
## Section 11: Network Diffusion{-}
[Network Diffusion](#NetworkDiffusion)
* [Diffusion Processes](#DiffusionProcesses)
* [Simulating Network Diffusion in R](#SimNetworkR)
+ [Simulated Networks](#DiffuseSimulatedNetworks)
+ [Empirical Networks](#DiffuseEmpiricalNetworks)
* [Evaluating Diffusion Models](#EvaluatingDiffusion)
## Section 12: Comparing Networks{-}
[Comparing Networks](#ComparingNetworks)
* [Known Node Correspondence](#KnownNode)
+ [Direct Comparison of Adjacency Matrices](#CompareAdjacencyMatrices)
+ [Quadratic Assignment Procedure](#QAP)
+ [DeltaCon](#DeltaCon)
* [Unknown Node Correspondence](#UnknownNode)
+ [Comparing Network Global and Local Statistics](#ComparingStatistics)
+ [Graph Kernel Methods](#NetworkKernel)
+ [Spectral Methods](#SpectralMethods)
+ [Portrait Divergence](#PortraitDivergence)
+ [Graphlet-based Methods](#GraphletMethods)
+ [Alignment-based Methods](#Alignment)
## ADDITIONAL INFORMATION AND MATERIALS{-}
[References and R Packages](https://book.archnetworks.net/references-and-r-packages.html)
[ArchNetSci GitHub Repository](https://github.com/mpeeples2008/ArchNetSci)