Graph/Network Visualization

Build graph/network structures using functions for stepwise addition and deletion of nodes and edges. Work with data available in tables for bulk addition of nodes, edges, and associated metadata. Use graph selections and traversals to apply changes to specific nodes or edges. A wide selection of graph algorithms allow for the analysis of graphs. Visualize the graphs and take advantage of any aesthetic properties assigned to nodes and edges.

Data Cloud Geometry (DCG): Using Random Walks to Find Community Structure in Social Network Analysis

Data cloud geometry (DCG) applies random walks in finding community structures for social networks. Fushing, VanderWaal, McCowan, & Koehl (2013) ().

Graph Plotting Methods, Psychometric Data Visualization and Graphical Model Estimation

Fork of qgraph - Weighted network visualization and analysis, as well as Gaussian graphical model computation. See Epskamp et al. (2012) .

Algebraic Tools for the Analysis of Multiple Social Networks

Algebraic procedures for analyses of multiple social networks are delivered with this package as described in Ostoic (2020) . 'multiplex' makes possible, among other things, to create and manipulate multiplex, multimode, and multilevel network data with different formats. Effective ways are available to treat multiple networks with routines that combine algebraic systems like the partially ordered semigroup with decomposition procedures or semiring structures with the relational bundles occurring in different types of multivariate networks. 'multiplex' provides also an algebraic approach for affiliation networks through Galois derivations between families of the pairs of subsets in the two domains of the network with visualization options.

Bayesian Network Modeling and Analysis

A "Shiny"" web application for creating interactive Bayesian Network models, learning the structure and parameters of Bayesian networks, and utilities for classic network analysis.

Tools for Identifying Important Nodes in Networks

Includes assorted tools for network analysis. Bridge centrality; goldbricker; MDS, PCA, & eigenmodel network plotting.

Fit, Simulate and Diagnose Models for Network Evolution Based on Exponential-Family Random Graph Models

An integrated set of extensions to the 'ergm' package to analyze and simulate network evolution based on exponential-family random graph models (ERGM). 'tergm' is a part of the 'statnet' suite of packages for network analysis. See Krivitsky and Handcock (2014) and Carnegie, Krivitsky, Hunter, and Goodreau (2015) .

Biological Structure Analysis

Utilities to process, organize and explore protein structure, sequence and dynamics data. Features include the ability to read and write structure, sequence and dynamic trajectory data, perform sequence and structure database searches, data summaries, atom selection, alignment, superposition, rigid core identification, clustering, torsion analysis, distance matrix analysis, structure and sequence conservation analysis, normal mode analysis, principal component analysis of heterogeneous structure data, and correlation network analysis from normal mode and molecular dynamics data. In addition, various utility functions are provided to enable the statistical and graphical power of the R environment to work with biological sequence and structural data. Please refer to the URLs below for more information.

Null Model Analysis for Ecological Networks

Null models to analyse ecological networks (e.g. food webs, flower-visitation networks, seed-dispersal networks) and detect resource preferences or non-random interactions among network nodes. Tools are provided to run null models, test for and plot preferences, plot and analyse bipartite networks, and export null model results in a form compatible with other network analysis packages. The underlying null model was developed by Agusti et al. (2003) Molecular Ecology and the full application to ecological networks by Vaughan et al. (2018) econullnetr: an R package using null models to analyse the structure of ecological networks and identify resource selection. Methods in Ecology & Evolution, .

Integrating Data Exchange and Analysis for Networks ('ideanet')

A suite of convenient tools for social network analysis geared toward students, entry-level users, and non-expert practitioners. ‘ideanet’ features unique functions for the processing and measurement of sociocentric and egocentric network data. These functions automatically generate node- and system-level measures commonly used in the analysis of these types of networks. Outputs from these functions maximize the ability of novice users to employ network measurements in further analyses while making all users less prone to common data analytic errors. Additionally, ‘ideanet’ features an R Shiny graphic user interface that allows novices to explore network data with minimal need for coding.