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NetworkToolbox (version 1.3.3)

Methods and Measures for Brain, Cognitive, and Psychometric Network Analysis

Description

Implements network analysis and graph theory measures used in neuroscience, cognitive science, and psychology. Methods include various filtering methods and approaches such as threshold, dependency (Kenett, Tumminello, Madi, Gur-Gershgoren, Mantegna, & Ben-Jacob, 2010 ), Information Filtering Networks (Barfuss, Massara, Di Matteo, & Aste, 2016 ), and Efficiency-Cost Optimization (Fallani, Latora, & Chavez, 2017 ). Brain methods include the recently developed Connectome Predictive Modeling (see references in package). Also implements several network measures including local network characteristics (e.g., centrality), community-level network characteristics (e.g., community centrality), global network characteristics (e.g., clustering coefficient), and various other measures associated with the reliability and reproducibility of network analysis.

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Version

Install

install.packages('NetworkToolbox')

Monthly Downloads

2,175

Version

1.3.3

License

GPL (>= 3.0)

Maintainer

Alexander Christensen

Last Published

January 11th, 2020

Functions in NetworkToolbox (1.3.3)

comm.str

Community Strength/Degree Centrality
desc

Variable Descriptive Statistics
conn

Network Connectivity
desc.all

Dataset Descriptive Statistics
hybrid

Hybrid Centrality
degree

Degree
gateway

Gateway Coefficient
cpm

Connectome Predictive Modeling
closeness

Closeness Centrality
binarize

Binarize Network
convert2igraph

Convert Network(s) to igraph's Format
comm.close

Community Closeness Centrality
MFCF

Maximally Filtered Clique Forest
leverage

Leverage Centrality
edgerep

Edge Replication
cor2cov

Convert Correlation Matrix to Covariance Matrix
core.items

Core Items
sim.chordal

Simulate Chordal Network
network.permutation

Permutation Test for Network Measures
neuralnetfilter

Neural Network Filter
comm.eigen

Community Eigenvector Centrality
sim.swn

Simulate Small-world Network
eigenvector

Eigenvector Centrality
kld

Kullback-Leibler Divergence
lattnet

Generates a Lattice Network
impact

Node Impact
node.multidimensional

Detects Node Crossings in a Network
convertConnBrainMat

Import CONN Toolbox Brain Matrices to R format
depend

Dependency Network Approach
depna

Dependency Neural Networks
participation

Participation Coefficient
smallworldness

Small-worldness Measure
louvain

Louvain Community Detection Algorithm
is.graphical

Determines if Network is Graphical
stable

Stabilizing Nodes
clustcoeff

Clustering Coefficient
threshold

Threshold Network Estimation Methods
strength

Node Strength
transitivity

Transitivity
reg

Regression Matrix
un.direct

Convert Directed Network to Undirected Network
pathlengths

Characteristic Path Lengths
resp.rep

Repeated Responses Check
randnet

Generates a Random Network
comcat

Communicating Nodes
flow.frac

Flow Fraction
diversity

Diversity Coefficient
distance

Distance
gain.functions

MFCF Gain Functions
rmse

Root Mean Square Error
network.coverage

Network Coverage
neoOpen

NEO-PI-3 Openness to Experience Data
rspbc

Randomized Shortest Paths Betweenness Centrality
adapt.a

Adaptive Alpha
betweenness

Betweenness Centrality
MaST

Maximum Spanning Tree
LoGo

Local/Global Inversion Method
ECO

ECO Neural Network Filter
TMFG

Triangulated Maximally Filtered Graph
behavOpen

NEO-PI-3 for Resting-state Data
NetworkToolbox-package

NetworkToolbox--package
ECOplusMaST

ECO+MaST Network Filter