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NetworkToolbox (version 1.3.2)

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-Gershogoren, 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

3,385

Version

1.3.2

License

GPL (>= 3.0)

Maintainer

Alexander Christensen

Last Published

October 28th, 2019

Functions in NetworkToolbox (1.3.2)

binarize

Binarize Network
comm.eigen

Community Eigenvector Centrality
depna

Dependency Neural Networks
depend

Dependency Network Approach
comm.close

Community Closeness Centrality
impact

Node Impact
MFCF

Maximally Filtered Clique Forest
is.graphical

Determines if Network is Graphical
gain.functions

MFCF Gain Functions
flow.frac

Flow Fraction
leverage

Leverage Centrality
closeness

Closeness Centrality
comcat

Communicating Nodes
clustcoeff

Clustering Coefficient
cpm

Connectome Predictive Modeling
diversity

Diversity Coefficient
edgerep

Edge Replication
neoOpen

NEO-PI-3 Openness to Experience Data
distance

Distance
eigenvector

Eigenvector Centrality
net.coverage

Network Coverage
neuralnetfilter

Neural Network Filter
degree

Degree
gateway

Gateway Coefficient
conn

Network Connectivity
cor2cov

Convert Correlation Matrix to Covariance Matrix
comm.str

Community Strength/Degree Centrality
convertConnBrainMat

Import CONN Toolbox Brain Matrices to R format
convert2igraph

Convert Network(s) to igraph's Format
desc.all

Dataset Descriptive Statistics
desc

Variable Descriptive Statistics
kld

Kullback-Leibler Divergence
core.items

Core Items
lattnet

Generates a Lattice Network
pathlengths

Characteristic Path Lengths
louvain

Louvain Community Detection Algorithm
sim.chordal

Simulate Chordal Network
sim.swn

Simulate Small-world Network
node.multidimensional

Detects Node Crossings in a Network
resp.rep

Repeated Responses Check
participation

Participation Coefficient
reg

Regression Matrix
node.redundant

Detects Redundant Nodes in a Network
hybrid

Hybrid Centrality
threshold

Threshold Network Estimation Methods
strength

Node Strength
randnet

Generates a Random Network
smallworldness

Small-worldness Measure
rmse

Root Mean Square Error
transitivity

Transitivity
rspbc

Randomized Shortest Paths Betweenness Centrality
un.direct

Convert Directed Network to Undirected Network
stable

Stabilizing Nodes
MaST

Maximum Spanning Tree
ECOplusMaST

ECO+MaST Network Filter
behavOpen

NEO-PI-3 for Resting-state Data
betweenness

Betweenness Centrality
TMFG

Triangulated Maximally Filtered Graph
LoGo

Local/Global Inversion Method
adapt.a

Adaptive Alpha
NetworkToolbox-package

NetworkToolbox--package
ECO

ECO Neural Network Filter