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NetworkToolbox (version 1.4.0)

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

1.4.0

License

GPL (>= 3.0)

Maintainer

Alexander Christensen

Last Published

March 8th, 2020

Functions in NetworkToolbox (1.4.0)

ECO

ECO Neural Network Filter
adapt.a

Adaptive Alpha
TMFG

Triangulated Maximally Filtered Graph
ECOplusMaST

ECO+MaST Network Filter
NetworkToolbox-package

NetworkToolbox--package
behavOpen

NEO-PI-3 for Resting-state Data
betweenness

Betweenness Centrality
convert2igraph

Convert Network(s) to igraph's Format
MaST

Maximum Spanning Tree
convertConnBrainMat

Import CONN Toolbox Brain Matrices to R format
comm.close

Community Closeness Centrality
comm.str

Community Strength/Degree Centrality
core.items

Core Items
impact

Node Impact
cor2cov

Convert Correlation Matrix to Covariance Matrix
desc

Variable Descriptive Statistics
conn

Network Connectivity
desc.all

Dataset Descriptive Statistics
hybrid

Hybrid Centrality
gateway

Gateway Coefficient
neoOpen

NEO-PI-3 Openness to Experience Data
degree

Degree
comm.eigen

Community Eigenvector Centrality
dCor.parallel

Parallelization of Distance Correlation for ROI Time Series
flow.frac

Flow Fraction
is.graphical

Determines if Network is Graphical
network.coverage

Network Coverage
LoGo

Local/Global Inversion Method
depend

Dependency Network Approach
MFCF

Maximally Filtered Clique Forest
binarize

Binarize Network
closeness

Closeness Centrality
gain.functions

MFCF Gain Functions
randnet

Generates a Random Network
pathlengths

Characteristic Path Lengths
kld

Kullback-Leibler Divergence
clustcoeff

Clustering Coefficient
dCor

Distance Correlation for ROI Time Series
cpm

Connectome Predictive Modeling
edgerep

Edge Replication
network.permutation

Permutation Test for Network Measures
eigenvector

Eigenvector Centrality
comcat

Communicating Nodes
neuralnetfilter

Neural Network Filter
lattnet

Generates a Lattice Network
depna

Dependency Neural Networks
node.multidimensional

Detects Node Crossings in a Network
distance

Distance
diversity

Diversity Coefficient
louvain

Louvain Community Detection Algorithm
smallworldness

Small-worldness Measure
leverage

Leverage Centrality
rmse

Root Mean Square Error
stable

Stabilizing Nodes
threshold

Threshold Network Estimation Methods
strength

Node Strength
reg

Regression Matrix
participation

Participation Coefficient
sim.chordal

Simulate Chordal Network
sim.swn

Simulate Small-world Network
transitivity

Transitivity
un.direct

Convert Directed Network to Undirected Network
rspbc

Randomized Shortest Paths Betweenness Centrality
resp.rep

Repeated Responses Check