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NetworkToolbox (version 1.4.2)

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-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

2,015

Version

1.4.2

License

GPL (>= 3.0)

Last Published

May 28th, 2021

Functions in NetworkToolbox (1.4.2)

LoGo

Local/Global Inversion Method
adapt.a

Adaptive Alpha
ECO

ECO Neural Network Filter
TMFG

Triangulated Maximally Filtered Graph
MaST

Maximum Spanning Tree
MFCF

Maximally Filtered Clique Forest
behavOpen

NEO-PI-3 for Resting-state Data
ECOplusMaST

ECO+MaST Network Filter
betweenness

Betweenness Centrality
NetworkToolbox-package

NetworkToolbox--package
comm.str

Community Strength/Degree Centrality
desc.all

Dataset Descriptive Statistics
desc

Variable Descriptive Statistics
convertConnBrainMat

Import CONN Toolbox Brain Matrices to R format
convert2igraph

Convert Network(s) to igraph's Format
dCor.parallel

Parallelization of Distance Correlation for ROI Time Series
clustcoeff

Clustering Coefficient
core.items

Core Items
comcat

Communicating Nodes
degree

Degree
cor2cov

Convert Correlation Matrix to Covariance Matrix
gateway

Gateway Coefficient
impact

Node Impact
is.graphical

Determines if Network is Graphical
comm.close

Community Closeness Centrality
neuralnetfilter

Neural Network Filter
distance

Distance
cpm

Connectome-based Predictive Modeling
comm.eigen

Community Eigenvector Centrality
dCor

Distance Correlation for ROI Time Series
diversity

Diversity Coefficient
leverage

Leverage Centrality
louvain

Louvain Community Detection Algorithm
closeness

Closeness Centrality
edgerep

Edge Replication
binarize

Binarize Network
openness

Four Inventories of Openness to Experience
depend

Dependency Network Approach
conn

Network Connectivity
network.permutation

Permutation Test for Network Measures
plot.cpm

Plots CPM results
network.coverage

Network Coverage
rmse

Root Mean Square Error
lattnet

Generates a Lattice Network
hybrid

Hybrid Centrality
kld

Kullback-Leibler Divergence
rspbc

Randomized Shortest Paths Betweenness Centrality
sim.chordal

Simulate Chordal Network
sim.swn

Simulate Small-world Network
depna

Dependency Neural Networks
randnet

Generates a Random Network
stable

Stabilizing Nodes
smallworldness

Small-worldness Measure
net.coverage

Network Coverage
eigenvector

Eigenvector Centrality
participation

Participation Coefficient
strength

Node Strength
pathlengths

Characteristic Path Lengths
neoOpen

NEO-PI-3 Openness to Experience Data
threshold

Threshold Network Estimation Methods
flow.frac

Flow Fraction
gain.functions

MFCF Gain Functions
reg

Regression Matrix
transitivity

Transitivity
resp.rep

Repeated Responses Check
un.direct

Convert Directed Network to Undirected Network