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NetworkToolbox (version 1.2.2)

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

2,053

Version

1.2.2

License

GPL (>= 3.0)

Maintainer

Alexander Christensen

Last Published

November 1st, 2018

Functions in NetworkToolbox (1.2.2)

adapt.a

Adaptive Alpha
comcat

Communicating Nodes
clustcoeff

Clustering Coefficient
degree

Degree
depend

Dependency Network Approach
ECO

ECO Neural Network Filter
diversity

Diversity Coefficient
ECOplusMaST

ECO+MaST Network Filter
edgerep

Edge Replication
reg

Regression Matrix
resp.rep

Repeated Responses Check
comm.str

Community Strength/Degree Centrality
conn

Network Connectivity
cpmEV

Connectome-based Predictive Modeling--External Validation
cpmFP

Connectome-based Predictive Modeling--Fingerprinting
eigenvector

Eigenvector Centrality
flow.frac

Flow Fraction
isSym

isSymmetric Wrapper Function
pathlengths

Characteristic Path Lengths
kld

Kullback-Leibler Divergence
randnet

Generates a Random Network
LoGo

Local/Global Sparse Inverse Covariance Matrix
MaST

Maximum Spanning Tree
stable

Stabilizing Nodes
bootgen

Bootstrapped Network Generalization
strength

Node Strength
bootgen.plot

Bootstrapped Network Generalization Plots
cpmFPperm

Connectome-based Predictive Modeling--Fingerprinting Permutation
desc.all

Dataset Descriptive Statisitcs
louvain

Louvain Community Detection Algorithm
distance

Distance
cpmIV

Connectome-based Predictive Modeling--Internal Validation
nams

Network Adjusted Mean/Sum
threshold

Threshold Filter
transitivity

Transitivity
betweenness

Betwenness Centrality
binarize

Binarize Network
centlist

List of Centrality Measures
closeness

Closeness Centrality
NetworkToolbox-package

NetworkToolbox--package
cor2cov

Convert Correlation Matrix to Covariance Matrix
TMFG

Triangulated Maximally Filtered Graph
comm.close

Community Closeness Centrality
comm.eigen

Community Eigenvector Centrality
core.items

Core Items
convert2igraph

Convert Network(s) to igraph's Format
gateway

Gateway Coefficient
convertConnBrainMat

Import CONN Toolbox Brain Matrices to R format
impact

Node Impact
is.graphical

Determines if Network is Graphical
rmse

Root Mean Square Error
desc

Variable Descriptive Statisitcs
depna

Dependency Neural Networks
hybrid

Hybrid Centrality
rspbc

Randomized Shortest Paths Betweenness Centrality
neoOpen

NEO-PI-3 Openness to Experience Data
net.coverage

Network Coverage
lattnet

Generates a Lattice Network
leverage

Leverage Centrality
sim.swn

Simulate Small-world Network
neuralnetfilter

Neural Network Filter
smallworldness

Small-worldness Measure
participation

Participation Coefficient
behavOpen

NEO-PI-3 for Resting-state Data