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NetworkToolbox (version 1.2.3)

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-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

1.2.3

License

GPL (>= 3.0)

Maintainer

Alexander Christensen

Last Published

January 31st, 2019

Functions in NetworkToolbox (1.2.3)

depna

Dependency Neural Networks
centlist

List of Centrality Measures
ECOplusMaST

ECO+MaST Network Filter
binarize

Binarize Network
gateway

Gateway Coefficient
hybrid

Hybrid Centrality
desc

Variable Descriptive Statisitcs
comm.str

Community Strength/Degree Centrality
behavOpen

NEO-PI-3 for Resting-state Data
nams

Network Adjusted Mean/Sum
convert2igraph

Convert Network(s) to igraph's Format
neoOpen

NEO-PI-3 Openness to Experience Data
clustcoeff

Clustering Coefficient
convertConnBrainMat

Import CONN Toolbox Brain Matrices to R format
conn

Network Connectivity
comm.close

Community Closeness Centrality
comcat

Communicating Nodes
closeness

Closeness Centrality
cpmEV

Connectome-based Predictive Modeling--External Validation
cor2cov

Convert Correlation Matrix to Covariance Matrix
core.items

Core Items
degree

Degree
cpmFP

Connectome-based Predictive Modeling--Fingerprinting
comm.eigen

Community Eigenvector Centrality
depend

Dependency Network Approach
cpmIV

Connectome-based Predictive Modeling--Internal Validation
cpmFPperm

Connectome-based Predictive Modeling--Fingerprinting Permutation
impact

Node Impact
diversity

Diversity Coefficient
edgerep

Edge Replication
is.graphical

Determines if Network is Graphical
eigenvector

Eigenvector Centrality
flow.frac

Flow Fraction
randnet

Generates a Random Network
reg

Regression Matrix
leverage

Leverage Centrality
louvain

Louvain Community Detection Algorithm
participation

Participation Coefficient
pathlengths

Characteristic Path Lengths
rspbc

Randomized Shortest Paths Betweenness Centrality
sim.swn

Simulate Small-world Network
kld

Kullback-Leibler Divergence
lattnet

Generates a Lattice Network
smallworldness

Small-worldness Measure
stable

Stabilizing Nodes
transitivity

Transitivity
net.coverage

Network Coverage
desc.all

Dataset Descriptive Statisitcs
distance

Distance
neuralnetfilter

Neural Network Filter
resp.rep

Repeated Responses Check
rmse

Root Mean Square Error
strength

Node Strength
threshold

Threshold Network Estimation Methods
ECO

ECO Neural Network Filter
LoGo

MaST

Maximum Spanning Tree
NetworkToolbox-package

NetworkToolbox--package
adapt.a

Adaptive Alpha
TMFG

Triangulated Maximally Filtered Graph
betweenness

Betweenness Centrality