Package: NetworkToolbox 1.4.3

NetworkToolbox: Methods and Measures for Brain, Cognitive, and Psychometric Network Analysis

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 <doi:10.1371/journal.pone.0015032>), Information Filtering Networks (Barfuss, Massara, Di Matteo, & Aste, 2016 <doi:10.1103/PhysRevE.94.062306>), and Efficiency-Cost Optimization (Fallani, Latora, & Chavez, 2017 <doi:10.1371/journal.pcbi.1005305>). 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.

Authors:Alexander Christensen [aut, cre], Guido Previde Massara [ctb]

NetworkToolbox_1.4.3.tar.gz
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NetworkToolbox.pdf |NetworkToolbox.html✨
NetworkToolbox/json (API)
NEWS

# Install 'NetworkToolbox' in R:

install.packages('NetworkToolbox', repos = c('https://alexchristensen.r-universe.dev', 'https://cloud.r-project.org'))

Bug tracker:https://github.com/alexchristensen/networktoolbox/issues

Datasets:

behavOpen - NEO-PI-3 for Resting-state Data
neoOpen - NEO-PI-3 Openness to Experience Data
openness - Four Inventories of Openness to Experience
openness.key - Four Inventories of Openness to Experience

On CRAN:

network-analysis

66 exports 21 stars 2.87 score 102 dependencies 3 dependents 4 mentions 97 scripts 1.5k downloads

Last updated 2 years agofrom:3fe11eb753. Checks:OK: 1 NOTE: 6. Indexed: yes.

Target	Result	Date
Doc / Vignettes	OK	Aug 28 2024
R-4.5-win	NOTE	Aug 28 2024
R-4.5-linux	NOTE	Aug 28 2024
R-4.4-win	NOTE	Aug 28 2024
R-4.4-mac	NOTE	Aug 28 2024
R-4.3-win	NOTE	Aug 28 2024
R-4.3-mac	NOTE	Aug 28 2024

Exports:adapt.a betweenness binarize closeness clustcoeff comcat comm.close comm.eigen comm.str conn convert2igraph convertConnBrainMat cor2cov core.items cpmEV cpmFP cpmFPperm cpmIV cpmIVperm cpmPlot dCor dCor.parallel degree depend depna desc desc.all distance diversity ECO ECOplusMaST edgerep eigenvector flow.frac gateway gfcnv_logdet hybrid impact is.graphical kld lattnet leverage LoGo louvain MaST MFCF net.coverage network.coverage network.permutation neuralnetfilter participation pathlengths randnet reg resp.rep rmse rspbc sim.chordal sim.swn smallworldness stable strength threshold TMFG transitivity un.direct

Dependencies:abind backports base64enc bslib cachem checkmate cli cluster codetools colorspace corpcor corrplot cpp11 data.table digest doParallel evaluate fansi farver fastmap fdrtool fontawesome foreach foreign Formula fs ggplot2 glasso glmnet glue GPArotation gridExtra gtable gtools highr Hmisc htmlTable htmltools htmlwidgets igraph IsingFit isoband iterators jpeg jquerylib jsonlite knitr labeling lattice lavaan lifecycle magrittr MASS Matrix memoise mgcv mime mnormt munsell nlme nnet numDeriv pbapply pbivnorm pillar pkgconfig plyr png ppcor psych pwr qgraph quadprog R.matlab R.methodsS3 R.oo R.utils R6 rappdirs RColorBrewer Rcpp RcppEigen reshape2 rlang rmarkdown rpart rstudioapi sass scales shape stringi stringr survival tibble tinytex utf8 vctrs viridis viridisLite withr xfun yaml

Help page	Topics
NetworkToolbox-package	NetworkToolbox-package NetworkToolbox
Adaptive Alpha	adapt.a
NEO-PI-3 for Resting-state Data	behavOpen
Betweenness Centrality	betweenness
Binarize Network	binarize
Closeness Centrality	closeness
Clustering Coefficient	clustcoeff
Communicating Nodes	comcat
Community Closeness Centrality	comm.close
Community Eigenvector Centrality	comm.eigen
Community Strength/Degree Centrality	comm.str
Network Connectivity	conn
Convert Network(s) to igraph's Format	convert2igraph
Import CONN Toolbox Brain Matrices to R format	convertConnBrainMat
Convert Correlation Matrix to Covariance Matrix	cor2cov
Core Items	core.items
Connectome-based Predictive Modeling	cpm cpmEV cpmFP cpmFPperm cpmIV cpmIVperm cpmPlot
Distance Correlation for ROI Time Series	dCor
Parallelization of Distance Correlation for ROI Time Series	dCor.parallel
Degree	degree
Dependency Network Approach	depend
Dependency Neural Networks	depna
Variable Descriptive Statistics	desc
Dataset Descriptive Statistics	desc.all
Distance	distance
Diversity Coefficient	diversity
ECO Neural Network Filter	ECO
ECO+MaST Network Filter	ECOplusMaST
Edge Replication	edgerep
Eigenvector Centrality	eigenvector
Flow Fraction	flow.frac
MFCF Gain Functions	gain.functions gdcnv_lmfit gfcnv_logdet gfcnv_logdet_val
Gateway Coefficient	gateway
Hybrid Centrality	hybrid
Node Impact	impact
Determines if Network is Graphical	is.graphical
Kullback-Leibler Divergence	kld
Generates a Lattice Network	lattnet
Leverage Centrality	leverage
Local/Global Inversion Method	LoGo
Louvain Community Detection Algorithm	louvain
Maximum Spanning Tree	MaST
Maximally Filtered Clique Forest	MFCF
NEO-PI-3 Openness to Experience Data	neoOpen
Network Coverage	net.coverage
Network Coverage	network.coverage
Permutation Test for Network Measures	network.permutation
Neural Network Filter	neuralnetfilter
Four Inventories of Openness to Experience	openness openness.key
Participation Coefficient	participation
Characteristic Path Lengths	pathlengths
Plots CPM results	plot.cpm
Generates a Random Network	randnet
Regression Matrix	reg
Repeated Responses Check	resp.rep
Root Mean Square Error	rmse
Randomized Shortest Paths Betweenness Centrality	rspbc
Simulate Chordal Network	sim.chordal
Simulate Small-world Network	sim.swn
Small-worldness Measure	smallworldness
Stabilizing Nodes	stable
Node Strength	strength
Threshold Network Estimation Methods	threshold
Triangulated Maximally Filtered Graph	TMFG
Transitivity	transitivity
Convert Directed Network to Undirected Network	un.direct

Package: NetworkToolbox 1.4.3

NetworkToolbox: Methods and Measures for Brain, Cognitive, and Psychometric Network Analysis

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