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
Changes in version 1.2.3
o removed isSym function
o fixed bugs in degree, strength, hybrid, and edgerep functions (symmetric matrix check is fixed)
o naming order bug fix in comcat
o removed bootgen and bootgen.plot functions (experimental funcitons that may return later)
o updated several functions' documentation
Changes in version 1.2.2
o comcat: added functionality to compute connectivity across communities or for each community
o stable: added closeness centrality
o desc: descriptive statistics function for a single variable
o desc.all: descriptive statistics function for a dataset
Changes in version 1.2.1
o updated comm.close algorithm: takes the reciprocal of the mean ASPL of each community
o LoGo: removed some arguments, added "..." for deprecated arguments (e.g., standardize)
o rep.resp: function to detect repetitive responding
Changes in version 1.2.0
o net.coverage: a function to examine the coverage of a subset of nodes in the network
o comm.close: a function to estimate the closeness centrality of communities in the network
o comm.eigen: a function to estimate the eigenvector centrality of communities in the network (based on the flow.frac function)
o comm.str: a function to estimate the strength/degree centrality of communities in the network
o flow.frac: a function to estimate the eigenvector centrality of a subset of nodes in the network
o core.items: a function to automatically determine core, intermediate, and peripheral items in the network
o commboot: removed
o removed splitsamp functions (will be brought back in a future update)
o removed options for weighted argument in network construction functions
o bootgenPlot changed to bootgen.plot
o significantly improved documentation and descriptions of all functions
o improved functionality of several functions
o updated citation
Changes in version 1.1.3
o nams: facet means are now adjusted relative to the overall score--improves estimate and makes adjusted means/sums equivalent to overall adjusted score
o edgerep: node label bug fixed
o bootstrapped functions: na.data argument bug fixed
o commboot: unweighted network option added
o updated citation
o semnetboot: removed and moved to package SemNetToolbox
o semnetmeas: removed and moved to package SemNetToolbox
o na.data bugs fixed throughout package
Changes in version 1.1.2
o bootgen: ensures graphical model for method = "LoGo"
o nams: adjusted algorithm
o sim.swn: added a function to simulate small-world networks and data
o PMFG: removed function due to inefficiency
o diversity: added a function to compute the diversity coefficient of nodes in the network
o gateway: added a function to compute the gateway coefficient of nodes in the network
o participation: added a function to compute the participation coefficient of nodes in the network
o edgerep: fixed bug in plot to display the strength of the replicated edges only and will display diagonal if diagonals are equivalent between the two matrices
o nams: added output for an overall network adjusted mean/sum score
o improved documentation
o added EBICglasso and Isingfit to bootgen and commboot function
o added back the kld and rmse function
o added network visualization of canonical and macro-scale region connectivity to cpmIV function
o LoGo: no longer outputs a list (only a matrix) and added a standardize argument for inverse correlation matrix as output (does not change partial correlation output)
Changes in Version 1.1.1
o LoGo: reversed sign bug fixed; cov.shrink no longer used for covariance matrix estimation
o is.graphical: updated with more efficient (inverse) covariance check
o bootgen: uses partial correlation significance for method = "LoGo"
Changes in Version 1.1.0
o new data files: NEO-PI-3 data for psychometric network analysis, verbal fluency files for semantic network analysis, behavioral NEO-PI-3 and an associated brain connectivity array for brain network analysis
o bootgen: no longer produces plots; added is.graphical function to automatically check if network is graphical when method = "LoGo"
o bootgenPlot: output from the bootgen function can now be input into a separate function to obtain plots. Contains an argument to also plot the bootstrapped network generalization method
o bootstrapping functions all include a seeds argument, which can be used to replicate the previous analysis using the Seeds output
o PMFG: now outputs a list to be used in Cytoscape visualization software (sparseList)
o reg: a function to perform regression for a dataset. An argument can set the type of regression and for the matrix to be symmetric
o nams: a function to calculate network adjusted mean or sum for data (based on the hybrid centrality)
o hybrid: added an option for "standard", "random", or "average" betweenness centrality to be used
o cpmIV: parallel processing now available for covariate estimation (defaults to max(cores) - 1)
o LoGo: corpcor's cov.shrink is now used for covariance estimation when argument normal = TRUE; added argument to check if network is graphical
o edgerep: includes a list of the replicated edges and their respective weights in each network. A plot for this information is also available (defaults to FALSE). Also includes an argument "corr" which allows the researcher to select different correlations for examining replicated edge weight relations
o is.graphical: function to check whether the network is graphical
o cor2cov: function to convert correlation matrix into a covariance matrix
o depend: fixed Fisher's z significance test
o kld: removed function