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