NEWS

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NetworkToolbox 1.4.3

• FIX: 'participation' coefficient values were in the reverse direction
• FIX: 'depend' diagonal fixed to 0 instead of 1

NetworkToolbox 1.4.2 (2021-05-28)

• ADD: full four inventories of openness to experience data from Christensen, Cotter, and Silvia (2019). See '?openness'
• FIX: 'lattnet' for larger networks

NetworkToolbox 1.4.1 (2020-12-07)

• ADD: k-folds validation is now implemented in 'cpmIV'
• NEW: 'cpmIVperm' allows for permutation of 'cpmIV' results
• FIX: NA communities throwing bad labels in 'stable' and 'comcat'
• FIX: 'diversity', 'gateway', and 'participation' bug when communities lengths equal one

NetworkToolbox 1.4.0 (2020-03-08)

• NEW: 'dCor.parallel' parallelizes the 'dCor' function to improve processing speed
• NEW: 'dCor' computes the distance correlation for time series data (intended for use with 'cpm')
• FIX: named communities into 'comcat' and 'stable'
• FIX: where 'comcat' and 'stable' treats 'NA' community membership as actual membership -- corrects 'EGAnet::net.loads' outputs
• FIX: 'comcat' and 'stable' for *EGAnet*

NetworkToolbox 1.3.3 (2020-01-10)

• 'node.redundant' function migrated to the *EGAnet* pacakge
• added the function 'network.permutation' to compute permutation tests for network measures
• changed name of 'net.coverage' to 'network.coverage'

NetworkToolbox 1.3.2 (2019-10-28)

• updated Description file
• updated citation

NetworkToolbox 1.3.1 (2019-09-27)

• 'TMFG' bug fix

NetworkToolbox 1.3.0 (2019-08-21)

• converged all Connectome Predictive Modeling into one documentation see '?cpm'
• migrated ‘net.scores' and 'net.loads' to ’EGAnet' package
• added several new functions to implement the latest state-of-the-art Information Filtering Network method: Maximally Filtered Clique Forest (MFCF; thanks Guido!)
• added Guido Previde Massara as a contributor
• changed name of function 'strength.dim' to 'lnet.loads' and updated documentation
• added information about 'NetworkToolbox' on package load
• changed name of function 'nams' to 'lnet.score', optimized function to be more efficient with large datasets, and updated documentation
• added function 'item.overlap' to detect redundant nodes in a network
• added function 'strength.dim' to identify within and between dimension node strength
• added 'absolute' argument for 'strength' and 'stable' functions (extension for EGA package)
• additional updates to documentation
• bug fix for one dimension in comcat function
• made 'rspbc' output a vector

NetworkToolbox 1.2.3 (2019-01-31)

• removed isSym function
• fixed bugs in degree, strength, hybrid, and edgerep functions (symmetric matrix check is fixed)
• naming order bug fix in comcat
• removed bootgen and bootgen.plot functions (experimental funcitons that may return later)
• updated several functions' documentation

NetworkToolbox 1.2.2 (2018-11-01)

• comcat: added functionality to compute connectivity across communities or for each community
• stable: added closeness centrality
• desc: descriptive statistics function for a single variable
• desc.all: descriptive statistics function for a dataset

NetworkToolbox 1.2.1 (2018-09-19)

• updated comm.close algorithm: takes the reciprocal of the mean ASPL of each community
• LoGo: removed some arguments, added "..." for deprecated arguments (e.g., standardize)
• rep.resp: function to detect repetitive responding

NetworkToolbox 1.2.0 (2018-07-25)

• net.coverage: a function to examine the coverage of a subset of nodes in the network
• comm.close: a function to estimate the closeness centrality of communities in the network
• comm.eigen: a function to estimate the eigenvector centrality of communities in the network (based on the flow.frac function)
• comm.str: a function to estimate the strength/degree centrality of communities in the network
• flow.frac: a function to estimate the eigenvector centrality of a subset of nodes in the network
• core.items: a function to automatically determine core, intermediate, and peripheral items in the network
• commboot: removed
• removed splitsamp functions (will be brought back in a future update)
• removed options for weighted argument in network construction functions
• bootgenPlot changed to bootgen.plot
• significantly improved documentation and descriptions of all functions
• improved functionality of several functions
• updated citation

NetworkToolbox 1.1.3

• nams: facet means are now adjusted relative to the overall score--improves estimate and makes adjusted means/sums equivalent to overall adjusted score
• edgerep: node label bug fixed
• bootstrapped functions: na.data argument bug fixed
• commboot: unweighted network option added
• updated citation
• semnetboot: removed and moved to package SemNetToolbox
• semnetmeas: removed and moved to package SemNetToolbox
• na.data bugs fixed throughout package

NetworkToolbox 1.1.2 (2018-04-29)

• bootgen: ensures graphical model for method = "LoGo"
• nams: adjusted algorithm
• sim.swn: added a function to simulate small-world networks and data
• PMFG: removed function due to inefficiency
• diversity: added a function to compute the diversity coefficient of nodes in the network
• gateway: added a function to compute the gateway coefficient of nodes in the network
• participation: added a function to compute the participation coefficient of nodes in the network
• 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
• nams: added output for an overall network adjusted mean/sum score
• improved documentation
• added EBICglasso and Isingfit to bootgen and commboot function
• added back the kld and rmse function
• added network visualization of canonical and macro-scale region connectivity to cpmIV function
• 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)

NetworkToolbox 1.1.1 (2018-03-25)

• LoGo: reversed sign bug fixed; cov.shrink no longer used for covariance matrix estimation
• is.graphical: updated with more efficient (inverse) covariance check
• bootgen: uses partial correlation significance for method = "LoGo"

NetworkToolbox 1.1.0 (2018-03-21)

• 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
• bootgen: no longer produces plots; added is.graphical function to automatically check if network is graphical when method = "LoGo"
• 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
• bootstrapping functions all include a seeds argument, which can be used to replicate the previous analysis using the Seeds output
• PMFG: now outputs a list to be used in Cytoscape visualization software (sparseList)
• reg: a function to perform regression for a dataset. An argument can set the type of regression and for the matrix to be symmetric
• nams: a function to calculate network adjusted mean or sum for data (based on the hybrid centrality)
• hybrid: added an option for "standard", "random", or "average" betweenness centrality to be used
• cpmIV: parallel processing now available for covariate estimation (defaults to max(cores) - 1)
• LoGo: corpcor's cov.shrink is now used for covariance estimation when argument normal = TRUE; added argument to check if network is graphical
• 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
• is.graphical: function to check whether the network is graphical
• cor2cov: function to convert correlation matrix into a covariance matrix
• depend: fixed Fisher's z significance test
• kld: removed function