Changes in Version 1.6 - Changed the way the pairwise, minimum and maximum sample sizes are computed for estimators using a correlation matrix as input with missing data. Thanks to Carl Falk. This might lead to different results compared to older bootnet versions! To recover old results, use the "pairwise_average_v1.5", "pairwise_minimum_v1.5", and "pairwise_maximum_v1.5" arguments in the sampleSize argument of the default functions. Changes in Version 1.5.6 - Included min_sum argument in the IsingFit default Changes in Version 1.5.5 - Small help file fix Changes in Version 1.5.4 - IsingSampler default set now always uses method = "uni" by default - Added min_sum and threshold options to defailt = "IsingSampler" - Fixed a small problem in the bootnet package help file Changes in Version 1.5.3 - Improved support for estimation functions with multiple networks of multiple types Changes in Version 1.5.2 - Fixed links in README.md Changes in Version 1.5.1 - Changed CRAN NOTE regarding class check - Fixed remaining deprecated dplyr functions - Fixed a bug with netSimulator and replicationSimulator print method Changes in Version 1.5 - Fixed a bug with bridge centrality indices being incorrectly labeled - Fixed a bug with that occured when using order = "sample" together with the subset argument - Removed calls to deprecated dplyr functions Changes in Version 1.4.7 - 'binarize' now makes values above the split 1 instead of below the split - The bootnet plot method now shows values for all centrality metrics when plotting difference tests. - the mgm default for tuning now defaults to 0.25 - Fixed a bug with bridge centrality indices being incorrectly labeled Changes in Version 1.4.6 - bootnet() now no longer re-estimates the network if the input is a bootnetResult - Several packages are now listed under Suggests instead of Imports - Included support for the GGMncv package Changes in Version 1.4.4 - Fixed a critical error when using multiple cores in R 4.0 on Mac Changes in Version 1.4 - Added the transformation functions 'quantile_transformation' and 'rank_transformation' - Several default sets now use corMethod = "cor" rather than corMethod = "cor_auto" by default! - Fixed a bug in case-drop bootstrap plotting method - "Sampled people" is now "Sampled cases" - Removed adalasso dependency due to CRAN removal - Added 'multiverse' function for multiverse-plots of bootstrap results Changes in Version 1.3 - Added the options pairwise_maximum, pairwise_minimum and pairwise_average to the sampleSize argument of several default functions - Old functionality in estimateNetwork and bootnet has been removed! This includes graphFun, estFun etcetera. - Some changes that lead to NEW DEFAULT BEHAVIOR: - Added the argument 'nonPositiveDefinite' to several default estimators, which will stop with an error when the input is different. - The sampleSize argument now defaults to "pairwise_average"! - All default functions are now by default locked unless used from within estimateNetwork - The plot method now better scales a margin on the top and bottom of the plot - ggmGenerator now generates thresholds more consistently, leading to unfiform data by default or skewed data if the 'skewFactor' argument is used - ggmGenerator can now simulate missing data using the 'missing' argument - corMethod = "spearman" is now supported in several default sets - Fixed a bug with BDgraph change in genGGM function Changes in Version 1.2.4 - Resolved a bug with expected influence crashing bootnet when empty networks were estimated Changes in Version 1.2.3 - More informative error when statistics are not included in the plot. - Updated psych to psychTools Changes in Version 1.2.2 - Added 'adjacency' argument to pcor default set, which allows for estimating a network with a fixed structure. - Fixed parametric bootstrapping Changes in Version 1.2.1 - corStability should now return the non-finite values warning less often Changes in Version 1.2 o New features: - Added support for statistics "bridgeStrength", "bridgeCloseness", "bridgeBetweenness", and "bridgeExpectedInfluence". Thanks to Payton Jones! - The statistics argument in bootnet can now be "all" - Added bootThreshold function to threshold a network based on bootstraps (e.g., bootstrapped interval includes 0) - Added bootInclude function to obtain a network of bootstrap inclusion probabilities - the 'statistics' argument in bootnet now defaults to c("edge","strength","outStrength","inStrength"). This means that closeness and betweenness are no longer stored by default! - corStability will now use all tested statistics by default o Updates: - The corStability function now accepts statistics written with an upper case first letter - Fixed a bug using default = "mgm" with only one binary variable - IsingFit and IsingSampler defaults now transform -1, 1 data to 0, 1 when computing network, then back when returning results - Included the 'includeDiagonal' argument to bootnet to include storing diagonal entries (self-loops) for directed networks only - Bootnet now copies the library used by the user to the clusters when using nCores > 1. This is important for checkpoint and packrat compatability - corStability now returns NA for incomputable correlations (e.g., due to infinite values) o Experimental: - Added default set "piecewiseIsing" for estimating Ising models while selecting participants on a sum-score (very experimental) - Added default set "SVAR_lavaan" for step-up structural VAR model selection using Lavaan (experimental) Changes in Version 1.1 - New supported default sets: - "cor" - Correlation networks - "TMFG" - Triangulated Maximally Filtered Graph - "LoGo"- Local/Global Sparse Inverse Covariance Matrix - "ggmModSelect" - Unregularized stepwise GGM model selection - "graphicalVAR" - LASSO regularized graphical VAR models - Some changes to mgm default: - mgm version >= 1.2 is now required - Renamed lev to level - Renamed degree to order, now defaults to 2 instead of 3 - Added binarySign argument. Now chosen by defult. - Added the 'replicationSimulator' function, which can be used to assess expected replicability of networks - Many default sets now support the 'principalDirection' argument, which can be used to multiply variables with the sign of the first principal component - plot method now supports split0 = TRUE, will show how often an edge was 0 and only show CIs of non-zero estimates (faded relative to proportion of times edge was zero). - Updated the 'genGGM' function to support various different network structures, with thanks to Mark Brandt! - Added RSPBC and Hybrid centrality, thanks to Alex Christensen - Added the 'alpha' argument to default set "pcor" - Added functionality for functions returning multiple graphs - Added outStrength, inStrength, outExpectedInfluence and inExpectedInfluence - Fixed a bug reporting the number of non-zero edges in the print methods - Added 'args' argument to netSimulator - Fixed a bug in which fun is not usuable in bootnet() - Added lambda.min.ratio argument to some estimators. Now defaults to 0.01 for default = "huge" - bootnet and netSimulator now show a progress bar (thanks to pbapply package) - plot method now shows bootstrapped mean in addition to sample value - The 'statistics' argument in bootnet and plot method now accept statistics with a upper case first letter, to be consistent with qgraph - CIstyle argument can now only be one value, and always defaults to quantiles Changes in Version 1.0.1 - missing = "fiml" is now supported for EBICglasso and pcor default sets - Relative importance networks now do not crash when the number of predictors is 0 or 1 - plotting bootnetResults now supports the labels argument - mgm default now uses matrices to resolve an error with the latest version of mgm - The plot method of networks estimated using 'estimateNetwork' now uses different defaults than qgraph! - cut defaults to NULL - theme defaults to "colorblind" - parallelEdge defaults to TRUE - layout always defaults to "spring" (rather than "circle" for undirected networks) Changes in Version 1.0.0: - Implemented the netSimulator function that allows for researchers to investigate sample size requirements and input arguments to estimateNetwork - Added genGGM, ggmGenerator, and IsingGenerator functions to be used in netSimulator - bootnet now stores less results and should have better memory usuage! Thanks to Giulio Costantini! - Fixed some bugs related to manual parametric bootstrap - EstimateNetwork now references packages used in a message - pcor default set now supports the argument 'threshold' - Fixed a bug where rule argument was not passed in bootnet default set - Bootnet now supports directed networks - Relative importance networks now implemented using default = "relimp" - Updated compatibility with MGM version 1.2.0 Changes in version 0.4: - estimateNetwork now accepts a custom estimation function using the argument 'fun' - Reworked default sets as functions! - This makes it easier to change common arguments, such as the EBIC tuning parameter - See the following functions for details: - bootnet_EBICglasso - bootnet_IsingFit - The corStability function now has a greatly improved output - Default set "IsingLL" has been renamed to "IsingSampler" - Default set "mgm" is now supported - labels argument is now supported in difference plots - Quantile now uses type = 6, this makes CIs slightly wider and therefore the difference test slightly more conservative Changes in version 0.3: - Eiko Fried joined the author list - Added 'estimateNetwork' function, allowing one to estimate the network structure from within bootnet - The plot method will run qgraph on the estimated network structure - The qgraph function getWmat can now be applied to networks estimated in bootnet. Allowing one to use, e.g., centralityPlot on a network estimated with 'estimateNetwork' - Added 'differenceTest' function to test for significant differences between edge weights and centrality indices - Added 'corStability' to compute the CS-coefficient as described in our paper: - Epskamp, S., Borsboom, D., & Fried, E. I. (2016). Estimating psychological networks and their accuracy: a tutorial paper. arXiv preprint, arXiv:1604.08462. - The plot method now supports 'plot = "difference"', to make plots of significant differences between edge-weights and centralities - New default sets: - "huge" - "adalasso" - 'nCores' argument added to bootnet to use parallel computing - bootnet print methods now print a list of relevant references on the network estimation procedure used - When EBICglasso is used as default set, variables that are made ordinal are now printed only when estimating the first network - Updated CITATION such that citation("bootnet") now references the pre-print - Bootnet now gives a message on loading that it is BETA software - Added 'statistics' argument to bootnet. Now, distance and length are not stored by default - Several minor bugfixes