Changes in version 1.8 (2026-03-19) o Updated nonconvex regularization to use mantar instead of GGMncv o Added multiple imputation as a missing data handling option for cross-sectional network analysis via the new cor_mantar functionality o Added nodewise regression with information-criterion based model selection as a method for estimating GGM network Changes in version 1.7.1 (2026-02-07) o Fixed compatibility with dplyr >= 1.2.0 (removal of dplyr::id()) o Replaced deprecated aes_string() with aes() + .data[[]] (ggplot2 >= 3.0.0) o Replaced deprecated dplyr underscore variants (filter_, mutate_, etc.) and funs() o Fixed cluster connection cleanup warnings when using nCores > 1 o Made GGMncv and huge optional dependencies (not in Suggests) while off CRAN Changes in version 1.7 o NA in weights matrix now leads to centrality indices not to be computed Changes in version 1.6 (2024-02-21) o 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 (2023-10-04) o Included min_sum argument in the IsingFit default Changes in version 1.5.5 (2023-08-22) o Small help file fix Changes in version 1.5.4 (2023-08-20) o IsingSampler default set now always uses method = "uni" by default o Added min_sum and threshold options to defailt = "IsingSampler" o Fixed a small problem in the bootnet package help file Changes in version 1.5.3 (2023-06-05) o Improved support for estimation functions with multiple networks of multiple types Changes in version 1.5.2 o Fixed links in README.md Changes in version 1.5.1 (2023-05-16) o Changed CRAN NOTE regarding class check o Fixed remaining deprecated dplyr functions o Fixed a bug with netSimulator and replicationSimulator print method Changes in version 1.5 (2021-10-25) o Fixed a bug with bridge centrality indices being incorrectly labeled o Fixed a bug with that occured when using order = "sample" together with the subset argument o Removed calls to deprecated dplyr functions Changes in version 1.4.7 o 'binarize' now makes values above the split 1 instead of below the split o The bootnet plot method now shows values for all centrality metrics when plotting difference tests. o the mgm default for tuning now defaults to 0.25 o Fixed a bug with bridge centrality indices being incorrectly labeled Changes in version 1.4.6 o bootnet() now no longer re-estimates the network if the input is a bootnetResult o Several packages are now listed under Suggests instead of Imports o Included support for the GGMncv package Changes in version 1.4.4 o Fixed a critical error when using multiple cores in R 4.0 on Mac Changes in version 1.4 (2020-05-10) o Added the transformation functions 'quantile_transformation' and 'rank_transformation' o Several default sets now use corMethod = "cor" rather than corMethod = "cor_auto" by default! o Fixed a bug in case-drop bootstrap plotting method o "Sampled people" is now "Sampled cases" o Removed adalasso dependency due to CRAN removal o Added 'multiverse' function for multiverse-plots of bootstrap results Changes in version 1.3 (2020-01-22) o Added the options pairwise_maximum, pairwise_minimum and pairwise_average to the sampleSize argument of several default functions o Old functionality in estimateNetwork and bootnet has been removed! This includes graphFun, estFun etcetera. o Some changes that lead to NEW DEFAULT BEHAVIOR: o Added the argument 'nonPositiveDefinite' to several default estimators, which will stop with an error when the input is different. o The sampleSize argument now defaults to "pairwise_average"! o All default functions are now by default locked unless used from within estimateNetwork o The plot method now better scales a margin on the top and bottom of the plot o ggmGenerator now generates thresholds more consistently, leading to unfiform data by default or skewed data if the 'skewFactor' argument is used o ggmGenerator can now simulate missing data using the 'missing' argument o corMethod = "spearman" is now supported in several default sets o Fixed a bug with BDgraph change in genGGM function Changes in version 1.2.4 (2019-08-08) o Resolved a bug with expected influence crashing bootnet when empty networks were estimated Changes in version 1.2.3 (2019-06-24) o More informative error when statistics are not included in the plot. o Updated psych to psychTools Changes in version 1.2.2 (2019-05-09) o Added 'adjacency' argument to pcor default set, which allows for estimating a network with a fixed structure. o Fixed parametric bootstrapping Changes in version 1.2.1 o corStability should now return the non-finite values warning less often Changes in version 1.2 (2019-01-24) 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 o New supported default sets: o "cor" - Correlation networks o "TMFG" - Triangulated Maximally Filtered Graph o "LoGo"- Local/Global Sparse Inverse Covariance Matrix o "ggmModSelect" - Unregularized stepwise GGM model selection o "graphicalVAR" - LASSO regularized graphical VAR models o Some changes to mgm default: o mgm version >= 1.2 is now required o Renamed lev to level o Renamed degree to order, now defaults to 2 instead of 3 o Added binarySign argument. Now chosen by defult. o Added the 'replicationSimulator' function, which can be used to assess expected replicability of networks o Many default sets now support the 'principalDirection' argument, which can be used to multiply variables with the sign of the first principal component o 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). o Updated the 'genGGM' function to support various different network structures, with thanks to Mark Brandt! o Added RSPBC and Hybrid centrality, thanks to Alex Christensen o Added the 'alpha' argument to default set "pcor" o Added functionality for functions returning multiple graphs o Added outStrength, inStrength, outExpectedInfluence and inExpectedInfluence o Fixed a bug reporting the number of non-zero edges in the print methods o Added 'args' argument to netSimulator o Fixed a bug in which fun is not usuable in bootnet() o Added lambda.min.ratio argument to some estimators. Now defaults to 0.01 for default = "huge" o bootnet and netSimulator now show a progress bar (thanks to pbapply package) o plot method now shows bootstrapped mean in addition to sample value o The 'statistics' argument in bootnet and plot method now accept statistics with a upper case first letter, to be consistent with qgraph o CIstyle argument can now only be one value, and always defaults to quantiles Changes in version 1.0.1 (2017-09-06) o missing = "fiml" is now supported for EBICglasso and pcor default sets o Relative importance networks now do not crash when the number of predictors is 0 or 1 o plotting bootnetResults now supports the labels argument o mgm default now uses matrices to resolve an error with the latest version of mgm o The plot method of networks estimated using 'estimateNetwork' now uses different defaults than qgraph! o cut defaults to NULL o theme defaults to "colorblind" o parallelEdge defaults to TRUE o layout always defaults to "spring" (rather than "circle" for undirected networks) Changes in version 1.0.0 (2017-05-04) o Implemented the netSimulator function that allows for researchers to investigate sample size requirements and input arguments to estimateNetwork o Added genGGM, ggmGenerator, and IsingGenerator functions to be used in netSimulator o bootnet now stores less results and should have better memory usuage! Thanks to Giulio Costantini! o Fixed some bugs related to manual parametric bootstrap o EstimateNetwork now references packages used in a message o pcor default set now supports the argument 'threshold' o Fixed a bug where rule argument was not passed in bootnet default set o Bootnet now supports directed networks o Relative importance networks now implemented using default = "relimp" o Updated compatibility with MGM version 1.2.0 Changes in version 0.4 (2017-01-17) o estimateNetwork now accepts a custom estimation function using the argument 'fun' o Reworked default sets as functions! o This makes it easier to change common arguments, such as the EBIC tuning parameter o See the following functions for details: o bootnet_EBICglasso o bootnet_IsingFit o The corStability function now has a greatly improved output o Default set "IsingLL" has been renamed to "IsingSampler" o Default set "mgm" is now supported o labels argument is now supported in difference plots o Quantile now uses type = 6, this makes CIs slightly wider and therefore the difference test slightly more conservative Changes in version 0.3 (2016-09-04) o Eiko Fried joined the author list o Added 'estimateNetwork' function, allowing one to estimate the network structure from within bootnet o The plot method will run qgraph on the estimated network structure o 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' o Added 'differenceTest' function to test for significant differences between edge weights and centrality indices o Added 'corStability' to compute the CS-coefficient as described in our paper: o Epskamp, S., Borsboom, D., & Fried, E. I. (2016). Estimating psychological networks and their accuracy: a tutorial paper. arXiv preprint, arXiv:1604.08462. o The plot method now supports 'plot = "difference"', to make plots of significant differences between edge-weights and centralities o New default sets: o "huge" o "adalasso" o 'nCores' argument added to bootnet to use parallel computing o bootnet print methods now print a list of relevant references on the network estimation procedure used o When EBICglasso is used as default set, variables that are made ordinal are now printed only when estimating the first network o Updated CITATION such that citation("bootnet") now references the pre-print o Bootnet now gives a message on loading that it is BETA software o Added 'statistics' argument to bootnet. Now, distance and length are not stored by default o Several minor bugfixes