NEWS

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bootnet 1.6 (2024-02-21)

• 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.

bootnet 1.5.6 (2023-10-04)

• Included min_sum argument in the IsingFit default

bootnet 1.5.5 (2023-08-22)

• Small help file fix

bootnet 1.5.4 (2023-08-20)

• 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

bootnet 1.5.3 (2023-06-05)

• Improved support for estimation functions with multiple networks of multiple types

bootnet 1.5.2

• Fixed links in README.md

bootnet 1.5.1 (2023-05-16)

• Changed CRAN NOTE regarding class check
• Fixed remaining deprecated dplyr functions
• Fixed a bug with netSimulator and replicationSimulator print method

bootnet 1.5 (2021-10-25)

• 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

bootnet 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

bootnet 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

bootnet 1.4.4

• Fixed a critical error when using multiple cores in R 4.0 on Mac

bootnet 1.4 (2020-05-10)

• 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

bootnet 1.3 (2020-01-22)

• 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

bootnet 1.2.4 (2019-08-08)

• Resolved a bug with expected influence crashing bootnet when empty networks were estimated

bootnet 1.2.3 (2019-06-24)

• More informative error when statistics are not included in the plot.
• Updated psych to psychTools

bootnet 1.2.2 (2019-05-09)

• Added 'adjacency' argument to pcor default set, which allows for estimating a network with a fixed structure.
• Fixed parametric bootstrapping

bootnet 1.2.1

• corStability should now return the non-finite values warning less often

bootnet 1.2 (2019-01-24)

• 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
• 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)
• 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)

bootnet 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

bootnet 1.0.1 (2017-09-06)

• 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)

bootnet 1.0.0 (2017-05-04)

• 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

bootnet 0.4 (2017-01-17)

• 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

bootnet 0.3 (2016-09-04)

• 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