Bootstrap Methods for Various Network Estimation Routines

Bootstrap methods to assess accuracy and stability of estimated network structures and centrality indices. Allows for flexible specification of any undirected network estimation procedure in R, and offers default sets for 'qgraph', 'IsingFit', 'IsingSampler', 'glasso', 'huge' and 'parcor' packages.


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

Reference manual

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1.0.1 by Sacha Epskamp, 10 months ago

Browse source code at

Authors: Sacha Epskamp and Eiko I. Fried

Documentation:   PDF Manual  

GPL-2 license

Imports methods, igraph, IsingFit, qgraph, dplyr, tidyr, gtools, corpcor, IsingSampler, mvtnorm, abind, Matrix, parallel, huge, parcor, mgm, relaimpo

Depends on ggplot2

Suggests psych

See at CRAN