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




