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Changelog

Source: NEWS.md

Changes in version 2.1.0

  • ADD: EGM and simEGM for model estimation and simulation of the Exploratory Graph Model, respectively

  • ADD: EGM.compare to compare EGM against EFA for most likely data generating mechanism

  • INTERNAL: fit function to calculate traditional, log-likelihood, and TEFI fit indices

Changes in version 2.0.8

CRAN release: 2024-09-28

  • FIX: issue with dynamic memory allocation in polychoric_matrix.c during CRAN’s install of the package

  • ADD: cosine similarity added as a default for auto.correlate and ‘corr’ arguments

Changes in version 2.0.7

CRAN release: 2024-09-02

  • FIX: mixed data with missing data in network.predictability

  • ADD: frobenius norm to compare networks

  • ADD: network.compare function to test for differences in network structures using three different metrics (Frobenius Norm, Jensen-Shannon Similarity, total network strength)

  • ADD: a general function called information to compute several information theory measures

  • UPDATE: default ‘loading.method’ for net.loads has been changed to “revised” moving forward – the previous default in versions <= 2.0.6 can be obtained using “original”

  • UPDATE: invariance handles more than 2 groups (plots up to 4 groups pairwise)

  • UPDATE: added ‘signed’ argument in jsd to allow for signed or absolute networks to be used in computations (includes downstream functions: infoCluster)

  • UPDATE: NEWS is now formatted in markdown

  • UPDATE: network.predictability uses R-squared and mean absolute error (MAE) for all node predictions

  • INTERNAL: network.generalizabilty was moved to be internal (needs some work yet)

  • INTERNAL: signs for net.loads uses the first eigenvector of the target network (rather than the custom obtain_signs function)

Changes in version 2.0.6

CRAN release: 2024-04-22

  • FIX: bug when using na.data = "listwise" in standard cor() function

  • FIX: update to revised network loadings signs: net.loads(..., loading.method = "experimental")

  • FIX: bug in argument ‘returnAllResults’ for EBICglasso.qgraph

  • FIX: bug when passing additional non-dimensionStability arguments into bootEGA

  • FIX: bug when printing hierEGA summary from bootEGA

  • UPDATE: colors in itemStability plots will match colors of hierEGA plot

  • UPDATE: network.predictability uses empirical inverse variances (rather than network-implied)

  • UPDATE: R-squared in continuous_accuracy helper uses Pearson’s correlation squared

Changes in version 2.0.5

CRAN release: 2024-03-15

  • FIX: ‘stroke’ parameter in hierEGA that broke with {ggplot2} update

  • ADD: network.predictability to predict new data based on a network

  • ADD: network.generalizability to estimate network generalizability to new data (leverages network.predictability)

  • UPDATE: new loadings (net.loads(..., loading.method = "experimental")) have been added to resolve issues in original loadings (e.g., signs, cross-loadings, standardization)

  • UPDATE: plot.bootEGA will output itemStability plot by default

  • UPDATE: dimensionStability output now included in bootEGA as output $stability

  • UPDATE: ‘rotate’ argument added to infoCluster plot to allow for different angle of dendrogram

  • DEPENDENCY: {fungible} is now ‘IMPORTS’ over ‘SUGGESTS’ for dependency in new loadings

  • DEPRECATED: typicalStructure and plot.typicalStructure have been deprecated to FALSE

Changes in version 2.0.4

CRAN release: 2024-01-22

  • FIX: plotting for infoCluster when there are grey lines involved (or not)

  • FIX: pass of multiple passes of resolution_parameter causing an error in {igraph} 2.0.0 for EGA.fit (see issue #148)

  • ADD: community.compare to perform permutation test to determine statistical significance of cluster similarity

  • UPDATE: moved reindex_memberships to helpers

  • UPDATE: reindex_memberships used in community.homogenize

Changes in version 2.0.3

CRAN release: 2023-11-17

  • FIX: freed edge.* arguments in compare.EGA.plots to allow full customization

  • UPDATE: optimizations for speed and memory in ergoInfo and boot.ergoInfo

  • DEPENDENCY: swapped out {ggdendro} for {dendextend}

Changes in version 2.0.2

CRAN release: 2023-10-25

  • FIX: ties for max gain in TMFG

  • FIX: continuous variables with few categories that are treated as ordinal in polychoric.matrix

  • FIX: character input for structure is now accepted

  • ADD: website pointing to different data check errors added to error output (hopefully, makes errors more understandable)

  • UPDATE: corr = "cor_auto" now performs qgraph::cor_auto in favor of legacy; previous behavior starting at 2.0.0 was t+ deprecate "cor_auto" in favor of "auto"; default remains corr = "auto"

  • UPDATE: compare.EGA.plots outputs $all and $individual for the plots

  • UPDATE: when structure is supplied for invariance, then configural check is skipped (structure is assumed to be invariant)

  • UPDATE: added data generation for model = "BGGM" and uni.method = "expand" in community.unidimensional

  • DEPENDENCY: {BGGM} has been removed until dependency chain on CRAN can be resolved

Changes in version 2.0.1

CRAN release: 2023-08-23

  • updated the polychoric C code to avoid out-of-bounds access errors

Changes in version 2.0.0

CRAN release: 2023-08-16

  • MAJOR REFACTOR: the update to version 2.0.0 includes many major changes that are designed to improve the speed, reliability, and reproducibility of {EGAnet}. The goal of these changes are to eliminate common errors and streamline the code in the package to prevent future error cases. There are several function additions that are provided to facilitate modular use of the {EGAnet} package

  • INTERNALS: function-specific internal functions and S3methods are now located in their respective .R files rather than elsewhere (e.g., “utils-EGAnet.R”)

  • SWAP: internal script usage of “utils-EGAnet.R” depracated for “helper.R” functions that are used across the package (no visible changes for the user)

  • NOTE: default objective function for Leiden algorithm is set to “modularity”

  • NOTE: default for Louvain unidimensional method is set to single-shot unless argument “consensus.method” or “consensus.iter” is specified

  • ADD: stricter *apply functions that are roughly equivalent to *apply but have stricter inputs/outputs (uses vapply as foundation; often, slightly faster)

  • ADD: community.consensus to apply the Consensus Clustering approach introduced by Lancichnetti & Fortunato (2012). Currently only available for the Louvain algorithm

  • ADD: community.detection to apply community detection algorithms as a standalone function

  • ADD: convenience function to convert an {igraph} object to a standard matrix (igraph2matrix)

  • ADD: modularity to compute standard (absolute values) and signed modularity (implemented in C)

  • ADD: polychoric.matrix to compute categorical correlations (implemented in C); handles missing data (“pairwise” or “listwise”) as well as empty cells in the joint frequency table (see documentation: ?polychoric.matrix)

  • ADD: auto.correlate now computes all correlations internally and no longer depends on external functions; categorical correlations are C based and bi/polyserial correlations are a simplified and vectorized version of {polycor}’s polyserial; substantial computational gains (between 10-25x faster than previous use of {qgraph}’s cor_auto)

  • ADD: network.estimation to handle all network estimation in {EGAnet}; includes Bayesian GGM from {BGGM} for more seamless incorporation of BEGA

  • ADD: community.unidimensional to apply different unidimensional community detection approaches; makes unidimensional community detection more modular and flexible

  • ADD: basic (internal) function to handle all network plots to keep changes centralized to a single function; extends flexbility to handle all {GGally}’s ggnet2 arguments

  • ADD: implemented reproducible parametric bootstrapping and random sampling (see https://github.com/hfgolino/EGAnet/wiki/Reproducibility-and-PRNG for more details)

  • ADD: implemented reproducible resampling bootstrapping and random sampling (see https://github.com/hfgolino/EGAnet/wiki/Reproducibility-and-PRNG for more details)

  • ADD: reproducible bootstrapping with seed setting that does not affect R’s seed and RNG (user’s seed will not be affected and will not affected bootstrapping seeds)

  • ADD: community.homogenize as a core function rather than internal (previously homogenize.membership); about 2.5x faster than the original version

  • ADD: convert2tidygraph for ggraph and tidygraph support – thanks to Dominique Makowski!

  • ADD: “multilevel” plotting support for hierEGA (only used when scores = "network" since factor scores don’t directly align with EGA detected dimensions)

  • ADD: internal functions shuffle and shuffle_replace to replace sample with and without replacement; performed in C and allows seed setting independent of R (about 2-3x faster)

  • ADD: xoshiro256++ PRNG for higher quailty random number generation, permutation, and resampling (~2x faster than runif and sample); based in C

  • ADD: Ziggurat method for random normal generation over top xoshiro256++ (2-5x faster than rnorm); based in C

  • ADD: configural invariance was added to invariance (see Details section)

  • ADD: genTEFI to compute the Generalized Total Entropy Fit Index solely; tefi serves as a general function to compute TEFI for all *EGA classes

  • REMOVE: signed.louvain until reproducibility can be sorted

  • REMOVE: methods.section and utils-EGAnet.methods.section to avoid space issues in ./R directory (1MB)

  • UPDATE: EBICglasso.qgraph and TMFG were optimized; TMFG is now 2x faster

  • UPDATE: TMFG can now directly estimate a GGM with the argument ‘partial = TRUE’; implements the Local-Global Inversion method from Barfuss et al. (2016)

  • UPDATE: switched on “Byte-Compile” (byte-compiles on our end and not when the user installs)

  • UPDATE: EGA.estimate and EGA core functions have been updated for seamless use with more basic functions network.estimation and community.* functions

  • UPDATE: S3method updates for EGA.estimate and EGA to provide estimation information

  • UPDATE: EGA.fit updated to be compatiable with all updates to EGA.estimate (other optimizations were implemented such as direct communtiy detection application and unique solution finding)

  • UPDATE: tefi updated with several checks (slightly slower for correlation matrix but much faster with raw data; includes data/matrix checks)

  • UPDATE: entropyFit uses more effective vectorization (about 5-7x faster)

  • UPDATE: Embed and glla made to be more efficient and includes an internal glla_setup function to avoid the same matrix calculations for every participant in a sample for dynEGA

  • UPDATE: riEGA updated to be compatiable with all lower-level updates (slightly faster)

  • UPDATE: wto updated to be fully vectorized (about 12x faster)

  • UPDATE: totalCor and totalCorMat updated to be fully vectorized (about 10x faster)

  • UPDATE: implemented internal fast.data.frame for more efficient data frame initialization when all values in data frame are the same

  • UPDATE: bootEGA allows flexibility to add any arguments from any EGA* functions; much faster due to optimizations across all functions (“resampling” is nearly as fast as “parametric”)

  • UPDATE: support for EGA.fit and riEGA added to bootEGA (support for hierEGA will be coming soon…)

  • UPDATE: itemStability has been updated and runs about 2.5x faster due to community.homogenize; S3methods were added; greater flexibility available in plotting but not much support (e.g., error checking) yet

  • UPDATE: dimensionStability has been updated and maintains speed gains from itemStability

  • UPDATE: dynEGA.ind.pop now calls dynEGA with level = c("individual", "population"); legacy dynEGA.ind.pop class is maintained across ergodicity functions

  • UPDATE: ergoInfo is about 2x faster

  • UPDATE: jsd received several internal functions to expedite procedures in infoCluster and jsd.ergoInfo

  • UPDATE: net.loads now includes ‘loading.method’ argument to allow for reproducibility with “BRM” implementation (and version 1.2.3); “experimental” implementation includes rotations alternative signs and cross-loading computation (potential future default)

  • UPDATE: net.scores is much simpler (internally) and quicker; seamlessly integrates with net.loads

  • UPDATE: compare.EGA.plots is faster, more flexible, and more reliable for comparing two or more plots

  • UPDATE: hierEGA is faster and has new S3 methods

  • UPDATE: S3 plotting for invariance

  • UPDATE: hierEGA + bootEGA integration for itemStability and dimensionStability (includes full S3 methods)

  • UPDATE: UVA supports legacy of inital conception in Christensen, Golino, and Silvia (EJP, 2020) but will no longer fix bugs related to: manual variable selection, “adapt” or “alpha” methods (warnings will be thrown)

  • UPDATE: streamlined UVA (about 4x faster); fixed bugs related to reverse coding issues

  • UPDATE: tefi now handles all EGA* function objects including hierEGA which computes generalized TEFI

  • UPDATE: documentation for all functions have been thoroughly revised to provide better instruction on how to use functions and their expected inputs

  • DEPENDENCY: removed {network} because it is no longer used for plotting; switched {sna} to IMPORTS rather than SUGGESTS

  • DEPENDENCY: removed {rstudioapi} from ‘Suggests’ because it was used in colortext and used in the package

  • DEPENDENCY: removed {matrixcalc} because it was only used for trace of a matrix (own internal function is used)

  • DEPENDENCY: {future} and {future.apply} are used for parallelization (better integration); includes internal function to check for available memory to not break in big data cases

  • DEPENDENCY: {progress} and {progressr} are used for progress bars (in parallelization)

  • DEPENDENCY: removed {psychTools} from ‘Suggests’ which was only used in examples

  • DEPENDENCY: removed {rmarkdown} from ‘Suggests’ since it wasn’t being used across the package

Changes in version 1.2.5.1

  • FIX: cross-loading bug in net.loads was leading to problems when there were negative cross-loadings

  • FIX: added psych::factor.scores scoring methods in net.scores

  • ADD: signed.louvain to estimate the Signed Louvain algorithm (implemented in C)

Changes in version 1.2.5

  • ADD: most_common_tefi method for EGA analyses

Changes in version 1.2.4

  • REMOVE: residualEGA has been removed in favor of riEGA (removes {OpenMx} dependency)

  • ADD: rotations to net.loads and net.scores

  • UPDATE: hierEGA only outputs specified output (no longer outputs all possible consensus methods and scores combinations – should be much faster)

Changes in version 1.2.3

CRAN release: 2022-09-05

  • FIX: many bug fixes related to latest update; functions have largely returned to stable status

  • UPDATE: Mac and Linux parallelizations have been optimized

  • UPDATE: documented examples are more efficient for CRAN checks

Changes in version 1.2.1

  • FIX: bootEGA read of bootstrap data (was not calling from datalist in do.call leading to perfect item stability)

  • FIX: number of possible colors expanded to 70 (increased from 40)

Changes in version 1.2.0

CRAN release: 2022-08-12

  • FIX: hex codes used in EGA plots

  • FIX: ordered = TRUE for categorical data in lavaan CFAs

  • UPDATE: consesnsus clustering is now used with Louvain in EGA

  • UPDATE: print/summary S3methods have been standardized

  • ADD/UPDATE: boot.ergoInfo has achieved functional working order. Results can be trusted to suggest whether dynamic data possess the ergodic property

  • ADD: information theoretic clustering algorithm for dynamic data is available in infoCluster

  • REMOVE: “alpha” and “adapt” options in UVA (removes {fitdistrplus} dependency)

  • REMOVE: {qgraph} plots are no longer available

  • ADD: convert2igraph is now a core function

  • ADD: Jensen-Shannon Divergence jsd for determining (dis)similarity between network strcutures

  • ADD: riEGA, EGA.fit, and hierEGA functionality to bootEGA

  • ADD: hierEGA functionality to itemStability and dimensionStability

  • UPDATE: “louvain” algorithm used as default for unidimensionality check in EGA

  • INTERNAL: cleaned up EGA and EGA.estimate; streamlined code; no user facing differences

Changes in version 1.1.0

CRAN release: 2022-05-10

  • FIX: CRAN note when if(class(object)). Replaced by if(is(object)).

  • FIX: bug in EGA.estimate when using the TMFG network method. The resulting EGA plot did not have the correct node names.

  • FIX: bug in UVA when trying to use sum score (reduce.method = "sum") in automated procedure

  • ADD: measurement invariance function for testing differences in network loadings between groups

  • UPDATE: itemStability now has a parameter structure in which the user can specify a given structure to test its stability.

  • ADD: riEGA implementing random-intercept EGA for wording effects

  • ADD: hierEGA implementing hierarchical EGA

  • FIX: consensus clustering for the Louvain algorithm

  • ADD: louvain algorithm with added optimization option using tefi

Changes in version 1.0.0

CRAN release: 2021-11-10

  • FIX: bug within the bootEGA function for type = "resampling".

  • UPDATE: default undimensionality adjustment has changed to leading eigenvalue (see Christensen, Garrido, & Golino, 2021 https://doi.org/10.31234/osf.io/hz89e). Previous unidimensionality adjustment in versions <= 0.9.8 can be applied using uni.method = "expand"

  • UPDATE: default UVA was changed type = "threshold"

  • UPDATE: UVA is now automated using auto = TRUE

  • DEFUNCT: dimStability will no longer be supported. Instead, use dimensionStability

  • REVAMP: itemStability has been recoded. Now includes error checking and more readable code

  • FIX: bug for plotting NA communities

  • FIX: bug for changing edge size in ‘GGally’ plotting

  • UPDATE: S3Methods for EGA.fit plotting

  • FIX: plotting parameters for bootEGA

  • FIX: redundancy output for adhoc check in UVA

  • FIX: latent variable with non-space separated entries in UVA (reduce.method = "latent")

  • UPDATE: UVA was added to methods.section

  • UPDATE: neural network weights in LCT (now only tests for factor or small-world network models)

  • UPDATE: citations

  • UPDATE: added seed argument for bootEGA to reproduce results

  • FIX: bug for Rand index in itemStability

Changes in version 0.9.8

CRAN release: 2021-02-16

  • UPDATE: Unidimensional check in EGA expands a correlation matrix (rather than generating variables; much more efficient)

  • ADD: color_palette_EGA New EGA palettes for plotting ggnet2 EGA network plots (see ?color_palette_EGA)

  • ADD: UVA or Unique Variable Analysis operates as a comprehensive handling of variable redundancy in multivariate data (see ?UVA)

  • DEFUNCT: node.redundant, node.redundant.names, and node.redundant.combine will be defunct in next version. Please use UVA

  • ADD: a new function to compute a parametric Bootstrap Test for the Ergodicity Information Index (see ?boot.ergoInfo)

  • ADD: basic Shiny functionality (EGA only)

  • ADD: a new function to compute a Monte-Carlo Test for the Ergodicity Information Index (see ?mctest.ergoInfo)

  • ADD: a new function to compute the Ergodicity Information Index (see ?ergoInfo)

  • UPDATE: new plotting scheme using network and GGally packages

  • ADD: a function to produce an automated Methods section for several functions (see ?methods.section)

  • UPDATE: bootEGA now implements the updated EGA algorithm

  • UPDATE: ega.wmt data (unidimensional)

  • UPDATE: itemStability plot defaults (“GGally” color scheme) and examples (manipulating plot)

  • ADD: total correlation (see ?totalCor and totalCorMat)

  • ADD: correlation argument (corr) for EGA, bootEGA, and UVA

  • FIX: GGally color palette when more than 9 dimensions

Changes in version 0.9.7

  • UPDATE: LCT neural network weights were updated (parametric relu activation function)

  • FIX: naming in EGA

  • FIX: output network matrix in EGA when data are input

  • UPDATE: citation version

  • UPDATE: node.redundant now provides a full plot of redundancies detected, descriptive statistics including the critical value, central tendency descriptive statistics, and the distribution the significant values were determined from (thanks to Luis Garrido for the suggestion!)

Changes in version 0.9.6

CRAN release: 2020-07-13

  • UPDATE: LCT updated with neural network implementation

Changes in version 0.9.5

  • ADD: loadings comparison test function added (see LCT)

  • FIX: named community memberships in itemStability and dimStability

  • UPDATE: plot, print, and summary methods all moved into single .R files (no effect on user’s end)

  • UPDATE: net.scores global score is improved and computes scores very close to CFA scores

  • FIX: additional argument calls for EGA.estimate (and EGA by extension)

  • UPDATE: message from EGA.estimate (and EGA by extension) reports both ‘gamma’ and ‘lambda.min.ratio’ arguments

  • FIX: upper quantile output from bootEGA

  • FIX: minor bugs in node.redundant, itemStability, and net.loads

Changes in version 0.9.4

  • MAJOR UPDATE: dimStability now computes proportion of exact dimension replications rather than items that replicate within dimension (this latter information can still be found in the output of itemStability under $mean.dim.rep)

  • FIX: net.loads for when dimensions equal one or the number of nodes in the network

  • FIX: naming typo with characters in itemStability

  • FIX: NAs in dimStability

  • FIX: weights of network in unidimensional structure of EGA are the same as multidimensional structure

  • UPDATE: Added a new function to simulate dynamic factor models simDFM

  • UPDATE: added internal functions for net.loads (see utils-net.loads)

  • FIX: ordering of names in itemStability

  • FIX: handling of NA communities in net.loads

  • UPDATE: Added output of the average replication of items in each dimension for itemStability

  • UPDATE: Revised ‘Network Scores’ vignette

  • UPDATE: net.loads functionality (cleaned up code)

  • UPDATE: S3Methods for net.loads

  • FIX: net.scores negative loadings corrected

Changes in version 0.9.3

CRAN release: 2020-03-05

  • New function and print, summary and plot methods: dynEGA

  • New functions: Embed and glla

Changes in version 0.9.2

  • UPDATE: add latent variable scores comparison to net.scores vignette

  • UPDATE: node.redundant.combine sets loadings equal to 1 when there are only two variables when the argument type = “latent”; warning also added from type = “sum”

  • FIX: node.redundant alpha types bug

  • updated itemStability (bug fixes)

  • updated node.redundant.combine (bug fixes, latent variable option)

  • major bug fix in net.loads: corrected loadings greater than 1 when there were many negative values

  • added EGA.estimate to clean up EGA code and allow for future implementations of different network estimation methods and community detection algorithms

  • updated EGA functionality: message for ‘gamma’ value used and EGA.estimate compatiability

  • removed iterators dependency

  • ordering and name fix in net.loads

  • auto-adjusts y-axis label size for itemStability plot based on number of nodes or length of node names

  • net.loads adjusted for larger values using absolute values and applying the sign afterwards

  • reverse coding update in net.loads

  • node.redundant.combine bug fix for reverse coding latent variables

  • added Louvain community detection to all EGA functions in EGAnet

  • functionality updates to node.redundant

  • swapped arguments ‘type’ and ‘method’ in the node.redundant function (fixed examples in other node.redundant functions)

  • updated citation

Changes in version 0.9.0

CRAN release: 2020-01-18

  • updated list of dependencies

  • added ORCiDs in Description file

  • corrected ordering of net.loads output

  • corrected standard error in bootEGA

  • citation update

  • added function dimStability to compute dimensional stability

  • added a series of functions for node.redundant, which facilitates detecting and combining redundant nodes in networks

  • updated the EGA.fit function, so now a correlation matrix can be used as well.

Changes in version 0.8.0

  • ‘bootEGA’ now computes time until bootstrap is finished

  • new functions ‘cmi’, ‘pmi’ and ‘residualEGA’ added: ‘cmi’ computes conditional mutual information, ‘pmi’ computes partial mutual information and residual EGA computes an EGA network controlling for wording effects

  • new dataset ‘optimism’ added

  • documentation and functionality for several functions updated

Changes in version 0.7.0

  • fixed ‘EGA’ bug in ‘bootEGA’ function; updated ‘bootEGA’ documentation; added progress messages

  • migrated ‘net.scores’ and ‘net.loads’ from ‘NetworkToolbox’ to ‘EGAnet’ package

  • functions ‘itemConfirm’ and ‘itemIdent’ have been merged into a single function called, ‘itemStability’

  • fixed item ordering in ‘itemStability’ output so dimensions are from least to greatest, the colors match the original community vector input, and updated average standardized network loadings to the ‘net.loads’ function

  • added datasets ‘ega.wmt’ and ‘boot.wmt’ for quick user-friendly examples (also removed all ‘’)

  • added package help page

  • added package load message

  • updated ‘itemStability’ algorithm (now can accept any number of ‘orig.wc’) and enforced ‘0’ to ‘1’ bounds on plot