Releases: hfgolino/EGAnet
{EGAnet} 2.0.7
Changes in version 2.0.7
-
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 customobtain_signs
function)
{EGAnet} 2.0.6
Changes in version 2.0.6
o FIX: bug when using na.data = "listwise"
in standard cor()
function
o FIX: update to revised network loadings signs
o FIX: bug in argument 'returnAllResults' for EBICglasso.qgraph
o FIX: bug when passing additional non-dimensionStability
arugments into bootEGA
o FIX: bug when printing hierEGA
summary from bootEGA
o UPDATE: colors in itemStability
plots will match colors of hierEGA
plot
o UPDATE: network.predictability
uses empirical inverse variances (rather than network-implied)
o UPDATE: R-squared in continuous_accuracy
helper uses formula for no intercept
{EGAnet} 2.0.5
Changes in version 2.0.5
o FIX: 'stroke' parameter in hierEGA
that broke with {ggplot2} update
o ADD: network.predictability
to predict new data based on a network
o ADD: network.generalizability
to estimate network generalizability to new data (leverages network.predictability
)
o UPDATE: new loadings (net.loads(..., loading.method = "experimental")
) have been added to resolve issues in original loadings (e.g., signs, cross-loadings, standardization)
o UPDATE: plot.bootEGA
will output itemStability
plot by default
o UPDATE: dimensionStability
output now included in bootEGA
as output $stability
o UPDATE: 'rotate' argument added to infoCluster
plot to allow for different angle of dendrogram
o DEPENDENCY: {fungible} is now 'IMPORTS' over 'SUGGESTS' for dependency in new loadings
o DEPRECATED: typicalStructure
and plot.typicalStructure
have been deprecated to FALSE
{EGAnet} 2.0.4
o FIX: plotting for infoCluster
when there are grey lines involved (or not)
o FIX: pass of multiple passes of resolution_parameter
causing an error in {igraph} 2.0.0 for EGA.fit
(see issue #148)
o ADD: community.compare
to perform permutation test to determine statistical significance of cluster similarity
o UPDATE: moved reindex_memberships
to helpers
o UPDATE: reindex_memberships
used in community.homogenize
{EGAnet} 2.0.3
Changes in version 2.0.3
-
FIX: freed
edge.*
arguments incompare.EGA.plots
to allow full customization -
UPDATE: optimizations for speed and memory in
ergoInfo
andboot.ergoInfo
-
DEPENDENCY: swapped out {ggdendro} for {dendextend}
{EGAnet} 2.0.2
Due to dependency issues, this release does not include Bayesian GGM capabilities. The functionality will return when the dependency issues can be resolved.
Changes in version 2.0.2
o FIX: ties for max gain in TMFG
o FIX: continuous variables with few categories that are treated as ordinal in polychoric.matrix
o FIX: character input for structure
is now accepted
o ADD: website pointing to different data check errors added to error output (hopefully, makes errors more understandable)
o UPDATE: corr = "cor_auto"
now performs qgraph::cor_auto
in favor of legacy; previous behavior starting at 2.0.0 was to deprecate "cor_auto"
in favor of "auto"
; default remains corr = "auto"
o UPDATE: compare.EGA.plots
outputs $all
and $individual
for the plots
o UPDATE: when structure
is supplied for invariance
, then configural check is skipped (structure is assumed to be invariant)
o UPDATE: added data generation for model = "BGGM"
and uni.method = "expand"
in community.unidimensional
o DEPENDENCY: {BGGM} has been removed until dependency chain on CRAN can be resolved
Changes in version 2.0.1
o updated the polychoric C code to avoid out-of-bounds access errors
{EGAnet} 2.0.0
To check out changes in version 2.0.0, see NEWS and What's Changed?
EGAnet 1.2.3
Major fixes to previous CRAN release version 1.2.0
If you've previously ran your analysis using version 1.2.0, we recommend re-running the analyses with version 1.2.3. There were some major bugs that may have affected your results.
Changes in 1.2.3
o FIX: many bug fixes related to latest update; functions have largely returned to stable status
o UPDATE: Mac and Linux parallelizations have been optimized
o UPDATE: documented examples are more efficient for CRAN checks
Changes in 1.2.1
o FIX: bootEGA
read of bootstrap data (was not calling from datalist
in do.call
leading to perfect item stability)
o FIX: number of possible colors expanded to 70 (increased from 40)
Changes in version 1.2.0
o FIX: hex codes used in EGA plots
o FIX: ordered = TRUE
for categorical data in lavaan CFAs
o UPDATE: consesnsus clustering is now used with Louvain in EGA
o UPDATE: print/summary S3methods have been standardized
o ADD/UPDATE: boot.ergoInfo
has achieved functional working order. Results can be trusted to suggest whether dynamic data possess the ergodic property
o ADD: information theoretic clustering algorithm for dynamic data is available in infoCluster
o REMOVE: "alpha" and "adapt" options in UVA
(removes {fitdistrplus} dependency)
o REMOVE: {qgraph} plots are no longer available
o ADD: convert2igraph
is now a core function
o ADD: Jensen-Shannon Divergence jsd
for determining (dis)similarity between network strcutures
o ADD: riEGA
, EGA.fit
, and hierEGA
functionality to bootEGA
o ADD: hierEGA
functionality to itemStability
and dimensionStability
o UPDATE: "louvain" algorithm used as default for unidimensionality check in EGA
o INTERNAL: cleaned up EGA
and EGA.estimate
; streamlined code; no user facing differences
Changes in version 1.1.0
o FIX: CRAN note when if(class(object))
. Replaced by if(is(object))
.
o FIX: bug in EGA.estimate
when using the TMFG network method. The resulting EGA plot did not have the correct node names.
o FIX: bug in UVA
when trying to use sum score (reduce.method = "sum"
) in automated procedure
o ADD: measurement invariance
function for testing differences in network loadings between groups
o UPDATE: itemStability
now has a parameter structure
in which the user can specify a given structure to test its stability.
o ADD: riEGA
implementing random-intercept EGA for wording effects
o ADD: hierEGA
implementing hierarchical EGA
o FIX: consensus clustering for the Louvain algorithm
o ADD: louvain
algorithm with added optimization option using tefi
EGAnet 1.0.0
Changes in version 1.0.0
o FIX: Bug within the bootEGA function for type = "resampling"
.
o 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"
O UPDATE: default UVA
was changed type = "threshold"
o UPDATE: UVA
is now automated using auto = TRUE
o DEFUNCT: dimStability
will no longer be supported. Instead, use dimensionStability
o REVAMP: itemStability
has been recoded. Now includes error checking and more readable code
o FIX: bug for plotting NA communities
o FIX: bug for changing edge size in 'GGally' plotting
o UPDATE: S3Methods for EGA.fit
plotting
o FIX: plotting parameters for bootEGA
o FIX: redundancy output for adhoc check in UVA
o FIX: latent variable with non-space separated entries in UVA
(reduce.method = "latent"
)
o UPDATE: UVA
was added to methods.section
o UPDATE: neural network weights in LCT
(now only tests for factor or small-world network models)
o UPDATE: citations
o UPDATE: added seed
argument for bootEGA
to reproduce results
o FIX: bug for Rand index in itemStability
Changes in version 0.9.8
o UPDATE: Unidimensional check in EGA
expands a correlation matrix (rather than generating variables; much more efficient)
o ADD: color_palette_EGA
New EGA palettes for plotting ggnet2
EGA network plots (see ?color_palette_EGA
)
o ADD: UVA
or Unique Variable Analysis operates as a comprehensive handling of variable redundancy in multivariate data (see ?UVA
)
o DEFUNCT: node.redundant
, node.redundant.names
, and node.redundant.combine
will be defunct in next version. Please use UVA
o ADD: a new function to compute a parametric Bootstrap Test for the Ergodicity Information Index (see ?boot.ergoInfo
)
o ADD: basic Shiny functionality (EGA
only)
o ADD: a new function to compute a Monte-Carlo Test for the Ergodicity Information Index (see ?mctest.ergoInfo
)
o ADD: a new function to compute the Ergodicity Information Index (see ?ergoInfo
)
o UPDATE: new plotting scheme using network and GGally packages
o ADD: a function to produce an automated Methods section for several functions (see ?methods.section
)
o UPDATE: bootEGA
now implements the updated EGA
algorithm
o UPDATE: ega.wmt data (unidimensional)
o UPDATE: itemStability
plot defaults ("GGally" color scheme) and examples (manipulating plot)
o ADD: total correlation (see ?totalCor
and totalCorMat
)
o ADD: correlation argument (corr) for EGA
, bootEGA
, and UVA
o FIX: GGally color palette when more than 9 dimensions
EGAnet 0.9.7
Changes in version 0.9.7
o UPDATE: LCT
neural network weights were updated (parametric relu activation function)
o FIX: naming in EGA
o FIX: output network matrix in EGA
when data are input
o UPDATE: citation version
o UPDATE: node.redundant
now provides a full plot of redundancies detected, descriptive statistics including the critical value, and the distribution the significant values were determined from
Changes in version 0.9.6
o UPDATE: LCT
updated with neural network implementation
Changes in version 0.9.5
o ADD: loadings comparison test function added (see LCT
)
o FIX: named community memberships in itemStability
and dimStability
o UPDATE: plot
, print
, and summary
methods all moved into single .R files (no effect on user's end)
o UPDATE: net.scores
global score is improved and computes scores very close to CFA scores
o FIX: additional argument calls for EGA.estimate
(and EGA
by extension)
o UPDATE: message from EGA.estimate
(and EGA
by extension) reports both 'gamma' and 'lambda.min.ratio' arguments
o FIX: upper quantile output from bootEGA
o FIX: minor bugs in node.redundant
, itemStability
, and net.loads
Changes in version 0.9.4
o 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)
o FIX: net.loads
for when dimensions equal one or the number of nodes in the network
o FIX: naming typo with characters in itemStability
o FIX: NAs in dimStability
o FIX: weights of network in unidimensional structure of EGA
are the same as multidimensional structure
o UPDATE: Added a new function to simulate dynamic factor models simDFM
o UPDATE: added internal functions for net.loads
(see utils-net.loads
)
o FIX: ordering of names in itemStability
o FIX: handling of NA communities in net.loads
o UPDATE: Added output of the average replication of items in each dimension for itemStability
o UPDATE: Revised 'Network Scores' vignette
o UPDATE: net.loads
functionality (cleaned up code)
o UPDATE: S3Methods for net.loads
o FIX: net.scores
negative loadings corrected
Changes in version 0.9.3
o New function and print, summary and plot methods: dynEGA
o New functions: Embed and glla
Changes in version 0.9.2
o UPDATE: add latent variable scores comparison to net.scores
vignette
o 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"
o FIX: node.redundant
alpha types bug
o updated itemStability
(bug fixes)
o updated node.redundant.combine
(bug fixes, latent variable option)
o major bug fix in net.loads
: corrected loadings greater than 1 when there were many negative values
o added EGA.estimate
to clean up EGA
code and allow for future implementations of different network estimation methods and community detection algorithms
o updated EGA
functionality: message for 'gamma' value used and EGA.estimate
compatiability
o removed iterators dependency
o ordering and name fix in net.loads
o auto-adjusts y-axis label size for itemStability
plot based on number of nodes or length of node names
o net.loads
adjusted for larger values using absolute values and applying the sign afterwards
o reverse coding update in net.loads
o node.redundant.combine
bug fix for reverse coding latent variables
o added Louvain community detection to all EGA functions in EGAnet
o functionality updates to node.redundant
o swapped arguments 'type' and 'method' in the node.redundant
function (fixed examples in other node.redundant functions)
o updated citation
Changes in version 0.9.0
o updated list of dependencies
o added ORCiDs in Description file
o corrected ordering of net.loads
output
o corrected standard error in bootEGA
o citation update
o added function dimStability
to compute dimensional stability
o added a series of functions for node.redundant
, which facilitates detecting and combining redundant nodes in networks
o updated the EGA.fit function, so now a correlation matrix can be used as well.
Changes in version 0.8.0
o 'bootEGA' now computes time until bootstrap is finished
o 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
o new dataset 'optimism' added
o documentation and functionality for several functions updated
Changes in version 0.7.0
o fixed 'EGA' bug in 'bootEGA' function; updated 'bootEGA' documentation; added progress messages
o migrated 'net.scores' and 'net.loads' from 'NetworkToolbox' to 'EGAnet' package
o functions 'itemConfirm' and 'itemIdent' have been merged into a single function called, 'itemStability'
o 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
o added datasets 'ega.wmt' and 'boot.wmt' for quick user-friendly examples (also removed all '\donttest')
o added package help page
o added package load message
o updated 'itemStability' algorithm (now can accept any number of 'orig.wc') and enforced '0' to '1' bounds on plot