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stats::lm
w/ stats::lm.wfit
:x$expert
is still formatted as per stats::lm
.equalPro=TRUE
).MoE_entropy
and MoE_AvePP
both gain the arg. group
for computing the average entropiesFALSE
, i.e. old behaviour.FARI
for computing the Frobenius (adjusted) Rand index between two soft &/or hard partitions.as.Mclust
for models w/ gating & expert covariates when expert.covar=TRUE
.matrixStats (>= 1.0.0)
+ related minor speed-ups.CITATION
commands & updated License: GPL (>= 3)
.MoE_gpairs
arg. diag.pars$show.dens=FALSE
added to toggle whetherMoE_Similarity
added and integrated into plot.MoEClust
.MoE_AvePP
added.MoE_mahala
for univariate data with (default) identity=FALSE
.<=1
observations (or equivalent):exp.init$malanabis=TRUE
(the default) introduced in v1.4.1,modelNames
are being fitted!MoE_entropy
added.summary
(and related print
) methods for MoECriterion
objects."EEE"
& "VVV"
models.G=0:X
in MoE_clust
without adding noise for G>0
, unlessmodelNames
when G=1
only.hc.meth
arg. in MoE_control
.z.list
in MoE_control
.MoE_mahala
arg. identity
(& related MoE_control
exp.init$identity
option) is now alsoFALSE
& TRUE
foridentity=FALSE
for univariate data is new).MoE_clust
bug when tau0
is specified but G
is not (introduced in last update).MoE_gpairs(response.type="density")
w/ expert covariates & noise component.MoE_gpairs
arg. density.pars$grid.size
now recycled as vector of length 2 if supplied as scalar.aitken
now returns ldiff
, the difference in log-likelihood estimates used for the stopping criterion.sapply
replaced with vapply
, with other negligible speed-ups.MoE_stepwise
:
fullMoE
(defaulting to FALSE
) which allows restricting the search to “full”initialModel
/initialG
is given, the "all"
option for noise.gate
& equalPro
"both"
whenever "all"
would unnecessarily duplicate candidate models.gating
&/or expert
have covariates that are already in initialModel
.G=1
equalPro
models w/ expert covariates only once.initialModel
and modelNames
interact:
initialModel
should be optimal w.r.t. model type.modelNames
are augmented with initialModel$modelName
if needs be.MoE_control
gains the arg. exp.init$estart
so the paper’s Algorithm 1 can work as intended:exp.init$estart
toggles the behaviour of init.z="random"
in the presence of expert covariatesexp.init$mahalanobis=TRUE
& nstarts > 1
: when FALSE
(the default/old behaviour), allTRUE
, only the single best random start obtained from this routine is subjected to the full EM.list(...)
defaults in MoE_control
/MoE_gpairs
.noise.gate
in MoE_compare
for G=1
models w/ noise & gating covariates.G
in MoE_clust
.MoE_stepwise()
(thanks, in part, to requests from Dr. Konstantinos Perrakis):
initialModel
arg. for specifying an initial model from which to begin the search,initialG
arg. as a simpler alternative when the only availablestepG
arg. (defaults to TRUE
) for fixing the number of componentsFALSE
).noise.gate
arg. now also invoked when adding components to models with gating covariatesequalPro
& noise.gate
args. gain new default "all"
(see documentation for details).network.data
argument.fitted
method for "MoEClust"
objects (a wrapper to predict.MoEClust
).predict
, fitted
, & residuals
methods for "MoE_gating"
objects, i.e. x$gating
.predict
, fitted
, & residuals
methods for "MoE_expert"
objects, i.e. x$expert
.predict.MoEClust
for models without expert network covariates.x$gating
object for equalPro=TRUE
models with a noise component.MoE_gpairs
:
expert_covar
(see below).mosaic.pars
gains logical arg. mfill=TRUE
, to toggle between filling select tiles with colourboxplot.pars
arg. added to allow customising boxplot and violin plot panels,scatter.pars$eci.col
: now governs colours of ellipses and regression lines.scatter.pars$uncert.pch
added; now plotting symbols in covariate-related scatterplotsresponse.type="uncertainty"
plots when uncert.cov
is TRUE
.expert_covar
gains the arg. weighted
to ensure cluster membership probabilities are properlyTRUE
,weighted=FALSE
is provided as an option for recovering the old (not recommended) behaviour.itmax
arg. to MoE_control
: the 3rd element of this arg. governs100
to1000
(thanks to a prompt from Dr. Georgios Karagiannis), which has the effect of slowing downnnet::multinom
but generally reduces the required number of EM iterations.MoE_compare
whenever the optimal model needs to be refitted.mclust::as.Mclust
& MoEClust::as.Mclust
:as.Mclust.MoEClust
now works regardless of order in which mclust
& MoEClust
are loaded.gating
& expert
formulas which are not found in network.data
.MoE_stepwise
speed-ups by avoiding duplication of initialisation for certain steps.MoE_stepwise
for univariate data sets without covariates.MoE_uncertainty
plots.MoE_control
arg. posidens=TRUE
ensures code no longer crashes when observationsposidens=FALSE
.MoE_control
gains the arg. asMclust
(FALSE
, by default) which modifies thestopping
and hcUse
arguments such that MoEClust
and mclust
behave similarlyMoE_gpairs
(thanks to Dr. Natasha De Manincor):
predict.MoEClust
when no newdata
is supplied to models with no gating covariates.MoE_clust
& MoE_stepwise
now coerce "character"
covariates to "factor"
(for later plotting).summary
method for MoE_expert
objects.print
& summary
methods for MoE_gating
objects if G=1
or equalPro=TRUE
.MoE_plotGate
.print.MoECompare
gains the args. maxi
, posidens=TRUE
, & rerank=FALSE
.lattice(>=0.12)
, matrixStats(>=0.53.1)
, & mclust(>=5.4)
in Imports:
.clustMD(>=1.2.1)
and geometry(>=0.4.0)
in Suggests:
.NCOL
/NROW
where appropriate.mclust
compatibility edits.summary.MoEClust
gains the printing-related arguments classification=TRUE
,parameters=FALSE
, and networks=FALSE
(thanks to a request from Prof. Kamel Gana).print
/summary
methods for MoE_gating
& MoE_expert
objects.G=1
models with expert network covariates.MoE_plotGate
, with new type
, pch
, and xlab
defaults.dimnames
to returned parameters
from MoE_clust()
.MoE_mahala
now correctly uses the covariance of resids
rather than the response.MoE_mahala
arg. identity
allow use of Euclidean distance instead:exp.init$identity
to MoE_control
.MoE_control
arg. exp.init$max.init
now defaults to .Machine$integer.max
.resids
arg. to MoE_mahala
.MoE_mahala
examples.predict.MoEClust
:
MAPy
), in addition to the (aggregated) predicted responses (y
).MAPresids
governs whether residuals are computed against MAPy
or y
.use.y
(see documentation for details).newdata
for models with no covariates of any kind.discard.noise=FALSE
.MoE_stepwise
bugs when
gating
or expert
are supplied.data
are supplied.summary
on x$gating
.noise_vol
now returns correction location for univariate data when reciprocal=TRUE
.donttest
examples.MoE_stepwise
:
network.data
and data
.z.list
from being suppliable.equalPro="yes"
& noise=TRUE
.MoE_control
arguments (also for MoE_clust
).discard.noise=TRUE
behaviour for MoE_clust
, predict.MoEClust
, &residuals.MoEClust
for models with a noise component fitted via "CEM"
.noise_vol
function and handling of noise.meth
arg. to MoE_control
.MoE_clust
output (see ?MoE_control
).MoE_stepwise
for conducting a greedy forward stepwiseMoE_control
& predict.MoEClust
gain the arg. discard.noise
:FALSE
retains old behaviour (see documentation for details).MoE_control
gains the arg. z.list
and the init.z
arg. gets the option "list"
:MoE_gpairs
:
uncert.cov
arg. added to control uncertainty point-size in panels with covariates.density.pars
gains arg. label.style
.scatter.pars
& stripplot.pars
gain args. noise.size
& size.noise
.barcode.pars$bar.col
slightly fixed from previous update."violin"
type plots now accurate for MAP panels.noise_vol
when method="ellipsoidhull"
.predict.MoEClust
when resid=TRUE
for models with expert covariates....
construct for residuals.MoEClust
.print.MoEClust
, print.summary_MoEClust
, & print.MoECompare
.gating
objects for equalPro=TRUE
models.parallel
package from Suggests:
.noise_vol
now also returns the location of the centre of mass of the regionpredict.MoEClust
for any models with a noise component (see below).MoE_gpairs
(see below).noise_vol
for data with >2 dimensionsmethod="ellipsoidhull"
, owing to a bug in the cluster
package.MoE_gpairs
plotting function:
expert.covar
(& also to as.Mclust
function).response.type="density"
for all models with a noise component.response.type="density"
for models with covariates of any kind.subset$data.ind
& subset$cov.ind
arguments.buffer
.MoE_plotGate
is now consistent with MoE_gpairs
.gating
& expert
formulas are handled:
~.-a-b
.~c-1
.I()
.drop_levels
& drop_constants
functions.MoE_compare
gains arg. noise.vol
for overriding the noise.meth
arg.:noise_vol()
fails.equalPro
models with noise component, and also added equalNoise
arg.MoE_control
, further controlling equalPro
in the presence of a noise component.predict.MoEClust
for the following special cases:
noise_vol
comment above).x.axis
arg. to MoE_plotGate
.tau0
can now also be supplied as a vector in the presence of gating covariates.expert_covar
for univariate models.MoE_estep
speed-up due to removal of unnecessary sweep()
.clustMD
is invoked, and added snow
package to Suggests:
.nnet
arg. MaxNWts
now passable to gating network multinom
call via MoE_control
.MoE_compare
.MoE_control
arg. algo
allows model fitting using the "EM"
or "CEM"
algorithm:
MoE_cstep
added.algo
option "cemEM"
allows running EM starting from convergence of CEM.LOGLIK
to MoE_clust
output, giving maximal log-likelihood values for all fitted models.
DF/ITERS
, etc., with associated printing/plotting functions.MoE_compare
, summary.MoEClust
, & MoE_plotCrit
accordingly.MoE_control
arg. nstarts
allows for multiple random starts when init.z="random"
.MoE_control
arg. tau0
provides another means of initialising the noise component.clustMD
is invoked for initialisation, models are now run more quickly in parallel.MoE_plotGate
now allows a user-specified x-axis against which mixing proportions are plotted.predict.MoEClust
function added: predicts cluster membership probability,noise.gate
option) accounted for.MoE_Uncertainty
added (callable within plot.MoEClust
):response.type="density"
to MoE_gpairs
now works properly for models withclustMD
package to Suggests:
. New MoE_control
argument exp.init$clustMD
isTRUE(exp.init$joint)
& clustMD
is loaded (defaults to FALSE
, works with noise).drop.break
arg. to MoE_control
for further control over the extra initialisationMoE_dens
for the EEE
& VVV
models by using already available Cholesky factors.MoE_control
arguments:
km.args
specifies kstarts
& kiters
when init.z="kmeans"
.init.z="hc"
& noise into hc.args
& noise.args
.hc.args
now also passed to call to mclust
when init.z="mclust"
.init.crit
("bic"
/"icl"
) controls selection of optimal mclust
/clustMD
init.z="mclust"
or isTRUE(exp.init$clustMD)
);init.z="mclust"
.ITERS
replaces iters
as the matrix of the number of EM iterations in MoE_clust
output:
iters
now gives this number for the optimal model.
ITERS
now behaves like BIC
/ICL
etc. in inheriting the "MoECriterion"
class.iters
now filters down to summary.MoEClust
and the associated printing function.ITERS
now filters down to MoE_compare
and the associated printing function.response.type="uncertainty"
MoE_gpairs
to better conform to mclust
: previously no transparency.subset
arg. to MoE_gpairs
now allows data.ind=0
or cov.ind=0
, allowing plotting ofMoE_gpairs
plots.sigs
arg. to MoE_dens
& MoE_estep
must now be a variance object, as per variance
MoE_clust
& mclust
output, the number of clusters G
,d
& modelName
is inferred from this object: the arg. modelName
was removed.MoE_clust
no longer returns an error if init.z="mclust"
when no gating/expert networkinit.z="hc"
is used to better reproduce mclust
output.resid.data
now returned by MoE_clust
as a list, to better conform to MoE_dens
.MoE_aitken
& MoE_qclass
to aitken
& quant_clust
, respectively.data
w/ missing values now dropped for gating/expert covariates too (MoE_clust
).linf
within aitken
& the associated stopping criterion.linf
estimate now returned for optimal model when stopping="aitken"
& G > 1.resid
& residuals
args. to as.Mclust
& MoE_gpairs
.MoE_plotCrit
, MoE_plotGate
& MoE_plotLogLik
now invisibly return relevant quantities.G=0
models when noise.init
is not supplied.drop_levels
to handle alphanumeric variable names and ordinal variables.MoE_compare
when a mix of models with and without a noise component are supplied.MoE_compare
when optimal model has to be re-fit due to mismatched criterion
.MoE_Uncertainty
plots.print.MoECompare
now has a digits
arg. to control rounding of printed output.MoE_clust
& MoE_compare
.drop_constants
.is.list(x)
with inherits(x, "list")
for stricter checking.MoE_clust
.mclust::clustCombi/clustCombiOptim
examples to as.Mclust
documentation.MoE_news
for accessing this NEWS
file.G
is at either end of the range considered.cat
/message
/warning
calls for printing clarity.usage
sections of multi-argument functions.MoEClust-package
help file (formerly just MoEClust
).MoE_control
gains the noise.gate
argument (defaults to TRUE
): when FALSE
,x$parameters$mean
is now reported as the posterior mean of the fitted values whenMoE_gpairs
plots when there are expert covariates.expert_covar
used to account for variability in the means, in the presenceMoE_control
gains the hcUse
argument (defaults to "VARS"
as per old mclust
versions).MoE_mahala
gains the squared
argument + speedup/matrix-inversion improvements.matrixStats
(on which MoEClust
already depended).MoE_gpairs
argument addEllipses
gains the option "both"
.equalPro=TRUE
in the presence of a noise component when there areMoE_gpairs
argument scatter.type
gains the options lm2
& ci2
for further controllm
& ci
type plots were beingMoE_mahala
and in expert network estimation with a noise component.G=0
models w/ noise component only can now be fitted without having to supply noise.init
.MoE_compare
now correctly prints noise information for sub-optimal models.stopping="relative"
: now conforms to mclust
.check.margin=FALSE
to calls to sweep()
.call.=FALSE
to all stop()
messages.grid
library.These binaries (installable software) and packages are in development.
They may not be fully stable and should be used with caution. We make no claims about them.
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