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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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