mclustOptions {mclust} | R Documentation |
Supplies a list of values including tolerances for singularity and convergence assessment, and an enumeration of models for use with MCLUST.
mclustOptions(eps, tol, itmax, equalPro, warnSingular, emModelNames, hcModelName, symbols)
eps |
A scalar tolerance associated with deciding when to terminate
computations due to computational singularity in
covariances. Smaller values of eps allow computations to
proceed nearer to singularity. The default is the relative machine
precision .Machine\$double.eps , which is approximately
$2e-16$ on IEEE-compliant machines.
|
tol |
A vector of length two giving relative convergence tolerances for the
loglikelihood and for parameter convergence in the inner loop for models
with iterative M-step ("VEI", "VEE", "VVE", "VEV"), respectively.
The default is c(1.e-5,1.e-5) .
|
itmax |
A vector of length two giving integer limits on the number of EM
iterations and on the number of iterations in the inner loop for
models with iterative M-step ("VEI", "VEE", "VVE", "VEV"),
respectively. The default is c(Inf,Inf) allowing termination
to be completely governed by tol .
|
equalPro |
Logical variable indicating whether or not the mixing proportions are
equal in the model. Default: equalPro = FALSE .
|
warnSingular |
A logical value indicating whether or not a warning should be issued
whenever a singularity is encountered. The default is
warnSingular = TRUE .
|
emModelNames |
A vector of character strings associated with multivariate models in
MCLUST. The default includes strings encoding all of the
multivariate models available: "EII": spherical, equal volume "VII": spherical, unequal volume "EEI": diagonal, equal volume and shape "VEI": diagonal, varying volume, equal shape "EVI": diagonal, equal volume, varying shape "VVI": diagonal, varying volume and shape "EEE": ellipsoidal, equal volume, shape, and orientation "EEV": ellipsoidal, equal volume and equal shape "VEV": ellipsoidal, equal shape "VVV": ellipsoidal, varying volume, shape, and orientation |
hcModelName |
A vector of two character strings giving the name of the model to be
used in the hierarchical clustering phase for univariate and
multivariate data, respectively, in EMclust and
EMclustN . The default is c("V","VVV") , giving the
unconstrained model in each case.
|
symbols |
A vector whose entries are either integers corresponding to graphics
symbols or single characters for plotting for
classifications. Classes are assigned symbols in the given
order. The default is
c(17,0,10,4,11,18,6,7,3,16,2,12,8,15,1,9,14,13,5) .
|
mclustOptions
is provided for assigning values
to the .Mclust
list, which is used
to supply default values to various functions in MCLUST.
Calls to mclustOptions
do not in themselves affect
the outcome of computations.
A named list in which the names are the names of the arguments and the values are the values supplied to the arguments.
C. Fraley and A. E. Raftery (2002a). Model-based clustering, discriminant analysis, and density estimation. Journal of the American Statistical Association 97:611-631. See http://www.stat.washington.edu/mclust.
C. Fraley and A. E. Raftery (2002b). MCLUST:Software for model-based clustering, density estimation and discriminant analysis. Technical Report, Department of Statistics, University of Washington. See http://www.stat.washington.edu/mclust.
data(iris) irisMatrix <- as.matrix(iris[,1:4]) irisClass <- iris[,5] .Mclust .Mclust <- mclustOptions(tol = 1.e-6, emModelNames = c("VII", "VVI", "VVV")) .Mclust irisBic <- EMclust(irisMatrix) summary(irisBic, irisMatrix) .Mclust <- mclustOptions() # restore default values .Mclust