version 5.4.8

Author: luca-scr

DESCRIPTION

@@ -1,9 +1,12 @@
 Package: mclust
-Version: 5.4.7
-Date: 2020-11-08
+Version: 5.4.8
+Date: 2021-11-05
 Title: Gaussian Mixture Modelling for Model-Based Clustering,
         Classification, and Density Estimation
-Description: Gaussian finite mixture models fitted via EM algorithm for model-based clustering, classification, and density estimation, including Bayesian regularization, dimension reduction for visualisation, and resampling-based inference.
+Description: Gaussian finite mixture models fitted via EM algorithm for
+  model-based clustering, classification, and density estimation, 
+  including Bayesian regularization, dimension reduction for 
+  visualisation, and resampling-based inference.
 Authors@R: c(person("Chris", "Fraley", role = "aut"),
              person("Adrian E.", "Raftery", role = "aut",
                     comment = c(ORCID = "0000-0002-6589-301X")),
@@ -26,11 +29,11 @@ ByteCompile: true
 NeedsCompilation: yes
 LazyData: yes
 Encoding: UTF-8
-Packaged: 2020-11-20 08:46:31 UTC; luca
+Packaged: 2021-11-05 11:30:47 UTC; luca
 Author: Chris Fraley [aut],
   Adrian E. Raftery [aut] (<https://orcid.org/0000-0002-6589-301X>),
   Luca Scrucca [aut, cre] (<https://orcid.org/0000-0003-3826-0484>),
   Thomas Brendan Murphy [ctb] (<https://orcid.org/0000-0002-5668-7046>),
   Michael Fop [ctb] (<https://orcid.org/0000-0003-3936-2757>)
 Maintainer: Luca Scrucca <[email protected]>
-Date/Publication: 2020-11-20 10:40:03 UTC
+Date/Publication: 2021-11-05 12:40:02 UTC

MD5

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 c1b81d23059192faf2b0fdb40b0bc0d2 *man/wreath.Rd
 2a6f9e9e044a78154d3cfda5936d6f48 *src/Makevars
 d784799104d2c2350f9350b268761a2b *src/dmvnorm.f
 394a717e565a6647678c758462d11eb2 *src/init.c
 5ddcdc7e9d5c82abda7bcb62fb594cb3 *src/mclust.f
 015387e2f8c8f04d9e8900f82002a925 *src/mclustaddson.f
-ab28dde3ab58c3103ae0440bd0e3d81c *vignettes/mclust.Rmd
-65f749d551420d943d4c097ff4bd7fdc *vignettes/vignette.css
+c7680542d4532804d5be21b3684986c7 *vignettes/mclust.Rmd
+71148153fcf7f0388c1ae6f5da2e9f06 *vignettes/vignette.css

NAMESPACE

@@ -60,7 +60,7 @@ export(hc, print.hc, plot.hc)
 S3method("print", "hc")
 S3method("plot", "hc")
 export(hcE, hcEEE, hcEII, hcV, hcVII, hcVVV)
-export(hclass, hcRandomPairs, randomPairs)
+export(hclass, hcRandomPairs, randomPairs, dupPartition)
 
 export(mclustBIC, print.mclustBIC, summary.mclustBIC, 
        print.summary.Mclust, plot.mclustBIC,

NEWS.md

@@ -1,11 +1,21 @@
-# mclust 5.4.7 (NOT ON CRAN)
+# mclust 5.4.8
+
+- `densityMclust()` by default draw a graph of the density estimate.
+- Fixed a bug in computing mixture density if the noise component is present.
+- Changed default behaviour of `hc()` when called to perform agglomerative hierarchical clustering instead of using for EM initialization.
+- The default `mclust.options("hcModelName")` now returns only the model to be used.
+- Changed default `partition` argument of `hc()` function by adding `dupPartion()` to remove data duplicates.
+- Added checks to `mclustBootstrapLRT()` to stop if an invalid `modelName` is provided or a one-component mixture model is provided. 
+- Extended the functionality of `cvMclustDA()` by including as cross-validated metrics both the classification error and the Brier score.
+- Updated info on dataset man pages. 
+
+# mclust 5.4.7
 
 - Updated plot method (dendrogram) for hierarchical clustering --- now based on classification likelihood.
 - Added `MclustSSC()` function (and related `print`, `summary`, `plot`, and `predict`, methods) for semi-supervised classification.
 - Exchanged order of models VEE and EVE to account for increasing complexity of EVE.
 - Added `cex` argument to `clPairs()` to control character expansion used in plotting symbols.
 - `em()` and `me()` have now `data` as first argument.
-- Added fish length data. 
 
 # mclust 5.4.6
 

R/bootstrap.R

@@ -13,6 +13,10 @@ mclustBootstrapLRT <- function(data, modelName = NULL,
   if(is.null(modelName))
     stop("A 'modelName' must be provided. Please see help(mclustModelNames) which describes the available models.")
   modelName <- modelName[1]
+  checkModelName(modelName)
+  if(grepl("X", modelName))
+    stop("Specified 'modelName' is only valid for one-component mixture.")
+  
   if(is.null(maxG))
   { 
     G <- seq.int(1, 9)
@@ -21,6 +25,7 @@ mclustBootstrapLRT <- function(data, modelName = NULL,
     maxG <- as.numeric(maxG)
     G <- seq.int(1, maxG+1) 
   }
+  
   BIC <- mclustBIC(data, G = G, modelNames = modelName, 
                    warn = FALSE, verbose = FALSE, ...)
 

R/clustCombi.R

@@ -6,7 +6,7 @@ clustCombi <- function(object = NULL, data = NULL, ...)
     { object <- Mclust(data, ...) }
   else
     { if(!inherits(object, "Mclust")) 
-        stop("object not of class \"Mclust\"")
+        stop("object not of class 'Mclust'")
       data <- object$data }
 	combiRes <- combi(data, object)
 	return(combiRes)
@@ -87,7 +87,7 @@ plot.clustCombi <- function(x, what = c("classification", "entropy", "tree"), ..
 {
   object <- x # Argh.  Really want to use object anyway
   if(!inherits(object, "clustCombi")) 
-    stop("object not of class \"clustCombi\"")
+    stop("object not of class 'clustCombi'")
   data <- object$MclustOutput$data
 
   what <- match.arg(what, several.ok = TRUE)
@@ -308,7 +308,7 @@ combiTree <- function(object, type = c("triangle", "rectangle"),
 { 
 
   if(!inherits(object, "clustCombi")) 
-    stop("object not of class \"clustCombi\"")
+    stop("object not of class 'clustCombi'")
   yaxis <- match.arg(yaxis, eval(formals(combiTree)$yaxis), several.ok = FALSE)
   type <- match.arg(type, eval(formals(combiTree)$type), several.ok = FALSE)