version 5.4.7

changbiHub · Nov 20, 2020 · 598224f · 598224f
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diff --git a/DESCRIPTION b/DESCRIPTION
@@ -1,6 +1,6 @@
 Package: mclust
-Version: 5.4.6
-Date: 2020-04-09
+Version: 5.4.7
+Date: 2020-11-08
 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.
@@ -26,11 +26,11 @@ ByteCompile: true
 NeedsCompilation: yes
 LazyData: yes
 Encoding: UTF-8
-Packaged: 2020-04-09 17:43:44 UTC; luca
+Packaged: 2020-11-20 08:46:31 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 <luca.scrucca@unipg.it>
-Date/Publication: 2020-04-11 14:30:08 UTC
+Date/Publication: 2020-11-20 10:40:03 UTC
diff --git a/MD5 b/MD5
@@ -1,158 +1,163 @@
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diff --git a/NAMESPACE b/NAMESPACE
@@ -56,13 +56,11 @@ export(clPairs, clPairsLegend, coordProj, randProj,
 
 export(priorControl, defaultPrior, hypvol)
 
-export(hc, print.hc, plot.hc, as.hclust.hc, as.dendrogram.hc)
+export(hc, print.hc, plot.hc)
 S3method("print", "hc")
 S3method("plot", "hc")
-S3method("as.hclust", "hc")
-S3method("as.dendrogram", "hc")
 export(hcE, hcEEE, hcEII, hcV, hcVII, hcVVV)
-export(hclass, randomPairs)
+export(hclass, hcRandomPairs, randomPairs)
 
 export(mclustBIC, print.mclustBIC, summary.mclustBIC, 
        print.summary.Mclust, plot.mclustBIC,
@@ -97,6 +95,14 @@ S3method("plot", "MclustDA")
 S3method("predict", "MclustDA")
 S3method("logLik", "MclustDA")
 
+export(MclustSSC, print.MclustSSC, summary.MclustSSC, print.summary.MclustSSC,
+       plot.MclustSSC, predict.MclustSSC)
+S3method("print", "MclustSSC")
+S3method("summary", "MclustSSC")
+S3method("print", "summary.MclustSSC")
+S3method("plot", "MclustSSC")
+S3method("predict", "MclustSSC")
+
 export(MclustDR, print.MclustDR, summary.MclustDR, print.summary.MclustDR,
        plot.MclustDR, plotEvalues.MclustDR, projpar.MclustDR, 
        predict.MclustDR, predict2D.MclustDR)

diff --git a/NEWS.md b/NEWS.md
@@ -1,3 +1,12 @@
+# mclust 5.4.7 (NOT ON CRAN)
+
+- 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
 
 - Fixed issues with source Fortran code with gfortran 10 as reported by CRAN.

diff --git a/R/graphics.R b/R/graphics.R
@@ -494,7 +494,7 @@ mvn2plot <- function(mu, sigma, k = 15, alone = FALSE,
 }
 
 clPairs <- function (data, classification, 
-                     symbols = NULL, colors = NULL, cex = 1, 
+                     symbols = NULL, colors = NULL, cex = NULL, 
                      labels = dimnames(data)[[2]], cex.labels = 1.5, 
                      gap = 0.2, grid = FALSE, ...) 
 {
@@ -532,6 +532,7 @@ clPairs <- function (data, classification,
     { colors <- rep( "black", l)
       warning("more colors needed")
   }
+	if(is.null(cex)) cex <- rep(1, l) 
   grid <- isTRUE(as.logical(grid))
 
   if(d > 2)
@@ -542,12 +543,12 @@ clPairs <- function (data, classification,
             },
             pch = symbols[classification], 
             col = colors[classification], 
+            cex = cex[classification], 
             gap = gap, 
-            cex = cex, 
             cex.labels = cex.labels,
             ...) }
   else if(d == 2)
-    { plot(data, cex = cex, 
+    { plot(data, cex = cex[classification],
             pch = symbols[classification], 
             col = colors[classification], 
             panel.first = if(grid) grid(),
@@ -556,10 +557,11 @@ clPairs <- function (data, classification,
   invisible(list(d = d,
                  class = levels(classification),
                  col = colors,
-                 pch = symbols[seq(l)]))
+                 pch = symbols[seq(l)],
+								 cex = cex))
 }
 
-clPairsLegend <- function(x, y, class, col, pch, box = TRUE, ...)
+clPairsLegend <- function(x, y, class, col, pch, cex, box = TRUE, ...)
 {
 
   usr <- par("usr")
@@ -581,9 +583,10 @@ clPairsLegend <- function(x, y, class, col, pch, box = TRUE, ...)
   dots$legend <- class
   dots$text.width <- max(strwidth(dots$title, units = "user"), 
                          strwidth(dots$legend, units = "user"))
-  dots$col <- col
-  dots$text.col <- col
-  dots$pch <- pch
+  dots$col <- if(missing(col)) 1 else col
+  dots$text.col <- if(missing(col)) 1 else col
+  dots$pch <- if(missing(pch)) 1 else pch
+	dots$cex <- if(missing(cex)) 1 else cex
   dots$title.col <- par("fg")
   dots$title.adj <- 0.1
   dots$xpd <- NA