fixing CRAN issues

DESCRIPTION

@@ -1,14 +1,15 @@
 Package: CEC
 Title: Cross-Entropy Clustering
 Version: 0.10.3
-Date: 2021-09-17
+Date: 2021-09-20
 Author: Konrad Kamieniecki [aut, cre], Przemyslaw Spurek [ctb]
 Maintainer: Konrad Kamieniecki <[email protected]>
-Description: CEC divides data into Gaussian type clusters. The implementation allows the simultaneous use of various type Gaussian mixture models, performs the reduction of unnecessary clusters and it's able to discover new groups. Based on Spurek, P. and Tabor, J. (2014) <doi:10.1016/j.patcog.2014.03.006>.
+Description: Clustering that splits data into Gaussian type clusters. The implementation allows the simultaneous use of various type Gaussian mixture models, performs the reduction of unnecessary clusters and it's able to discover new groups. Based on Spurek, P. and Tabor, J. (2014) <doi:10.1016/j.patcog.2014.03.006>.
 ByteCompile: true
 URL: https://github.com/azureblue/cec
 Encoding: UTF-8
 NeedsCompilation: yes
 SystemRequirements: C++11
 License: GPL-3
 Imports: graphics, methods, stats, utils
+Packaged: 2021-09-20 21:50:01 UTC; konrad

R/cec.R

@@ -7,15 +7,15 @@ cec <- function(
     param,
     centers.init  = c("kmeans++", "random"), 
     card.min      = "5%",
-    keep.removed  = F,
-    interactive   = F,
+    keep.removed  = FALSE,
+    interactive   = FALSE,
     threads       = 1,
-    split         = F,
+    split         = FALSE,
     split.depth   = 8,
     split.tries   = 5,
     split.limit   = 100,
     split.initial.starts = 1,
-    readline      = T
+    readline      = TRUE
 )
 {
     # check arguments  
@@ -207,13 +207,14 @@ cec.interactive <- function(
     param,
     centers.init  = c("kmeans++", "random"), 
     card.min      = "5%",
-    keep.removed  = F,
-    readline      = T
+    keep.removed  = FALSE,
+    readline      = TRUE
 )
 {
     par 
     {
         old.ask = par()["ask"]   
+        on.exit(par(old.ask))
         n = ncol(x)
         if (n != 2) 
             stop("interactive mode available only for 2-dimensional data")    
@@ -261,7 +262,6 @@ cec.interactive <- function(
             i = i + 1
         }    
         plot(Z, ellipses="TRUE")
-        par(ask = old.ask)
         if (readline)
             ignore = readline(prompt="Press <Enter>:")
 

R/plot.cec.R

@@ -1,4 +1,4 @@
-plot.cec <- function(x, col, cex = 0.5, pch = 19, cex.centers = 1, pch.centers = 8, ellipses.lwd = 4, ellipses = TRUE, model = T, xlab, ylab, ...)
+plot.cec <- function(x, col, cex = 0.5, pch = 19, cex.centers = 1, pch.centers = 8, ellipses.lwd = 4, ellipses = TRUE, model = TRUE, xlab, ylab, ...)
 {
     if (ncol (x $ data) != 2 )
         stop("plotting available only for 2-dimensional data")
@@ -45,4 +45,4 @@ plot.cec <- function(x, col, cex = 0.5, pch = 19, cex.centers = 1, pch.centers =
                     finally = {})     
             }
     }  
-}
+}

man/CEC-package.Rd

@@ -22,4 +22,12 @@ Konrad Kamieniecki
 \seealso{
 \code{\link{cec}}
 }
-\keyword{ clustering, entropy, gaussian, kmeans }
+
+\keyword{cluster}
+\keyword{models}
+\keyword{multivariate}
+\keyword{package}
+\concept{entropy}
+\concept{gaussian}
+\concept{gaussian mixture models}
+\concept{kmeans}

man/ball.Rd

@@ -41,6 +41,4 @@ M = ball(4000, 0.9)
 plot(M, cex = 0.5, pch = 19)
 }
 
-\keyword{ ~ball }
-\keyword{ ~points }
-\keyword{ ~uniform }
+\keyword{datagen}

man/cec.Rd

@@ -12,9 +12,9 @@ Performs Cross-Entropy Clustering on a data matrix.
 \usage{
 cec(x, centers, type = c("covariance", "fixedr", "spherical", "diagonal",  
 "eigenvalues", "mean", "all"), iter.max = 25, nstart = 1, param,
-centers.init = c("kmeans++", "random"), card.min = "5\%", keep.removed = F, 
-interactive = F, threads = 1, split = F, split.depth = 8, split.tries = 5, 
-split.limit = 100, split.initial.starts = 1,readline = T)
+centers.init = c("kmeans++", "random"), card.min = "5\%", keep.removed = FALSE, 
+interactive = FALSE, threads = 1, split = FALSE, split.depth = 8, split.tries = 5, 
+split.limit = 100, split.initial.starts = 1, readline = TRUE)
 }
 
 \arguments{
@@ -56,7 +56,7 @@ only if the \code{centers} argument is a number or a vector.
 If the \code{centers} argument is a vector, \code{length(centers)} clusterings will be performed
 for each start and the total number of clusterings will be \code{length(centers) * nstart}.
 
-If the split mode is on (\code{split = T}), it's rarely desired use change this parameter as the whole procedure (initial clustering + split) will be performed \code{nstart} times.
+If the split mode is on (\code{split = TRUE}), it's rarely desired use change this parameter as the whole procedure (initial clustering + split) will be performed \code{nstart} times.
 }
 
 \item{centers.init}{
@@ -182,7 +182,8 @@ m2 = matrix(rnorm(2000, mean = 3, sd = 1.5), ncol = 2)
 m3 = matrix(rnorm(2000, mean = 3, sd = 1), ncol = 2)
 m3[,2] = m3[,2] - 5
 m = rbind(m1, m2, m3)
-par(ask = TRUE)
+oldpar = par(ask = TRUE)
+on.exit(par(oldpar))
 plot(m, cex = 0.5, pch = 19)
 ## Clustering result:
 Z = cec(m, 10, iter.max = 100, card.min="7\%")
@@ -223,5 +224,13 @@ Spurek, P. and Tabor, J. (2014)
 Cross-Entropy Clustering
 \emph{Pattern Recognition} \bold{47, 9} 3046--3059
 }
-\keyword{ ~cec }
-\keyword{ ~clustering }
+
+\keyword{cluster}
+\keyword{models}
+\keyword{multivariate}
+\keyword{package}
+\concept{entropy}
+\concept{gaussian}
+\concept{gaussian mixture models}
+\concept{kmeans}
+

man/mouseset.Rd

@@ -59,7 +59,4 @@ right.ear.dist=2.5, dim=2)
 plot(M, cex = 0.5, pch = 19)
 }
 
-\keyword{ ~mouse}
-\keyword{ ~mouseset}
-\keyword{ ~points}
-\keyword{ ~uniform}
+\keyword{datagen}

man/plot.cec.Rd

@@ -13,7 +13,7 @@ Ellipses are drawn with regards to the covariance (either model or sample) of ea
 
 \usage{
 \method{plot}{cec}(x, col, cex = 0.5, pch = 19, cex.centers = 1, pch.centers = 8, 
-ellipses.lwd = 4, ellipses = TRUE, model = T, xlab, ylab, ...)
+ellipses.lwd = 4, ellipses = TRUE, model = TRUE, xlab, ylab, ...)
 }
 
 \arguments{
@@ -67,6 +67,8 @@ Arguments are passed to \code{plot} function when drawing data points.
 }
 }
 
+\value{No return value.}
+
 \seealso{
 \code{\link{print.cec}}
 }
@@ -75,5 +77,5 @@ Arguments are passed to \code{plot} function when drawing data points.
 ## See the examples of function cec.
 }
 
-\keyword{ ~plot }
-\keyword{ ~cec }
+\keyword{hplot}
+

man/print.cec.Rd

@@ -24,13 +24,12 @@ Ignored.
 }
 }
 
+\value{Returns the summary of the \code{cec} function result as text.}
+
 \seealso{
 \code{\link{plot.cec}}
 }
 
 \examples{
 ## See the examples of function cec.
 }
-
-\keyword{ ~print }
-\keyword{ ~cec }

man/run.cec.tests.Rd

@@ -14,6 +14,5 @@ defining each test case. This is also used for R CMD check.
 run.cec.tests()
 }
 
-\keyword{ ~tests }
-\keyword{ ~unit }
-\keyword{ ~cec }
+\value{No return value. Stops with error when a test fails.}
+\concept{unit testing}