Merge pull request #14 from snoweye/master

snoweye · web-flow · commit 14f70761e1fd · 2016-09-22T19:59:44.000-04:00
0.1-8 on CRAN
diff --git a/DESCRIPTION b/DESCRIPTION
@@ -1,6 +1,6 @@
 Package: pmclust
-Version: 0.1-7
-Date: 2016-06-07
+Version: 0.1-8
+Date: 2016-09-21
 Title: Parallel Model-Based Clustering using
         Expectation-Gathering-Maximization Algorithm for Finite Mixture
         Gaussian Model
@@ -30,7 +30,3 @@ BugReports: http://group.r-pbd.org/
 MailingList: Please send questions and comments regarding pbdR to
         RBigData@gmail.com
 NeedsCompilation: yes
-Packaged: 2016-01-24 20:10:34 UTC; snoweye
-Author: Wei-Chen Chen [aut, cre],
-  George Ostrouchov [aut]
-Maintainer: Wei-Chen Chen <wccsnow@gmail.com>
diff --git a/inst/CITATION b/inst/CITATION
@@ -6,8 +6,8 @@ citEntry(
   author = personList(as.person("W.-C. Chen"), as.person("G. Ostrouchov")),
   year = "2012",
   note = "R Package",
-  url = "http://cran.r-project.org/package=pmclust",
-  textVersion = "W.-C. Chen, G. Ostrouchov (2012). pmclust: Parallel Model-Based Clustering. R Package, URL http://cran.r-project.org/package=pmclust",
+  url = "https://cran.r-project.org/package=pmclust",
+  textVersion = "W.-C. Chen, G. Ostrouchov (2012). pmclust: Parallel Model-Based Clustering. R Package, URL https://cran.r-project.org/package=pmclust",
   key = "Chen2012pmclustpackage"
 )
 
@@ -17,8 +17,8 @@ citEntry(
   author = personList(as.person("W.-C. Chen"), as.person("G. Ostrouchov")),
   year = "2012",
   note = "R Vignette",
-  url = "http://cran.r-project.org/package=pmclust",
-  textVersion = "W.-C. Chen, G. Ostrouchov (2014). A Quick Guide for the pmclust Package. R Vignette, URL http://cran.r-project.org/package=pmclust",
+  url = "https://cran.r-project.org/package=pmclust",
+  textVersion = "W.-C. Chen, G. Ostrouchov (2014). A Quick Guide for the pmclust Package. R Vignette, URL https://cran.r-project.org/package=pmclust",
   key = "Chen2012pmclustvignette"
 )
 
diff --git a/inst/tests/dmat_em.r b/inst/tests/dmat_em.r
diff --git a/inst/tests/dmat_kmeans.r b/inst/tests/dmat_kmeans.r
diff --git a/inst/tests/iris_EMCluster.r b/inst/tests/iris_EMCluster.r
diff --git a/inst/tests/iris_em_dmat.r b/inst/tests/iris_em_dmat.r
diff --git a/inst/tests/iris_em_spmd.r b/inst/tests/iris_em_spmd.r
diff --git a/inst/tests/iris_kmeans_dmat.r b/inst/tests/iris_kmeans_dmat.r
diff --git a/inst/tests/iris_kmeans_spmd.r b/inst/tests/iris_kmeans_spmd.r
diff --git a/man/00_pmclust-package.Rd b/man/00_pmclust-package.Rd
@@ -43,8 +43,8 @@
   dispersions.
 }
 \references{
-  High Performance Statistical Computing (HPSC) Website:
-  \url{http://thirteen-01.stat.iastate.edu/snoweye/hpsc/}
+  % High Performance Statistical Computing (HPSC) Website:
+  % \url{http://thirteen-01.stat.iastate.edu/snoweye/hpsc/}
 
   Programming with Big Data in R Website:
   \url{http://r-pbd.org/}
diff --git a/man/01-pmclust_pkmeans.Rd b/man/01-pmclust_pkmeans.Rd
@@ -46,8 +46,8 @@
   for details.
 }
 \references{
-  High Performance Statistical Computing (HPSC) Website:
-  \url{http://thirteen-01.stat.iastate.edu/snoweye/hpsc/}
+  % High Performance Statistical Computing (HPSC) Website:
+  % \url{http://thirteen-01.stat.iastate.edu/snoweye/hpsc/}
 
   Programming with Big Data in R Website:
   \url{http://r-pbd.org/}
diff --git a/man/10_d.readme.Rd b/man/10_d.readme.Rd
@@ -80,8 +80,8 @@
   such as \code{.pmclustEnv$CONTROL}.
 }
 \references{
-  High Performance Statistical Computing (HPSC) Website:
-  \url{http://thirteen-01.stat.iastate.edu/snoweye/hpsc/}
+  % High Performance Statistical Computing (HPSC) Website:
+  % \url{http://thirteen-01.stat.iastate.edu/snoweye/hpsc/}
 
   Programming with Big Data in R Website:
   \url{http://r-pbd.org/}
diff --git a/man/11_d.set.global.Rd b/man/11_d.set.global.Rd
@@ -65,8 +65,8 @@
   set by this function.
 }
 \references{
-  High Performance Statistical Computing (HPSC) Website:
-  \url{http://thirteen-01.stat.iastate.edu/snoweye/hpsc/}
+  % High Performance Statistical Computing (HPSC) Website:
+  % \url{http://thirteen-01.stat.iastate.edu/snoweye/hpsc/}
 
   Programming with Big Data in R Website:
   \url{http://r-pbd.org/}
diff --git a/man/12_d.param.Rd b/man/12_d.param.Rd
@@ -39,8 +39,8 @@
   are only used in computing.
 }
 \references{
-  High Performance Statistical Computing (HPSC) Website:
-  \url{http://thirteen-01.stat.iastate.edu/snoweye/hpsc/}
+  % High Performance Statistical Computing (HPSC) Website:
+  % \url{http://thirteen-01.stat.iastate.edu/snoweye/hpsc/}
 
   Programming with Big Data in R Website:
   \url{http://r-pbd.org/}
diff --git a/man/13_d.control.Rd b/man/13_d.control.Rd
@@ -63,8 +63,8 @@
   See \code{\link{e.step}} for more information about computing.
 }
 \references{
-  High Performance Statistical Computing (HPSC) Website:
-  \url{http://thirteen-01.stat.iastate.edu/snoweye/hpsc/}
+  % High Performance Statistical Computing (HPSC) Website:
+  % \url{http://thirteen-01.stat.iastate.edu/snoweye/hpsc/}
 
   Programming with Big Data in R Website:
   \url{http://r-pbd.org/}
diff --git a/man/20-assign.N.sample.Rd b/man/20-assign.N.sample.Rd
@@ -38,8 +38,8 @@
   \code{N.spmd} for \code{ID.spmd}.
 }
 \references{
-  High Performance Statistical Computing (HPSC) Website:
-  \url{http://thirteen-01.stat.iastate.edu/snoweye/hpsc/}
+  % High Performance Statistical Computing (HPSC) Website:
+  % \url{http://thirteen-01.stat.iastate.edu/snoweye/hpsc/}
 
   Programming with Big Data in R Website:
   \url{http://r-pbd.org/}
diff --git a/man/30-em.one.Rd b/man/30-em.one.Rd
@@ -40,8 +40,8 @@
   for details.
 }
 \references{
-  High Performance Statistical Computing (HPSC) Website:
-  \url{http://thirteen-01.stat.iastate.edu/snoweye/hpsc/}
+  % High Performance Statistical Computing (HPSC) Website:
+  % \url{http://thirteen-01.stat.iastate.edu/snoweye/hpsc/}
 
   Programming with Big Data in R Website:
   \url{http://r-pbd.org/}
diff --git a/man/30-em.one.e.Rd b/man/30-em.one.e.Rd
@@ -47,8 +47,8 @@
   See \code{\link{CONTROL}} for details about constrains on E- and M-steps.
 }
 \references{
-  High Performance Statistical Computing (HPSC) Website:
-  \url{http://thirteen-01.stat.iastate.edu/snoweye/hpsc/}
+  % High Performance Statistical Computing (HPSC) Website:
+  % \url{http://thirteen-01.stat.iastate.edu/snoweye/hpsc/}
 
   Programming with Big Data in R Website:
   \url{http://r-pbd.org/}
diff --git a/man/30-em.one.m.Rd b/man/30-em.one.m.Rd
@@ -29,8 +29,8 @@
   likelihood for the current iteration.
 }
 \references{
-  High Performance Statistical Computing (HPSC) Website:
-  \url{http://thirteen-01.stat.iastate.edu/snoweye/hpsc/}
+  % High Performance Statistical Computing (HPSC) Website:
+  % \url{http://thirteen-01.stat.iastate.edu/snoweye/hpsc/}
 
   Programming with Big Data in R Website:
   \url{http://r-pbd.org/}
diff --git a/man/30-em_initial.Rd b/man/30-em_initial.Rd
@@ -67,8 +67,8 @@
   for details.
 }
 \references{
-  High Performance Statistical Computing (HPSC) Website:
-  \url{http://thirteen-01.stat.iastate.edu/snoweye/hpsc/}
+  % High Performance Statistical Computing (HPSC) Website:
+  % \url{http://thirteen-01.stat.iastate.edu/snoweye/hpsc/}
 
   Programming with Big Data in R Website:
   \url{http://r-pbd.org/}
diff --git a/man/30-em_like.Rd b/man/30-em_like.Rd
@@ -50,8 +50,8 @@
   for details.
 }
 \references{
-  High Performance Statistical Computing (HPSC) Website:
-  \url{http://thirteen-01.stat.iastate.edu/snoweye/hpsc/}
+  % High Performance Statistical Computing (HPSC) Website:
+  % \url{http://thirteen-01.stat.iastate.edu/snoweye/hpsc/}
 
   Programming with Big Data in R Website:
   \url{http://r-pbd.org/}
diff --git a/man/40-generate.MixSim.Rd b/man/40-generate.MixSim.Rd
@@ -58,8 +58,8 @@
   \emph{Journal of Statistical Software},
   (accepted).
 
-  High Performance Statistical Computing (HPSC) Website:
-  \url{http://thirteen-01.stat.iastate.edu/snoweye/hpsc/}
+  % High Performance Statistical Computing (HPSC) Website:
+  % \url{http://thirteen-01.stat.iastate.edu/snoweye/hpsc/}
 
   Programming with Big Data in R Website:
   \url{http://r-pbd.org/}
diff --git a/man/40-generate.basic.Rd b/man/40-generate.basic.Rd
@@ -55,8 +55,8 @@
 }
 }
 \references{
-  High Performance Statistical Computing (HPSC) Website:
-  \url{http://thirteen-01.stat.iastate.edu/snoweye/hpsc/}
+  % High Performance Statistical Computing (HPSC) Website:
+  % \url{http://thirteen-01.stat.iastate.edu/snoweye/hpsc/}
 
   Programming with Big Data in R Website:
   \url{http://r-pbd.org/}
diff --git a/man/41-get.N.CLASS.Rd b/man/41-get.N.CLASS.Rd
@@ -42,8 +42,8 @@
   Programming with Big Data in R Website:
   \url{http://r-pbd.org/}
 
-  High Performance Statistical Computing (HPSC) Website:
-  \url{http://thirteen-01.stat.iastate.edu/snoweye/hpsc/}
+  % High Performance Statistical Computing (HPSC) Website:
+  % \url{http://thirteen-01.stat.iastate.edu/snoweye/hpsc/}
 }
 \author{
   Wei-Chen Chen \email{wccsnow@gmail.com} and George Ostrouchov.
diff --git a/man/50-as.dmat.spmd.Rd b/man/50-as.dmat.spmd.Rd
@@ -32,8 +32,8 @@
   A \code{ddmatrix} is returned.
 }
 \references{
-  High Performance Statistical Computing (HPSC) Website:
-  \url{http://thirteen-01.stat.iastate.edu/snoweye/hpsc/}
+  % High Performance Statistical Computing (HPSC) Website:
+  % \url{http://thirteen-01.stat.iastate.edu/snoweye/hpsc/}
 
   Programming with Big Data in R Website:
   \url{http://r-pbd.org/}
diff --git a/man/50-indep.logL.Rd b/man/50-indep.logL.Rd
@@ -32,8 +32,8 @@
   large difference indicates bugs of code or illness of data.
 }
 \references{
-  High Performance Statistical Computing (HPSC) Website:
-  \url{http://thirteen-01.stat.iastate.edu/snoweye/hpsc/}
+  % High Performance Statistical Computing (HPSC) Website:
+  % \url{http://thirteen-01.stat.iastate.edu/snoweye/hpsc/}
 
   Programming with Big Data in R Website:
   \url{http://r-pbd.org/}
diff --git a/man/50-mb.print.Rd b/man/50-mb.print.Rd
@@ -20,8 +20,8 @@
   Summarized messages will print/cat on screen by default.
 }
 \references{
-  High Performance Statistical Computing (HPSC) Website:
-  \url{http://thirteen-01.stat.iastate.edu/snoweye/hpsc/}
+  % High Performance Statistical Computing (HPSC) Website:
+  % \url{http://thirteen-01.stat.iastate.edu/snoweye/hpsc/}
 
   Programming with Big Data in R Website:
   \url{http://r-pbd.org/}
diff --git a/man/50-update.class.Rd b/man/50-update.class.Rd
@@ -26,8 +26,8 @@
   \code{\link{CLASS.spmd}} will be updated.
 }
 \references{
-  High Performance Statistical Computing (HPSC) Website:
-  \url{http://thirteen-01.stat.iastate.edu/snoweye/hpsc/}
+  % High Performance Statistical Computing (HPSC) Website:
+  % \url{http://thirteen-01.stat.iastate.edu/snoweye/hpsc/}
 
   Programming with Big Data in R Website:
   \url{http://r-pbd.org/}
diff --git a/man/60-print.Rd b/man/60-print.Rd
@@ -21,8 +21,8 @@
   The results will cat or print on the STDOUT by default.
 }
 \references{
-  High Performance Statistical Computing (HPSC) Website:
-  \url{http://thirteen-01.stat.iastate.edu/snoweye/hpsc/}
+  % High Performance Statistical Computing (HPSC) Website:
+  % \url{http://thirteen-01.stat.iastate.edu/snoweye/hpsc/}
 
   Programming with Big Data in R Website:
   \url{http://r-pbd.org/}
