[Distr-commits] r949 - in branches/distr-2.6/pkg: distr/inst distr/man distr/vignettes distrDoc/inst distrDoc/vignettes distrEllipse/inst distrEx/inst distrMod/inst distrRmetrics/inst distrSim/inst distrTEst/inst distrTeach/inst distrTeach/man
noreply at r-forge.r-project.org
noreply at r-forge.r-project.org
Sun Aug 10 14:41:00 CEST 2014
Author: ruckdeschel
Date: 2014-08-10 14:41:00 +0200 (Sun, 10 Aug 2014)
New Revision: 949
Modified:
branches/distr-2.6/pkg/distr/inst/NEWS
branches/distr-2.6/pkg/distr/man/0distr-package.Rd
branches/distr-2.6/pkg/distr/man/ConvPow.Rd
branches/distr-2.6/pkg/distr/man/operators-methods.Rd
branches/distr-2.6/pkg/distr/vignettes/newDistributions.Rnw
branches/distr-2.6/pkg/distrDoc/inst/CITATION
branches/distr-2.6/pkg/distrDoc/inst/NEWS
branches/distr-2.6/pkg/distrDoc/vignettes/distr.Rnw
branches/distr-2.6/pkg/distrEllipse/inst/NEWS
branches/distr-2.6/pkg/distrEx/inst/NEWS
branches/distr-2.6/pkg/distrMod/inst/NEWS
branches/distr-2.6/pkg/distrRmetrics/inst/NEWS
branches/distr-2.6/pkg/distrSim/inst/NEWS
branches/distr-2.6/pkg/distrTEst/inst/NEWS
branches/distr-2.6/pkg/distrTeach/inst/NEWS
branches/distr-2.6/pkg/distrTeach/man/IllustCLT.Rd
Log:
updated NEWS entries and references
Modified: branches/distr-2.6/pkg/distr/inst/NEWS
===================================================================
--- branches/distr-2.6/pkg/distr/inst/NEWS 2014-08-08 16:53:55 UTC (rev 948)
+++ branches/distr-2.6/pkg/distr/inst/NEWS 2014-08-10 12:41:00 UTC (rev 949)
@@ -8,6 +8,38 @@
information)
##############
+v 2.6
+##############
+
+user visible changes
++ added reference to JSS paper in IllustCLT
++ updated references in vignette 'newDistributions'
+
+under the hood:
+
+-qqplot:
+ + (already there for a while) gains argument 'debug' to be able to
+ trace where computation of confidence bounds fails; this 'debug'
+ argument has now been enhanced in the sense that now more detailed
+ information about which helper function was the culprit and where
+ (uniroot/optimize) this happens
+-qqbounds:
+ + the respective helper functions .BinomCI.nosym, .BinomCI,
+ .q2kolmogorov capsulate their calls to uniroot / optimize in
+ individual try-catches (instead of / on top of the one in
+ qqbounds itself) so that in case of several evaluations (e.g. in
+ pointwise CIs) at least a subset of valid points is produced.
+ In addition the search interval is now more flexible: it is bound
+ away from 0 below and from the upper bound from above, and this
+ bound moves to the respective lower/upper bounds in up to 20 trials.
+ Also, the search interval for .q2kolmogorov if argument 'exact' is
+ TRUE (i.e., if pKolmogorov2x is called) has been refined. This
+ should make the simultaneous intervals more stable.
+ + re-included faster right-tail approximation in C-code K(int n, double d)
+ included from R-Core (was commented out there) [ks.c in folder src in
+ tar-ball, ll 153-155]
+
+##############
v 2.5.3
##############
Modified: branches/distr-2.6/pkg/distr/man/0distr-package.Rd
===================================================================
--- branches/distr-2.6/pkg/distr/man/0distr-package.Rd 2014-08-08 16:53:55 UTC (rev 948)
+++ branches/distr-2.6/pkg/distr/man/0distr-package.Rd 2014-08-10 12:41:00 UTC (rev 949)
@@ -336,6 +336,11 @@
S4 Classes for Distributions, \emph{R News}, \emph{6}(2), 2-6.
\url{http://CRAN.R-project.org/doc/Rnews/Rnews_2006-2.pdf}
+P. Ruckdeschel and M. Kohl (2014):
+ General purpose convolution algorithm for distributions
+ in S4-Classes by means of FFT. \emph{J. Statist. Softw.}
+ \bold{59}(4): 1-25.
+
a vignette for packages \pkg{distr}, \pkg{distrSim}, \pkg{distrTEst}, and
\pkg{distrEx} is included into the mere documentation package \pkg{distrDoc}
and may be called by
Modified: branches/distr-2.6/pkg/distr/man/ConvPow.Rd
===================================================================
--- branches/distr-2.6/pkg/distr/man/ConvPow.Rd 2014-08-08 16:53:55 UTC (rev 948)
+++ branches/distr-2.6/pkg/distr/man/ConvPow.Rd 2014-08-10 12:41:00 UTC (rev 949)
@@ -91,11 +91,10 @@
}
\references{
-Kohl, M., Ruckdeschel, P., Stabla, T. (2005):
+Kohl, M., Ruckdeschel, P., (2014):
General purpose convolution algorithm for distributions
- in S4-Classes by means of FFT.
- Technical report, Feb. 2005. Also available in
-\url{http://www.uni-bayreuth.de/departments/math/org/mathe7/RUCKDESCHEL/pubs/comp.pdf}
+ in S4-Classes by means of FFT. \emph{J. Statist. Softw.}
+ \bold{59}(4): 1-25.
}
\concept{convolution for distributions}
Modified: branches/distr-2.6/pkg/distr/man/operators-methods.Rd
===================================================================
--- branches/distr-2.6/pkg/distr/man/operators-methods.Rd 2014-08-08 16:53:55 UTC (rev 948)
+++ branches/distr-2.6/pkg/distr/man/operators-methods.Rd 2014-08-10 12:41:00 UTC (rev 949)
@@ -335,6 +335,13 @@
1.2 ^ N
abs(N) ^ 1.3
}
+\references{
+Ruckdeschel, P., Kohl, M.(2014):
+ General purpose convolution algorithm for distributions
+ in S4-Classes by means of FFT. \emph{J. Statist. Softw.}
+ \bold{59}(4): 1-25.
+}
+
\keyword{math}
\keyword{distribution}
\keyword{arith}
Modified: branches/distr-2.6/pkg/distr/vignettes/newDistributions.Rnw
===================================================================
--- branches/distr-2.6/pkg/distr/vignettes/newDistributions.Rnw 2014-08-08 16:53:55 UTC (rev 948)
+++ branches/distr-2.6/pkg/distr/vignettes/newDistributions.Rnw 2014-08-10 12:41:00 UTC (rev 949)
@@ -390,14 +390,13 @@
\begin{thebibliography}{2}
\bibitem{K:R:S:04}
-Kohl M., Ruckdeschel P. and Stabla T.
+Ruckdeschel P. and Kohl, M. (2014):
\newblock {General Purpose Convolution Algorithm for Distributions in S4-Classes
by means of FFT}.
-\newblock unpublished manual
+\newblock {\em J. Statist. Software\/}, {\bf 59}(4): 1--25.
-
\bibitem{R:K:S:C:04}
-Ruckdeschel P., Kohl M., Stabla T., and Camphausen F.
+Ruckdeschel P., Kohl M., Stabla T., and Camphausen F. (2006):
\newblock {S4 Classes for Distributions.}
\newblock {\em R-News\/}, {\bf 6}(2): 10--13.
\newblock http://CRAN.R-project.org/doc/Rnews/Rnews\_2006-2.pdf
Modified: branches/distr-2.6/pkg/distrDoc/inst/CITATION
===================================================================
--- branches/distr-2.6/pkg/distrDoc/inst/CITATION 2014-08-08 16:53:55 UTC (rev 948)
+++ branches/distr-2.6/pkg/distrDoc/inst/CITATION 2014-08-10 12:41:00 UTC (rev 949)
@@ -18,3 +18,23 @@
pdf = "http://CRAN.R-project.org/doc/Rnews/Rnews_2006-2.pdf",
textVersion = paste("Ruckdeschel, P., Kohl, M., Stabla, T., & Camphausen, F. (2006)",
"S4 Classes for Distributions"))
+
+citEntry(entry = "Article",
+ title = "General Purpose Convolution Algorithm in {S}4 Classes by Means of FFT",
+ author = personList(as.person("Peter Ruckdeschel"),
+ as.person("Matthias Kohl")),
+ journal = "Journal of Statistical Software",
+ year = "2014",
+ volume = "59",
+ number = "4",
+ pages = "1--25",
+ url = "http://www.jstatsoft.org/v59/i04/",
+ textVersion =
+ paste("Peter Ruckdeschel, Matthias Kohl (2014).",
+ "General Purpose Convolution Algorithm in S4 Classes by Means of FFT.",
+ "Journal of Statistical Software, 59(4), 1-25.",
+ "URL http://www.jstatsoft.org/v59/i04/."),
+ header = "If you employ convolution, please also cite:"
+)
+
+
\ No newline at end of file
Modified: branches/distr-2.6/pkg/distrDoc/inst/NEWS
===================================================================
--- branches/distr-2.6/pkg/distrDoc/inst/NEWS 2014-08-08 16:53:55 UTC (rev 948)
+++ branches/distr-2.6/pkg/distrDoc/inst/NEWS 2014-08-10 12:41:00 UTC (rev 949)
@@ -8,6 +8,19 @@
information)
##############
+v 2.6
+##############
+
+user-visible CHANGES:
+
++ updated CITATION file
++ removed some outdated references from uni-bayreuth
++ updated references in vignette distr.Rnw
+
+under the hood
++ added svn-properties to distr.Rnw
+
+##############
v 2.5
##############
Modified: branches/distr-2.6/pkg/distrDoc/vignettes/distr.Rnw
===================================================================
--- branches/distr-2.6/pkg/distrDoc/vignettes/distr.Rnw 2014-08-08 16:53:55 UTC (rev 948)
+++ branches/distr-2.6/pkg/distrDoc/vignettes/distr.Rnw 2014-08-10 12:41:00 UTC (rev 949)
@@ -3564,7 +3564,7 @@
\begin{thebibliography}{8}
\bibitem{Beng:03}
-Bengtsson H.
+Bengtsson H. (2003):
\newblock The {R.oo} package - object-oriented programming with references using
standard {R} code.
\newblock In: Hornik K., Leisch F. and Zeileis A. (Eds.) {\em
@@ -3573,43 +3573,43 @@
\newblock Published as http://www.ci.tuwien.ac.at/Conferences/DSC-2003/
\bibitem{Cham:98}
-Chambers J.M.
+Chambers J.M. (1998):
\newblock {\em {Programming with data. A guide to the S language}\/}.
\newblock {Springer}.
\newblock http://cm.bell-labs.com/stat/Sbook/index.html
\bibitem{OOPGent}
-Gentleman R.
+Gentleman R. (2003):
\newblock {\em Object Orientated Programming. Slides of a Short Course held in
Auckland\/}.
\newblock http://www.stat.auckland.ac.nz/S-Workshop/Gentleman/Methods.pdf
\bibitem{MK:05}
-Kohl M.
+Kohl M. (2005):
\newblock {\em Numerical Contributions to the Asymptotic Theory of Robustness\/}.
\newblock {Dissertation}, Universit\"at Bayreuth.
\newblock See also http://stamats.de/ThesisMKohl.pdf
\bibitem{K:R:S:04}
-Kohl M., Ruckdeschel P. and Stabla T.
-\newblock {General Purpose Convolution Algorithm for Distributions in S4-Classes
+Ruckdeschel P. and Kohl, M. (2014):
+\newblock {General Purpose Convolution Algorithm for Distributions in S4-Classes
by means of FFT}.
-\newblock unpublished manual
+\newblock {\em J. Statist. Software\/}, {\bf 59}(4): 1--25.
\bibitem{NumR:92}
-Press W.H., Teukolsky S.A., Vetterling W.T. and Flannery B.P.
+Press W.H., Teukolsky S.A., Vetterling W.T. and Flannery B.P. (1992):
\newblock {\em {Numerical recipes in C. The art of scientific computing.}\/}
\newblock {Cambridge Univ. Press}, 2. Aufl.
\bibitem{Ric:88}
-Rice J.A.
+Rice J.A. (1988):
\newblock {\em {Mathematical statistics and data analysis}\/}.
\newblock The Wadsworth \& Brooks/Cole Statistics/Probability Series.
{Wadsworth \& Brooks/Cole Advanced Books \& Software}, Pacific Grove,
California.
\bibitem{R:K:S:C:04}
-Ruckdeschel P., Kohl M., Stabla T., and Camphausen F.
+Ruckdeschel P., Kohl M., Stabla T., and Camphausen F. (2006):
\newblock {S4 Classes for Distributions.}
\newblock {\em R-News\/}, {\bf 6}(2): 10--13.
\newblock http://CRAN.R-project.org/doc/Rnews/Rnews\_2006-2.pdf
Modified: branches/distr-2.6/pkg/distrEllipse/inst/NEWS
===================================================================
--- branches/distr-2.6/pkg/distrEllipse/inst/NEWS 2014-08-08 16:53:55 UTC (rev 948)
+++ branches/distr-2.6/pkg/distrEllipse/inst/NEWS 2014-08-10 12:41:00 UTC (rev 949)
@@ -8,6 +8,16 @@
information)
##############
+v 2.6
+##############
+
+under the hood:
+
++ removed ::: internal dependencies (within distr-Fam of pkgs) by copying
+ respective routines
+
+
+##############
v 2.5
##############
Modified: branches/distr-2.6/pkg/distrEx/inst/NEWS
===================================================================
--- branches/distr-2.6/pkg/distrEx/inst/NEWS 2014-08-08 16:53:55 UTC (rev 948)
+++ branches/distr-2.6/pkg/distrEx/inst/NEWS 2014-08-10 12:41:00 UTC (rev 949)
@@ -6,6 +6,16 @@
package-individual development, but rather are chosen for the
distrXXX family as a whole in order to ease updating "depends"
information)
+
+##############
+v 2.6
+##############
+
+under the hood:
++ used delayedAssign() for assignment of .mv2RobExtremes() to
+ former package internal constants EULERMASCHERONICONSTANT and
+ APERYCONSTANT)
+
##############
v 2.5
Modified: branches/distr-2.6/pkg/distrMod/inst/NEWS
===================================================================
--- branches/distr-2.6/pkg/distrMod/inst/NEWS 2014-08-08 16:53:55 UTC (rev 948)
+++ branches/distr-2.6/pkg/distrMod/inst/NEWS 2014-08-10 12:41:00 UTC (rev 949)
@@ -8,6 +8,38 @@
information)
##############
+v 2.6
+##############
+
+user-visible CHANGES:
++ introduced dropZeroDensity argument to ML estimators
+
+GENERAL ENHANCEMENTS:
+
+under the hood:
++ zero dropping (see argument 'dropZeroDensity' above)
+ --Optimizers like optim require finite values, so get problems when
+ negative loglikelihood is evaluated, so optionally, and by default,
+ values with density/likelihood 0 are dropped from optimization
++ removed ::: internal dependencies (within distr-Fam of pkgs) by copying
+ respective routines
++ qqplot:
+ * (already there for a while) gains ability to interchange x- and y-
+ axis by argument 'datax' for compatibility with other qqplots
+ * gains new methods for object of class "Estimate" (which could also be
+ seen as "fitted" objects...)
++ returnlevelplot
+ * similar
++ new .checkEstClassForParamFamily-method to be able to cast an estimator
+ to a return class specific to the resp. parametric famil
+
+ BUGFIXES:
+
++ fixed issue with slot withPosRestr in ParamFamParameter.R
++ fixed issue with check.validity (reported by B.Spangl)
++ fixed some minor issue in existsPIC (in case we get 0 matrix, and less strict tolerance)
+
+##############
v 2.5
##############
Modified: branches/distr-2.6/pkg/distrRmetrics/inst/NEWS
===================================================================
--- branches/distr-2.6/pkg/distrRmetrics/inst/NEWS 2014-08-08 16:53:55 UTC (rev 948)
+++ branches/distr-2.6/pkg/distrRmetrics/inst/NEWS 2014-08-10 12:41:00 UTC (rev 949)
@@ -8,6 +8,12 @@
information)
##############
+v 2.6
+##############
+
+No extra changes this time
+
+##############
v 2.5
##############
Modified: branches/distr-2.6/pkg/distrSim/inst/NEWS
===================================================================
--- branches/distr-2.6/pkg/distrSim/inst/NEWS 2014-08-08 16:53:55 UTC (rev 948)
+++ branches/distr-2.6/pkg/distrSim/inst/NEWS 2014-08-10 12:41:00 UTC (rev 949)
@@ -8,6 +8,12 @@
information)
##############
+v 2.6
+##############
+
+No extra changes this time
+
+##############
v 2.5
##############
Modified: branches/distr-2.6/pkg/distrTEst/inst/NEWS
===================================================================
--- branches/distr-2.6/pkg/distrTEst/inst/NEWS 2014-08-08 16:53:55 UTC (rev 948)
+++ branches/distr-2.6/pkg/distrTEst/inst/NEWS 2014-08-10 12:41:00 UTC (rev 949)
@@ -3,6 +3,12 @@
######################################################################
##############
+v 2.6
+##############
+
+No extra changes this time
+
+##############
v 2.5
##############
Modified: branches/distr-2.6/pkg/distrTeach/inst/NEWS
===================================================================
--- branches/distr-2.6/pkg/distrTeach/inst/NEWS 2014-08-08 16:53:55 UTC (rev 948)
+++ branches/distr-2.6/pkg/distrTeach/inst/NEWS 2014-08-10 12:41:00 UTC (rev 949)
@@ -8,6 +8,19 @@
information)
##############
+v 2.6
+##############
+
+user visible changes:
+
++ added reference to JSS-paper in help to IllustCLT
+
+under the hood:
+
++ removed ::: internal dependencies (within distr-Fam of pkgs) by copying
+ respective routines
+
+##############
v 2.5
##############
Modified: branches/distr-2.6/pkg/distrTeach/man/IllustCLT.Rd
===================================================================
--- branches/distr-2.6/pkg/distrTeach/man/IllustCLT.Rd 2014-08-08 16:53:55 UTC (rev 948)
+++ branches/distr-2.6/pkg/distrTeach/man/IllustCLT.Rd 2014-08-10 12:41:00 UTC (rev 949)
@@ -43,6 +43,14 @@
illustrateCLT(Distr = Pois(lambda = 2)+Unif(), len = 20)
illustrateCLT.tcl(Distr = Unif(), k = 4, "Unif()")
}
+
+\references{
+Kohl, M., Ruckdeschel, P., (2014):
+ General purpose convolution algorithm for distributions
+ in S4-Classes by means of FFT. \emph{J. Statist. Softw.}
+ \bold{59}(4): 1-25.
+}
+
\keyword{distribution}
\keyword{methods}
\concept{illustration}
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