[Robast-commits] r1234 - in branches/robast-1.3/pkg: ROptEst/inst ROptEst/man ROptEstOld/R ROptEstOld/inst ROptEstOld/man RandVar/inst RandVar/man RandVar/vignettes RobAStBase/inst RobAStBase/man RobAStRDA/inst RobAStRDA/man RobExtremes/R RobExtremes/inst RobExtremes/man RobLox/inst RobLox/man RobLoxBioC/inst RobLoxBioC/inst/scripts RobLoxBioC/man
noreply at r-forge.r-project.org
noreply at r-forge.r-project.org
Fri Apr 22 12:44:54 CEST 2022
Author: ruckdeschel
Date: 2022-04-22 12:44:53 +0200 (Fri, 22 Apr 2022)
New Revision: 1234
Modified:
branches/robast-1.3/pkg/ROptEst/inst/NEWS
branches/robast-1.3/pkg/ROptEst/man/0ROptEst-package.Rd
branches/robast-1.3/pkg/ROptEstOld/R/Expectation.R
branches/robast-1.3/pkg/ROptEstOld/R/Functionals.R
branches/robast-1.3/pkg/ROptEstOld/R/Gumbel.R
branches/robast-1.3/pkg/ROptEstOld/R/Kurtosis.R
branches/robast-1.3/pkg/ROptEstOld/R/Skewness.R
branches/robast-1.3/pkg/ROptEstOld/inst/NEWS
branches/robast-1.3/pkg/ROptEstOld/man/ROptEstOldConstants.Rd
branches/robast-1.3/pkg/RandVar/inst/NEWS
branches/robast-1.3/pkg/RandVar/man/0RandVar-package.Rd
branches/robast-1.3/pkg/RandVar/vignettes/RandVar.Rnw
branches/robast-1.3/pkg/RobAStBase/inst/NEWS
branches/robast-1.3/pkg/RobAStBase/man/0RobAStBase-package.Rd
branches/robast-1.3/pkg/RobAStRDA/inst/NEWS
branches/robast-1.3/pkg/RobAStRDA/man/0RobRDA-package.Rd
branches/robast-1.3/pkg/RobExtremes/R/Expectation.R
branches/robast-1.3/pkg/RobExtremes/R/Functionals.R
branches/robast-1.3/pkg/RobExtremes/R/Gumbel.R
branches/robast-1.3/pkg/RobExtremes/R/Kurtosis.R
branches/robast-1.3/pkg/RobExtremes/R/Skewness.R
branches/robast-1.3/pkg/RobExtremes/inst/NEWS
branches/robast-1.3/pkg/RobExtremes/man/0RobExtremes-package.Rd
branches/robast-1.3/pkg/RobExtremes/man/RobExtremesConstants.Rd
branches/robast-1.3/pkg/RobLox/inst/NEWS
branches/robast-1.3/pkg/RobLox/man/finiteSampleCorrection.Rd
branches/robast-1.3/pkg/RobLox/man/roblox.Rd
branches/robast-1.3/pkg/RobLox/man/rowRoblox.Rd
branches/robast-1.3/pkg/RobLox/man/showdown.Rd
branches/robast-1.3/pkg/RobLoxBioC/inst/NEWS
branches/robast-1.3/pkg/RobLoxBioC/inst/scripts/AffymetrixExample.R
branches/robast-1.3/pkg/RobLoxBioC/inst/scripts/AffymetrixReproducibility.R
branches/robast-1.3/pkg/RobLoxBioC/inst/scripts/IlluminaExample.R
branches/robast-1.3/pkg/RobLoxBioC/inst/scripts/IlluminaReproducibility.R
branches/robast-1.3/pkg/RobLoxBioC/man/0RobLoxBioC-package.Rd
branches/robast-1.3/pkg/RobLoxBioC/man/robloxbioc.Rd
Log:
[robast, devel branch 1.3] triggered by a mail from the CRAN maintainers to fix a broken mail address, I browsed through all packages to fix broken URLs and to change URLs from http to https where possible
Modified: branches/robast-1.3/pkg/ROptEst/inst/NEWS
===================================================================
--- branches/robast-1.3/pkg/ROptEst/inst/NEWS 2021-07-28 14:39:58 UTC (rev 1233)
+++ branches/robast-1.3/pkg/ROptEst/inst/NEWS 2022-04-22 10:44:53 UTC (rev 1234)
@@ -14,6 +14,7 @@
under the hood:
+ in calls of form do.call(E, .....) we only use functions with one argument;
(in calls where a function was passed on as argument, this threw errors...)
++ fixed some broken URLs and changed URLs from http to https where possible
#######################################
version 1.2.1
Modified: branches/robast-1.3/pkg/ROptEst/man/0ROptEst-package.Rd
===================================================================
--- branches/robast-1.3/pkg/ROptEst/man/0ROptEst-package.Rd 2021-07-28 14:39:58 UTC (rev 1233)
+++ branches/robast-1.3/pkg/ROptEst/man/0ROptEst-package.Rd 2022-04-22 10:44:53 UTC (rev 1234)
@@ -21,7 +21,7 @@
ByteCompile: \tab yes \cr
Encoding: \tab latin1 \cr
License: \tab LGPL-3 \cr
-URL: \tab http://robast.r-forge.r-project.org/\cr
+URL: \tab https://robast.r-forge.r-project.org/\cr
VCS/SVNRevision: \tab 1213 \cr
}
}
Modified: branches/robast-1.3/pkg/ROptEstOld/R/Expectation.R
===================================================================
--- branches/robast-1.3/pkg/ROptEstOld/R/Expectation.R 2021-07-28 14:39:58 UTC (rev 1233)
+++ branches/robast-1.3/pkg/ROptEstOld/R/Expectation.R 2022-04-22 10:44:53 UTC (rev 1234)
@@ -31,4 +31,4 @@
else
return(E(as(object,"AbscontDistribution"), low=low, upp=upp, ...))
})
-## http://mathworld.wolfram.com/GumbelDistribution.html
+## https://mathworld.wolfram.com/GumbelDistribution.html
Modified: branches/robast-1.3/pkg/ROptEstOld/R/Functionals.R
===================================================================
--- branches/robast-1.3/pkg/ROptEstOld/R/Functionals.R 2021-07-28 14:39:58 UTC (rev 1233)
+++ branches/robast-1.3/pkg/ROptEstOld/R/Functionals.R 2022-04-22 10:44:53 UTC (rev 1234)
@@ -11,5 +11,5 @@
else{ b <- scale(x)
return(b^2 * pi^2/6)
}})
-## http://mathworld.wolfram.com/GumbelDistribution.html
+## https://mathworld.wolfram.com/GumbelDistribution.html
Modified: branches/robast-1.3/pkg/ROptEstOld/R/Gumbel.R
===================================================================
--- branches/robast-1.3/pkg/ROptEstOld/R/Gumbel.R 2021-07-28 14:39:58 UTC (rev 1233)
+++ branches/robast-1.3/pkg/ROptEstOld/R/Gumbel.R 2022-04-22 10:44:53 UTC (rev 1234)
@@ -46,10 +46,10 @@
})
### Euler Mascheroni constant:
-EULERMASCHERONICONSTANT <- -digamma(1) ### after http://mathworld.wolfram.com/Euler-MascheroniConstant.html (48)
+EULERMASCHERONICONSTANT <- -digamma(1) ### after https://mathworld.wolfram.com/Euler-MascheroniConstant.html (48)
### Apéry constant
##local helper function:
.fctApery <- function(n) (-1)^n*choose(2*n,n)*n^3
##
-APERYCONSTANT <- -sum(sapply(1:50,.fctApery)^(-1))*5/2 ## after http://mathworld.wolfram.com/AperysConstant.html (8)
+APERYCONSTANT <- -sum(sapply(1:50,.fctApery)^(-1))*5/2 ## after https://mathworld.wolfram.com/AperysConstant.html (8)
Modified: branches/robast-1.3/pkg/ROptEstOld/R/Kurtosis.R
===================================================================
--- branches/robast-1.3/pkg/ROptEstOld/R/Kurtosis.R 2021-07-28 14:39:58 UTC (rev 1233)
+++ branches/robast-1.3/pkg/ROptEstOld/R/Kurtosis.R 2022-04-22 10:44:53 UTC (rev 1234)
@@ -15,10 +15,10 @@
return(kurtosis(as(x,"AbscontDistribution"),...))
else{
return(12/5)
-# http://mathworld.wolfram.com/GumbelDistribution.html
+# https://mathworld.wolfram.com/GumbelDistribution.html
}
})
-### source http://en.wikipedia.org/wiki/Generalized_extreme_value_distribution
-### http://en.wikipedia.org/wiki/Gumbel_distribution
-### http://en.wikipedia.org/wiki/Riemann_zeta_function
+### source https://en.wikipedia.org/wiki/Generalized_extreme_value_distribution
+### https://en.wikipedia.org/wiki/Gumbel_distribution
+### https://en.wikipedia.org/wiki/Riemann_zeta_function
Modified: branches/robast-1.3/pkg/ROptEstOld/R/Skewness.R
===================================================================
--- branches/robast-1.3/pkg/ROptEstOld/R/Skewness.R 2021-07-28 14:39:58 UTC (rev 1233)
+++ branches/robast-1.3/pkg/ROptEstOld/R/Skewness.R 2022-04-22 10:44:53 UTC (rev 1234)
@@ -10,7 +10,7 @@
return(skewness(as(x,"AbscontDistribution"),...))
else{
return( -12 * sqrt(6) * APERYCONSTANT / pi^3 )
-# http://mathworld.wolfram.com/GumbelDistribution.html
+# https://mathworld.wolfram.com/GumbelDistribution.html
}
})
Modified: branches/robast-1.3/pkg/ROptEstOld/inst/NEWS
===================================================================
--- branches/robast-1.3/pkg/ROptEstOld/inst/NEWS 2021-07-28 14:39:58 UTC (rev 1233)
+++ branches/robast-1.3/pkg/ROptEstOld/inst/NEWS 2022-04-22 10:44:53 UTC (rev 1234)
@@ -8,6 +8,13 @@
information)
#######################################
+version 1.3
+#######################################
+
+under the hood:
++ fixed some broken URLs and changed URLs from http to https where possible
+
+#######################################
version 1.2
#######################################
Modified: branches/robast-1.3/pkg/ROptEstOld/man/ROptEstOldConstants.Rd
===================================================================
--- branches/robast-1.3/pkg/ROptEstOld/man/ROptEstOldConstants.Rd 2021-07-28 14:39:58 UTC (rev 1233)
+++ branches/robast-1.3/pkg/ROptEstOld/man/ROptEstOldConstants.Rd 2022-04-22 10:44:53 UTC (rev 1234)
@@ -17,11 +17,11 @@
\itemize{
\item \code{EULERMASCHERONICONSTANT}: the Euler Mascheroni constant
\deqn{\gamma=-\Gamma'(1)}{gamma=-digamma(1)}
- given in \url{http://mathworld.wolfram.com/Euler-MascheroniConstant.html} (48);
+ given in \url{https://mathworld.wolfram.com/Euler-MascheroniConstant.html} (48);
\item \code{APERYCONSTANT}: the \enc{Apéry}{Apery} constant
\deqn{\zeta(3)= \frac{5}{2} (\sum_{k\ge 1}\frac{(-1)^{k-1}}{k^3 {2k\choose k}})}{
zeta(3) = 5/2 sum_{k>=0} (-1)^(k-1)/(k^3 * choose(2k,k))}
- as given in \url{http://mathworld.wolfram.com/AperysConstant.html}, equation (8);
+ as given in \url{https://mathworld.wolfram.com/AperysConstant.html}, equation (8);
}
These are implemented as variables in the \pkg{ROptEstOld} name space taking
Modified: branches/robast-1.3/pkg/RandVar/inst/NEWS
===================================================================
--- branches/robast-1.3/pkg/RandVar/inst/NEWS 2021-07-28 14:39:58 UTC (rev 1233)
+++ branches/robast-1.3/pkg/RandVar/inst/NEWS 2022-04-22 10:44:53 UTC (rev 1234)
@@ -8,6 +8,13 @@
information)
#######################################
+version 1.3
+#######################################
+
+under the hood:
++ fixed some broken URLs and changed URLs from http to https where possible
+
+#######################################
version 1.2
#######################################
Modified: branches/robast-1.3/pkg/RandVar/man/0RandVar-package.Rd
===================================================================
--- branches/robast-1.3/pkg/RandVar/man/0RandVar-package.Rd 2021-07-28 14:39:58 UTC (rev 1233)
+++ branches/robast-1.3/pkg/RandVar/man/0RandVar-package.Rd 2022-04-22 10:44:53 UTC (rev 1234)
@@ -17,7 +17,7 @@
Imports: \tab startupmsg \cr
ByteCompile: \tab yes \cr
License: \tab LGPL-3 \cr
-URL: \tab http://robast.r-forge.r-project.org/\cr
+URL: \tab https://robast.r-forge.r-project.org/\cr
VCS/SVNRevision: \tab 1228 \cr
}
}
@@ -28,6 +28,7 @@
\references{
M. Kohl (2005). Numerical Contributions to the Asymptotic Theory of Robustness.
Dissertation. University of Bayreuth.
+ See also https://www.stamats.de/wp-content/uploads/2018/04/ThesisMKohl.pdf
}
\seealso{
\code{\link[distr:0distr-package]{distr-package}}, \code{\link[distrEx:0distrEx-package]{distrEx-package}}
Modified: branches/robast-1.3/pkg/RandVar/vignettes/RandVar.Rnw
===================================================================
--- branches/robast-1.3/pkg/RandVar/vignettes/RandVar.Rnw 2021-07-28 14:39:58 UTC (rev 1233)
+++ branches/robast-1.3/pkg/RandVar/vignettes/RandVar.Rnw 2022-04-22 10:44:53 UTC (rev 1234)
@@ -27,7 +27,7 @@
\usepackage{ifpdf}
\definecolor{darkblue}{rgb}{0.0,0.0,0.75}
\usepackage[%
-baseurl={http://www.stamats.de},%
+baseurl={https://www.stamats.de},%
pdftitle={RandVar: Implementation of random variables by means of S4 classes and methods},%
pdfauthor={Matthias Kohl},%
pdfsubject={RandVar},%
@@ -256,18 +256,18 @@
Chambers J.M.
\newblock {\em {Programming with data. A guide to the S language}\/}.
\newblock {Springer}.
-\newblock http://cm.bell-labs.com/stat/Sbook/index.html
+\newblock https://cm.bell-labs.com/stat/Sbook/index.html
\bibitem{Gent:03}
Gentleman R.
\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
+\newblock https://www.stat.auckland.ac.nz/S-Workshop/Gentleman/Methods.pdf
\bibitem{MK:05}
Kohl M.
\newblock {\em Numerical Contributions to the Asymptotic Theory of Robustness\/}.
\newblock {Dissertation}, Universit\"at Bayreuth.
-\newblock See also http://stamats.de/ThesisMKohl.pdf
+\newblock See also https://www.stamats.de/wp-content/uploads/2018/04/ThesisMKohl.pdf
\bibitem{distr}
Ruckdeschel P., Kohl M., Stabla T., and Camphausen F.
@@ -274,7 +274,6 @@
\newblock {S4 Classes for Distributions.}
\newblock {\em R-News\/}, {\bf 6}(2): 10--13.
\newblock https://CRAN.R-project.org/doc/Rnews/Rnews\_2006-2.pdf
-\newblock See also {http://www.uni-bayreuth.de/departments/math/org/mathe7/RUCKDESCHEL/pubs/distr.pdf}
\end{thebibliography}
% -------------------------------------------------------------------------------
Modified: branches/robast-1.3/pkg/RobAStBase/inst/NEWS
===================================================================
--- branches/robast-1.3/pkg/RobAStBase/inst/NEWS 2021-07-28 14:39:58 UTC (rev 1233)
+++ branches/robast-1.3/pkg/RobAStBase/inst/NEWS 2022-04-22 10:44:53 UTC (rev 1234)
@@ -11,6 +11,9 @@
version 1.3
#######################################
+under the hood:
++ fixed some broken URLs and changed URLs from http to https where possible
+
#######################################
version 1.2.1
#######################################
Modified: branches/robast-1.3/pkg/RobAStBase/man/0RobAStBase-package.Rd
===================================================================
--- branches/robast-1.3/pkg/RobAStBase/man/0RobAStBase-package.Rd 2021-07-28 14:39:58 UTC (rev 1233)
+++ branches/robast-1.3/pkg/RobAStBase/man/0RobAStBase-package.Rd 2022-04-22 10:44:53 UTC (rev 1234)
@@ -20,7 +20,7 @@
ByteCompile: \tab yes \cr
Encoding: \tab latin1 \cr
License: \tab LGPL-3 \cr
-URL: \tab http://robast.r-forge.r-project.org/\cr
+URL: \tab https://robast.r-forge.r-project.org/\cr
VCS/SVNRevision: \tab 1205 \cr
}
}
@@ -31,6 +31,7 @@
\references{
M. Kohl (2005). Numerical Contributions to the Asymptotic Theory of Robustness.
Dissertation. University of Bayreuth.
+ See also https://www.stamats.de/wp-content/uploads/2018/04/ThesisMKohl.pdf
}
\seealso{
\code{\link[distr:0distr-package]{distr-package}},
Modified: branches/robast-1.3/pkg/RobAStRDA/inst/NEWS
===================================================================
--- branches/robast-1.3/pkg/RobAStRDA/inst/NEWS 2021-07-28 14:39:58 UTC (rev 1233)
+++ branches/robast-1.3/pkg/RobAStRDA/inst/NEWS 2022-04-22 10:44:53 UTC (rev 1234)
@@ -14,6 +14,7 @@
+ removed LazyData tag in DESCRIPTION and replaced it by SysDataCompression: xz
+ removed pre 3.0 branches
+ hence: need R>=3.5.0 to be able to use version 3 save-ing/compression
++ fixed some broken URLs and changed URLs from http to https where possible
#######################################
version 1.1
Modified: branches/robast-1.3/pkg/RobAStRDA/man/0RobRDA-package.Rd
===================================================================
--- branches/robast-1.3/pkg/RobAStRDA/man/0RobRDA-package.Rd 2021-07-28 14:39:58 UTC (rev 1233)
+++ branches/robast-1.3/pkg/RobAStRDA/man/0RobRDA-package.Rd 2022-04-22 10:44:53 UTC (rev 1234)
@@ -37,7 +37,7 @@
LazyData: \tab yes \cr
ByteCompile: \tab yes \cr
License: \tab LGPL-3 \cr
-URL: \tab http://robast.r-forge.r-project.org/\cr
+URL: \tab https://robast.r-forge.r-project.org/\cr
VCS/SVNRevision: \tab 1205 \cr
}
}
Modified: branches/robast-1.3/pkg/RobExtremes/R/Expectation.R
===================================================================
--- branches/robast-1.3/pkg/RobExtremes/R/Expectation.R 2021-07-28 14:39:58 UTC (rev 1233)
+++ branches/robast-1.3/pkg/RobExtremes/R/Expectation.R 2022-04-22 10:44:53 UTC (rev 1234)
@@ -25,7 +25,7 @@
diagnostic = diagnostic))
})
-### source http://mathworld.wolfram.com/ParetoDistribution.html
+### source https://mathworld.wolfram.com/ParetoDistribution.html
setMethod("E", signature(object = "Gumbel",
@@ -43,7 +43,7 @@
return(E(object=object,fun=function(x)x, low=low, upp=upp, ...,
diagnostic = diagnostic))
})
-## http://mathworld.wolfram.com/GumbelDistribution.html
+## https://mathworld.wolfram.com/GumbelDistribution.html
setMethod("E", signature(object = "GPareto",
fun = "missing",
@@ -65,7 +65,7 @@
diagnostic = diagnostic))
})
-### source http://en.wikipedia.org/wiki/Pareto_distribution
+### source https://en.wikipedia.org/wiki/Pareto_distribution
setMethod("E", signature(object = "DistributionsIntegratingByQuantiles",
fun = "function",
Modified: branches/robast-1.3/pkg/RobExtremes/R/Functionals.R
===================================================================
--- branches/robast-1.3/pkg/RobExtremes/R/Functionals.R 2021-07-28 14:39:58 UTC (rev 1233)
+++ branches/robast-1.3/pkg/RobExtremes/R/Functionals.R 2022-04-22 10:44:53 UTC (rev 1234)
@@ -14,7 +14,7 @@
if(!propagate.names){names(ret.v) <- NULL}
return(ret.v)
}})
-### source http://mathworld.wolfram.com/ParetoDistribution.html
+### source https://mathworld.wolfram.com/ParetoDistribution.html
setMethod("var", signature(x = "Gumbel"),
function(x, propagate.names=getdistrExOption("propagate.names.functionals"), ...){
@@ -30,7 +30,7 @@
if(!propagate.names){names(ret.v) <- NULL}
return(ret.v)
}})
-## http://mathworld.wolfram.com/GumbelDistribution.html
+## https://mathworld.wolfram.com/GumbelDistribution.html
setMethod("var", signature(x = "GPareto"),
function(x, propagate.names=getdistrExOption("propagate.names.functionals"), ...){
@@ -47,7 +47,7 @@
if(!propagate.names){names(ret.v) <- NULL}
return(ret.v)
}})
-### source http://en.wikipedia.org/wiki/Pareto_distribution
+### source https://en.wikipedia.org/wiki/Pareto_distribution
setMethod("var", signature(x = "GEV"),
@@ -66,7 +66,7 @@
if(!propagate.names){names(ret.v) <- NULL}
return(ret.v)
}})
-### http://en.wikipedia.org/wiki/Generalized_extreme_value_distribution
+### https://en.wikipedia.org/wiki/Generalized_extreme_value_distribution
#################################################################
# some exact medians
Modified: branches/robast-1.3/pkg/RobExtremes/R/Gumbel.R
===================================================================
--- branches/robast-1.3/pkg/RobExtremes/R/Gumbel.R 2021-07-28 14:39:58 UTC (rev 1233)
+++ branches/robast-1.3/pkg/RobExtremes/R/Gumbel.R 2022-04-22 10:44:53 UTC (rev 1234)
@@ -49,10 +49,10 @@
})
### Euler Mascheroni constant:
-EULERMASCHERONICONSTANT <- -digamma(1) ### after http://mathworld.wolfram.com/Euler-MascheroniConstant.html (48)
+EULERMASCHERONICONSTANT <- -digamma(1) ### after https://mathworld.wolfram.com/Euler-MascheroniConstant.html (48)
### Apéry constant
##local helper function:
.fctApery <- function(n) (-1)^n*choose(2*n,n)*n^3
##
-APERYCONSTANT <- -sum(sapply(1:50,.fctApery)^(-1))*5/2 ## after http://mathworld.wolfram.com/AperysConstant.html (8)
+APERYCONSTANT <- -sum(sapply(1:50,.fctApery)^(-1))*5/2 ## after https://mathworld.wolfram.com/AperysConstant.html (8)
Modified: branches/robast-1.3/pkg/RobExtremes/R/Kurtosis.R
===================================================================
--- branches/robast-1.3/pkg/RobExtremes/R/Kurtosis.R 2021-07-28 14:39:58 UTC (rev 1233)
+++ branches/robast-1.3/pkg/RobExtremes/R/Kurtosis.R 2022-04-22 10:44:53 UTC (rev 1234)
@@ -22,7 +22,7 @@
}
}
})
-### source http://mathworld.wolfram.com/ParetoDistribution.html
+### source https://mathworld.wolfram.com/ParetoDistribution.html
setMethod("kurtosis", signature(x = "Gumbel"),
function(x, ...){
@@ -35,7 +35,7 @@
return(kurtosis(as(x,"AbscontDistribution"),...))
else{
return(12/5)
-# http://mathworld.wolfram.com/GumbelDistribution.html
+# https://mathworld.wolfram.com/GumbelDistribution.html
}
})
@@ -78,6 +78,6 @@
return(ret.v)
}}
})
-### source http://en.wikipedia.org/wiki/Generalized_extreme_value_distribution
-### http://en.wikipedia.org/wiki/Gumbel_distribution
-### http://en.wikipedia.org/wiki/Riemann_zeta_function
+### source https://en.wikipedia.org/wiki/Generalized_extreme_value_distribution
+### https://en.wikipedia.org/wiki/Gumbel_distribution
+### https://en.wikipedia.org/wiki/Riemann_zeta_function
Modified: branches/robast-1.3/pkg/RobExtremes/R/Skewness.R
===================================================================
--- branches/robast-1.3/pkg/RobExtremes/R/Skewness.R 2021-07-28 14:39:58 UTC (rev 1233)
+++ branches/robast-1.3/pkg/RobExtremes/R/Skewness.R 2022-04-22 10:44:53 UTC (rev 1234)
@@ -18,7 +18,7 @@
return(ret.v)
}}
})
-### source http://mathworld.wolfram.com/ParetoDistribution.html
+### source https://mathworld.wolfram.com/ParetoDistribution.html
setMethod("skewness", signature(x = "Gumbel"),
function(x, ...){
@@ -31,7 +31,7 @@
return(skewness(as(x,"AbscontDistribution"),...))
else{
return( -12 * sqrt(6) * APERYCONSTANT / pi^3 )
-# http://mathworld.wolfram.com/GumbelDistribution.html
+# https://mathworld.wolfram.com/GumbelDistribution.html
}
})
@@ -75,6 +75,6 @@
}}
})
-### source http://en.wikipedia.org/wiki/Generalized_extreme_value_distribution
-### http://en.wikipedia.org/wiki/Gumbel_distribution
-### http://en.wikipedia.org/wiki/Riemann_zeta_function
+### source https://en.wikipedia.org/wiki/Generalized_extreme_value_distribution
+### https://en.wikipedia.org/wiki/Gumbel_distribution
+### https://en.wikipedia.org/wiki/Riemann_zeta_function
Modified: branches/robast-1.3/pkg/RobExtremes/inst/NEWS
===================================================================
--- branches/robast-1.3/pkg/RobExtremes/inst/NEWS 2021-07-28 14:39:58 UTC (rev 1233)
+++ branches/robast-1.3/pkg/RobExtremes/inst/NEWS 2022-04-22 10:44:53 UTC (rev 1234)
@@ -17,6 +17,9 @@
obtained from parameter coordinates should be propagated to return values
of specific S4 methods for functionals for Gumbel, GEV, GPD, Pareto
+under the hood
++ fixed some broken URLs and changed URLs from http to https where possible
+
#######################################
version 1.2
#######################################
Modified: branches/robast-1.3/pkg/RobExtremes/man/0RobExtremes-package.Rd
===================================================================
--- branches/robast-1.3/pkg/RobExtremes/man/0RobExtremes-package.Rd 2021-07-28 14:39:58 UTC (rev 1233)
+++ branches/robast-1.3/pkg/RobExtremes/man/0RobExtremes-package.Rd 2022-04-22 10:44:53 UTC (rev 1234)
@@ -130,7 +130,7 @@
ByteCompile: \tab yes \cr
LazyLoad: \tab yes \cr
License: \tab LGPL-3 \cr
-URL: \tab http://robast.r-forge.r-project.org/\cr
+URL: \tab https://robast.r-forge.r-project.org/\cr
Encoding: \tab latin1 \cr
VCS/SVNRevision: \tab 1205 \cr
}
@@ -267,7 +267,7 @@
\references{
M. Kohl (2005): \emph{Numerical Contributions to the Asymptotic
Theory of Robustness.} PhD Thesis. Bayreuth. Available as
-\url{http://r-kurs.de/RRlong.pdf}
+\url{https://www.stamats.de/wp-content/uploads/2018/04/ThesisMKohl.pdf}
P. Ruckdeschel, M. Kohl, T. Stabla, F. Camphausen (2006):
S4 Classes for Distributions, \emph{R News}, \emph{6}(2), 2-6.
@@ -290,7 +290,7 @@
and \pkg{RobExtremes} is included into the mere documentation package \pkg{distrDoc}
and may be called by \code{require("distrDoc");vignette("distr")}.
-A homepage to this package is available under \url{http://robast.r-forge.r-project.org/}.
+A homepage to this package is available under \url{https://robast.r-forge.r-project.org/}.
}
Modified: branches/robast-1.3/pkg/RobExtremes/man/RobExtremesConstants.Rd
===================================================================
--- branches/robast-1.3/pkg/RobExtremes/man/RobExtremesConstants.Rd 2021-07-28 14:39:58 UTC (rev 1233)
+++ branches/robast-1.3/pkg/RobExtremes/man/RobExtremesConstants.Rd 2022-04-22 10:44:53 UTC (rev 1234)
@@ -17,11 +17,11 @@
\itemize{
\item \code{EULERMASCHERONICONSTANT}: the Euler Mascheroni constant
\deqn{\gamma=-\Gamma'(1)}{gamma=-digamma(1)}
- given in \url{http://mathworld.wolfram.com/Euler-MascheroniConstant.html} (48);
+ given in \url{https://mathworld.wolfram.com/Euler-MascheroniConstant.html} (48);
\item \code{APERYCONSTANT}: the \enc{Apéry}{Apery} constant
\deqn{\zeta(3)= \frac{5}{2} (\sum_{k\ge 1}\frac{(-1)^{k-1}}{k^3 {2k\choose k}})}{
zeta(3) = 5/2 sum_{k>=0} (-1)^(k-1)/(k^3 * choose(2k,k))}
- as given in \url{http://mathworld.wolfram.com/AperysConstant.html}, equation (8);
+ as given in \url{https://mathworld.wolfram.com/AperysConstant.html}, equation (8);
}
These are implemented as variables in the \pkg{RobExtremes} name space taking
Modified: branches/robast-1.3/pkg/RobLox/inst/NEWS
===================================================================
--- branches/robast-1.3/pkg/RobLox/inst/NEWS 2021-07-28 14:39:58 UTC (rev 1233)
+++ branches/robast-1.3/pkg/RobLox/inst/NEWS 2022-04-22 10:44:53 UTC (rev 1234)
@@ -8,6 +8,13 @@
information)
#######################################
+version 1.3
+#######################################
+
+under the hood
++ fixed some broken URLs and changed URLs from http to https where possible
+
+#######################################
version 1.2
#######################################
Modified: branches/robast-1.3/pkg/RobLox/man/finiteSampleCorrection.Rd
===================================================================
--- branches/robast-1.3/pkg/RobLox/man/finiteSampleCorrection.Rd 2021-07-28 14:39:58 UTC (rev 1233)
+++ branches/robast-1.3/pkg/RobLox/man/finiteSampleCorrection.Rd 2022-04-22 10:44:53 UTC (rev 1234)
@@ -36,7 +36,7 @@
Rieder, H., Kohl, M. and Ruckdeschel, P. (2008) The Costs of not Knowing
the Radius. Statistical Methods and Applications \emph{17}(1) 13-40.
- Extended version: \url{http://r-kurs.de/RRlong.pdf}
+ Extended version: \url{https://uol.de/f/5/inst/mathe/personen/peter.ruckdeschel/Rr.pdf}
}
\author{Matthias Kohl \email{Matthias.Kohl at stamats.de}}
%\note{}
Modified: branches/robast-1.3/pkg/RobLox/man/roblox.Rd
===================================================================
--- branches/robast-1.3/pkg/RobLox/man/roblox.Rd 2021-07-28 14:39:58 UTC (rev 1233)
+++ branches/robast-1.3/pkg/RobLox/man/roblox.Rd 2022-04-22 10:44:53 UTC (rev 1234)
@@ -77,7 +77,7 @@
Rieder, H., Kohl, M. and Ruckdeschel, P. (2008) The Costs of not Knowing
the Radius. Statistical Methods and Applications \emph{17}(1) 13-40.
- Extended version: \url{http://r-kurs.de/RRlong.pdf}
+ Extended version: \url{https://uol.de/f/5/inst/mathe/personen/peter.ruckdeschel/Rr.pdf}
M. Kohl, P. Ruckdeschel, and H. Rieder (2010). Infinitesimally Robust Estimation
in General Smoothly Parametrized Models. \emph{Statistical Methods and Application},
Modified: branches/robast-1.3/pkg/RobLox/man/rowRoblox.Rd
===================================================================
--- branches/robast-1.3/pkg/RobLox/man/rowRoblox.Rd 2021-07-28 14:39:58 UTC (rev 1233)
+++ branches/robast-1.3/pkg/RobLox/man/rowRoblox.Rd 2022-04-22 10:44:53 UTC (rev 1234)
@@ -87,7 +87,7 @@
Rieder, H., Kohl, M. and Ruckdeschel, P. (2008) The Costs of not Knowing
the Radius. Statistical Methods and Applications \emph{17}(1) 13-40.
- Extended version: \url{http://r-kurs.de/RRlong.pdf}
+ Extended version: \url{https://uol.de/f/5/inst/mathe/personen/peter.ruckdeschel/Rr.pdf}
M. Kohl, P. Ruckdeschel, and H. Rieder (2010). Infinitesimally Robust Estimation
in General Smoothly Parametrized Models. \emph{Statistical Methods and Application},
Modified: branches/robast-1.3/pkg/RobLox/man/showdown.Rd
===================================================================
--- branches/robast-1.3/pkg/RobLox/man/showdown.Rd 2021-07-28 14:39:58 UTC (rev 1233)
+++ branches/robast-1.3/pkg/RobLox/man/showdown.Rd 2022-04-22 10:44:53 UTC (rev 1234)
@@ -57,7 +57,7 @@
Rieder, H., Kohl, M. and Ruckdeschel, P. (2008) The Costs of not Knowing
the Radius. Statistical Methods and Applications \emph{17}(1) 13-40.
- Extended version: \url{http://r-kurs.de/RRlong.pdf}
+ Extended version: \url{https://uol.de/f/5/inst/mathe/personen/peter.ruckdeschel/Rr.pdf}
M. Kohl, P. Ruckdeschel, and H. Rieder (2010). Infinitesimally Robust Estimation
in General Smoothly Parametrized Models. \emph{Statistical Methods and Application},
Modified: branches/robast-1.3/pkg/RobLoxBioC/inst/NEWS
===================================================================
--- branches/robast-1.3/pkg/RobLoxBioC/inst/NEWS 2021-07-28 14:39:58 UTC (rev 1233)
+++ branches/robast-1.3/pkg/RobLoxBioC/inst/NEWS 2022-04-22 10:44:53 UTC (rev 1234)
@@ -8,6 +8,13 @@
information)
#######################################
+version 1.3
+#######################################
+
+under the hood
++ fixed some broken URLs and changed URLs from http to https where possible
+
+#######################################
version 1.1
#######################################
Modified: branches/robast-1.3/pkg/RobLoxBioC/inst/scripts/AffymetrixExample.R
===================================================================
--- branches/robast-1.3/pkg/RobLoxBioC/inst/scripts/AffymetrixExample.R 2021-07-28 14:39:58 UTC (rev 1233)
+++ branches/robast-1.3/pkg/RobLoxBioC/inst/scripts/AffymetrixExample.R 2022-04-22 10:44:53 UTC (rev 1234)
@@ -16,10 +16,10 @@
###############################################################################
## Data
## Spike-in hgu95a data:
-## http://www.biostat.jhsph.edu/~ririzarr/affycomp/spikein.tgz
+## https://www.biostat.jhsph.edu/~ririzarr/affycomp/spikein.tgz
##
## Spike-in hgu133a data:
-## http://www.biostat.jhsph.edu/~ririzarr/affycomp/hgu133spikein.tgz
+## https://www.biostat.jhsph.edu/~ririzarr/affycomp/hgu133spikein.tgz
##
## Dilution data:
## The links:
@@ -76,10 +76,10 @@
system.time(minKD.hgu133a <- KolmogorovMinDist(spikein.hgu133a, Norm()))
## load the results from R-forge ...
-con <- url("http://robast.r-forge.r-project.org/data/minKD_hgu95a.RData")
+con <- url("https://robast.r-forge.r-project.org/data/minKD_hgu95a.RData")
load(file = con)
close(con)
-con <- url("http://robast.r-forge.r-project.org/data/minKD_hgu133a.RData")
+con <- url("https://robast.r-forge.r-project.org/data/minKD_hgu133a.RData")
load(file = con)
close(con)
@@ -106,7 +106,7 @@
colnames(minKD.norm) <- ns
## load the results from R-forge
-con <- url("http://robast.r-forge.r-project.org/data/minKD_norm.RData")
+con <- url("https://robast.r-forge.r-project.org/data/minKD_norm.RData")
load(file = con)
close(con)
Modified: branches/robast-1.3/pkg/RobLoxBioC/inst/scripts/AffymetrixReproducibility.R
===================================================================
--- branches/robast-1.3/pkg/RobLoxBioC/inst/scripts/AffymetrixReproducibility.R 2021-07-28 14:39:58 UTC (rev 1233)
+++ branches/robast-1.3/pkg/RobLoxBioC/inst/scripts/AffymetrixReproducibility.R 2022-04-22 10:44:53 UTC (rev 1234)
@@ -18,7 +18,7 @@
system.time(minKD.D <- KolmogorovMinDist(refD, Norm()))
## load the results for random normal samples from R-forge
-con <- url("http://robast.r-forge.r-project.org/data/minKD_norm.RData")
+con <- url("https://robast.r-forge.r-project.org/data/minKD_norm.RData")
load(file = con)
close(con)
Modified: branches/robast-1.3/pkg/RobLoxBioC/inst/scripts/IlluminaExample.R
===================================================================
--- branches/robast-1.3/pkg/RobLoxBioC/inst/scripts/IlluminaExample.R 2021-07-28 14:39:58 UTC (rev 1233)
+++ branches/robast-1.3/pkg/RobLoxBioC/inst/scripts/IlluminaExample.R 2022-04-22 10:44:53 UTC (rev 1234)
@@ -17,6 +17,7 @@
## Data:
## Can be obtained via
## http://www.compbio.group.cam.ac.uk/Resources/spike/index.html
+## [20220422: URL seems to be broken]
###############################################################################
## Load the required packages
@@ -55,10 +56,10 @@
save(minKD.Illumina.log, compress = TRUE, file = "minKD_Illumina_log.RData")
## load the results from R-forge ...
-con <- url("http://robast.r-forge.r-project.org/data/minKD_Illumina.RData")
+con <- url("https://robast.r-forge.r-project.org/data/minKD_Illumina.RData")
load(file = con)
close(con)
-con <- url("http://robast.r-forge.r-project.org/data/minKD_Illumina_log.RData")
+con <- url("https://robast.r-forge.r-project.org/data/minKD_Illumina_log.RData")
load(file = con)
close(con)
@@ -78,7 +79,7 @@
}
## load the results from R-forge
-con <- url("http://robast.r-forge.r-project.org/data/minKD_Illumina_norm.RData")
+con <- url("https://robast.r-forge.r-project.org/data/minKD_Illumina_norm.RData")
load(file = con)
close(con)
@@ -246,6 +247,7 @@
## The following example is based on the R code of Mark Dunning and Matt Ritchie
## available under
## http://www.compbio.group.cam.ac.uk/Resources/spike/scripts/Analysis.R
+## [20220422: URL seems to be broken]
##
## This file was slightly adapted and code for the computation of
## rmx-estimators was added.
Modified: branches/robast-1.3/pkg/RobLoxBioC/inst/scripts/IlluminaReproducibility.R
===================================================================
--- branches/robast-1.3/pkg/RobLoxBioC/inst/scripts/IlluminaReproducibility.R 2021-07-28 14:39:58 UTC (rev 1233)
+++ branches/robast-1.3/pkg/RobLoxBioC/inst/scripts/IlluminaReproducibility.R 2022-04-22 10:44:53 UTC (rev 1234)
@@ -17,6 +17,7 @@
## Data:
## Can be obtained via
## http://www.compbio.group.cam.ac.uk/Resources/spike/index.html
+## [20220422: URL seems to be broken]
###############################################################################
## Load the required packages
Modified: branches/robast-1.3/pkg/RobLoxBioC/man/0RobLoxBioC-package.Rd
===================================================================
--- branches/robast-1.3/pkg/RobLoxBioC/man/0RobLoxBioC-package.Rd 2021-07-28 14:39:58 UTC (rev 1233)
+++ branches/robast-1.3/pkg/RobLoxBioC/man/0RobLoxBioC-package.Rd 2022-04-22 10:44:53 UTC (rev 1234)
@@ -21,7 +21,7 @@
illuminaHumanv3.db \cr
ByteCompile: \tab yes \cr
License: \tab LGPL-3 \cr
-URL: \tab http://robast.r-forge.r-project.org/\cr
+URL: \tab https://robast.r-forge.r-project.org/\cr
VCS/SVNRevision: \tab 1205 \cr
Encoding: \tab latin1 \cr
}
@@ -44,7 +44,7 @@
Rieder, H., Kohl, M. and Ruckdeschel, P. (2008) The Costs of not Knowing
the Radius. \emph{Statistical Methods and Applications} \bold{17}(1) 13-40.
- Extended version: \url{http://r-kurs.de/RRlong.pdf}
+ Extended version: \url{https://uol.de/f/5/inst/mathe/personen/peter.ruckdeschel/Rr.pdf}
}
\seealso{
\code{\link[RobLox]{roblox}}, \code{\link[RobLox]{rowRoblox}}
Modified: branches/robast-1.3/pkg/RobLoxBioC/man/robloxbioc.Rd
===================================================================
--- branches/robast-1.3/pkg/RobLoxBioC/man/robloxbioc.Rd 2021-07-28 14:39:58 UTC (rev 1233)
+++ branches/robast-1.3/pkg/RobLoxBioC/man/robloxbioc.Rd 2022-04-22 10:44:53 UTC (rev 1234)
@@ -125,7 +125,7 @@
Rieder, H., Kohl, M. and Ruckdeschel, P. (2008) The Costs of not Knowing
the Radius. \emph{Statistical Methods and Applications} \bold{17}(1) 13-40.
- Extended version: \url{http://r-kurs.de/RRlong.pdf}
+ Extended version: \url{https://uol.de/f/5/inst/mathe/personen/peter.ruckdeschel/Rr.pdf}
}
\author{Matthias Kohl \email{Matthias.Kohl at stamats.de},
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