[Distr-commits] r1344 - in pkg: distrMod distrMod/inst distrMod/man distrMod/tests/Examples utils
noreply at r-forge.r-project.org
noreply at r-forge.r-project.org
Wed May 1 01:16:26 CEST 2019
Author: ruckdeschel
Date: 2019-05-01 01:16:26 +0200 (Wed, 01 May 2019)
New Revision: 1344
Modified:
pkg/distrMod/DESCRIPTION
pkg/distrMod/inst/NEWS
pkg/distrMod/man/0distrMod-package.Rd
pkg/distrMod/man/InfoNorm.Rd
pkg/distrMod/man/NormType-class.Rd
pkg/distrMod/man/NormType.Rd
pkg/distrMod/man/QFNorm.Rd
pkg/distrMod/man/SelfNorm.Rd
pkg/distrMod/man/returnlevelplot.Rd
pkg/distrMod/tests/Examples/distrMod-Ex.Rout.save
pkg/utils/DESCRIPTIONutilsExamples.R
Log:
[distrMod] trunk -- in response to K. Hornik's mails from Apr 30, 2019, we created version 2.8.2 for submission to CRAN in order to fix the issues detected on
<https://cran.r-project.org/web/checks/check_results_distrMod.html>
Modified: pkg/distrMod/DESCRIPTION
===================================================================
--- pkg/distrMod/DESCRIPTION 2019-04-30 21:12:49 UTC (rev 1343)
+++ pkg/distrMod/DESCRIPTION 2019-04-30 23:16:26 UTC (rev 1344)
@@ -1,6 +1,6 @@
Package: distrMod
-Version: 2.8.1
-Date: 2019-04-07
+Version: 2.8.2
+Date: 2019-04-30
Title: Object Oriented Implementation of Probability Models
Description: Implements S4 classes for probability models based on packages 'distr' and
'distrEx'.
@@ -18,4 +18,4 @@
URL: http://distr.r-forge.r-project.org/
LastChangedDate: {$LastChangedDate$}
LastChangedRevision: {$LastChangedRevision$}
-VCS/SVNRevision: 1337
+VCS/SVNRevision: 1342
Modified: pkg/distrMod/inst/NEWS
===================================================================
--- pkg/distrMod/inst/NEWS 2019-04-30 21:12:49 UTC (rev 1343)
+++ pkg/distrMod/inst/NEWS 2019-04-30 23:16:26 UTC (rev 1344)
@@ -8,6 +8,13 @@
information)
##############
+v 2.8.2
+##############
+under the hood:
++ inserted some ## IGNORE_RDIFF_BEGIN comments to prevent NOTES when comparing R.out.save to
+ R.out on varying architectures, e.g. Rblas/ATLAS
+
+##############
v 2.8.1
##############
user-visible CHANGES:
Modified: pkg/distrMod/man/0distrMod-package.Rd
===================================================================
--- pkg/distrMod/man/0distrMod-package.Rd 2019-04-30 21:12:49 UTC (rev 1343)
+++ pkg/distrMod/man/0distrMod-package.Rd 2019-04-30 23:16:26 UTC (rev 1344)
@@ -13,8 +13,8 @@
\details{
\tabular{ll}{
Package: \tab distrMod \cr
-Version: \tab 2.8.1 \cr
-Date: \tab 2019-04-07 \cr
+Version: \tab 2.8.2 \cr
+Date: \tab 2019-04-30 \cr
Depends: \tab R(>= 3.4), distr(>= 2.8.0), distrEx(>= 2.8.0), RandVar(>= 1.2.0), MASS, stats4,methods \cr
Imports: \tab startupmsg, sfsmisc, graphics, stats, grDevices \cr
Suggests: \tab ismev, evd, \cr
@@ -22,7 +22,7 @@
ByteCompile: \tab yes \cr
License: \tab LGPL-3 \cr
URL: \tab http://distr.r-forge.r-project.org/\cr
-VCS/SVNRevision: \tab 1337 \cr
+VCS/SVNRevision: \tab 1342 \cr
}}
\section{Classes}{
\preformatted{
Modified: pkg/distrMod/man/InfoNorm.Rd
===================================================================
--- pkg/distrMod/man/InfoNorm.Rd 2019-04-30 21:12:49 UTC (rev 1343)
+++ pkg/distrMod/man/InfoNorm.Rd 2019-04-30 23:16:26 UTC (rev 1344)
@@ -19,10 +19,12 @@
%\note{}
\seealso{\code{\link{InfoNorm-class}}}
\examples{
+ ## IGNORE_RDIFF_BEGIN
InfoNorm()
## The function is currently defined as
function(){ new("InfoNorm") }
+ ## IGNORE_RDIFF_END
}
\concept{asymptotic covariance}
\concept{risk}
Modified: pkg/distrMod/man/NormType-class.Rd
===================================================================
--- pkg/distrMod/man/NormType-class.Rd 2019-04-30 21:12:49 UTC (rev 1343)
+++ pkg/distrMod/man/NormType-class.Rd 2019-04-30 23:16:26 UTC (rev 1344)
@@ -40,9 +40,11 @@
%\note{}
\seealso{\code{\link{BiasType-class}}}
\examples{
+ ## IGNORE_RDIFF_BEGIN
EuclNorm <- NormType("EuclideanNorm",EuclideanNorm)
fct(EuclNorm)
name(EuclNorm)
+ ## IGNORE_RDIFF_END
}
\concept{asymptotic risk}
\concept{bias}
Modified: pkg/distrMod/man/NormType.Rd
===================================================================
--- pkg/distrMod/man/NormType.Rd 2019-04-30 21:12:49 UTC (rev 1343)
+++ pkg/distrMod/man/NormType.Rd 2019-04-30 23:16:26 UTC (rev 1344)
@@ -22,7 +22,9 @@
%\note{}
\seealso{\code{\link{NormType-class}}}
\examples{
+ ## IGNORE_RDIFF_BEGIN
NormType()
+ ## IGNORE_RDIFF_END
}
\concept{asymptotic covariance}
\concept{risk}
Modified: pkg/distrMod/man/QFNorm.Rd
===================================================================
--- pkg/distrMod/man/QFNorm.Rd 2019-04-30 21:12:49 UTC (rev 1343)
+++ pkg/distrMod/man/QFNorm.Rd 2019-04-30 23:16:26 UTC (rev 1344)
@@ -27,7 +27,9 @@
QFNorm()
## The function is currently defined as
+ ## IGNORE_RDIFF_BEGIN
function(){ new("QFNorm") }
+ ## IGNORE_RDIFF_END
}
\concept{asymptotic covariance}
\concept{risk}
Modified: pkg/distrMod/man/SelfNorm.Rd
===================================================================
--- pkg/distrMod/man/SelfNorm.Rd 2019-04-30 21:12:49 UTC (rev 1343)
+++ pkg/distrMod/man/SelfNorm.Rd 2019-04-30 23:16:26 UTC (rev 1344)
@@ -19,10 +19,12 @@
%\note{}
\seealso{\code{\link{SelfNorm-class}}}
\examples{
+ ## IGNORE_RDIFF_BEGIN
SelfNorm()
## The function is currently defined as
function(){ new("SelfNorm") }
+ ## IGNORE_RDIFF_END
}
\concept{asymptotic covariance}
\concept{risk}
Modified: pkg/distrMod/man/returnlevelplot.Rd
===================================================================
--- pkg/distrMod/man/returnlevelplot.Rd 2019-04-30 21:12:49 UTC (rev 1343)
+++ pkg/distrMod/man/returnlevelplot.Rd 2019-04-30 23:16:26 UTC (rev 1344)
@@ -255,6 +255,11 @@
returnlevelplot(r(Norm(15,sqrt(30)))(40), Chisq(df=15))
### more could be seen after installing RobExtremes and ismev
#
+
+## IGNORE_RDIFF_BEGIN
+\donttest{ ## at R CMD check --as-cran, it does not find package cluster
+ ## when trying to attach package rrcov
+ ## so remove this from testing
if(require(RobExtremes) && require(ismev)){
data(portpirie)
@@ -270,6 +275,9 @@
gpdfit <- gpd.fit(rain,10) ## taken from example from ismev::gpd.fit
GPDF <- GParetoFamily(scale=gpdfit$mle[1],shape=gpdfit$mle[2],loc=10)
returnlevelplot(rain, GPDF, MaxOrPOT="POT", xlim=c(1e-1,1e3))
-}}
+}
+}
+ ## IGNORE_RDIFF_END
+}
\keyword{hplot}
\keyword{distribution}
Modified: pkg/distrMod/tests/Examples/distrMod-Ex.Rout.save
===================================================================
--- pkg/distrMod/tests/Examples/distrMod-Ex.Rout.save 2019-04-30 21:12:49 UTC (rev 1343)
+++ pkg/distrMod/tests/Examples/distrMod-Ex.Rout.save 2019-04-30 23:16:26 UTC (rev 1344)
@@ -92,7 +92,7 @@
Loading required package: MASS
Loading required package: stats4
:distrMod> Object Oriented Implementation of Probability Models
-:distrMod> (version 2.8.1)
+:distrMod> (version 2.8.2)
:distrMod>
:distrMod> Some functions from pkg's 'base' and 'stats' are
:distrMod> intentionally masked ---see distrModMASK().
@@ -419,7 +419,7 @@
dimnames = list(nms, nms0))
list(fval = fval0, mat = mat0)
}
-<bytecode: 0x000000000d34f360>
+<bytecode: 0x000000000c79b9f0>
Trafo / derivative matrix at which estimate was produced:
scale shape
shape 0.000 1
@@ -620,7 +620,7 @@
1)/c(scale = 1)
return(y)
}
-<environment: 0x000000000e638530>
+<environment: 0x0000000014dade30>
> checkL2deriv(E1)
precision of centering: -2.042661e-06
@@ -777,6 +777,7 @@
>
> ### ** Examples
>
+> ## IGNORE_RDIFF_BEGIN
> InfoNorm()
An object of class "InfoNorm"
Slot "QuadForm":
@@ -789,8 +790,8 @@
Slot "fct":
function(x) QuadFormNorm(x, A = A)
-<bytecode: 0x000000000d5f1b98>
-<environment: 0x000000000d5f5498>
+<bytecode: 0x000000000da8bab8>
+<environment: 0x000000000da89dc8>
>
> ## The function is currently defined as
@@ -799,6 +800,7 @@
{
new("InfoNorm")
}
+> ## IGNORE_RDIFF_END
>
>
>
@@ -1072,7 +1074,7 @@
1)/c(meanlog = 1)
return(y)
}
-<environment: 0x00000000065c9f70>
+<environment: 0x0000000014f39200>
> checkL2deriv(L1)
precision of centering: -0.003003394
@@ -2103,6 +2105,7 @@
>
> ### ** Examples
>
+> ## IGNORE_RDIFF_BEGIN
> EuclNorm <- NormType("EuclideanNorm",EuclideanNorm)
> fct(EuclNorm)
function(x){
@@ -2111,10 +2114,11 @@
else
return(sqrt(colSums(x^2)))
}
-<bytecode: 0x000000000d7b0298>
+<bytecode: 0x00000000119b69b0>
<environment: namespace:distrMod>
> name(EuclNorm)
[1] "EuclideanNorm"
+> ## IGNORE_RDIFF_END
>
>
>
@@ -2131,6 +2135,7 @@
>
> ### ** Examples
>
+> ## IGNORE_RDIFF_BEGIN
> NormType()
An object of class "NormType"
Slot "name":
@@ -2143,9 +2148,10 @@
else
return(sqrt(colSums(x^2)))
}
-<bytecode: 0x000000000d7b0298>
+<bytecode: 0x00000000119b69b0>
<environment: namespace:distrMod>
+> ## IGNORE_RDIFF_END
>
>
>
@@ -2598,16 +2604,18 @@
Slot "fct":
function(x) QuadFormNorm(x, A= A0)
-<bytecode: 0x0000000014108388>
-<environment: 0x0000000014109fd0>
+<bytecode: 0x0000000015964f78>
+<environment: 0x0000000015968b18>
>
> ## The function is currently defined as
+> ## IGNORE_RDIFF_BEGIN
> function(){ new("QFNorm") }
function ()
{
new("QFNorm")
}
+> ## IGNORE_RDIFF_END
>
>
>
@@ -2624,6 +2632,7 @@
>
> ### ** Examples
>
+> ## IGNORE_RDIFF_BEGIN
> SelfNorm()
An object of class "SelfNorm"
Slot "QuadForm":
@@ -2636,8 +2645,8 @@
Slot "fct":
function(x) QuadFormNorm(x, A = A)
-<bytecode: 0x00000000138dd9d0>
-<environment: 0x00000000138e33d8>
+<bytecode: 0x0000000014f9e188>
+<environment: 0x000000001316a788>
>
> ## The function is currently defined as
@@ -2646,6 +2655,7 @@
{
new("SelfNorm")
}
+> ## IGNORE_RDIFF_END
>
>
>
@@ -3655,7 +3665,7 @@
dimnames(mat) <- list(nfval, c("mean", "sd"))
return(list(fval = fval, mat = mat))
}
-<bytecode: 0x0000000014f4f340>
+<bytecode: 0x0000000014ac1948>
> print(param(NS), show.details = "minimal")
An object of class "ParamWithScaleFamParameter"
name: location and scale
@@ -3704,7 +3714,7 @@
dimnames(mat) <- list(nfval, c("mean", "sd"))
return(list(fval = fval, mat = mat))
}
-<bytecode: 0x0000000014f4f340>
+<bytecode: 0x0000000014ac1948>
Trafo / derivative matrix:
mean sd
mu/sig 0.3668695 -0.3024814
@@ -3747,7 +3757,7 @@
dimnames(mat) <- list(nfval, c("mean", "sd"))
return(list(fval = fval, mat = mat))
}
-<bytecode: 0x0000000014f4f340>
+<bytecode: 0x0000000014ac1948>
Trafo / derivative matrix:
mean sd
mu/sig 0.3669 -0.3025
@@ -3827,132 +3837,13 @@
> returnlevelplot(r(Norm(15,sqrt(30)))(40), Chisq(df=15))
> ### more could be seen after installing RobExtremes and ismev
> #
-> if(require(RobExtremes) && require(ismev)){
-+
-+ data(portpirie)
-+ gevfit <- gev.fit(portpirie[,2]) ## taken from example from ismev::gev.fit
-+ GEVF <- GEVFamily(scale=gevfit$mle[2],shape=gevfit$mle[3],loc=gevfit$mle[1])
-+ erg <- returnlevelplot(portpirie[,2], GEVF)
-+ print(names(erg))
-+ print(names(erg$plotArgs))
-+ print(names(erg$IdLineArgs))
-+ returnlevelplot(portpirie[,2], GEVF, datax=TRUE)
-+
-+ data(rain)
-+ gpdfit <- gpd.fit(rain,10) ## taken from example from ismev::gpd.fit
-+ GPDF <- GParetoFamily(scale=gpdfit$mle[1],shape=gpdfit$mle[2],loc=10)
-+ returnlevelplot(rain, GPDF, MaxOrPOT="POT", xlim=c(1e-1,1e3))
-+ }
-Loading required package: RobExtremes
-Loading required package: ROptEst
-Loading required package: RobAStBase
-Loading required package: rrcov
-Loading required package: robustbase
-Scalable Robust Estimators with High Breakdown Point (version 1.4-7)
-
-:RobAStBase> Robust Asymptotic Statistics (version 1.2.0)
-:RobAStBase>
-:RobAStBase> Some functions from pkg's 'stats' and 'graphics'
-:RobAStBase> are intentionally masked ---see RobAStBaseMASK().
-:RobAStBase>
-:RobAStBase> Note that global options are controlled by
-:RobAStBase> RobAStBaseoptions() ---c.f. ?"RobAStBaseoptions".
-:RobAStBase>
-:RobAStBase> For more information see ?"RobAStBase",
-:RobAStBase> NEWS("RobAStBase"), as well as
-:RobAStBase> http://robast.r-forge.r-project.org/
-
-
-Attaching package: 'RobAStBase'
-
-The following object is masked from 'package:graphics':
-
- clip
-
-Loading required package: evd
-:RobExtremes> Optimally Robust Estimation for Extreme Value
-:RobExtremes> Distributions (version 1.2.0)
-:RobExtremes>
-:RobExtremes>
-:RobExtremes> For more information see ?"RobExtremes",
-:RobExtremes> NEWS("RobExtremes"), as well as
-:RobExtremes> http://robast.r-forge.r-project.org/
-
-
-Attaching package: 'RobExtremes'
-
-The following objects are masked from 'package:robustbase':
-
- Qn, Sn
-
-Loading required package: ismev
-Loading required package: mgcv
-Loading required package: nlme
-
-Attaching package: 'nlme'
-
-The following object is masked from 'package:rrcov':
-
- getData
-
-The following object is masked from 'package:RandVar':
-
- Dim
-
-This is mgcv 1.8-28. For overview type 'help("mgcv-package")'.
-
-Attaching package: 'ismev'
-
-The following objects are masked from 'package:RobExtremes':
-
- gev.diag, gev.prof, gev.profxi, gpd.diag, gpd.prof, gpd.profxi
-
-$conv
-[1] 0
-
-$nllh
-[1] -4.339058
-
-$mle
-[1] 3.87474692 0.19804120 -0.05008773
-
-$se
-[1] 0.02793211 0.02024610 0.09825633
-
- [1] "call" "dots" "args" "plotArgs" "pointArgs"
- [6] "usr" "IdLineArgs" "ret.x" "ret.y" "qqb.crit"
-[11] "qqb.err"
- [1] "x" "y" "log" "type" "xlab" "ylab" "main" "pch" "cex" "col"
-[1] "" "" "col" "lty" "lwd"
-$threshold
-[1] 10
-
-$nexc
-[1] 2003
-
-$conv
-[1] 0
-
-$nllh
-[1] 6123.465
-
-$mle
-[1] 7.43768624 0.05045225
-
-$rate
-[1] 0.1142547
-
-$se
-[1] 0.23606472 0.02256649
-
>
+> ## IGNORE_RDIFF_BEGIN
+> ## IGNORE_RDIFF_END
>
+>
+>
> cleanEx()
-
-detaching 'package:ismev', 'package:mgcv', 'package:nlme',
- 'package:RobExtremes', 'package:evd', 'package:ROptEst',
- 'package:RobAStBase', 'package:rrcov', 'package:robustbase'
-
> nameEx("symmetricBias-class")
> ### * symmetricBias-class
>
@@ -4144,7 +4035,7 @@
(0.2113366) (1.9183645)
> ## confidence interval
> confint(res)
-A[n] asymptotic (LAN-based) confidence interval:
+A[n] asymptotic (CLT-based) confidence interval:
2.5 % 97.5 %
mu/sig 0.4102811 1.238705
sig^2 3.6698685 11.189719
@@ -4189,7 +4080,7 @@
> res <- trafoEst(mtrafo, res0)
> ## confidence interval
> confint(res)
-A[n] asymptotic (LAN-based) confidence interval:
+A[n] asymptotic (CLT-based) confidence interval:
2.5 % 97.5 %
mu/sig 0.4102811 1.238705
sig^2 3.6698685 11.189719
@@ -4232,7 +4123,7 @@
> cleanEx()
> options(digits = 7L)
> base::cat("Time elapsed: ", proc.time() - base::get("ptime", pos = 'CheckExEnv'),"\n")
-Time elapsed: 29.69 0.99 31.06 NA NA
+Time elapsed: 30.2 0.66 31.53 NA NA
> grDevices::dev.off()
null device
1
Modified: pkg/utils/DESCRIPTIONutilsExamples.R
===================================================================
--- pkg/utils/DESCRIPTIONutilsExamples.R 2019-04-30 21:12:49 UTC (rev 1343)
+++ pkg/utils/DESCRIPTIONutilsExamples.R 2019-04-30 23:16:26 UTC (rev 1344)
@@ -188,6 +188,24 @@
ReqDistrPkgVersion =ReqDistrPkgVersion0)
}
+if(FALSE){## Version 2.8 in trunk fourth shift 20190430
+Pkgs <- c("distrMod")
+Names <- c("Version")
+Values <- matrix(c("2.8.2"),1,length(Pkgs))
+ReqRVersion0 <- c(rep("R(>= 3.4)",length(Pkgs)))
+ReqDistrPkgVersion0 <- vector("list",length(Pkgs))
+names(ReqDistrPkgVersion0) <- Pkgs
+ReqDistrPkgVersion0[["RandVar"]] <- NA
+for(pk in Pkgs) ReqDistrPkgVersion0[[pk]] <- c("distr"="distr(>= 2.8.0)",
+ "distrEx"="distrEx(>= 2.8.0)","distrMod"="distrMod(>= 2.8.2)",
+ "RandVar"="RandVar(>= 1.2.0)")
+colnames(Values) <- names(ReqRVersion0) <- Pkgs
+rownames(Values) <- Names
+changeDescription(startDir = "C:/rtest/distr",names=Names,
+ pkgs=Pkgs, values=Values,ReqRVersion =ReqRVersion0,
+ ReqDistrPkgVersion =ReqDistrPkgVersion0)
+}
+
if(FALSE){## Version 2.8 in branch
Pkgs <- c("startupmsg",
"distr", "distrEx", "distrDoc", "distrEllipse", "distrRmetrics",
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