[Mboost-commits] r821 - in pkg/mboostPatch: . R inst man tests tests/Examples vignettes
noreply at r-forge.r-project.org
noreply at r-forge.r-project.org
Mon Dec 15 18:50:35 CET 2014
Author: hofner
Date: 2014-12-15 18:50:34 +0100 (Mon, 15 Dec 2014)
New Revision: 821
Added:
pkg/mboostPatch/tests/birds_Biometrics.R
Removed:
pkg/mboostPatch/tests/birds_Biometrics.R
Modified:
pkg/mboostPatch/DESCRIPTION
pkg/mboostPatch/NAMESPACE
pkg/mboostPatch/R/AAA.R
pkg/mboostPatch/R/methods.R
pkg/mboostPatch/inst/NEWS.Rd
pkg/mboostPatch/man/mboost_package.Rd
pkg/mboostPatch/man/methods.Rd
pkg/mboostPatch/tests/Examples/mboost-Ex.Rout.save
pkg/mboostPatch/tests/birds_Biometrics.Rout.save
pkg/mboostPatch/tests/bugfixes.Rout.save
pkg/mboostPatch/tests/regtest-baselearner.Rout.save
pkg/mboostPatch/tests/regtest-blackboost.Rout.save
pkg/mboostPatch/tests/regtest-family.Rout.save
pkg/mboostPatch/tests/regtest-gamboost.Rout.save
pkg/mboostPatch/tests/regtest-glmboost.Rout.save
pkg/mboostPatch/tests/regtest-hatmatrix.Rout.save
pkg/mboostPatch/tests/regtest-inference.Rout.save
pkg/mboostPatch/vignettes/SurvivalEnsembles.Rout.save
pkg/mboostPatch/vignettes/mboost.Rout.save
pkg/mboostPatch/vignettes/mboost_illustrations.Rout.save
pkg/mboostPatch/vignettes/mboost_tutorial.Rout.save
Log:
Prepare release mboost 2.4-1
- re-export selected() from package stabs
- instead to the file NEWS we now refer to news(package = "mboost")
- updated test results
Modified: pkg/mboostPatch/DESCRIPTION
===================================================================
--- pkg/mboostPatch/DESCRIPTION 2014-12-15 17:50:31 UTC (rev 820)
+++ pkg/mboostPatch/DESCRIPTION 2014-12-15 17:50:34 UTC (rev 821)
@@ -1,7 +1,7 @@
Package: mboost
Title: Model-Based Boosting
Version: 2.4-1
-Date: 2014-xx-yy
+Date: 2014-12-15
Authors at R: c(person("Torsten", "Hothorn", role = c("aut", "cre"),
email = "Torsten.Hothorn at R-project.org"),
person("Peter", "Buehlmann", role = "aut"),
Modified: pkg/mboostPatch/NAMESPACE
===================================================================
--- pkg/mboostPatch/NAMESPACE 2014-12-15 17:50:31 UTC (rev 820)
+++ pkg/mboostPatch/NAMESPACE 2014-12-15 17:50:34 UTC (rev 821)
@@ -21,7 +21,8 @@
ExpectReg, NBinomial, PropOdds, Weibull, Loglog, Lognormal, AUC, mboost_fit,
Huber, AdaExp, Gehan, CoxPH, Hurdle, Multinomial, FP, IPCweights,
cvrisk, cv, bbs,
- bols, bspatial, brandom, btree, bss, bns, brad, bmono, bmrf, buser, survFit, selected.mboost,
+ bols, bspatial, brandom, btree, bss, bns, brad, bmono, bmrf, buser,
+ survFit, selected, selected.mboost,
nuisance, "%+%", "%X%", "%O%", extract, risk, "mstop<-",
stabsel.mboost, stabsel_parameters.mboost, confint.mboost, confint.glmboost)
###, basesel, fitsel)
Modified: pkg/mboostPatch/R/AAA.R
===================================================================
--- pkg/mboostPatch/R/AAA.R 2014-12-15 17:50:31 UTC (rev 820)
+++ pkg/mboostPatch/R/AAA.R 2014-12-15 17:50:34 UTC (rev 821)
@@ -29,7 +29,8 @@
vers <- packageDescription("mboost")[["Version"]]
packageStartupMessage("This is mboost ", vers, ". ", "See ",
- sQuote("package?mboost"), " and the NEWS file\n",
+ sQuote("package?mboost"), " and ",
+ sQuote('news(package = "mboost")'), "\n",
"for a complete list of changes.\n",
appendLF = TRUE)
return(TRUE)
Modified: pkg/mboostPatch/R/methods.R
===================================================================
--- pkg/mboostPatch/R/methods.R 2014-12-15 17:50:31 UTC (rev 820)
+++ pkg/mboostPatch/R/methods.R 2014-12-15 17:50:34 UTC (rev 821)
@@ -444,6 +444,9 @@
ret[which]
}
+#selected <- function(object, ...)
+# UseMethod("selected", object)
+
selected.mboost <- function(object, ...)
object$xselect()
Modified: pkg/mboostPatch/inst/NEWS.Rd
===================================================================
--- pkg/mboostPatch/inst/NEWS.Rd 2014-12-15 17:50:31 UTC (rev 820)
+++ pkg/mboostPatch/inst/NEWS.Rd 2014-12-15 17:50:34 UTC (rev 821)
@@ -1,21 +1,19 @@
\name{NEWS}
\title{News for Package 'mboost'}
-\section{Changes in mboost version 2.4-1 (2014-xx-yy)}{
-\subsection{User-visible changes}{
+\section{Changes in mboost version 2.4-1 (2014-12-15)}{
+ \subsection{Miscellaneous}{
\itemize{
\item Moved generic definition of \code{selected} to \pkg{stabs}
which is required anyway (thus, \pkg{stabs} >= 0.5-0 is now
required)
- }
- }
- \subsection{Miscellaneous}{
- \itemize{
\item load AML dataset (\file{AML_Bullinger.rda}) from package
\pkg{TH.data}
\item Updated references (for stability selection, confidence
intervals and constrained regression)
\item fixed \file{inst/CITATION}
+ \item Refer to \code{news(package = "mboost")} instead of to the
+ \file{NEWS} file.
}
}
\subsection{Bug-fixes}{
@@ -362,7 +360,7 @@
design matrix corresponding to contrasts of factors
when an intercept term is present leading to faster risk
minimization in these cases.
- \item coef.glmboost: New argument `off2int = TRUE' adds the
+ \item coef.glmboost: New argument \code{off2int = TRUE} adds the
offset to the intercept. In addition, the intercept
term is now adjusted for centered covariates.
\item check for infinite residuals in mboost_fit(). Especially
@@ -390,7 +388,7 @@
\section{Changes in mboost version 2.0-0 (2010-02-01)}{
\itemize{
\item generic implementation of component-wise functional gradient
- boosting in `mboost_fit', specialized code for linear,
+ boosting in \code{mboost_fit}, specialized code for linear,
additive and interaction models removed
\item new families available for ordinal, expectile and censored regression
\item computations potentially based on package Matrix
@@ -429,7 +427,7 @@
\section{Changes in mboost version 1.1-3 (2009-09-21)}{
\itemize{
\item better x-axes in plot.cvrisk and possibility to change xlab
- \item parallel cvrisk on Unix systems only (`multicore' isn't safe on windows)
+ \item parallel cvrisk on Unix systems only (\pkg{multicore} isn't safe on windows)
\item included new penalty for ordinal predictors (in bols())
\item corrected bug in bspatial (centering was not used for Xna)
\item removed output of dfbase (which is seldom used) in gamboost
@@ -441,7 +439,7 @@
\section{Changes in mboost version 1.1-2 (2009-07-21)}{
\itemize{
\item better weights and boundary knots handling in bspatial
- \item cvrisk runs in parallel if package `multicore' is available
+ \item cvrisk runs in parallel if package \pkg{multicore} is available
\item errors removed and minor improvements in the manuals
\item center = TRUE in glmboost did only apply to numeric (not integer)
predictors
@@ -501,7 +499,7 @@
\item new btree() base-learner for gamboost() available
\item fix inconsistencies in regression tests
\item add coef.gamboost
- \item new generic `survFit'
+ \item new generic \code{survFit}
\item cosmetics for trace = TRUE
}
}
@@ -524,8 +522,8 @@
}
\section{Changes in mboost version 0.6-2}{
\itemize{
- \item move `mboost' to R-forge
- \item improvements in `gamboost':
+ \item move \pkg{mboost} to R-forge
+ \item improvements in \code{gamboost}:
\item P-splines as base learners available
\item new formula interface for specifying the base learner
\item new plot.gamboost
@@ -542,7 +540,7 @@
\item gamboost() now allows for user-specified base learners
via the formula interface
\item gamboost.matrix(x = x, ...) requires colnames being set
- for `x'
+ for \code{x}
\item na.action = na.omit fix for g\{al\}mboost()
}
}
@@ -566,13 +564,13 @@
}
\section{Changes in mboost version 0.5-5 (2007-04-25)}{
\itemize{
- \item `westbc' regenerated
+ \item \code{westbc} regenerated
\item LazyLoad: yes (no SaveImage: yes)
}
}
\section{Changes in mboost version 0.5-4 (2007-04-18)}{
\itemize{
- \item plot() method for `glmboost' objects visualizing the
+ \item plot() method for \code{glmboost} objects visualizing the
coefficient path (feature request by Axel Benner <benner at dkfz.de>).
\item predict(newdata = <matrix>) was broken for gamboost(),
thanks to Max Kuhn <Max.Kuhn at pfizer.com> for spotting this.
@@ -586,7 +584,7 @@
}
\section{Changes in mboost version 0.5-2 (2007-02-28)}{
\itemize{
- \item some performance improvements for `glmboost()'
+ \item some performance improvements for \code{glmboost()}
\item blackboost() is now generic with formula and x, y interface
\item plot() method for cvrisk() and AIC() output now allows for ylim
specification without troubles
@@ -599,12 +597,12 @@
}
\section{Changes in mboost version 0.5-0 (2007-01-30)}{
\itemize{
- \item new `baselearner' argument to `gamboost' allowing to
+ \item new \code{baselearner} argument to \code{gamboost} allowing to
specify difference component-wise base-learners to
be used. Currently implemented: "ssp" for smoothing splines
(default), "bsp" for B-splines and "ols" for linear models.
The latter two haven't been tested yet.
- \item The `dfbase' arguments now applies to each covariate and
+ \item The \code{dfbase} arguments now applies to each covariate and
no longer to each column of the design matrix.
\item cvrisk() for blackboost() was broken, totally :-(
\item centered covariates were returned by glmboost() and gamboost()
@@ -612,12 +610,12 @@
\item check for y being positive counts when family = "Poisson()"[B
\item checks for Poisson() logLik() and AIC() methods
\item fire a warning when all u > 0 or u < 0
- \item update vignette `mboost_illustrations'
+ \item update vignette \file{mboost_illustrations}
}
}
\section{Changes in mboost version 0.4-17 (2007-01-15)}{
\itemize{
- \item fix problem with `dfbase' in `gamboost', spotted by
+ \item fix problem with \code{dfbase} in \code{gamboost}, spotted by
Karin Eckel <Karin.Eckel at imbe.imed.uni-erlangen.de>
}
}
@@ -653,8 +651,8 @@
}
\section{Changes in mboost version 0.4-11 (2006-09-07)}{
\itemize{
- \item add `contrasts.arg' argument to `glmboost.formula'
- \item more meaningful default for `grid' in `cvrisk'
+ \item add \code{contrasts.arg} argument to \code{glmboost.formula}
+ \item more meaningful default for \code{grid} in \code{cvrisk}
\item R-2.4.0 fixes
}
}
@@ -669,28 +667,28 @@
}
\section{Changes in mboost version 0.4-9 (2006-07-17)}{
\itemize{
- \item some small speed improvements in `gamboost'
- \item handle factors in `gamboost' properly (via a linear model)
- \item the dfbase argument can take a vector now (in `gamboost')
+ \item some small speed improvements in \code{gamboost}
+ \item handle factors in \code{gamboost} properly (via a linear model)
+ \item the dfbase argument can take a vector now (in \code{gamboost})
\item update and improve entries in DESCRIPTION
\item documentation updates
}
}
\section{Changes in mboost version 0.4-8 (2006-07-05)}{
\itemize{
- \item Huber() is `Huber Error', not `Huber Absolute Error'
- \item added `CoxPH' family object for fitting Cox models
+ \item Huber() is \sQuote{Huber Error}, not \sQuote{Huber Absolute Error}
+ \item added \code{CoxPH} family object for fitting Cox models
\item remove inst/LaTeX
- \item use NROW / NCOL more often (now that `y' may be a `Surv' object)
- \item implement `cvrisk', a general cross-validation function for the
+ \item use NROW / NCOL more often (now that \code{y} may be a \code{Surv} object)
+ \item implement \code{cvrisk}, a general cross-validation function for the
empirical risk and a corresponding plot method
\item unify risk computations in all three fitting functions
- \item unify names for `gb' objects
+ \item unify names for \code{gb} objects
\item allow for out-of-bag risk computations
\item some cosmetics
\item update keywords in Rd-files
\item risk was always 0 in Huber()@risk when d was chosen adaptively
- \item pData(westbc)$nodal.y has levels `negative' and `positive'
+ \item pData(westbc)$nodal.y has levels \code{negative} and \code{positive}
(lymph node status)
}
}
@@ -698,15 +696,15 @@
\itemize{
\item add src/Makevars (required for Windows builds)
\item make sure objects that are modified at C-level get _copied_ in
- `blackboost'
+ \code{blackboost}
}
}
\section{Changes in mboost version 0.4-6 (2006-06-14)}{
\itemize{
- \item some minor `codetools' fixes: removed unused variables
+ \item some minor \code{codetools} fixes: removed unused variables
and an out-dated function
- \item add `codetools' checks to regression tests
+ \item add \code{codetools} checks to regression tests
\item fix xlab in plot.gbAIC
- `mboost' version 0.4-5 published on CRAN 2006-06-13
+ \item \pkg{mboost} version 0.4-5 published on CRAN 2006-06-13
}
}
Modified: pkg/mboostPatch/man/mboost_package.Rd
===================================================================
--- pkg/mboostPatch/man/mboost_package.Rd 2014-12-15 17:50:31 UTC (rev 820)
+++ pkg/mboostPatch/man/mboost_package.Rd 2014-12-15 17:50:34 UTC (rev 821)
@@ -19,7 +19,7 @@
Package: \tab mboost\cr
Type: \tab Package\cr
Version: \tab 2.4-1\cr
-Date: \tab 2014-xx-yy\cr
+Date: \tab 2014-12-15\cr
License: \tab GPL-2\cr
LazyLoad: \tab yes\cr
LazyData: \tab yes\cr
@@ -69,7 +69,7 @@
selection with other fitting functions. A generic function for
\code{"mboost"} models is implemented in \pkg{mboost}.
- For more changes see NEWS file.
+ \bold{For more changes see}\cr\code{news(Version >= "2.4-0", package = "mboost")}
}
\section{NEWS in 2.3-series}{
@@ -93,7 +93,7 @@
(based on out-of-bag data) during fitting to \code{boost_control}.
}
- For more changes see NEWS file.
+ \bold{For more changes see}\cr\code{news(Version >= "2.3-0", package = "mboost")}
}
\section{NEWS in 2.2-series}{
@@ -124,7 +124,7 @@
boundaries (per default).
}
- For more changes see NEWS file.
+ \bold{For more changes see}\cr\code{news(Version >= "2.2-0" & Version < "2.3-0", package = "mboost")}
}
\section{NEWS in 2.1-series}{
@@ -138,7 +138,7 @@
Starting from this version, we now also automatically center the
variables in \code{\link{glmboost}} (argument \code{center = TRUE}).
- A complete list of changes can be found in the NEWS file.
+ \bold{For more changes see}\cr\code{news(Version >= "2.1-0" & Version < "2.2-0", package = "mboost")}
}
\section{NEWS in 2.0-series}{
@@ -168,6 +168,8 @@
The most important advancement is a generic implementation
of the optimizer in function \code{\link{mboost_fit}}.
+ \bold{For more changes see}\cr\code{news(Version >= "2.0-0" & Version < "2.1-0", package = "mboost")}
+
}
\author{
Torsten Hothorn \email{Torsten.Hothorn at R-project.org},\cr
Modified: pkg/mboostPatch/man/methods.Rd
===================================================================
--- pkg/mboostPatch/man/methods.Rd 2014-12-15 17:50:31 UTC (rev 820)
+++ pkg/mboostPatch/man/methods.Rd 2014-12-15 17:50:34 UTC (rev 821)
@@ -45,6 +45,7 @@
\alias{hatvalues.gamboost}
\alias{hatvalues.glmboost}
+\alias{selected}
\alias{selected.mboost}
\alias{nuisance}
Modified: pkg/mboostPatch/tests/Examples/mboost-Ex.Rout.save
===================================================================
--- pkg/mboostPatch/tests/Examples/mboost-Ex.Rout.save 2014-12-15 17:50:31 UTC (rev 820)
+++ pkg/mboostPatch/tests/Examples/mboost-Ex.Rout.save 2014-12-15 17:50:34 UTC (rev 821)
@@ -35,7 +35,7 @@
> library('mboost')
Loading required package: parallel
Loading required package: stabs
-This is mboost 2.4-1. See ‘package?mboost’ and the NEWS file
+This is mboost 2.4-1. See ‘package?mboost’ and ‘news(package = "mboost")’
for a complete list of changes.
>
@@ -3323,7 +3323,7 @@
> ###
> options(digits = 7L)
> base::cat("Time elapsed: ", proc.time() - base::get("ptime", pos = 'CheckExEnv'),"\n")
-Time elapsed: 15.536 0.68 19.097 2.326 0.227
+Time elapsed: 15.457 0.544 18.843 1.57 0.183
> grDevices::dev.off()
null device
1
Deleted: pkg/mboostPatch/tests/birds_Biometrics.R
===================================================================
--- pkg/mboostPatch/tests/birds_Biometrics.R 2014-12-15 17:50:31 UTC (rev 820)
+++ pkg/mboostPatch/tests/birds_Biometrics.R 2014-12-15 17:50:34 UTC (rev 821)
@@ -1 +0,0 @@
-link ../inst/birds_Biometrics.R
\ No newline at end of file
Added: pkg/mboostPatch/tests/birds_Biometrics.R
===================================================================
--- pkg/mboostPatch/tests/birds_Biometrics.R (rev 0)
+++ pkg/mboostPatch/tests/birds_Biometrics.R 2014-12-15 17:50:34 UTC (rev 821)
@@ -0,0 +1,98 @@
+
+library("mboost")
+data("birds", package = "TH.data")
+
+# define characteristics of the boosting algorithm
+bcr <- boost_control(mstop=200, trace=TRUE)
+
+# estimation of a purely linear GLM
+fm <- SG5 ~ bols(GST) + bols(DBH) + bols(AOT) + bols(AFS) + bols(DWC) +
+ bols(LOG)
+sp <- gamboost(fm, data = birds, family = Poisson(), control = bcr)
+
+# extract and plot AIC curve against iteration index and determine stopping
+# iteration
+birdsaic <- AIC(sp, "classical")
+plot(birdsaic)
+ms <- mstop(birdsaic)
+
+# selection frequencies of the model terms
+table(sp$xselect()[1:ms])
+
+# estimated coefficients
+coef(sp[ms])
+
+# re-define boosting iterations
+bcr <- boost_control(mstop=500, trace=TRUE)
+
+# Variable selection in a GLM without spatial component
+fm <- SG4 ~ bols(GST) + bols(DBH) + bols(AOT) + bols(AFS) + bols(DWC) +
+ bols(LOG)
+sp <- gamboost(fm, data = birds, family = Poisson(), control = bcr)
+table(sp$xselect())
+coef(sp, which=1:6)
+
+# Variable selection in a GLM with high df spatial component
+fm <- SG4 ~ bols(GST) + bols(DBH) + bols(AOT) + bols(AFS) + bols(DWC) +
+ bols(LOG) + bspatial(x_gk, y_gk, df=5, differences=1, knots=c(12,12))
+sp <- gamboost(fm, data = birds, family = Poisson(), control = bcr)
+table(sp$xselect())
+coef(sp, which=1:6)
+
+# Variable selection in a GLM with small df spatial component
+fm <- SG4 ~ bols(GST) + bols(DBH) + bols(AOT) + bols(AFS) + bols(DWC) +
+ bols(LOG) + bspatial(x_gk, y_gk, df=1, differences=1, knots=c(12,12), center=TRUE)
+sp <- gamboost(fm, data = birds, family = Poisson(), control = bcr)
+table(sp$xselect())
+coef(sp, which=1:6)
+
+
+# Geoadditive regression model without centering
+fm <- SG5 ~ bbs(GST) + bbs(DBH) + bbs(AOT) + bbs(AFS) + bbs(DWC) +
+ bbs(LOG) + bspatial(x_gk, y_gk, df=4, differences=1, knots=c(12,12))
+sp <- gamboost(fm, data = birds, family = Poisson(), control = bcr)
+plot(sp)
+
+# Geoadditive regression model with centering
+
+fm <- SG5 ~ bols(GST) + bbs(GST, df=1, center=TRUE) +
+ bols(AOT) + bbs(AOT, df=1, center=TRUE) +
+ bols(AFS) + bbs(AFS, df=1, center=TRUE) +
+ bols(DWC) + bbs(DWC, df=1, center=TRUE) +
+ bols(LOG) + bbs(LOG, df=1, center=TRUE) +
+ bspatial(x_gk, y_gk, df=1, differences=1, knots=c(12,12),
+ center=TRUE)
+sp <- gamboost(fm, data = birds, family = Poisson(), control = bcr)
+plot(sp)
+
+
+# re-define boosting iterations
+bcr <- boost_control(mstop=200, trace=TRUE)
+
+# transform covariates to [0,1]
+birds$GST <- (birds$GST-min(birds$GST))/(max(birds$GST)-min(birds$GST))
+birds$AOT <- (birds$AOT-min(birds$AOT))/(max(birds$AOT)-min(birds$AOT))
+birds$AFS <- (birds$AFS-min(birds$AFS))/(max(birds$AFS)-min(birds$AFS))
+birds$DWC <- (birds$DWC-min(birds$DWC))/(max(birds$DWC)-min(birds$DWC))
+birds$LOG <- (birds$LOG-min(birds$LOG))/(max(birds$LOG)-min(birds$LOG))
+
+# Space-varying coefficient models (with centered spatial effects)
+fm <- SG5 ~ bols(GST) + bspatial(x_gk, y_gk, by = GST, df=1, differences=1,
+ knots=c(12, 12), center=TRUE) +
+ bols(AOT) + bspatial(x_gk, y_gk, by = AOT, df=1, differences=1,
+ knots=c(12, 12), center=TRUE) +
+ bols(AFS) + bspatial(x_gk, y_gk, by = AFS, df=1, differences=1,
+ knots=c(12, 12), center=TRUE) +
+ bols(DWC) + bspatial(x_gk, y_gk, by = DWC, df=1, differences=1,
+ knots=c(12, 12), center=TRUE) +
+ bols(LOG) + bspatial(x_gk, y_gk, by = LOG, df=1, differences=1,
+ knots=c(12, 12), center=TRUE) +
+ bspatial(x_gk, y_gk, df=1, differences=1, knots=c(12, 12),
+ center=TRUE)
+sp <- gamboost(fm, data = birds, family = Poisson(), control = bcr)
+plot(sp, which = "GST")
+plot(sp, which = "AOT")
+plot(sp, which = "AFS")
+plot(sp, which = "DWC")
+plot(sp, which = "LOG")
+
Modified: pkg/mboostPatch/tests/birds_Biometrics.Rout.save
===================================================================
--- pkg/mboostPatch/tests/birds_Biometrics.Rout.save 2014-12-15 17:50:31 UTC (rev 820)
+++ pkg/mboostPatch/tests/birds_Biometrics.Rout.save 2014-12-15 17:50:34 UTC (rev 821)
@@ -19,7 +19,7 @@
> library("mboost")
Loading required package: parallel
Loading required package: stabs
-This is mboost 2.4-1. See 'package?mboost' and the NEWS file
+This is mboost 2.4-1. See 'package?mboost' and 'news(package = "mboost")'
for a complete list of changes.
> data("birds", package = "TH.data")
@@ -315,4 +315,4 @@
>
> proc.time()
user system elapsed
- 19.935 0.696 21.177
+ 20.078 0.342 21.018
Modified: pkg/mboostPatch/tests/bugfixes.Rout.save
===================================================================
--- pkg/mboostPatch/tests/bugfixes.Rout.save 2014-12-15 17:50:31 UTC (rev 820)
+++ pkg/mboostPatch/tests/bugfixes.Rout.save 2014-12-15 17:50:34 UTC (rev 821)
@@ -20,7 +20,7 @@
Loading required package: mboost
Loading required package: parallel
Loading required package: stabs
-This is mboost 2.4-1. See 'package?mboost' and the NEWS file
+This is mboost 2.4-1. See 'package?mboost' and 'news(package = "mboost")'
for a complete list of changes.
> require("Matrix")
@@ -743,4 +743,4 @@
>
> proc.time()
user system elapsed
- 27.983 0.489 28.889
+ 28.136 0.475 29.138
Modified: pkg/mboostPatch/tests/regtest-baselearner.Rout.save
===================================================================
--- pkg/mboostPatch/tests/regtest-baselearner.Rout.save 2014-12-15 17:50:31 UTC (rev 820)
+++ pkg/mboostPatch/tests/regtest-baselearner.Rout.save 2014-12-15 17:50:34 UTC (rev 821)
@@ -19,7 +19,7 @@
> library("mboost")
Loading required package: parallel
Loading required package: stabs
-This is mboost 2.4-1. See 'package?mboost' and the NEWS file
+This is mboost 2.4-1. See 'package?mboost' and 'news(package = "mboost")'
for a complete list of changes.
> attach(asNamespace("mboost"))
@@ -1203,4 +1203,4 @@
>
> proc.time()
user system elapsed
- 33.789 1.594 35.922
+ 33.272 0.514 34.343
Modified: pkg/mboostPatch/tests/regtest-blackboost.Rout.save
===================================================================
--- pkg/mboostPatch/tests/regtest-blackboost.Rout.save 2014-12-15 17:50:31 UTC (rev 820)
+++ pkg/mboostPatch/tests/regtest-blackboost.Rout.save 2014-12-15 17:50:34 UTC (rev 821)
@@ -20,7 +20,7 @@
Loading required package: mboost
Loading required package: parallel
Loading required package: stabs
-This is mboost 2.4-1. See 'package?mboost' and the NEWS file
+This is mboost 2.4-1. See 'package?mboost' and 'news(package = "mboost")'
for a complete list of changes.
> if (require("party")) {
@@ -211,4 +211,4 @@
>
> proc.time()
user system elapsed
- 8.502 0.171 8.888
+ 8.407 0.225 9.009
Modified: pkg/mboostPatch/tests/regtest-family.Rout.save
===================================================================
--- pkg/mboostPatch/tests/regtest-family.Rout.save 2014-12-15 17:50:31 UTC (rev 820)
+++ pkg/mboostPatch/tests/regtest-family.Rout.save 2014-12-15 17:50:34 UTC (rev 821)
@@ -19,7 +19,7 @@
> library("mboost")
Loading required package: parallel
Loading required package: stabs
-This is mboost 2.4-1. See 'package?mboost' and the NEWS file
+This is mboost 2.4-1. See 'package?mboost' and 'news(package = "mboost")'
for a complete list of changes.
>
@@ -404,4 +404,4 @@
>
> proc.time()
user system elapsed
- 16.036 0.203 16.416
+ 16.272 0.166 16.638
Modified: pkg/mboostPatch/tests/regtest-gamboost.Rout.save
===================================================================
--- pkg/mboostPatch/tests/regtest-gamboost.Rout.save 2014-12-15 17:50:31 UTC (rev 820)
+++ pkg/mboostPatch/tests/regtest-gamboost.Rout.save 2014-12-15 17:50:34 UTC (rev 821)
@@ -20,7 +20,7 @@
Loading required package: mboost
Loading required package: parallel
Loading required package: stabs
-This is mboost 2.4-1. See 'package?mboost' and the NEWS file
+This is mboost 2.4-1. See 'package?mboost' and 'news(package = "mboost")'
for a complete list of changes.
> require("survival")
@@ -515,4 +515,4 @@
>
> proc.time()
user system elapsed
- 11.326 0.308 11.928
+ 11.083 0.441 11.826
Modified: pkg/mboostPatch/tests/regtest-glmboost.Rout.save
===================================================================
--- pkg/mboostPatch/tests/regtest-glmboost.Rout.save 2014-12-15 17:50:31 UTC (rev 820)
+++ pkg/mboostPatch/tests/regtest-glmboost.Rout.save 2014-12-15 17:50:34 UTC (rev 821)
@@ -20,7 +20,7 @@
Loading required package: mboost
Loading required package: parallel
Loading required package: stabs
-This is mboost 2.4-1. See 'package?mboost' and the NEWS file
+This is mboost 2.4-1. See 'package?mboost' and 'news(package = "mboost")'
for a complete list of changes.
>
@@ -598,4 +598,4 @@
>
> proc.time()
user system elapsed
- 15.562 0.104 15.815
+ 15.638 0.326 16.135
Modified: pkg/mboostPatch/tests/regtest-hatmatrix.Rout.save
===================================================================
--- pkg/mboostPatch/tests/regtest-hatmatrix.Rout.save 2014-12-15 17:50:31 UTC (rev 820)
+++ pkg/mboostPatch/tests/regtest-hatmatrix.Rout.save 2014-12-15 17:50:34 UTC (rev 821)
@@ -19,7 +19,7 @@
> library("mboost")
Loading required package: parallel
Loading required package: stabs
-This is mboost 2.4-1. See 'package?mboost' and the NEWS file
+This is mboost 2.4-1. See 'package?mboost' and 'news(package = "mboost")'
for a complete list of changes.
>
@@ -84,4 +84,4 @@
>
> proc.time()
user system elapsed
- 2.169 0.100 2.312
+ 2.156 0.103 2.308
Modified: pkg/mboostPatch/tests/regtest-inference.Rout.save
===================================================================
--- pkg/mboostPatch/tests/regtest-inference.Rout.save 2014-12-15 17:50:31 UTC (rev 820)
+++ pkg/mboostPatch/tests/regtest-inference.Rout.save 2014-12-15 17:50:34 UTC (rev 821)
@@ -19,7 +19,7 @@
Loading required package: mboost
Loading required package: parallel
Loading required package: stabs
-This is mboost 2.4-1. See 'package?mboost' and the NEWS file
+This is mboost 2.4-1. See 'package?mboost' and 'news(package = "mboost")'
for a complete list of changes.
> attach(asNamespace("mboost"))
@@ -207,4 +207,4 @@
>
> proc.time()
user system elapsed
- 48.422 5.464 48.206
+ 48.243 5.671 48.205
Modified: pkg/mboostPatch/vignettes/SurvivalEnsembles.Rout.save
===================================================================
--- pkg/mboostPatch/vignettes/SurvivalEnsembles.Rout.save 2014-12-15 17:50:31 UTC (rev 820)
+++ pkg/mboostPatch/vignettes/SurvivalEnsembles.Rout.save 2014-12-15 17:50:34 UTC (rev 821)
@@ -1,7 +1,8 @@
> source("setup.R")
Loading required package: parallel
-This is mboost 2.4-0. See ‘package?mboost’ and the NEWS file
+Loading required package: stabs
+This is mboost 2.4-1. See ‘package?mboost’ and ‘news(package = "mboost")’
for a complete list of changes.
@@ -39,6 +40,13 @@
Loading required package: modeltools
Loading required package: stats4
+Attaching package: ‘modeltools’
+
+The following object is masked from ‘package:stabs’:
+
+ parameters
+
+
> set.seed(290875)
> CEX <- 0.85
@@ -48,7 +56,8 @@
+ d <- obs - pred
+ plot(m, d, xlab = "(Observed + Predicted) / 2" .... [TRUNCATED]
-> load(system.file("AML_Bullinger.Rda", package = "mboost"))
+> load(file.path(path.package(package = "TH.data"),
++ "rda", "AML_Bullinger.rda"))
> AMLw <- IPCweights(Surv(clinical$time, clinical$event))
@@ -325,4 +334,4 @@
*** Run successfully completed ***
> proc.time()
user system elapsed
- 8.157 0.381 8.760
+ 7.954 0.224 8.387
Modified: pkg/mboostPatch/vignettes/mboost.Rout.save
===================================================================
--- pkg/mboostPatch/vignettes/mboost.Rout.save 2014-12-15 17:50:31 UTC (rev 820)
+++ pkg/mboostPatch/vignettes/mboost.Rout.save 2014-12-15 17:50:34 UTC (rev 821)
@@ -7,7 +7,8 @@
+ dependencies = TRUE)
Loading required package: mboost
Loading required package: parallel
-This is mboost 2.4-0. See ‘package?mboost’ and the NEWS file
+Loading required package: stabs
+This is mboost 2.4-1. See ‘package?mboost’ and ‘news(package = "mboost")’
for a complete list of changes.
@@ -29,6 +30,13 @@
Loading required package: modeltools
Loading required package: stats4
+Attaching package: ‘modeltools’
+
+The following object is masked from ‘package:stabs’:
+
+ parameters
+
+
> library("party")
> if (file.exists("model.Rda")) {
@@ -155,4 +163,4 @@
*** Run successfully completed ***
> proc.time()
user system elapsed
- 42.153 0.279 45.487
+ 42.362 0.239 46.004
Modified: pkg/mboostPatch/vignettes/mboost_illustrations.Rout.save
===================================================================
--- pkg/mboostPatch/vignettes/mboost_illustrations.Rout.save 2014-12-15 17:50:31 UTC (rev 820)
+++ pkg/mboostPatch/vignettes/mboost_illustrations.Rout.save 2014-12-15 17:50:34 UTC (rev 821)
@@ -1,7 +1,8 @@
> source("setup.R")
Loading required package: parallel
-This is mboost 2.4-0. See ‘package?mboost’ and the NEWS file
+Loading required package: stabs
+This is mboost 2.4-1. See ‘package?mboost’ and ‘news(package = "mboost")’
for a complete list of changes.
@@ -327,4 +328,4 @@
*** Run successfully completed ***
> proc.time()
user system elapsed
- 13.021 0.227 13.407
+ 13.022 0.227 13.390
Modified: pkg/mboostPatch/vignettes/mboost_tutorial.Rout.save
===================================================================
--- pkg/mboostPatch/vignettes/mboost_tutorial.Rout.save 2014-12-15 17:50:31 UTC (rev 820)
+++ pkg/mboostPatch/vignettes/mboost_tutorial.Rout.save 2014-12-15 17:50:34 UTC (rev 821)
@@ -6,16 +6,17 @@
> if (any(is.na(pd))) {
+ install.packages("mboost", repos = "http://cran.at.r-project.org")
+ pd <- packageDescription("mboost")
-+ .... [TRUNCATED]
++ }
> if (compareVersion(pd$Version, "2.1-0") < 0) {
+ warning("Current version of mboost is installed!")
-+ install.packages("mboost", repos .... [TRUNCATED]
++ install.packages("mboost", repos = "ht ..." ... [TRUNCATED]
> require("mboost")
Loading required package: mboost
Loading required package: parallel
-This is mboost 2.4-0. See ‘package?mboost’ and the NEWS file
+Loading required package: stabs
+This is mboost 2.4-1. See ‘package?mboost’ and ‘news(package = "mboost")’
for a complete list of changes.
@@ -687,4 +688,4 @@
*** Run successfully completed ***
> proc.time()
user system elapsed
- 13.124 0.359 13.845
+ 13.149 0.371 13.969
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