[Mboost-commits] r798 - / pkg/mboostDevel pkg/mboostDevel/inst
noreply at r-forge.r-project.org
noreply at r-forge.r-project.org
Fri Sep 26 10:15:48 CEST 2014
Author: hofner
Date: 2014-09-26 10:15:48 +0200 (Fri, 26 Sep 2014)
New Revision: 798
Modified:
pkg/mboostDevel/.Rbuildignore
pkg/mboostDevel/.RbuildignoreCRAN
pkg/mboostDevel/NAMESPACE
pkg/mboostDevel/inst/NEWS.Rd
svn_release.txt
Log:
- updated release SOPs (w.r.t. NEWS.Rd)
- updated NEWS
- import parallel to make R CMD check happy
- changes in .Rbuildignore and .RbuildignoreCRAN w.r.t. NEWS.Rd
Modified: pkg/mboostDevel/.Rbuildignore
===================================================================
--- pkg/mboostDevel/.Rbuildignore 2014-09-25 18:34:43 UTC (rev 797)
+++ pkg/mboostDevel/.Rbuildignore 2014-09-26 08:15:48 UTC (rev 798)
@@ -2,4 +2,5 @@
to_do_list.txt
^\..*
.*/auto
-
+inst/NEWS.html
+inst/NEWS.pdf
Modified: pkg/mboostDevel/.RbuildignoreCRAN
===================================================================
--- pkg/mboostDevel/.RbuildignoreCRAN 2014-09-25 18:34:43 UTC (rev 797)
+++ pkg/mboostDevel/.RbuildignoreCRAN 2014-09-26 08:15:48 UTC (rev 798)
@@ -4,3 +4,5 @@
^\..*
.*/auto
vignettes/.*\.Rout\.save$
+inst/NEWS.html
+inst/NEWS.pdf
\ No newline at end of file
Modified: pkg/mboostDevel/NAMESPACE
===================================================================
--- pkg/mboostDevel/NAMESPACE 2014-09-25 18:34:43 UTC (rev 797)
+++ pkg/mboostDevel/NAMESPACE 2014-09-26 08:15:48 UTC (rev 798)
@@ -3,6 +3,7 @@
import(stats)
import(Matrix)
+import(parallel)
importFrom(survival, Surv, survfit)
importFrom(splines, bs, splineDesign)
importFrom(lattice, levelplot)
Modified: pkg/mboostDevel/inst/NEWS.Rd
===================================================================
--- pkg/mboostDevel/inst/NEWS.Rd 2014-09-25 18:34:43 UTC (rev 797)
+++ pkg/mboostDevel/inst/NEWS.Rd 2014-09-26 08:15:48 UTC (rev 798)
@@ -15,10 +15,10 @@
\item \code{stabsel} has been moved to the new package \pkg{stabs}
- \item changed vignette \code{mboost_tutorial} to reflect latest
+ \item changed vignette \file{mboost_tutorial} to reflect latest
changes in \pkg{mboost}.
- \item changed plain text \code{NEWS} to \code{inst/NEWS.Rd}
+ \item changed plain text \file{NEWS} to \file{inst/NEWS.Rd}
}
\subsection{Bugfixes}{
\itemize{
@@ -81,82 +81,90 @@
\itemize{
\item fixed bugs in survival families:
\itemize{
- \item offset in all survival families was based on max(survtime) instead
- of max(log(survtime));
- \item offset in CoxPH can't be computed from Cox Partial LH as constants
- are canceled out; Use fixed offset instead;
+ \item \code{offset} in all survival families was based on
+ \code{max(survtime)} instead of \code{max(log(survtime))};
+ \item \code{offset} in \code{CoxPH} can't be computed from Cox
+ Partial LH as constants are canceled out; Use fixed \code{offset}
+ instead;
}
\item speed up checking of manual by changing some computations (e.g. reduce
- mstop) or exclude code from checking via \\dontrun\{\}
- \item removed dependency on ipred (replaced with TH.data)
+ \code{mstop}) or exclude code from checking via \code{\\dontrun\{\}}
+ \item removed dependency on \pkg{ipred} (replaced with \pkg{TH.data})
\item small improvements in manual
}
}
\section{Changes in mboost version 2.2-2 (2013-02-08, r703)}{
\itemize{
- \item bbs(..., center = "spectralDecomp") computes the spectral
+ \item \code{bbs(..., center = "spectralDecomp")} computes the spectral
decomposition of the penalty matrix and the penalized part of the
- design matrix is defined by this decomposition. Experiments show
- that \code{bols(x) + bbs(x, center = "spectralDecomp")} is a little
- better in recovering the true underlying functions than the default
- \code{bols(x) + bbs(x, center = TRUE)} or, equivalently,
- \code{bols(x) + bbs(x, center = "differenceMatrix")}. For
- \code{bbs(x, y, center = TRUE)} or \code{bmrf(x, center = TRUE)},
+ design matrix is defined by this decomposition.
+
+ Experiments show that \code{bols(x) + bbs(x, center = "spectralDecomp")}
+ is a little better in recovering the true underlying functions than
+ the default \code{bols(x) + bbs(x, center = TRUE)} or, equivalently,
+ \code{bols(x) + bbs(x, center = "differenceMatrix")}.
+
+ For \code{bbs(x, y, center = TRUE)} or \code{bmrf(x, center = TRUE)},
the spectral decomposition is (and was) always used.
- \item fixed bug in stabsel: '...' was not passed to cvrisk and thus one could
- not specify options for mclapply
- \item fixed bug in brandom: now really use contrasts.arg = "contr.dummy" per
- default.
- \item removed tests/ folder and .Rout.save files for vignettes from the CRAN
- release
+ \item fixed bug in \code{stabsel}: \code{'...'} was not passed to
+ \code{cvrisk} and thus one could not specify options for \code{mclapply}
+ \item fixed bug in \code{brandom}: now really use
+ \code{contrasts.arg = "contr.dummy"} per default.
+ \item removed \code{tests/} folder and \code{.Rout.save} files for
+ vignettes from the CRAN release
\item small improvements in manual
}
}
\section{Changes in mboost version 2.2-1 (2013-01-14, r694)}{
\itemize{
- \item included warnings in stabsel() for better guidiance of the
- user:
+ \item included warnings in \code{stabsel()} for better
+ guidiance of the user:
\itemize{
- \item A warning is issued if the upper bound for the FWER in stability
- selection is greater (by a certain margin) than the specified bound.
- \item A warning is also issued if mstop is too small to select
- q variables.
+ \item A warning is issued if the upper bound for the
+ \code{FWER} in stability selection is greater (by a certain
+ margin) than the specified bound.
+ \item A warning is also issued if \code{mstop} is too small to select
+ \code{q} variables.
}
- \item improved output of errors and warnings in stabsel.
- \item suppress the notes from package Matrix about method ambiguity
- ("Note: method with signature ... chosen, ... would also be valid")
+ \item improved output of errors and warnings in \code{stabsel}.
+ \item suppress the notes from package \pkg{Matrix} about method ambiguity
+ (\code{"Note: method with signature ... chosen, ... would also be valid"})
\item updated manual on base-learners to reflect the change in the default for
degrees of freedom (addtionally, all options are now discussed in a
- separate section of the baselearner manual)
- \item updated vignette mboost_tutorial
- \item updated mboost_package.Rd:
- now all important changes since mboost 2.0 are documented there
- \item changed roles of contributers to ctb
- \item suggested packages are now only used inside if(require(pkg)) statements
+ separate section of the base-learner manual)
+ \item updated vignette \file{mboost_tutorial}
+ \item updated \file{mboost_package.Rd}:
+ now all important changes since \pkg{mboost} 2.0 are documented there
+ \item changed roles of contributers to \code{ctb}
+ \item suggested packages are now only used inside \code{if(require(pkg))} statements
\item changed startup message
}
}
\section{Changes in mboost version 2.2-0 (2012-11-21, r680)}{
\itemize{
- \item switch from packages `multicore' and`snow' to `parallel'
- \item changed behavior of bols(x, intercept = FALSE) when x is a factor:
- now the intercept is simply dropped from the design matrix;
- coding can be specified as usually for factors.
- \item changed default for options("mboost_dftraceS") to FALSE, i.e.,
+ \item switch from packages \pkg{multicore} and \pkg{snow} to \pkg{parallel}
+ \item changed behavior of \code{bols(x, intercept = FALSE)} when
+ \code{x} is a factor:
+ \itemize{
+ \item now the intercept is simply dropped from the design matrix
+ \item coding can be specified as usually for factors.
+ }
+ \item changed default for \code{options("mboost_dftraceS")} to \code{FALSE}, i.e.,
degrees of freedom are now computed from smoothing parameter
as described in B. Hofner, T. Hothorn, T. Kneib, M. Schmid (2011).
\item changed computation of B-spline basis at the boundaries:
now also use equidistant knots in the boundaries (per default)
- \item improved plot function when dealing with spatial plots
- (now builds suitable grid based on the observations if no newdata is given)
- \item increased default number of subsampling replicates in stabsel to 100
- \item [experimental] bmono() now implements constraints at the boundaries of
- (monotonic) P-splines
- \item [experimental] added family Gehan() for rank-based estimation of survival models
- in an accelerated failure time framework (contributed by Brent Johnson
- <bajohn3 at emory.edu>)
+ \item improved \code{plot} function when dealing with spatial plots
+ (now builds suitable grid based on the observations if no
+ \code{newdata} is given)
+ \item increased default number of subsampling replicates in \code{stabsel} to 100
+ \item [experimental] \code{bmono()} now implements constraints at the boundaries of
+ (monotonic) P-splines
+ \item [experimental] added family \code{Gehan()} for rank-based
+ estimation of survival models in an accelerated failure time
+ framework (contributed by Brent Johnson \email{bajohn3 at emory.edu})
}
}
\section{Changes in mboost version 2.1-3 (2012-09-27, r672)}{
Modified: svn_release.txt
===================================================================
--- svn_release.txt 2014-09-25 18:34:43 UTC (rev 797)
+++ svn_release.txt 2014-09-26 08:15:48 UTC (rev 798)
@@ -178,6 +178,8 @@
How to preview NEWS.Rd files
----------------------------
- library(tools)
- Rd2HTML("NEWS.Rd", out = "NEWS.html")
- Rd2latex("NEWS.Rd", out = "NEWS.tex")
+ For HTML preview:
+ R CMD Rdconv -t 'html' -o 'NEWS.html' NEWS.Rd && firefox NEWS.html
+
+ and for PDF preview:
+ R CMD Rd2pdf NEWS.Rd
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