Author: Nicolas Turenne
Diff between svcR versions 1.6.2 dated 2009-09-12 and 1.6.3 dated 2009-12-21
Title: svcR package
Description: svcR implements a support vector machine technique for
clustering It includes choice between three kinds of kernel.
Original cluster labeling and export of clusters. Format of
data require 3 files: matrix, attributes, variables.
svcR-1.6.2/svcR/data/term_att.txt |only
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svcR-1.6.3/svcR/NAMESPACE | 5 +-
svcR-1.6.3/svcR/R/display.R | 29 ++++++++--------
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21 files changed, 68 insertions(+), 86 deletions(-)
Author: Terry Therneau, original R port by Thomas Lumley
Title: Survival analysis, including penalised likelihood.
Description: survival analysis: descriptive statistics, two-sample
tests, parametric accelerated failure models, Cox model.
Delayed entry (truncation) allowed for all models; interval
censoring for parametric models. Case-cohort designs.
Diff between survival versions 2.35-7 dated 2009-09-09 and 2.35-8 dated 2009-12-21
survival-2.35-7/survival/Notes |only survival-2.35-7/survival/tests/r_standord.R |only survival-2.35-7/survival/tests/r_standord.Rout.save |only survival-2.35-8/survival/Changelog | 36 + survival-2.35-8/survival/DESCRIPTION | 8 survival-2.35-8/survival/R/aareg.taper.S | 2 survival-2.35-8/survival/R/agexact.fit.S | 2 survival-2.35-8/survival/R/agreg.fit.S | 2 survival-2.35-8/survival/R/basehaz.S | 2 survival-2.35-8/survival/R/cluster.S | 2 survival-2.35-8/survival/R/coxpenal.df.S | 2 survival-2.35-8/survival/R/coxph.S | 7 survival-2.35-8/survival/R/coxph.fit.S | 2 survival-2.35-8/survival/R/coxph.rvar.S | 2 survival-2.35-8/survival/R/coxph.wtest.S | 2 survival-2.35-8/survival/R/dsurvreg.S | 2 survival-2.35-8/survival/R/frailty.S | 2 survival-2.35-8/survival/R/frailty.brent.S | 2 survival-2.35-8/survival/R/frailty.controlaic.S | 2 survival-2.35-8/survival/R/frailty.controldf.S | 6 survival-2.35-8/survival/R/frailty.controlgam.S | 2 survival-2.35-8/survival/R/frailty.controlgauss.S | 2 survival-2.35-8/survival/R/frailty.gamma.S | 4 survival-2.35-8/survival/R/frailty.gammacon.S | 2 survival-2.35-8/survival/R/frailty.gaussian.S | 5 survival-2.35-8/survival/R/frailty.t.S | 4 survival-2.35-8/survival/R/is.na.coxph.penalty.S | 2 survival-2.35-8/survival/R/labels.survreg.S | 2 survival-2.35-8/survival/R/lines.aareg.S | 2 survival-2.35-8/survival/R/lines.survfit.coxph.S | 2 survival-2.35-8/survival/R/model.matrix.coxph.R | 12 survival-2.35-8/survival/R/plot.aareg.S | 2 survival-2.35-8/survival/R/plot.survfit.S | 6 survival-2.35-8/survival/R/points.survfit.S | 2 survival-2.35-8/survival/R/predict.coxph.S | 18 survival-2.35-8/survival/R/predict.survreg.penal.S | 2 survival-2.35-8/survival/R/print.cox.zph.S | 2 survival-2.35-8/survival/R/print.coxph.S | 2 survival-2.35-8/survival/R/print.coxph.null.S | 2 survival-2.35-8/survival/R/print.coxph.penal.S | 2 survival-2.35-8/survival/R/print.ratetable.S | 2 survival-2.35-8/survival/R/print.summary.survfit.S | 2 survival-2.35-8/survival/R/print.summary.survreg.S | 2 survival-2.35-8/survival/R/print.survdiff.S | 2 survival-2.35-8/survival/R/print.survexp.S | 2 survival-2.35-8/survival/R/print.survreg.S | 2 survival-2.35-8/survival/R/print.survreg.penal.S | 2 survival-2.35-8/survival/R/residuals.survreg.S | 352 +++++++++---------- survival-2.35-8/survival/R/residuals.survreg.penal.S | 2 survival-2.35-8/survival/R/ridge.S | 2 survival-2.35-8/survival/R/strata.S | 2 survival-2.35-8/survival/R/summary.ratetable.S | 2 survival-2.35-8/survival/R/summary.survreg.S | 2 survival-2.35-8/survival/R/survdiff.S | 2 survival-2.35-8/survival/R/survdiff.fit.S | 2 survival-2.35-8/survival/R/survexp.cfit.S | 2 survival-2.35-8/survival/R/survfitCI.S | 4 survival-2.35-8/survival/R/survreg.S | 17 survival-2.35-8/survival/R/survreg.old.S | 2 survival-2.35-8/survival/R/tcut.S | 2 survival-2.35-8/survival/R/untangle.specials.S | 2 survival-2.35-8/survival/data/survexp.mn.R | 11 survival-2.35-8/survival/inst |only survival-2.35-8/survival/man/anova.coxph.Rd | 7 survival-2.35-8/survival/man/survreg.Rd | 11 survival-2.35-8/survival/src/agexact.c | 2 survival-2.35-8/survival/src/agscore.c | 2 survival-2.35-8/survival/src/agsurv1.c | 2 survival-2.35-8/survival/src/agsurv2.c | 2 survival-2.35-8/survival/src/chinv3.c | 2 survival-2.35-8/survival/src/cholesky3.c | 2 survival-2.35-8/survival/src/chsolve2.c | 4 survival-2.35-8/survival/src/chsolve3.c | 2 survival-2.35-8/survival/src/coxfit2.c | 2 survival-2.35-8/survival/src/coxmart.c | 2 survival-2.35-8/survival/src/coxph_wtest.c | 2 survival-2.35-8/survival/src/coxscho.c | 3 survival-2.35-8/survival/src/pyears2.c | 2 survival-2.35-8/survival/src/pystep.c | 2 survival-2.35-8/survival/src/survConcordance.c | 2 survival-2.35-8/survival/src/survdiff2.c | 2 survival-2.35-8/survival/src/survfit4.c | 2 survival-2.35-8/survival/src/survreg6.c | 3 survival-2.35-8/survival/tests/book1.Rout.save | 34 + survival-2.35-8/survival/tests/book2.Rout.save | 34 + survival-2.35-8/survival/tests/book3.Rout.save | 49 +- survival-2.35-8/survival/tests/book4.Rout.save | 49 +- survival-2.35-8/survival/tests/factor2.Rout.save | 13 survival-2.35-8/survival/tests/r_stanford.R |only survival-2.35-8/survival/tests/r_stanford.Rout.save |only survival-2.35-8/survival/tests/survreg2.R |only 91 files changed, 481 insertions(+), 336 deletions(-)
Author: Hemant Ishwaran
Diff between randomSurvivalForest versions 3.5.1 dated 2008-09-05 and 3.6.0 dated 2009-12-21
More information about randomSurvivalForest at CRAN
Title: Ishwaran and Kogalur's Random Survival Forest
Description: Ensemble survival analysis based on a random forest of
trees using random inputs.
randomSurvivalForest-3.5.1/randomSurvivalForest/R/interaction.rsf.R |only
randomSurvivalForest-3.5.1/randomSurvivalForest/data/burn.txt |only
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randomSurvivalForest-3.6.0/randomSurvivalForest/R/plot.error.R | 338 +
randomSurvivalForest-3.6.0/randomSurvivalForest/R/plot.proximity.R | 145
randomSurvivalForest-3.6.0/randomSurvivalForest/R/plot.rsf.R | 145
randomSurvivalForest-3.6.0/randomSurvivalForest/R/plot.variable.R | 186
randomSurvivalForest-3.6.0/randomSurvivalForest/R/pmml2rsf.R | 141
randomSurvivalForest-3.6.0/randomSurvivalForest/R/predict.rsf.R | 433 +-
randomSurvivalForest-3.6.0/randomSurvivalForest/R/print.rsf.R | 195
randomSurvivalForest-3.6.0/randomSurvivalForest/R/randomSurvivalForest.R | 141
randomSurvivalForest-3.6.0/randomSurvivalForest/R/rsf.R | 141
randomSurvivalForest-3.6.0/randomSurvivalForest/R/rsf.default.R | 540 +-
randomSurvivalForest-3.6.0/randomSurvivalForest/R/rsf.formula.R | 141
randomSurvivalForest-3.6.0/randomSurvivalForest/R/rsf.news.R | 141
randomSurvivalForest-3.6.0/randomSurvivalForest/R/rsf2pmml.R | 433 +-
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randomSurvivalForest-3.6.0/randomSurvivalForest/man/plot.error.Rd | 27
randomSurvivalForest-3.6.0/randomSurvivalForest/man/plot.proximity.Rd | 3
randomSurvivalForest-3.6.0/randomSurvivalForest/man/plot.variable.Rd | 49
randomSurvivalForest-3.6.0/randomSurvivalForest/man/pmml2rsf.Rd | 6
randomSurvivalForest-3.6.0/randomSurvivalForest/man/predict.rsf.Rd | 151
randomSurvivalForest-3.6.0/randomSurvivalForest/man/rsf.Rd | 525 +-
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randomSurvivalForest-3.6.0/randomSurvivalForest/src/extern.h | 189
randomSurvivalForest-3.6.0/randomSurvivalForest/src/factor.h | 141
randomSurvivalForest-3.6.0/randomSurvivalForest/src/global.h | 218 -
randomSurvivalForest-3.6.0/randomSurvivalForest/src/node.h | 147
randomSurvivalForest-3.6.0/randomSurvivalForest/src/nodeOps.c |only
randomSurvivalForest-3.6.0/randomSurvivalForest/src/nodeOps.h |only
randomSurvivalForest-3.6.0/randomSurvivalForest/src/nrutil.c | 473 +-
randomSurvivalForest-3.6.0/randomSurvivalForest/src/nrutil.h | 430 +-
randomSurvivalForest-3.6.0/randomSurvivalForest/src/rsf.c | 1146 ++---
randomSurvivalForest-3.6.0/randomSurvivalForest/src/rsf.h | 154
randomSurvivalForest-3.6.0/randomSurvivalForest/src/rsfBootstrap.c | 163
randomSurvivalForest-3.6.0/randomSurvivalForest/src/rsfBootstrap.h | 146
randomSurvivalForest-3.6.0/randomSurvivalForest/src/rsfEntry.c | 242 -
randomSurvivalForest-3.6.0/randomSurvivalForest/src/rsfEntry.h | 157
randomSurvivalForest-3.6.0/randomSurvivalForest/src/rsfFactorOps.c | 231 -
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randomSurvivalForest-3.6.0/randomSurvivalForest/src/rsfImportance.h |only
randomSurvivalForest-3.6.0/randomSurvivalForest/src/rsfImpute.c | 652 ++-
randomSurvivalForest-3.6.0/randomSurvivalForest/src/rsfImpute.h | 151
randomSurvivalForest-3.6.0/randomSurvivalForest/src/rsfSplit.c | 1090 ++++-
randomSurvivalForest-3.6.0/randomSurvivalForest/src/rsfSplit.h | 148
randomSurvivalForest-3.6.0/randomSurvivalForest/src/rsfSplitUtil.c | 400 +
randomSurvivalForest-3.6.0/randomSurvivalForest/src/rsfSplitUtil.h | 158
randomSurvivalForest-3.6.0/randomSurvivalForest/src/rsfStack.c | 1115 ++++-
randomSurvivalForest-3.6.0/randomSurvivalForest/src/rsfStack.h | 168
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randomSurvivalForest-3.6.0/randomSurvivalForest/src/rsfUtil.c | 2115 +++++-----
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99 files changed, 9657 insertions(+), 5579 deletions(-)
Permanent link
Author: Guido Schwarzer
Diff between meta versions 1.1-4 dated 2009-11-04 and 1.1-5 dated 2009-12-21
Title: Meta-Analysis with R
Description: Fixed and random effects meta-analysis. Functions for
tests of bias, forest and funnel plot.
ChangeLog | 6 ++++++
DESCRIPTION | 8 ++++----
R/forest.R | 18 ++++++++++--------
man/forest.Rd | 4 +++-
4 files changed, 23 insertions(+), 13 deletions(-)
Author: Nicholas J. Lewin-Koh and Roger Bivand, contributions by Edzer
J. Pebesma, Eric Archer, Adrian Baddeley, Hans-Jörg Bibiko,
Stéphane Dray, David Forrest, Michael Friendly, Patrick
Giraudoux, Duncan Golicher, Virgilio Gómez Rubio, Patrick
Hausmann, Thomas Jagger, Sebastian P. Luque, Don MacQueen,
Andrew Niccolai, Tom Short and Ben Stabler
Title: Tools for reading and handling spatial objects
Description: Set of tools for manipulating and reading geographic data,
in particular ESRI shapefiles; C code used from shapelib. It
includes binary access to GSHHS shoreline files. The package
also provides interface wrappers for exchanging spatial objects
with packages such as PBSmapping, spatstat, maps, RArcInfo,
Stata tmap, WinBUGS, Mondrian, and others.
Diff between maptools versions 0.7-28 dated 2009-12-03 and 0.7-29 dated 2009-12-21
ChangeLog | 17 ++++++++++++++- DESCRIPTION | 10 ++++----- INDEX | 1 NAMESPACE | 3 ++ R/CCmaps.R |only inst/ChangeLog | 17 ++++++++++++++- inst/share/gshhs_c.b |binary inst/share/wdb_borders_c.b |binary man/CCmaps.Rd |only man/Rgshhs.Rd | 11 ++-------- man/spRbind-methods.Rd | 17 +++++++++++++++ src/Rgshhs.c | 29 +++++++++++++++++++++----- src/Rgshhs.h | 49 +++++++++++++++++++++++++++++++++------------ 13 files changed, 121 insertions(+), 33 deletions(-)
Author: Roger Bivand
Diff between classInt versions 0.1-13 dated 2009-10-20 and 0.1-14 dated 2009-12-21
Title: Choose univariate class intervals
Description: A package for choosing univariate class intervals for
mapping or other graphics purposes
ChangeLog | 9 +++++++++
DESCRIPTION | 8 ++++----
R/classInt.R | 12 ++++++++++++
inst/ChangeLog | 9 +++++++++
man/classIntervals.Rd | 8 +++++---
5 files changed, 39 insertions(+), 7 deletions(-)
Author: Aniko Szabo, Lisa Pappas
Title: Estimating oncogenetic trees
Description: Contains functions to construct and evaluate directed tree
structures that model the process of occurrence of genetic
alterations during carcinogenesis.
Diff between Oncotree versions 0.3 dated 2009-03-12 and 0.3.1 dated 2009-12-21
DESCRIPTION | 10 ++++++---- inst/doc/Oncotree_vignette.pdf |binary man/oncotree.fit.Rd | 6 +++--- 3 files changed, 9 insertions(+), 7 deletions(-)
Author: John R. Wallace
Diff between Imap versions 1.0 dated 2009-12-18 and 1.01 dated 2009-12-21
Title: Interactive Mapping
Description: Zoom in and out of maps or any supplied lines or points,
with control for color, poly fill, and aspect.
DESCRIPTION | 8 ++++----
man/IMAP-package.Rd | 6 +++---
man/imap.Rd | 6 +++---
man/imap.ll.Rd | 7 +++++--
man/select.pts.Rd | 6 +++---
5 files changed, 18 insertions(+), 15 deletions(-)
Author: Uwe Ligges
Diff between tuneR versions 0.2-12 dated 2009-11-19 and 0.2-13 dated 2009-12-21
Title: Analysis of music
Description: Collection of tools to analyze music, handling wave files,
transcription, ...
DESCRIPTION | 8 ++++----
man/WaveIO.Rd | 2 +-
2 files changed, 5 insertions(+), 5 deletions(-)
Author: Martin Kober
Title: String Kernel Methods for kernlab
Description: Gapped and word-based string kernels for use with kernlab
Diff between stringkernels versions 0.8.7 dated 2009-09-23 and 0.8.8 dated 2009-12-21
DESCRIPTION | 8 ++++---- NAMESPACE | 2 +- 2 files changed, 5 insertions(+), 5 deletions(-)
Author: Justin Donaldson
Title: A simple toolbar GUI for brushing RGL plots
Description: sculpt3d is a GTK+ toolbar that allows for more
interactive control of a dataset inside the RGL plot window.
Controls for simple brushing, highlighting, labeling, and
mouseMode changes are provided by point-and-click rather than
through the R terminal interface.
Diff between sculpt3d versions 0.2-1 dated 2009-08-27 and 0.2-2 dated 2009-12-21
DESCRIPTION | 8 ++++---- NEWS | 2 ++ R/sculpt3d-internal.R | 22 ++++++---------------- 3 files changed, 12 insertions(+), 20 deletions(-)
Author: Torsten Hothorn, Frank Bretz and Peter Westfall and Richard M.
Heiberger and Andre Schuetzenmeister
Title: Simultaneous Inference in General Parametric Models
Description: Simultaneous tests and confidence intervals for general
linear hypotheses in parametric models, including linear,
generalized linear, linear mixed effects, and survival models.
Diff between multcomp versions 1.1-2 dated 2009-09-10 and 1.1-3 dated 2009-12-21
multcomp-1.1-2/multcomp/inst/doc/chfls1.bbl |only multcomp-1.1-2/multcomp/inst/doc/chfls1.blg |only multcomp-1.1-3/multcomp/DESCRIPTION | 13 multcomp-1.1-3/multcomp/NEWS | 12 multcomp-1.1-3/multcomp/R/cld.R | 2 multcomp-1.1-3/multcomp/R/helpers.R | 88 multcomp-1.1-3/multcomp/R/mcp.R | 5 multcomp-1.1-3/multcomp/R/print.R | 13 multcomp-1.1-3/multcomp/data/sbp.R |only multcomp-1.1-3/multcomp/inst/CHANGES | 12 multcomp-1.1-3/multcomp/inst/doc/chfls1.pdf |binary multcomp-1.1-3/multcomp/inst/doc/generalsiminf.pdf | 1642 +++++------ multcomp-1.1-3/multcomp/inst/doc/multcomp-examples.pdf |binary multcomp-1.1-3/multcomp/man/glht.Rd | 2 multcomp-1.1-3/multcomp/man/sbp.Rd |only multcomp-1.1-3/multcomp/man/trees513.Rd | 6 multcomp-1.1-3/multcomp/tests/Examples/multcomp-Ex.Rout.save | 81 multcomp-1.1-3/multcomp/tests/bugfix.R | 19 multcomp-1.1-3/multcomp/tests/bugfix.Rout.save | 27 multcomp-1.1-3/multcomp/tests/codetools-checks.Rout.save | 2 multcomp-1.1-3/multcomp/tests/regtest-Tukey.Rout.save | 2 multcomp-1.1-3/multcomp/tests/regtest-anova.Rout.save |only multcomp-1.1-3/multcomp/tests/regtest-interface.Rout.save | 2 multcomp-1.1-3/multcomp/tests/regtest-lme.Rout.save |only 24 files changed, 1031 insertions(+), 897 deletions(-)
Author: Adelino Ferreira da Silva
Diff between cudaBayesreg versions 0.1-1 dated 2009-10-19 and 0.2-1 dated 2009-12-21
Title: CUDA Parallel Implementation of a Bayesian Multilevel Model for
fMRI Data Analysis
Description: Compute Unified Device Architecture (CUDA) is a software
platform for massively parallel high-performance computing on
NVIDIA GPUs. This package provides a CUDA implementation of a
Bayesian multilevel model for the analysis of brain fMRI data.
A fMRI data set consists of time series of volume data in 4D
space. Typically, volumes are collected as slices of 64 x 64
"voxels". Analysis of fMRI data often relies on fitting linear
regression models at each voxel of the brain. The volume of the
data to be processed, and the type of statistical analysis to
perform in fMRI analysis, call for high-performance computing
strategies. In this package, the CUDA programming model uses a
separate thread for fitting a linear regression model at each
voxel in parallel. The global statistical model implements a
Gibbs Sampler for hierarchical linear models with a normal
prior. This model has been proposed by Rossi, Allenby and
McCulloch in "Bayesian Statistics and Marketing", Chapter 3,
and is referred to as "rhierLinearModel" in the R-package
"bayesm". A notebook equipped with a NVIDIA "GeForce 8400M GS"
card having Compute Capability 1.1 has been used in the tests.
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cudaBayesreg-0.2-1/cudaBayesreg/R/post.tseries.R | 2
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cudaBayesreg-0.2-1/cudaBayesreg/configure.ac | 2
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cudaBayesreg-0.2-1/cudaBayesreg/data/mask.nii |binary
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cudaBayesreg-0.2-1/cudaBayesreg/src/cudaMultireg.cu | 85 ++++++-----
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cudaBayesreg-0.2-1/cudaBayesreg/src/d_rngNR.cu | 23 ++-
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21 files changed, 159 insertions(+), 136 deletions(-)
Author: Dirk Eddelbuettel
Title: C++ classes to embed R in C++ applications
Description: C++ classes to embed R in C++ applications The RInside
packages makes it easier to have 'R inside' your C++
application by providing a few wrapper classes.
As R itself is embedded into your application, a shared library build
of R is required. This works on Linux, OS X and even on Windows
provided you use the same tools used to build R itself.
Several examples are provided in the examples/ directory of the
installed package, and Doxygen-generated documentation of the
C++ classes is included as well.
Diff between RInside versions 0.1.1 dated 2009-09-28 and 0.2.0 dated 2009-12-21
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