Author: Max Kuhn. Contributions from Jed Wing, Steve Weston, Andre
Williams, Chris Keefer and Allan Engelhardt
Title: Classification and Regression Training
Description: Misc functions for training and plotting classification
and regression models
Diff between caret versions 4.27 dated 2009-11-05 and 4.30 dated 2009-11-09
caret-4.27/caret/inst/doc/caretMisc.tex |only caret-4.27/caret/inst/doc/caretSelection.tex |only caret-4.27/caret/inst/doc/caretTrain.tex |only caret-4.27/caret/inst/doc/caretVarImp.tex |only caret-4.30/caret/DESCRIPTION | 14 caret-4.30/caret/R/createGrid.R | 4 caret-4.30/caret/R/createModel.R | 50 + caret-4.30/caret/R/extractPrediction.R | 10 caret-4.30/caret/R/extractProb.R | 12 caret-4.30/caret/R/makeCubistFiles.R |only caret-4.30/caret/R/misc.R | 52 + caret-4.30/caret/R/plotClassProbs.R | 83 +- caret-4.30/caret/R/predictionFunction.R | 20 caret-4.30/caret/R/predictors.R | 7 caret-4.30/caret/R/probFunction.R | 20 caret-4.30/caret/R/selection.R | 5 caret-4.30/caret/R/train.default.R | 2 caret-4.30/caret/inst/CHANGES | 30 + caret-4.30/caret/inst/doc/caretMisc.pdf | 758 +++++++++++++-------------- caret-4.30/caret/inst/doc/caretSelection.pdf | 325 +++++------ caret-4.30/caret/inst/doc/caretTrain.Rnw | 17 caret-4.30/caret/inst/doc/caretTrain.pdf |binary caret-4.30/caret/inst/doc/caretVarImp.pdf | 199 +++---- caret-4.30/caret/man/extractPrediction.Rd | 1 caret-4.30/caret/man/plotClassProbs.Rd | 63 +- caret-4.30/caret/man/plsda.Rd | 13 caret-4.30/caret/man/train.Rd | 6 27 files changed, 958 insertions(+), 733 deletions(-)
Author: Michal Juraska
Diff between speff2trial versions 1.0.0 dated 2009-07-02 and 1.0.1 dated 2009-11-09
Title: Semiparametric efficient estimation for a two-sample treatment
effect
Description: The package performs estimation and testing of the
treatment effect in a 2-group randomized clinical trial with a
quantitative, dichotomous, or right-censored time-to-event
endpoint. The method improves efficiency by leveraging baseline
predictors of the endpoint. The inverse probability weighting
technique of Robins, Rotnitzky, and Zhao (JASA, 1994) is used
to provide unbiased estimation when the endpoint is missing at
random.
DESCRIPTION | 21
NAMESPACE | 7
R/print.summary.speffSurv.R |only
R/speffSurv.R |only
R/summary.speffSurv.R |only
data/ACTG175.txt | 4280 ++++++++++++++++++++++----------------------
man/ACTG175.Rd | 25
man/speffSurv.Rd |only
man/summaryspeffSurv.Rd |only
9 files changed, 2170 insertions(+), 2163 deletions(-)
Author: Han Lin Shang and Rob J Hyndman
Title: Rainbow plots, bagplots and boxplots for functional data
Description: Functions and datasets for functional data display and
outlier detection.
Diff between rainbow versions 1.5 dated 2009-10-08 and 1.6 dated 2009-11-09
CHANGELOG | 2 ++ DESCRIPTION | 8 ++++---- NAMESPACE | 3 ++- R/SVDplot.R |only man/SVDplot.Rd |only man/fboxplot.Rd | 3 +++ 6 files changed, 11 insertions(+), 5 deletions(-)
Author: Stephen Milborrow derived from mda:mars by Trevor Hastie and
Rob Tibshirani.
Title: Multivariate Adaptive Regression Spline Models
Description: Build regression models using the techniques in Friedman's
papers "Fast MARS" and "Multivariate Adaptive Regression
Splines". (The term "MARS" is copyrighted and thus not used in
the name of the package.)
Diff between earth versions 2.3-5 dated 2009-10-09 and 2.4-0 dated 2009-11-09
DESCRIPTION | 6 NEWS | 6 R/earth.R | 2 man/earth.Rd | 64 man/evimp.Rd | 16 man/format.earth.Rd | 34 man/mars.to.earth.Rd | 2 man/model.matrix.earth.Rd | 44 man/predict.earth.Rd | 2 man/summary.earth.Rd | 20 man/update.earth.Rd | 26 src/earth.c | 45 src/earth.h | 16 src/tests/test.earth.big.Rout.save | 61 src/tests/test.earth.cv.Rout.save | 743 +++--- src/tests/test.earth.full.R | 3 src/tests/test.earth.full.Rout.save | 3964 ++++++++++++++++++------------------ src/tests/test.earth.glm.Rout.save | 449 ++-- src/tests/test.earthc.out.save | 2861 +++++++++++++------------ src/tests/test.earthmain.out.save | 37 src/tests/test.plotd.R | 30 src/tests/test.plotd.Rout.save | 30 src/tests/test.plotmo.R | 14 src/tests/test.plotmo.Rout.save | 1553 +++++++------- tests/test.earth.Rout.save | 156 - 25 files changed, 5126 insertions(+), 5058 deletions(-)
Author: Ingmar Visser
Diff between depmix versions 0.9.6 dated 2009-07-18 and 0.9.7 dated 2009-11-09
Title: Dependent Mixture Models
Description: Fit (multigroup) mixtures of latent Markov models on mixed
categorical and continuous (timeseries) data
CHANGES | 6 ++++++
DESCRIPTION | 10 +++++-----
README | 4 ++--
man/markovdata.Rd | 2 +-
4 files changed, 14 insertions(+), 8 deletions(-)
Author: Tianqing Liu, Nan Lin, Ningzhong Shi and Baoxue Zhang
Title: Order-restricted Information Criterion-based Clustering
Algorithm
Description: ORIClust is a user-friendly R-based software package for
gene clustering. Clusters are given by genes matched to
prespecified profiles across various ordered treatment groups.
It is particularly useful for analyzing data obtained from
short time-course or dose-response microarray experiments.
Diff between ORIClust versions 1.0-0 dated 2009-09-18 and 1.0-1 dated 2009-11-09
DESCRIPTION | 6 +++--- R/ORICC1.R | 27 +++++++++++++++++---------- R/ORICC2.R | 34 +++++++++++++++++++++++++--------- man/Breast.Rd | 2 +- man/ORICC1-package.Rd | 2 +- man/ORICC2-package.Rd | 2 +- man/complete.profile.Rd | 2 +- man/cyclical.max.min.Rd | 2 +- man/cyclical.min.max.Rd | 2 +- man/decreasing.Rd | 2 +- man/down.up.Rd | 2 +- man/flat.pattern.Rd | 2 +- man/increasing.Rd | 2 +- man/isodecre.Rd | 2 +- man/isoincre.Rd | 2 +- man/up.down.Rd | 2 +- 16 files changed, 58 insertions(+), 35 deletions(-)
Author: Klaus Nordhausen, Seija Sirkia, Hannu Oja, David E. Tyler
Title: Tools for Multivariate Nonparametrics
Description: Tools for multivariate nonparametrics, as location tests
based on marginal ranks, spatial median and spatial signs
computation, Hotelling's T-test, estimates of shape
Diff between ICSNP versions 1.0-5 dated 2009-09-12 and 1.0-6 dated 2009-11-09
DESCRIPTION | 8 ++++---- NAMESPACE | 2 +- R/HP.loc.test.R |only R/vdw.loc.R | 3 ++- data/LASERI.txt |only inst/CHANGES | 7 +++++++ man/HP.loc.test.Rd |only man/ICSNP-package.Rd | 4 ++-- man/LASERI.Rd |only man/pulmonary.Rd | 3 +++ 10 files changed, 19 insertions(+), 8 deletions(-)
Author: Steve Su
Title: Fitting Single and Mixture of Generalised Lambda Distributions
(RS and FMKL) using Discretised and Maximum Likelihood Methods
Description: The fitting algorithms considered in this package have two
major objectives. One is to provide a smoothing device to fit
distributions to data using the weight and unweighted
discretised approach based on the bin width of the histogram.
The other is to provide a definitive fit to the data set using
the maximum likelihood estimation. Diagnostics on goodness of
fit can be done via qqplots, KS-resample tests and comparing
mean, variance, skewness and kurtosis of the data with the
fitted distribution.
Diff between GLDEX versions 1.0.3.3 dated 2009-11-01 and 1.0.3.4 dated 2009-11-09
DESCRIPTION | 8 +++---- R/qqplot.gld.R | 31 +++++++++++++++++------------ R/qqplot.gld.bi.R | 53 ++++++++++++++++++++++++++++++++------------------- man/GLDEX.package.Rd | 4 +-- 4 files changed, 58 insertions(+), 38 deletions(-)
Author: Dongjun Chung
Diff between spls versions 1.1-0 dated 2009-05-20 and 2.1-0 dated 2009-11-09
Title: Sparse Partial Least Squares (SPLS) Regression and
Classification
Description: This package provides functions for fitting a Sparse
Partial Least Squares Regression and Classification
spls-1.1-0/spls/inst/doc/Rplots.pdf |only
spls-2.1-0/spls/DESCRIPTION | 10 ++++-----
spls-2.1-0/spls/R/cv.sgpls.R |only
spls-2.1-0/spls/R/cv.sgpls.binary.R |only
spls-2.1-0/spls/R/cv.sgpls.multi.R |only
spls-2.1-0/spls/R/cv.split.R |only
spls-2.1-0/spls/R/cv.splsda.R |only
spls-2.1-0/spls/R/predict.sgpls.R |only
spls-2.1-0/spls/R/predict.splsda.R |only
spls-2.1-0/spls/R/print.sgpls.R |only
spls-2.1-0/spls/R/print.splsda.R |only
spls-2.1-0/spls/R/sgpls.R |only
spls-2.1-0/spls/R/sgpls.binary.R |only
spls-2.1-0/spls/R/sgpls.multi.R |only
spls-2.1-0/spls/R/spls.R | 2 -
spls-2.1-0/spls/R/splsda.R |only
spls-2.1-0/spls/R/wpls.R |only
spls-2.1-0/spls/data/filelist | 4 ++-
spls-2.1-0/spls/data/lymphoma.RData |only
spls-2.1-0/spls/data/prostate.RData |only
spls-2.1-0/spls/inst/doc/spls-example.pdf |binary
spls-2.1-0/spls/man/ci.spls.Rd | 32 +++++++++++++++---------------
spls-2.1-0/spls/man/coefplot.spls.Rd | 17 ++++++++-------
spls-2.1-0/spls/man/correct.spls.Rd | 19 +++++++++--------
spls-2.1-0/spls/man/cv.sgpls.Rd |only
spls-2.1-0/spls/man/cv.spls.Rd | 25 ++++++++++++-----------
spls-2.1-0/spls/man/cv.splsda.Rd |only
spls-2.1-0/spls/man/lymphoma.Rd |only
spls-2.1-0/spls/man/mice.Rd | 13 +++++-------
spls-2.1-0/spls/man/plot.spls.Rd | 7 +++---
spls-2.1-0/spls/man/predict.sgpls.Rd |only
spls-2.1-0/spls/man/predict.spls.Rd | 9 ++++----
spls-2.1-0/spls/man/predict.splsda.Rd |only
spls-2.1-0/spls/man/print.sgpls.Rd |only
spls-2.1-0/spls/man/print.spls.Rd | 9 ++++----
spls-2.1-0/spls/man/print.splsda.Rd |only
spls-2.1-0/spls/man/prostate.Rd |only
spls-2.1-0/spls/man/sgpls.Rd |only
spls-2.1-0/spls/man/spls-internal.Rd | 26 +++++++++++++++++++++++-
spls-2.1-0/spls/man/spls.Rd | 23 +++++++++++----------
spls-2.1-0/spls/man/splsda.Rd |only
spls-2.1-0/spls/man/yeast.Rd | 14 ++++++-------
42 files changed, 121 insertions(+), 89 deletions(-)