Title: sos
Diff between sos versions 1.3-0 dated 2010-06-23 and 1.3-1 dated 2011-07-06
Description: R related Search Engines
Author: Spencer Graves, Sundar Dorai-Raj, and Romain Francois
Maintainer: Spencer Graves
DESCRIPTION | 8 +++----
R/Extract.findFn.R |only
R/findFn.R | 54 +++++++++++++++++++++++++++-----------------------
R/writeFindFn2xls.R | 2 -
inst/doc/sos.pdf |binary
man/Extract.findFn.Rd |only
man/findFn.Rd | 7 +++++-
7 files changed, 41 insertions(+), 30 deletions(-)
Title: RVM Binary Classification
Diff between rvmbinary versions 0.1 dated 2011-04-11 and 0.1.2 dated 2011-07-06
Description: Performs binary classification of data using a Relevance
Vector Machine
Author: Robert Lowe
Maintainer: Robert Lowe
DESCRIPTION | 6 ++--
R/gaus.R | 4 +-
R/gauspredict.R | 71 +++++++++++++++++++++++++++++++++++--------------
man/aa.Rd | 5 ++-
man/aapredict.Rd | 5 ++-
man/gaus.Rd | 5 ++-
man/gauspredict.Rd | 5 ++-
man/rvmbinary.Rd | 5 ++-
src/fullstatistics.cpp | 11 ++++---
src/fullstatistics.h | 9 ++----
src/main.cpp | 24 +++++++++++-----
11 files changed, 104 insertions(+), 46 deletions(-)
Title: statistical methods for analysing multivariate abundance data
Diff between mvabund versions 2.2-4 dated 2011-06-30 and 2.2-5.3 dated 2011-07-06
Description: A set of tools for displaying, modeling and analysing
multivariate abundance data in community ecology. See
mvabund-package.Rd for details of overall package organization.
The package is implemented with the Gnu Scientific Library
(http://www.gnu.org/software/gsl/) and Rcpp
(http://dirk.eddelbuettel.com/code/rcpp.html) R / C++ classes.
Author: Yi Wang, Ulrike Naumann, Stephen Wright and David Warton
Maintainer: Yi Wang
DESCRIPTION | 12 -
R/anova.manyglm.R | 121 +++++------
R/anova.manylm.R | 396 ++++++++++++++++----------------------
R/cooks.distance.manylm.R | 4
R/default.plot.manyglm.R | 4
R/default.plot.manylm.R | 17 -
R/default.print.summary.manyglm.R | 4
R/deviance.manylm.R | 6
R/manyglm.R | 2
R/manylm.R | 7
R/predict.manylm.R | 2
R/print.summary.manylm.R | 2
src/Makevars.win | 9
src/RtoAnovaCpp.cpp | 51 ++--
src/RtoGlm.cpp | 32 +--
src/RtoGlmAnova.cpp | 65 +++---
src/RtoGlmSmry.cpp | 72 +++---
src/RtoSmryCpp.cpp | 71 +++---
src/anova.cpp | 38 +--
src/calctest.cpp | 119 +++++------
src/glm.cpp | 26 +-
src/glmtest.cpp | 94 ++++-----
src/io.cpp | 12 -
src/resampTest.h | 87 ++++----
src/rmv.h | 12 -
src/rnd.cpp | 20 -
src/simutility.cpp | 52 ++--
src/summary.cpp | 85 ++++----
tests |only
29 files changed, 692 insertions(+), 730 deletions(-)
Title: Inferences for ratios of coefficients in the general linear
model
Diff between mratios versions 1.3.15 dated 2011-03-24 and 1.3.16 dated 2011-07-06
Description: With this package, it is possible to perform
(simultaneous) inferences for ratios of linear combinations of
coefficients in the general linear model. In particular, tests
and confidence interval estimations for ratios of treatment
means in the normal one-way layout and confidence interval
estimations like in (multiple) slope ratio and parallel line
assays can be carried out. Moreover, it is possible to
calculate the sample sizes required in comparisons with a
control based on relative margins. For the simple two-sample
problem, functions for a t-test for ratio-formatted hypotheses
and the corresponding Fieller-type confidence interval are
provided assuming homogeneous or heterogeneous group variances.
Author: Gemechis Dilba Djira, Mario Hasler, Daniel Gerhard, Frank
Schaarschmidt
Maintainer: Frank Schaarschmidt
DESCRIPTION | 8 ++++----
R/ratioVH.R | 16 ++++++++--------
R/simtest.ratioI.R | 6 +++---
3 files changed, 15 insertions(+), 15 deletions(-)
Title: Jitter/CI Plot with Ordered Points Below the Limit of Detection
Diff between limitplot versions 1.0 dated 2010-04-15 and 1.2 dated 2011-07-06
Description: Values below a specified limit of detection are stacked in
rows in order to reduce overplotting and create a clear
graphical representation of your data.
Author: Omar E. Olmedo
Maintainer: Omar E. Olmedo
DESCRIPTION | 11 +--
NAMESPACE |only
R/limitplot.R | 169 +++++++++++--------------------------------------------
R/plotBox.R |only
R/plotInit.R |only
R/plotStack.R |only
README |only
man/limitplot.Rd | 33 ++++++----
8 files changed, 60 insertions(+), 153 deletions(-)
Title: Regularization paths for regression models with grouped
covariates
Diff between grpreg versions 1.2-0 dated 2011-06-22 and 1.2-1 dated 2011-07-06
Description: Efficient algorithms for fitting the regularization path
for linear or logistic regression models penalized by the group
lasso, group bridge, or group MCP methods. The algorithm is
based on the idea of a locally approximated coordinate descent.
Author: Patrick Breheny
Maintainer: Patrick Breheny
DESCRIPTION | 10 +++++-----
1 file changed, 5 insertions(+), 5 deletions(-)
Title: R package for parsing and manipulating edit rules
Diff between editrules versions 0.7-1 dated 2011-06-29 and 0.8 dated 2011-07-06
Description: Facilitates reading and manipulation of linear
(in)equalities, converting them into matrix format (and vice
versa) and checking if data are valid according to these rules.
Sets of linear edits can be manipulated using Fourier-Motzkin
elimination and variable substitution and solving error
localization problems based on the generalized principle of
Felligi and Holt.
Author: Edwin de Jonge, Mark van der Loo
Maintainer: Edwin de Jonge
editrules-0.7-1/editrules/R/choicepoint.R |only
editrules-0.7-1/editrules/man/choicepoint.Rd |only
editrules-0.7-1/editrules/man/iter.choicepoint.Rd |only
editrules-0.7-1/editrules/man/print.choicepoint.Rd |only
editrules-0.8/editrules/DESCRIPTION | 8
editrules-0.8/editrules/NAMESPACE | 10
editrules-0.8/editrules/NEWS | 12
editrules-0.8/editrules/R/backtracker.R |only
editrules-0.8/editrules/R/editmatrix.R | 38
editrules-0.8/editrules/R/editmatrixAttr.R | 14
editrules-0.8/editrules/R/eliminate.R | 23
editrules-0.8/editrules/R/errorLocalizer.R | 36
editrules-0.8/editrules/R/pkg.R | 34
editrules-0.8/editrules/R/reduce.R | 29
editrules-0.8/editrules/inst/doc/Sweave.sty | 6
editrules-0.8/editrules/inst/doc/editrules-categorical.pdf |binary
editrules-0.8/editrules/inst/doc/editrules-linear.Snw | 771 +++++-----
editrules-0.8/editrules/inst/doc/editrules-linear.bbl | 31
editrules-0.8/editrules/inst/doc/editrules-linear.blg | 68
editrules-0.8/editrules/inst/doc/editrules-linear.dvi |binary
editrules-0.8/editrules/inst/doc/editrules-linear.pdf |binary
editrules-0.8/editrules/inst/doc/editrules.bib | 46
editrules-0.8/editrules/inst/doc/texput.log |only
editrules-0.8/editrules/inst/doc/tree.tex |only
editrules-0.8/editrules/inst/doc/tree.tex.aux |only
editrules-0.8/editrules/inst/doc/x.log |only
editrules-0.8/editrules/inst/tests/testFourierMotzkin.R | 18
editrules-0.8/editrules/inst/tests/testIsObviouslyInfeasible.R |only
editrules-0.8/editrules/inst/tests/testIsObviouslyRedundant.R |only
editrules-0.8/editrules/inst/tests/testeditmatrix.R | 1
editrules-0.8/editrules/man/as.character.editmatrix.Rd | 5
editrules-0.8/editrules/man/as.editmatrix.Rd | 8
editrules-0.8/editrules/man/as.expression.editmatrix.Rd | 5
editrules-0.8/editrules/man/backtracker.Rd |only
editrules-0.8/editrules/man/editmatrix.Rd | 4
editrules-0.8/editrules/man/editrules-package.Rd | 24
editrules-0.8/editrules/man/errorLocalizer.Rd | 16
editrules-0.8/editrules/man/getA.Rd | 1
editrules-0.8/editrules/man/getb.Rd | 1
editrules-0.8/editrules/man/isObviouslyInfeasible.Rd | 2
editrules-0.8/editrules/man/iter.backtracker.Rd |only
editrules-0.8/editrules/man/print.backtracker.Rd |only
editrules-0.8/editrules/man/substValue.Rd | 7
43 files changed, 670 insertions(+), 548 deletions(-)
Title: Classification and Regression Training
Diff between caret versions 4.91 dated 2011-06-09 and 4.92 dated 2011-07-06
Description: Misc functions for training and plotting classification
and regression models
Author: Max Kuhn. Contributions from Jed Wing, Steve Weston, Andre
Williams, Chris Keefer and Allan Engelhardt
Maintainer: Max Kuhn
DESCRIPTION | 11 +-
R/createGrid.R | 1
R/createModel.R | 21 ++++
R/misc.R | 26 +++++
R/modelLookup.R | 54 ++++++++++--
R/plot.train.R | 11 ++
R/preProcess.R | 1
R/predictionFunction.R | 83 ++++++++++++------
R/resamples.R | 193 ++++++++++++++++++++++++++++++++++++--------
R/rfe.R | 43 +++++----
R/selectByFilter.R | 35 ++++---
R/selection.R | 3
R/train.default.R | 26 ++++-
R/trainControl.R | 2
inst/NEWS | 35 +++++++
inst/doc/caretMisc.pdf |binary
inst/doc/caretSelection.pdf |binary
inst/doc/caretTrain.Rnw | 17 +++
inst/doc/caretTrain.pdf |binary
inst/doc/caretVarImp.pdf |binary
man/lattice.resamples.Rd | 9 +-
man/rfeControl.Rd | 2
man/sbfControl.Rd | 2
man/train.Rd | 13 ++
man/trainControl.Rd | 2
25 files changed, 467 insertions(+), 123 deletions(-)
Title: Six Sigma Tools for Quality and Process Improvement
Diff between SixSigma versions 0.2.1 dated 2011-04-01 and 0.3.0 dated 2011-07-06
Description: This package contains functions and utilities to perform
Statistical Analysis for Six Sigma methodology. Through its
outline DMAIC (Define, Measure, Analyze, Improve, Control), you
can manage several Quality Management studies. The current
version includes Capability Analysis, Gage R&R Study,
Confidence Interval, Cause-and-effect diagram and Process Map.
There will be new functions very soon for Capability Analysis,
Control Charts, Reliability, OC Curves, Regression and Design
of Experiments. See ?SixSigma for an Introduction.
Author: Emilio Lopez, Andres Redchuk, Javier M.Moguerza
Maintainer: Emilio Lopez
DESCRIPTION | 21 +++++++++++----------
INDEX | 9 +++++++--
R/SixSigma.R |only
R/ss.ca.R |only
R/ss.heli.R |only
R/ss.rr.R | 2 +-
data/ss.data.ca.RData |only
inst/doc |only
man/ss.ca.indices.Rd |only
man/ss.ca.yield.Rd |only
man/ss.data.ca.Rd |only
man/ss.heli.Rd |only
man/ss.study.ca.Rd |only
13 files changed, 19 insertions(+), 13 deletions(-)
Title: Seamless R and C++ Integration
Diff between Rcpp versions 0.9.4 dated 2011-04-12 and 0.9.5 dated 2011-07-06
Description: The Rcpp package provides a C++ library which facilitates
the integration of R and C++.
R data types (SEXP) are matched to C++ objects in a class hierarchy.
All R types are supported (vectors, functions, environment, etc
...) and each type is mapped to a dedicated class. For
example, numeric vectors are represented as instances of the
Rcpp::NumericVector class, environments are represented as
instances of Rcpp::Environment, functions are represented as
Rcpp::Function, etc ... The "Rcpp-introduction" vignette
provides a good entry point to Rcpp.
Conversion from C++ to R and back is driven by the templates Rcpp::wrap
and Rcpp::as which are highly flexible and extensible, as
documented in the "Rcpp-extending" vignette.
Rcpp also provides Rcpp modules, a framework that allows exposing C++
functions and classes to the R level. The "Rcpp-modules"
vignette details the current set of features of Rcpp-modules.
Rcpp includes a concept called Rcpp sugar that brings many R functions
into C++. Sugar takes advantage of lazy evaluation and
expression templates to achieve great performance while
exposing a syntax that is much nicer to use than the equivalent
low-level loop code. The "Rcpp-sugar" vignette gives an
overview of the feature.
Several examples are included, and 753 unit tests in 338 unit test
functions provide additional usage examples.
An earlier version of Rcpp, containing what we now call the 'classic
Rcpp API' was written during 2005 and 2006 by Dominick Samperi.
This code has been factored out of Rcpp into the package
RcppClassic and it is still available for code relying on this
interface. New development should use this package instead.
Author: Dirk Eddelbuettel and Romain Francois, with contributions by
Douglas Bates and John Chambers
Maintainer: Dirk Eddelbuettel and Romain Francois
ChangeLog | 74
DESCRIPTION | 10
R/00_classes.R | 3
R/Module.R | 16
R/loadRcppModules.R | 10
R/populate.R | 10
R/tools.R | 13
R/zzz.R | 3
cleanup | 2
inst/NEWS | 21
inst/doc/Rcpp-FAQ.pdf |binary
inst/doc/Rcpp-FAQ/Rcpp-FAQ.Rnw | 62
inst/doc/Rcpp-extending.pdf |binary
inst/doc/Rcpp-introduction.pdf |binary
inst/doc/Rcpp-modules.pdf |binary
inst/doc/Rcpp-modules/Rcpp-modules.Rnw | 7
inst/doc/Rcpp-package.pdf |binary
inst/doc/Rcpp-quickref.pdf |binary
inst/doc/Rcpp-quickref/Rcpp-quickref.Rnw | 59
inst/doc/Rcpp-sugar.pdf |binary
inst/doc/Rcpp-unitTests.pdf |binary
inst/doc/Rcpp.bib | 4
inst/doc/unitTests-results/Rcpp-unitTests.html | 18
inst/doc/unitTests-results/Rcpp-unitTests.txt | 49
inst/examples/OpenMP |only
inst/include/Rcpp/Module.h | 33
inst/include/Rcpp/config.h | 2
inst/include/Rcpp/internal/wrap.h | 5
inst/include/Rcpp/module/Module_generated_CppMethod.h | 2902 +++++++++++++++++-
inst/include/Rcpp/stats/random/rlnorm.h | 14
inst/include/Rcpp/stats/random/rnorm.h | 4
inst/include/Rcpp/sugar/functions/functions.h | 3
inst/include/Rcpp/sugar/functions/mean.h |only
inst/include/Rcpp/sugar/functions/sd.h |only
inst/include/Rcpp/sugar/functions/sum.h | 4
inst/include/Rcpp/sugar/functions/var.h |only
inst/include/Rcpp/vector/Vector.h | 4
inst/skeleton/zzz.R | 1
inst/unitTests/runit.wrap.R | 25
man/CppClass-class.Rd | 2
man/loadRcppModules.Rd | 6
src/Module.cpp | 1
42 files changed, 3252 insertions(+), 115 deletions(-)
Title: Joint Optimization Plot
Diff between JOP versions 2.0.2 dated 2011-06-15 and 2.0.3 dated 2011-07-06
Description: JOP is a tool for simultanous optimization of multiple
responses and visualization of the results. The visualization
is done by the joint optimization plot introduced by Kuhnt and
Erbruegge (2004).
Author: Sonja Kuhnt and Nikolaus Rudak
Maintainer: Nikolaus Rudak
DESCRIPTION | 8 ++++----
R/locate.R | 30 +++++++++++++++---------------
R/oplot.R | 18 +++++++++---------
man/JOP-package.Rd | 4 ++--
4 files changed, 30 insertions(+), 30 deletions(-)
Title: gpseq: Using the generalized Poisson distribution to model
sequence read counts from high throughput sequencing
experiments
Diff between GPseq versions 0.4 dated 2011-01-11 and 0.5 dated 2011-07-06
Description: Some functions for modeling sequence read counts as a
generalized poisson model and to use this model for detecting
differentially expressed genes in different conditions and
differentially spliced exons.
Author: Sudeep Srivastava, Liang Chen
Maintainer: Sudeep Srivastava
DESCRIPTION | 6 +++---
R/wrapper2.R | 9 +++------
2 files changed, 6 insertions(+), 9 deletions(-)
Title: Find biomarkers in two-class discrimination problems
Diff between BioMark versions 0.2.6 dated 2011-02-08 and 0.3.0 dated 2011-07-06
Description: The package implements PCLDA, PLSDA, and several t-tests
to find those variables that allow for adequate discrimination
between two classes. Apart from the usual approaches based on
the size of model coefficients, a set of functions is provided
that assess the stability of the potential biomarkers under
crossvalidation.
Author: Ron Wehrens, Pietro Franceschi
Maintainer: Ron Wehrens
CHANGES |only
DESCRIPTION | 10 +-
R/biom.HC.R |only
R/biom.coef.R | 32 ++----
R/biom.options.R |only
R/biom.stab.R | 14 +-
R/gen.data.R | 2
R/get.biom.R | 247 +++++++++++++++++++++++++++++++++++++++-------------
R/roc.R | 12 +-
TODO |only
data/SpikeNeg.RData |only
data/SpikePos.RData |only
man/HCthresh.Rd |only
man/ROC.Rd | 96 ++++++++------------
man/SpikedApple.Rd |only
man/auxBiom.Rd |only
man/biom.options.Rd |only
man/gen.data.Rd | 9 +
man/get.biom.Rd | 169 ++++++++++++++---------------------
man/get.segments.Rd | 6 -
man/scalefun.Rd | 3
man/spikedApples.Rd | 7 +
22 files changed, 349 insertions(+), 258 deletions(-)