Title: IRT Separate Calibration Linking Methods
Diff between plink versions 1.2-3 dated 2010-04-19 and 1.2-4 dated 2010-07-26
Description: This package uses item response theory methods to compute
linking constants and conduct chain linking of unidimensional
or multidimensional tests for multiple groups under a common
item design. The unidimensional methods include the Mean/Mean,
Mean/Sigma, Haebara, and Stocking-Lord methods for dichotomous
(1PL, 2PL and 3PL) and/or polytomous (graded response, partial
credit/generalized partial credit, nominal, and multiple-choice
model) items. The multidimensional methods include the
Reckase-Martineau method and extensions of the Haebara and
Stocking-Lord method using a single dilation parameter,
multiple dilation parameters, or the Oshima, Davey, & Lee
approach for multidimensional extensions of all the
unidimensional dichotomous and polytomous item response models.
The package also includes functions for importing item and/or
ability parameters from common IRT software, conducting IRT
true score and observed score equating, and plotting item
response curves/surfaces, vector plots, and comparison plots
for examining parameter drift.
Author: Jonathan P. Weeks
Maintainer: Jonathan P. Weeks
DESCRIPTION | 8 ++++----
R/plot.R | 3 +--
inst/CITATION | 30 +++++++++++++++++-------------
inst/NEWS | 5 +++++
inst/doc |only
man/as.irt.pars.Rd | 7 +++++++
man/as.poly.mod.Rd | 7 +++++++
man/combine.pars.Rd | 7 +++++++
man/drm-methods.Rd | 5 +++++
man/equate-methods.Rd | 5 +++++
man/gpcm-methods.Rd | 5 +++++
man/grm-methods.Rd | 5 +++++
man/mcm-methods.Rd | 5 +++++
man/nrm-methods.Rd | 5 +++++
man/plink-methods.Rd | 5 +++++
man/plink-package.Rd | 10 +++++++++-
man/plot.irt.prob.Rd | 7 +++++++
man/read.bilog.Rd | 5 +++++
man/summary.irt.pars.Rd | 7 +++++++
19 files changed, 111 insertions(+), 20 deletions(-)
Title: N-Gram Based Text Categorization
Diff between textcat versions 0.0-3 dated 2010-06-24 and 0.0-4 dated 2010-07-26
Description: Text categorization based on n-grams
Author: Kurt Hornik, Johannes Rauch, Christian Buchta, Ingo Feinerer
Maintainer: Kurt Hornik
DESCRIPTION | 6 +++---
R/sysdata.rda |binary
2 files changed, 3 insertions(+), 3 deletions(-)
Title: Data Structures and Algorithms for Relations
Diff between relations versions 0.5-7 dated 2010-03-08 and 0.5-8 dated 2010-07-26
Description: Data structures and algorithms for k-ary relations with
arbitrary domains, featuring relational algebra, predicate
functions, and fitters for consensus relations.
Author: Kurt Hornik and David Meyer
Maintainer: Kurt Hornik
DESCRIPTION | 8 ++++----
NEWS | 4 ++++
inst/NEWS | 4 ++++
inst/doc/relations.pdf |binary
man/impute.Rd | 8 ++++++--
5 files changed, 18 insertions(+), 6 deletions(-)
Title: Spherical Trigonometry
Diff between geosphere versions 1.2-4 dated 2010-06-25 and 1.2-7 dated 2010-07-26
Description: Spherical trigonometry for geographic applications
Author: Robert J. Hijmans, Ed Williams, Chris Vennes
Maintainer: Robert J. Hijmans
DESCRIPTION | 10 +++++-----
R/mercator.R | 14 ++++++++------
R/randomCoordinates.R |only
R/regularCoordinates.R |only
inst/doc/geosphere.Rnw | 21 +++++++++++++++++----
inst/doc/geosphere.pdf |binary
man/randomCoordinates.Rd |only
7 files changed, 30 insertions(+), 15 deletions(-)
Title: Partial Least Squares Data Analysis Methods
Diff between plspm versions 0.1-7 dated 2010-07-24 and 0.1-8 dated 2010-07-26
Description: Partial Least Squares (PLS) methods with emphasis on
structural equation models with latent variables.
Author: Gaston Sanchez
Maintainer: Gaston Sanchez
DESCRIPTION | 8
R/it.reb.R | 18 -
R/local.models.R | 12
R/plspm-internal.R | 601 +++++++++++++++++++++++++++++++++++++-----------
R/plspm.R | 32 +-
R/plspm.fit.R | 31 +-
R/plspm.groups.R | 44 +--
R/print.local.models.R | 2
R/print.summary.plspm.R | 27 +-
R/rebus.test.R | 14 -
R/res.clus.R | 14 -
R/summary.plspm.R | 4
man/plspm-package.Rd | 4
man/plspm.Rd | 18 -
14 files changed, 611 insertions(+), 218 deletions(-)
Title: Tools for evaluating collinearity
Diff between perturb versions 2.03 dated 2007-12-07 and 2.04 dated 2010-07-26
Description: "perturb" evaluates collinearity by adding random noise to
selected variables. "colldiag" calculates condition numbers and
variance decomposition proportions to test for collinearity and
uncover its sources.
Author: John Hendrickx
Maintainer: John Hendrickx
DESCRIPTION | 24 +++++++++++++++---------
man/perturb.Rd | 2 +-
man/reclassify.Rd | 4 ++--
3 files changed, 18 insertions(+), 12 deletions(-)
Title: Generic Functions for R
Diff between caroline versions 0.1-8 dated 2010-02-12 and 0.2-0 dated 2010-07-26
Description: The caroline package is a collection of generic functions
useful for various applications.
Author: David M. Schruth
Maintainer: David M. Schruth
DESCRIPTION | 10 ++--
NAMESPACE | 2
R/plots.R | 122 -------------------------------------------------
R/system.R | 50 ++++++++++++++++++--
R/violins.R |only
man/parseArgStrings.Rd |only
man/violins.Rd | 18 +++++--
man/write.delim.Rd |only
8 files changed, 66 insertions(+), 136 deletions(-)
Title: Seamless R and C++ Integration
Diff between Rcpp versions 0.8.4 dated 2010-07-15 and 0.8.5 dated 2010-07-26
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 735 unit tests in 329 unit test
functions provide additional usage examples.
Author: Dirk Eddelbuettel and Romain Francois, with contributions by
Simon Urbanek, David Reiss and Douglas Bates; based on code
written during 2005 and 2006 by Dominick Samperi
Maintainer: Dirk Eddelbuettel and Romain Francois
Rcpp-0.8.4/Rcpp/src/cxx0x |only
Rcpp-0.8.5/Rcpp/DESCRIPTION | 63 ++----
Rcpp-0.8.5/Rcpp/NEWS | 15 +
Rcpp-0.8.5/Rcpp/TODO | 68 ++-----
Rcpp-0.8.5/Rcpp/inst/ChangeLog | 40 ++++
Rcpp-0.8.5/Rcpp/inst/doc/Rcpp-FAQ.pdf |binary
Rcpp-0.8.5/Rcpp/inst/doc/Rcpp-extending.pdf |binary
Rcpp-0.8.5/Rcpp/inst/doc/Rcpp-introduction.pdf |binary
Rcpp-0.8.5/Rcpp/inst/doc/Rcpp-modules.pdf |binary
Rcpp-0.8.5/Rcpp/inst/doc/Rcpp-sugar.pdf |binary
Rcpp-0.8.5/Rcpp/inst/doc/Rcpp-unitTests.pdf |binary
Rcpp-0.8.5/Rcpp/inst/doc/unitTests-results/Rcpp-unitTests.html | 6
Rcpp-0.8.5/Rcpp/inst/doc/unitTests-results/Rcpp-unitTests.txt | 72 +++----
Rcpp-0.8.5/Rcpp/inst/include/Rcpp/vector/Vector.h | 28 +--
Rcpp-0.8.5/Rcpp/man/CppClass-class.Rd | 2
Rcpp-0.8.5/Rcpp/man/CppObject-class.Rd | 2
Rcpp-0.8.5/Rcpp/man/Rcpp-package.Rd | 93 +---------
Rcpp-0.8.5/Rcpp/src/Date.cpp | 8
Rcpp-0.8.5/Rcpp/src/Makevars | 11 -
Rcpp-0.8.5/Rcpp/src/Makevars.win | 8
Rcpp-0.8.5/Rcpp/src/RObject.cpp | 17 -
21 files changed, 192 insertions(+), 241 deletions(-)
Title: Ornstein-Uhlenbeck models for phylogenetic comparative
hypotheses
Diff between ouch versions 2.6-2 dated 2010-06-24 and 2.7-1 dated 2010-07-26
Description: Fit and compare Ornstein-Uhlenbeck models for evolution
along a phylogenetic tree.
Author: Aaron A. King
Maintainer: Aaron A. King
DESCRIPTION | 10 +++++-----
R/hansen.R | 32 +++++++++++++++++---------------
inst/ChangeLog | 18 ++++++++++++++++++
3 files changed, 40 insertions(+), 20 deletions(-)
Title: Companion to Applied Regression
Diff between car versions 1.2-16 dated 2009-10-11 and 2.0-0 dated 2010-07-26
Description: This package accompanies J. Fox and S. Weisberg, An R
Companion to Applied Regression, Second Edition, Sage,
forthcoming.
Author: John Fox
Maintainer: John Fox
car-1.2-16/car/.project |only
car-1.2-16/car/R/Ask.R |only
car-1.2-16/car/R/Axes.R |only
car-1.2-16/car/R/Var.R |only
car-1.2-16/car/R/av.plots.R |only
car-1.2-16/car/R/box.cox.R |only
car-1.2-16/car/R/box.cox.powers.R |only
car-1.2-16/car/R/box.cox.var.R |only
car-1.2-16/car/R/box.tidwell.R |only
car-1.2-16/car/R/ceres.plots.R |only
car-1.2-16/car/R/cookd.R |only
car-1.2-16/car/R/cr.plots.R |only
car-1.2-16/car/R/durbin.watson.R |only
car-1.2-16/car/R/levene.test.R |only
car-1.2-16/car/R/leverage.plots.R |only
car-1.2-16/car/R/linear.hypothesis.R |only
car-1.2-16/car/R/n.bins.R |only
car-1.2-16/car/R/ncv.test.R |only
car-1.2-16/car/R/outlier.test.R |only
car-1.2-16/car/R/qq.plot.R |only
car-1.2-16/car/R/reg.line.R |only
car-1.2-16/car/R/scatterplot.matrix.R |only
car-1.2-16/car/R/spread.level.plot.R |only
car-1.2-16/car/data/Can.pop.rda |only
car-1.2-16/car/data/US.pop.rda |only
car-1.2-16/car/inst |only
car-1.2-16/car/man/Ask.Rd |only
car-1.2-16/car/man/Can.pop.Rd |only
car-1.2-16/car/man/Transformation.Axes.Rd |only
car-1.2-16/car/man/US.pop.Rd |only
car-1.2-16/car/man/Var.Rd |only
car-1.2-16/car/man/av.plots.Rd |only
car-1.2-16/car/man/box.cox.Rd |only
car-1.2-16/car/man/box.cox.powers.Rd |only
car-1.2-16/car/man/box.cox.var.Rd |only
car-1.2-16/car/man/box.tidwell.Rd |only
car-1.2-16/car/man/car-internal.Rd |only
car-1.2-16/car/man/ceres.plots.Rd |only
car-1.2-16/car/man/cookd.Rd |only
car-1.2-16/car/man/cr.plots.Rd |only
car-1.2-16/car/man/durbin.watson.Rd |only
car-1.2-16/car/man/levene.test.Rd |only
car-1.2-16/car/man/leverage.plots.Rd |only
car-1.2-16/car/man/linear.hypothesis.Rd |only
car-1.2-16/car/man/n.bins.Rd |only
car-1.2-16/car/man/ncv.test.Rd |only
car-1.2-16/car/man/outlier.test.Rd |only
car-1.2-16/car/man/qq.plot.Rd |only
car-1.2-16/car/man/reg.line.Rd |only
car-1.2-16/car/man/scatterplot.matrix.Rd |only
car-1.2-16/car/man/spread.level.plot.Rd |only
car-2.0-0/car/DESCRIPTION | 40 -
car-2.0-0/car/NAMESPACE | 306 ++++++----
car-2.0-0/car/NEWS |only
car-2.0-0/car/R/Anova.R | 858 +++++++++++++++++++-----------
car-2.0-0/car/R/Boxplot.R |only
car-2.0-0/car/R/Ellipse.R | 225 ++++---
car-2.0-0/car/R/TransformationAxes.R |only
car-2.0-0/car/R/avPlots.R |only
car-2.0-0/car/R/bootCase.R |only
car-2.0-0/car/R/boxCox.R |only
car-2.0-0/car/R/boxCoxVariable.R |only
car-2.0-0/car/R/boxTidwell.R |only
car-2.0-0/car/R/car-deprecated.R |only
car-2.0-0/car/R/carWeb.R |only
car-2.0-0/car/R/ceresPlots.R |only
car-2.0-0/car/R/coefTable.R |only
car-2.0-0/car/R/crPlots.R |only
car-2.0-0/car/R/deltaMethod.R |only
car-2.0-0/car/R/dfbetaPlots.R |only
car-2.0-0/car/R/durbinWatsonTest.R |only
car-2.0-0/car/R/hccm.R | 67 +-
car-2.0-0/car/R/infIndexPlot.R |only
car-2.0-0/car/R/influencePlot.R | 66 +-
car-2.0-0/car/R/invResPlot.R |only
car-2.0-0/car/R/invTranPlot.R |only
car-2.0-0/car/R/leveneTest.R |only
car-2.0-0/car/R/leveragePlots.R |only
car-2.0-0/car/R/linearHypothesis.R |only
car-2.0-0/car/R/logit.R | 28
car-2.0-0/car/R/marginalModelPlot.R |only
car-2.0-0/car/R/ncvTest.R |only
car-2.0-0/car/R/outlierTest.R |only
car-2.0-0/car/R/panel.car.R | 11
car-2.0-0/car/R/powerTransform.R |only
car-2.0-0/car/R/qqPlot.R |only
car-2.0-0/car/R/recode.R | 6
car-2.0-0/car/R/regLine.R |only
car-2.0-0/car/R/residualPlots.R |only
car-2.0-0/car/R/scatter3d.R |only
car-2.0-0/car/R/scatterplot.R | 510 ++++++++++-------
car-2.0-0/car/R/scatterplotMatrix.R |only
car-2.0-0/car/R/showLabels.R |only
car-2.0-0/car/R/sigmaHat.R |only
car-2.0-0/car/R/spreadLevelPlot.R |only
car-2.0-0/car/R/subsets.R | 95 +--
car-2.0-0/car/R/symbox.R | 38 -
car-2.0-0/car/R/utility-functions.R | 360 ++++++++----
car-2.0-0/car/R/vif.R | 63 +-
car-2.0-0/car/R/wcrossprod.R |only
car-2.0-0/car/R/which.names.R | 10
car-2.0-0/car/data/AMSsurvey.rda |only
car-2.0-0/car/data/CanPop.rda |only
car-2.0-0/car/data/Depredations.rda |only
car-2.0-0/car/data/Freedman.rda |binary
car-2.0-0/car/data/Highway1.rda |only
car-2.0-0/car/data/Prestige.rda |binary
car-2.0-0/car/data/Salaries.rda |only
car-2.0-0/car/data/Transact.rda |only
car-2.0-0/car/data/USPop.rda |only
car-2.0-0/car/data/Vocab.rda |binary
car-2.0-0/car/data/WeightLoss.rda |only
car-2.0-0/car/data/Wool.rda |only
car-2.0-0/car/man/AMSsurvey.Rd |only
car-2.0-0/car/man/Angell.Rd | 5
car-2.0-0/car/man/Anova.Rd | 85 ++
car-2.0-0/car/man/Anscombe.Rd | 6
car-2.0-0/car/man/Baumann.Rd | 13
car-2.0-0/car/man/Bfox.Rd | 7
car-2.0-0/car/man/Boxplot.Rd |only
car-2.0-0/car/man/Burt.Rd | 4
car-2.0-0/car/man/CanPop.Rd |only
car-2.0-0/car/man/Chile.Rd | 8
car-2.0-0/car/man/Chirot.Rd | 5
car-2.0-0/car/man/Contrasts.Rd | 13
car-2.0-0/car/man/Davis.Rd | 8
car-2.0-0/car/man/DavisThin.Rd | 7
car-2.0-0/car/man/Depredations.Rd |only
car-2.0-0/car/man/Duncan.Rd | 11
car-2.0-0/car/man/Ellipses.Rd | 50 +
car-2.0-0/car/man/Ericksen.Rd | 8
car-2.0-0/car/man/Florida.Rd | 4
car-2.0-0/car/man/Freedman.Rd | 7
car-2.0-0/car/man/Friendly.Rd | 13
car-2.0-0/car/man/Ginzberg.Rd | 5
car-2.0-0/car/man/Greene.Rd | 37 -
car-2.0-0/car/man/Guyer.Rd | 8
car-2.0-0/car/man/Hartnagel.Rd | 5
car-2.0-0/car/man/Highway1.Rd |only
car-2.0-0/car/man/Leinhardt.Rd | 10
car-2.0-0/car/man/Mandel.Rd | 5
car-2.0-0/car/man/Migration.Rd | 6
car-2.0-0/car/man/Moore.Rd | 8
car-2.0-0/car/man/Mroz.Rd | 7
car-2.0-0/car/man/OBrienKaiser.Rd | 4
car-2.0-0/car/man/Ornstein.Rd | 8
car-2.0-0/car/man/Pottery.Rd | 7
car-2.0-0/car/man/Prestige.Rd | 8
car-2.0-0/car/man/Robey.Rd | 5
car-2.0-0/car/man/SLID.Rd | 10
car-2.0-0/car/man/Sahlins.Rd | 5
car-2.0-0/car/man/Salaries.Rd |only
car-2.0-0/car/man/Soils.Rd | 12
car-2.0-0/car/man/States.Rd | 4
car-2.0-0/car/man/Transact.Rd |only
car-2.0-0/car/man/TransformationAxes.Rd |only
car-2.0-0/car/man/UN.Rd | 12
car-2.0-0/car/man/USPop.Rd |only
car-2.0-0/car/man/Vocab.Rd | 21
car-2.0-0/car/man/WeightLoss.Rd |only
car-2.0-0/car/man/Womenlf.Rd | 10
car-2.0-0/car/man/Wool.Rd |only
car-2.0-0/car/man/avPlots.Rd |only
car-2.0-0/car/man/bcPower.Rd |only
car-2.0-0/car/man/bootCase.Rd |only
car-2.0-0/car/man/boxCox.Rd |only
car-2.0-0/car/man/boxCoxVariable.Rd |only
car-2.0-0/car/man/boxTidwell.Rd |only
car-2.0-0/car/man/car-deprecated.Rd |only
car-2.0-0/car/man/car-package.Rd | 120 ----
car-2.0-0/car/man/carWeb.Rd |only
car-2.0-0/car/man/ceresPlots.Rd |only
car-2.0-0/car/man/coefTable.Rd |only
car-2.0-0/car/man/crPlots.Rd |only
car-2.0-0/car/man/deltaMethod.Rd |only
car-2.0-0/car/man/dfbetaPlots.Rd |only
car-2.0-0/car/man/durbinWatsonTest.Rd |only
car-2.0-0/car/man/estimateTransform.Rd |only
car-2.0-0/car/man/hccm.Rd | 29 -
car-2.0-0/car/man/infIndexPlot.Rd |only
car-2.0-0/car/man/influencePlot.Rd | 60 +-
car-2.0-0/car/man/invResPlot.Rd |only
car-2.0-0/car/man/invTranPlot.Rd |only
car-2.0-0/car/man/leveneTest.Rd |only
car-2.0-0/car/man/leveragePlots.Rd |only
car-2.0-0/car/man/linearHypothesis.Rd |only
car-2.0-0/car/man/logit.Rd | 11
car-2.0-0/car/man/marginalModelPlot.Rd |only
car-2.0-0/car/man/ncvTest.Rd |only
car-2.0-0/car/man/outlierTest.Rd |only
car-2.0-0/car/man/panel.car.Rd | 12
car-2.0-0/car/man/plot.powerTransform.Rd |only
car-2.0-0/car/man/powerTransform.Rd |only
car-2.0-0/car/man/qqPlot.Rd |only
car-2.0-0/car/man/recode.Rd | 19
car-2.0-0/car/man/regLine.Rd |only
car-2.0-0/car/man/residualPlots.Rd |only
car-2.0-0/car/man/scatter3d.Rd |only
car-2.0-0/car/man/scatterplot.Rd | 120 ++--
car-2.0-0/car/man/scatterplotMatrix.Rd |only
car-2.0-0/car/man/showLabels.Rd |only
car-2.0-0/car/man/sigmaHat.Rd |only
car-2.0-0/car/man/some.Rd | 8
car-2.0-0/car/man/spreadLevelPlot.Rd |only
car-2.0-0/car/man/subsets.Rd | 28
car-2.0-0/car/man/symbox.Rd | 37 -
car-2.0-0/car/man/testTransform.Rd |only
car-2.0-0/car/man/vif.Rd | 24
car-2.0-0/car/man/wcrossprod.Rd |only
car-2.0-0/car/man/which.names.Rd | 12
210 files changed, 2184 insertions(+), 1430 deletions(-)
Title: BioPhysConnectoR
Diff between BioPhysConnectoR versions 1.6-4 dated 2010-05-28 and 1.6-5 dated 2010-07-26
More information about BioPhysConnectoR at CRAN
Description: Utilities and functions to investigate the relation
between biomolecular structures, their interactions, and the
evolutionary information revealed in sequence alignments of
these molecules.
Author: Franziska Hoffgaard
Maintainer: Franziska Hoffgaard
DESCRIPTION | 8 ++---
R/get.mie.r | 20 +++++++-------
man/BioPhysConnectoR-package.Rd | 6 ++--
man/get.mie.Rd | 3 +-
src/meths.c | 56 ++++++++++++++++++++++++++++------------
5 files changed, 60 insertions(+), 33 deletions(-)
Permanent link
Title: Relevant Functions for Gene Expression Analysis, Especially in
Breast Cancer.
Diff between genefu versions 1.0.5 dated 2010-04-15 and 1.0.8 dated 2010-07-26
Description: R package providing various functions relevant for gene
expression analysis with emphasis on breast cancer.
Author: Benjamin Haibe-Kains, Gianluca Bontempi, John Quackenbush,
Christos Sotiriou
Maintainer: Benjamin Haibe-Kains
genefu-1.0.5/genefu/data/sbtgene.rda |only
genefu-1.0.5/genefu/data/sbtmod1.rda |only
genefu-1.0.5/genefu/data/sbtmod2.rda |only
genefu-1.0.5/genefu/man/sbtgene.Rd |only
genefu-1.0.5/genefu/man/sbtmod1.Rd |only
genefu-1.0.5/genefu/man/sbtmod2.Rd |only
genefu-1.0.8/genefu/DESCRIPTION | 9 +-
genefu-1.0.8/genefu/R/bimod.R | 6 +
genefu-1.0.8/genefu/R/genius.R | 2
genefu-1.0.8/genefu/R/intrinsic.cluster.R | 8 +-
genefu-1.0.8/genefu/R/intrinsic.cluster.predict.R | 58 ++++++++++++------
genefu-1.0.8/genefu/R/pik3cags.R |only
genefu-1.0.8/genefu/R/ps.cluster.R | 19 ++++-
genefu-1.0.8/genefu/R/strescR.R |only
genefu-1.0.8/genefu/R/subtype.cluster.R | 2
genefu-1.0.8/genefu/R/subtype.cluster.predict.R | 2
genefu-1.0.8/genefu/data/pam50.rda |binary
genefu-1.0.8/genefu/data/pam50.robust.rda |only
genefu-1.0.8/genefu/data/pam50.scale.rda |only
genefu-1.0.8/genefu/data/scmgene.rda |only
genefu-1.0.8/genefu/data/scmod1.rda |only
genefu-1.0.8/genefu/data/scmod2.rda |only
genefu-1.0.8/genefu/data/sig.pik3cags.rda |only
genefu-1.0.8/genefu/data/ssp2003.rda |binary
genefu-1.0.8/genefu/data/ssp2003.robust.rda |only
genefu-1.0.8/genefu/data/ssp2003.scale.rda |only
genefu-1.0.8/genefu/data/ssp2006.rda |binary
genefu-1.0.8/genefu/data/ssp2006.robust.rda |only
genefu-1.0.8/genefu/data/ssp2006.scale.rda |only
genefu-1.0.8/genefu/inst/extdata/loi2010_pik3cags.csv |only
genefu-1.0.8/genefu/man/bimod.Rd | 11 ++-
genefu-1.0.8/genefu/man/compare.proto.cor.Rd | 2
genefu-1.0.8/genefu/man/compute.proto.cor.meta.Rd | 2
genefu-1.0.8/genefu/man/genefu-package.Rd | 7 --
genefu-1.0.8/genefu/man/intrinsic.cluster.Rd | 2
genefu-1.0.8/genefu/man/intrinsic.cluster.predict.Rd | 2
genefu-1.0.8/genefu/man/pam50.Rd | 26 ++++++--
genefu-1.0.8/genefu/man/pik3cags.Rd |only
genefu-1.0.8/genefu/man/scmgene.Rd |only
genefu-1.0.8/genefu/man/scmod1.Rd |only
genefu-1.0.8/genefu/man/scmod2.Rd |only
genefu-1.0.8/genefu/man/sig.pik3cags.Rd |only
genefu-1.0.8/genefu/man/sig.score.Rd | 2
genefu-1.0.8/genefu/man/sig.tamr13.Rd | 2
genefu-1.0.8/genefu/man/ssp2003.Rd | 24 +++++--
genefu-1.0.8/genefu/man/ssp2006.Rd | 24 +++++--
genefu-1.0.8/genefu/man/strescR.Rd |only
genefu-1.0.8/genefu/man/subtype.cluster.Rd | 18 ++---
genefu-1.0.8/genefu/man/subtype.cluster.predict.Rd | 10 +--
49 files changed, 162 insertions(+), 76 deletions(-)
Title: Introduction to Probability and Statistics Using R
Diff between IPSUR versions 0.1-2 dated 2007-01-13 and 1.0 dated 2010-07-26
Description: This package contains the Sweave source code used to
generate IPSUR, an introductory probability and statistics
textbook, alongside other supplementary materials such as the
parsed R code for the book and data for the examples and
exercises. The book is released under the GNU Free
Documentation License.
Author: G. Jay Kerns
Maintainer: G. Jay Kerns
IPSUR-0.1-2/IPSUR/NAMESPACE |only
IPSUR-0.1-2/IPSUR/R/Recode.R |only
IPSUR-0.1-2/IPSUR/R/cluster.R |only
IPSUR-0.1-2/IPSUR/R/commander.R |only
IPSUR-0.1-2/IPSUR/R/data-menu.R |only
IPSUR-0.1-2/IPSUR/R/distributions-menu.R |only
IPSUR-0.1-2/IPSUR/R/distributions-plotDistributions-menu.R |only
IPSUR-0.1-2/IPSUR/R/distributions-sample.R |only
IPSUR-0.1-2/IPSUR/R/file-menu.R |only
IPSUR-0.1-2/IPSUR/R/graphs-menu.R |only
IPSUR-0.1-2/IPSUR/R/linePlot.R |only
IPSUR-0.1-2/IPSUR/R/model-menu.R |only
IPSUR-0.1-2/IPSUR/R/sciviews-specific.R |only
IPSUR-0.1-2/IPSUR/R/startup.R |only
IPSUR-0.1-2/IPSUR/R/statistics-dimensional-menu.R |only
IPSUR-0.1-2/IPSUR/R/statistics-means-menu.R |only
IPSUR-0.1-2/IPSUR/R/statistics-models-menu.R |only
IPSUR-0.1-2/IPSUR/R/statistics-nonparametric-menu.R |only
IPSUR-0.1-2/IPSUR/R/statistics-proportions-menu.R |only
IPSUR-0.1-2/IPSUR/R/statistics-summaries-menu.R |only
IPSUR-0.1-2/IPSUR/R/statistics-tables-menu.R |only
IPSUR-0.1-2/IPSUR/R/statistics-variances-menu.R |only
IPSUR-0.1-2/IPSUR/R/utilities.R |only
IPSUR-0.1-2/IPSUR/R/zIPSUR-Hist.R |only
IPSUR-0.1-2/IPSUR/R/zIPSUR-Misc.R |only
IPSUR-0.1-2/IPSUR/R/zIPSUR-barPlotSumm.r |only
IPSUR-0.1-2/IPSUR/R/zIPSUR-commander.R |only
IPSUR-0.1-2/IPSUR/R/zIPSUR-continuous-probability-menu.R |only
IPSUR-0.1-2/IPSUR/R/zIPSUR-discrete-probability-menu.R |only
IPSUR-0.1-2/IPSUR/R/zIPSUR-distributions-sample.R |only
IPSUR-0.1-2/IPSUR/R/zIPSUR-enterTableProportionsTest.r |only
IPSUR-0.1-2/IPSUR/R/zIPSUR-graphs-menu.R |only
IPSUR-0.1-2/IPSUR/R/zIPSUR-linePlot.R |only
IPSUR-0.1-2/IPSUR/R/zIPSUR-multiSamplePropTest.r |only
IPSUR-0.1-2/IPSUR/R/zIPSUR-power.R |only
IPSUR-0.1-2/IPSUR/R/zIPSUR-simulate-probability-menu.R |only
IPSUR-0.1-2/IPSUR/R/zIPSUR-startup.R |only
IPSUR-0.1-2/IPSUR/R/zIPSUR-statistics-summaries-menu.R |only
IPSUR-0.1-2/IPSUR/R/zIPSUR-statistics-tables-menu.R |only
IPSUR-0.1-2/IPSUR/data/BloodPressure.txt |only
IPSUR-0.1-2/IPSUR/data/FeedingTimes.txt |only
IPSUR-0.1-2/IPSUR/data/RcmdrTestDrive.txt |only
IPSUR-0.1-2/IPSUR/inst/CHANGES |only
IPSUR-0.1-2/IPSUR/inst/FEATURES |only
IPSUR-0.1-2/IPSUR/inst/doc/Getting-Started-with-the-Rcmdr.pdf |only
IPSUR-0.1-2/IPSUR/inst/doc/RcmdrTestDrive-story.pdf |only
IPSUR-0.1-2/IPSUR/inst/etc |only
IPSUR-0.1-2/IPSUR/inst/po |only
IPSUR-0.1-2/IPSUR/man/BloodPressure.Rd |only
IPSUR-0.1-2/IPSUR/man/Commander.Rd |only
IPSUR-0.1-2/IPSUR/man/Compute.Rd |only
IPSUR-0.1-2/IPSUR/man/Confint.Rd |only
IPSUR-0.1-2/IPSUR/man/FeedingTimes.Rd |only
IPSUR-0.1-2/IPSUR/man/Hist.Rd |only
IPSUR-0.1-2/IPSUR/man/IPSURgetAnswer.Rd |only
IPSUR-0.1-2/IPSUR/man/IPSURweb.Rd |only
IPSUR-0.1-2/IPSUR/man/KMeans.Rd |only
IPSUR-0.1-2/IPSUR/man/Rcmdr-package.Rd |only
IPSUR-0.1-2/IPSUR/man/Rcmdr.Utilities.Rd |only
IPSUR-0.1-2/IPSUR/man/Rcmdr.sciviews-specific.Rd |only
IPSUR-0.1-2/IPSUR/man/RcmdrPager.Rd |only
IPSUR-0.1-2/IPSUR/man/RcmdrTestDrive.rd |only
IPSUR-0.1-2/IPSUR/man/Recode.Rd |only
IPSUR-0.1-2/IPSUR/man/Scatter3DDialog.Rd |only
IPSUR-0.1-2/IPSUR/man/assignCluster.Rd |only
IPSUR-0.1-2/IPSUR/man/bin.var.Rd |only
IPSUR-0.1-2/IPSUR/man/birthday.ipsur.Rd |only
IPSUR-0.1-2/IPSUR/man/colPercents.Rd |only
IPSUR-0.1-2/IPSUR/man/generalizedLinearModel.Rd |only
IPSUR-0.1-2/IPSUR/man/hierarchicalCluster.Rd |only
IPSUR-0.1-2/IPSUR/man/linearModel.Rd |only
IPSUR-0.1-2/IPSUR/man/numSummary.Rd |only
IPSUR-0.1-2/IPSUR/man/partial.cor.Rd |only
IPSUR-0.1-2/IPSUR/man/plotMeans.Rd |only
IPSUR-0.1-2/IPSUR/man/reliability.Rd |only
IPSUR-0.1-2/IPSUR/man/scatter3d.Rd |only
IPSUR-0.1-2/IPSUR/man/stem.leaf.Rd |only
IPSUR-0.1-2/IPSUR/po |only
IPSUR-1.0/IPSUR/DESCRIPTION | 39 +++---
IPSUR-1.0/IPSUR/LICENSE |only
IPSUR-1.0/IPSUR/R/clt.R |only
IPSUR-1.0/IPSUR/R/ipsur.R |only
IPSUR-1.0/IPSUR/R/plothtest.R |only
IPSUR-1.0/IPSUR/data/IPSUR.RData |only
IPSUR-1.0/IPSUR/inst/IPSUR.R |only
IPSUR-1.0/IPSUR/inst/doc/IPSUR.Rnw |only
IPSUR-1.0/IPSUR/inst/doc/IPSUR.bib |only
IPSUR-1.0/IPSUR/inst/doc/IPSUR.pdf |only
IPSUR-1.0/IPSUR/man/IPSUR-data.Rd |only
IPSUR-1.0/IPSUR/man/IPSUR-package.Rd | 64 ++++------
IPSUR-1.0/IPSUR/man/IPSUR.Utilities.Rd | 39 ------
IPSUR-1.0/IPSUR/man/clt.Rd |only
IPSUR-1.0/IPSUR/man/plothtest.Rd |only
93 files changed, 59 insertions(+), 83 deletions(-)
Title: Cambial Activity and wood formation data processing,
visualisation and analysis using R
Diff between CAVIAR versions 0.1-0 dated 2010-03-11 and 1.1-0 dated 2010-07-26
Description: Allows processing, visualisation and analysis of data
coming from cambial activity and wood formation monitoring
studies.
Author: Cyrille Rathgeber
Maintainer: Cyrille Rathgeber
CAVIAR-0.1-0/CAVIAR/inst/CITATION.rtf |only
CAVIAR-1.1-0/CAVIAR/DESCRIPTION | 8 ++---
CAVIAR-1.1-0/CAVIAR/R/averageRF.R |only
CAVIAR-1.1-0/CAVIAR/R/computeBootstrapTest.R | 6 ++++
CAVIAR-1.1-0/CAVIAR/R/computeCriticalDates.R | 35 ++++++++++++++++++------
CAVIAR-1.1-0/CAVIAR/R/computeRCN.R |only
CAVIAR-1.1-0/CAVIAR/R/fitGompertz.R |only
CAVIAR-1.1-0/CAVIAR/inst/CITATION |only
CAVIAR-1.1-0/CAVIAR/man/AMA2006.Rd | 8 ++++-
CAVIAR-1.1-0/CAVIAR/man/CAVIAR-package.Rd | 28 ++++++++++---------
CAVIAR-1.1-0/CAVIAR/man/averageRF.Rd |only
CAVIAR-1.1-0/CAVIAR/man/computeBootstrapTest.Rd | 6 ++--
CAVIAR-1.1-0/CAVIAR/man/computeCriticalDates.Rd | 8 ++---
CAVIAR-1.1-0/CAVIAR/man/computeRCN.Rd |only
CAVIAR-1.1-0/CAVIAR/man/fitGompertz.Rd |only
CAVIAR-1.1-0/CAVIAR/man/plotWoodCalendar.Rd | 6 ++--
16 files changed, 69 insertions(+), 36 deletions(-)
Title: Multivariate, Interactive Visualization
Diff between mvgraph versions 1.1 dated 2009-05-25 and 1.2 dated 2010-07-26
Description: This package offers different possibilities to visualize
multivariate data
Author: Moritz Gschwandtner
Maintainer: Moritz Gschwandtner
DESCRIPTION | 8 ++++----
configure | 7 +++++--
src/Makevars | 4 ++--
src/Makevars.in | 2 +-
src/moc_groupwidget.cpp | 20 +++++++++++++-------
src/moc_icondialog.cpp | 18 ++++++++++++------
src/moc_iconview.cpp | 20 +++++++++++++-------
src/moc_identifywidget.cpp | 20 +++++++++++++-------
src/moc_infowidget.cpp | 20 +++++++++++++-------
src/moc_legendwidget.cpp | 18 ++++++++++++------
src/moc_multiDialog.cpp | 20 +++++++++++++-------
src/moc_rotatewidget.cpp | 20 +++++++++++++-------
src/moc_selectdialog.cpp | 20 +++++++++++++-------
src/moc_spinview.cpp | 20 +++++++++++++-------
src/moc_spinwidget.cpp | 20 +++++++++++++-------
15 files changed, 153 insertions(+), 84 deletions(-)
Title: ODBC Database Access
Diff between RODBC versions 1.3-1 dated 2009-10-12 and 1.3-2 dated 2010-07-26
Description: An ODBC database interface
Author: Brian Ripley, and from 1999 to Oct 2002 Michael Lapsley
Maintainer: Brian Ripley
ChangeLog | 9 +++++
DESCRIPTION | 8 ++--
R/win.R | 6 +++
inst/doc/RODBC.Rnw | 57 ++++++++++++++++++++-------------
inst/doc/RODBC.pdf |binary
inst/po/de |only
inst/po/en@quot/LC_MESSAGES/R-RODBC.mo |binary
inst/po/en@quot/LC_MESSAGES/RODBC.mo |binary
man/odbcConnect.Rd | 24 +++++++++----
po/R-RODBC.pot | 7 ++--
po/R-de.po |only
po/R-en@quot.po | 9 +++--
po/RODBC.pot | 46 +++++++++++++-------------
po/de.po |only
po/en@quot.po | 54 +++++++++++++++----------------
src/RODBC.c | 1
16 files changed, 133 insertions(+), 88 deletions(-)
Title: Bayesian inference for exponential random graph models
Diff between Bergm versions 1.2 dated 2010-06-01 and 1.3 dated 2010-07-26
Description: Functions implementing Bayesian estimation for exponential
random graph models via exchange algorithm
Author: Alberto Caimo and Nial Friel
Maintainer: Alberto Caimo
DESCRIPTION | 8 +--
R/bergm.R | 125 +++++++++++++++++++++++++++++---------------------------
R/mcmc.output.R | 2
man/bergm.Rd | 24 +++++-----
4 files changed, 82 insertions(+), 77 deletions(-)
Title: Rmetrics - Financial Time Series Objects
Diff between timeSeries versions 2120.88 dated 2010-07-06 and 2120.89 dated 2010-07-26
Description: Environment for teaching "Financial Engineering and
Computational Finance"
Author: Diethelm Wuertz and Yohan Chalabi
Maintainer: Rmetrics Core Team
ChangeLog | 17 +++++++
DESCRIPTION | 10 ++--
R/base-apply.R | 18 ++++---
R/base-cbind.R | 3 -
R/base-diff.R | 13 ++---
R/base-rowCumsums.R | 79 ++++++++-------------------------
R/fin-runlengths.R | 3 +
R/methods-mathOps.R | 33 ++++++--------
R/stats-lag.R | 20 +++-----
R/stats-na.omit.R | 110 +++++++++++------------------------------------
R/timeSeries-finCenter.R | 15 +-----
11 files changed, 119 insertions(+), 202 deletions(-)
Title: Rmetrics - Chronological and Calendarical Objects
Diff between timeDate versions 2120.89 dated 2010-07-06 and 2120.90 dated 2010-07-26
Description: Environment for teaching "Financial Engineering and
Computational Finance"
Author: Diethelm Wuertz and Yohan Chalabi with contributions from
Martin Maechler, Joe W. Byers, and others
Maintainer: Rmetrics Core Team
timeDate-2120.89/timeDate/inst/DocCopying.pdf |only
timeDate-2120.90/timeDate/ChangeLog | 13 +++++++++++++
timeDate-2120.90/timeDate/DESCRIPTION | 10 +++++-----
3 files changed, 18 insertions(+), 5 deletions(-)
Title: Modelling and analysis of real-time PCR data
Diff between qpcR versions 1.2-8 dated 2010-06-18 and 1.2-9 dated 2010-07-26
Description: Model fitting, optimal model selection and calculation of
various features that are essential in the analysis of
quantitative real-time polymerase chain reaction (qPCR).
Author: Andrej-Nikolai Spiess
Maintainer: Andrej-Nikolai Spiess
DESCRIPTION | 6 +++---
R/Rsq.R | 13 +++++++++----
R/modlist.r | 6 +++++-
R/pcrfit.r | 13 +++++++++----
R/ratiocalc.r | 6 +++---
R/sliwin.R | 4 +++-
data/qpcR_functions.rda |binary
man/Rsq.Rd | 4 +++-
man/pcrfit.Rd | 5 +++--
man/qpcR_functions.rd | 6 ++++++
10 files changed, 44 insertions(+), 19 deletions(-)
Title: Support package for aroma.affymetrix et al.
Diff between aroma.core versions 1.6.0 dated 2010-05-16 and 1.7.0 dated 2010-07-26
Description: This package is a private support package for
aroma.affymetrix et al. The methods and classes of this
package are independent of platform. Its API is in alpha and
beta stage.
Author: Henrik Bengtsson
Maintainer: Henrik Bengtsson
DESCRIPTION | 12 -
R/AromaTabularBinaryFile.R | 35 ++-
R/AromaUnitFracBCnBinarySet.R | 6
R/AromaUnitSignalBinarySet.writeDataFrame.R | 6
R/AromaUnitTotalCnBinarySet.R | 7
R/ChromosomalModel.R | 76 +------
R/CopyNumberRegions.EXT.R |only
R/CopyNumberRegions.R | 33 +++
R/RawGenomicSignals.R | 47 ++++
R/as.NnnImage.matrix.R | 9
R/doCBS.CopyNumberDataSet.R | 46 ----
R/doCBS.CopyNumberDataSetTuple.R |only
R/doCBS.character.R | 99 +++++++++-
R/getAromaFullNameTranslatorSet.R |only
incl/999.missingdocs.txt | 18 +
inst/NEWS | 57 +++++
inst/bin/nohupR | 8
inst/testScripts/system/CnSegmentation/segmentByPruneCBS.R |only
inst/testScripts/system/CnSegmentation/test20100719,SEG,pruneCalls.Rex |only
man/AromaCellTabularBinaryFile.Rd | 2
man/AromaMicroarrayDataFile.Rd | 2
man/AromaMicroarrayDataSet.Rd | 5
man/AromaMicroarrayDataSetTuple.Rd | 2
man/AromaMicroarrayTabularBinaryFile.Rd | 2
man/AromaTabularBinaryFile.Rd | 2
man/AromaTabularBinarySet.Rd | 4
man/AromaUnitCallFile.Rd | 2
man/AromaUnitCallSet.Rd | 6
man/AromaUnitFracBCnBinaryFile.Rd | 2
man/AromaUnitFracBCnBinarySet.Rd | 7
man/AromaUnitGenotypeCallFile.Rd | 2
man/AromaUnitGenotypeCallSet.Rd | 6
man/AromaUnitSignalBinaryFile.Rd | 2
man/AromaUnitSignalBinarySet.Rd | 5
man/AromaUnitTabularBinaryFile.Rd | 2
man/AromaUnitTotalCnBinaryFile.Rd | 2
man/AromaUnitTotalCnBinarySet.Rd | 7
man/AromaUnitTypesFile.Rd | 2
man/Non-documented_objects.Rd | 27 ++
man/RawAlleleBFractions.Rd | 2
man/RawCopyNumbers.Rd | 2
man/RawGenomicSignals.Rd | 1
man/RawMirroredAlleleBFractions.Rd | 2
man/RawSequenceReads.Rd | 2
man/SegmentedAlleleBFractions.Rd | 2
man/SegmentedCopyNumbers.Rd | 2
46 files changed, 397 insertions(+), 166 deletions(-)
Title: Analysis of large Affymetrix microarray data sets
Diff between aroma.affymetrix versions 1.6.0 dated 2010-05-16 and 1.7.0 dated 2010-07-26
More information about aroma.affymetrix at CRAN
Description: This package implements classes for files and sets of
files for various Affymetrix file formats, e.g.
AffymetrixCdfFile, AffymetrixCelFile, and AffymetrixCelSet.
These are designed to be memory efficient but still being fast.
The idea is to keep all data on file and only read data into
memory when needed. Clever caching mechanisms are used to
minimize the overhead of data IO. All of the above is hidden
in the package API and for the developer (and the end user),
the data is queried as if it lives in memory. With this design
it is only the diskspace that limits the number of arrays that
can be analyzed.
Author: Henrik Bengtsson
Maintainer: Henrik Bengtsson
aroma.affymetrix-1.6.0/aroma.affymetrix/R/Env2Cdf.R |only
aroma.affymetrix-1.6.0/aroma.affymetrix/R/PdInfo2Cdf.R |only
aroma.affymetrix-1.7.0/aroma.affymetrix/DESCRIPTION | 18
aroma.affymetrix-1.7.0/aroma.affymetrix/R/999.AromaAffymetrix.R | 6
aroma.affymetrix-1.7.0/aroma.affymetrix/R/AffymetrixCdfFile.PLOT.R | 9
aroma.affymetrix-1.7.0/aroma.affymetrix/R/AffymetrixCelSet.R | 333 ----------
aroma.affymetrix-1.7.0/aroma.affymetrix/R/AffymetrixCelSet.getAverageFile.R |only
aroma.affymetrix-1.7.0/aroma.affymetrix/R/AffymetrixProbeTabFile.R | 7
aroma.affymetrix-1.7.0/aroma.affymetrix/R/ChipEffectSet.R | 22
aroma.affymetrix-1.7.0/aroma.affymetrix/R/doCRMAv1.R | 20
aroma.affymetrix-1.7.0/aroma.affymetrix/R/doCRMAv2.R | 7
aroma.affymetrix-1.7.0/aroma.affymetrix/R/doRMA.R |only
aroma.affymetrix-1.7.0/aroma.affymetrix/R/env2Cdf.R |only
aroma.affymetrix-1.7.0/aroma.affymetrix/R/pdInfo2Cdf.R |only
aroma.affymetrix-1.7.0/aroma.affymetrix/incl/999.missingdocs.txt | 7
aroma.affymetrix-1.7.0/aroma.affymetrix/inst/NEWS | 57 +
aroma.affymetrix-1.7.0/aroma.affymetrix/inst/annotationData/dataSets |only
aroma.affymetrix-1.7.0/aroma.affymetrix/inst/annotationData/samples |only
aroma.affymetrix-1.7.0/aroma.affymetrix/inst/downloadScripts |only
aroma.affymetrix-1.7.0/aroma.affymetrix/inst/testScripts/system/chipTypes/GenomeWideSNP_6/test20090211,6.0,CRMAv2,TotalFreqB.R | 2
aroma.affymetrix-1.7.0/aroma.affymetrix/inst/testScripts/system/chipTypes/GenomeWideSNP_6/test20090322,6.0,CRMAv2,GCN.R | 2
aroma.affymetrix-1.7.0/aroma.affymetrix/inst/testScripts/system/chipTypes/GenomeWideSNP_6/test20100422,6.0,doCRMAv2.R | 15
aroma.affymetrix-1.7.0/aroma.affymetrix/inst/testScripts/system/chipTypes/Mapping10K_Xba142/test20070726c,10K,CN,segmentation.R | 2
aroma.affymetrix-1.7.0/aroma.affymetrix/inst/testScripts/system/chipTypes/Mapping10K_Xba142/test20081204,10K,CRMAv2,ASCN.R | 2
aroma.affymetrix-1.7.0/aroma.affymetrix/inst/testScripts/system/chipTypes/Mapping10K_Xba142/test20081217,10K,CRMAv2,ASCN,1array.R | 2
aroma.affymetrix-1.7.0/aroma.affymetrix/inst/testScripts/system/chipTypes/Mapping10K_Xba142/test20090211,10K,CRMAv2,TotalFreqB.R | 2
aroma.affymetrix-1.7.0/aroma.affymetrix/inst/testScripts/system/chipTypes/Mapping10K_Xba142/test20100620,10K,doCRMAv2,ASCN.R |only
aroma.affymetrix-1.7.0/aroma.affymetrix/inst/testScripts/system/chipTypes/Mapping250K_Nsp,Sty/test20090116,250K,TumorNormal,ASCN.R | 4
aroma.affymetrix-1.7.0/aroma.affymetrix/inst/testScripts/system/chipTypes/Mapping250K_Nsp,Sty/test20090117,250K,TumorNormal,ASCN,pairy.R | 2
aroma.affymetrix-1.7.0/aroma.affymetrix/inst/testScripts/system/chipTypes/Mapping50K_Hind240,Xba240/test20100525,100K,CRMA,exportCNs.R |only
aroma.affymetrix-1.7.0/aroma.affymetrix/inst/testScripts/system/chipTypes/Mapping50K_Hind240,Xba240/test20100525,100K,doCBS,tuple.R |only
aroma.affymetrix-1.7.0/aroma.affymetrix/inst/testScripts/system/chipTypes/Mapping50K_Hind240,Xba240/test20100526,100K,tuple,fnt.R |only
aroma.affymetrix-1.7.0/aroma.affymetrix/man/AffymetrixCdfFile.Rd | 2
aroma.affymetrix-1.7.0/aroma.affymetrix/man/AffymetrixCelFile.Rd | 2
aroma.affymetrix-1.7.0/aroma.affymetrix/man/AffymetrixCelSet.Rd | 7
aroma.affymetrix-1.7.0/aroma.affymetrix/man/AffymetrixCelSetTuple.Rd | 2
aroma.affymetrix-1.7.0/aroma.affymetrix/man/AffymetrixCnChpSet.Rd | 6
aroma.affymetrix-1.7.0/aroma.affymetrix/man/AffymetrixFile.Rd | 2
aroma.affymetrix-1.7.0/aroma.affymetrix/man/AffymetrixFileSet.Rd | 6
aroma.affymetrix-1.7.0/aroma.affymetrix/man/AffymetrixProbeTabFile.Rd | 2
aroma.affymetrix-1.7.0/aroma.affymetrix/man/AromaChipTypeAnnotationFile.Rd | 2
aroma.affymetrix-1.7.0/aroma.affymetrix/man/ChipEffectFile.Rd | 2
aroma.affymetrix-1.7.0/aroma.affymetrix/man/ChipEffectSet.Rd | 8
aroma.affymetrix-1.7.0/aroma.affymetrix/man/CnChipEffectFile.Rd | 2
aroma.affymetrix-1.7.0/aroma.affymetrix/man/CnChipEffectSet.Rd | 8
aroma.affymetrix-1.7.0/aroma.affymetrix/man/CnProbeAffinityFile.Rd | 2
aroma.affymetrix-1.7.0/aroma.affymetrix/man/CnagCfhFile.Rd | 2
aroma.affymetrix-1.7.0/aroma.affymetrix/man/CnagCfhSet.Rd | 4
aroma.affymetrix-1.7.0/aroma.affymetrix/man/CrlmmParametersFile.Rd | 6
aroma.affymetrix-1.7.0/aroma.affymetrix/man/CrlmmParametersSet.Rd | 6
aroma.affymetrix-1.7.0/aroma.affymetrix/man/DChipCdfBinFile.Rd | 2
aroma.affymetrix-1.7.0/aroma.affymetrix/man/DChipDcpFile.Rd | 2
aroma.affymetrix-1.7.0/aroma.affymetrix/man/DChipDcpSet.Rd | 6
aroma.affymetrix-1.7.0/aroma.affymetrix/man/DChipGenomeInformation.Rd | 2
aroma.affymetrix-1.7.0/aroma.affymetrix/man/DChipSnpInformation.Rd | 2
aroma.affymetrix-1.7.0/aroma.affymetrix/man/ExonChipEffectFile.Rd | 2
aroma.affymetrix-1.7.0/aroma.affymetrix/man/ExonChipEffectSet.Rd | 8
aroma.affymetrix-1.7.0/aroma.affymetrix/man/ExonProbeAffinityFile.Rd | 2
aroma.affymetrix-1.7.0/aroma.affymetrix/man/FirmaFile.Rd | 2
aroma.affymetrix-1.7.0/aroma.affymetrix/man/FirmaSet.Rd | 8
aroma.affymetrix-1.7.0/aroma.affymetrix/man/GenomeInformation.Rd | 2
aroma.affymetrix-1.7.0/aroma.affymetrix/man/Non-documented_objects.Rd | 11
aroma.affymetrix-1.7.0/aroma.affymetrix/man/ParameterCelFile.Rd | 2
aroma.affymetrix-1.7.0/aroma.affymetrix/man/ParameterCelSet.Rd | 8
aroma.affymetrix-1.7.0/aroma.affymetrix/man/ProbeAffinityFile.Rd | 2
aroma.affymetrix-1.7.0/aroma.affymetrix/man/QualityAssessmentFile.Rd | 2
aroma.affymetrix-1.7.0/aroma.affymetrix/man/QualityAssessmentSet.Rd | 8
aroma.affymetrix-1.7.0/aroma.affymetrix/man/ResidualFile.Rd | 2
aroma.affymetrix-1.7.0/aroma.affymetrix/man/ResidualSet.Rd | 8
aroma.affymetrix-1.7.0/aroma.affymetrix/man/SnpChipEffectFile.Rd | 2
aroma.affymetrix-1.7.0/aroma.affymetrix/man/SnpChipEffectSet.Rd | 8
aroma.affymetrix-1.7.0/aroma.affymetrix/man/SnpInformation.Rd | 2
aroma.affymetrix-1.7.0/aroma.affymetrix/man/SnpProbeAffinityFile.Rd | 2
aroma.affymetrix-1.7.0/aroma.affymetrix/man/UgpGenomeInformation.Rd | 2
aroma.affymetrix-1.7.0/aroma.affymetrix/man/WeightsFile.Rd | 2
aroma.affymetrix-1.7.0/aroma.affymetrix/man/WeightsSet.Rd | 8
aroma.affymetrix-1.7.0/aroma.affymetrix/man/getAverageFile.AffymetrixCelSet.Rd | 3
aroma.affymetrix-1.7.0/aroma.affymetrix/man/pdInfo2Cdf.Rd |only
78 files changed, 273 insertions(+), 427 deletions(-)
Permanent link
Title: Various programming utilities
Diff between R.utils versions 1.4.3 dated 2010-07-03 and 1.4.4 dated 2010-07-26
Description: This package provides utility classes and methods useful
when programming in R and developing R packages.
Author: Henrik Bengtsson
Maintainer: Henrik Bengtsson
DESCRIPTION | 10 +++++-----
R/arrayIndex.R | 24 +++++++++++++++++-------
R/getCommonPrefix.R | 6 +++++-
incl/getAbsolutePath.Rex |only
inst/NEWS | 8 +++++++-
man/arrayIndex.Rd | 4 +++-
6 files changed, 37 insertions(+), 15 deletions(-)
Title: Spatial Point Pattern analysis, model-fitting, simulation, tests
Diff between spatstat versions 1.19-3 dated 2010-06-17 and 1.20-1 dated 2010-07-26
Description: A package for analysing spatial data, mainly Spatial Point
Patterns, including multitype/marked points and spatial
covariates, in any two-dimensional spatial region. Also
supports three-dimensional point patterns, and space-time point
patterns in any number of dimensions. Contains functions for
plotting spatial data, exploratory data analysis,
model-fitting, simulation, spatial sampling, model diagnostics,
and formal inference. Data types include point patterns, line
segment patterns, spatial windows, pixel images and
tessellations. Point process models can be fitted to point
pattern data. Cluster type models are fitted by the method of
minimum contrast. Very general Gibbs point process models can
be fitted to point pattern data using a function ppm similar to
lm or glm. Models may include dependence on covariates,
interpoint interaction and dependence on marks. Fitted models
can be simulated automatically. Also provides facilities for
formal inference (such as chi-squared tests) and model
diagnostics (including simulation envelopes, residuals,
residual plots and Q-Q plots).
Author: Adrian Baddeley
Maintainer: Adrian Baddeley
DESCRIPTION | 34 ++---
NEWS | 100 +++++++++++++++
R/areainter.R | 15 +-
R/as.im.R | 33 +++--
R/badgey.R | 51 +++++++-
R/deltametric.R | 8 +
R/density.psp.R | 2
R/dg.S | 56 ++++++++
R/dgs.R |only
R/distbdry.S | 3
R/eval.im.R | 11 -
R/fiksel.R | 59 +++++++++
R/geyer.S | 85 +++++++++++++
R/hardcore.R | 22 +++
R/images.R | 65 ++++------
R/infline.R | 4
R/inforder.family.R | 13 --
R/mpl.R | 282 ++++++++++++++++++++++++++++++++-------------
R/options.R | 5
R/ord.family.S | 12 -
R/pairsat.family.S | 46 ++++---
R/pairwise.family.S | 29 +++-
R/plot.im.R | 4
R/plot.owin.S | 6
R/ppmclass.R | 4
R/ppp.S | 10 +
R/predict.ppm.S | 65 +++-------
R/profilepl.R | 11 +
R/psp.R | 4
R/quadclass.S | 12 +
R/quadratcount.R | 13 +-
R/random.S | 6
R/randommk.R | 4
R/rmhmodel.ppm.R | 13 +-
R/strauss.S | 137 +++++++++++++++------
R/strausshard.S | 22 +++
R/summary.im.R | 4
R/tess.R | 16 +-
R/weights.S | 9 -
inst/doc/shapefiles.pdf |binary
man/DiggleGatesStibbard.Rd |only
man/Hardcore.Rd | 4
man/im.Rd | 56 +++++---
man/internal.Rd | 40 +++++-
man/nncross.Rd | 2
man/ppm.Rd | 2
man/rmhmodel.default.Rd | 15 +-
man/rmhmodel.ppm.Rd | 14 +-
man/spatstat-package.Rd | 7 -
src/Ediggatsti.c |only
src/Ediggra.c |only
src/Efiksel.c |only
src/Egeyer.c |only
src/Estrauss.c |only
src/areaint.c | 99 ++++++++-------
src/badgey.c | 151 +++++++++++++-----------
src/dgs.c | 47 ++++---
src/diggra.c | 68 ++++++----
src/fiksel.c | 67 ++++++----
src/geyer.c | 94 ++++++++-------
src/hardcore.c | 39 +++---
src/lennard.c | 94 +++++++++++----
src/lookup.c | 94 ++++++++-------
src/methas.c | 19 +--
src/methas.h | 15 +-
src/sftcr.c | 40 +++---
src/straush.c | 58 +++++----
src/straushm.c | 101 ++++++++--------
src/strauss.c | 50 ++++---
src/straussm.c | 80 +++++++-----
tests/fastgeyer.R |only
71 files changed, 1681 insertions(+), 850 deletions(-)
Title: Base package for phylogenetic structures and comparative data
Diff between phylobase versions 0.6.0 dated 2010-07-24 and 0.6.1 dated 2010-07-26
Description: Provides a base S4 class for comparative methods,
incorporating one or more trees and trait data
Author: R Hackathon et al. (alphabetically: Ben Bolker, Marguerite
Butler, Peter Cowan, Damien de Vienne, Dirk Eddelbuettel, Mark
Holder, Thibaut Jombart, Steve Kembel, Francois Michonneau,
David Orme, Brian O'Meara, Emmanuel Paradis, Jim Regetz,
Derrick Zwickl)
Maintainer: Ben Bolker
DESCRIPTION | 8 ++++----
NEWS | 8 ++++++++
inst/doc/developer.pdf |binary
inst/doc/phylobase.pdf |binary
src/ncl/nxsstring.h | 6 +++---
src/nxsmultiformat.cpp | 27 ++++++++++++++++-----------
src/nxsstring.cpp | 4 ++--
7 files changed, 33 insertions(+), 20 deletions(-)
Title: Testing Linear Regression Models
Diff between lmtest versions 0.9-26 dated 2009-12-07 and 0.9-27 dated 2010-07-26
Description: A collection of tests, data sets, and examples for
diagnostic checking in linear regression models. Furthermore,
some generic tools for inference in parametric models are
provided.
Author: Torsten Hothorn, Achim Zeileis, Giovanni Millo, David Mitchell
Maintainer: Achim Zeileis
DESCRIPTION | 14 ++++++++------
NEWS | 6 ++++++
R/grangertest.R | 2 +-
inst/doc/lmtest-intro.pdf |binary
4 files changed, 15 insertions(+), 7 deletions(-)
Title: Utilities for working with formulas, expressions, calls and
other R objects
Diff between formula.tools versions 0.20.0 dated 2010-05-03 and 1.0.1 dated 2010-07-26
Description: This package provides a number of useful utilities for
working with formulas, expressions, calls, names, symbols and
other R objects. This package was designed to greatly
facilitate symbolic manupulation using native R objects.
Author: Christopher Brown
Maintainer: Christopher Brown
formula.tools-0.20.0/formula.tools/R/not.in.R |only
formula.tools-0.20.0/formula.tools/R/operators.R |only
formula.tools-0.20.0/formula.tools/R/sysdata.rda |only
formula.tools-0.20.0/formula.tools/man/not.in.Rd |only
formula.tools-0.20.0/formula.tools/man/operators.Rd |only
formula.tools-1.0.1/formula.tools/ChangeLog | 49 +++++
formula.tools-1.0.1/formula.tools/DESCRIPTION | 17 -
formula.tools-1.0.1/formula.tools/NAMESPACE | 2
formula.tools-1.0.1/formula.tools/R/get.vars.R | 57 +-----
formula.tools-1.0.1/formula.tools/R/invert.R | 18 +
formula.tools-1.0.1/formula.tools/R/is.one.sided.R | 73 ++++---
formula.tools-1.0.1/formula.tools/R/lhs.R | 75 +++----
formula.tools-1.0.1/formula.tools/R/lhs.vars.R | 6
formula.tools-1.0.1/formula.tools/R/op.R | 71 +++++--
formula.tools-1.0.1/formula.tools/R/op.type.R | 18 +
formula.tools-1.0.1/formula.tools/R/rhs.R | 94 +++++-----
formula.tools-1.0.1/formula.tools/R/rhs.vars.R | 8
formula.tools-1.0.1/formula.tools/R/terms.R | 6
formula.tools-1.0.1/formula.tools/R/which.class.R | 3
formula.tools-1.0.1/formula.tools/R/zzz.R | 38 ++--
formula.tools-1.0.1/formula.tools/TODO | 12 +
formula.tools-1.0.1/formula.tools/man/formula.parts-methods.Rd | 20 +-
formula.tools-1.0.1/formula.tools/man/formula.tools-package.Rd | 12 -
formula.tools-1.0.1/formula.tools/man/is.one.sided.Rd | 5
formula.tools-1.0.1/formula.tools/tests |only
25 files changed, 336 insertions(+), 248 deletions(-)
Title: Bayesian Nonparametric and Semiparametric Analysis
Diff between DPpackage versions 1.1-0 dated 2010-03-15 and 1.1-1 dated 2010-07-26
Description: This package contains functions to perform inference via
simulation from the posterior distributions for Bayesian
nonparametric and semiparametric models. Although the name of
the package was motivated by the Dirichlet Process prior, the
package considers and will consider other priors on functional
spaces. So far, DPpackage includes models considering Dirichlet
Processes, Dependent Dirichlet Processes, Dependent Poisson-
Dirichlet Processes, Hierarchical Dirichlet Processes, Polya
Trees, Mixtures of Triangular distributions, and Random
Bernstein polynomials priors. The package also includes models
considering Penalized B-Splines. Currently the package includes
semiparametric models for marginal and conditional density
estimation, ROC curve analysis, interval censored data, binary
regression models, generalized linear mixed models, IRT type
models, and generalized additive models. The package also
contains functions to compute Pseudo-Bayes factors for model
comparison, and to elicitate the precision parameter of the
Dirichlet Process. To maximize computational efficiency, the
actual sampling for each model is done in compiled FORTRAN. The
functions return objects which can be subsequently analyzed
with functions provided in the coda package.
Author: Alejandro Jara
Maintainer: Alejandro Jara
DESCRIPTION | 8 ++++----
LICENSE | 23 ++++++++++++-----------
NAMESPACE | 12 ++++++++++++
R/DPMdencens.R |only
R/DPdensity.R | 2 +-
R/DPrandom.R | 4 ++--
man/DPMdencens.Rd |only
man/DPdensity.Rd | 4 ++--
man/LDPDdoublyint.Rd | 5 ++---
man/PTsampler.Rd | 2 +-
src/DPMdencens.f |only
src/DPbivdensityg.f | 5 +++++
src/DPbivdensityn.f | 5 +++++
src/DPdensityg.f | 5 +++++
src/DPdensityn.f | 5 +++++
src/DPdensityreg.f | 5 +++++
src/DPglmmprob.f | 1 +
src/HDPMcdensity.f | 20 ++++++++++++--------
src/HDPMdensity.f | 14 ++++++++++++--
src/ToolsSweep.f | 4 ++--
20 files changed, 88 insertions(+), 36 deletions(-)