Title: Rcpp integration for Armadillo templated linear algebra library
Description: R and Armadillo integration using Rcpp Armadillo is a
templated C++ linear algebra library (by Conrad Sanderson) that
aims towards a good balance between speed and ease of use.
Integer, floating point and complex numbers are supported, as
well as a subset of trigonometric and statistics functions.
Various matrix decompositions are provided through optional
integration with LAPACK and ATLAS libraries.
A delayed evaluation approach is employed (during compile time) to
combine several operations into one, and to reduce (or
eliminate) the need for temporaries. This is accomplished
through recursive templates and template meta-programming.
This library is useful if C++ has been decided as the language of
choice (due to speed and/or integration capabilities), rather
than another language.
The RcppArmadillo package includes the header files from the templated
Armadillo library (currently version 2.2.1). Thus users do not
need to install Armadillo itself in order to use RcppArmadillo.
This Armadillo integration provides a nice illustration of the
capabilities of the Rcpp package for seamless R and C++
integration.
Armadillo is licensed under the GNU LGPL version 3 or later, while
RcppArmadillo (the Rcpp bindings/bridge to Armadillo) is
licenses under the GNU GPL version 2 or later, as is the rest
of Rcpp.
Author: Romain Francois, Dirk Eddelbuettel and Doug Bates
Maintainer: Romain Francois, Dirk Eddelbuettel and Doug Bates
Diff between RcppArmadillo versions 0.2.27 dated 2011-07-23 and 0.2.28 dated 2011-08-02
ChangeLog | 6 ++++++ DESCRIPTION | 10 +++++----- inst/NEWS | 13 +++++++++++++ inst/include/armadillo_bits/arma_version.hpp | 6 +++--- inst/include/armadillo_bits/fn_det.hpp | 7 +++++-- inst/include/armadillo_bits/glue_cor_meat.hpp | 4 ++-- inst/include/armadillo_bits/glue_cov_meat.hpp | 8 ++++---- inst/include/armadillo_bits/op_cor_meat.hpp | 8 ++++---- inst/include/armadillo_bits/op_cov_meat.hpp | 12 ++++++------ inst/include/armadillo_bits/running_stat_vec_meat.hpp | 4 ++-- 10 files changed, 50 insertions(+), 28 deletions(-)
Title: Reads, annotates, and normalizes reverse phase protein array
data
Description: Reads in sampledescription and slidedescription files and
annotates the expression values taken from gpr files. After
Normalization data can be presented in boxplots, heatmaps or
dotplots.
Author: Heiko Mannsperger with contributions of Stephan Gade
Maintainer: Heiko Mannsperger
Diff between RPPanalyzer versions 1.0.3 dated 2010-05-28 and 1.0.4 dated 2011-08-02
RPPanalyzer-1.0.3/RPPanalyzer/data/S1.gpr |only RPPanalyzer-1.0.3/RPPanalyzer/data/S2.gpr |only RPPanalyzer-1.0.3/RPPanalyzer/data/S4.gpr |only RPPanalyzer-1.0.3/RPPanalyzer/data/sampledescription.txt |only RPPanalyzer-1.0.3/RPPanalyzer/data/slidedescription.txt |only RPPanalyzer-1.0.4/RPPanalyzer/DESCRIPTION | 10 +- RPPanalyzer-1.0.4/RPPanalyzer/R/calcSuperCurve.R | 2 RPPanalyzer-1.0.4/RPPanalyzer/R/createColumnIndices.R | 37 ++++++- RPPanalyzer-1.0.4/RPPanalyzer/R/pick.high.conc.R | 2 RPPanalyzer-1.0.4/RPPanalyzer/R/read.gpr.R | 36 ++++++- RPPanalyzer-1.0.4/RPPanalyzer/R/read.slidedescription.R | 59 +++++++++--- RPPanalyzer-1.0.4/RPPanalyzer/R/sample.median.R | 10 ++ RPPanalyzer-1.0.4/RPPanalyzer/R/wilcox.plot.groups.R | 2 RPPanalyzer-1.0.4/RPPanalyzer/data/sampledescription.txt.gz |only RPPanalyzer-1.0.4/RPPanalyzer/data/slidedescription.txt.gz |only RPPanalyzer-1.0.4/RPPanalyzer/inst/doc/RPPanalyzer.pdf |binary RPPanalyzer-1.0.4/RPPanalyzer/inst/doc/b2-clj4700dn-p2 |only RPPanalyzer-1.0.4/RPPanalyzer/inst/extdata |only RPPanalyzer-1.0.4/RPPanalyzer/man/HKdata.Rd | 2 RPPanalyzer-1.0.4/RPPanalyzer/man/read.Data.Rd | 3 20 files changed, 132 insertions(+), 31 deletions(-)
Title: Estimation, simulation and visualization of Hierarchical
Archimedean Copulae (HAC)
Description: Package provides the estimation of the structure and the
parameters, simulation methods and structural plots of
high-dimensional Hierarchical Archimedean Copulae (HAC).
Author: Ostap Okhrin
Maintainer: Ostap Okhrin
Diff between HAC versions 0.1-1 dated 2011-07-29 and 0.1-2 dated 2011-08-02
ChangeLog |only DESCRIPTION | 8 ++++---- R/copula_empirical.r | 39 +++++++++++++++++++++------------------ R/copula_estimate.r | 18 +++++++++++++++--- man/emp.copula.Rd | 9 ++++++--- man/estimate.copula.Rd | 9 ++++++++- 6 files changed, 54 insertions(+), 29 deletions(-)
Title: Core methods and classes used by aroma.* package part of The
Aroma Project
Description: This package contains core methods and classes used by
higher-level aroma.* packages part of the Aroma Project, e.g.
aroma.affymetrix and aroma.cn. Its API should be considered to
be in alpha and beta versions, and is mostly of interest to
developers.
Author: Henrik Bengtsson
Maintainer: Henrik Bengtsson
Diff between aroma.core versions 2.1.3 dated 2011-08-01 and 2.1.4 dated 2011-08-02
aroma.core-2.1.3/aroma.core/NAMESPACE |only aroma.core-2.1.4/aroma.core/DESCRIPTION | 10 +++++----- aroma.core-2.1.4/aroma.core/R/zzz.R | 1 + aroma.core-2.1.4/aroma.core/inst/NEWS | 5 +++++ 4 files changed, 11 insertions(+), 5 deletions(-)
Title: Overlays on Google map tiles in R
Description: This package serves two purposes: (i) Provide a
comfortable R interface to query the Google server for static
maps, and (ii) Use the map as a background image to overlay
plots within R. This requires proper coordinate scaling. NOTE:
To do anything but downloading static map tiles, RgoogleMaps
needs EITHER png OR ReadImages OR rimage installed ! png
(default) is your package if you prefer png file format and
ReadImages or rimage if you prefer jpg format. In the latter
cases, you will also need the libjpeg library installed.
Author: Markus Loecher
Maintainer: "Markus Loecher, Sense Networks"
Diff between RgoogleMaps versions 1.1.9.13 dated 2011-07-26 and 1.1.9.15 dated 2011-08-02
DESCRIPTION | 10 +++++----- R/PlotArrowsOnStaticMap.R | 1 + R/PlotOnStaticMap.R | 2 +- R/PlotPolysOnStaticMap.R | 5 +++-- R/TextOnStaticMap.R |only man/GetMap.Rd | 2 +- man/GetMap.bbox.Rd | 2 +- man/PlotOnStaticMap.Rd | 2 +- man/PlotPolysOnStaticMap.Rd | 8 ++++---- man/RgoogleMaps-package.Rd | 6 +++--- man/TextOnStaticMap.Rd |only 11 files changed, 20 insertions(+), 18 deletions(-)
Title: Text Classification Using Low-memory Multinomial Logistic
Regression
Description: maxent is an R package with tools for text classification
using multinomial logistic regression, also known as maximum
entropy. The focus of this maximum entropy classifier is to
minimize memory consumption on very large datasets,
particularly sparse document-term matrices represented by the
tm package.
Author: Timothy P. Jurka
Maintainer: Timothy P. Jurka
Diff between maxent versions 1.2 dated 2011-07-30 and 1.2.1 dated 2011-08-02
maxent-1.2.1/maxent/DESCRIPTION | 10 +++++----- maxent-1.2.1/maxent/data/NYTimes.csv.gz |only maxent-1.2.1/maxent/data/datalist |only maxent-1.2.1/maxent/man/NYTimes.Rd | 2 +- maxent-1.2.1/maxent/man/as.compressed.matrix.Rd | 2 +- maxent-1.2.1/maxent/man/load.model.Rd | 2 +- maxent-1.2.1/maxent/man/maxent-class.Rd | 2 +- maxent-1.2.1/maxent/man/maxent-package.Rd | 6 +++--- maxent-1.2.1/maxent/man/maxent.Rd | 2 +- maxent-1.2.1/maxent/man/predict.maxent.Rd | 2 +- maxent-1.2.1/maxent/man/save.model.Rd | 2 +- maxent-1.2/maxent/data/NYTimes.csv |only 12 files changed, 15 insertions(+), 15 deletions(-)
Title: Get XKCD comic from R
Description: This package allows the visualization of your favorite
XKCD comic strip directly from R. XKCD web comic content is
provided under the Creative Commons Attribution-NonCommercial
2.5 License.
Author: Paolo Sonego
Maintainer: Paolo Sonego
Diff between RXKCD versions 1.2 dated 2011-07-26 and 1.4 dated 2011-08-02
DESCRIPTION | 10 +++++----- R/getXKCD.R | 49 ++++++++++++++++++------------------------------- man/getXKCD.Rd | 3 ++- 3 files changed, 25 insertions(+), 37 deletions(-)
Title: Inverse Regression for Text Analysis
Description: A suite of tools for text and sentiment mining. This
includes the `mnlm' function, for sparse multinomial logistic
regression, `pls', a concise partial least squares routine, and
the `topics' function, for efficient estimation and dimension
selection in latent topic models.
Author: Matt Taddy
Maintainer: Matt Taddy
Diff between textir versions 1.6 dated 2011-06-09 and 1.6-1 dated 2011-08-02
ChangeLog | 10 ++++++++-- DESCRIPTION | 8 ++++---- R/topics.R | 10 +++++++--- man/congress109.Rd | 16 ++++++++++------ man/predict.mnlm.Rd | 21 +++++++++++++++++++++ man/summary.topics.Rd | 2 +- man/we8there.Rd | 8 +++----- man/wsjibm.Rd | 2 +- 8 files changed, 55 insertions(+), 22 deletions(-)
Title: Frailty models using maximum penalized likelihood estimation
Description: Frailtypack now fits several classes of frailty models
using Penalized Likelihood on the hazard function. 1) A shared
gamma frailty model and Cox proportional hazards model. Left
truncated, censored data and strata (max=2) are allowed.
Clustered and recurrent survival times can be studied (the
Andersen-Gill(1982) approach has been implemented for recurrent
events). An automatic choice of the smoothing parameter is
possible using an approximated cross-validation procedure. 2)
Additive frailty models for proportional hazards models with
two correlated random effects (intercept random effect with
random slope). 3) Nested frailty models for hierarchically
clustered data (with 2 levels of clustering) by including two
iid gamma random effects. 4) Joint frailty models in the
context of joint modelling of recurrent events with terminal
event.
Author: Juan R Gonzalez, Virginie Rondeau
Maintainer: Juan R Gonzalez
Diff between frailtypack versions 2.2-16 dated 2010-10-13 and 2.2-17 dated 2011-08-02
frailtypack-2.2-16/frailtypack/src/additive.f |only frailtypack-2.2-16/frailtypack/src/frailtypack.f |only frailtypack-2.2-16/frailtypack/src/general.f |only frailtypack-2.2-16/frailtypack/src/joint.f |only frailtypack-2.2-16/frailtypack/src/nested.f |only frailtypack-2.2-17/frailtypack/DESCRIPTION | 19 frailtypack-2.2-17/frailtypack/R/additivePenal.R | 99 - frailtypack-2.2-17/frailtypack/R/frailtyPenal.R | 995 ++++++++------- frailtypack-2.2-17/frailtypack/R/print.additivePenal.R | 40 frailtypack-2.2-17/frailtypack/R/print.frailtyPenal.R | 56 frailtypack-2.2-17/frailtypack/R/print.jointPenal.R | 119 + frailtypack-2.2-17/frailtypack/R/print.nestedPenal.R | 41 frailtypack-2.2-17/frailtypack/data/dataJoint.R |only frailtypack-2.2-17/frailtypack/data/filelist | 4 frailtypack-2.2-17/frailtypack/man/JointfrailtyPenal.Rd | 415 +++--- frailtypack-2.2-17/frailtypack/man/NestedfrailtyPenal.Rd | 36 frailtypack-2.2-17/frailtypack/man/additivePenal.Rd | 22 frailtypack-2.2-17/frailtypack/man/dataJoint.Rd |only frailtypack-2.2-17/frailtypack/man/frailtyPenal.Rd | 27 frailtypack-2.2-17/frailtypack/man/plotFrailtyPenal.Rd | 3 frailtypack-2.2-17/frailtypack/man/plotJointPenal.Rd | 4 frailtypack-2.2-17/frailtypack/man/printNestedPenal.Rd | 2 frailtypack-2.2-17/frailtypack/src/aaOptim.f90 |only frailtypack-2.2-17/frailtypack/src/additive.f90 |only frailtypack-2.2-17/frailtypack/src/frailtypack.f90 |only frailtypack-2.2-17/frailtypack/src/joint.f90 |only frailtypack-2.2-17/frailtypack/src/nested.f90 |only 27 files changed, 1065 insertions(+), 817 deletions(-)
Title: Analysis of large Affymetrix microarray data sets
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. To install, do:
source("http://www.aroma-project.org/hbLite.R");
hbInstall("aroma.affymetrix").
Author: Henrik Bengtsson
Maintainer: Henrik Bengtsson
Diff between aroma.affymetrix versions 2.1.0 dated 2011-04-09 and 2.1.6 dated 2011-08-02
aroma.affymetrix-2.1.0/aroma.affymetrix/inst/buildScripts/chipTypes/GenomeWideSNP_6/.Rhistory |only aroma.affymetrix-2.1.6/aroma.affymetrix/DESCRIPTION | 18 - aroma.affymetrix-2.1.6/aroma.affymetrix/R/999.AromaAffymetrix.R | 18 + aroma.affymetrix-2.1.6/aroma.affymetrix/R/AffymetrixCdfFile.MONOCELL.R | 8 aroma.affymetrix-2.1.6/aroma.affymetrix/R/AffymetrixCdfFile.UNIQUE.R | 108 +++++- aroma.affymetrix-2.1.6/aroma.affymetrix/R/AffymetrixNetAffxCsvFile.XTRS.R | 161 +++++++--- aroma.affymetrix-2.1.6/aroma.affymetrix/R/AllelicCrosstalkCalibration.getSetsOfProbes.R | 2 aroma.affymetrix-2.1.6/aroma.affymetrix/R/ChipEffectSet.extractExpressionSet.R |only aroma.affymetrix-2.1.6/aroma.affymetrix/R/CrlmmModel.R | 4 aroma.affymetrix-2.1.6/aroma.affymetrix/R/zzz.R | 12 aroma.affymetrix-2.1.6/aroma.affymetrix/incl/999.missingdocs.txt | 2 aroma.affymetrix-2.1.6/aroma.affymetrix/inst/NEWS | 40 ++ aroma.affymetrix-2.1.6/aroma.affymetrix/inst/buildScripts/chipTypes/Canine_2/Canine_2,ACS.R | 2 aroma.affymetrix-2.1.6/aroma.affymetrix/inst/buildScripts/chipTypes/Cytogenetics_Array/Cytogenetics_Array,ACS.R | 2 aroma.affymetrix-2.1.6/aroma.affymetrix/inst/buildScripts/chipTypes/Cytogenetics_Array/na28/Cytogenetics_Array,UGP,na28.R | 6 aroma.affymetrix-2.1.6/aroma.affymetrix/inst/buildScripts/chipTypes/DogSty06m520431/DogSty06m520431,ACS.R | 2 aroma.affymetrix-2.1.6/aroma.affymetrix/inst/buildScripts/chipTypes/GenomeWideSNP_5/na26/GenomeWideSNP_5,UFL,na26,GWS6.R | 4 aroma.affymetrix-2.1.6/aroma.affymetrix/inst/buildScripts/chipTypes/GenomeWideSNP_5/na26/GenomeWideSNP_5,UFL,na26.R | 2 aroma.affymetrix-2.1.6/aroma.affymetrix/inst/buildScripts/chipTypes/GenomeWideSNP_5/na26/GenomeWideSNP_5,UGP,na26.R | 4 aroma.affymetrix-2.1.6/aroma.affymetrix/inst/buildScripts/chipTypes/GenomeWideSNP_5/na26/GenomeWideSNP_5,default,UGP+UFL,na26.R | 2 aroma.affymetrix-2.1.6/aroma.affymetrix/inst/buildScripts/chipTypes/GenomeWideSNP_6/GenomeWideSNP_6,UFL.R | 7 aroma.affymetrix-2.1.6/aroma.affymetrix/inst/buildScripts/chipTypes/GenomeWideSNP_6/GenomeWideSNP_6,UGP.R | 3 aroma.affymetrix-2.1.6/aroma.affymetrix/inst/buildScripts/chipTypes/GenomeWideSNP_6/GenomeWideSNP_6,default,UGP+UFL.R | 3 aroma.affymetrix-2.1.6/aroma.affymetrix/inst/buildScripts/chipTypes/GenomeWideSNP_6/na26/GenomeWideSNP_6,UFL,na26.R | 2 aroma.affymetrix-2.1.6/aroma.affymetrix/inst/buildScripts/chipTypes/GenomeWideSNP_6/na26/GenomeWideSNP_6,UGP,na26.R | 4 aroma.affymetrix-2.1.6/aroma.affymetrix/inst/buildScripts/chipTypes/GenomeWideSNP_6/na26/GenomeWideSNP_6,default,UGP+UFL,na26.R | 2 aroma.affymetrix-2.1.6/aroma.affymetrix/inst/buildScripts/chipTypes/GenomeWideSNP_6/na27.1/GenomeWideSNP_6,UFL,na27.1.R | 2 aroma.affymetrix-2.1.6/aroma.affymetrix/inst/buildScripts/chipTypes/GenomeWideSNP_6/na27.1/GenomeWideSNP_6,UGP,na27.1.R | 6 aroma.affymetrix-2.1.6/aroma.affymetrix/inst/buildScripts/chipTypes/GenomeWideSNP_6/na27.1/GenomeWideSNP_6,default,UGP+UFL,na27.1.R | 2 aroma.affymetrix-2.1.6/aroma.affymetrix/inst/buildScripts/chipTypes/GenomeWideSNP_6/na27/GenomeWideSNP_6,UGC,na27.R | 2 aroma.affymetrix-2.1.6/aroma.affymetrix/inst/buildScripts/chipTypes/GenomeWideSNP_6/na30/GenomeWideSNP_6,UFL,na30.R | 2 aroma.affymetrix-2.1.6/aroma.affymetrix/inst/buildScripts/chipTypes/GenomeWideSNP_6/na30/GenomeWideSNP_6,UGP,na30.R | 4 aroma.affymetrix-2.1.6/aroma.affymetrix/inst/buildScripts/chipTypes/GenomeWideSNP_6/na31 |only aroma.affymetrix-2.1.6/aroma.affymetrix/inst/buildScripts/chipTypes/HG-Focus/HG-Focus,ACS.R | 2 aroma.affymetrix-2.1.6/aroma.affymetrix/inst/buildScripts/chipTypes/HuEx-1_0-st-v2/HuEx-1_0-st-v2,ACS.R | 2 aroma.affymetrix-2.1.6/aroma.affymetrix/inst/buildScripts/chipTypes/HuGene-1_0-st-v1/HuGene-1_0-st-v1,ACS.R | 2 aroma.affymetrix-2.1.6/aroma.affymetrix/inst/buildScripts/chipTypes/HuGene-1_0-st-v1/HuGene-1_0-st-v1,NetAffx.R |only aroma.affymetrix-2.1.6/aroma.affymetrix/inst/buildScripts/chipTypes/MOUSEDIVm520650/MOUSEDIVm520650,ACS.R | 2 aroma.affymetrix-2.1.6/aroma.affymetrix/inst/buildScripts/chipTypes/MOUSEDIVm520650/na30/MOUSEDIVm520650,UFL,na30.R | 2 aroma.affymetrix-2.1.6/aroma.affymetrix/inst/buildScripts/chipTypes/MOUSEDIVm520650/na30/MOUSEDIVm520650,UGP,na30.R | 4 aroma.affymetrix-2.1.6/aroma.affymetrix/inst/buildScripts/chipTypes/Mapping10K_Xba131/Mapping10K_Xba131,ACS.R | 2 aroma.affymetrix-2.1.6/aroma.affymetrix/inst/buildScripts/chipTypes/Mapping10K_Xba131/na26/Mapping10K_Xba131,UFL,na26.R | 4 aroma.affymetrix-2.1.6/aroma.affymetrix/inst/buildScripts/chipTypes/Mapping10K_Xba131/na26/Mapping10K_Xba131,UGP,na26.R | 6 aroma.affymetrix-2.1.6/aroma.affymetrix/inst/buildScripts/chipTypes/Mapping10K_Xba142/Mapping10K_Xba142,ACS.R | 2 aroma.affymetrix-2.1.6/aroma.affymetrix/inst/buildScripts/chipTypes/Mapping10K_Xba142/na26/Mapping10K_Xba142,UFL,na26.R | 4 aroma.affymetrix-2.1.6/aroma.affymetrix/inst/buildScripts/chipTypes/Mapping10K_Xba142/na26/Mapping10K_Xba142,UGP,na26.R | 6 aroma.affymetrix-2.1.6/aroma.affymetrix/inst/buildScripts/chipTypes/Mapping250K_Nsp/na26/Mapping250K_Nsp,UFL,na26.R | 4 aroma.affymetrix-2.1.6/aroma.affymetrix/inst/buildScripts/chipTypes/Mapping250K_Nsp/na26/Mapping250K_Nsp,UGP,na26.R | 6 aroma.affymetrix-2.1.6/aroma.affymetrix/inst/buildScripts/chipTypes/Mapping250K_Nsp/na28/Mapping250K_Nsp,UGC,na28.R | 2 aroma.affymetrix-2.1.6/aroma.affymetrix/inst/buildScripts/chipTypes/Mapping250K_Nsp/na31/Mapping250K_Nsp,UFL,na31.R | 4 aroma.affymetrix-2.1.6/aroma.affymetrix/inst/buildScripts/chipTypes/Mapping250K_Nsp/na31/Mapping250K_Nsp,UGP,na31.R | 6 aroma.affymetrix-2.1.6/aroma.affymetrix/inst/buildScripts/chipTypes/Mapping250K_Sty/na26/Mapping250K_Sty,UFL,na26.R | 4 aroma.affymetrix-2.1.6/aroma.affymetrix/inst/buildScripts/chipTypes/Mapping250K_Sty/na26/Mapping250K_Sty,UGP,na26.R | 6 aroma.affymetrix-2.1.6/aroma.affymetrix/inst/buildScripts/chipTypes/Mapping250K_Sty/na28/Mapping250K_Sty,UGC,na28.R | 2 aroma.affymetrix-2.1.6/aroma.affymetrix/inst/buildScripts/chipTypes/Mapping250K_Sty/na31/Mapping250K_Sty,UFL,na31.R | 4 aroma.affymetrix-2.1.6/aroma.affymetrix/inst/buildScripts/chipTypes/Mapping250K_Sty/na31/Mapping250K_Sty,UGP,na31.R | 6 aroma.affymetrix-2.1.6/aroma.affymetrix/inst/buildScripts/chipTypes/Mapping50K_Hind240/Mapping50K_Hind240,UFL.R | 3 aroma.affymetrix-2.1.6/aroma.affymetrix/inst/buildScripts/chipTypes/Mapping50K_Hind240/Mapping50K_Xba240,UGP.R | 3 aroma.affymetrix-2.1.6/aroma.affymetrix/inst/buildScripts/chipTypes/Mapping50K_Hind240/na26/Mapping50K_Hind240,UFL,na26.R | 4 aroma.affymetrix-2.1.6/aroma.affymetrix/inst/buildScripts/chipTypes/Mapping50K_Hind240/na26/Mapping50K_Hind240,UGP,na26.R | 6 aroma.affymetrix-2.1.6/aroma.affymetrix/inst/buildScripts/chipTypes/Mapping50K_Xba240/Mapping50K_Xba240,ACS.R | 2 aroma.affymetrix-2.1.6/aroma.affymetrix/inst/buildScripts/chipTypes/Mapping50K_Xba240/Mapping50K_Xba240,UFL.R | 5 aroma.affymetrix-2.1.6/aroma.affymetrix/inst/buildScripts/chipTypes/Mapping50K_Xba240/Mapping50K_Xba240,UGP.R | 5 aroma.affymetrix-2.1.6/aroma.affymetrix/inst/buildScripts/chipTypes/Mapping50K_Xba240/na26/Mapping50K_Xba240,UFL,na26.R | 4 aroma.affymetrix-2.1.6/aroma.affymetrix/inst/buildScripts/chipTypes/Mapping50K_Xba240/na26/Mapping50K_Xba240,UGP,na26.R | 6 aroma.affymetrix-2.1.6/aroma.affymetrix/inst/buildScripts/chipTypes/MoGene-1_0-st-v1/MoGene-1_0-st-v1,ACS.R | 5 aroma.affymetrix-2.1.6/aroma.affymetrix/inst/testScripts/system/chipTypes/HG-U133_Plus_2/test20110709,doRMA,extractExpressionSet.R |only aroma.affymetrix-2.1.6/aroma.affymetrix/inst/testScripts/system/chipTypes/HG-U133_Plus_2/test20110709,doRMA.R |only aroma.affymetrix-2.1.6/aroma.affymetrix/inst/testScripts/system/chipTypes/Mm_PromPR_v02 |only aroma.affymetrix-2.1.6/aroma.affymetrix/man/AbstractProbeSequenceNormalization.Rd | 2 aroma.affymetrix-2.1.6/aroma.affymetrix/man/AdditiveCovariatesNormalization.Rd | 2 aroma.affymetrix-2.1.6/aroma.affymetrix/man/AffineCnPlm.Rd | 2 aroma.affymetrix-2.1.6/aroma.affymetrix/man/AffinePlm.Rd | 2 aroma.affymetrix-2.1.6/aroma.affymetrix/man/AffineSnpPlm.Rd | 2 aroma.affymetrix-2.1.6/aroma.affymetrix/man/AffymetrixCdfFile.Rd | 4 aroma.affymetrix-2.1.6/aroma.affymetrix/man/AffymetrixCelFile.Rd | 2 aroma.affymetrix-2.1.6/aroma.affymetrix/man/AffymetrixCelSet.Rd | 4 aroma.affymetrix-2.1.6/aroma.affymetrix/man/AffymetrixCelSetReporter.Rd | 2 aroma.affymetrix-2.1.6/aroma.affymetrix/man/AffymetrixCelSetTuple.Rd | 2 aroma.affymetrix-2.1.6/aroma.affymetrix/man/AffymetrixCnChpSet.Rd | 4 aroma.affymetrix-2.1.6/aroma.affymetrix/man/AffymetrixFile.Rd | 2 aroma.affymetrix-2.1.6/aroma.affymetrix/man/AffymetrixFileSet.Rd | 4 aroma.affymetrix-2.1.6/aroma.affymetrix/man/AffymetrixFileSetReporter.Rd | 2 aroma.affymetrix-2.1.6/aroma.affymetrix/man/AffymetrixProbeTabFile.Rd | 2 aroma.affymetrix-2.1.6/aroma.affymetrix/man/AlleleSummation.Rd | 2 aroma.affymetrix-2.1.6/aroma.affymetrix/man/AllelicCrosstalkCalibration.Rd | 2 aroma.affymetrix-2.1.6/aroma.affymetrix/man/AromaChipTypeAnnotationFile.Rd | 2 aroma.affymetrix-2.1.6/aroma.affymetrix/man/ArrayExplorer.Rd | 2 aroma.affymetrix-2.1.6/aroma.affymetrix/man/AvgCnPlm.Rd | 2 aroma.affymetrix-2.1.6/aroma.affymetrix/man/AvgPlm.Rd | 2 aroma.affymetrix-2.1.6/aroma.affymetrix/man/AvgSnpPlm.Rd | 2 aroma.affymetrix-2.1.6/aroma.affymetrix/man/BackgroundCorrection.Rd | 2 aroma.affymetrix-2.1.6/aroma.affymetrix/man/BaseCountNormalization.Rd | 2 aroma.affymetrix-2.1.6/aroma.affymetrix/man/BasePositionNormalization.Rd | 2 aroma.affymetrix-2.1.6/aroma.affymetrix/man/ChipEffectFile.Rd | 2 aroma.affymetrix-2.1.6/aroma.affymetrix/man/ChipEffectGroupMerge.Rd | 2 aroma.affymetrix-2.1.6/aroma.affymetrix/man/ChipEffectSet.Rd | 5 aroma.affymetrix-2.1.6/aroma.affymetrix/man/ChipEffectTransform.Rd | 2 aroma.affymetrix-2.1.6/aroma.affymetrix/man/CnChipEffectFile.Rd | 2 aroma.affymetrix-2.1.6/aroma.affymetrix/man/CnChipEffectSet.Rd | 6 aroma.affymetrix-2.1.6/aroma.affymetrix/man/CnProbeAffinityFile.Rd | 2 aroma.affymetrix-2.1.6/aroma.affymetrix/man/CnagCfhFile.Rd | 2 aroma.affymetrix-2.1.6/aroma.affymetrix/man/CnagCfhSet.Rd | 4 aroma.affymetrix-2.1.6/aroma.affymetrix/man/CrlmmParametersFile.Rd | 2 aroma.affymetrix-2.1.6/aroma.affymetrix/man/CrlmmParametersSet.Rd | 4 aroma.affymetrix-2.1.6/aroma.affymetrix/man/DChipCdfBinFile.Rd | 2 aroma.affymetrix-2.1.6/aroma.affymetrix/man/DChipDcpFile.Rd | 2 aroma.affymetrix-2.1.6/aroma.affymetrix/man/DChipDcpSet.Rd | 4 aroma.affymetrix-2.1.6/aroma.affymetrix/man/DChipGenomeInformation.Rd | 2 aroma.affymetrix-2.1.6/aroma.affymetrix/man/DChipQuantileNormalization.Rd | 4 aroma.affymetrix-2.1.6/aroma.affymetrix/man/DChipSnpInformation.Rd | 2 aroma.affymetrix-2.1.6/aroma.affymetrix/man/ExonChipEffectFile.Rd | 2 aroma.affymetrix-2.1.6/aroma.affymetrix/man/ExonChipEffectSet.Rd | 6 aroma.affymetrix-2.1.6/aroma.affymetrix/man/ExonProbeAffinityFile.Rd | 2 aroma.affymetrix-2.1.6/aroma.affymetrix/man/ExonRmaPlm.Rd | 2 aroma.affymetrix-2.1.6/aroma.affymetrix/man/FirmaFile.Rd | 2 aroma.affymetrix-2.1.6/aroma.affymetrix/man/FirmaModel.Rd | 2 aroma.affymetrix-2.1.6/aroma.affymetrix/man/FirmaSet.Rd | 4 aroma.affymetrix-2.1.6/aroma.affymetrix/man/FragmentEquivalentClassNormalization.Rd | 2 aroma.affymetrix-2.1.6/aroma.affymetrix/man/FragmentLengthNormalization.Rd | 2 aroma.affymetrix-2.1.6/aroma.affymetrix/man/GcContentNormalization.Rd | 2 aroma.affymetrix-2.1.6/aroma.affymetrix/man/GcContentNormalization2.Rd | 2 aroma.affymetrix-2.1.6/aroma.affymetrix/man/GcRmaBackgroundCorrection.Rd | 2 aroma.affymetrix-2.1.6/aroma.affymetrix/man/GenericReporter.Rd | 2 aroma.affymetrix-2.1.6/aroma.affymetrix/man/GenomeInformation.Rd | 2 aroma.affymetrix-2.1.6/aroma.affymetrix/man/HetLogAddCnPlm.Rd | 2 aroma.affymetrix-2.1.6/aroma.affymetrix/man/HetLogAddPlm.Rd | 2 aroma.affymetrix-2.1.6/aroma.affymetrix/man/HetLogAddSnpPlm.Rd | 2 aroma.affymetrix-2.1.6/aroma.affymetrix/man/LimmaBackgroundCorrection.Rd | 2 aroma.affymetrix-2.1.6/aroma.affymetrix/man/LinearModelProbeSequenceNormalization.Rd | 2 aroma.affymetrix-2.1.6/aroma.affymetrix/man/MatNormalization.Rd | 2 aroma.affymetrix-2.1.6/aroma.affymetrix/man/MatSmoothing.Rd | 2 aroma.affymetrix-2.1.6/aroma.affymetrix/man/MbeiCnPlm.Rd | 2 aroma.affymetrix-2.1.6/aroma.affymetrix/man/MbeiPlm.Rd | 2 aroma.affymetrix-2.1.6/aroma.affymetrix/man/MbeiSnpPlm.Rd | 2 aroma.affymetrix-2.1.6/aroma.affymetrix/man/Model.Rd | 2 aroma.affymetrix-2.1.6/aroma.affymetrix/man/MultiArrayUnitModel.Rd | 2 aroma.affymetrix-2.1.6/aroma.affymetrix/man/Non-documented_objects.Rd | 6 aroma.affymetrix-2.1.6/aroma.affymetrix/man/NormExpBackgroundCorrection.Rd | 2 aroma.affymetrix-2.1.6/aroma.affymetrix/man/OpticalBackgroundCorrection.Rd | 2 aroma.affymetrix-2.1.6/aroma.affymetrix/man/ParameterCelFile.Rd | 2 aroma.affymetrix-2.1.6/aroma.affymetrix/man/ParameterCelSet.Rd | 4 aroma.affymetrix-2.1.6/aroma.affymetrix/man/ProbeAffinityFile.Rd | 2 aroma.affymetrix-2.1.6/aroma.affymetrix/man/ProbeLevelModel.Rd | 2 aroma.affymetrix-2.1.6/aroma.affymetrix/man/ProbeLevelTransform.Rd | 2 aroma.affymetrix-2.1.6/aroma.affymetrix/man/ProbeLevelTransform3.Rd | 2 aroma.affymetrix-2.1.6/aroma.affymetrix/man/QualityAssessmentFile.Rd | 2 aroma.affymetrix-2.1.6/aroma.affymetrix/man/QualityAssessmentModel.Rd | 2 aroma.affymetrix-2.1.6/aroma.affymetrix/man/QualityAssessmentSet.Rd | 4 aroma.affymetrix-2.1.6/aroma.affymetrix/man/QuantileNormalization.Rd | 2 aroma.affymetrix-2.1.6/aroma.affymetrix/man/ReseqCrosstalkCalibration.Rd | 2 aroma.affymetrix-2.1.6/aroma.affymetrix/man/ResidualFile.Rd | 2 aroma.affymetrix-2.1.6/aroma.affymetrix/man/ResidualSet.Rd | 4 aroma.affymetrix-2.1.6/aroma.affymetrix/man/RmaBackgroundCorrection.Rd | 2 aroma.affymetrix-2.1.6/aroma.affymetrix/man/RmaCnPlm.Rd | 2 aroma.affymetrix-2.1.6/aroma.affymetrix/man/RmaPlm.Rd | 2 aroma.affymetrix-2.1.6/aroma.affymetrix/man/RmaSnpPlm.Rd | 2 aroma.affymetrix-2.1.6/aroma.affymetrix/man/ScaleNormalization.Rd | 2 aroma.affymetrix-2.1.6/aroma.affymetrix/man/ScaleNormalization3.Rd | 2 aroma.affymetrix-2.1.6/aroma.affymetrix/man/SingleArrayUnitModel.Rd | 2 aroma.affymetrix-2.1.6/aroma.affymetrix/man/SmoothMultiarrayModel.Rd | 4 aroma.affymetrix-2.1.6/aroma.affymetrix/man/SmoothRmaModel.Rd | 4 aroma.affymetrix-2.1.6/aroma.affymetrix/man/SnpChipEffectFile.Rd | 2 aroma.affymetrix-2.1.6/aroma.affymetrix/man/SnpChipEffectGroupMerge.Rd | 2 aroma.affymetrix-2.1.6/aroma.affymetrix/man/SnpChipEffectSet.Rd | 6 aroma.affymetrix-2.1.6/aroma.affymetrix/man/SnpInformation.Rd | 2 aroma.affymetrix-2.1.6/aroma.affymetrix/man/SnpProbeAffinityFile.Rd | 2 aroma.affymetrix-2.1.6/aroma.affymetrix/man/SpatialReporter.Rd | 2 aroma.affymetrix-2.1.6/aroma.affymetrix/man/TransformReport.Rd | 2 aroma.affymetrix-2.1.6/aroma.affymetrix/man/UgpGenomeInformation.Rd | 2 aroma.affymetrix-2.1.6/aroma.affymetrix/man/UnitModel.Rd | 2 aroma.affymetrix-2.1.6/aroma.affymetrix/man/UnitTypeScaleNormalization.Rd | 2 aroma.affymetrix-2.1.6/aroma.affymetrix/man/WeightsFile.Rd | 2 aroma.affymetrix-2.1.6/aroma.affymetrix/man/WeightsSet.Rd | 4 aroma.affymetrix-2.1.6/aroma.affymetrix/man/createMonocellCdf.AffymetrixCdfFile.Rd | 3 aroma.affymetrix-2.1.6/aroma.affymetrix/man/createUniqueCdf.AffymetrixCdfFile.Rd | 14 aroma.affymetrix-2.1.6/aroma.affymetrix/man/extractExpressionSet.ChipEffectSet.Rd |only aroma.affymetrix-2.1.6/aroma.affymetrix/man/getImage.AffymetrixCelFile.Rd | 3 178 files changed, 540 insertions(+), 300 deletions(-)
More information about aroma.affymetrix at CRAN
Permanent link
Title: Data Analysis And Graphics data and functions
Description: various data sets used in examples and exercises in the
book Maindonald, J.H. and Braun, W.J. (2003, 2007, 2010) "Data
Analysis and Graphics Using R".
Author: John Maindonald and W. John Braun
Maintainer: W. John Braun
Diff between DAAG versions 1.07 dated 2011-07-22 and 1.08 dated 2011-08-02
DESCRIPTION | 8 ++++---- R/bestset.noise.R | 34 ++++++++++++++++++---------------- R/bestsetNoise.R | 34 ++++++++++++++++++---------------- R/bsnCV.R | 41 ++++++++++++++++++++--------------------- man/bestsetNoise.Rd | 22 ++++++++++++---------- 5 files changed, 72 insertions(+), 67 deletions(-)