Title: Calculate afc
Diff between afc versions 1.0 dated 2009-02-18 and 1.03 dated 2010-01-07
Description: Package to calculate the Generalized Discrimination Score
(also known as Two Alternatives Forced Choice Score (2AFC)
Author: Andreas Weigel
Maintainer: Andreas Weigel
DESCRIPTION | 13 ++++++++-----
R/afc.mp.R | 34 ++++++++++++++++++----------------
man/afc-package.Rd | 8 +++-----
man/afc.np.Rd | 2 +-
4 files changed, 30 insertions(+), 27 deletions(-)
Title: Methods for Tree-based Local Adaptive Thresholding
Diff between treethresh versions 0.1-4 dated 2010-01-04 and 0.1-5 dated 2010-01-07
Description: This package implements TreeThresh, a locally adaptive
version of EbayesThresh.
Author: Ludger Evers
Maintainer: Ludger Evers
DESCRIPTION | 8
inst/doc/treethresh.Rnw | 2
inst/doc/treethresh.pdf | 4162 ++++++++++++++++++++++------------------------
man/coefficients.Rd | 3
man/row263.Rd | 2
man/trees.Rd | 2
man/treethresh.Rd | 2
man/wavelet.treethresh.Rd | 9
man/wtthresh.Rd | 2
9 files changed, 2028 insertions(+), 2164 deletions(-)
Title: Implementation of the hydrological model TOPMODEL in R
Diff between topmodel versions 0.7.0 dated 2009-08-16 and 0.7.1 dated 2010-01-07
Description: Set of hydrological functions including an R
implementation of the hydrological model TOPMODEL, which is
based on the 1995 FORTRAN version by Keith Beven. From version
0.7.0, the package is put into maintenance mode. New functions
for hydrological analysis are now developed as part of the
RHydro package. RHydro can be found on R-forge and is built on
a set of dedicated S4 classes.
Author: Wouter Buytaert
Maintainer: Wouter Buytaert
DESCRIPTION | 8 -
R/infiltration.R | 14 +-
man/NSeff.Rd | 4
man/infiltration.Rd | 8 -
man/make.classes.Rd | 8 -
man/subcatch.Rd | 4
man/topidx.Rd | 2
src/flowlength.c | 14 +-
src/get_f.c | 345 +++++++++++++++++++++++++---------------------------
src/infiltration.c | 18 +-
10 files changed, 209 insertions(+), 216 deletions(-)
Title: tnet: Software for Analysis of Weighted, Two-mode, and
Longitudinal networks
Diff between tnet versions 0.1.3 dated 2009-11-26 and 0.1.4 dated 2010-01-07
Description: R package to analyse weighted, two-mode, and longitudinal
networks.
Author: Tore Opsahl
Maintainer: Tore Opsahl
tnet-0.1.3/tnet/data/OnlineComm.f1000.rdata |only
tnet-0.1.3/tnet/man/Cross.Parker.Consulting.net.info.Rd |only
tnet-0.1.3/tnet/man/Cross.Parker.Consulting.net.value.Rd |only
tnet-0.1.3/tnet/man/Cross.Parker.Consulting.node.gender.Rd |only
tnet-0.1.3/tnet/man/Cross.Parker.Consulting.node.location.Rd |only
tnet-0.1.3/tnet/man/Cross.Parker.Consulting.node.orglevel.Rd |only
tnet-0.1.3/tnet/man/Cross.Parker.Consulting.node.region.Rd |only
tnet-0.1.3/tnet/man/Cross.Parker.Manufacturing.net.aware.Rd |only
tnet-0.1.3/tnet/man/Cross.Parker.Manufacturing.net.info.Rd |only
tnet-0.1.3/tnet/man/Cross.Parker.Manufacturing.node.location.Rd |only
tnet-0.1.3/tnet/man/Cross.Parker.Manufacturing.node.orglevel.Rd |only
tnet-0.1.3/tnet/man/Cross.Parker.Manufacturing.node.tenure.Rd |only
tnet-0.1.3/tnet/man/Freemans.EIES.net.1.n48.Rd |only
tnet-0.1.3/tnet/man/Freemans.EIES.net.2.n48.Rd |only
tnet-0.1.3/tnet/man/Freemans.EIES.net.3.n32.Rd |only
tnet-0.1.3/tnet/man/Freemans.EIES.node.Citations.n32.Rd |only
tnet-0.1.3/tnet/man/Freemans.EIES.node.Discipline.n32.Rd |only
tnet-0.1.3/tnet/man/Newman.Condmat.95.99.net.1mode.wNewman.Rd |only
tnet-0.1.3/tnet/man/Newman.Condmat.95.99.net.2mode.Rd |only
tnet-0.1.3/tnet/man/OnlineComm.f1000.lnet.Rd |only
tnet-0.1.3/tnet/man/celegans.n306.net.Rd |only
tnet-0.1.4/tnet/DESCRIPTION | 8 -
tnet-0.1.4/tnet/R/as.tnet.R | 19 ++++
tnet-0.1.4/tnet/R/clustering_tm.R | 11 +-
tnet-0.1.4/tnet/R/clustering_tm_local.R |only
tnet-0.1.4/tnet/R/rg_tm.R | 20 ++--
tnet-0.1.4/tnet/R/rg_w.R | 41 ++++++----
tnet-0.1.4/tnet/R/weighted_richclub_w.R | 2
tnet-0.1.4/tnet/data/Cross.Parker.Consulting.RData |binary
tnet-0.1.4/tnet/data/Cross.Parker.Manufacturing.RData |binary
tnet-0.1.4/tnet/data/Davis.Southern.women.RData |only
tnet-0.1.4/tnet/data/Freemans.EIES.RData |binary
tnet-0.1.4/tnet/data/Newman.Condmat.95.99.RData |binary
tnet-0.1.4/tnet/data/OnlineSocialNetwork.n1899.RData |only
tnet-0.1.4/tnet/data/USairport.n500.RData |binary
tnet-0.1.4/tnet/data/celegans.n306.RData |binary
tnet-0.1.4/tnet/man/Cross.Parker.Consulting.Rd |only
tnet-0.1.4/tnet/man/Cross.Parker.Manufacturing.Rd |only
tnet-0.1.4/tnet/man/Davis.Southern.women.Rd |only
tnet-0.1.4/tnet/man/Freemans.EIES.Rd |only
tnet-0.1.4/tnet/man/Newman.Condmat.95.99.Rd |only
tnet-0.1.4/tnet/man/OnlineSocialNetwork.n1899.Rd |only
tnet-0.1.4/tnet/man/USairport.n500.net.Rd | 2
tnet-0.1.4/tnet/man/as.tnet.Rd | 2
tnet-0.1.4/tnet/man/betweenness_w.Rd | 2
tnet-0.1.4/tnet/man/celegans.n306.Rd |only
tnet-0.1.4/tnet/man/clustering_tm_local.Rd |only
tnet-0.1.4/tnet/man/degree_w.Rd | 4
tnet-0.1.4/tnet/man/projecting_tm.Rd | 2
tnet-0.1.4/tnet/man/rg_reshuffling_tm.Rd | 8 -
tnet-0.1.4/tnet/man/rg_tm.Rd | 2
tnet-0.1.4/tnet/man/rg_w.Rd | 2
tnet-0.1.4/tnet/man/weighted_richclub_tm.Rd | 8 -
tnet-0.1.4/tnet/man/weighted_richclub_w.Rd | 2
54 files changed, 86 insertions(+), 49 deletions(-)
Title: Calculates parameters of the seawater carbonate system
Diff between seacarb versions 2.2 dated 2009-10-07 and 2.3 dated 2010-01-07
Description: Calculates parameters of the seawater carbonate system
Author: Heloise Lavigne and Aurelien Proye and Jean-Pierre Gattuso.
Portions of code and/or corrections were contributed by
Jean-Marie Epitalon, Andreas Hofmann, Bernard Gentili, Jim Orr
and Karline Soetaert
Maintainer: Jean-Pierre Gattuso
ChangeLog | 369 ++++++++++++++++++++++++++++++----------------------------
DESCRIPTION | 8 -
R/oa.R |only
R/ppH.R | 8 -
man/buffer.Rd | 2
man/carb.Rd | 12 -
man/oa.Rd |only
man/pHconv.Rd | 2
man/pmix.Rd | 2
man/ppH.Rd | 17 --
man/psi.Rd | 2
11 files changed, 218 insertions(+), 204 deletions(-)
Title: R Workspace and Directory Management
Diff between rwm versions 1.27 dated 2008-09-10 and 1.35 dated 2010-01-07
Description: R workspace and directory management functions. The
workspace functions are loosed similar to commands used in APL
for managing workspaces but with enhancements to manage the
present working directory and command history as well
Author: A.I. McLeod
Maintainer: A.I. McLeod
rwm-1.27/rwm/INDEX |only
rwm-1.27/rwm/R/InitializeRWM.R |only
rwm-1.27/rwm/R/TestRWMSetup.R |only
rwm-1.27/rwm/R/continuews.R |only
rwm-1.27/rwm/doc |only
rwm-1.27/rwm/man/InitializeRWM.Rd |only
rwm-1.27/rwm/man/TestRWMSetup.Rd |only
rwm-1.27/rwm/man/continuews.Rd |only
rwm-1.35/rwm/DESCRIPTION | 28 ++--
rwm-1.35/rwm/R/attachws.R |only
rwm-1.35/rwm/R/clearws.R | 40 +++---
rwm-1.35/rwm/R/cws.R |only
rwm-1.35/rwm/R/initrwm.R |only
rwm-1.35/rwm/R/loadws.R | 224 +++++++++++++++++++++-----------------
rwm-1.35/rwm/R/rwm-internal.R | 21 +--
rwm-1.35/rwm/R/savews.R | 162 +++++++++++++++------------
rwm-1.35/rwm/R/testrwm.R |only
rwm-1.35/rwm/inst |only
rwm-1.35/rwm/man/attachws.Rd |only
rwm-1.35/rwm/man/clearws.Rd | 112 +++++++++----------
rwm-1.35/rwm/man/cws.Rd |only
rwm-1.35/rwm/man/initrwm.Rd |only
rwm-1.35/rwm/man/loadws.Rd | 185 ++++++++++++++++---------------
rwm-1.35/rwm/man/rwm-package.Rd | 198 +++++++++++++++++----------------
rwm-1.35/rwm/man/savews.Rd | 171 ++++++++++++++++-------------
rwm-1.35/rwm/man/testrwm.Rd |only
26 files changed, 617 insertions(+), 524 deletions(-)
Title: Local Regression, Likelihood and Density Estimation.
Diff between locfit versions 1.5-4 dated 2007-11-27 and 1.5-5 dated 2010-01-07
Description: Local Regression, Likelihood and density estimation.
Author: Catherine Loader
Maintainer: Andy Liaw
DESCRIPTION | 25 +--
R/locfit.r | 316 ++++++++++++++++++++++----------------------
man/mcyc.Rd | 4
man/plot.preplot.locfit.Rd | 4
man/plot.scb.Rd | 2
man/preplot.locfit.Rd | 4
man/print.gcvplot.Rd | 2
man/print.lfeval.Rd | 2
man/print.preplot.locfit.Rd | 2
man/print.scb.Rd | 4
man/store.Rd | 4
man/trimod.Rd | 1
src/fitted.c | 2
src/local.h | 3
src/m_icirc.c | 2
src/procv.c | 2
16 files changed, 191 insertions(+), 188 deletions(-)
Title: Graphical Cluster Explorer
Diff between gcExplorer versions 0.9-1 dated 2009-05-06 and 0.9-2 dated 2010-01-07
Description: Visualize cluster results and investigate additional
properties of clusters using interactive neighbourhood graphs.
By clicking on the node representing the cluster, information
about the cluster is provided using additional graphics or
summary statistics. For microarray data, tables with links to
genetic databases like NCBI Entrez Gene can be created for each
cluster.
Author: Theresa Scharl, Ingo Voglhuber, Friedrich Leisch
Maintainer: Theresa Scharl
DESCRIPTION | 12 +++----
NAMESPACE | 2 -
R/clnorm.R | 4 +-
R/comp_test.R | 13 ++++---
R/edgeTest.R | 6 +--
R/gcModify.R | 5 ++
R/gcProfile.R | 10 +++--
R/go.details.R | 90 +++++++++++++++++++++++++++++++++++++++++------------
inst/CITATION | 2 -
man/clnorm.Rd | 4 +-
man/clusterPlot.Rd | 5 +-
man/comp_test.Rd | 5 +-
man/edgeTest.Rd | 6 ++-
man/fitsod.Rd | 6 +--
man/gcModify.Rd | 4 +-
man/gcProfile.Rd | 5 +-
man/go.details.Rd | 8 +++-
man/oxygen.Rd | 2 -
man/ps19.Rd | 4 +-
19 files changed, 130 insertions(+), 63 deletions(-)
Title: Fuzzy Set Ordination
Diff between fso versions 1.0-1 dated 2007-07-16 and 1.2-0 dated 2010-01-07
Description: Fuzzy set ordination is a multivariate analysis used in
ecology to relate the composition of samples to possible
explanatory variables. While differing in theory and method,
in practice, the use is similar to "constrained ordination."
The package contains plotting and summary functions as well as
the analyses
Author: David W. Roberts
Maintainer: David W. Roberts
DESCRIPTION | 26 +++++++------
R/fso.R | 107 ++++++++++++++++++++++++++++++++++++++++++++++++++++---
inst |only
man/fso.Rd | 10 ++---
man/mfso.Rd | 13 +++---
man/plot.fso.Rd | 6 +--
man/plot.mfso.Rd | 25 ++++++++++++
man/step.mfso.Rd | 8 ++--
svn-commit.tmp |only
9 files changed, 161 insertions(+), 34 deletions(-)
Title: CCMN and other noRMalizatioN methods for metabolomics data
Diff between crmn versions 0.0.10 dated 2010-01-06 and 0.0.11 dated 2010-01-07
Description: Implements the Cross-contribution Compensating Multiple
standard Normalization (CCMN) method and other normalization
algorithms.
Author: Henning Redestig
Maintainer: Henning Redestig
DESCRIPTION | 6 +++---
R/norm.R | 8 ++++++--
inst/doc/crmn.pdf |binary
3 files changed, 9 insertions(+), 5 deletions(-)
Title: Bayesian network structure learning
Diff between bnlearn versions 1.7 dated 2009-10-26 and 1.8 dated 2010-01-07
Description: Bayesian network structure learning via constraint-based
(also known as 'conditional independence'), score-based and
hybrid algorithms. This package implements the Grow-Shrink (GS)
algorithm, the Incremental Association (IAMB) algorithm, the
Interleaved-IAMB (Inter-IAMB) algorithm, the Fast-IAMB
(Fast-IAMB) algorithm, the Max-Min Parents and Children (MMPC)
algorithm, the Hill-Climbing (HC) greedy search algorithm, the
Tabu Search (TABU) algorithm, the Max-Min Hill-Climbing (MMHC)
algorithm and the two-stage Restricted Maximization (RSMAX2)
algorithm for both discrete and Gaussian networks, along with
many score functions and conditional independence tests. Some
utility functions (model comparison and manipulation, random
data generation, arc orientation testing, simple and advanced
plots) are included, as well as basic parametric and bootstrap
inference functions.
Author: Marco Scutari
Maintainer: Marco Scutari
bnlearn-1.7/bnlearn/R/cpdag.R |only
bnlearn-1.8/bnlearn/Changelog | 22 ++
bnlearn-1.8/bnlearn/DESCRIPTION | 22 +-
bnlearn-1.8/bnlearn/NAMESPACE | 3
bnlearn-1.8/bnlearn/R/backend-indep.R | 2
bnlearn-1.8/bnlearn/R/choose.direction.R | 6
bnlearn-1.8/bnlearn/R/fast-iamb.R | 15 +
bnlearn-1.8/bnlearn/R/frontend-fit.R | 2
bnlearn-1.8/bnlearn/R/frontend-graph.R | 4
bnlearn-1.8/bnlearn/R/frontend-learning.R | 35 +++-
bnlearn-1.8/bnlearn/R/frontend-nodes.R | 36 +---
bnlearn-1.8/bnlearn/R/globals.R | 22 +-
bnlearn-1.8/bnlearn/R/graph-generation.R | 18 +-
bnlearn-1.8/bnlearn/R/grow-shrink.R | 143 +++++++++---------
bnlearn-1.8/bnlearn/R/hill-climbing.R | 4
bnlearn-1.8/bnlearn/R/incremental-association.R | 2
bnlearn-1.8/bnlearn/R/inter-iamb.R | 2
bnlearn-1.8/bnlearn/R/learning-algorithms.R | 52 ++++--
bnlearn-1.8/bnlearn/R/mvber.R | 2
bnlearn-1.8/bnlearn/R/tabu.R |only
bnlearn-1.8/bnlearn/R/test.R | 86 +++++-----
bnlearn-1.8/bnlearn/R/utils-graph.R | 52 ++----
bnlearn-1.8/bnlearn/R/utils-misc.R | 7
bnlearn-1.8/bnlearn/R/utils-sanitization.R | 127 ++++++++++++++-
bnlearn-1.8/bnlearn/data/hailfinder.rda |only
bnlearn-1.8/bnlearn/data/insurance.rda |only
bnlearn-1.8/bnlearn/inst/bibtex/bnlearn.bib | 71 ++++++++
bnlearn-1.8/bnlearn/inst/network.scripts/hailfinder.R |only
bnlearn-1.8/bnlearn/inst/network.scripts/insurance.R |only
bnlearn-1.8/bnlearn/man/alarm.Rd | 3
bnlearn-1.8/bnlearn/man/bn.fit.Rd | 3
bnlearn-1.8/bnlearn/man/bnlearn-package.Rd | 33 ++--
bnlearn-1.8/bnlearn/man/ci.test.Rd | 11 +
bnlearn-1.8/bnlearn/man/graph.Rd | 4
bnlearn-1.8/bnlearn/man/graphgen.Rd | 30 ++-
bnlearn-1.8/bnlearn/man/hailfinder.Rd |only
bnlearn-1.8/bnlearn/man/hc.Rd | 19 +-
bnlearn-1.8/bnlearn/man/hybrid.Rd | 27 +--
bnlearn-1.8/bnlearn/man/insurance.Rd |only
bnlearn-1.8/bnlearn/man/mb.Rd | 10 -
bnlearn-1.8/bnlearn/man/modelstring.Rd | 2
bnlearn-1.8/bnlearn/man/ordering.Rd | 4
bnlearn-1.8/bnlearn/src/allocations.c | 48 +++++-
bnlearn-1.8/bnlearn/src/bn.recovery.c | 12 -
bnlearn-1.8/bnlearn/src/common.c | 62 +++++++
bnlearn-1.8/bnlearn/src/common.h | 22 ++
bnlearn-1.8/bnlearn/src/configurations.c | 34 +++-
bnlearn-1.8/bnlearn/src/cpdag.c |only
bnlearn-1.8/bnlearn/src/graph.generation.c | 42 +++--
bnlearn-1.8/bnlearn/src/hc.cache.lookup.c | 12 -
bnlearn-1.8/bnlearn/src/is.dag.c | 12 -
bnlearn-1.8/bnlearn/src/monte.carlo.c | 141 -----------------
bnlearn-1.8/bnlearn/src/mvber.c | 6
bnlearn-1.8/bnlearn/src/path.c | 97 ++++++++++++
bnlearn-1.8/bnlearn/src/pdag2dag.c | 14 -
bnlearn-1.8/bnlearn/src/shrinkage.c |only
bnlearn-1.8/bnlearn/src/symmetric.c |only
bnlearn-1.8/bnlearn/src/tabu.c |only
58 files changed, 871 insertions(+), 512 deletions(-)
Title: Scalable Least-Angle Regression and Lasso
Diff between biglars versions 1.0 dated 2010-01-05 and 1.0.1 dated 2010-01-07
Description: Least-angle regression, lasso and stepwise regression for
numeric datasets in which the number of observations is greater
than the number of predictors. The functions can be used with
the ff library to accomodate datasets that are too large to be
held in memory.
Author: Mark Seligman, Chris Fraley, Tim Hesterberg
Maintainer: Mark Seligman
ChangeLog |only
DESCRIPTION | 6 +++---
src/Makevars |only
3 files changed, 3 insertions(+), 3 deletions(-)
Title: Support package for aroma.affymetrix et al.
Diff between aroma.core versions 1.3.1 dated 2009-11-03 and 1.4.0 dated 2010-01-07
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
aroma.core-1.3.1/aroma.core/R/getCommonPrefix.R |only
aroma.core-1.3.1/aroma.core/R/print.GenericSummary.R |only
aroma.core-1.3.1/aroma.core/man/extract.AromaMicroarrayDataSetTuple.Rd |only
aroma.core-1.3.1/aroma.core/man/getArrayTuple.AromaMicroarrayDataSetTuple.Rd |only
aroma.core-1.3.1/aroma.core/man/getArrays.AromaMicroarrayDataSetTuple.Rd |only
aroma.core-1.3.1/aroma.core/man/getArrays.Explorer.Rd |only
aroma.core-1.3.1/aroma.core/man/getTableOfArrays.AromaMicroarrayDataSetTuple.Rd |only
aroma.core-1.3.1/aroma.core/man/indexOfArrays.AromaMicroarrayDataSetTuple.Rd |only
aroma.core-1.3.1/aroma.core/man/nbrOfArrays.AromaMicroarrayDataSetTuple.Rd |only
aroma.core-1.4.0/aroma.core/DESCRIPTION | 21
aroma.core-1.4.0/aroma.core/R/AromaCellPositionFile.R | 4
aroma.core-1.4.0/aroma.core/R/AromaCellSequenceFile.R | 16
aroma.core-1.4.0/aroma.core/R/AromaCellSequenceFile.REPEATS.R | 2
aroma.core-1.4.0/aroma.core/R/AromaMicroarrayDataFile.R | 8
aroma.core-1.4.0/aroma.core/R/AromaMicroarrayDataSet.ATTRS.R | 4
aroma.core-1.4.0/aroma.core/R/AromaMicroarrayDataSet.EXT.R |only
aroma.core-1.4.0/aroma.core/R/AromaMicroarrayDataSet.R | 8
aroma.core-1.4.0/aroma.core/R/AromaMicroarrayDataSetTuple.DEPRECATED.R |only
aroma.core-1.4.0/aroma.core/R/AromaMicroarrayDataSetTuple.R | 960 ++--------
aroma.core-1.4.0/aroma.core/R/AromaTabularBinaryFile.R | 22
aroma.core-1.4.0/aroma.core/R/AromaTabularBinarySet.R | 8
aroma.core-1.4.0/aroma.core/R/AromaTransform.R | 5
aroma.core-1.4.0/aroma.core/R/AromaUflFile.R |only
aroma.core-1.4.0/aroma.core/R/AromaUgpFile.R | 5
aroma.core-1.4.0/aroma.core/R/AromaUnitCallFile.R | 28
aroma.core-1.4.0/aroma.core/R/AromaUnitFracBCnBinarySet.R | 6
aroma.core-1.4.0/aroma.core/R/AromaUnitGenotypeCallFile.R | 5
aroma.core-1.4.0/aroma.core/R/AromaUnitSignalBinaryFile.R | 26
aroma.core-1.4.0/aroma.core/R/AromaUnitTabularBinaryFile.R | 12
aroma.core-1.4.0/aroma.core/R/AromaUnitTotalCnBinaryFile.R | 73
aroma.core-1.4.0/aroma.core/R/AromaUnitTotalCnBinaryFile.xam.R |only
aroma.core-1.4.0/aroma.core/R/AromaUnitTotalCnBinarySet.R | 251 ++
aroma.core-1.4.0/aroma.core/R/AromaUnitTotalCnBinarySetTuple.R |only
aroma.core-1.4.0/aroma.core/R/AromaUnitTypesFile.R | 4
aroma.core-1.4.0/aroma.core/R/CbsModel.R |only
aroma.core-1.4.0/aroma.core/R/ChromosomalModel.R |only
aroma.core-1.4.0/aroma.core/R/ChromosomalModel.drawCytoband.R |only
aroma.core-1.4.0/aroma.core/R/ChromosomeExplorer.R |only
aroma.core-1.4.0/aroma.core/R/CopyNumberChromosomalModel.R |only
aroma.core-1.4.0/aroma.core/R/CopyNumberChromosomalModel.newPlot.R |only
aroma.core-1.4.0/aroma.core/R/CopyNumberChromosomalModel.plotChromosomesLayers.R |only
aroma.core-1.4.0/aroma.core/R/CopyNumberChromosomalModel.plotFitLayers.R |only
aroma.core-1.4.0/aroma.core/R/CopyNumberChromosomalModel.plotRawCopyNumbers.R |only
aroma.core-1.4.0/aroma.core/R/CopyNumberChromosomalModel.plotSampleLayers.R |only
aroma.core-1.4.0/aroma.core/R/CopyNumberDataSetTuple.R |only
aroma.core-1.4.0/aroma.core/R/CopyNumberOutliers.FOREIGN.R |only
aroma.core-1.4.0/aroma.core/R/CopyNumberOutliers.R | 4
aroma.core-1.4.0/aroma.core/R/CopyNumberRegions.R | 4
aroma.core-1.4.0/aroma.core/R/CopyNumberSegmentationModel.R |only
aroma.core-1.4.0/aroma.core/R/CopyNumberSegmentationModel.plot.R |only
aroma.core-1.4.0/aroma.core/R/CopyNumberSegmentationModel.plotCopyNumberRegionLayers.R |only
aroma.core-1.4.0/aroma.core/R/Explorer.R | 33
aroma.core-1.4.0/aroma.core/R/GladModel.R |only
aroma.core-1.4.0/aroma.core/R/GladModel.onFitAddGenotypeCalls.R |only
aroma.core-1.4.0/aroma.core/R/HaarSegModel.R |only
aroma.core-1.4.0/aroma.core/R/MPCBS.EXTS.R |only
aroma.core-1.4.0/aroma.core/R/RawCopyNumberModel.R |only
aroma.core-1.4.0/aroma.core/R/RawCopyNumbers.R | 40
aroma.core-1.4.0/aroma.core/R/RawGenomicSignals.OPS.R | 6
aroma.core-1.4.0/aroma.core/R/RawGenomicSignals.R | 11
aroma.core-1.4.0/aroma.core/R/RawGenomicSignals.append.R | 4
aroma.core-1.4.0/aroma.core/R/RawGenomicSignals.segmentByMPCBS.R |only
aroma.core-1.4.0/aroma.core/R/RawSequenceReads.EXTRAS.R | 20
aroma.core-1.4.0/aroma.core/R/SampleAnnotationSet.R | 3
aroma.core-1.4.0/aroma.core/R/TextUnitNamesFile.R | 2
aroma.core-1.4.0/aroma.core/R/UnitAnnotationDataFile.R | 38
aroma.core-1.4.0/aroma.core/R/profileCGH.drawExtraAnnotations.R |only
aroma.core-1.4.0/aroma.core/R/profileCGH.plot.R |only
aroma.core-1.4.0/aroma.core/R/profileCGH.plotProfile2.R |only
aroma.core-1.4.0/aroma.core/R/profileCGH.plotRawCNs.R |only
aroma.core-1.4.0/aroma.core/incl/999.missingdocs.txt | 537 +++--
aroma.core-1.4.0/aroma.core/inst/NEWS | 82
aroma.core-1.4.0/aroma.core/inst/reports/includes/js/ChromosomeExplorer3.1/ChromosomeExplorer.js | 9
aroma.core-1.4.0/aroma.core/inst/reports/templates/html/ArrayExplorer/ArrayExplorer.html | 2
aroma.core-1.4.0/aroma.core/inst/reports/templates/html/ChromosomeExplorer/ChromosomeExplorer.html | 7
aroma.core-1.4.0/aroma.core/inst/reports/templates/rsp/ChromosomeExplorer3/ChromosomeExplorer.onLoad.js.rsp | 1
aroma.core-1.4.0/aroma.core/man/AromaMicroarrayDataFile.Rd | 2
aroma.core-1.4.0/aroma.core/man/AromaMicroarrayDataSet.Rd | 7
aroma.core-1.4.0/aroma.core/man/AromaMicroarrayDataSetTuple.Rd | 38
aroma.core-1.4.0/aroma.core/man/AromaMicroarrayTabularBinaryFile.Rd | 2
aroma.core-1.4.0/aroma.core/man/AromaTabularBinaryFile.Rd | 2
aroma.core-1.4.0/aroma.core/man/AromaUnitCallFile.Rd | 2
aroma.core-1.4.0/aroma.core/man/AromaUnitFracBCnBinaryFile.Rd | 2
aroma.core-1.4.0/aroma.core/man/AromaUnitGenotypeCallFile.Rd | 2
aroma.core-1.4.0/aroma.core/man/AromaUnitSignalBinaryFile.Rd | 1
aroma.core-1.4.0/aroma.core/man/AromaUnitTabularBinaryFile.Rd | 11
aroma.core-1.4.0/aroma.core/man/AromaUnitTotalCnBinaryFile.Rd | 16
aroma.core-1.4.0/aroma.core/man/AromaUnitTotalCnBinarySet.Rd | 14
aroma.core-1.4.0/aroma.core/man/AromaUnitTypesFile.Rd | 4
aroma.core-1.4.0/aroma.core/man/BinnedScatter.Rd | 2
aroma.core-1.4.0/aroma.core/man/CbsModel.Rd |only
aroma.core-1.4.0/aroma.core/man/ChromosomalModel.Rd |only
aroma.core-1.4.0/aroma.core/man/ChromosomeExplorer.Rd |only
aroma.core-1.4.0/aroma.core/man/CopyNumberChromosomalModel.Rd |only
aroma.core-1.4.0/aroma.core/man/CopyNumberSegmentationModel.Rd |only
aroma.core-1.4.0/aroma.core/man/Explorer.Rd | 4
aroma.core-1.4.0/aroma.core/man/GladModel.Rd |only
aroma.core-1.4.0/aroma.core/man/HaarSegModel.Rd |only
aroma.core-1.4.0/aroma.core/man/Non-documented_objects.Rd | 512 +++--
aroma.core-1.4.0/aroma.core/man/RawCopyNumberModel.Rd |only
aroma.core-1.4.0/aroma.core/man/RawCopyNumbers.Rd | 1
aroma.core-1.4.0/aroma.core/man/RawGenomicSignals.Rd | 2
aroma.core-1.4.0/aroma.core/man/SegmentedCopyNumbers.Rd | 2
aroma.core-1.4.0/aroma.core/man/UnitAnnotationDataFile.Rd | 7
aroma.core-1.4.0/aroma.core/man/UnitNamesFile.Rd | 4
aroma.core-1.4.0/aroma.core/man/UnitTypesFile.Rd | 4
aroma.core-1.4.0/aroma.core/man/estimateSds.CopyNumberChromosomalModel.Rd |only
aroma.core-1.4.0/aroma.core/man/extractRawCopyNumbers.CopyNumberChromosomalModel.Rd |only
aroma.core-1.4.0/aroma.core/man/fit.CopyNumberChromosomalModel.Rd |only
aroma.core-1.4.0/aroma.core/man/fit.CopyNumberSegmentationModel.Rd |only
aroma.core-1.4.0/aroma.core/man/getChipType.ChromosomalModel.Rd |only
aroma.core-1.4.0/aroma.core/man/getChromosomes.ChromosomalModel.Rd |only
aroma.core-1.4.0/aroma.core/man/getChromosomes.ChromosomeExplorer.Rd |only
aroma.core-1.4.0/aroma.core/man/getModel.ChromosomeExplorer.Rd |only
aroma.core-1.4.0/aroma.core/man/getNames.ChromosomalModel.Rd |only
aroma.core-1.4.0/aroma.core/man/getNames.Explorer.Rd |only
aroma.core-1.4.0/aroma.core/man/nbrOfArrays.ChromosomalModel.Rd |only
aroma.core-1.4.0/aroma.core/man/nbrOfChipTypes.AromaMicroarrayDataSetTuple.Rd | 1
aroma.core-1.4.0/aroma.core/man/nbrOfChipTypes.ChromosomalModel.Rd |only
aroma.core-1.4.0/aroma.core/man/process.ChromosomeExplorer.Rd |only
aroma.core-1.4.0/aroma.core/man/setArrays.ChromosomeExplorer.Rd |only
aroma.core-1.4.0/aroma.core/man/updateSamplesFile.ChromosomeExplorer.Rd |only
122 files changed, 1673 insertions(+), 1240 deletions(-)
Title: Analysis of large Affymetrix microarray data sets
Diff between aroma.affymetrix versions 1.3.0 dated 2009-11-03 and 1.4.0 dated 2010-01-07
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 what number of arrays can
be analyzed.
Author: Henrik Bengtsson
Maintainer: Henrik Bengtsson
aroma.affymetrix-1.3.0/aroma.affymetrix/R/AromaUflFile.R |only
aroma.affymetrix-1.3.0/aroma.affymetrix/R/AromaUflFile.summaryOfUnits.R |only
aroma.affymetrix-1.3.0/aroma.affymetrix/R/CbsModel.R |only
aroma.affymetrix-1.3.0/aroma.affymetrix/R/ChromosomalModel.R |only
aroma.affymetrix-1.3.0/aroma.affymetrix/R/ChromosomalModel.drawCytoband.R |only
aroma.affymetrix-1.3.0/aroma.affymetrix/R/ChromosomeExplorer.R |only
aroma.affymetrix-1.3.0/aroma.affymetrix/R/CopyNumberChromosomalModel.R |only
aroma.affymetrix-1.3.0/aroma.affymetrix/R/CopyNumberChromosomalModel.newPlot.R |only
aroma.affymetrix-1.3.0/aroma.affymetrix/R/CopyNumberChromosomalModel.plotChromosomesLayers.R |only
aroma.affymetrix-1.3.0/aroma.affymetrix/R/CopyNumberChromosomalModel.plotFitLayers.R |only
aroma.affymetrix-1.3.0/aroma.affymetrix/R/CopyNumberChromosomalModel.plotRawCopyNumbers.R |only
aroma.affymetrix-1.3.0/aroma.affymetrix/R/CopyNumberChromosomalModel.plotSampleLayers.R |only
aroma.affymetrix-1.3.0/aroma.affymetrix/R/CopyNumberOutliers.FOREIGN.R |only
aroma.affymetrix-1.3.0/aroma.affymetrix/R/CopyNumberSegmentationModel.R |only
aroma.affymetrix-1.3.0/aroma.affymetrix/R/CopyNumberSegmentationModel.plot.R |only
aroma.affymetrix-1.3.0/aroma.affymetrix/R/CopyNumberSegmentationModel.plotCopyNumberRegionLayers.R |only
aroma.affymetrix-1.3.0/aroma.affymetrix/R/GladModel.R |only
aroma.affymetrix-1.3.0/aroma.affymetrix/R/GladModel.onFitAddGenotypeCalls.R |only
aroma.affymetrix-1.3.0/aroma.affymetrix/R/HaarSegModel.R |only
aroma.affymetrix-1.3.0/aroma.affymetrix/R/RawCopyNumberModel.R |only
aroma.affymetrix-1.3.0/aroma.affymetrix/R/profileCGH.drawExtraAnnotations.R |only
aroma.affymetrix-1.3.0/aroma.affymetrix/R/profileCGH.plot.R |only
aroma.affymetrix-1.3.0/aroma.affymetrix/R/profileCGH.plotProfile2.R |only
aroma.affymetrix-1.3.0/aroma.affymetrix/R/profileCGH.plotRawCNs.R |only
aroma.affymetrix-1.3.0/aroma.affymetrix/man/CbsModel.Rd |only
aroma.affymetrix-1.3.0/aroma.affymetrix/man/ChromosomalModel.Rd |only
aroma.affymetrix-1.3.0/aroma.affymetrix/man/ChromosomeExplorer.Rd |only
aroma.affymetrix-1.3.0/aroma.affymetrix/man/CopyNumberChromosomalModel.Rd |only
aroma.affymetrix-1.3.0/aroma.affymetrix/man/CopyNumberSegmentationModel.Rd |only
aroma.affymetrix-1.3.0/aroma.affymetrix/man/GladModel.Rd |only
aroma.affymetrix-1.3.0/aroma.affymetrix/man/HaarSegModel.Rd |only
aroma.affymetrix-1.3.0/aroma.affymetrix/man/RawCopyNumberModel.Rd |only
aroma.affymetrix-1.3.0/aroma.affymetrix/man/estimateSds.CopyNumberChromosomalModel.Rd |only
aroma.affymetrix-1.3.0/aroma.affymetrix/man/fit.CopyNumberChromosomalModel.Rd |only
aroma.affymetrix-1.3.0/aroma.affymetrix/man/fit.CopyNumberSegmentationModel.Rd |only
aroma.affymetrix-1.3.0/aroma.affymetrix/man/getArrays.ChromosomalModel.Rd |only
aroma.affymetrix-1.3.0/aroma.affymetrix/man/getChipType.ChromosomalModel.Rd |only
aroma.affymetrix-1.3.0/aroma.affymetrix/man/getChromosomes.ChromosomalModel.Rd |only
aroma.affymetrix-1.3.0/aroma.affymetrix/man/getChromosomes.ChromosomeExplorer.Rd |only
aroma.affymetrix-1.3.0/aroma.affymetrix/man/getModel.ChromosomeExplorer.Rd |only
aroma.affymetrix-1.3.0/aroma.affymetrix/man/getTableOfArrays.ChromosomalModel.Rd |only
aroma.affymetrix-1.3.0/aroma.affymetrix/man/indexOfArrays.ChromosomalModel.Rd |only
aroma.affymetrix-1.3.0/aroma.affymetrix/man/nbrOfArrays.ChromosomalModel.Rd |only
aroma.affymetrix-1.3.0/aroma.affymetrix/man/nbrOfChipTypes.ChromosomalModel.Rd |only
aroma.affymetrix-1.3.0/aroma.affymetrix/man/process.ChromosomeExplorer.Rd |only
aroma.affymetrix-1.3.0/aroma.affymetrix/man/setArrays.ChromosomeExplorer.Rd |only
aroma.affymetrix-1.3.0/aroma.affymetrix/man/updateSamplesFile.ChromosomeExplorer.Rd |only
aroma.affymetrix-1.4.0/aroma.affymetrix/DESCRIPTION | 19
aroma.affymetrix-1.4.0/aroma.affymetrix/R/999.AromaAffymetrix.R | 2
aroma.affymetrix-1.4.0/aroma.affymetrix/R/ASCRMAv2.R |only
aroma.affymetrix-1.4.0/aroma.affymetrix/R/AdditiveCovariatesNormalization.R | 9
aroma.affymetrix-1.4.0/aroma.affymetrix/R/AffymetrixCdfFile.R | 27
aroma.affymetrix-1.4.0/aroma.affymetrix/R/AffymetrixCdfFile.getAlleleCellPairs.R | 2
aroma.affymetrix-1.4.0/aroma.affymetrix/R/AffymetrixCdfFile.getCellQuartets.R | 2
aroma.affymetrix-1.4.0/aroma.affymetrix/R/AffymetrixCdfFile.getSubsetOfCellIndices.R | 4
aroma.affymetrix-1.4.0/aroma.affymetrix/R/AffymetrixCdfFile.getSubsetOfUnits.R | 4
aroma.affymetrix-1.4.0/aroma.affymetrix/R/AffymetrixCdfFile.getUnitGroupCellMap.R | 2
aroma.affymetrix-1.4.0/aroma.affymetrix/R/AffymetrixCdfFile.readDataFrame.R | 2
aroma.affymetrix-1.4.0/aroma.affymetrix/R/AffymetrixCelFile.BG.R | 3
aroma.affymetrix-1.4.0/aroma.affymetrix/R/AffymetrixCelFile.PLOT.R | 7
aroma.affymetrix-1.4.0/aroma.affymetrix/R/AffymetrixCelFile.R | 9
aroma.affymetrix-1.4.0/aroma.affymetrix/R/AffymetrixCelFile.allocateFromCdf.R | 4
aroma.affymetrix-1.4.0/aroma.affymetrix/R/AffymetrixCelFile.extractMatrix.R | 2
aroma.affymetrix-1.4.0/aroma.affymetrix/R/AffymetrixCelFile.normalizeQuantile.R | 3
aroma.affymetrix-1.4.0/aroma.affymetrix/R/AffymetrixCelSet.R | 28
aroma.affymetrix-1.4.0/aroma.affymetrix/R/AffymetrixCelSet.extractMatrix.R | 2
aroma.affymetrix-1.4.0/aroma.affymetrix/R/AffymetrixCelSet.xtras.R | 5
aroma.affymetrix-1.4.0/aroma.affymetrix/R/AffymetrixCelSetTuple.R | 8
aroma.affymetrix-1.4.0/aroma.affymetrix/R/AffymetrixCnChpFile.R | 7
aroma.affymetrix-1.4.0/aroma.affymetrix/R/AffymetrixCnChpSet.R | 11
aroma.affymetrix-1.4.0/aroma.affymetrix/R/AffymetrixFileSet.R | 4
aroma.affymetrix-1.4.0/aroma.affymetrix/R/AffymetrixFileSetReporter.R | 5
aroma.affymetrix-1.4.0/aroma.affymetrix/R/AffymetrixNetAffxCsvFile.R | 2
aroma.affymetrix-1.4.0/aroma.affymetrix/R/AlleleSummation.R | 5
aroma.affymetrix-1.4.0/aroma.affymetrix/R/AllelicCrosstalkCalibration.PLOT.R | 4
aroma.affymetrix-1.4.0/aroma.affymetrix/R/AllelicCrosstalkCalibration.R | 11
aroma.affymetrix-1.4.0/aroma.affymetrix/R/AromaCellMatchScoreFile.AFFX.R | 36
aroma.affymetrix-1.4.0/aroma.affymetrix/R/AromaCellMatchScoreFile.R | 4
aroma.affymetrix-1.4.0/aroma.affymetrix/R/AromaCellPositionFile.AFFX.R | 35
aroma.affymetrix-1.4.0/aroma.affymetrix/R/AromaCellSequenceFile.AFFX.R | 12
aroma.affymetrix-1.4.0/aroma.affymetrix/R/AromaPipeline.R |only
aroma.affymetrix-1.4.0/aroma.affymetrix/R/AromaUfcFile.R | 6
aroma.affymetrix-1.4.0/aroma.affymetrix/R/AromaUflFile.AFFX.R |only
aroma.affymetrix-1.4.0/aroma.affymetrix/R/AromaUgpFile.AFFX.R | 14
aroma.affymetrix-1.4.0/aroma.affymetrix/R/AromaUnitGcContentFile.AFFX.R | 4
aroma.affymetrix-1.4.0/aroma.affymetrix/R/AromaUnitTabularBinaryFile.AFFX.R | 12
aroma.affymetrix-1.4.0/aroma.affymetrix/R/ArrayExplorer.R | 26
aroma.affymetrix-1.4.0/aroma.affymetrix/R/BaseCountNormalization.R | 6
aroma.affymetrix-1.4.0/aroma.affymetrix/R/BasePositionNormalization.getFit.R | 2
aroma.affymetrix-1.4.0/aroma.affymetrix/R/ChipEffectFile.fromDataFile.R | 6
aroma.affymetrix-1.4.0/aroma.affymetrix/R/ChipEffectFile.getUnitGroupCellMatrixMap.R | 8
aroma.affymetrix-1.4.0/aroma.affymetrix/R/ChipEffectFile.xam.R | 60
aroma.affymetrix-1.4.0/aroma.affymetrix/R/ChipEffectGroupMerge.R | 3
aroma.affymetrix-1.4.0/aroma.affymetrix/R/ChipEffectNnn.extractChromosomalDataFrame.R | 2
aroma.affymetrix-1.4.0/aroma.affymetrix/R/ChipEffectSet.R | 2
aroma.affymetrix-1.4.0/aroma.affymetrix/R/ChipEffectSet.STATS.R | 12
aroma.affymetrix-1.4.0/aroma.affymetrix/R/ChipEffectSet.extractTheta.R | 4
aroma.affymetrix-1.4.0/aroma.affymetrix/R/ChipEffectSet.xam.R | 60
aroma.affymetrix-1.4.0/aroma.affymetrix/R/ChipEffectSetTuple.R | 23
aroma.affymetrix-1.4.0/aroma.affymetrix/R/ChipEffectTransform.R | 5
aroma.affymetrix-1.4.0/aroma.affymetrix/R/ChromosomalModel.AFFX.R |only
aroma.affymetrix-1.4.0/aroma.affymetrix/R/CnChipEffectFile.R | 70
aroma.affymetrix-1.4.0/aroma.affymetrix/R/CnChipEffectSet.R | 20
aroma.affymetrix-1.4.0/aroma.affymetrix/R/CnChipEffectSet.importFromApt.R | 4
aroma.affymetrix-1.4.0/aroma.affymetrix/R/CnChipEffectSet.importFromDChip.R | 4
aroma.affymetrix-1.4.0/aroma.affymetrix/R/CnChipEffectSet.writeWig.R | 7
aroma.affymetrix-1.4.0/aroma.affymetrix/R/CnChipEffectSetTuple.R |only
aroma.affymetrix-1.4.0/aroma.affymetrix/R/CnagCfhFile.R | 6
aroma.affymetrix-1.4.0/aroma.affymetrix/R/CnagCfhSet.R | 16
aroma.affymetrix-1.4.0/aroma.affymetrix/R/CopyNumberChromosomalModel.AFFX.R |only
aroma.affymetrix-1.4.0/aroma.affymetrix/R/CopyNumberChromosomalModel.applyCCF.R | 21
aroma.affymetrix-1.4.0/aroma.affymetrix/R/CrlmmModel.R | 7
aroma.affymetrix-1.4.0/aroma.affymetrix/R/DChipCdfBinFile.R | 4
aroma.affymetrix-1.4.0/aroma.affymetrix/R/DChipCdfBinFile.mapToUnitNamesFile.R | 4
aroma.affymetrix-1.4.0/aroma.affymetrix/R/DChipDcpFile.R | 18
aroma.affymetrix-1.4.0/aroma.affymetrix/R/DChipDcpSet.R | 4
aroma.affymetrix-1.4.0/aroma.affymetrix/R/DChipGenomeInformation.R | 2
aroma.affymetrix-1.4.0/aroma.affymetrix/R/FirmaFile.R | 6
aroma.affymetrix-1.4.0/aroma.affymetrix/R/FirmaModel.R | 6
aroma.affymetrix-1.4.0/aroma.affymetrix/R/FragmentEquivalentClassNormalization.R | 8
aroma.affymetrix-1.4.0/aroma.affymetrix/R/FragmentLengthNormalization.R | 10
aroma.affymetrix-1.4.0/aroma.affymetrix/R/GcContentNormalization.R | 9
aroma.affymetrix-1.4.0/aroma.affymetrix/R/GcContentNormalization2.R | 2
aroma.affymetrix-1.4.0/aroma.affymetrix/R/GcContentNormalization2.plotCovariateEffects.R | 4
aroma.affymetrix-1.4.0/aroma.affymetrix/R/GenomeInformation.AFFX.R | 4
aroma.affymetrix-1.4.0/aroma.affymetrix/R/LinearModelProbeSequenceNormalization.R | 8
aroma.affymetrix-1.4.0/aroma.affymetrix/R/MatSmoothing.R | 2
aroma.affymetrix-1.4.0/aroma.affymetrix/R/Model.R | 4
aroma.affymetrix-1.4.0/aroma.affymetrix/R/ParameterCelFile.extractNnn.R | 2
aroma.affymetrix-1.4.0/aroma.affymetrix/R/ParameterCelSet.R | 2
aroma.affymetrix-1.4.0/aroma.affymetrix/R/ProbeLevelModel.fit.R | 2
aroma.affymetrix-1.4.0/aroma.affymetrix/R/ProbeLevelTransform3.R | 18
aroma.affymetrix-1.4.0/aroma.affymetrix/R/QualityAssessmentModel.R | 3
aroma.affymetrix-1.4.0/aroma.affymetrix/R/ReseqCrosstalkCalibration.R | 9
aroma.affymetrix-1.4.0/aroma.affymetrix/R/ResidualFile.R | 6
aroma.affymetrix-1.4.0/aroma.affymetrix/R/ResidualSet.R | 3
aroma.affymetrix-1.4.0/aroma.affymetrix/R/ScaleNormalization.R | 3
aroma.affymetrix-1.4.0/aroma.affymetrix/R/ScaleNormalization3.R | 8
aroma.affymetrix-1.4.0/aroma.affymetrix/R/SingleArrayUnitModel.R | 2
aroma.affymetrix-1.4.0/aroma.affymetrix/R/SingleArrayUnitModel.fit.R | 4
aroma.affymetrix-1.4.0/aroma.affymetrix/R/SmoothMultiarrayModel.R | 4
aroma.affymetrix-1.4.0/aroma.affymetrix/R/SmoothMultiarrayModel.fit.R | 4
aroma.affymetrix-1.4.0/aroma.affymetrix/R/SnpChipEffectFile.R | 2
aroma.affymetrix-1.4.0/aroma.affymetrix/R/SnpChipEffectFile.extractTotalAndFracB.R | 4
aroma.affymetrix-1.4.0/aroma.affymetrix/R/SnpChipEffectNnn.extractCNT.R | 9
aroma.affymetrix-1.4.0/aroma.affymetrix/R/SnpChipEffectSet.extractSnpCnvQSet.R | 2
aroma.affymetrix-1.4.0/aroma.affymetrix/R/SnpChipEffectSet.extractSnpQSet.R | 2
aroma.affymetrix-1.4.0/aroma.affymetrix/R/SnpChipEffectSet.extractTotalAndFreqB.R | 2
aroma.affymetrix-1.4.0/aroma.affymetrix/R/SnpInformation.R | 4
aroma.affymetrix-1.4.0/aroma.affymetrix/R/SpatialReporter.R | 14
aroma.affymetrix-1.4.0/aroma.affymetrix/R/TransformReport.R | 13
aroma.affymetrix-1.4.0/aroma.affymetrix/R/UflSnpInformation.R | 7
aroma.affymetrix-1.4.0/aroma.affymetrix/R/UgpGenomeInformation.R | 6
aroma.affymetrix-1.4.0/aroma.affymetrix/R/UnitModel.R | 4
aroma.affymetrix-1.4.0/aroma.affymetrix/R/UnitTypeScaleNormalization.R | 8
aroma.affymetrix-1.4.0/aroma.affymetrix/R/WeightsFile.R | 6
aroma.affymetrix-1.4.0/aroma.affymetrix/R/doCRMA.R | 3
aroma.affymetrix-1.4.0/aroma.affymetrix/R/readCfhUnits.R | 2
aroma.affymetrix-1.4.0/aroma.affymetrix/incl/999.missingdocs.txt | 1163 +++-------
aroma.affymetrix-1.4.0/aroma.affymetrix/inst/NEWS | 55
aroma.affymetrix-1.4.0/aroma.affymetrix/inst/testScripts/replication/chipTypes/HG-U133_Plus_2/affyPLM,fitPLM.R | 8
aroma.affymetrix-1.4.0/aroma.affymetrix/inst/testScripts/robustness |only
aroma.affymetrix-1.4.0/aroma.affymetrix/inst/testScripts/system/chipTypes/Mapping10K_Xba142/test20070726,10K,QA.R | 71
aroma.affymetrix-1.4.0/aroma.affymetrix/inst/testScripts/system/chipTypes/Mapping10K_Xba142/test20081217,10K,CRMAv2,ASCN,1array.R | 9
aroma.affymetrix-1.4.0/aroma.affymetrix/inst/testScripts/system/chipTypes/Mapping10K_Xba142/test20091120,10K,ASB,segmentation.R |only
aroma.affymetrix-1.4.0/aroma.affymetrix/inst/testScripts/system/chipTypes/Mapping10K_Xba142/test20100104,10K,CRMAv2,subset.R |only
aroma.affymetrix-1.4.0/aroma.affymetrix/inst/testScripts/system/chipTypes/Mapping50K_Hind240,Xba240/test20070412,100K,CN.R | 5
aroma.affymetrix-1.4.0/aroma.affymetrix/man/AffymetrixCdfFile.Rd | 4
aroma.affymetrix-1.4.0/aroma.affymetrix/man/AffymetrixCelFile.Rd | 2
aroma.affymetrix-1.4.0/aroma.affymetrix/man/AffymetrixCelSet.Rd | 2
aroma.affymetrix-1.4.0/aroma.affymetrix/man/AffymetrixCelSetTuple.Rd | 18
aroma.affymetrix-1.4.0/aroma.affymetrix/man/AffymetrixCnChpSet.Rd | 2
aroma.affymetrix-1.4.0/aroma.affymetrix/man/AffymetrixFile.Rd | 2
aroma.affymetrix-1.4.0/aroma.affymetrix/man/AffymetrixFileSet.Rd | 2
aroma.affymetrix-1.4.0/aroma.affymetrix/man/AromaChipTypeAnnotationFile.Rd | 2
aroma.affymetrix-1.4.0/aroma.affymetrix/man/ArrayExplorer.Rd | 2
aroma.affymetrix-1.4.0/aroma.affymetrix/man/ChipEffectFile.Rd | 2
aroma.affymetrix-1.4.0/aroma.affymetrix/man/ChipEffectSet.Rd | 2
aroma.affymetrix-1.4.0/aroma.affymetrix/man/CnChipEffectFile.Rd | 13
aroma.affymetrix-1.4.0/aroma.affymetrix/man/CnChipEffectSet.Rd | 14
aroma.affymetrix-1.4.0/aroma.affymetrix/man/CnProbeAffinityFile.Rd | 2
aroma.affymetrix-1.4.0/aroma.affymetrix/man/CnagCfhFile.Rd | 2
aroma.affymetrix-1.4.0/aroma.affymetrix/man/CrlmmParametersFile.Rd | 2
aroma.affymetrix-1.4.0/aroma.affymetrix/man/DChipCdfBinFile.Rd | 4
aroma.affymetrix-1.4.0/aroma.affymetrix/man/DChipDcpFile.Rd | 2
aroma.affymetrix-1.4.0/aroma.affymetrix/man/DChipDcpSet.Rd | 2
aroma.affymetrix-1.4.0/aroma.affymetrix/man/ExonChipEffectFile.Rd | 2
aroma.affymetrix-1.4.0/aroma.affymetrix/man/ExonChipEffectSet.Rd | 2
aroma.affymetrix-1.4.0/aroma.affymetrix/man/ExonProbeAffinityFile.Rd | 2
aroma.affymetrix-1.4.0/aroma.affymetrix/man/ExonRmaPlm.Rd | 14
aroma.affymetrix-1.4.0/aroma.affymetrix/man/FirmaFile.Rd | 2
aroma.affymetrix-1.4.0/aroma.affymetrix/man/FirmaSet.Rd | 2
aroma.affymetrix-1.4.0/aroma.affymetrix/man/HetLogAddCnPlm.Rd | 4
aroma.affymetrix-1.4.0/aroma.affymetrix/man/HetLogAddPlm.Rd | 6
aroma.affymetrix-1.4.0/aroma.affymetrix/man/HetLogAddSnpPlm.Rd | 4
aroma.affymetrix-1.4.0/aroma.affymetrix/man/Model.Rd | 2
aroma.affymetrix-1.4.0/aroma.affymetrix/man/MultiArrayUnitModel.Rd | 2
aroma.affymetrix-1.4.0/aroma.affymetrix/man/Non-documented_objects.Rd | 1163 +++-------
aroma.affymetrix-1.4.0/aroma.affymetrix/man/ParameterCelFile.Rd | 2
aroma.affymetrix-1.4.0/aroma.affymetrix/man/ParameterCelSet.Rd | 2
aroma.affymetrix-1.4.0/aroma.affymetrix/man/ProbeAffinityFile.Rd | 2
aroma.affymetrix-1.4.0/aroma.affymetrix/man/ProbeLevelModel.Rd | 2
aroma.affymetrix-1.4.0/aroma.affymetrix/man/QualityAssessmentFile.Rd | 2
aroma.affymetrix-1.4.0/aroma.affymetrix/man/QualityAssessmentSet.Rd | 2
aroma.affymetrix-1.4.0/aroma.affymetrix/man/ResidualFile.Rd | 2
aroma.affymetrix-1.4.0/aroma.affymetrix/man/ResidualSet.Rd | 2
aroma.affymetrix-1.4.0/aroma.affymetrix/man/RmaCnPlm.Rd | 4
aroma.affymetrix-1.4.0/aroma.affymetrix/man/RmaPlm.Rd | 5
aroma.affymetrix-1.4.0/aroma.affymetrix/man/RmaSnpPlm.Rd | 4
aroma.affymetrix-1.4.0/aroma.affymetrix/man/SmoothMultiarrayModel.Rd | 6
aroma.affymetrix-1.4.0/aroma.affymetrix/man/SmoothRmaModel.Rd | 4
aroma.affymetrix-1.4.0/aroma.affymetrix/man/SnpChipEffectFile.Rd | 2
aroma.affymetrix-1.4.0/aroma.affymetrix/man/SnpChipEffectSet.Rd | 2
aroma.affymetrix-1.4.0/aroma.affymetrix/man/SnpProbeAffinityFile.Rd | 2
aroma.affymetrix-1.4.0/aroma.affymetrix/man/UnitModel.Rd | 2
aroma.affymetrix-1.4.0/aroma.affymetrix/man/WeightsFile.Rd | 2
aroma.affymetrix-1.4.0/aroma.affymetrix/man/WeightsSet.Rd | 2
aroma.affymetrix-1.4.0/aroma.affymetrix/man/setArrays.ArrayExplorer.Rd | 2
218 files changed, 1519 insertions(+), 2074 deletions(-)
Permanent link
Title: SQLite interface for R
Diff between RSQLite versions 0.8-0 dated 2009-12-22 and 0.8-1 dated 2010-01-07
Description: Database Interface R driver for SQLite. This package
embeds the SQLite database engine in R and provides an
interface compliant with the DBI package. The source for the
SQLite engine (version 3.6.21) is included.
Author: David A. James
Maintainer: Seth Falcon
DESCRIPTION | 6 +--
R/SQLiteSupport.R | 31 ++++++++++------
a.out.dSYM/Contents/Resources/DWARF/a.out |binary
inst/NEWS | 21 ++++++++++
inst/UnitTests/basic_type_test.R | 12 ++++++
inst/UnitTests/bind_data_test.R | 9 ++++
inst/UnitTests/sqliteCopyDatabase_test.R | 17 +++++++-
man/sqliteCopyDatabase.Rd | 58 ++++++++++++++++++++----------
src/RS-DBI.c | 2 -
src/RS-DBI.h | 2 -
src/RS-SQLite.c | 43 ++++++++--------------
src/RS-SQLite.h | 2 -
12 files changed, 141 insertions(+), 62 deletions(-)
Title: C++ classes to embed R in C++ applications
Diff between RInside versions 0.2.0 dated 2009-12-21 and 0.2.1 dated 2010-01-07
Description: C++ classes to embed R in C++ applications The RInside
packages makes it easier to have 'R inside' your C++
application by providing a few wrapper classes.
As R itself is embedded into your application, a shared library build
of R is required. This works on Linux, OS X and even on Windows
provided you use the same tools used to build R itself.
Several examples are provided in the examples/ directory of the
installed package, and Doxygen-generated documentation of the
C++ classes is included as well.
Author: Dirk Eddelbuettel
Maintainer: Dirk Eddelbuettel
COPYING |only
DESCRIPTION | 10 +++++-----
inst/ChangeLog | 22 ++++++++++++++++++++++
src/Makefile | 19 +++++++++++++++++--
src/Makefile.win | 21 ++++++++++++++++++---
src/MemBuf.cpp | 19 +++++++++++++++++--
src/MemBuf.h | 19 +++++++++++++++++--
src/RInside.cpp | 27 +++++++++++++++++++++++----
src/RInside.h | 22 ++++++++++++++++++++--
src/setenv.c | 26 +++++++++++++++++++++-----
src/tools/unix2dos.r |only
11 files changed, 160 insertions(+), 25 deletions(-)
Title: Algorithms and framework for Nonnegative Matrix Factorization
(NMF).
Diff between NMF versions 0.2.2 dated 2009-11-26 and 0.2.3 dated 2010-01-07
Description: This package provides a framework to perform Non-negative
Matrix Factorization (NMF). It implements a set of already
published algorithms and seeding methods, and provides a
framework to test, develop and plug new/custom algorithms.
Author: Renaud Gaujoux
Maintainer: Renaud Gaujoux
DESCRIPTION | 16
NAMESPACE | 31
NEWS |only
R/Bioc-layer.R | 178 +-
R/NMF-class.R | 272 +++-
R/NMFSet-class.R | 21
R/nmf-package.R | 5
R/nmf.R | 4
inst/doc/NMF-vignette.Rnw | 91 +
inst/doc/NMF-vignette.pdf | 2883 ++++++++++++++++++++++++----------------------
man/Bioc-layer.Rd | 2
man/NMF-class.Rd | 24
man/NMF-deprecated.Rd |only
man/NMF-internals.Rd | 1
man/NMF-package.Rd |only
man/NMF-utils.Rd | 157 +-
man/NMFSet-class.Rd | 29
man/NMFfit-class.Rd | 2
man/NMFstd-class.Rd | 2
man/advanced.Rd | 2
man/nmf-methods.Rd | 20
21 files changed, 2187 insertions(+), 1553 deletions(-)
Title: Kalman filter and smoothers for exponential family state space
models.
Diff between KFAS versions 0.4.9 dated 2009-12-29 and 0.5.0 dated 2010-01-07
Description: Package KFAS provides functions for Kalman filtering,
state, disturbance and simulation smoothing, forecasting and
simulation of state space models. All functions can use exact
diffuse initialisation when distributions of some or all
elements of initial state vector are unknown. Filtering, state
smoothing and simulation functions use sequential processing
algorithm, which is faster than standard approach, and it also
allows singularity of prediction error variance matrix. KFAS
also contains function for computing the likelihood of
exponential family state space models and function for state
smoothing of exponential family state space models.
Author: Jouni Helske
Maintainer: Jouni Helske
KFAS-0.4.9/KFAS/elinankoodeja |only
KFAS-0.4.9/KFAS/src/expf.f90 |only
KFAS-0.5.0/KFAS/DESCRIPTION | 8
KFAS-0.5.0/KFAS/R/KFAS.R | 285 +++++++++---------
KFAS-0.5.0/KFAS/man/efsmoother.Rd | 2
KFAS-0.5.0/KFAS/man/kf.Rd | 4
KFAS-0.5.0/KFAS/man/simsmoother.Rd | 4
KFAS-0.5.0/KFAS/src/Makevars | 2
KFAS-0.5.0/KFAS/src/eflik.f90 | 82 ++---
KFAS-0.5.0/KFAS/src/eflik0.f90 |only
KFAS-0.5.0/KFAS/src/kf.f90 | 566 ++++++++++++++++++++----------------
KFAS-0.5.0/KFAS/src/ks.f90 | 266 +++++++++-------
KFAS-0.5.0/KFAS/src/simsmoother.f90 | 420 +++++++++++++-------------
13 files changed, 877 insertions(+), 762 deletions(-)