Title: Create cryptographic hash digests of R objects
Diff between digest versions 0.5.2 dated 2012-03-15 and 0.6.0 dated 2012-11-25
Description: The digest package provides a function 'digest()' for the
creation of hash digests of arbitrary R objects (using the md5,
sha-1, sha-256 and crc32 algorithms) permitting easy comparison
of R language objects, as well as a function 'hmac()' to create
hash-based message authentication code.
The md5 algorithm by Ron Rivest is specified in RFC 1321, the SHA-1 and
SHA-256 algorithms are specified in FIPS-180-1 and FIPS-180-2,
and the crc32 algorithm is described in
ftp://ftp.rocksoft.com/cliens/rocksoft/papers/crc_v3.txt.
For md5, sha-1 and sha-256, this package uses a small standalone
implementations that were provided by Christophe Devine. For
crc32, code from the zlib library is used. For sha-512, an
implementation by Aaron D. Gifford is used.
Please note that this package is not meant to be deployed for
cryptographic purposes for which more comprehensive (and widely
tested) libraries such as OpenSSL should be used.
Author: Dirk Eddelbuettel
Maintainer: Dirk Eddelbuettel
ChangeLog | 36 +++
DESCRIPTION | 19 +
MD5 | 20 +-
R/digest.R | 7
R/hmac.R | 4
man/digest.Rd | 23 ++
man/hmac.Rd | 7
src/digest.c | 430 ++++++++++++++++++++++++++-------------------
src/sha2.c |only
src/sha2.h |only
tests/digestTest.R | 35 +++
tests/digestTest.Rout.save | 65 ++++++
12 files changed, 433 insertions(+), 213 deletions(-)
Title: Base package for phylogenetic structures and comparative data
Diff between phylobase versions 0.6.4 dated 2012-11-20 and 0.6.5 dated 2012-11-25
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
phylobase-0.6.4/phylobase/tests/doRUnit.Rout.save |only
phylobase-0.6.5/phylobase/DESCRIPTION | 13 --
phylobase-0.6.5/phylobase/MD5 | 41 ++++---
phylobase-0.6.5/phylobase/data/geospiza.rda |binary
phylobase-0.6.5/phylobase/data/geospiza_raw.rda |binary
phylobase-0.6.5/phylobase/data/owls4.rda |only
phylobase-0.6.5/phylobase/inst/doc/developer.pdf |binary
phylobase-0.6.5/phylobase/inst/doc/phylobase.pdf |binary
phylobase-0.6.5/phylobase/inst/unitTests/report.html |only
phylobase-0.6.5/phylobase/inst/unitTests/report.txt |only
phylobase-0.6.5/phylobase/inst/unitTests/reportSummary.txt |only
phylobase-0.6.5/phylobase/man/owls4.Rd |only
phylobase-0.6.5/phylobase/src/nxstreesblock.cpp | 20 +--
phylobase-0.6.5/phylobase/tests/RUnit-tests.R |only
phylobase-0.6.5/phylobase/tests/RUnit-tests.Rout.save |only
phylobase-0.6.5/phylobase/tests/dUnit.Rout.save |only
phylobase-0.6.5/phylobase/tests/makeNewOut |only
phylobase-0.6.5/phylobase/tests/misctests.Rout.save | 16 +--
phylobase-0.6.5/phylobase/tests/nexusdata.Rout.save | 8 -
phylobase-0.6.5/phylobase/tests/phylo4dtests.Rout.save | 12 +-
phylobase-0.6.5/phylobase/tests/phylosubtest.Rout.save | 12 +-
phylobase-0.6.5/phylobase/tests/phylotorture.Rout.save | 22 +++-
phylobase-0.6.5/phylobase/tests/plottest.R | 6 -
phylobase-0.6.5/phylobase/tests/plottest.Rout.save | 52 ++--------
phylobase-0.6.5/phylobase/tests/roundtrip.Rout.save | 14 +-
phylobase-0.6.5/phylobase/tests/roundtripUnit-tests.Rout.save |only
phylobase-0.6.5/phylobase/tests/testprune.Rout.save | 12 +-
27 files changed, 110 insertions(+), 118 deletions(-)
Title: Multidimensional Item Response Theory
Diff between mirt versions 0.4.1 dated 2012-10-23 and 0.4.2 dated 2012-11-25
Description: Analysis of dichotomous and polytomous response data using
latent trait models under the Item Response Theory paradigm.
Includes univariate and multivariate one-, two-, three-, and
four-parameter logistic models, graded response models, rating
scale graded response models, generalized partial credit
models, nominal models, multiple choice models, and
multivariate partially-compensatory models. These can be used
in an exploratory or confirmatory manner with optional user
defined linear constraints. Exploratory models can be estimated
via quadrature or stochastic methods, a generalized
confirmatory bi-factor analysis is included, and confirmatory
models can be fit with a Metropolis-Hastings Robbins-Monro
algorithm which can include polynomial or product constructed
latent traits. Additionally, multiple group analysis may be
performed for unidimensional or multidimensional item response
models for detecting differential item functioning.
Author: Phil Chalmers [aut, cre]
Maintainer: Phil Chalmers
DESCRIPTION | 9
MD5 | 133 +-
NAMESPACE | 69 -
NEWS | 590 ++++++-----
R/00-classes.R | 137 +-
R/01-itemtypes.R | 145 +-
R/02-item_methods.R | 1813 +++++++++++-------------------------
R/03-estimation.R | 841 ++++++++--------
R/04-derivatives.R |only
R/Confirmatory-methods.R | 463 ++++-----
R/EMstep.group.R | 528 +++++-----
R/Exploratory-methods.R | 598 +++++------
R/LoadPars.R | 781 +++++++--------
R/MHRM.group.R | 605 ++++++------
R/MultipleGroup-methods.R | 226 ++--
R/PrepData.R | 302 ++---
R/bfactor.R | 368 +++----
R/calcLogLik.R | 308 +++---
R/confmirt.R | 572 +++++------
R/confmirt.model.R | 104 +-
R/extract.item.R | 52 -
R/fscores.R | 279 -----
R/fscores.internal.R |only
R/itemfit.R | 279 ++---
R/iteminfo.R | 77 -
R/itemplot.R | 260 -----
R/itemplot.internal.R |only
R/mirt-package.R | 166 +--
R/mirt.R | 762 +++++++--------
R/model.elements.R | 195 +--
R/multipleGroup.R | 452 ++++----
R/personfit.R | 234 ++--
R/polymirt.R | 40
R/read.mirt.R |only
R/simdata.R | 349 +++---
R/utils.R | 907 +++++++++---------
R/wald.R | 184 +--
inst/CITATION | 38
inst/doc/mirt-presentation-2012.Rnw | 8
inst/tests/confmods/modelcombo | 6
inst/tests/confmods/modelquad | 4
inst/tests/test-bfactor.R | 158 +--
inst/tests/test-confmirtOne.R | 60 -
inst/tests/test-confmirtTwo.R | 134 +-
inst/tests/test-mirtOne.R | 98 -
inst/tests/test-mirtTwo.R | 88 -
inst/tests/test-multipleGroupOne.R | 86 -
inst/tests/test-multipleGroupTwo.R | 78 -
man/ConfirmatoryClass-class.Rd | 122 +-
man/ExploratoryClass-class.Rd | 126 +-
man/MultipleGroupClass-class.Rd | 124 +-
man/bfactor.Rd | 451 ++++----
man/calcLogLik-methods.Rd | 94 -
man/confmirt.Rd | 753 +++++++-------
man/confmirt.model.Rd | 114 +-
man/extract.item.Rd | 56 -
man/fscores.Rd | 123 +-
man/itemfit.Rd | 144 +-
man/iteminfo.Rd | 79 -
man/itemplot.Rd | 113 +-
man/mirt-package.Rd | 74 -
man/mirt.Rd | 971 +++++++++----------
man/multipleGroup.Rd | 595 +++++------
man/personfit.Rd | 117 +-
man/polymirt.Rd | 54 -
man/read.mirt.Rd |only
man/simdata.Rd | 337 +++---
man/wald.Rd | 128 +-
src/Makevars.win | 8
src/traceLinePts.cpp | 13
70 files changed, 8710 insertions(+), 9472 deletions(-)
Title: doBy - Groupwise summary statistics, general linear contrasts,
population means (least-squares-means), and other utilities
Diff between doBy versions 4.5-3 dated 2012-05-19 and 4.5-5 dated 2012-11-25
Description: doBy originally contained facilities to 'do something' to
data where data is partitioned 'by' some variables which define
groupings of data - hence the name doBy. doBy contains a
variety of utilities including:
1) Facilities for groupwise computations of summary statistics and
other facilities for working with grouped data.
2) General linear contrasts and LSMEANS (least-squares-means also known
as population means),
3) other utilities.
Author: Søren Højsgaard
Maintainer: Søren Højsgaard
doBy-4.5-3/doBy/R/Rmarkup.R |only
doBy-4.5-3/doBy/inst/Rmarkup |only
doBy-4.5-3/doBy/man/Rmarkup.Rd |only
doBy-4.5-3/doBy/vignettes |only
doBy-4.5-5/doBy/ChangeLog | 27 ++++-
doBy-4.5-5/doBy/DESCRIPTION | 37 ++++----
doBy-4.5-5/doBy/MD5 | 91 +++++++++----------
doBy-4.5-5/doBy/R/BY-subsetBy.R | 27 ++++-
doBy-4.5-5/doBy/R/popMeans.R | 7 +
doBy-4.5-5/doBy/R/timeSinceEvent.R | 148 +++++++++++++++++++-------------
doBy-4.5-5/doBy/data/NIRmilk.csv.xz |only
doBy-4.5-5/doBy/data/NIRmilk.rda |only
doBy-4.5-5/doBy/data/carcass.txt.bz2 |only
doBy-4.5-5/doBy/data/carcassall.txt.bz2 |only
doBy-4.5-5/doBy/data/codstom.rda |binary
doBy-4.5-5/doBy/data/datalist | 3
doBy-4.5-5/doBy/data/dietox.rda |binary
doBy-4.5-5/doBy/data/milkman.RData |binary
doBy-4.5-5/doBy/doBy-Ex.R | 43 ++++-----
doBy-4.5-5/doBy/inst/doc/doBy.Rnw | 2
doBy-4.5-5/doBy/inst/doc/doBy.pdf |binary
doBy-4.5-5/doBy/inst/doc/figure |only
doBy-4.5-5/doBy/inst/doc/popMeans.Rnw | 17 ---
doBy-4.5-5/doBy/inst/doc/popMeans.pdf |binary
doBy-4.5-5/doBy/man/DATA-NIRmilk.Rd |only
doBy-4.5-5/doBy/man/DATA-carcass.Rd |only
doBy-4.5-5/doBy/man/doBy-internal.Rd | 6 +
doBy-4.5-5/doBy/man/doBy.Rd | 3
doBy-4.5-5/doBy/man/esticon.Rd | 4
doBy-4.5-5/doBy/man/firstlastobs.Rd | 3
doBy-4.5-5/doBy/man/lapplyBy.Rd | 3
doBy-4.5-5/doBy/man/lmBy.Rd | 6 -
doBy-4.5-5/doBy/man/orderBy.Rd | 4
doBy-4.5-5/doBy/man/popMeans.Rd | 14 +--
doBy-4.5-5/doBy/man/recodeVar.Rd | 3
doBy-4.5-5/doBy/man/renameCol.Rd | 4
doBy-4.5-5/doBy/man/sampleBy.Rd | 3
doBy-4.5-5/doBy/man/scaleBy.Rd | 3
doBy-4.5-5/doBy/man/splitBy.Rd | 3
doBy-4.5-5/doBy/man/subSeq.Rd | 4
doBy-4.5-5/doBy/man/subsetBy.Rd | 3
doBy-4.5-5/doBy/man/summaryBy.Rd | 2
doBy-4.5-5/doBy/man/timeSinceEvent.Rd | 5 -
doBy-4.5-5/doBy/man/transformBy.Rd | 4
doBy-4.5-5/doBy/man/which.maxn.Rd | 4
45 files changed, 277 insertions(+), 206 deletions(-)
Title: Core methods and classes used by aroma.* packages part of The
Aroma Framework
Diff between aroma.core versions 2.6.0 dated 2012-09-06 and 2.7.0 dated 2012-11-25
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
aroma.core-2.6.0/aroma.core/R/FileMatrix.importFromTable.R |only
aroma.core-2.6.0/aroma.core/R/downloadPackagePatch.R |only
aroma.core-2.6.0/aroma.core/R/patchPackage.R |only
aroma.core-2.6.0/aroma.core/R/private.assertDigest.R |only
aroma.core-2.6.0/aroma.core/inst/reports/includes/css/ChromosomeExplorer3.4.css |only
aroma.core-2.6.0/aroma.core/inst/reports/includes/js/ArrayExplorer3.4 |only
aroma.core-2.6.0/aroma.core/inst/reports/includes/js/ChromosomeExplorer3.4 |only
aroma.core-2.6.0/aroma.core/inst/reports/templates/html/ArrayExplorer/ArrayExplorer1.0 |only
aroma.core-2.6.0/aroma.core/inst/reports/templates/html/ArrayExplorer/ArrayExplorer3.3 |only
aroma.core-2.6.0/aroma.core/inst/reports/templates/html/ArrayExplorer/ArrayExplorer3.4 |only
aroma.core-2.6.0/aroma.core/inst/reports/templates/html/ChromosomeExplorer/ChromosomeExplorer3.1 |only
aroma.core-2.6.0/aroma.core/inst/reports/templates/html/ChromosomeExplorer/ChromosomeExplorer3.2 |only
aroma.core-2.6.0/aroma.core/inst/reports/templates/html/ChromosomeExplorer/ChromosomeExplorer3.3 |only
aroma.core-2.6.0/aroma.core/inst/reports/templates/html/ChromosomeExplorer/ChromosomeExplorer3.4 |only
aroma.core-2.6.0/aroma.core/inst/reports/templates/html/ChromosomeExplorer/ChromosomeExplorer4.html |only
aroma.core-2.6.0/aroma.core/inst/reports/templates/rsp/ArrayExplorer1.0 |only
aroma.core-2.6.0/aroma.core/inst/reports/templates/rsp/ArrayExplorer3.3 |only
aroma.core-2.6.0/aroma.core/inst/reports/templates/rsp/ArrayExplorer3.4 |only
aroma.core-2.6.0/aroma.core/inst/reports/templates/rsp/ChromosomeExplorer3 |only
aroma.core-2.6.0/aroma.core/inst/reports/templates/rsp/ChromosomeExplorer3.4 |only
aroma.core-2.7.0/aroma.core/DESCRIPTION | 30
aroma.core-2.7.0/aroma.core/MD5 | 471 +++---
aroma.core-2.7.0/aroma.core/NAMESPACE | 26
aroma.core-2.7.0/aroma.core/R/009.setup.R | 2
aroma.core-2.7.0/aroma.core/R/999.DEPRECATED,downloadPackagePatch.R |only
aroma.core-2.7.0/aroma.core/R/999.DEPRECATED,patchPackage.R |only
aroma.core-2.7.0/aroma.core/R/999.DEPRECATED.R |only
aroma.core-2.7.0/aroma.core/R/999.package.R | 3
aroma.core-2.7.0/aroma.core/R/AromaCellCpgFile.R | 14
aroma.core-2.7.0/aroma.core/R/AromaCellPositionFile.R | 14
aroma.core-2.7.0/aroma.core/R/AromaCellSequenceFile.R | 82 -
aroma.core-2.7.0/aroma.core/R/AromaCellSequenceFile.REPEATS.R | 18
aroma.core-2.7.0/aroma.core/R/AromaCellSequenceFile.SNPs.R | 19
aroma.core-2.7.0/aroma.core/R/AromaGenomeTextFile.R | 6
aroma.core-2.7.0/aroma.core/R/AromaMicroarrayDataFile.ATTRS.R | 2
aroma.core-2.7.0/aroma.core/R/AromaMicroarrayDataFile.PLOT.R | 8
aroma.core-2.7.0/aroma.core/R/AromaMicroarrayDataFile.R | 16
aroma.core-2.7.0/aroma.core/R/AromaMicroarrayDataSet.ATTRS.R | 2
aroma.core-2.7.0/aroma.core/R/AromaMicroarrayDataSet.EXT.R | 4
aroma.core-2.7.0/aroma.core/R/AromaMicroarrayDataSet.R | 10
aroma.core-2.7.0/aroma.core/R/AromaMicroarrayDataSetTuple.R | 14
aroma.core-2.7.0/aroma.core/R/AromaMicroarrayTabularBinaryFile.R | 11
aroma.core-2.7.0/aroma.core/R/AromaPlatform.R | 8
aroma.core-2.7.0/aroma.core/R/AromaPlatformInterface.R | 2
aroma.core-2.7.0/aroma.core/R/AromaRepository.R | 16
aroma.core-2.7.0/aroma.core/R/AromaTabularBinaryFile.R | 74 -
aroma.core-2.7.0/aroma.core/R/AromaTabularBinarySet.ATTRS.R | 4
aroma.core-2.7.0/aroma.core/R/AromaTabularBinarySet.R | 6
aroma.core-2.7.0/aroma.core/R/AromaTransform.R | 116 -
aroma.core-2.7.0/aroma.core/R/AromaUcscGenomeTextFile.R | 4
aroma.core-2.7.0/aroma.core/R/AromaUflFile.R | 24
aroma.core-2.7.0/aroma.core/R/AromaUgpFile.R | 18
aroma.core-2.7.0/aroma.core/R/AromaUgpFile.plotCoverageMap.R | 4
aroma.core-2.7.0/aroma.core/R/AromaUnitCallFile.R | 18
aroma.core-2.7.0/aroma.core/R/AromaUnitCallSet.R | 12
aroma.core-2.7.0/aroma.core/R/AromaUnitChromosomeTabularBinaryFile.R | 37
aroma.core-2.7.0/aroma.core/R/AromaUnitFracBCnBinarySet.R | 2
aroma.core-2.7.0/aroma.core/R/AromaUnitFracBCnBinarySet.exportFracBDiffSet.R | 6
aroma.core-2.7.0/aroma.core/R/AromaUnitGcContentFile.R |only
aroma.core-2.7.0/aroma.core/R/AromaUnitGenotypeCallFile.R | 26
aroma.core-2.7.0/aroma.core/R/AromaUnitGenotypeCallSet.R | 12
aroma.core-2.7.0/aroma.core/R/AromaUnitPscnBinaryFile.R | 9
aroma.core-2.7.0/aroma.core/R/AromaUnitPscnBinarySet.R | 678 ++++-----
aroma.core-2.7.0/aroma.core/R/AromaUnitSignalBinaryFile.R | 22
aroma.core-2.7.0/aroma.core/R/AromaUnitSignalBinaryFile.writeDataFrame.R | 4
aroma.core-2.7.0/aroma.core/R/AromaUnitSignalBinarySet.R | 7
aroma.core-2.7.0/aroma.core/R/AromaUnitSignalBinarySet.writeDataFrame.R | 16
aroma.core-2.7.0/aroma.core/R/AromaUnitTabularBinaryFile.R | 26
aroma.core-2.7.0/aroma.core/R/AromaUnitTabularBinaryFile.writeDataFrame.R | 4
aroma.core-2.7.0/aroma.core/R/AromaUnitTotalCnBinaryFile.extractPSCNArray.R | 4
aroma.core-2.7.0/aroma.core/R/AromaUnitTotalCnBinaryFile.xam.R | 45
aroma.core-2.7.0/aroma.core/R/AromaUnitTotalCnBinaryFileList.R | 464 +++---
aroma.core-2.7.0/aroma.core/R/AromaUnitTotalCnBinarySet.R | 732 +++++-----
aroma.core-2.7.0/aroma.core/R/AromaUnitTotalCnBinarySet.exportAromaUnitPscnBinarySet.R | 31
aroma.core-2.7.0/aroma.core/R/AromaUnitTotalCnBinarySet.exportTotalCnRatioSet.R | 4
aroma.core-2.7.0/aroma.core/R/AromaUnitTotalCnBinarySetTuple.R | 4
aroma.core-2.7.0/aroma.core/R/AromaUnitTypesFile.R | 6
aroma.core-2.7.0/aroma.core/R/BasicObject.asThis.R | 2
aroma.core-2.7.0/aroma.core/R/BinnedScatter.R | 2
aroma.core-2.7.0/aroma.core/R/CbsModel.R | 2
aroma.core-2.7.0/aroma.core/R/CbsSegmentationDataSet.R | 6
aroma.core-2.7.0/aroma.core/R/ChromosomalModel.R | 60
aroma.core-2.7.0/aroma.core/R/ChromosomeExplorer.R | 66
aroma.core-2.7.0/aroma.core/R/CopyNumberChromosomalModel.R | 658 +++++---
aroma.core-2.7.0/aroma.core/R/CopyNumberChromosomalModel.plotChromosomesLayers.R | 22
aroma.core-2.7.0/aroma.core/R/CopyNumberChromosomalModel.plotFitLayers.R | 4
aroma.core-2.7.0/aroma.core/R/CopyNumberChromosomalModel.plotRawCopyNumbers.R | 9
aroma.core-2.7.0/aroma.core/R/CopyNumberChromosomalModel.plotSampleLayers.R | 4
aroma.core-2.7.0/aroma.core/R/CopyNumberDataSetTuple.R | 8
aroma.core-2.7.0/aroma.core/R/CopyNumberOutliers.FOREIGN.R | 2
aroma.core-2.7.0/aroma.core/R/CopyNumberOutliers.R | 4
aroma.core-2.7.0/aroma.core/R/CopyNumberRegions.EXT.R | 4
aroma.core-2.7.0/aroma.core/R/CopyNumberRegions.R | 6
aroma.core-2.7.0/aroma.core/R/CopyNumberSegmentationModel.R | 65
aroma.core-2.7.0/aroma.core/R/CopyNumberSegmentationModel.plot.R | 7
aroma.core-2.7.0/aroma.core/R/CopyNumberSegmentationModel.plotCopyNumberRegionLayers.R | 6
aroma.core-2.7.0/aroma.core/R/Explorer.R | 110 +
aroma.core-2.7.0/aroma.core/R/GLAD.EXTS.R | 2
aroma.core-2.7.0/aroma.core/R/GenericTabularFileSet.calculateAverageColumnAcrossFiles.R | 4
aroma.core-2.7.0/aroma.core/R/GladModel.R | 16
aroma.core-2.7.0/aroma.core/R/HaarSegModel.R | 4
aroma.core-2.7.0/aroma.core/R/Image.EXTS.R | 3
aroma.core-2.7.0/aroma.core/R/MPCBS.EXTS.R | 4
aroma.core-2.7.0/aroma.core/R/PairedPSCNData.PLOT.R | 2
aroma.core-2.7.0/aroma.core/R/ParametersInterface.R |only
aroma.core-2.7.0/aroma.core/R/ProbePositionEffects.R | 42
aroma.core-2.7.0/aroma.core/R/RasterImage.R | 14
aroma.core-2.7.0/aroma.core/R/RawAlleleBFractions.R | 2
aroma.core-2.7.0/aroma.core/R/RawCopyNumberModel.R | 6
aroma.core-2.7.0/aroma.core/R/RawCopyNumbers.R | 7
aroma.core-2.7.0/aroma.core/R/RawGenomicSignals.R | 48
aroma.core-2.7.0/aroma.core/R/RawGenomicSignals.SEG.R | 280 +--
aroma.core-2.7.0/aroma.core/R/RawGenomicSignals.segmentByCBS.R | 642 ++++----
aroma.core-2.7.0/aroma.core/R/RawGenomicSignals.segmentByGLAD.R | 590 ++++----
aroma.core-2.7.0/aroma.core/R/RawGenomicSignals.segmentByHaarSeg.R | 550 +++----
aroma.core-2.7.0/aroma.core/R/RawGenomicSignals.segmentByMPCBS.R | 562 +++----
aroma.core-2.7.0/aroma.core/R/RawMirroredAlleleBFractions.R | 2
aroma.core-2.7.0/aroma.core/R/RawSequenceReads.EXTRAS.R | 6
aroma.core-2.7.0/aroma.core/R/RawSequenceReads.R | 2
aroma.core-2.7.0/aroma.core/R/RichDataFrame.R | 12
aroma.core-2.7.0/aroma.core/R/SampleAnnotationFile.R | 6
aroma.core-2.7.0/aroma.core/R/SampleAnnotationSet.R | 10
aroma.core-2.7.0/aroma.core/R/SegmentationDataSet.R | 380 ++---
aroma.core-2.7.0/aroma.core/R/SegmentedGenomicSignalsInterface.COLS.R | 194 +-
aroma.core-2.7.0/aroma.core/R/SegmentedGenomicSignalsInterface.R | 30
aroma.core-2.7.0/aroma.core/R/TextUnitNamesFile.R | 43
aroma.core-2.7.0/aroma.core/R/UnitAnnotationDataFile.R | 8
aroma.core-2.7.0/aroma.core/R/colBinnedSmoothing.R | 20
aroma.core-2.7.0/aroma.core/R/colGaussianSmoothing.R | 6
aroma.core-2.7.0/aroma.core/R/colKernelSmoothing.R | 6
aroma.core-2.7.0/aroma.core/R/convertTable.R | 2
aroma.core-2.7.0/aroma.core/R/doCBS.CopyNumberDataSetTuple.R | 2
aroma.core-2.7.0/aroma.core/R/doCBS.character.R | 2
aroma.core-2.7.0/aroma.core/R/findAnnotationData.R | 14
aroma.core-2.7.0/aroma.core/R/fitMultiDimensionalCone.matrix.R | 4
aroma.core-2.7.0/aroma.core/R/fitWHLAPLM.matrix.R | 4
aroma.core-2.7.0/aroma.core/R/fitWHRCModel.matrix.R | 4
aroma.core-2.7.0/aroma.core/R/getAromaFullNameTranslatorSet.R | 4
aroma.core-2.7.0/aroma.core/R/getCommonListElements.R | 2
aroma.core-2.7.0/aroma.core/R/getProbePositionEffectDesignMatrix.R | 8
aroma.core-2.7.0/aroma.core/R/lapplyInChunks.R | 4
aroma.core-2.7.0/aroma.core/R/matrixBlockPolish.matrix.R | 6
aroma.core-2.7.0/aroma.core/R/mergeBoxplotStats.list.R | 4
aroma.core-2.7.0/aroma.core/R/norm2d.matrix.R | 176 +-
aroma.core-2.7.0/aroma.core/R/processTime.R | 2
aroma.core-2.7.0/aroma.core/R/remap.R | 86 -
aroma.core-2.7.0/aroma.core/R/requireWithMemory.R | 2
aroma.core-2.7.0/aroma.core/R/smoothWRMA.matrix.R | 4
aroma.core-2.7.0/aroma.core/R/smoothWSA.matrix.R | 4
aroma.core-2.7.0/aroma.core/R/stringTree.R | 268 +--
aroma.core-2.7.0/aroma.core/incl/999.missingdocs.txt | 36
aroma.core-2.7.0/aroma.core/incl/RawGenomicSignals.SEG,MP.Rex | 2
aroma.core-2.7.0/aroma.core/incl/RawGenomicSignals.SEG.Rex | 8
aroma.core-2.7.0/aroma.core/inst/NEWS | 124 +
aroma.core-2.7.0/aroma.core/inst/reports/includes/css/ChromosomeExplorer.css |only
aroma.core-2.7.0/aroma.core/inst/reports/includes/css/figures.css | 2
aroma.core-2.7.0/aroma.core/inst/reports/includes/js/ArrayExplorer |only
aroma.core-2.7.0/aroma.core/inst/reports/includes/js/ChromosomeExplorer |only
aroma.core-2.7.0/aroma.core/inst/reports/includes/js/Scrollbar2d.js | 12
aroma.core-2.7.0/aroma.core/inst/reports/includes/js/domUtils.js | 15
aroma.core-2.7.0/aroma.core/inst/reports/templates/html/ArrayExplorer/ArrayExplorer.html | 8
aroma.core-2.7.0/aroma.core/inst/reports/templates/html/ChromosomeExplorer/ChromosomeExplorer.html | 15
aroma.core-2.7.0/aroma.core/inst/reports/templates/html/archive |only
aroma.core-2.7.0/aroma.core/inst/reports/templates/rsp/ArrayExplorer/setupExplorer.js.rsp | 2
aroma.core-2.7.0/aroma.core/inst/reports/templates/rsp/ChromosomeExplorer |only
aroma.core-2.7.0/aroma.core/inst/reports/templates/rsp/archive |only
aroma.core-2.7.0/aroma.core/man/AbstractCNData.Rd | 2
aroma.core-2.7.0/aroma.core/man/AbstractPSCNData.Rd | 2
aroma.core-2.7.0/aroma.core/man/AromaCellTabularBinaryFile.Rd | 23
aroma.core-2.7.0/aroma.core/man/AromaGenomeTextFile.Rd | 20
aroma.core-2.7.0/aroma.core/man/AromaMicroarrayDataFile.Rd | 5
aroma.core-2.7.0/aroma.core/man/AromaMicroarrayDataSet.Rd | 6
aroma.core-2.7.0/aroma.core/man/AromaMicroarrayDataSetTuple.Rd | 5
aroma.core-2.7.0/aroma.core/man/AromaMicroarrayTabularBinaryFile.Rd | 25
aroma.core-2.7.0/aroma.core/man/AromaPlatform.Rd | 4
aroma.core-2.7.0/aroma.core/man/AromaRepository.Rd | 2
aroma.core-2.7.0/aroma.core/man/AromaTabularBinaryFile.Rd | 23
aroma.core-2.7.0/aroma.core/man/AromaTabularBinarySet.Rd | 8
aroma.core-2.7.0/aroma.core/man/AromaTransform.Rd | 14
aroma.core-2.7.0/aroma.core/man/AromaUnitCallFile.Rd | 24
aroma.core-2.7.0/aroma.core/man/AromaUnitCallSet.Rd | 6
aroma.core-2.7.0/aroma.core/man/AromaUnitFracBCnBinaryFile.Rd | 23
aroma.core-2.7.0/aroma.core/man/AromaUnitFracBCnBinarySet.Rd | 5
aroma.core-2.7.0/aroma.core/man/AromaUnitGenotypeCallFile.Rd | 26
aroma.core-2.7.0/aroma.core/man/AromaUnitGenotypeCallSet.Rd | 5
aroma.core-2.7.0/aroma.core/man/AromaUnitPscnBinaryFile.Rd | 27
aroma.core-2.7.0/aroma.core/man/AromaUnitPscnBinarySet.Rd | 4
aroma.core-2.7.0/aroma.core/man/AromaUnitSignalBinaryFile.Rd | 26
aroma.core-2.7.0/aroma.core/man/AromaUnitSignalBinarySet.Rd | 6
aroma.core-2.7.0/aroma.core/man/AromaUnitTabularBinaryFile.Rd | 29
aroma.core-2.7.0/aroma.core/man/AromaUnitTotalCnBinaryFile.Rd | 26
aroma.core-2.7.0/aroma.core/man/AromaUnitTotalCnBinarySet.Rd | 4
aroma.core-2.7.0/aroma.core/man/AromaUnitTypesFile.Rd | 28
aroma.core-2.7.0/aroma.core/man/BinnedScatter.Rd | 2
aroma.core-2.7.0/aroma.core/man/CbsModel.Rd | 10
aroma.core-2.7.0/aroma.core/man/ChromosomalModel.Rd | 7
aroma.core-2.7.0/aroma.core/man/ChromosomeExplorer.Rd | 9
aroma.core-2.7.0/aroma.core/man/CopyNumberChromosomalModel.Rd | 18
aroma.core-2.7.0/aroma.core/man/CopyNumberSegmentationModel.Rd | 7
aroma.core-2.7.0/aroma.core/man/Explorer.Rd | 14
aroma.core-2.7.0/aroma.core/man/GladModel.Rd | 7
aroma.core-2.7.0/aroma.core/man/HaarSegModel.Rd | 10
aroma.core-2.7.0/aroma.core/man/Non-documented_objects.Rd | 37
aroma.core-2.7.0/aroma.core/man/NonPairedPSCNData.Rd | 2
aroma.core-2.7.0/aroma.core/man/PairedPSCNData.Rd | 2
aroma.core-2.7.0/aroma.core/man/ParametersInterface.Rd |only
aroma.core-2.7.0/aroma.core/man/RawAlleleBFractions.Rd | 2
aroma.core-2.7.0/aroma.core/man/RawCopyNumberModel.Rd | 11
aroma.core-2.7.0/aroma.core/man/RawCopyNumbers.Rd | 2
aroma.core-2.7.0/aroma.core/man/RawGenomicSignals.Rd | 11
aroma.core-2.7.0/aroma.core/man/RawMirroredAlleleBFractions.Rd | 2
aroma.core-2.7.0/aroma.core/man/RawSequenceReads.Rd | 2
aroma.core-2.7.0/aroma.core/man/SegmentedAlleleBFractions.Rd | 2
aroma.core-2.7.0/aroma.core/man/SegmentedCopyNumbers.Rd | 2
aroma.core-2.7.0/aroma.core/man/SegmentedGenomicSignalsInterface.Rd | 2
aroma.core-2.7.0/aroma.core/man/UnitAnnotationDataFile.Rd | 2
aroma.core-2.7.0/aroma.core/man/aroma.core-package.Rd | 3
aroma.core-2.7.0/aroma.core/man/as.GrayscaleImage.matrix.Rd | 2
aroma.core-2.7.0/aroma.core/man/colBinnedSmoothing.matrix.Rd | 2
aroma.core-2.7.0/aroma.core/man/colKernelSmoothing.matrix.Rd | 2
aroma.core-2.7.0/aroma.core/man/downloadPackagePatch.Rd | 2
aroma.core-2.7.0/aroma.core/man/estimateSds.CopyNumberChromosomalModel.Rd | 2
aroma.core-2.7.0/aroma.core/man/fit.CopyNumberSegmentationModel.Rd | 4
aroma.core-2.7.0/aroma.core/man/getParameters.ParametersInterface.Rd |only
aroma.core-2.7.0/aroma.core/man/getParametersAsString.ParametersInterface.Rd |only
aroma.core-2.7.0/aroma.core/man/getPath.AromaTransform.Rd | 10
aroma.core-2.7.0/aroma.core/man/getPath.Explorer.Rd |only
aroma.core-2.7.0/aroma.core/man/getRootPath.AromaTransform.Rd |only
aroma.core-2.7.0/aroma.core/man/getRootPath.Explorer.Rd |only
aroma.core-2.7.0/aroma.core/man/patchPackage.Rd | 2
aroma.core-2.7.0/aroma.core/man/segmentByCBS.RawGenomicSignals.Rd | 8
aroma.core-2.7.0/aroma.core/man/segmentByMPCBS.RawGenomicSignals.Rd | 2
aroma.core-2.7.0/aroma.core/man/setAlias.Explorer.Rd | 2
aroma.core-2.7.0/aroma.core/tests/RawCopyNumbers,states.R | 10
aroma.core-2.7.0/aroma.core/tests/RawCopyNumbers.R | 6
aroma.core-2.7.0/aroma.core/tests/RawGenomicSignals.R | 14
aroma.core-2.7.0/aroma.core/tests/RawGenomicSignals.SEG,MP.R | 2
aroma.core-2.7.0/aroma.core/tests/RawGenomicSignals.SEG.R | 8
aroma.core-2.7.0/aroma.core/tests/RichDataFrame.R | 6
aroma.core-2.7.0/aroma.core/tests/SegmentedCopyNumbers.R | 6
240 files changed, 4763 insertions(+), 4444 deletions(-)