Title: Methods for Temporal Disaggregation and Interpolation of Time
Series
Diff between tempdisagg versions 0.21 dated 2013-02-12 and 0.22 dated 2013-08-04
Description: Temporal disaggregation methods are used to disaggregate
and interpolate a low frequency time series to a higher
frequency series. This can be done without additional
information or by exploiting the information contained in one
or more indicators. All disaggregation methods ensure that
either the sum, the average, the first or the last value of the
resulting high frequency series is consistent with the low
frequency series.
Author: Christoph Sax, Peter Steiner
Maintainer: Christoph Sax
tempdisagg-0.21/tempdisagg/man/swisspharma.Rd |only
tempdisagg-0.21/tempdisagg/man/tempdisagg-internal.Rd |only
tempdisagg-0.21/tempdisagg/news.txt |only
tempdisagg-0.22/tempdisagg/DESCRIPTION | 25 -
tempdisagg-0.22/tempdisagg/MD5 | 34 +
tempdisagg-0.22/tempdisagg/NAMESPACE | 11
tempdisagg-0.22/tempdisagg/NEWS |only
tempdisagg-0.22/tempdisagg/R/ta.R | 87 +++-
tempdisagg-0.22/tempdisagg/R/td.R | 258 ++++++++++++--
tempdisagg-0.22/tempdisagg/R/td.calc.R | 4
tempdisagg-0.22/tempdisagg/R/td.output.R | 152 ++++++--
tempdisagg-0.22/tempdisagg/R/td.sub.R | 38 +-
tempdisagg-0.22/tempdisagg/R/tempdisagg-package.R |only
tempdisagg-0.22/tempdisagg/README.md |only
tempdisagg-0.22/tempdisagg/demo |only
tempdisagg-0.22/tempdisagg/man/exports.m.Rd |only
tempdisagg-0.22/tempdisagg/man/plot.td.Rd | 34 +
tempdisagg-0.22/tempdisagg/man/predict.td.Rd | 37 +-
tempdisagg-0.22/tempdisagg/man/summary.td.Rd | 77 ++--
tempdisagg-0.22/tempdisagg/man/ta.Rd | 46 +-
tempdisagg-0.22/tempdisagg/man/td.Rd | 324 ++++++++++++------
tempdisagg-0.22/tempdisagg/man/tempdisagg-package.Rd |only
22 files changed, 798 insertions(+), 329 deletions(-)
Title: CalMaTe - Improved allele-specific copy number of SNP arrays for
downstream segmentation
Diff between calmate versions 0.10.0 dated 2013-01-08 and 0.10.2 dated 2013-08-04
Description: A multi-array post-processing method of allele-specific copy-number estimates (ASCNs)
Author: Maria Ortiz, Ander Aramburu, Henrik Bengtsson, Pierre Neuvial, Angel Rubio
Maintainer: Henrik Bengtsson
calmate-0.10.0/calmate/incl |only
calmate-0.10.2/calmate/DESCRIPTION | 30 -
calmate-0.10.2/calmate/MD5 | 35 -
calmate-0.10.2/calmate/NAMESPACE | 5
calmate-0.10.2/calmate/inst/NEWS | 14
calmate-0.10.2/calmate/man/CalMaTeCalibration.Rd | 372 ++++++-------
calmate-0.10.2/calmate/man/Non-documented_objects.Rd | 138 ++--
calmate-0.10.2/calmate/man/calmate-package.Rd | 108 +--
calmate-0.10.2/calmate/man/calmateByThetaAB.array.Rd | 199 +++---
calmate-0.10.2/calmate/man/calmateByTotalAndFracB.array.Rd | 190 +++---
calmate-0.10.2/calmate/man/fitCalMaTe.matrix.Rd | 122 ++--
calmate-0.10.2/calmate/man/fitCalMaTeCNprobes.matrix.Rd | 76 +-
calmate-0.10.2/calmate/man/fitCalMaTeInternal.Rd | 172 +++---
calmate-0.10.2/calmate/man/thetaAB2TotalAndFracB.array.Rd | 106 +--
calmate-0.10.2/calmate/tests/calmateByThetaAB.R | 6
calmate-0.10.2/calmate/tests/testScriptCalMaTe1.R | 10
16 files changed, 800 insertions(+), 783 deletions(-)
Title: Rcpp integration for Armadillo templated linear algebra library
Diff between RcppArmadillo versions 0.3.900.0 dated 2013-06-05 and 0.3.900.7 dated 2013-08-04
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 3.900.7). 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 MPL 2.0, while RcppArmadillo (the Rcpp
bindings/bridge to Armadillo) is licensed under the GNU GPL version 2
or later, as is the rest of Rcpp.
Author: Romain Francois, Dirk Eddelbuettel and Doug Bates
Maintainer: Dirk Eddelbuettel
RcppArmadillo-0.3.900.0/RcppArmadillo/debian |only
RcppArmadillo-0.3.900.7/RcppArmadillo/ChangeLog | 24 ++
RcppArmadillo-0.3.900.7/RcppArmadillo/DESCRIPTION | 53 ++--
RcppArmadillo-0.3.900.7/RcppArmadillo/MD5 | 99 ++++----
RcppArmadillo-0.3.900.7/RcppArmadillo/inst/NEWS.Rd | 17 +
RcppArmadillo-0.3.900.7/RcppArmadillo/inst/doc/RcppArmadillo-intro.pdf |binary
RcppArmadillo-0.3.900.7/RcppArmadillo/inst/doc/RcppArmadillo-unitTests.pdf |binary
RcppArmadillo-0.3.900.7/RcppArmadillo/inst/doc/unitTests-results/RcppArmadillo-unitTests.html | 4
RcppArmadillo-0.3.900.7/RcppArmadillo/inst/doc/unitTests-results/RcppArmadillo-unitTests.txt | 2
RcppArmadillo-0.3.900.7/RcppArmadillo/inst/examples/fastLm.r | 20 -
RcppArmadillo-0.3.900.7/RcppArmadillo/inst/examples/kalman/benchmark.R | 3
RcppArmadillo-0.3.900.7/RcppArmadillo/inst/examples/kalman/firstExample.R | 9
RcppArmadillo-0.3.900.7/RcppArmadillo/inst/examples/varSimulation.r | 44 ++-
RcppArmadillo-0.3.900.7/RcppArmadillo/inst/include/RcppArmadillo/Col_meat.h | 3
RcppArmadillo-0.3.900.7/RcppArmadillo/inst/include/RcppArmadillo/Mat_meat.h | 4
RcppArmadillo-0.3.900.7/RcppArmadillo/inst/include/RcppArmadillo/Row_meat.h | 3
RcppArmadillo-0.3.900.7/RcppArmadillo/inst/include/armadillo | 7
RcppArmadillo-0.3.900.7/RcppArmadillo/inst/include/armadillo_bits/Cube_bones.hpp | 2
RcppArmadillo-0.3.900.7/RcppArmadillo/inst/include/armadillo_bits/GenCube_bones.hpp | 1
RcppArmadillo-0.3.900.7/RcppArmadillo/inst/include/armadillo_bits/Gen_bones.hpp | 1
RcppArmadillo-0.3.900.7/RcppArmadillo/inst/include/armadillo_bits/Mat_bones.hpp | 7
RcppArmadillo-0.3.900.7/RcppArmadillo/inst/include/armadillo_bits/Proxy.hpp | 48 ++++
RcppArmadillo-0.3.900.7/RcppArmadillo/inst/include/armadillo_bits/ProxyCube.hpp | 4
RcppArmadillo-0.3.900.7/RcppArmadillo/inst/include/armadillo_bits/SpMat_meat.hpp | 4
RcppArmadillo-0.3.900.7/RcppArmadillo/inst/include/armadillo_bits/SpValProxy_bones.hpp | 4
RcppArmadillo-0.3.900.7/RcppArmadillo/inst/include/armadillo_bits/SpValProxy_meat.hpp | 4
RcppArmadillo-0.3.900.7/RcppArmadillo/inst/include/armadillo_bits/arma_version.hpp | 2
RcppArmadillo-0.3.900.7/RcppArmadillo/inst/include/armadillo_bits/arrayops_bones.hpp | 4
RcppArmadillo-0.3.900.7/RcppArmadillo/inst/include/armadillo_bits/arrayops_meat.hpp | 113 ++--------
RcppArmadillo-0.3.900.7/RcppArmadillo/inst/include/armadillo_bits/compiler_setup.hpp | 101 ++++++--
RcppArmadillo-0.3.900.7/RcppArmadillo/inst/include/armadillo_bits/compiler_setup_post.hpp |only
RcppArmadillo-0.3.900.7/RcppArmadillo/inst/include/armadillo_bits/eGlueCube_meat.hpp | 9
RcppArmadillo-0.3.900.7/RcppArmadillo/inst/include/armadillo_bits/eGlue_meat.hpp | 10
RcppArmadillo-0.3.900.7/RcppArmadillo/inst/include/armadillo_bits/eglue_core_meat.hpp | 5
RcppArmadillo-0.3.900.7/RcppArmadillo/inst/include/armadillo_bits/eop_aux.hpp | 13 -
RcppArmadillo-0.3.900.7/RcppArmadillo/inst/include/armadillo_bits/eop_core_meat.hpp | 3
RcppArmadillo-0.3.900.7/RcppArmadillo/inst/include/armadillo_bits/field_bones.hpp | 2
RcppArmadillo-0.3.900.7/RcppArmadillo/inst/include/armadillo_bits/field_meat.hpp | 3
RcppArmadillo-0.3.900.7/RcppArmadillo/inst/include/armadillo_bits/fn_as_scalar.hpp | 6
RcppArmadillo-0.3.900.7/RcppArmadillo/inst/include/armadillo_bits/glue_cross_meat.hpp | 72 ++++--
RcppArmadillo-0.3.900.7/RcppArmadillo/inst/include/armadillo_bits/glue_mixed_meat.hpp | 68 +++++-
RcppArmadillo-0.3.900.7/RcppArmadillo/inst/include/armadillo_bits/memory.hpp | 2
RcppArmadillo-0.3.900.7/RcppArmadillo/inst/include/armadillo_bits/op_median_meat.hpp | 4
RcppArmadillo-0.3.900.7/RcppArmadillo/inst/include/armadillo_bits/op_reshape_meat.hpp | 56 +---
RcppArmadillo-0.3.900.7/RcppArmadillo/inst/include/armadillo_bits/xvec_htrans_bones.hpp | 2
RcppArmadillo-0.3.900.7/RcppArmadillo/inst/include/armadillo_bits/xvec_htrans_meat.hpp | 12 +
RcppArmadillo-0.3.900.7/RcppArmadillo/inst/unitTests/runTests.R | 58 ++---
RcppArmadillo-0.3.900.7/RcppArmadillo/inst/unitTests/runit.RcppArmadillo.R | 4
48 files changed, 530 insertions(+), 386 deletions(-)
Title: Various confidence interval methods for proportions
Diff between PropCIs versions 0.2-0 dated 2013-01-22 and 0.2-4 dated 2013-08-04
Description: Computes two-sample confidence intervals for single, paired and independent proportions
Author: Ralph Scherer
Maintainer: Ralph Scherer
DESCRIPTION | 14 ++++++++------
MD5 | 9 +++++----
NAMESPACE | 6 +-----
NEWS | 41 ++++++++++++++++++++---------------------
README.md |only
man/PropCIs-package.Rd | 8 ++++----
6 files changed, 38 insertions(+), 40 deletions(-)
Title: Penalized likelihood factor analysis via nonconvex penalty
Diff between fanc versions 1.7 dated 2013-03-17 and 1.12 dated 2013-08-04
Description: An R package "fanc" computes the penalized maximum
likelihood estimates of factor loadings and unique variances
for various tuning parameters. The pathwise coordinate descent
along with EM algorithm is used. This package also includes a
new graphical tool which outputs path diagram, goodness-of-fit
indices and model selection criteria for each regularization
parameter. The user can change the regularization parameter by
manipulating scrollbars, which is helpful to find a suitable
value of regularization parameter.
Author: Kei Hirose, Michio Yamamoto
Maintainer: Kei Hirose
fanc-1.12/fanc/DESCRIPTION | 8
fanc-1.12/fanc/MD5 | 16
fanc-1.12/fanc/NAMESPACE | 9
fanc-1.12/fanc/R/fanc.R | 158 +++--
fanc-1.12/fanc/R/out.fanc.R | 58 +
fanc-1.12/fanc/R/plot.fanc.R | 1149 +++++++++++++++++++--------------------
fanc-1.12/fanc/man/fanc.Rd | 87 +-
fanc-1.12/fanc/man/out.fanc.Rd | 2
fanc-1.12/fanc/src/fancC_v1.12.c |only
fanc-1.7/fanc/src/fancC_v1.7.c |only
10 files changed, 792 insertions(+), 695 deletions(-)
Title: Functions for actuarial scientists
Diff between CompLognormal versions 2.0 dated 2012-10-05 and 3.0 dated 2013-08-04
Description: Computes the probability density function, cumulative distribution function, quantile function, random numbers of any composite model based on the lognormal distribution.
Author: Saralees Nadarajah
Maintainer: Saralees Nadarajah
DESCRIPTION | 13 ++---
MD5 | 10 +--
R/CompLognormal.R | 110 ++++++++++++++++++++++---------------------
man/CompLognormal-package.Rd | 8 +--
man/pcomplnorm.Rd | 3 -
man/qcomplnorm.Rd | 3 -
6 files changed, 76 insertions(+), 71 deletions(-)
Title: Core methods and classes used by aroma.* packages part of The
Aroma Framework
Diff between aroma.core versions 2.9.0 dated 2013-04-25 and 2.10.0 dated 2013-08-04
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-2.10.0/aroma.core/DESCRIPTION | 37 -
aroma.core-2.10.0/aroma.core/MD5 | 258 +++++-----
aroma.core-2.10.0/aroma.core/NAMESPACE | 25
aroma.core-2.10.0/aroma.core/R/006.fixVarArgs.R | 9
aroma.core-2.10.0/aroma.core/R/008.BioC.R |only
aroma.core-2.10.0/aroma.core/R/AromaCellCpgFile.R | 35 -
aroma.core-2.10.0/aroma.core/R/AromaCellPositionFile.R | 31 -
aroma.core-2.10.0/aroma.core/R/AromaCellSequenceFile.R | 145 +++--
aroma.core-2.10.0/aroma.core/R/AromaCellSequenceFile.REPEATS.R | 12
aroma.core-2.10.0/aroma.core/R/AromaCellSequenceFile.SNPs.R | 28 -
aroma.core-2.10.0/aroma.core/R/AromaRepository.R | 32 -
aroma.core-2.10.0/aroma.core/R/AromaTabularBinaryFile.R | 146 ++---
aroma.core-2.10.0/aroma.core/R/AromaTransform.R | 101 ++-
aroma.core-2.10.0/aroma.core/R/AromaUflFile.R | 18
aroma.core-2.10.0/aroma.core/R/AromaUgpFile.R | 22
aroma.core-2.10.0/aroma.core/R/AromaUnitCallFile.R | 15
aroma.core-2.10.0/aroma.core/R/AromaUnitFracBCnBinarySet.exportFracBDiffSet.R | 22
aroma.core-2.10.0/aroma.core/R/AromaUnitGenotypeCallFile.R | 67 +-
aroma.core-2.10.0/aroma.core/R/AromaUnitPscnBinarySet.R | 39 -
aroma.core-2.10.0/aroma.core/R/AromaUnitSignalBinaryFile.R | 26 -
aroma.core-2.10.0/aroma.core/R/AromaUnitSignalBinaryFile.writeDataFrame.R | 43 -
aroma.core-2.10.0/aroma.core/R/AromaUnitSignalBinarySet.writeDataFrame.R | 60 +-
aroma.core-2.10.0/aroma.core/R/AromaUnitTabularBinaryFile.writeDataFrame.R | 41 -
aroma.core-2.10.0/aroma.core/R/AromaUnitTotalCnBinaryFileList.R | 19
aroma.core-2.10.0/aroma.core/R/AromaUnitTotalCnBinarySet.R | 31 -
aroma.core-2.10.0/aroma.core/R/AromaUnitTotalCnBinarySet.exportAromaUnitPscnBinarySet.R | 18
aroma.core-2.10.0/aroma.core/R/AromaUnitTotalCnBinarySet.exportTotalCnRatioSet.R | 26 -
aroma.core-2.10.0/aroma.core/R/BinnedScatter.R | 14
aroma.core-2.10.0/aroma.core/R/CopyNumberChromosomalModel.R | 153 +++--
aroma.core-2.10.0/aroma.core/R/CopyNumberChromosomalModel.plotChromosomesLayers.R | 24
aroma.core-2.10.0/aroma.core/R/CopyNumberChromosomalModel.plotFitLayers.R | 24
aroma.core-2.10.0/aroma.core/R/CopyNumberChromosomalModel.plotSampleLayers.R | 34 -
aroma.core-2.10.0/aroma.core/R/CopyNumberRegions.R | 11
aroma.core-2.10.0/aroma.core/R/CopyNumberSegmentationModel.R | 79 +--
aroma.core-2.10.0/aroma.core/R/CopyNumberSegmentationModel.plot.R | 40 -
aroma.core-2.10.0/aroma.core/R/GLAD.EXTS.R | 38 -
aroma.core-2.10.0/aroma.core/R/GenericTabularFileSet.calculateAverageColumnAcrossFiles.R | 14
aroma.core-2.10.0/aroma.core/R/GladModel.R | 35 -
aroma.core-2.10.0/aroma.core/R/GladModel.onFitAddGenotypeCalls.R | 19
aroma.core-2.10.0/aroma.core/R/MPCBS.EXTS.R | 11
aroma.core-2.10.0/aroma.core/R/PairedPSCNData.R | 37 -
aroma.core-2.10.0/aroma.core/R/ProbePositionEffects.R | 68 +-
aroma.core-2.10.0/aroma.core/R/RasterImage.R | 74 +-
aroma.core-2.10.0/aroma.core/R/RawGenomicSignals.R | 70 +-
aroma.core-2.10.0/aroma.core/R/RawGenomicSignals.SEG.R | 16
aroma.core-2.10.0/aroma.core/R/RawGenomicSignals.segmentByCBS.R | 35 -
aroma.core-2.10.0/aroma.core/R/RawGenomicSignals.segmentByGLAD.R | 18
aroma.core-2.10.0/aroma.core/R/RawGenomicSignals.segmentByHaarSeg.R | 16
aroma.core-2.10.0/aroma.core/R/RawGenomicSignals.segmentByMPCBS.R | 20
aroma.core-2.10.0/aroma.core/R/RichDataFrame.R | 15
aroma.core-2.10.0/aroma.core/R/SampleAnnotationFile.R | 21
aroma.core-2.10.0/aroma.core/R/SegmentedGenomicSignalsInterface.R | 59 +-
aroma.core-2.10.0/aroma.core/R/convertTable.R | 11
aroma.core-2.10.0/aroma.core/R/doCBS.R |only
aroma.core-2.10.0/aroma.core/R/drawCytoband2.R | 41 -
aroma.core-2.10.0/aroma.core/R/findAnnotationData.R | 37 -
aroma.core-2.10.0/aroma.core/R/fitGenotypeCone.matrix.R | 29 -
aroma.core-2.10.0/aroma.core/R/fitMultiDimensionalCone.matrix.R | 20
aroma.core-2.10.0/aroma.core/R/fitSplineBlockPolish.matrix.R | 9
aroma.core-2.10.0/aroma.core/R/fitWHRCModel.matrix.R | 4
aroma.core-2.10.0/aroma.core/R/fitWRMA.matrix.R | 2
aroma.core-2.10.0/aroma.core/R/getProbePositionEffectDesignMatrix.R | 14
aroma.core-2.10.0/aroma.core/R/lapplyInChunks.R | 12
aroma.core-2.10.0/aroma.core/R/matrixBlockPolish.matrix.R | 40 -
aroma.core-2.10.0/aroma.core/R/norm2d.matrix.R | 11
aroma.core-2.10.0/aroma.core/R/profileCGH.plotProfile2.R | 56 +-
aroma.core-2.10.0/aroma.core/R/profileCGH.plotRawCNs.R | 30 -
aroma.core-2.10.0/aroma.core/R/remap.R | 3
aroma.core-2.10.0/aroma.core/R/smoothWRMA.matrix.R | 26 -
aroma.core-2.10.0/aroma.core/R/smoothWSA.matrix.R | 28 -
aroma.core-2.10.0/aroma.core/inst/NEWS | 44 +
aroma.core-2.10.0/aroma.core/man/AbstractCNData.Rd | 2
aroma.core-2.10.0/aroma.core/man/AbstractPSCNData.Rd | 2
aroma.core-2.10.0/aroma.core/man/AromaCellCpgFile.Rd | 38 -
aroma.core-2.10.0/aroma.core/man/AromaCellPositionFile.Rd | 38 -
aroma.core-2.10.0/aroma.core/man/AromaGenomeTextFile.Rd | 16
aroma.core-2.10.0/aroma.core/man/AromaRepository.Rd | 34 -
aroma.core-2.10.0/aroma.core/man/AromaTabularBinaryFile.Rd | 36 -
aroma.core-2.10.0/aroma.core/man/AromaTransform.Rd | 46 -
aroma.core-2.10.0/aroma.core/man/AromaUnitCallFile.Rd | 28 -
aroma.core-2.10.0/aroma.core/man/AromaUnitGenotypeCallFile.Rd | 28 -
aroma.core-2.10.0/aroma.core/man/AromaUnitPscnBinarySet.Rd | 30 -
aroma.core-2.10.0/aroma.core/man/AromaUnitSignalBinaryFile.Rd | 34 -
aroma.core-2.10.0/aroma.core/man/AromaUnitTotalCnBinarySet.Rd | 30 -
aroma.core-2.10.0/aroma.core/man/BinnedScatter.Rd | 44 -
aroma.core-2.10.0/aroma.core/man/CopyNumberChromosomalModel.Rd | 65 +-
aroma.core-2.10.0/aroma.core/man/CopyNumberSegmentationModel.Rd | 30 -
aroma.core-2.10.0/aroma.core/man/GladModel.Rd | 92 +--
aroma.core-2.10.0/aroma.core/man/Non-documented_objects.Rd | 8
aroma.core-2.10.0/aroma.core/man/NonPairedPSCNData.Rd | 2
aroma.core-2.10.0/aroma.core/man/PairedPSCNData.Rd | 83 +--
aroma.core-2.10.0/aroma.core/man/RawAlleleBFractions.Rd | 2
aroma.core-2.10.0/aroma.core/man/RawCopyNumbers.Rd | 22
aroma.core-2.10.0/aroma.core/man/RawGenomicSignals.Rd | 48 -
aroma.core-2.10.0/aroma.core/man/RawMirroredAlleleBFractions.Rd | 2
aroma.core-2.10.0/aroma.core/man/RawSequenceReads.Rd | 4
aroma.core-2.10.0/aroma.core/man/SegmentedAlleleBFractions.Rd | 2
aroma.core-2.10.0/aroma.core/man/SegmentedCopyNumbers.Rd | 14
aroma.core-2.10.0/aroma.core/man/SegmentedGenomicSignalsInterface.Rd | 26 -
aroma.core-2.10.0/aroma.core/man/allocate.AromaTabularBinaryFile.Rd | 7
aroma.core-2.10.0/aroma.core/man/as.GrayscaleImage.matrix.Rd | 3
aroma.core-2.10.0/aroma.core/man/colBinnedSmoothing.matrix.Rd | 14
aroma.core-2.10.0/aroma.core/man/colKernelSmoothing.matrix.Rd | 4
aroma.core-2.10.0/aroma.core/man/doCBS.Rd |only
aroma.core-2.10.0/aroma.core/man/downloadChipTypeFile.AromaRepository.Rd | 3
aroma.core-2.10.0/aroma.core/man/downloadFile.AromaRepository.Rd | 3
aroma.core-2.10.0/aroma.core/man/downloadPackagePatch.Rd | 3
aroma.core-2.10.0/aroma.core/man/estimateSds.CopyNumberChromosomalModel.Rd | 3
aroma.core-2.10.0/aroma.core/man/estimateStandardDeviation.RawGenomicSignals.Rd | 3
aroma.core-2.10.0/aroma.core/man/extractRawCopyNumbers.CopyNumberChromosomalModel.Rd | 3
aroma.core-2.10.0/aroma.core/man/findAnnotationData.Rd | 63 +-
aroma.core-2.10.0/aroma.core/man/findFilesTodo.AromaTransform.Rd |only
aroma.core-2.10.0/aroma.core/man/fit.CopyNumberSegmentationModel.Rd | 4
aroma.core-2.10.0/aroma.core/man/fitGenotypeCone.matrix.Rd | 56 +-
aroma.core-2.10.0/aroma.core/man/fitGenotypeConeBySfit.matrix.Rd | 92 +--
aroma.core-2.10.0/aroma.core/man/fitMultiDimensionalCone.matrix.Rd | 131 ++---
aroma.core-2.10.0/aroma.core/man/isDone.AromaTransform.Rd | 5
aroma.core-2.10.0/aroma.core/man/listFiles.AromaRepository.Rd | 3
aroma.core-2.10.0/aroma.core/man/matrixBlockPolish.matrix.Rd | 73 +-
aroma.core-2.10.0/aroma.core/man/patchPackage.Rd | 3
aroma.core-2.10.0/aroma.core/man/plotTracks.PairedPSCNData.Rd | 5
aroma.core-2.10.0/aroma.core/man/process.ChromosomeExplorer.Rd | 3
aroma.core-2.10.0/aroma.core/man/processTime.Rd | 3
aroma.core-2.10.0/aroma.core/man/segmentByCBS.RawGenomicSignals.Rd | 94 +--
aroma.core-2.10.0/aroma.core/man/segmentByGLAD.RawGenomicSignals.Rd | 65 +-
aroma.core-2.10.0/aroma.core/man/segmentByHaarSeg.RawGenomicSignals.Rd | 52 +-
aroma.core-2.10.0/aroma.core/man/segmentByMPCBS.RawGenomicSignals.Rd | 50 -
aroma.core-2.10.0/aroma.core/man/writeDataFrame.AromaUnitSignalBinaryFile.Rd | 6
aroma.core-2.10.0/aroma.core/man/writeDataFrame.AromaUnitSignalBinarySet.Rd | 6
aroma.core-2.10.0/aroma.core/man/writeDataFrame.AromaUnitTabularBinaryFile.Rd | 6
aroma.core-2.9.0/aroma.core/R/doCBS.CopyNumberDataSet.R |only
aroma.core-2.9.0/aroma.core/R/doCBS.CopyNumberDataSetTuple.R |only
aroma.core-2.9.0/aroma.core/R/doCBS.character.R |only
aroma.core-2.9.0/aroma.core/man/doCBS.character.Rd |only
134 files changed, 2290 insertions(+), 1950 deletions(-)
Title: Search contributed R packages, sort by package
Diff between sos versions 1.3-5 dated 2012-07-28 and 1.3-7 dated 2013-08-04
Description: Search contributed R packages, sort by package
Author: Spencer Graves, Sundar Dorai-Raj, and Romain Francois
Maintainer: Spencer Graves
DESCRIPTION | 14 +++++++------
MD5 | 15 +++++++------
NAMESPACE | 4 +--
R/PackageSum2.R | 9 +++++++-
R/findFn.R | 20 ++++++++++++------
R/writeFindFn2xls.R | 56 +++++++++++++++++++++++++++++++++++++++-------------
inst/doc/sos.R |only
inst/doc/sos.pdf |binary
man/findFn.Rd | 24 ++++++++++++++++++++++
9 files changed, 106 insertions(+), 36 deletions(-)
Title: Retrieve and plot Google n-gram data
Diff between ngramr versions 1.2.2 dated 2013-07-23 and 1.3.0 dated 2013-08-04
Description: Retrieve and plot word frequencies through time from the Google
Ngram Viewer
Author: Sean Carmody
Maintainer: Sean Carmody
DESCRIPTION | 12 +++++++-----
MD5 | 27 +++++++++++++++++----------
NAMESPACE | 2 ++
NEWS | 23 +++++++++++++++++++++++
R/add_count.R |only
R/data.R |only
R/ggram.R | 37 +++++++++++++++++++++++++++----------
R/ngram.R | 17 +++++++++++++++--
R/ngrami.R | 5 +++++
R/ngramw.R | 1 +
R/print.R |only
R/sysdata.rda |only
R/utilities.R |only
README.md | 11 ++++++++++-
man/ggram.Rd | 30 ++++++++++++++++++++++--------
man/hacker.Rd |only
man/ngram.Rd | 11 ++++++++---
man/print.ngram.Rd |only
18 files changed, 137 insertions(+), 39 deletions(-)
Title: R companion to "Curve and Surface Fitting with Splines"
Diff between DierckxSpline versions 1.1-8 dated 2013-01-21 and 1.1-9 dated 2013-08-04
Description:
This package provides a wrapper to the FITPACK routines written by
Paul Dierckx. The original Fortran is available from
http://www.netlib.org/dierckx
2012.02.15: This package is broken.
Currently, it seems NOT to have any users and is not worth fixing.
These FITPACK routines are over 20 years old and may be obsolete.
If you want to fix it, I will happily make you the maintainer.
Spencer Graves
Author: Sundar Dorai-Raj and Spencer Graves
Maintainer: Spencer Graves
DESCRIPTION | 27 +++++++++++++++------------
MD5 | 8 ++++----
R/splineZeros.R | 27 +++++++++++++++------------
man/curfit.free.knot.Rd | 7 ++++++-
man/titanium.Rd | 6 +++++-
5 files changed, 45 insertions(+), 30 deletions(-)