Author: Benjamin Haibe-Kains, Christos Sotiriou, Gianluca Bontempi
Title: Performance Assessment and Comparison for Survival Analysis
Description: R package providing functions to assess and to compare the
performance of risk prediction (survival) models.
Diff between survcomp versions 1.1.2 dated 2009-06-05 and 1.1.3 dated 2009-11-13
DESCRIPTION | 6 +++--- man/concordance.index.Rd | 2 +- man/fisherz.Rd | 2 +- man/sbrier.score2proba.Rd | 2 +- man/score2proba.Rd | 2 +- man/survcomp-package.Rd | 4 ++-- 6 files changed, 9 insertions(+), 9 deletions(-)
Author: Jerome Sueur
Diff between seewave versions 1.5.5 dated 2009-06-26 and 1.5.6 dated 2009-11-13
Title: Time wave analysis and graphical representation
Description: seewave provides functions for analysing, manipulating,
displaying, editing and synthesizing time waves (particularly
sound). This package processes time analysis (oscillograms and
envelopes), spectral content, resonance quality factor,
entropy, cross correlation and autocorrelation, zero-crossing,
dominant frequency, analytic signal, frequency coherence, 2D
and 3D spectrograms and many other analyses.
seewave-1.5.5/seewave/man/dynspec.rd |only
seewave-1.5.5/seewave/man/echo.rd |only
seewave-1.5.5/seewave/man/fadew.rd |only
seewave-1.5.5/seewave/man/fdoppler.rd |only
seewave-1.5.5/seewave/man/field.rd |only
seewave-1.5.5/seewave/man/noise.Rd |only
seewave-1.5.5/seewave/man/repw.rd |only
seewave-1.5.5/seewave/man/seewave.internal.rd |only
seewave-1.5.5/seewave/man/setenv.rd |only
seewave-1.5.5/seewave/man/wasp.rd |only
seewave-1.5.5/seewave/man/zapsilw.rd |only
seewave-1.5.5/seewave/man/zc.rd |only
seewave-1.5.6/seewave/DESCRIPTION | 13
seewave-1.5.6/seewave/NAMESPACE |only
seewave-1.5.6/seewave/NEWS | 38
seewave-1.5.6/seewave/R/seewave.r | 776 +++++++-----
seewave-1.5.6/seewave/data/orni.R | 5
seewave-1.5.6/seewave/data/peewit.R | 5
seewave-1.5.6/seewave/data/pellucens.R | 5
seewave-1.5.6/seewave/data/sheep.R | 5
seewave-1.5.6/seewave/data/tico.R | 5
seewave-1.5.6/seewave/demo/seewave.R | 6
seewave-1.5.6/seewave/inst/doc/seewave_IO.pdf | 1576 +++++++++++++-------------
seewave-1.5.6/seewave/inst/doc/seewave_IO.rnw | 94 -
seewave-1.5.6/seewave/man/H.Rd | 8
seewave-1.5.6/seewave/man/Q.Rd | 16
seewave-1.5.6/seewave/man/addsilw.Rd | 28
seewave-1.5.6/seewave/man/afilter.Rd | 22
seewave-1.5.6/seewave/man/ama.Rd | 38
seewave-1.5.6/seewave/man/autoc.Rd | 8
seewave-1.5.6/seewave/man/ccoh.Rd | 88 -
seewave-1.5.6/seewave/man/ceps.Rd | 64 -
seewave-1.5.6/seewave/man/cepstro.Rd | 57
seewave-1.5.6/seewave/man/coh.Rd | 50
seewave-1.5.6/seewave/man/corenv.Rd | 55
seewave-1.5.6/seewave/man/covspectro.Rd | 56
seewave-1.5.6/seewave/man/crest.Rd | 8
seewave-1.5.6/seewave/man/csh.Rd | 20
seewave-1.5.6/seewave/man/cutw.Rd | 38
seewave-1.5.6/seewave/man/deletew.Rd | 39
seewave-1.5.6/seewave/man/dfreq.Rd | 22
seewave-1.5.6/seewave/man/diffenv.Rd | 38
seewave-1.5.6/seewave/man/diffspec.Rd | 60
seewave-1.5.6/seewave/man/diffwave.Rd | 39
seewave-1.5.6/seewave/man/discrets.Rd | 42
seewave-1.5.6/seewave/man/drawenv.Rd | 40
seewave-1.5.6/seewave/man/dynspec.Rd |only
seewave-1.5.6/seewave/man/echo.Rd |only
seewave-1.5.6/seewave/man/env.Rd | 8
seewave-1.5.6/seewave/man/export.Rd | 30
seewave-1.5.6/seewave/man/fadew.Rd |only
seewave-1.5.6/seewave/man/fdoppler.Rd |only
seewave-1.5.6/seewave/man/ffilter.Rd | 37
seewave-1.5.6/seewave/man/field.Rd |only
seewave-1.5.6/seewave/man/fir.Rd | 39
seewave-1.5.6/seewave/man/fma.Rd | 32
seewave-1.5.6/seewave/man/ftwindow.Rd | 12
seewave-1.5.6/seewave/man/fund.Rd | 10
seewave-1.5.6/seewave/man/hilbert.Rd | 10
seewave-1.5.6/seewave/man/ifreq.Rd | 52
seewave-1.5.6/seewave/man/lfs.Rd | 38
seewave-1.5.6/seewave/man/listen.Rd | 43
seewave-1.5.6/seewave/man/meandB.Rd |only
seewave-1.5.6/seewave/man/meanspec.Rd | 54
seewave-1.5.6/seewave/man/mel.Rd | 36
seewave-1.5.6/seewave/man/micsens.Rd | 18
seewave-1.5.6/seewave/man/moredB.Rd | 10
seewave-1.5.6/seewave/man/mutew.Rd | 34
seewave-1.5.6/seewave/man/noisew.Rd |only
seewave-1.5.6/seewave/man/orni.Rd | 18
seewave-1.5.6/seewave/man/oscillo.Rd | 55
seewave-1.5.6/seewave/man/oscilloST.Rd | 33
seewave-1.5.6/seewave/man/pastew.Rd | 49
seewave-1.5.6/seewave/man/peewit.Rd | 19
seewave-1.5.6/seewave/man/pellucens.Rd | 6
seewave-1.5.6/seewave/man/pulse.Rd | 16
seewave-1.5.6/seewave/man/repw.Rd |only
seewave-1.5.6/seewave/man/resamp.Rd | 22
seewave-1.5.6/seewave/man/revw.Rd | 36
seewave-1.5.6/seewave/man/rmam.Rd | 31
seewave-1.5.6/seewave/man/rmnoise.Rd | 26
seewave-1.5.6/seewave/man/rmoffset.Rd | 20
seewave-1.5.6/seewave/man/rms.Rd | 4
seewave-1.5.6/seewave/man/savewav.Rd | 30
seewave-1.5.6/seewave/man/seedata.Rd |only
seewave-1.5.6/seewave/man/seewave.internal.Rd |only
seewave-1.5.6/seewave/man/seewave.package.Rd | 40
seewave-1.5.6/seewave/man/setenv.Rd |only
seewave-1.5.6/seewave/man/sfm.Rd | 26
seewave-1.5.6/seewave/man/sh.Rd | 32
seewave-1.5.6/seewave/man/sheep.Rd | 10
seewave-1.5.6/seewave/man/simspec.Rd | 48
seewave-1.5.6/seewave/man/spec.Rd | 55
seewave-1.5.6/seewave/man/specprop.Rd | 62 -
seewave-1.5.6/seewave/man/spectro.Rd | 117 +
seewave-1.5.6/seewave/man/spectro3D.Rd | 72 -
seewave-1.5.6/seewave/man/symba.Rd | 66 -
seewave-1.5.6/seewave/man/synth.Rd | 64 -
seewave-1.5.6/seewave/man/th.Rd | 32
seewave-1.5.6/seewave/man/tico.Rd | 22
seewave-1.5.6/seewave/man/timer.Rd | 55
seewave-1.5.6/seewave/man/wasp.Rd |only
seewave-1.5.6/seewave/man/wav2flac.Rd | 4
seewave-1.5.6/seewave/man/wf.Rd | 41
seewave-1.5.6/seewave/man/zapsilw.Rd |only
seewave-1.5.6/seewave/man/zc.Rd |only
106 files changed, 2496 insertions(+), 2442 deletions(-)
Author: Steve Juggins
Title: Analysis of Quaternary Science Data
Description: Functions for the analysis of Quaternary science data,
including constrained clustering, WA, WAPLS, IKFA, MLRC and MAT
transfer functions, and stratigraphic diagrams.
Diff between rioja versions 0.5-5 dated 2009-10-28 and 0.5-6 dated 2009-11-13
DESCRIPTION | 10 +++++----- inst/CITATION | 4 ++-- inst/ChangeLog | 45 ++++++++++++++++----------------------------- man/read.CEP.Rd | 2 +- man/read.Tilia.Rd | 4 +++- man/rioja.package.Rd | 4 ++-- 6 files changed, 29 insertions(+), 40 deletions(-)
Author: Roger Bivand, Friedrich Leisch and Martin Maechler
Title: Bitmap Images (``Pixel Maps'')
Description: Functions for import, export, plotting and other
manipulations of bitmapped images.
Diff between pixmap versions 0.4-9 dated 2008-07-04 and 0.4-10 dated 2009-11-13
pixmap-0.4-10/pixmap/DESCRIPTION | 12 +++++++----- pixmap-0.4-10/pixmap/NEWS | 8 ++++++++ pixmap-0.4-10/pixmap/R/pnm.R | 2 -- pixmap-0.4-10/pixmap/man/pnm.Rd | 3 ++- pixmap-0.4-9/pixmap/inst/NEWS |only 5 files changed, 17 insertions(+), 8 deletions(-)
Author: Patrick Giraudoux
Diff between pgirmess versions 1.4.1 dated 2009-11-08 and 1.4.2 dated 2009-11-13
Title: Data analysis in ecology
Description: Miscellaneous functions for analysis and display of
ecological and spatial data
DESCRIPTION | 8 ++++----
man/gps2gpx.rd | 4 ++--
man/kruskalmc.Rd | 15 +++++----------
man/readVista.rd | 2 +-
man/uploadGPS.rd | 2 +-
5 files changed, 13 insertions(+), 18 deletions(-)
Author: Christopher Jackson
Diff between msm versions 0.9.3 dated 2009-08-26 and 0.9.4 dated 2009-11-13
Title: Multi-state Markov and hidden Markov models in continuous time
Description: Functions for fitting general continuous-time Markov and
hidden Markov multi-state models to longitudinal data. Both
Markov transition rates and the hidden Markov output process
can be modelled in terms of covariates. A variety of
observation schemes are supported, including processes observed
at arbitrary times, completely-observed processes, and censored
states.
msm-0.9.3/msm/tests/Rplots.pdf |only
msm-0.9.3/msm/tests/debug.dat |only
msm-0.9.4/msm/ChangeLog | 31 +++++++++++++++++++++++-
msm-0.9.4/msm/DESCRIPTION | 8 +++---
msm-0.9.4/msm/R/constants.R | 7 +++++
msm-0.9.4/msm/R/msm.R | 37 ++++++++++++++++-------------
msm-0.9.4/msm/R/outputs.R | 22 +++++++++--------
msm-0.9.4/msm/R/pearson.R | 8 +++---
msm-0.9.4/msm/inst/NEWS | 20 +++++++++++++++
msm-0.9.4/msm/inst/doc/msm-manual.pdf |binary
msm-0.9.4/msm/man/MatrixExp.Rd | 3 +-
msm-0.9.4/msm/man/deltamethod.Rd | 2 -
msm-0.9.4/msm/man/pmatrix.msm.Rd | 9 +++++--
msm-0.9.4/msm/man/pmatrix.piecewise.msm.Rd | 5 +++
msm-0.9.4/msm/src/analyticp.c | 33 +++++++------------------
msm-0.9.4/msm/src/doc/msm-manual.Rnw | 10 ++++---
msm-0.9.4/msm/src/lik.c | 16 +++++++++---
msm-0.9.4/msm/tests/boot.R | 31 +++++++++++++++++++++++-
msm-0.9.4/msm/tests/deriv-debug.R |only
msm-0.9.4/msm/tests/deriv.R | 2 -
msm-0.9.4/msm/tests/simple.R | 23 ++++++++++++++----
21 files changed, 190 insertions(+), 77 deletions(-)
Author: Henrik Bengtsson
Diff between matrixStats versions 0.1.6 dated 2009-06-18 and 0.1.8 dated 2009-11-13
Title: Methods that apply to rows and columns of a matrix
Description: This packages provides methods operating on rows and
columns of matrices. The methods are optimized for speed and
memory. This package is currently in a beta phase. Make sure
to read the 'Roadmap' section in the package help.
DESCRIPTION | 8 ++--
R/rowRanges.R | 7 ++-
R/rowTabulates.R | 12 +++++-
inst/NEWS | 15 ++++++++
man/matrixStats-package.Rd | 2 -
tests/rowRanges.R | 83 ++++++++++++++++++++++++---------------------
6 files changed, 81 insertions(+), 46 deletions(-)
Author: Vinzenz Erhardt
Title: Generate correlated count random variables
Description: Generate high-dimensional correlated count random
variables with a prespecified Pearson correlation.
Diff between corcounts versions 1.3 dated 2009-10-09 and 1.4 dated 2009-11-13
DESCRIPTION | 8 +-- R/modified.cvine.alg.R | 4 - R/modified.cvine.alg.reg.R | 4 - R/rcounts.R | 102 +++++++++++++++++++++++------------------- R/rcounts.reg.R | 107 +++++++++++++++++++++++++-------------------- man/corcounts-package.Rd | 4 - 6 files changed, 127 insertions(+), 102 deletions(-)
Author: Nicola Lama
Diff between vbmp versions 1.12.0 dated 2009-05-10 and 1.14.0 dated 2009-11-13
Title: Variational Bayesian Multinomial Probit Regression
Description: Variational Bayesian Multinomial Probit Regression with
Gaussian Process Priors. It estimates class membership
posterior probability employing variational and sparse
approximation to the full posterior. This software also
incorporates feature weighting by means of Automatic Relevance
Determination.
DESCRIPTION | 8 ++++----
data/BRCA12.RData |binary
inst/doc/vbmp.pdf |binary
3 files changed, 4 insertions(+), 4 deletions(-)
Author: Jeff Gentry
Diff between twitteR versions 0.1.2 dated 2009-10-20 and 0.1.3 dated 2009-11-13
Title: R based Twitter client
Description: Provides an interface to the Twitter web API
DESCRIPTION | 6 +++---
R/dm.R | 14 +++-----------
R/json.R | 13 ++++++-------
R/search.R | 18 +++++++++++++++---
R/status.R | 6 +-----
R/toys.R |only
inst/doc/twitteR.Rnw | 17 +++++++++++++++--
inst/doc/twitteR.pdf |binary
man/Rtweets.Rd | 3 ++-
man/search.Rd |only
man/taskStatus.Rd |only
11 files changed, 45 insertions(+), 32 deletions(-)
Author: Alan Dabney
Diff between qvalue versions 1.18.0 dated 2009-05-10 and 1.20.0 dated 2009-11-13
Title: Q-value estimation for false discovery rate control
Description: This package takes a list of p-values resulting from the
simultaneous testing of many hypotheses and estimates their
q-values. The q-value of a test measures the proportion of
false positives incurred (called the false discovery rate) when
that particular test is called significant. Various plots are
automatically generated, allowing one to make sensible
significance cut-offs. Several mathematical results have
recently been shown on the conservative accuracy of the
estimated q-values from this software. The software can be
applied to problems in genomics, brain imaging, astrophysics,
and data mining.
qvalue-1.18.0/qvalue/inst/doc/my-qvalue-results.txt |only
qvalue-1.18.0/qvalue/inst/doc/qvalue.tex |only
qvalue-1.20.0/qvalue/DESCRIPTION | 6 +-
qvalue-1.20.0/qvalue/data/hedenfalk.RData |binary
qvalue-1.20.0/qvalue/inst/doc/qvalue-002.eps | 2
qvalue-1.20.0/qvalue/inst/doc/qvalue-002.pdf | 26 +++++-----
qvalue-1.20.0/qvalue/inst/doc/qvalue-004.eps | 2
qvalue-1.20.0/qvalue/inst/doc/qvalue-004.pdf | 26 +++++-----
qvalue-1.20.0/qvalue/inst/doc/qvalue-006.eps | 2
qvalue-1.20.0/qvalue/inst/doc/qvalue-006.pdf | 49 +++++---------------
qvalue-1.20.0/qvalue/inst/doc/qvalue.pdf |binary
11 files changed, 49 insertions(+), 64 deletions(-)
Author: T. Hastie, R. Tibshirani, Balasubramanian Narasimhan, Gil Chu
Title: Pam: prediction analysis for microarrays
Description: Some functions for sample classification in microarrays
Diff between pamr versions 1.42.0 dated 2009-05-10 and 1.44.0 dated 2009-11-13
DESCRIPTION | 6 +++--- 1 file changed, 3 insertions(+), 3 deletions(-)
Author: Mark V. Bravington
Diff between mvbutils versions 2.2.0 dated 2008-11-06 and 2.5.0 dated 2009-11-13
Title: Workspace organization, code and documentation editing, package
prep and editing, etc.
Description: Hierarchical workspace tree, code editing and backup, easy
package prep, editing of packages while loaded, per-object
lazy-loading, easy documentation, macro functions, and
miscellaneous utilities. Needed by debug package.
mvbutils-2.2.0/mvbutils/man/autoFF.Rd |only
mvbutils-2.2.0/mvbutils/man/mvbutils-operators.Rd |only
mvbutils-2.2.0/mvbutils/man/mvbutils-utils.Rd |only
mvbutils-2.5.0/mvbutils/DESCRIPTION | 30
mvbutils-2.5.0/mvbutils/INDEX | 17
mvbutils-2.5.0/mvbutils/NAMESPACE | 16
mvbutils-2.5.0/mvbutils/R/mvbutils.R | 2230 +++++++++++----
mvbutils-2.5.0/mvbutils/R/sysdata.rda |binary
mvbutils-2.5.0/mvbutils/man/00mvbutils-package.Rd | 58
mvbutils-2.5.0/mvbutils/man/Save.Rd | 12
mvbutils-2.5.0/mvbutils/man/add.flatdoc.to.Rd | 14
mvbutils-2.5.0/mvbutils/man/as.data.frame.I.Rd | 2
mvbutils-2.5.0/mvbutils/man/cd.Rd | 40
mvbutils-2.5.0/mvbutils/man/cdfind.Rd | 2
mvbutils-2.5.0/mvbutils/man/do.in.envir.Rd | 2
mvbutils-2.5.0/mvbutils/man/doc2Rd.Rd | 67
mvbutils-2.5.0/mvbutils/man/dochelp.Rd | 4
mvbutils-2.5.0/mvbutils/man/dont.lockBindings.Rd | 18
mvbutils-2.5.0/mvbutils/man/find.documented.Rd | 14
mvbutils-2.5.0/mvbutils/man/fix.order.Rd | 2
mvbutils-2.5.0/mvbutils/man/fixr.Rd | 74
mvbutils-2.5.0/mvbutils/man/flatdoc.Rd | 87
mvbutils-2.5.0/mvbutils/man/foodweb.Rd | 13
mvbutils-2.5.0/mvbutils/man/get.backup.Rd | 10
mvbutils-2.5.0/mvbutils/man/help2flatdoc.Rd | 17
mvbutils-2.5.0/mvbutils/man/local.on.exit.Rd | 4
mvbutils-2.5.0/mvbutils/man/lsize.Rd | 4
mvbutils-2.5.0/mvbutils/man/maintain.packages.Rd | 20
mvbutils-2.5.0/mvbutils/man/make.NAMESPACE.Rd | 13
mvbutils-2.5.0/mvbutils/man/make.usage.section.Rd | 4
mvbutils-2.5.0/mvbutils/man/mcut.Rd |only
mvbutils-2.5.0/mvbutils/man/mlazy.Rd | 27
mvbutils-2.5.0/mvbutils/man/mlocal.Rd | 8
mvbutils-2.5.0/mvbutils/man/move.Rd | 2
mvbutils-2.5.0/mvbutils/man/mvb.sys.parent.Rd | 2
mvbutils-2.5.0/mvbutils/man/mvbutils.operators.Rd |only
mvbutils-2.5.0/mvbutils/man/mvbutils.packaging.tools.Rd |only
mvbutils-2.5.0/mvbutils/man/mvbutils.utils.Rd |only
mvbutils-2.5.0/mvbutils/man/my.index.Rd | 2
mvbutils-2.5.0/mvbutils/man/pre.install.Rd | 120
mvbutils-2.5.0/mvbutils/man/rm.pkg.Rd | 2
mvbutils-2.5.0/mvbutils/man/setup.mcache.Rd | 4
mvbutils-2.5.0/mvbutils/man/source.mvb.Rd | 11
mvbutils-2.5.0/mvbutils/man/task.home.Rd | 2
mvbutils-2.5.0/mvbutils/man/unpackage.Rd |only
mvbutils-2.5.0/mvbutils/man/write.sourceable.function.Rd | 17
46 files changed, 2087 insertions(+), 884 deletions(-)
Author: Katherine S. Pollard, Houston N. Gilbert, Yongchao Ge, Sandra
Taylor, Sandrine Dudoit
Title: Resampling-based multiple hypothesis testing
Description: Non-parametric bootstrap and permutation resampling-based
multiple testing procedures (including empirical Bayes methods)
for controlling the family-wise error rate (FWER), generalized
family-wise error rate (gFWER), tail probability of the
proportion of false positives (TPPFP), and false discovery rate
(FDR). Several choices of bootstrap-based null distribution
are implemented (centered, centered and scaled,
quantile-transformed). Single-step and step-wise methods are
available. Tests based on a variety of t- and F-statistics
(including t-statistics based on regression parameters from
linear and survival models as well as those based on
correlation parameters) are included. When probing hypotheses
with t-statistics, users may also select a potentially faster
null distribution which is multivariate normal with mean zero
and variance covariance matrix derived from the vector
influence function. Results are reported in terms of adjusted
p-values, confidence regions and test statistic cutoffs. The
procedures are directly applicable to identifying
differentially expressed genes in DNA microarray experiments.
Diff between multtest versions 2.1.3 dated 2009-10-22 and 2.2.0 dated 2009-11-13
DESCRIPTION | 6 +++--- 1 file changed, 3 insertions(+), 3 deletions(-)
Author: Hao Wu, modified by Hyuna Yang and Keith Sheppard with ideas
from Gary Churchill, Katie Kerr and Xiangqin Cui.
Title: Tools for analyzing Micro Array experiments
Description: Analysis of N-dye Micro Array experiment using mixed model
effect. Containing anlysis of variance, permutation and
bootstrap, cluster and consensus tree.
Diff between maanova versions 1.14.0 dated 2009-05-10 and 1.16.0 dated 2009-11-13
maanova-1.14.0/maanova/inst/doc/maanova.bbl |only maanova-1.14.0/maanova/inst/doc/maanova.blg |only maanova-1.16.0/maanova/DESCRIPTION | 6 maanova-1.16.0/maanova/R/read.madata.R | 172 +++- maanova-1.16.0/maanova/R/util.R | 2 maanova-1.16.0/maanova/R/volcano.R | 704 +++++++++--------- maanova-1.16.0/maanova/inst/doc/abf1.tex | 4 maanova-1.16.0/maanova/inst/doc/camda.tex | 2 maanova-1.16.0/maanova/inst/doc/maanova.pdf | 962 ++++++++++++------------- maanova-1.16.0/maanova/man/arrayview.Rd | 4 maanova-1.16.0/maanova/man/fitmaanova.Rd | 6 maanova-1.16.0/maanova/man/fom.Rd | 2 maanova-1.16.0/maanova/man/geneprofile.Rd | 2 maanova-1.16.0/maanova/man/gridcheck.Rd | 2 maanova-1.16.0/maanova/man/macluster.Rd | 6 maanova-1.16.0/maanova/man/matest.Rd | 3 maanova-1.16.0/maanova/man/read.madata.Rd | 10 maanova-1.16.0/maanova/man/subset.madata.Rd | 4 maanova-1.16.0/maanova/man/transform.madata.Rd | 4 maanova-1.16.0/maanova/man/varplot.Rd | 2 20 files changed, 1006 insertions(+), 891 deletions(-)
Author: Christophe Genolini
Title: K-Means for Longitudinal Data (KmL)
Description: KmL is an implementation of k-means specificaly design to
deal with longitudinal data. It provide facilities to deal with
missing value and propose a graphical interphace for chosing
the correct number of clusters.
Diff between kml versions 0.9.2 dated 2009-02-19 and 1.0 dated 2009-11-13
kml-0.9.2/kml/R/artificialLongData.r |only kml-0.9.2/kml/R/function.r |only kml-0.9.2/kml/R/imputation.r |only kml-0.9.2/kml/R/longData-Partition.r |only kml-0.9.2/kml/R/longData.r |only kml-0.9.2/kml/R/partition.r |only kml-0.9.2/kml/man/ArtificialLongData-class.Rd |only kml-0.9.2/kml/man/generateArtificialLongData.Rd |only kml-0.9.2/kml/man/plotCalinski.Rd |only kml-0.9.2/kml/man/plotSubGroups.Rd |only kml-0.9.2/kml/man/plotTraj.Rd |only kml-0.9.2/kml/testsDev/.svn |only kml-0.9.2/kml/testsDev/cld2.Rdata |only kml-0.9.2/kml/testsDev/cld3n.Rdata |only kml-0.9.2/kml/testsDev/cld4.Rdata |only kml-0.9.2/kml/testsDev/cld5.Rdata |only kml-0.9.2/kml/testsDev/essaiExport1-CLUSTERS.csv |only kml-0.9.2/kml/testsDev/essaiExport1-CRITERS.csv |only kml-0.9.2/kml/testsDev/essaiExport2-CLUSTERS.csv |only kml-0.9.2/kml/testsDev/essaiExport2-CRITERS.csv |only kml-0.9.2/kml/testsDev/essaiExport3-CLUSTERS.csv |only kml-0.9.2/kml/testsDev/essaiExport3-CRITERS.csv |only kml-0.9.2/kml/testsDev/essaiExport4-CLUSTERS.csv |only kml-0.9.2/kml/testsDev/essaiExport4-CRITERS.csv |only kml-1.0/kml/DESCRIPTION | 35 - kml-1.0/kml/NAMESPACE | 20 kml-1.0/kml/NAMESPACE.Ex |only kml-1.0/kml/R/clusterizLongData.r | 684 ++++++++--------------- kml-1.0/kml/R/clusterization.r | 113 +-- kml-1.0/kml/R/global.r | 35 - kml-1.0/kml/R/kml.r |only kml-1.0/kml/_man |only kml-1.0/kml/man.zip |only kml-1.0/kml/man/ClusterizLongData-class.Rd | 180 +++--- kml-1.0/kml/man/Clusterization-class.Rd | 107 +-- kml-1.0/kml/man/affectIndiv.Rd |only kml-1.0/kml/man/affectIndivGeneralized.Rd |only kml-1.0/kml/man/as.clusterizLongData.Rd | 79 +- kml-1.0/kml/man/calculCenterGeneralized.Rd |only kml-1.0/kml/man/calculMean.Rd |only kml-1.0/kml/man/choice.Rd | 92 +-- kml-1.0/kml/man/clusterizLongData.Rd | 54 + kml-1.0/kml/man/clusterization.Rd |only kml-1.0/kml/man/exportClusterization.Rd |only kml-1.0/kml/man/kml-internal.Rd | 22 kml-1.0/kml/man/kml-package.Rd | 71 +- kml-1.0/kml/man/kml.Rd | 157 +++-- kml-1.0/kml/man/partitionInitialise.Rd |only kml-1.0/kml/man/plot.Rd | 93 ++- kml-1.0/kml/man/plotAll.Rd | 152 ++--- kml-1.0/kml/man/plotCriterion.Rd |only kml-1.0/kml/man/updateClusterizLongData.Rd |only kml-1.0/kml/man/updateClusterization.Rd |only kml-1.0/kml/src/kml.c | 466 ++++++++++++++- kml-1.0/kml/src/kml.h | 37 + kml-1.0/kml/testsDev/Object.Rdata |binary kml-1.0/kml/testsDev/a.Rdata |only kml-1.0/kml/testsDev/allTest.Rdata |only kml-1.0/kml/testsDev/cld3.Rdata |binary kml-1.0/kml/testsDev/testArtificialLongData.r | 27 kml-1.0/kml/testsDev/testClusterizLongData.r | 243 ++++---- kml-1.0/kml/testsDev/testClusterization.r | 123 ++-- kml-1.0/kml/testsDev/testFunction.r | 2 kml-1.0/kml/testsDev/testKml.r |only kml-1.0/kml/testsDev/testKml2.r |only kml-1.0/kml/testsDev/testKml3.r |only kml-1.0/kml/toDo.txt |only 67 files changed, 1615 insertions(+), 1177 deletions(-)
Author: Sebastien Dejean, Ignacio Gonzalez and Kim-Anh Le Cao
Title: Integrate Omics data project
Description: The package supplies two efficients methodologies:
regularized CCA and sparse PLS to unravel relationships between
two heterogeneous data sets of size (nxp) and (nxq) where the p
and q variables are measured on the same samples or individuals
n. These data may come from high throughput technologies, such
as omics data (e.g. transcriptomics, metabolomics or proteomics
data) that require an integrative or joint analysis. However,
integrOmics can also be applied to any other large data sets
where p+q>>n. rCCA is a regularized version of CCA to deal with
the large number of variables. sPLS allows variable selection
in a one step procedure and two frameworks are proposed:
regression and canonical analysis. Numerous graphical outputs
are provided to help interpreting the results.
Diff between integrOmics versions 2.4 dated 2009-09-23 and 2.5 dated 2009-11-13
DESCRIPTION | 6 NAMESPACE | 15 - R/cim.R | 505 ++++++++++++++++++++++++++--------------------------- R/cim.rcc.R | 70 ++++--- R/cim.spls.R |only R/network.rcc.R | 13 - R/network.spls.R | 438 +++++++++++++++++++++++++++++++++------------ R/rcc.R | 4 R/spls.R | 2 man/cim.Rd | 44 ++++ man/network.Rd | 47 ++-- man/plot3dIndiv.Rd | 1 man/plot3dVar.Rd | 4 man/plotIndiv.Rd | 2 man/plotVar.Rd | 2 man/spls.Rd | 2 16 files changed, 697 insertions(+), 458 deletions(-)
Author: Trevor Hastie, Robert Tibshirani, Balasubramanian Narasimhan,
Gilbert Chu
Title: impute: Imputation for microarray data
Description: Imputation for microarray data (currently KNN only)
Diff between impute versions 1.18.0 dated 2009-09-22 and 1.20.0 dated 2009-11-13
DESCRIPTION | 6 +++--- data/khanmiss.rda |binary 2 files changed, 3 insertions(+), 3 deletions(-)
Author: Katherine S. Pollard, with Mark J. van der Laan
Diff between hopach versions 2.4.0 dated 2009-05-10 and 2.6.0 dated 2009-11-13
Title: Hierarchical Ordered Partitioning and Collapsing Hybrid (HOPACH)
Description: The HOPACH clustering algorithm builds a hierarchical tree
of clusters by recursively partitioning a data set, while
ordering and possibly collapsing clusters at each level. The
algorithm uses the Mean/Median Split Silhouette (MSS) criteria
to identify the level of the tree with maximally homogeneous
clusters. It also runs the tree down to produce a final ordered
list of the elements. The non-parametric bootstrap allows one
to estimate the probability that each element belongs to each
cluster (fuzzy clustering).
DESCRIPTION | 6
inst/doc/hopach.pdf | 407 +++++++++++++++++++++++++++-------------------------
2 files changed, 217 insertions(+), 196 deletions(-)
Author: Dan Carr
Diff between hexbin versions 1.18.0 dated 2009-05-10 and 1.20.0 dated 2009-11-13
Title: Hexagonal Binning Routines
Description: Binning and plotting functions for hexagonal bins. Now
uses and relies on grid graphics and formal (S4) classes and
methods.
ChangeLog | 11
DESCRIPTION | 9
R/grid.hexagons.R | 13
R/hexbin.s4.R | 8
inst/doc/hexagon_binning.pdf |65301 +++++++++++++++++++++----------------------
man/colramp.Rd | 4
man/hexList.Rd | 2
man/hexVP-class.Rd | 12
man/hexViewport.Rd | 5
man/hexplom.Rd | 5
man/panel.hexboxplot.Rd | 2
man/panel.hexloess.Rd | 12
man/plotMAhex.Rd | 2
man/pushHexport.Rd | 5
14 files changed, 32190 insertions(+), 33201 deletions(-)
Author: Patrick Breheny
Title: Regularization paths for regression models with grouped
covariates
Description: Efficient algorithms for fitting the regularization path
for linear or logistic regression models penalized by the group
lasso, group bridge, or group MCP methods. The algorithm is
based on the idea of a locally approximated coordinate descent.
Diff between grpreg versions 1.0 dated 2008-11-24 and 1.1 dated 2009-11-13
grpreg-1.0/grpreg/R/formatData.R |only grpreg-1.0/grpreg/R/formatPar.R |only grpreg-1.1/grpreg/DESCRIPTION | 20 ++- grpreg-1.1/grpreg/R/calcL.R | 10 - grpreg-1.1/grpreg/R/criteria.R | 13 +- grpreg-1.1/grpreg/R/grpreg.R | 44 ++++--- grpreg-1.1/grpreg/R/plot.R | 44 ++----- grpreg-1.1/grpreg/R/print.R | 2 grpreg-1.1/grpreg/R/select.R | 10 - grpreg-1.1/grpreg/R/setupLambda.R |only grpreg-1.1/grpreg/R/unstandardize.R | 6 - grpreg-1.1/grpreg/man/grpreg-internal.Rd | 25 +--- grpreg-1.1/grpreg/man/grpreg-package.Rd | 40 ++---- grpreg-1.1/grpreg/man/grpreg.Rd | 183 ++++++++++++++++--------------- grpreg-1.1/grpreg/man/plot.grpreg.Rd | 43 +++---- grpreg-1.1/grpreg/man/select.grpreg.Rd | 47 +++---- grpreg-1.1/grpreg/src/grpreg.c | 136 +++++++++++------------ grpreg-1.1/grpreg/tests/test.R | 40 +----- 18 files changed, 319 insertions(+), 344 deletions(-)
Author: R. Gentleman, Elizabeth Whalen, W. Huber, S. Falcon
Title: graph: A package to handle graph data structures
Description: A package that implements some simple graph handling
capabilities.
Diff between graph versions 1.22.2 dated 2009-05-10 and 1.24.1 dated 2009-11-13
graph-1.22.2/graph/src/Makevars.win |only graph-1.24.1/graph/DESCRIPTION | 6 +++--- graph-1.24.1/graph/R/graphNEL.R | 18 +++++++++--------- graph-1.24.1/graph/R/methods-graphAM.R | 8 +++++--- graph-1.24.1/graph/R/zzz.R | 2 +- graph-1.24.1/graph/inst/doc/GraphClass.pdf |binary graph-1.24.1/graph/inst/doc/clusterGraph.pdf |binary graph-1.24.1/graph/inst/doc/graph.pdf |binary graph-1.24.1/graph/inst/doc/graphAttributes.pdf |binary graph-1.24.1/graph/inst/unitTests/graphAM_test.R | 16 ++++++++++++++++ graph-1.24.1/graph/inst/unitTests/graphNEL_test.R | 11 +++++++---- graph-1.24.1/graph/man/DFS.Rd | 2 +- graph-1.24.1/graph/man/IMCA.Rd | 2 +- graph-1.24.1/graph/man/combineNodes.Rd | 4 ++-- graph-1.24.1/graph/man/fromGXL-methods.Rd | 2 +- graph-1.24.1/graph/man/graph-class.Rd | 4 +++- graph-1.24.1/graph/man/graphAM-class.Rd | 2 -- graph-1.24.1/graph/man/matrix2Graph.Rd | 10 ++++++---- graph-1.24.1/graph/man/renderInfo-class.Rd | 2 +- graph-1.24.1/graph/man/toDotR-methods.Rd | 4 ++-- graph-1.24.1/graph/src/Makevars | 3 ++- 21 files changed, 60 insertions(+), 36 deletions(-)
Author: Beiying Ding
Title: Classification using generalized partial least squares
Description: Classification using generalized partial least squares for
two-group and multi-group (more than 2 group) classification.
Diff between gpls versions 1.16.0 dated 2009-05-10 and 1.18.0 dated 2009-11-13
DESCRIPTION | 6 +++--- NAMESPACE | 4 +++- R/glpls1a.R | 13 +++++++++++-- inst/doc/gpls.pdf |binary 4 files changed, 17 insertions(+), 6 deletions(-)
Author: Holger Froehlich
Diff between gene2pathway versions 1.2.0 dated 2009-05-10 and 1.4.0 dated 2009-11-13
Title: Prediction of KEGG pathway membership for individual genes based
on InterPro domain signatures
Description: The package takes a list of genes and predicts to which
KEGG pathway each gene maps to. This is done by looking at the
InterPro domains of each gene. Each prediction is assigned a
confidence score. The package also allows to predict connected
component membership of genes within signaling pathways.
Separate models for each organism supported by KEGG can be
trained.
DESCRIPTION | 8 ++++----
R/gene2pathway.signaltrans.R | 9 +++++----
inst/doc/gene2pathway.pdf |binary
3 files changed, 9 insertions(+), 8 deletions(-)
Author: John Verzani
Title: Toolkit implementation of the gWidgets API for use with web
pages
Description: Port of the gWidgets API to www using a local server or
RApache (http://biostat.mc.vanderbilt.edu/rapache/index.html)
to link R with a web page, The Ext JavaScript libararies are
used to create and manipulate widgets. (www.extjs.com)
Diff between gWidgetsWWW versions 0.0-12 dated 2009-11-01 and 0.0-13 dated 2009-11-13
DESCRIPTION | 6 +-- NEWS | 10 ++++++ R/LocalVersion.R | 60 ++++++++++++++++++++++++------------- inst/Examples/ex-index.R | 2 - inst/basehtml/images/extanim32.gif |only inst/basehtml/index.gWWW | 17 +++++++--- inst/doc/gWidgetsWWW.pdf |binary inst/scripts/gWidgetsWWWrun.R | 25 ++++++++++++--- inst/tcl/mini1.1.tcl | 46 ++++++++++++++++++---------- man/localServerStart.Rd | 2 - 10 files changed, 118 insertions(+), 50 deletions(-)
Author: Mark V. Bravington
Diff between debug versions 1.2.0 dated 2008-10-27 and 1.2.1 dated 2009-11-13
Title: MVB's debugger for R
Description: Debugger for R functions, with code display, graceful
error recovery, line-numbered conditional breakpoints, access
to exit code, flow control, and full keyboard input.
DESCRIPTION | 28 +++++-----
INDEX | 14 ++---
R/debug.R | 133 ++++++++++++++++++++++++++++++++-----------------
inst/changes.txt | 2
man/00debug-package.Rd | 28 ++++++----
man/bp.Rd | 18 +++---
man/fun.locator.Rd | 10 ++-
man/get.retval.Rd | 10 ++-
man/go-skip-qqq.Rd | 5 -
man/is.mtraced.Rd | 5 +
man/mtrace.Rd | 22 ++++----
11 files changed, 167 insertions(+), 108 deletions(-)
Author: Nusrat Rabbee
Diff between RLMM versions 1.6.0 dated 2009-05-10 and 1.8.0 dated 2009-11-13
Title: A Genotype Calling Algorithm for Affymetrix SNP Arrays
Description: A classification algorithm, based on a multi-chip,
multi-SNP approach for Affymetrix SNP arrays. Using a large
training sample where the genotype labels are known, this
aglorithm will obtain more accurate classification results on
new data. RLMM is based on a robust, linear model and uses the
Mahalanobis distance for classification. The chip-to-chip
non-biological variation is removed through normalization. This
model-based algorithm captures the similarities across genotype
groups and probes, as well as thousands other SNPs for accurate
classification. NOTE: 100K-Xba only at for now.
DESCRIPTION | 10 -
inst/doc/RLMM.pdf | 288 ++++++++++++++++++++++++++----------------------------
2 files changed, 148 insertions(+), 150 deletions(-)
Author: Vince Carey
Diff between RBGL versions 1.20.0 dated 2009-05-10 and 1.22.0 dated 2009-11-13
Title: An interface to the BOOST graph library
Description: A fairly extensive and comprehensive interface to the
graph algorithms contained in the BOOST library.
RBGL-1.20.0/RBGL/man/kolmogorovMaxFlow.Rd |only
RBGL-1.20.0/RBGL/man/lengauerTarjanDominatorTree.Rd |only
RBGL-1.22.0/RBGL/DESCRIPTION | 6
RBGL-1.22.0/RBGL/NAMESPACE | 5
RBGL-1.22.0/RBGL/R/interfaces.R | 241 ++-
RBGL-1.22.0/RBGL/inst/doc/RBGL.Rnw | 6
RBGL-1.22.0/RBGL/inst/doc/RBGL.pdf | 1224 +++++++---------
RBGL-1.22.0/RBGL/man/RBGL.overview.Rd | 4
RBGL-1.22.0/RBGL/man/chrobakPayneStraightLineDrawing.Rd | 21
RBGL-1.22.0/RBGL/man/connectedComp.Rd | 2
RBGL-1.22.0/RBGL/man/dominatorTree.Rd | 3
RBGL-1.22.0/RBGL/man/edgeConn.Rd | 2
RBGL-1.22.0/RBGL/man/edmondsMaxCardinalityMatching.Rd | 29
RBGL-1.22.0/RBGL/man/edmondsOptimumBranching.Rd |only
RBGL-1.22.0/RBGL/man/extractPath.Rd | 2
RBGL-1.22.0/RBGL/man/incrConnComp.Rd | 2
RBGL-1.22.0/RBGL/man/isKuratowskiSubgraph.Rd | 22
RBGL-1.22.0/RBGL/man/isStraightLineDrawing.Rd | 28
RBGL-1.22.0/RBGL/man/makeBiconnectedPlanar.Rd | 19
RBGL-1.22.0/RBGL/man/makeConnected.Rd | 16
RBGL-1.22.0/RBGL/man/makeMaximalPlanar.Rd | 16
RBGL-1.22.0/RBGL/man/maxFlow.Rd | 14
RBGL-1.22.0/RBGL/man/planarCanonicalOrdering.Rd | 19
RBGL-1.22.0/RBGL/man/planarFaceTraversal.Rd | 19
RBGL-1.22.0/RBGL/man/sp.between.Rd | 2
RBGL-1.22.0/RBGL/man/strongComp.Rd | 2
RBGL-1.22.0/RBGL/src/boostIncl.tar.gz |binary
RBGL-1.22.0/RBGL/src/edmonds_optimum_branching.cpp |only
RBGL-1.22.0/RBGL/src/edmonds_optimum_branching.hpp |only
RBGL-1.22.0/RBGL/src/edmonds_optimum_branching_impl.hpp |only
RBGL-1.22.0/RBGL/src/mincut.cpp | 36
RBGL-1.22.0/RBGL/src/mincut.hpp | 2
RBGL-1.22.0/RBGL/src/planar.cpp |only
RBGL-1.22.0/RBGL/src/sna.cpp | 4
34 files changed, 1071 insertions(+), 675 deletions(-)
Author: David Rocke, Geun Cheol Lee, and John Tillinghast.
Title: LMGene Software for Date Transformation and Identification of
Differentially Expressed Genes in Gene Expression Arrays
Description: LMGene package for analysis of microarray data using a
linear model and glog data transformation in the R statistical
package.
Diff between LMGene versions 1.14.0 dated 2009-05-10 and 1.16.0 dated 2009-11-13
DESCRIPTION | 10 +++++----- data/sample.eS.RData |binary inst/doc/LMGene.pdf |binary 3 files changed, 5 insertions(+), 5 deletions(-)
Author: R. Gentleman and Alain Vandal .
Title: NPMLE for Censored and Truncated Data
Description: Many functions for computing the NPMLE for censored and
truncated data.
Diff between Icens versions 1.16.0 dated 2009-05-10 and 1.18.0 dated 2009-11-13
DESCRIPTION | 6 +++--- man/Plotboxes.Rd | 2 +- 2 files changed, 4 insertions(+), 4 deletions(-)
Author: Dongxiao Zhu and Youjuan Li
Title: Multivariate Correlation Estimator and Statistical Inference
Procedures.
Description: Multivariate correlation estimation and statistical
inference. See package vignette.
Diff between CORREP versions 1.10.0 dated 2009-05-10 and 1.12.0 dated 2009-11-13
DESCRIPTION | 6 +++--- inst/doc/CORREP.pdf |binary 2 files changed, 3 insertions(+), 3 deletions(-)