Title: subset quantile normalization
Diff between SQN versions 1.0.4 dated 2011-08-03 and 1.0.5 dated 2012-08-13
Description: Normalization based a subset of negative control probes as
described in 'Subset quantile normalization using negative
control features'. Wu Z, Aryee MJ, J Comput Biol. 2010
Oct;17(10):1385-95 [PMID 20976876].
Author: Zhijin(Jean) Wu, Martin Aryee
Maintainer: Martin Aryee
DESCRIPTION | 18 ++++++++++--------
MD5 |only
NAMESPACE |only
3 files changed, 10 insertions(+), 8 deletions(-)
Title: Hartigan's dip test statistic for unimodality - corrected code
Diff between diptest versions 0.75-3 dated 2012-04-18 and 0.75-4 dated 2012-08-13
Description: Compute Hartigan's dip test statistic for unimodality
Author: Martin Maechler (originally from Fortran and S-plus by Dario
Ringach, NYU.edu)
Maintainer: Martin Maechler
ChangeLog | 9 ++++
DESCRIPTION | 8 ++--
MD5 | 21 ++++++-----
NAMESPACE | 2 -
R/dip.R | 11 +++---
R/dipTest.R | 11 ++++--
data/qDiptab.R | 4 --
inst/doc/diptest-issues.Rnw-ss |only
inst/doc/diptest-issues.pdf |binary
src/dip.c | 74 ++++++++++++++++++++++++++++++++++-------
tests/ex1.Rout.save | 38 ++++++++++++---------
tests/sim1.Rout.save | 11 +++---
12 files changed, 133 insertions(+), 56 deletions(-)
Title: Pretty Heatmaps
Diff between pheatmap versions 0.6.1 dated 2012-03-08 and 0.7 dated 2012-08-13
Description: A package for drawing pretty heatmaps in R. The ordinary
heatmap function in R has several drawbacks when it comes to
producing publication quality heatmaps. It is hard to produce
pictures with consistent text, cell and overall sizes and
shapes. The function pheatmap tries to alleviate the problems
by offering more fine grained control over heatmap dimensions
and appearance.
Author: Raivo Kolde
Maintainer: Raivo Kolde
pheatmap-0.6.1/pheatmap/run_roxygen.r |only
pheatmap-0.7/pheatmap/DESCRIPTION | 26 +-
pheatmap-0.7/pheatmap/MD5 | 12
pheatmap-0.7/pheatmap/NEWS |only
pheatmap-0.7/pheatmap/R/pheatmap-package.r |only
pheatmap-0.7/pheatmap/R/pheatmap.r | 113 ++++++--
pheatmap-0.7/pheatmap/README.md |only
pheatmap-0.7/pheatmap/man/pheatmap-package.Rd | 20 -
pheatmap-0.7/pheatmap/man/pheatmap.Rd | 328 ++++++++++++++++----------
9 files changed, 327 insertions(+), 172 deletions(-)
Title: Functions for nonlinear least squares solutions
Diff between nlmrt versions 2012-8.11 dated 2012-08-12 and 2012-8.12 dated 2012-08-13
Description: nlmrt provides tools for working with nonlinear least
squares problems using a calling structure similar to, but much
simpler than, that of the nls() function. Moreover, where nls()
specifically does NOT deal with small or zero residual
problems, nlmrt is quite happy to solve them. It also attempts
to be more robust in finding solutions, thereby avoiding
'singular gradient' messages that arise in the Gauss-Newton
method within nls(). The Marquardt-Nash approach in nlmrt
generally works more reliably to get a solution, though this
may be one of a set of possibilities, and may also be
statistically unsatisfactory.
Author: John C. Nash
Maintainer:
nlmrt-2012-8.11/nlmrt/Makefile |only
nlmrt-2012-8.12/nlmrt/DESCRIPTION | 10 ++--
nlmrt-2012-8.12/nlmrt/MD5 | 19 +++----
nlmrt-2012-8.12/nlmrt/R/modgr.R | 10 ++--
nlmrt-2012-8.12/nlmrt/inst/doc/nlmrt-vignette.pdf |binary
nlmrt-2012-8.12/nlmrt/man/model2grfun.Rd | 48 +++++++++++--------
nlmrt-2012-8.12/nlmrt/man/model2jacfun.Rd | 50 ++++++++++++--------
nlmrt-2012-8.12/nlmrt/man/model2resfun.Rd | 53 +++++++++++-----------
nlmrt-2012-8.12/nlmrt/man/model2ssfun.Rd | 42 ++++++++---------
nlmrt-2012-8.12/nlmrt/man/modgr.Rd | 20 +++++---
nlmrt-2012-8.12/nlmrt/man/modss.Rd | 13 +++--
11 files changed, 146 insertions(+), 119 deletions(-)
Title: NCBI2R-An R package to navigate and annotate genes and SNPs
Diff between NCBI2R versions 1.4.1 dated 2012-07-17 and 1.4.2 dated 2012-08-13
Description: NCBI2R is an R package that annotates lists of SNPs and/or
genes, with current information from NCBI, including LD
information. Functions are provided that with one command will
provide annotation of the results from genome wide association
studies to provide a broader context of their meaning. Other
functions enable comparisons between a user's GWA results, and
candidate snp/gene lists that are created from keywords, such
as specific diseases, phenotypes or gene ontology terms.
Commands are simple to follow and designed to work with R
objects to integrate into existing workflows. The output
produces text fields and weblinks to more information for items
such as: gene descriptions, nucleotide positions, OMIM,
pathways, phenotypes, and lists of interacting and neighboring
genes. Annotation can then be used in R for further analysis,
or the objects can be customized for use in spreadsheet
programs or web browsers. The NCBI2R package wasdesigned to
allow those performing genome analysis to produce output that
could easily be understood by a person not familiar with R.
Please see the website at http://NCBI2R.wordpress.com for more
information. The internet is required for almost all of these
functions. Use the function PrintNCBI2RInfo() for information.
Author: Scott Melville
Maintainer: Scott Melville
DESCRIPTION | 8 ++++----
MD5 | 13 +++++++------
R/AnnotateSNPList.r | 3 ++-
R/GetGeneInfo.r | 35 +++++++++++++++++++++++------------
R/MergeSNPsGenes.r | 5 ++---
R/SplitGenes.r | 5 +++--
R/check.package.r | 1 +
R/order.to.original.list.r |only
8 files changed, 42 insertions(+), 28 deletions(-)
Title: Multivariate Dependence with Copulas
Diff between copula versions 0.999-0 dated 2012-07-30 and 0.999-1 dated 2012-08-13
Description: Classes (S4) of commonly used elliptical, Archimedean,
extreme value and some more copula families. Methods for
density, distribution, random number generation, bivariate
dependence measures, perspective and contour plots. Fitting
copula models including variance estimates. Independence and
serial (univariate and multivariate) independence tests, and
other copula related tests. Goodness-of-fit tests for copulas
based on multipliers, the parametric bootstrap with several
transformation options. Merged former package 'nacopula' for
nested Archimedean copulas: Efficient sampling algorithms,
various estimators, goodness-of-fit tests and related tools and
special functions.
Author: Marius Hofert
Maintainer: Martin Maechler
DESCRIPTION | 46 +++-----
MD5 | 91 ++++++++--------
NAMESPACE | 2
R/Classes.R | 9 +
R/Copula.R | 25 ++--
R/amhCopula.R | 25 +++-
R/aux-acopula.R | 79 +++++++++++--
R/claytonCopula.R | 3
R/cop_objects.R | 34 ++----
R/derCdfPdf.R | 191 +++++++++++++++++++--------------
R/ellipCopula.R | 8 -
R/estimation.R | 10 -
R/fitCopula.R | 243 ++++++++++++++++++++++++-------------------
R/frankCopula.R | 3
R/gof.R | 16 +-
R/gofEVTests.R | 8 -
R/gofTests.R | 41 +++----
R/joeCopula.R | 7 -
R/tCopula.R | 80 ++++++++------
TODO | 15 +-
demo/dDiag-plots.R | 7 +
demo/fitting-tests.R | 97 ++---------------
demo/logL-vis.R | 18 ++-
do-now.org | 5
feature-table.org | 4
inst/Rsource/tstFit-fn.R |only
inst/doc/Frank-Rmpfr.Rnw | 6 -
inst/doc/Frank-Rmpfr.pdf |binary
inst/doc/nacopula-pkg.Rnw | 1
inst/doc/nacopula-pkg.pdf |binary
inst/doc/nacopula.bib | 8 +
man/Sibuya.Rd | 1
man/copula-package.Rd |only
man/dDiag.Rd | 4
man/empcop.Rd | 6 -
man/evTestA.Rd | 14 +-
man/exchEVTest.Rd | 58 +++++-----
man/fitCopula.Rd | 6 -
man/fitMvdc.Rd | 11 +
man/indepTest.Rd | 36 +++---
man/log1mexp.Rd | 13 --
man/tauAMH.Rd | 105 +++++++++++++-----
man/timing.Rd | 4
tests/estim-ex.R | 13 +-
tests/fitting-ex.R |only
tests/moments.R | 10 -
tests/tail-pcopula.R | 5
tests/tail-pcopula.Rout.save | 21 +--
48 files changed, 765 insertions(+), 624 deletions(-)
Title: Analytic Solutions for (ground-water) Boussinesq Equation
Diff between boussinesq versions 1.0 dated 2011-12-07 and 1.0.1 dated 2012-08-13
Description: This package is a collection of R functions implemented
from published and available analytic solutions for the
One-Dimensional Boussinesq Equation (ground-water). In
particular, the function "beq.lin" is the analytic solution of
the linearized form of Boussinesq Equation between two
different head-based boundary (Dirichlet) conditions;
"beq.song" is the non-linear power-series analytic solution of
the motion of a wetting front over a dry bedrock (Song at al,
2007, see complete reference on function documentation).
Bugs/comments/questions/collaboration of any kind are warmly
welcomed.
Author: Emanuele Cordano
Maintainer: Emanuele Cordano
DESCRIPTION | 26 ++++++++++++++------------
MD5 | 2 +-
2 files changed, 15 insertions(+), 13 deletions(-)
Title: Vector analysis using graphical and analytical methods in 3D
Diff between VecStatGraphs3D versions 1.2 dated 2011-06-27 and 1.3 dated 2012-08-13
More information about VecStatGraphs3D at CRAN
Description: This package performs a 3D statistical analysis, both
numerical and graphic, of a set of vectors. Since a vector has
three components (a module and two angles) vector analysis is
performed in two stages: modules are analyzed by means of
linear statistics and orientations are analyzed by spherical
statistics. Tests and spherical statistic parameters are
accompanied by a full range of graphing: vector maps, density
maps, distribution modules and angles. The tests, spherical
statistic parameters and graphs allow us detecting another
distribution properties (I.e. anisotropy) and outliers.
Author: Juan Carlos Ruiz Cuetos, Maria Eugenia Polo Garcia, Pablo
Garcia Rodriguez
Maintainer: Pablo Garcia Rodriguez
DESCRIPTION | 13 ++++-----
MD5 |only
NAMESPACE |only
R/CorrectType3D.R | 6 ++--
R/DrawDensity3D.R | 2 -
R/LoadData3D.R | 25 +++++++++----------
R/MeanDirection3D.R | 6 ++--
R/Vectors3D.R | 2 -
man/AllAngleStatistics.Rd | 4 +--
man/AllModuleStatistics3D.Rd | 4 +--
man/ArithmeticMean3D.Rd | 4 +--
man/ConcentrationParameter3D.Rd | 4 +--
man/DrawDensity3D.Rd | 4 +--
man/DrawModuleAndAngleDistribution3D.Rd | 4 +--
man/LoadData3D.Rd | 38 ++++++++++-------------------
man/MaxValue3D.Rd | 4 +--
man/MeanDirection3D.Rd | 4 +--
man/MeanModule3D.Rd | 4 +--
man/MinValue3D.Rd | 4 +--
man/ModulePopulationStandardDeviation3D.Rd | 4 +--
man/ModulePopulationVariance3D.Rd | 4 +--
man/ModuleStandardDeviation3D.Rd | 4 +--
man/ModuleSum3D.Rd | 4 +--
man/ModuleVariance3D.Rd | 4 +--
man/NumberOfElements3D.Rd | 4 +--
man/Range3D.Rd | 4 +--
man/RayleighTest3D.Rd | 2 -
man/SphericalStandardError3D.Rd | 4 +--
man/StandardError3D.Rd | 4 +--
man/VecStatGraphs3D-package.Rd | 8 +++---
30 files changed, 84 insertions(+), 94 deletions(-)
Permanent link
Title: Vector analysis using graphical and analytical methods in 2D
Diff between VecStatGraphs2D versions 1.4 dated 2011-05-23 and 1.5 dated 2012-08-13
More information about VecStatGraphs2D at CRAN
Description: This package performs a 2D statistical analysis, both
numerical and graphic, of a set of vectors. Since a vector has
two components (module and azimuth) vector analysis is
performed in three stages: modules are analyzed by means of
linear statistics, azimuths are analyzed by circular
statistics, and the joint analysis of modules and azimuths is
done using density maps that allow detecting another
distribution properties (I.e. anisotropy) and outliers. Tests
and circular statistic parameters have associated a full range
of graphing: histograms, maps of distributions, point maps,
vector maps, density maps, distribution modules and azimuths.
Author: Ruiz-Cuetos, J.C., Polo, M.E., Rodriguez, P.G.
Maintainer: Pablo Garcia Rodriguez
DESCRIPTION | 11 +++++------
MD5 |only
NAMESPACE |only
R/CircularDispersal.R | 2 +-
R/CorrectType.R | 6 +++---
R/DrawDensityMap.R | 4 ++--
R/DrawDistribution.R | 2 +-
R/DrawHistogram.R | 7 ++++---
R/DrawModuleAndAzimuthDistribution.R | 2 +-
R/DrawPoints.R | 2 +-
R/DrawVectors.R | 2 +-
R/KurtosisAzimuthCoefficient.R | 14 +++++++++++++-
R/LoadData.R | 24 +++++++++++++-----------
R/MeanAzimuth.R | 6 +++---
R/RayleighTest.R | 17 +++++++++++------
R/SkewnessAzimuthCoefficient.R | 15 ++++++++++++++-
R/VonMisesParameter.R | 6 +++---
man/AllAzimuthStatistics.Rd | 4 ++--
man/AllModuleStatistics.Rd | 4 ++--
man/ArithmeticMean.Rd | 4 ++--
man/CircularDispersal.Rd | 6 +++---
man/CircularStandardDeviation.Rd | 4 ++--
man/CircularVariance.Rd | 4 ++--
man/DrawDensityMap.Rd | 4 ++--
man/DrawDistribution.Rd | 4 ++--
man/DrawHistogram.Rd | 12 ++++++------
man/DrawModuleAndAzimuthDistribution.Rd | 4 ++--
man/DrawPoints.Rd | 4 ++--
man/DrawVectors.Rd | 6 +++---
man/KurtosisAzimuthCoefficient.Rd | 4 ++--
man/KurtosisModuleCoefficient.Rd | 4 ++--
man/LoadData.Rd | 23 ++++++++++++-----------
man/MaxValue.Rd | 4 ++--
man/MeanAzimuth.Rd | 4 ++--
man/MeanModule.Rd | 4 ++--
man/MinValue.Rd | 4 ++--
man/ModulePopulationStandardDeviation.Rd | 4 ++--
man/ModulePopulationVariance.Rd | 4 ++--
man/ModuleStandardDeviation.Rd | 4 ++--
man/ModuleSum.Rd | 4 ++--
man/ModuleVariance.Rd | 4 ++--
man/NumberOfElements.Rd | 4 ++--
man/Range.Rd | 4 ++--
man/RaoTest.Rd | 4 ++--
man/RayleighTest.Rd | 4 ++--
man/SkewnessAzimuthCoefficient.Rd | 4 ++--
man/SkewnessModuleCoefficient.Rd | 4 ++--
man/StandardError.Rd | 4 ++--
man/ValuationOfUniformity.Rd | 4 ++--
man/VecStatGraphs2D-package.Rd | 6 +++---
man/VonMisesParameter.Rd | 4 ++--
51 files changed, 161 insertions(+), 128 deletions(-)
Permanent link
Title: Threshold exceedences and multivariate extremes
Diff between texmex versions 1.2 dated 2011-11-18 and 1.3 dated 2012-08-13
Description: Conditional multivariate extreme value modelling using the
approach of Heffernan and Tawn.
Author: Harry Southworth, Janet E. Heffernan
Maintainer: Harry Southworth
texmex-1.2/texmex/R/rl.gpd.R |only
texmex-1.2/texmex/man/summer.Rd |only
texmex-1.2/texmex/man/winter.Rd |only
texmex-1.3/texmex/CHANGES | 23
texmex-1.3/texmex/DESCRIPTION | 14
texmex-1.3/texmex/MD5 | 142 ++---
texmex-1.3/texmex/NAMESPACE |only
texmex-1.3/texmex/R/bgpdSetSeed.R | 9
texmex-1.3/texmex/R/bootgpd.R | 27
texmex-1.3/texmex/R/bootmex.R | 108 +--
texmex-1.3/texmex/R/chi.R | 505 +++++++++---------
texmex-1.3/texmex/R/coefficients.gpd.R | 12
texmex-1.3/texmex/R/coefficients.migpd.R | 5
texmex-1.3/texmex/R/copulas.R | 180 +++---
texmex-1.3/texmex/R/dgpd.R | 49 -
texmex-1.3/texmex/R/efficient.closures.R |only
texmex-1.3/texmex/R/endPoint.R |only
texmex-1.3/texmex/R/extremalIndex.R |only
texmex-1.3/texmex/R/gpd.R | 529 +++++++++----------
texmex-1.3/texmex/R/gpd.fit.R | 75 +-
texmex-1.3/texmex/R/gpdRangeFit.R | 11
texmex-1.3/texmex/R/hist.gpd.R | 13
texmex-1.3/texmex/R/info.gpd.R | 41 -
texmex-1.3/texmex/R/mex.R | 7
texmex-1.3/texmex/R/mexDependence.R | 106 +--
texmex-1.3/texmex/R/mexDependenceLowLevelFunctions.R | 144 ++---
texmex-1.3/texmex/R/mexRangeFit.R | 180 +++---
texmex-1.3/texmex/R/migpd.R | 24
texmex-1.3/texmex/R/migpdCoefs.R | 10
texmex-1.3/texmex/R/mrlPlot.R | 3
texmex-1.3/texmex/R/mspearman.R | 2
texmex-1.3/texmex/R/multivariate.cauchy.R |only
texmex-1.3/texmex/R/pgpd.R | 25
texmex-1.3/texmex/R/plot.bgpd.R | 49 -
texmex-1.3/texmex/R/plot.bootmex.R | 4
texmex-1.3/texmex/R/plot.gpd.R | 13
texmex-1.3/texmex/R/plot.mex.R | 256 ++++-----
texmex-1.3/texmex/R/plot.mexPrediction.R | 18
texmex-1.3/texmex/R/plot.predict.link.gpd.R |only
texmex-1.3/texmex/R/plotrl.gpd.R |only
texmex-1.3/texmex/R/predict.gpd.R |only
texmex-1.3/texmex/R/predict.mex.R | 77 +-
texmex-1.3/texmex/R/print.bootmex.R | 2
texmex-1.3/texmex/R/print.mexDependence.R | 2
texmex-1.3/texmex/R/qgpd.R | 6
texmex-1.3/texmex/R/rMaxAR.R |only
texmex-1.3/texmex/R/revTransform.R | 20
texmex-1.3/texmex/R/rgpd.R | 35 -
texmex-1.3/texmex/R/summary.bgpd.R | 2
texmex-1.3/texmex/R/summary.predict.mex.R | 8
texmex-1.3/texmex/R/testingFunctions.R | 154 +++--
texmex-1.3/texmex/R/thinAndBurn.bgpd.R | 186 +++---
texmex-1.3/texmex/R/validate.texmex.R | 2
texmex-1.3/texmex/inst |only
texmex-1.3/texmex/man/MCS.Rd | 32 -
texmex-1.3/texmex/man/airPollution.Rd |only
texmex-1.3/texmex/man/bootgpd.Rd | 16
texmex-1.3/texmex/man/bootmex.Rd | 166 ++---
texmex-1.3/texmex/man/chi.Rd | 65 +-
texmex-1.3/texmex/man/copula.Rd | 16
texmex-1.3/texmex/man/dgpd.Rd | 6
texmex-1.3/texmex/man/edf.Rd | 3
texmex-1.3/texmex/man/endPoint.Rd |only
texmex-1.3/texmex/man/extremalIndex.Rd |only
texmex-1.3/texmex/man/gpd.Rd | 88 +--
texmex-1.3/texmex/man/gpdRangeFit.Rd | 13
texmex-1.3/texmex/man/mex.Rd | 77 +-
texmex-1.3/texmex/man/mexDependence.Rd | 168 ++----
texmex-1.3/texmex/man/mexRangeFit.Rd | 123 ++--
texmex-1.3/texmex/man/migpd.Rd | 226 +++-----
texmex-1.3/texmex/man/migpdCoefs.Rd | 11
texmex-1.3/texmex/man/mrlPlot.Rd | 11
texmex-1.3/texmex/man/predict.gpd.Rd |only
texmex-1.3/texmex/man/rl.Rd |only
texmex-1.3/texmex/man/texmex-internal.Rd | 61 +-
texmex-1.3/texmex/man/texmex-package.Rd | 22
texmex-1.3/texmex/man/texmexMethods.Rd |only
texmex-1.3/texmex/man/thinAndBurn.Rd | 93 +--
texmex-1.3/texmex/man/validate.texmex.Rd | 16
texmex-1.3/texmex/src |only
80 files changed, 2176 insertions(+), 2115 deletions(-)
Title: Supervised and unsupervised self-organising maps
Diff between kohonen versions 2.0.9 dated 2012-01-09 and 2.0.10 dated 2012-08-13
Description: Supervised and unsupervised self-organising maps
Author: Ron Wehrens
Maintainer: Ron Wehrens
CHANGES | 7 ++++++-
DESCRIPTION | 6 +++---
MD5 | 8 ++++----
R/plot.kohonen.R | 19 +++++++------------
man/plot.kohonen.Rd | 8 ++++++--
5 files changed, 26 insertions(+), 22 deletions(-)
Title: Dependent Mixture Models - Hidden Markov Models of GLMs and
Other Distributions in S4
Diff between depmixS4 versions 1.2-0 dated 2012-06-21 and 1.2-1 dated 2012-08-13
Description: Fit latent (hidden) Markov models on mixed categorical and
continuous (timeseries) data, otherwise known as dependent
mixture models
Author: Ingmar Visser
Maintainer: Ingmar Visser
DESCRIPTION | 8 ++++----
MD5 | 12 ++++++------
NEWS | 6 +++++-
R/EM.R | 29 ++++++++++++++++++-----------
R/fb.R | 2 +-
inst/doc/depmixS4.pdf |binary
man/depmixS4-package.Rd | 4 ++--
7 files changed, 36 insertions(+), 25 deletions(-)
Title: Earthquake Traveltime Calculations for 1-D Earth Models
Diff between TauP.R versions 1.0 dated 2011-05-23 and 1.1 dated 2012-08-13
Description: Evaluates traveltimes and ray paths using predefined Earth
(or other planet) models. Includes phase plotting routines.
The IASP91 and AK135 Earth models are included, and most
important arrival phases can be evaluated.
Author: Jake Anderson, Jonathan Lees; largely translated from the TTBOX
Matlab toolbox by Martin Knapmeyer
(http://www.dr-knapmeyer.de/downloads/)
Maintainer: Jake Anderson
DESCRIPTION | 13 ++++++++-----
MD5 |only
NAMESPACE |only
R/Earthplot.R | 16 ++++++++--------
R/Rayfan.R | 4 ++--
man/AnalyzeLVZ.Rd | 9 +--------
man/CalcTP.Rd | 7 -------
man/CalcTPsum.Rd | 8 +-------
man/CalcXP.Rd | 8 +-------
man/CalcXPsum.Rd | 8 +-------
man/ConvAng2p.Rd | 12 +-----------
man/ConvP2Vdepthinv.Rd | 12 +-----------
man/ConvVdepth2p.Rd | 13 ++-----------
man/DistSummary.Rd | 3 +--
man/Earthplot.Rd | 14 +++-----------
man/EmptyModel.Rd | 11 ++---------
man/FindDiscon.Rd | 7 -------
man/FindDist4p.Rd | 9 +--------
man/FindP4Dist.Rd | 11 +++--------
man/FindPrange.Rd | 11 ++---------
man/FindRoots.Rd | 11 ++---------
man/FindTime4p.Rd | 12 +++---------
man/HoneP.Rd | 18 +++---------------
man/ImproveModel.Rd | 8 +-------
man/InterpModel.Rd | 11 ++---------
man/LVZSmp.Rd | 11 ++---------
man/LinInterp.Rd | 8 +-------
man/MakePscan.Rd | 15 +--------------
man/OptimizeDist.Rd | 16 +++-------------
man/PolarPlot.Rd | 16 ++--------------
man/ReadND.Rd | 8 --------
man/SlopeInt.Rd | 11 ++---------
man/StripRepetitions.Rd | 11 ++---------
man/TauP.R-package.Rd | 7 ++++---
man/TransformF2Sz.Rd | 15 +--------------
man/ak135.Rd | 6 +-----
man/iasp91.Rd | 5 +----
man/meshgrid.Rd | 35 +++++++++++++++++++++++------------
man/model.Rd | 6 +-----
man/polaraxis.Rd | 12 ++----------
40 files changed, 95 insertions(+), 323 deletions(-)
Title: C++ classes to embed R in C++ applications
Diff between RInside versions 0.2.6 dated 2012-01-12 and 0.2.7 dated 2012-08-13
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 C++ wrapper class providing the R
interpreter.
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.
Numerous examples are provided in the six subdirectories of the
examples/ directory of the installed package: standard, mpi
(for parallel computing) qt (showing how to embed RInside
inside a Qt application), wt (showing how to build a
'web-application' using the Wt toolkit), armadillo (for RInside
use with RcppArmadillo) and eigen (for RInside use with
RcppEigen).
Doxygen-generated documentation of the C++ classes is available at the
RInside website as well.
Author: Dirk Eddelbuettel and Romain Francois
Maintainer: Dirk Eddelbuettel
RInside-0.2.6/RInside/inst/NEWS |only
RInside-0.2.7/RInside/ChangeLog | 42 +++++
RInside-0.2.7/RInside/DESCRIPTION | 26 ++-
RInside-0.2.7/RInside/MD5 | 32 ++--
RInside-0.2.7/RInside/cleanup | 2
RInside-0.2.7/RInside/inst/NEWS.Rd |only
RInside-0.2.7/RInside/inst/examples/armadillo |only
RInside-0.2.7/RInside/inst/examples/eigen |only
RInside-0.2.7/RInside/inst/examples/standard/Makefile.win | 5
RInside-0.2.7/RInside/inst/examples/standard/cmake/CMakeLists.txt | 75 +++++++---
RInside-0.2.7/RInside/inst/examples/standard/rinside_sample12.cpp |only
RInside-0.2.7/RInside/inst/examples/standard/rinside_sample4.cpp | 20 +-
RInside-0.2.7/RInside/inst/examples/wt/Makefile | 23 ++-
RInside-0.2.7/RInside/inst/examples/wt/wtdensity.cpp | 19 ++
RInside-0.2.7/RInside/inst/examples/wt/wtdensity.css |only
RInside-0.2.7/RInside/inst/examples/wt/wtdensity.xml |only
RInside-0.2.7/RInside/inst/examples/wt/wtdensityPlain.cpp |only
RInside-0.2.7/RInside/inst/include/RInsideAutoloads.h | 18 ++
RInside-0.2.7/RInside/inst/include/RInsideEnvVars.h | 5
19 files changed, 197 insertions(+), 70 deletions(-)
Title: Nonparametric kernel estimation of the distribution function.
Bandwidth selection and estimation of related functions.
Diff between kerdiest versions 1.1 dated 2011-03-31 and 1.2 dated 2012-08-13
Description: Nonparametric kernel distribution function estimation is
performed. Three automatic bandwidth selection methods for
nonparametric kernel distribution function estimation are
implemented: the plug-in of Altman and Leger, the plug-in of
Polansky and Baker, and the modified cross-validation of
Bowman, Hall and Prvan. The exceedance function, the mean
return period and the return level are also computed.
Author: Alejandro Quintela del Rio and Graciela Estevez Perez
Maintainer: Alejandro Quintela del Rio
DESCRIPTION | 11 +++++------
INDEX | 2 +-
MD5 |only
NAMESPACE | 2 +-
R/A1_k.R | 1 -
R/A2_k.R | 1 -
R/ALbw.R | 3 +--
R/CVbw.R | 3 +--
R/PBbw.R | 3 +--
R/derivative_kernel_function.R | 1 -
R/derivative_normal_kernel.R | 1 -
R/dichotomy_fun.R | 1 -
R/ef.R | 1 -
R/functional.R | 1 -
R/kde.R | 1 -
R/kernel_distribution_without_i.R | 1 -
R/kernel_function.R | 1 -
R/kernel_function_distribution.R | 1 -
R/mrp.R | 1 -
R/mu2_k.R | 1 -
R/rl.R | 1 -
R/ro_k.R | 1 -
R/simp_int.R | 1 -
data/nwip.rda |binary
data/saltriver.rda |binary
inst |only
man/ALbw.Rd | 6 ++++++
man/CVbw.Rd | 6 ++++++
man/PBbw.Rd | 6 ++++++
man/ef.Rd | 6 ++++++
man/kde.Rd | 8 +++++++-
man/kerdiest-internal.Rd |only
man/kerdiest-package.Rd | 8 +++++++-
man/mrp.Rd | 7 ++++++-
man/nwip.Rd | 6 ++++++
man/rl.Rd | 6 ++++++
man/saltriver.Rd | 6 ++++++
37 files changed, 72 insertions(+), 33 deletions(-)
Title: Statistical Analysis and Data Display: Heiberger and Holland
Diff between HH versions 2.3-15 dated 2012-05-21 and 2.3-17 dated 2012-08-13
Description: Support software for Statistical Analysis and Data Display
(Springer, ISBN 0-387-40270-5). This contemporary presentation
of statistical methods features extensive use of graphical
displays for exploring data and for displaying the analysis.
The authors demonstrate how to analyze data---showing code,
graphics, and accompanying computer listings---for all the
methods they cover. They emphasize how to construct and
interpret graphs, discuss principles of graphical design, and
show how accompanying traditional tabular results are used to
confirm the visual impressions derived directly from the
graphs. Many of the graphical formats are novel and appear here
for the first time in print. All chapters have exercises.
Author: Richard M. Heiberger
Maintainer: Richard M. Heiberger
HH-2.3-15/HH/.Data |only
HH-2.3-15/HH/inst/HH.Data |only
HH-2.3-15/HH/inst/data_setup |only
HH-2.3-15/HH/inst/datasets |only
HH-2.3-15/HH/inst/h2 |only
HH-2.3-15/HH/inst/xls |only
HH-2.3-17/HH/DESCRIPTION | 10
HH-2.3-17/HH/MD5 | 368 +-------------------------------
HH-2.3-17/HH/R/hh.R | 39 +++
HH-2.3-17/HH/R/intxplot.s | 4
HH-2.3-17/HH/R/likert.R | 16 -
HH-2.3-17/HH/R/zzz.R | 2
HH-2.3-17/HH/demo/MMC.catalystm.R | 2
HH-2.3-17/HH/demo/book.plots.r | 2
HH-2.3-17/HH/demo/likert-paper.r | 4
HH-2.3-17/HH/inst/scripts/Ch05-iinf.r | 4
HH-2.3-17/HH/inst/scripts/Ch14-apple3.r | 15 -
HH-2.3-17/HH/man/hh.Rd | 17 +
HH-2.3-17/HH/man/likert.Rd | 6
19 files changed, 102 insertions(+), 387 deletions(-)
Title: Comparison of groups
Diff between cg versions 0.9-4 dated 2012-03-11 and 0.9-5 dated 2012-08-13
Description: cg is comprehensive data analysis software, and stands for
"compare groups." Its genesis and evolution are driven by
common needs to compare administrations, conditions, etc. in
medicine research & development. The current version provides
comparisons of unpaired samples, i.e. a linear model with one
factor of at least two levels. Good data graphs, modern
statistical methods, and useful displays of results are
emphasized.
Author: Bill Pikounis and John Oleynick
Maintainer: Bill Pikounis
DESCRIPTION | 10 +++++-----
MD5 | 12 ++++++------
R/generics.R | 25 +++++++++++++++++++------
R/p02DescriptiveOneFactorData.R | 2 +-
R/utilities.R | 2 +-
inst/CHANGES | 8 ++++++++
man/cg-package.Rd | 10 +++++-----
7 files changed, 45 insertions(+), 24 deletions(-)
Title: Tuning Insensitive Graph Estimation and Regression
Diff between bigmatrix versions 0.9.2 dated 2012-08-06 and 0.9.3 dated 2012-08-13
Description: The package "bigmatrix" solves for the precision matrix
estimations with two different methods. The first is the tuning
insensitive graph estimation and regression implemented with
scaled Lasso. Another method is by estimating at a grid of
values for the constrained lambda and the augmented Lagrangian
multiplier rho based on constrained L1 minimization for sparse
precision matrix estimation, which guarantees positive definite
output by projected augmented Lagrangian method and further
accelerates the algorithm via coordinate descent and active set
methods.
Author: Xingguo Li, Tuo Zhao, Lie Wang and Han Liu
Maintainer: Xingguo LI
DESCRIPTION | 8 ++++----
MD5 | 44 ++++++++++++++++++++++----------------------
NAMESPACE | 1 +
R/tiger.R | 19 +++++++++++++++----
R/tiger.clime.R | 3 ++-
R/tiger.generator.R | 14 +++++++++++---
R/tiger.slasso.R | 2 +-
man/bigmatrix-package.Rd | 2 +-
man/plot.roc.Rd | 2 +-
man/plot.select.Rd | 2 +-
man/plot.sim.Rd | 2 +-
man/plot.tiger.Rd | 2 +-
man/print.roc.Rd | 2 +-
man/print.select.Rd | 2 +-
man/print.sim.Rd | 2 +-
man/print.tiger.Rd | 2 +-
man/tiger-internal.Rd | 8 +++-----
man/tiger.Rd | 9 ++++++---
man/tiger.generator.Rd | 6 +++---
man/tiger.plot.Rd | 2 +-
man/tiger.roc.Rd | 2 +-
man/tiger.select.Rd | 2 +-
src/tiger_clime.c | 3 ++-
23 files changed, 82 insertions(+), 59 deletions(-)