Author: Graham Williams
Diff between rattle versions 2.4.40 dated 2009-03-03 and 2.4.41 dated 2009-03-04
Title: A graphical user interface for data mining in R using GTK
Description: Rattle (the R Analytic Tool To Learn Easily) provides a
Gnome (RGtk2) based interface to R functionality for data mining.
The aim is to provide a simple and intuitive interface
that allows a user to quickly load data from a CSV file
(or via ODBC), transform and explore the data,
build and evaluate models, and export models as PMML (predictive
modelling markup language) or as scores. All of this with knowing little
about R. All R commands are logged and commented through the log tab
and so available to the user as a script file or as an aide to the user to
interact directly with R itself. Rattle also exports a number of utility
functions and the graphical user interface, invoked as rattle(), does
not need to be run to deploy these.
DESCRIPTION | 6 +++---
R/rattle.R | 2 +-
man/rattle.Rd | 7 ++++++-
3 files changed, 10 insertions(+), 5 deletions(-)
Author: Kaspar Rufibach
Diff between modehunt versions 1.0.3 dated 2008-08-25 and 1.0.4 dated 2009-03-04
Title: Multiscale Analysis for Density Functions
Description: Given independent and identically distributed observations X(1), ..., X(n) from a density f,
this package provides five methods to perform a multiscale analysis about f as well as the necessary critical
values. The first method, introduced in Duembgen and Walther (2008), provides simultaneous confidence statements
for the existence and location of local increases (or decreases) of f, based on all intervals I(all) spanned by
any two observations X(j), X(k). The second method approximates the latter approach by using only a subset of
I(all) and is therefore computationally much more efficient, but asymptotically equivalent. Omitting the additive
correction term Gamma in either method offers another two approaches which are more powerful on small scales and
less powerful on large scales, however, not asymptotically minimax optimal anymore. Finally, the block procedure is a
compromise between adding Gamma or not, having intermediate power properties. The latter is again asymptotically
equivalent to the first and was introduced in Rufibach and Walther (2007).
CHANGES | 9 +++++++--
DESCRIPTION | 10 +++++-----
man/cvModeAll.Rd | 2 +-
man/cvModeApprox.Rd | 2 +-
man/cvModeBlock.Rd | 2 +-
man/minimalIntervals.Rd | 2 +-
man/modeHunting.Rd | 4 ++--
man/modeHuntingApprox.Rd | 4 ++--
man/modeHuntingBlock.Rd | 4 ++--
man/modehunt-package.Rd | 8 ++++----
10 files changed, 26 insertions(+), 21 deletions(-)
Author: Oscar Rueda
Diff between RJaCGH versions 1.5.7 dated 2008-10-22 and 2.0.0 dated 2009-03-04
Title: Reversible Jump MCMC for the analysis of CGH arrays.
Description: Bayesian analysis of CGH microarrays fitting Hidden Markov Chain models.
The selection of the number of states is made via their posterior probability
computed by Reversible Jump Markov Chain Monte Carlo Methods. Also
returns probabilistic common regions for gains/losses.
RJaCGH-1.5.7/RJaCGH/man/chainsSelect.Rd |only
RJaCGH-1.5.7/RJaCGH/man/collapseChain.Rd |only
RJaCGH-1.5.7/RJaCGH/man/gelman.rubin.plot.Rd |only
RJaCGH-1.5.7/RJaCGH/man/genome.plot.Rd |only
RJaCGH-1.5.7/RJaCGH/man/model.averaging.Rd |only
RJaCGH-2.0.0/RJaCGH/Changes | 7
RJaCGH-2.0.0/RJaCGH/DESCRIPTION | 14
RJaCGH-2.0.0/RJaCGH/NAMESPACE | 39
RJaCGH-2.0.0/RJaCGH/R/RJaCGH.R | 3988 +++++-----
RJaCGH-2.0.0/RJaCGH/inst/doc/Implementing_pREC_in_C.pdf |binary
RJaCGH-2.0.0/RJaCGH/inst/doc/RJaCGH.pdf |binary
RJaCGH-2.0.0/RJaCGH/inst/doc/Recurrent-regions-COBRA-reprint.pdf |only
RJaCGH-2.0.0/RJaCGH/man/Q.NH.Rd | 8
RJaCGH-2.0.0/RJaCGH/man/RJaCGH.Rd | 46
RJaCGH-2.0.0/RJaCGH/man/genomePlot.Rd |only
RJaCGH-2.0.0/RJaCGH/man/modelAveraging.Rd |only
RJaCGH-2.0.0/RJaCGH/man/normal.HMM.likelihood.NH.C.Rd | 2
RJaCGH-2.0.0/RJaCGH/man/pREC_A.Rd | 21
RJaCGH-2.0.0/RJaCGH/man/pREC_S.Rd | 17
RJaCGH-2.0.0/RJaCGH/man/plot.Q.NH.Rd | 4
RJaCGH-2.0.0/RJaCGH/man/plot.RJaCGH.Rd | 71
RJaCGH-2.0.0/RJaCGH/man/plot.pREC_S.Rd | 2
RJaCGH-2.0.0/RJaCGH/man/print.pREC_A.Rd | 4
RJaCGH-2.0.0/RJaCGH/man/print.pREC_S.Rd | 2
RJaCGH-2.0.0/RJaCGH/man/print.summary.RJaCGH.Rd | 12
RJaCGH-2.0.0/RJaCGH/man/relabelStates.Rd | 29
RJaCGH-2.0.0/RJaCGH/man/smoothMeans.Rd | 35
RJaCGH-2.0.0/RJaCGH/man/snijders.Rd | 10
RJaCGH-2.0.0/RJaCGH/man/states.Rd | 19
RJaCGH-2.0.0/RJaCGH/man/summary.RJaCGH.Rd | 42
RJaCGH-2.0.0/RJaCGH/man/trace.plot.Rd | 25
RJaCGH-2.0.0/RJaCGH/src/nnhl.c | 233
32 files changed, 2344 insertions(+), 2286 deletions(-)
Author: Bjoern Bornkamp, Jose Pinheiro and Frank Bretz
Title: Design and Analysis of Dose-Finding Studies
Description: This package implements a methodology for the design and analysis of
dose-response studies that combines aspects of multiple comparison procedures
and modeling approaches (Bretz, Pinheiro and Branson, 2005, Biometrics 61, 738-748).
The package provides tools for the analysis of dose finding trials as well as a variety
of tools necessary to plan a trial to be conducted with the MCPMod methodology.
Diff between MCPMod versions 1.0-1 dated 2009-02-13 and 1.0-2 dated 2009-03-04
ChangeLog | 4 DESCRIPTION | 6 R/analysisMM.R | 2 inst/doc/MCPMod.pdf | 2302 +++++++++++++++++++++++++------------------------- man/MCPMod-package.Rd | 4 5 files changed, 1170 insertions(+), 1148 deletions(-)
Author: Kaspar Rufibach
Diff between logcondens versions 1.3.2 dated 2008-07-16 and 1.3.3 dated 2009-03-04
Title: Estimate a Log-Concave Probability Density from iid Observations
Description: Given independent and identically distributed observations X(1), ..., X(n), this package allows to
compute a concave, piecewise linear function phi on [X(1), X(n)] with knots only in {X(1), X(2), ..., X(n)}
such that L(phi) = sum_{i=1}^n W(i)*phi(X(i)) - int_{X(1)}^{X(n)} exp(phi(x)) dx is maximal, for some
weights W(1), ..., W(n) s.t. sum_{i=1}^n W(i) = 1. According to the results in Duembgen and Rufibach (2009),
this function phi maximizes the ordinary log-likelihood sum_{i=1}^n W(i)*phi(X(i))
under the constraint that phi is concave. The corresponding function exp(phi) is a log-concave probability density.
Two algorithms are offered: An active set algorithm and one based on the pool-adjacent-violaters algorithm.
CHANGES | 9
DESCRIPTION | 8
inst/doc/logcondens_vignette.pdf | 1163 ++++++++++++++++++++-------------------
man/activeSetLogCon.Rd | 4
man/icmaLogCon.Rd | 1
man/intECDF.Rd | 8
man/intF.Rd | 8
man/logcondens-package.Rd | 12
man/robust.Rd | 1
9 files changed, 643 insertions(+), 571 deletions(-)
Author: Ismail Ahmed & Antoine Poncet
Title: Pharmacovigilance signal detection methods extended to the multiple comparison setting.
Description: PhViD proposes the main pharmacovigilance signal detection methods extended to the multiple comparison setting. Those functions can be used as standard R functions or through an user friendly interface (PhViD.gui)
Diff between PhViD versions 1.0 dated 2009-03-03 and 1.0.1 dated 2009-03-04
DESCRIPTION | 6 +++--- 1 file changed, 3 insertions(+), 3 deletions(-)
Author: Julien Barnier
Title: Functions to make R usage in social sciences easier (in french)
Description: This package provides functions for beginners and social sciences students or researchers. Currently it includes functions for cross-tabulation, weighting, results export, and maps plotting. The documentation and help pages are written in french.
Diff between rgrs versions 0.2-6 dated 2009-02-25 and 0.2-8 dated 2009-03-04
DESCRIPTION | 12 +++++++----- man/Cartographie.Rd | 4 ++-- man/copie.Rd | 2 +- man/copie.proptab.Rd | 2 +- 4 files changed, 11 insertions(+), 9 deletions(-)
Author: Kaspar Rufibach
Title: Generate LaTeX tables of descriptive statistics
Description: The functions in this package are especially helpful when writing reports of data analysis using Sweave.
Diff between reporttools versions 1.0.1 dated 2008-11-13 and 1.0.2 dated 2009-03-04
CHANGES | 13 ++++ DESCRIPTION | 6 +- R/NAtoCategory.R | 10 ++- R/displayCI.R | 6 +- R/displayKbyC.R | 4 - R/eliminateNA.R | 11 +--- R/tableContinuous.R | 123 ++++++++++++++++++++++++++++++--------------- R/tableDate.R | 29 +++++----- R/tableNominal.R | 19 +++--- R/transformVarNames.R | 2 man/checkDateSuccession.Rd | 4 - man/displayCI.Rd | 10 ++- man/displayKbyC.Rd | 12 ++-- man/reporttools-package.Rd | 12 ++-- man/tableContinuous.Rd | 48 +++++++++++++---- man/tableDate.Rd | 30 ++++++---- man/tableNominal.Rd | 14 ++--- 17 files changed, 224 insertions(+), 129 deletions(-)
Author: Petr Savicky
Diff between pspearman versions 0.1-9 dated 2009-02-11 and 0.1-10 dated 2009-03-04
Title: Spearman's rank correlation test
Description: Spearman's rank correlation test with improved accuracy
CHANGELOG |only
DESCRIPTION | 6 +++---
R/spearman.test.R | 2 +-
3 files changed, 4 insertions(+), 4 deletions(-)
Author: Chong Gu
Diff between gss versions 1.0-2 dated 2008-09-07 and 1.0-3 dated 2009-03-04
Title: General Smoothing Splines
Description: A comprehensive package for structural multivariate
function estimation using smoothing splines.
ChangeLog | 7 +++++++
DESCRIPTION | 4 ++--
R/grkpk.R | 40 +++++++++++++++++++++++++++++++++-------
R/mkterm.R | 8 ++++----
R/predict.ssanova.R | 17 ++++++-----------
R/rkpk.R | 40 +++++++++++++++++++++++++++++++++-------
6 files changed, 85 insertions(+), 31 deletions(-)
Author: K. Gerald van den Boogaart
Diff between compositions versions 0.91-6 dated 2007-04-13 and 1.01-1 dated 2009-03-04
Title: Compositional Data Analysis
Description: The package provides functions for the consistent analysis of
compositional data (e.g. portions of substances) and positive numbers
(e.g. concentrations) in the way proposed by Aitchison and Pawlowsky-Glahn.
ChangeLog | 28
DESCRIPTION | 13
INDEX | 95
NAMESPACE |only
R/3d.R | 40
R/FunctionOutliers.R |only
R/OldStuff.R |only
R/and.R |only
R/binary.R |only
R/codadendrogram.R | 39
R/compositions.R | 4454 ++++++++++++++++++++++++++-----------
R/robust.R |only
R/zerotreatment.R |only
R/zzz.R | 34
data/SimulatedAmounts.RData |binary
inst/doc/UsingCompositions.aux | 12
inst/doc/UsingCompositions.dvi |binary
inst/doc/UsingCompositions.log | 1852 ++++++++++++++-
inst/doc/UsingCompositions.pdf |binary
inst/doc/UsingCompositions.tex | 14
inst/doc/UsingCompositions.tex.flc | 6
man/Activity10.Rd | 1
man/Activity31.Rd | 1
man/AnimalVegetation.Rd | 1
man/ArcticLake.Rd | 3
man/Bayesite.Rd | 1
man/Blood23.Rd | 1
man/Boxite.Rd | 1
man/ClamEast.Rd | 3
man/ClamWest.Rd | 3
man/Coxite.Rd | 1
man/DiagnosticProb.Rd | 1
man/Firework.Rd | 5
man/Glacial.Rd | 1
man/Hongite.Rd | 1
man/Kongite.Rd | 1
man/Metabolites.Rd | 7
man/PogoJump.Rd | 3
man/Sediments.Rd | 13
man/SerumProtein.Rd | 12
man/ShiftOperators.Rd | 1
man/SimulatedAmounts.Rd | 53
man/Skulls.Rd | 1
man/SkyeAFM.Rd | 1
man/Supervisor.Rd | 15
man/WhiteCells.Rd | 11
man/Yatquat.Rd | 3
man/acomp.Rd | 12
man/acompmargin.Rd | 14
man/alr.Rd | 12
man/aplus.Rd | 7
man/apt.Rd | 15
man/asdataframe.Rd | 2
man/balancebase.Rd |only
man/barplot.Rd | 32
man/binary.Rd |only
man/boxplot.Rd | 57
man/cdt.Rd | 40
man/clo.Rd | 1
man/clr.Rd | 12
man/clr2ilr.Rd | 11
man/clusterfinder.Rd |only
man/codadendrogram.Rd | 27
man/coloredbiplot.Rd |only
man/colorsforoutliers.Rd |only
man/compmiss.Rd | 159 -
man/compositions.Rd | 37
man/cor.Rd | 21
man/cpt.Rd | 18
man/dist.Rd | 13
man/ellipses.Rd | 61
man/endmemberCoordinates.Rd | 4
man/geometricmean.Rd | 24
man/getdetectionlimit.Rd | 10
man/groupparts.Rd | 8
man/gsiadd.Rd | 26
man/gsiaddclass.Rd | 4
man/gsicall.Rd | 6
man/gsiclosespread.Rd | 8
man/gsicoorinfo.Rd | 26
man/gsicsum.Rd | 26
man/gsidiagExtract.Rd | 10
man/gsidiagGenerate.Rd | 6
man/gsidrop.Rd | 9
man/gsieps.Rd | 4
man/gsieq.Rd | 8
man/gsiexpandrcomp.Rd | 4
man/gsifiltercall.Rd | 16
man/gsigetD.Rd | 6
man/gsigetbalstruct.Rd |only
man/gsiinternal.Rd | 19
man/gsiinvperm.Rd | 6
man/gsiisSingleRow.Rd | 4
man/gsimap01.Rd | 13
man/gsimargin.Rd | 9
man/gsimerge2signary.Rd | 4
man/gsipairrelativeMatrix.Rd | 9
man/gsipairs.Rd | 7
man/gsiplain.Rd | 10
man/gsiplotmargin.Rd | 8
man/gsirecode.Rd | 11
man/gsireset3d.Rd | 6
man/gsisimshape.Rd | 12
man/gsispreadToIsoSpace.Rd | 8
man/gsisvdsolve.Rd | 21
man/gsitextpanel.Rd | 7
man/gsivarwithlosts.Rd |only
man/idt.Rd | 44
man/iit.Rd | 14
man/ilr.Rd | 10
man/ilrBase.Rd | 4
man/ilt.Rd | 13
man/ipt.Rd | 23
man/isAcomp.Rd | 2
man/ismahalanobisoutlier.Rd |only
man/lines.Rd | 21
man/mahalanobisdist.Rd |only
man/meanAcomp.Rd | 25
man/meanrow.Rd | 16
man/missingProjector.Rd | 4
man/missingsummary.Rd | 5
man/mix2compositions.Rd | 4
man/mixRead.Rd | 16
man/mvar.Rd | 3
man/norm.Rd | 1
man/oneOrDataset.Rd | 2
man/outlierclassifier.Rd |only
man/outlierplot.Rd |only
man/outliers.Rd |only
man/pairwisePlot.Rd |only
man/perturbe.Rd | 2
man/plot.Rd | 73
man/plot3d.Rd | 6
man/plot3dacomp.Rd | 14
man/plot3daplus.Rd | 3
man/plot3drmult.Rd | 3
man/plot3drplus.Rd | 4
man/plotpos.Rd | 50
man/powerofmatrix.Rd | 7
man/princompacomp.Rd | 9
man/princompaplus.Rd | 8
man/princomprcomp.Rd | 12
man/princomprmult.Rd | 13
man/princomprplus.Rd | 8
man/print.Rd |only
man/rDirichlet.Rd | 2
man/rcomp.Rd | 12
man/rcompmargin.Rd | 11
man/readgeoeas.Rd | 15
man/replot.Rd |only
man/rmahalanobis.Rd |only
man/rnorm.Rd | 2
man/robustness.Rd |only
man/rplus.Rd | 7
man/runif.Rd | 2
man/scalar.Rd | 2
man/scale.Rd | 40
man/segments.Rd | 15
man/simplemissingplot.Rd |only
man/simulatemissing.Rd | 2
man/straight.Rd | 12
man/summaryAcomp.Rd | 5
man/summaryAplus.Rd | 21
man/summaryRcomp.Rd | 7
man/sumprojector.Rd | 3
man/ternaryAxis.Rd |only
man/totals.Rd | 2
man/ult.Rd | 12
man/varAcomp.Rd | 34
man/variation.Rd | 17
man/zeroreplace.Rd | 4
tests/CheckGeometry.R |only
tests/CheckGeometry.Rout |only
tests/RobustTest.R |only
tests/RobustTest.Rout |only
tests/TAGS |only
tests/TestMissing.R | 38
tests/TestMissing.Rout |only
tests/TestSimp.R | 54
tests/TestSimp.Rout |only
tests/acheck.R |only
tests/missings.R | 2
tests/missings.Rout |only
tests/myfirst.kin |only
tests/quickcheck.R |only
185 files changed, 6221 insertions(+), 2161 deletions(-)
Author: Rasmus E. Benestad
Diff between clim.pact versions 2.2-29 dated 2009-02-04 and 2.2-30 dated 2009-03-04
Title: Climate analysis and empirical-statistical downscaling (ESD) package for monthly and daily data.
Description: The package contains R functions for retrieving data, making climate analysis and downscaling of monthly mean and daily mean global climate scenarios. (Windows-users may need to obtain the 'ncdf' package from URL 'http://www.stats.ox.ac.uk/pub/RWin/' to get clim.pact to work). The package is also described in the book 'Empirical-Statistical Downscaling (http://www.worldscibooks.com/environsci/6908.html)
DESCRIPTION | 6 +++---
R/cdfcont.R | 2 +-
R/retrieve.nc.R | 19 +++++++++++++++----
R/upper.case.R | 1 +
4 files changed, 20 insertions(+), 8 deletions(-)
Author: Juan R González, Lluís Armengol, Elisabet Guinó, Xavier Solé, and Víctor Moreno
Title: SNPs-based whole genome association studies
Description: This package carries out most common analysis when performing whole genome association studies. These analyses include descriptive statistics and exploratory analysis of missing values, calculation of Hardy-Weinberg equilibrium, analysis of association based on generalized linear models (either for quantitative or binary traits), and analysis of multiple SNPs (haplotype and epistasis analysis). Permutation test and related tests (sum statistic and truncated product) are also implemented.
Diff between SNPassoc versions 1.5-6 dated 2009-02-06 and 1.5-7 dated 2009-03-04
DESCRIPTION | 6 ++-- R/LD.R | 60 ------------------------------------------------ R/print.LD.R |only inst/docs/changelog.txt | 4 +++ 4 files changed, 7 insertions(+), 63 deletions(-)
Author: Dirk Eddelbuettel
Diff between RQuantLib versions 0.2.10 dated 2008-12-04 and 0.2.11 dated 2009-03-04
Title: R interface to the QuantLib library
Description: The RQuantLib package makes selected parts of QuantLib
visible to the R user. Currently some basic option pricing
functions are included, as well as fixed-income functions that
can be used for interest rate curve construction and Bermuda
swaption pricing. Further software contributions are welcome.
The QuantLib project aims to provide a comprehensive software
framework for quantitative finance. The goal is to provide a
standard open source library for quantitative analysis,
modeling, trading, and risk management of financial
assets.
The Windows binary version is self-contained and does not require
a QuantLib (or Boost) installation.
RQuantLib use the Rcpp R/C++ interface class library. See the Rcpp
package on CRAN (or R-Forge) for more information on Rcpp.
Note that while RQuantLib's code is licensed under the GPL (v2 or
later), QuantLib itself is released under a somewhat less
restrictive Open Source license (see QuantLib-License.txt).
RQuantLib-0.2.10/RQuantLib/inst/Rcpp-license.txt |only
RQuantLib-0.2.11/RQuantLib/DESCRIPTION | 10 +++++-----
RQuantLib-0.2.11/RQuantLib/configure.in | 6 +++---
RQuantLib-0.2.11/RQuantLib/inst/ChangeLog | 10 ++++++++++
RQuantLib-0.2.11/RQuantLib/src/barrier_binary.cpp | 16 ++++++++--------
RQuantLib-0.2.11/RQuantLib/src/bermudan.cpp | 15 ++++++++-------
RQuantLib-0.2.11/RQuantLib/src/curves.cpp | 19 ++++++++++---------
RQuantLib-0.2.11/RQuantLib/src/discount.cpp | 11 ++++++-----
RQuantLib-0.2.11/RQuantLib/src/implieds.cpp | 8 ++++----
RQuantLib-0.2.11/RQuantLib/src/rquantlib.hpp | 14 +++++++-------
RQuantLib-0.2.11/RQuantLib/src/utils.cpp | 4 ++--
RQuantLib-0.2.11/RQuantLib/src/vanilla.cpp | 8 ++++----
12 files changed, 67 insertions(+), 54 deletions(-)