Author: Hadley Wickham
Title: Testthat code. Tools to make testing fun :)
Description: A testing package specifically tailored for R that's fun,
flexible and easy to set up.
Diff between testthat versions 0.1 dated 2009-11-17 and 0.1.1 dated 2009-11-30
DESCRIPTION | 11 ++++++----- R/colour-text.r | 4 +++- 2 files changed, 9 insertions(+), 6 deletions(-)
Author: Thoralf Mildenberger, Henrike Weinert, Sebastian Tiemeyer
Title: 28 benchmark densities from Berlinet/Devroye (1994)
Description: Full implementation of the 28 distributions introduced as
benchmarks for nonparametric density estimation by Berlinet and
Devroye (1994). Includes densities, cdfs, quantile functions
and generators for samples as well as additional information on
features of the densities. Also contains the 4 histogram
densities used in Rozenholc/Mildenberger/Gather (2009).
Diff between benchden versions 1.0.2 dated 2009-09-28 and 1.0.3 dated 2009-11-30
DESCRIPTION | 8 ++++---- man/bhisto.Rd | 5 +++-- man/dhisto.Rd | 5 +++-- man/histo.Rd | 5 +++-- 4 files changed, 13 insertions(+), 10 deletions(-)
Author: Jeffrey M. Dick
Title: Chemical Thermodynamics and Activity Diagrams
Description: Calculation of the standard molal thermodynamic properties
and chemical affinities of reactions between and among
minerals, inorganic, organic, and/or biomolecular aqueous and
crystalline species. Incorporation of an extensive database of
thermodynamic properties of species and algorithms for
computing the standard thermodynamic properties of neutral and
ionized proteins from amino acid group contributions.
Generation of chemical speciation and predominance diagrams for
stable and metastable equilibrium in open systems as a function
of temperature, pressure, and chemical activities or fugacities
of basis species.
Diff between CHNOSZ versions 0.8 dated 2009-04-23 and 0.9 dated 2009-11-30
CHNOSZ-0.8/CHNOSZ/R/diversity.R |only CHNOSZ-0.8/CHNOSZ/man/chnosz.Rd |only CHNOSZ-0.8/CHNOSZ/man/diversity.Rd |only CHNOSZ-0.9/CHNOSZ/DESCRIPTION | 13 CHNOSZ-0.9/CHNOSZ/R/affinity.R | 75 +- CHNOSZ-0.9/CHNOSZ/R/diagram.R | 574 +++++++++++---- CHNOSZ-0.9/CHNOSZ/R/eos.R | 10 CHNOSZ-0.9/CHNOSZ/R/eqdata.R |only CHNOSZ-0.9/CHNOSZ/R/info.R | 117 +-- CHNOSZ-0.9/CHNOSZ/R/protein.R | 166 ++-- CHNOSZ-0.9/CHNOSZ/R/species.R | 33 CHNOSZ-0.9/CHNOSZ/R/subcrt.R | 92 +- CHNOSZ-0.9/CHNOSZ/R/thermo.R | 1196 ++++++++++++++++++++++++++++++-- CHNOSZ-0.9/CHNOSZ/R/transfer.R | 6 CHNOSZ-0.9/CHNOSZ/R/water.R | 53 - CHNOSZ-0.9/CHNOSZ/data/OBIGT.csv | 586 ++++++++------- CHNOSZ-0.9/CHNOSZ/data/SOJSH.csv |only CHNOSZ-0.9/CHNOSZ/data/opt.csv | 4 CHNOSZ-0.9/CHNOSZ/data/protein.csv | 56 + CHNOSZ-0.9/CHNOSZ/data/thermo.R | 3 CHNOSZ-0.9/CHNOSZ/inst/CITATION |only CHNOSZ-0.9/CHNOSZ/inst/NEWS | 24 CHNOSZ-0.9/CHNOSZ/inst/doc |only CHNOSZ-0.9/CHNOSZ/man/CHNOSZ-package.Rd |only CHNOSZ-0.9/CHNOSZ/man/affinity.Rd | 291 +++---- CHNOSZ-0.9/CHNOSZ/man/basis.Rd | 73 - CHNOSZ-0.9/CHNOSZ/man/buffer.Rd | 187 ++--- CHNOSZ-0.9/CHNOSZ/man/data.Rd | 126 ++- CHNOSZ-0.9/CHNOSZ/man/diagram.Rd | 679 +++++++++--------- CHNOSZ-0.9/CHNOSZ/man/eos.Rd | 36 CHNOSZ-0.9/CHNOSZ/man/eqdata.Rd |only CHNOSZ-0.9/CHNOSZ/man/get.protein.Rd | 332 +++++--- CHNOSZ-0.9/CHNOSZ/man/info.Rd | 59 - CHNOSZ-0.9/CHNOSZ/man/ionize.Rd | 189 ++--- CHNOSZ-0.9/CHNOSZ/man/makeup.Rd | 56 - CHNOSZ-0.9/CHNOSZ/man/nuts.Rd | 38 - CHNOSZ-0.9/CHNOSZ/man/protein.Rd | 220 ++--- CHNOSZ-0.9/CHNOSZ/man/revisit.Rd |only CHNOSZ-0.9/CHNOSZ/man/species.Rd | 31 CHNOSZ-0.9/CHNOSZ/man/subcrt.Rd | 356 ++++----- CHNOSZ-0.9/CHNOSZ/man/transfer.Rd | 72 - CHNOSZ-0.9/CHNOSZ/man/utilities.Rd | 315 +++++--- CHNOSZ-0.9/CHNOSZ/man/water.Rd | 79 +- 43 files changed, 3966 insertions(+), 2181 deletions(-)
Author: Christopher Brown
Title: Implements hash/associated arrays/dictionaries
Description: This package implements a data structure similar to hashes
in Perl and dictionaries in Python but with a purposefully R
flavor.
Diff between hash versions 1.0.3 dated 2009-11-05 and 1.10.0 dated 2009-11-30
ChangeLog | 26 ++++++++++++++++++ DESCRIPTION | 8 ++--- R/Class-hash.R | 71 +++++++++++++++++++------------------------------- R/invert.R | 6 +--- R/set.R | 8 ++++- R/zzz.R | 10 +++---- man/hash-accessors.Rd | 18 ++++++------ man/hash-class.Rd | 2 - man/hash-package.Rd | 4 +- man/invert.Rd | 6 ++-- tests/set.R | 10 ++++++- 11 files changed, 95 insertions(+), 74 deletions(-)
Author: Nagiza F. Samatova
Title: A seamless interface to perform parallel computation on linear
algebra problems using the ScaLAPACK library.
Description: An R add-on package capable of carrying out parallel
computation through a single function call from the R
environment. It uses the high-performance ScaLAPACK library for
the linear algebra computations.
Diff between RScaLAPACK versions 0.5.1 dated 2005-09-03 and 0.6.1 dated 2009-11-30
RScaLAPACK-0.5.1/RScaLAPACK/COPYRIGHT |only RScaLAPACK-0.5.1/RScaLAPACK/configure.win |only RScaLAPACK-0.5.1/RScaLAPACK/html |only RScaLAPACK-0.5.1/RScaLAPACK/src/Makefile |only RScaLAPACK-0.6.1/RScaLAPACK/DESCRIPTION | 28 RScaLAPACK-0.6.1/RScaLAPACK/R/HLRscalapack.R | 137 RScaLAPACK-0.6.1/RScaLAPACK/R/ParallelAgent.R | 2 RScaLAPACK-0.6.1/RScaLAPACK/R/Rscalapack.R | 382 ++ RScaLAPACK-0.6.1/RScaLAPACK/R/StartUpLam.R.in | 1 RScaLAPACK-0.6.1/RScaLAPACK/R/StartUpMpich2.R.in | 3 RScaLAPACK-0.6.1/RScaLAPACK/R/StartUpOmpi.R.in |only RScaLAPACK-0.6.1/RScaLAPACK/README | 284 - RScaLAPACK-0.6.1/RScaLAPACK/configure | 3340 +++++++++++++---------- RScaLAPACK-0.6.1/RScaLAPACK/configure.in | 340 +- RScaLAPACK-0.6.1/RScaLAPACK/demo/RScaLAPACK.R | 1 RScaLAPACK-0.6.1/RScaLAPACK/man/Rfactanal.Rd | 16 RScaLAPACK-0.6.1/RScaLAPACK/man/RgridExit.Rd | 1 RScaLAPACK-0.6.1/RScaLAPACK/man/RgridInfo.Rd |only RScaLAPACK-0.6.1/RScaLAPACK/man/RgridInit.Rd | 13 RScaLAPACK-0.6.1/RScaLAPACK/man/Rpdgemm.Rd | 13 RScaLAPACK-0.6.1/RScaLAPACK/man/Rpdgeqrf.Rd | 10 RScaLAPACK-0.6.1/RScaLAPACK/man/Rpdgesv.Rd | 14 RScaLAPACK-0.6.1/RScaLAPACK/man/Rpdgesvd.Rd | 14 RScaLAPACK-0.6.1/RScaLAPACK/man/Rpdpotrf.Rd | 7 RScaLAPACK-0.6.1/RScaLAPACK/man/Rpdpotri.Rd | 18 RScaLAPACK-0.6.1/RScaLAPACK/man/Rpdsyevd.Rd | 10 RScaLAPACK-0.6.1/RScaLAPACK/man/Rpprcomp.Rd | 6 RScaLAPACK-0.6.1/RScaLAPACK/man/Rprincomp.Rd | 10 RScaLAPACK-0.6.1/RScaLAPACK/man/Rquit.Rd | 1 RScaLAPACK-0.6.1/RScaLAPACK/man/Rvarimax.Rd | 20 RScaLAPACK-0.6.1/RScaLAPACK/man/other.Rd | 2 RScaLAPACK-0.6.1/RScaLAPACK/src/CRDriver.c | 1 RScaLAPACK-0.6.1/RScaLAPACK/src/CRcollectData.f | 1 RScaLAPACK-0.6.1/RScaLAPACK/src/CRdistData.f | 1 RScaLAPACK-0.6.1/RScaLAPACK/src/CRscalapack.c | 105 RScaLAPACK-0.6.1/RScaLAPACK/src/CRscalapack.h | 13 RScaLAPACK-0.6.1/RScaLAPACK/src/Makefile.in | 38 RScaLAPACK-0.6.1/RScaLAPACK/src/PAdistData.c | 1 RScaLAPACK-0.6.1/RScaLAPACK/src/ParallelAgent.c | 93 RScaLAPACK-0.6.1/RScaLAPACK/src/ParallelAgent.h | 13 RScaLAPACK-0.6.1/RScaLAPACK/src/callpdgemm.f | 1 RScaLAPACK-0.6.1/RScaLAPACK/src/callpdgeqrf.f | 1 RScaLAPACK-0.6.1/RScaLAPACK/src/callpdgesv.f | 1 RScaLAPACK-0.6.1/RScaLAPACK/src/callpdgesvd.f | 1 RScaLAPACK-0.6.1/RScaLAPACK/src/callpdpotrf.f | 1 RScaLAPACK-0.6.1/RScaLAPACK/src/callpdpotri.f | 1 RScaLAPACK-0.6.1/RScaLAPACK/src/callpdsyevd.f | 13 47 files changed, 3069 insertions(+), 1889 deletions(-)
Author: Thomas Lumley, Achim Zeileis
Title: Robust Covariance Matrix Estimators
Description: Model-robust standard error estimators for
cross-sectional, time series and longitudinal data.
Diff between sandwich versions 2.2-2 dated 2009-11-17 and 2.2-3 dated 2009-11-30
DESCRIPTION | 8 ++++---- NAMESPACE | 1 + NEWS | 5 +++++ R/bread.R | 8 ++++++++ inst/doc/sandwich-OOP.pdf |binary inst/doc/sandwich.pdf |binary man/bread.Rd | 1 + 7 files changed, 19 insertions(+), 4 deletions(-)
Author: Rolf Turner
Title: Hidden Markov models with discrete non-parametric observation
distributions.
Description: Fits hidden Markov models with discrete non-parametric
observation distributions to data sets. Simulates data from
such models. Finds most probable underlying hidden states and
most probable sequences of such states.
Diff between hmm.discnp versions 0.1-0 dated 2009-09-28 and 0.1-1 dated 2009-11-30
ChangeLog | 27 ++++++++++++++++++++++++++- DESCRIPTION | 8 ++++---- R/First.R | 4 ++-- R/ffun.R | 1 + R/revise.rho.R | 1 + R/sp.R | 1 + 6 files changed, 35 insertions(+), 7 deletions(-)
Author: Jonathan M. Lees
Title: Seismic Time Series Analysis Tools
Description: Multiple interactive codes to analyze seismic data, via,
spectrum analysis, wavelet transforms, particle motion,
hodograms.
Diff between RSEIS versions 2.2-0 dated 2009-10-15 and 2.3-1 dated 2009-11-30
DESCRIPTION | 8 - R/DOsgram.R | 2 R/GETARAIC.R | 6 R/JGET.seis.R | 109 +++++----------- R/JSAC.seis.R |only R/JSEGY.seis.R |only R/MTMgabor.R | 71 ++++++++-- R/Mine.Teles.R |only R/Mine.seis.R | 6 R/PICK.GEN.R | 201 +++++++++++++++++++++++++++++ R/PLOT.ALLPX.R | 3 R/TTteles.R | 10 + R/blankevol.R |only R/correct.moveout.R |only R/dateList.R |only R/dateStamp.R |only R/doGABOR.AR.R | 9 - R/doGABOR.MTM.R | 7 - R/evolAR.R | 19 +- R/getPDEcsv.R |only R/getPDEscreen.R |only R/getseis24.R | 18 ++ R/getseisinfo.R | 21 ++- R/insertNAs.R |only R/makeDB.R | 15 +- R/mtapspec.R | 2 R/parse.pde.R |only R/parseFN2STA.R | 31 +++- R/plotevol.R | 332 +++++++++++++++++++++---------------------------- R/plotevol2.R |only R/prepSEIS.R | 18 ++ R/selstas.R |only R/setwpix.R | 2 R/sysinfo.R |only inst/doc/hodo.pdf |binary inst/doc/rseis.pdf |binary man/GETARAIC.Rd | 7 - man/JGET.seis.Rd | 87 +++++++++++- man/JSAC.seis.Rd |only man/MTMgabor.Rd | 18 +- man/Mine.Teles.Rd |only man/Mine.seis.Rd | 41 +++++- man/RSEIS-package.Rd | 4 man/Zdate.Rd | 13 + man/correct.moveout.Rd |only man/doGABOR.AR.Rd | 5 man/doGABOR.MTM.Rd | 24 ++- man/getPDEcsv.Rd |only man/insertNAs.Rd |only man/makeDB.Rd | 29 +++- man/parse.pde.Rd |only man/parseFN2STA.Rd | 13 + man/plotevol.Rd | 20 ++ man/selstas.Rd |only man/sysinfo.Rd |only src/jget_seis.c | 52 +++++++ src/sac.h | 2 57 files changed, 840 insertions(+), 365 deletions(-)
Author: Etienne Lalibert�, Bill Shipley
Title: Measuring functional diversity (FD) from multiple traits, and
other tools for functional ecology
Description: FD is a package to compute different multidimensional FD
indices. It implements a distance-based framework to measure FD
that allows any number and type of functional traits, and can
also consider species relative abundances. It also contains
other useful tools for functional ecology.
Diff between FD versions 1.0-1 dated 2009-10-26 and 1.0-5 dated 2009-11-30
FD-1.0-1/FD/R/zzz.R |only FD-1.0-5/FD/DESCRIPTION | 16 +++++++++------- FD-1.0-5/FD/NAMESPACE | 3 ++- FD-1.0-5/FD/R/functcomp.R | 12 ++++++++---- FD-1.0-5/FD/R/maxent.R |only FD-1.0-5/FD/inst/CITATION | 8 ++++---- FD-1.0-5/FD/inst/NEWS | 16 ++++++++++++++++ FD-1.0-5/FD/man/FD-package.Rd | 10 +++++----- FD-1.0-5/FD/man/functcomp.Rd | 11 +++++++---- FD-1.0-5/FD/man/gowdis.Rd | 1 - FD-1.0-5/FD/man/maxent.Rd |only 11 files changed, 51 insertions(+), 26 deletions(-)
Author: Roeland Kindt
Title: GUI for biodiversity and community ecology analysis
Description: This package provides a GUI (Graphical User Interface, via
the R-Commander) and some utility functions (often based on the
vegan package) for statistical analysis of biodiversity and
ecological communities, including species accumulation curves,
diversity indices, Renyi profiles, GLMs for analysis of species
abundance and presence-absence, distance matrices, Mantel
tests, and cluster, constrained and unconstrained ordination
analysis. A book on biodiversity and community ecology analysis
is available for free download from the website.
Diff between BiodiversityR versions 1.4 dated 2009-10-23 and 1.4.2 dated 2009-11-30
BiodiversityR-1.4.2/BiodiversityR/DESCRIPTION | 8 +- BiodiversityR-1.4.2/BiodiversityR/NAMESPACE | 2 BiodiversityR-1.4.2/BiodiversityR/inst/etc/BiodiversityGUI.R | 36 +++++------ BiodiversityR-1.4.2/BiodiversityR/man/BiodiversityRGUI.Rd | 4 - BiodiversityR-1.4.2/BiodiversityR/man/ordisymbol.Rd | 17 ----- BiodiversityR-1.4/BiodiversityR/R/ordihull.centroids.R |only BiodiversityR-1.4/BiodiversityR/R/ordispider.centroids.R |only 7 files changed, 25 insertions(+), 42 deletions(-)
Author: Matthias Templ, Karel Hron, Peter Filzmoser
Title: Robust Estimation for Compositional Data.
Description: The package includes methods for imputation of
compositional data including robust methods, (robust) outlier
detection for compositional data, (robust) principal component
analysis for compositional data, (robust) factor analysis for
compositional data and (robust) Anderson-Darling normality
tests for compositional data as well as popular log-ratio
transformations (alr, clr, ilr, and their inverse
transformations).
Diff between robCompositions versions 1.2.2 dated 2009-05-08 and 1.3.2 dated 2009-11-29
robCompositions-1.2.2/robCompositions/data/aitchison359.rda |only robCompositions-1.2.2/robCompositions/data/aitchison360.rda |only robCompositions-1.2.2/robCompositions/data/aitchison395.rda |only robCompositions-1.2.2/robCompositions/inst/doc/Rplots.pdf |only robCompositions-1.2.2/robCompositions/inst/doc/hs_err_pid1448.log |only robCompositions-1.2.2/robCompositions/inst/doc/hs_err_pid2256.log |only robCompositions-1.2.2/robCompositions/inst/doc/hs_err_pid2848.log |only robCompositions-1.2.2/robCompositions/inst/doc/hs_err_pid3600.log |only robCompositions-1.2.2/robCompositions/inst/doc/normalityAD.aux |only robCompositions-1.2.2/robCompositions/inst/doc/normalityAD.bbl |only robCompositions-1.2.2/robCompositions/inst/doc/normalityAD.blg |only robCompositions-1.2.2/robCompositions/inst/doc/normalityAD.log |only robCompositions-1.2.2/robCompositions/inst/doc/normalityAD.out |only robCompositions-1.2.2/robCompositions/inst/doc/refPCSn.log |only robCompositions-1.2.2/robCompositions/inst/texput.log |only robCompositions-1.2.2/robCompositions/man/aitchison359.Rd |only robCompositions-1.2.2/robCompositions/man/aitchison360.Rd |only robCompositions-1.2.2/robCompositions/man/aitchison395.Rd |only robCompositions-1.3.2/robCompositions/.project |only robCompositions-1.3.2/robCompositions/DESCRIPTION | 14 robCompositions-1.3.2/robCompositions/NAMESPACE | 7 robCompositions-1.3.2/robCompositions/R/aDist.R | 1 robCompositions-1.3.2/robCompositions/R/adtest.R | 15 robCompositions-1.3.2/robCompositions/R/alr.R |only robCompositions-1.3.2/robCompositions/R/alrEM.R | 12 robCompositions-1.3.2/robCompositions/R/clr.R |only robCompositions-1.3.2/robCompositions/R/constSum.R |only robCompositions-1.3.2/robCompositions/R/impCoda.R | 21 robCompositions-1.3.2/robCompositions/R/impKNNa.R | 4 robCompositions-1.3.2/robCompositions/R/impPCA.R | 2 robCompositions-1.3.2/robCompositions/R/invalr.R |only robCompositions-1.3.2/robCompositions/R/invclr.R |only robCompositions-1.3.2/robCompositions/R/invilr.R | 1 robCompositions-1.3.2/robCompositions/R/plot.imp.R | 4 robCompositions-1.3.2/robCompositions/R/robVariation.R | 10 robCompositions-1.3.2/robCompositions/data/arcticLake.rda |only robCompositions-1.3.2/robCompositions/data/expenditures.rda |only robCompositions-1.3.2/robCompositions/data/phd.rda |only robCompositions-1.3.2/robCompositions/data/skyeLavas.rda |only robCompositions-1.3.2/robCompositions/inst/doc/Landkarten.zip |only robCompositions-1.3.2/robCompositions/inst/doc/bw09.xls |only robCompositions-1.3.2/robCompositions/inst/doc/compLW.R |only robCompositions-1.3.2/robCompositions/inst/doc/eu09.xls |only robCompositions-1.3.2/robCompositions/inst/doc/imputation.R |only robCompositions-1.3.2/robCompositions/inst/doc/imputation.Rnw | 19 robCompositions-1.3.2/robCompositions/inst/doc/imputation.pdf | 6952 +++++----- robCompositions-1.3.2/robCompositions/inst/doc/lw03.csv |only robCompositions-1.3.2/robCompositions/inst/doc/lw03.xlw |only robCompositions-1.3.2/robCompositions/inst/doc/lw09-1.xls |only robCompositions-1.3.2/robCompositions/inst/doc/lw09.csv |only robCompositions-1.3.2/robCompositions/inst/doc/nr08.xls |only robCompositions-1.3.2/robCompositions/inst/doc/ooeWahl.pdf |only robCompositions-1.3.2/robCompositions/inst/doc/testingTests.R |only robCompositions-1.3.2/robCompositions/inst/doc/vb00.xlw |only robCompositions-1.3.2/robCompositions/man/aDist.Rd | 4 robCompositions-1.3.2/robCompositions/man/adjust.Rd | 4 robCompositions-1.3.2/robCompositions/man/alr.Rd |only robCompositions-1.3.2/robCompositions/man/alrEM.Rd | 5 robCompositions-1.3.2/robCompositions/man/arcticLake.Rd |only robCompositions-1.3.2/robCompositions/man/clr.Rd |only robCompositions-1.3.2/robCompositions/man/constSum.Rd |only robCompositions-1.3.2/robCompositions/man/expenditures.Rd |only robCompositions-1.3.2/robCompositions/man/ilr.Rd | 3 robCompositions-1.3.2/robCompositions/man/impCoda.Rd | 4 robCompositions-1.3.2/robCompositions/man/impKNNa.Rd | 4 robCompositions-1.3.2/robCompositions/man/invalr.Rd |only robCompositions-1.3.2/robCompositions/man/invclr.Rd |only robCompositions-1.3.2/robCompositions/man/invilr.Rd | 7 robCompositions-1.3.2/robCompositions/man/outCoDa.Rd | 4 robCompositions-1.3.2/robCompositions/man/pcaCoDa.Rd | 4 robCompositions-1.3.2/robCompositions/man/pfa.Rd | 4 robCompositions-1.3.2/robCompositions/man/phd.Rd |only robCompositions-1.3.2/robCompositions/man/plot.imp.Rd | 10 robCompositions-1.3.2/robCompositions/man/plot.outCoDa.Rd | 4 robCompositions-1.3.2/robCompositions/man/plot.pcaCoDa.Rd | 4 robCompositions-1.3.2/robCompositions/man/print.imp.Rd | 8 robCompositions-1.3.2/robCompositions/man/print.outCoDa.Rd | 4 robCompositions-1.3.2/robCompositions/man/print.pcaCoDa.Rd | 4 robCompositions-1.3.2/robCompositions/man/robCompositions-package.Rd | 17 robCompositions-1.3.2/robCompositions/man/robVariation.Rd | 14 robCompositions-1.3.2/robCompositions/man/skyeLavas.Rd |only robCompositions-1.3.2/robCompositions/man/summary.imp.Rd | 10 robCompositions-1.3.2/robCompositions/tests/rz.R | 8 83 files changed, 3610 insertions(+), 3578 deletions(-)
More information about robCompositions at CRAN
Permanent link
Author: Matthias Templ, Andreas Alfons
Title: Visualization and Imputation of Missing Values
Description: This package introduces new tools for the visualization of
missing values in R, which can be used for exploring the data
and the structure of the missing values. Depending on this
structure, they may help to identify the mechanism generating
the missings. A graphical user interface allows an easy
handling of the implemented plot methods.
Diff between VIM versions 1.3 dated 2009-04-19 and 1.3.2 dated 2009-11-29
.project |only DESCRIPTION | 12 ++++++------ NAMESPACE | 2 ++ R/aggr.R | 1 + R/irmi.R |only R/scattmatrixMiss.R | 2 ++ data/SBS2524.rda |only inst/doc |only man/SBS2524.Rd |only man/irmi.Rd |only man/matrixplot.Rd | 2 +- 11 files changed, 12 insertions(+), 7 deletions(-)
Author: Kurt Hornik, with contributions from Christian Buchta, Torsten
Hothorn, Alexandros Karatzoglou, David Meyer, and Achim Zeileis
Title: R/Weka interface
Description: An R interface to Weka (Version 3.6.1). Weka is a
collection of machine learning algorithms for data mining tasks
written in Java, containing tools for data pre-processing,
classification, regression, clustering, association rules, and
visualization. Both the R interface and Weka itself are
contained in the RWeka package. For more information on Weka
see http://www.cs.waikato.ac.nz/~ml/weka/.
Diff between RWeka versions 0.3-23 dated 2009-10-30 and 0.3-24 dated 2009-11-29
CHANGELOG | 8 ++++++++ DESCRIPTION | 8 ++++---- R/classifiers.R | 2 +- 3 files changed, 13 insertions(+), 5 deletions(-)
Author: Matthias Templ
Title: Statistical Disclosure Control methods for the generation of
public- and scientific-use files.
Description: Data from statistical agencies and other institutions are
mostly confidential. This package can be used for the
generation of save (micro)data, i.e. for the generation of
public- and scientific-use files. The package includes also a
graphical user interface.
Diff between sdcMicro versions 2.6.2 dated 2009-10-22 and 2.6.3 dated 2009-11-29
sdcMicro-2.6.2/sdcMicro/inst/doc/Rplots.pdf |only sdcMicro-2.6.3/sdcMicro/DESCRIPTION | 10 ++--- sdcMicro-2.6.3/sdcMicro/R/addNoise.r | 41 +++++++++++++++++++++ sdcMicro-2.6.3/sdcMicro/R/sdcGUI.r | 38 ++++++++++++------- sdcMicro-2.6.3/sdcMicro/R/zzz.R | 2 - sdcMicro-2.6.3/sdcMicro/inst/doc/psfig.sty |only sdcMicro-2.6.3/sdcMicro/inst/doc/sdcMicroPaper.pdf |binary 7 files changed, 72 insertions(+), 19 deletions(-)
Author: Graham Williams
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.
Diff between rattle versions 2.5.6 dated 2009-11-24 and 2.5.7 dated 2009-11-29
DESCRIPTION | 8 ++++---- R/evaluate.R | 4 ++-- R/hclust.R | 6 ++++-- R/kmeans.R | 6 ++++-- R/model.R | 6 ++++-- R/nnet.R | 6 ++++-- R/rattle.R | 15 ++++++++++++--- R/rpart.R | 6 ++++-- R/survival.R | 14 ++++---------- inst/etc/rattle.glade | 11 +++++++++++ man/internal.Rd | 1 + 11 files changed, 54 insertions(+), 29 deletions(-)
Author: J. R. M. Hosking
Title: Regional frequency analysis using L-moments
Description: Functions for regional frequency analysis using the
methods of J. R. M. Hosking and J. R. Wallis (1997), "Regional
frequency analysis: an approach based on L-moments".
Diff between lmomRFA versions 2.1 dated 2009-07-18 and 2.2 dated 2009-11-29
DESCRIPTION | 8 ++++---- NEWS | 18 ++++++++++++++---- R/lmomRFA.r | 32 +++++++++++++++++++------------- man/Cascades.Rd | 2 +- man/evplot.rfd.Rd | 5 +++-- man/regfit.Rd | 6 +++--- man/regquant.Rd | 1 - man/regquantbounds.Rd | 1 - man/regsimh.Rd | 6 +++--- man/regsimq.Rd | 6 +++--- man/regtst.Rd | 12 ++++++------ man/sitequant.Rd | 1 - 12 files changed, 56 insertions(+), 42 deletions(-)
Author: J. R. M. Hosking
Title: L-moments
Description: Functions related to L-moments: computation of L-moments
of distributions and data samples; parameter estimation;
L-moment ratio diagram; plot vs. quantiles of an extreme-value
distribution.
Diff between lmom versions 1.4 dated 2009-07-18 and 1.5 dated 2009-11-29
DESCRIPTION | 8 ++++---- NEWS | 16 +++++++++++++++- R/lmom.r | 47 +++++++++++++++++++++++++---------------------- man/lmr-functions.Rd | 15 +-------------- man/lmrdpoints.Rd | 1 - man/lmrp.Rd | 4 ++-- man/pelp.Rd | 18 ++---------------- 7 files changed, 49 insertions(+), 60 deletions(-)
Author: David Hajage
Title: Export R objects to several markup languages
Description: Coerce R object to asciidoc, txt2tags, restructuredText or
org syntax. Package comes with a set of drivers for Sweave.
Diff between ascii versions 0.4-1 dated 2009-11-26 and 0.4-2 dated 2009-11-29
DESCRIPTION | 6 +-- NAMESPACE | 2 + NEWS | 9 ++++ R/asciiDescr.r | 3 + R/asciiHmisc.r | 2 - R/asciiSurvival.r | 108 ++++++++++++++++++++++++++++++++++++++++++++++++++++++ R/misc.r | 4 +- man/ascii.Rd | 15 +++++++ 8 files changed, 140 insertions(+), 9 deletions(-)
Author: Jonathan M. Lees
Title: Read in WIN format data
Description: Reads in WIN pickfile and waveform file, prepares data for
RSEIS
Diff between WINRPACK versions 1.0-9 dated 2009-09-28 and 1.1-0 dated 2009-11-29
DESCRIPTION | 6 +++--- inst/doc/WIN2R.pdf |binary man/WINRPACK-package.Rd | 2 +- src/win2R.c | 6 +++--- src/win2asc.c | 4 ++-- 5 files changed, 9 insertions(+), 9 deletions(-)
Author: Andrew D. Martin
Title: Markov chain Monte Carlo (MCMC) Package
Description: This package contains functions to perform Bayesian
inference using posterior simulation for a number of
statistical models. Most simulation is done in compiled C++
written in the Scythe Statistical Library Version 1.0.2. All
models return coda mcmc objects that can then be summarized
using the coda package. MCMCpack also contains some useful
utility functions, including some additional density functions
and pseudo-random number generators for statistical
distributions, a general purpose Metropolis sampling algorithm,
and tools for visualization.
Diff between MCMCpack versions 1.0-4 dated 2009-09-08 and 1.0-5 dated 2009-11-29
DESCRIPTION | 10 HISTORY | 4 NAMESPACE | 1 R/MCMCirtHier1d.R | 4 R/MCMCirtKdHet.R |only man/MCMCirtKdHet.Rd |only src/MCMCirtKdHet.cc |only src/MCMCoprobit.cc | 568 ++++++++++++++++++++++++++-------------------------- 8 files changed, 296 insertions(+), 291 deletions(-)
Author: David Ardia and Katharine Mullen
Title: Global optimization by differential evolution
Description: This package provides the DEoptim function which performs
global optimization by differential evolution.
Diff between DEoptim versions 2.0-1 dated 2009-10-07 and 2.0-3 dated 2009-11-29
DEoptim-2.0-1/DEoptim/R/zzz.R |only DEoptim-2.0-1/DEoptim/inst/CITATION |only DEoptim-2.0-1/DEoptim/src/de.h |only DEoptim-2.0-1/DEoptim/src/sort.c |only DEoptim-2.0-3/DEoptim/DESCRIPTION | 10 DEoptim-2.0-3/DEoptim/NAMESPACE | 3 DEoptim-2.0-3/DEoptim/NEWS | 69 + DEoptim-2.0-3/DEoptim/R/DEoptim.R | 18 DEoptim-2.0-3/DEoptim/R/methods.R | 98 +- DEoptim-2.0-3/DEoptim/THANKS | 6 DEoptim-2.0-3/DEoptim/inst/citation |only DEoptim-2.0-3/DEoptim/man/DEoptim.Rd | 27 DEoptim-2.0-3/DEoptim/man/DEoptim.control.Rd | 28 DEoptim-2.0-3/DEoptim/src/de4_0.c | 1066 ++++++++++++++------------- DEoptim-2.0-3/DEoptim/src/evaluate.c | 33 DEoptim-2.0-3/DEoptim/src/get_element.c | 8 16 files changed, 749 insertions(+), 617 deletions(-)
Author: Nicole Kraemer, Mikio L. Braun
Title: Degrees of Freedom and Confidence Intervals for Partial Least
Squares Regression
Description: The plsdof package provides Degrees of Freedom estimates
for Kernel Partial Least Squares Regression and its kernel
extension. The package also provides model selection based on
various information criteria (aic, bic, gmdl) and based on
cross-validation. For linear Partial Least Squares, the package
computes the approximate distribution of the regression
coefficients. This allows the construction of confidence
intervals and tests.
Diff between plsdof versions 0.1 dated 2009-11-16 and 0.1-1 dated 2009-11-27
DESCRIPTION | 24 ++++++++++++++---------- R/coef.plsdof.R |only R/dA.R |only R/dvvtz.R | 24 +++++++++++++----------- R/kernel.pls.fit.R | 2 +- R/linear.pls.R |only R/vcov.plsdof.R |only man/coef.plsdof.Rd |only man/dA.Rd |only man/kernel.pls.Rd | 4 ++-- man/kernel.pls.fit.Rd | 1 + man/linear.pls.Rd |only man/plsdof-package.Rd | 11 ++++++----- man/vcov.plsdof.Rd |only 14 files changed, 37 insertions(+), 29 deletions(-)
Author: Klaus Schliep
Title: Phylogenetic analysis in R
Description: Phylogenetic analysis in R (Estimation of phylogenetic
trees and networks using Maximum Likelihood, Maximum Parsimony,
Distance methods & Hadamard conjugation)
Diff between phangorn versions 0.99-3 dated 2009-10-30 and 0.99-4 dated 2009-11-27
ChangeLog | 18 DESCRIPTION | 8 NAMESPACE | 9 R/phylo.R | 1318 +++++++++++++++++++++------------------------ data/Laurasiatherian.RData |binary data/chloroplast.RData |binary data/yeast.RData |binary inst/doc/Rplots.pdf | 4 inst/doc/Trees.pdf |binary inst/doc/phangorn.bib | 15 man/phyDat.Rd | 10 src/init.c | 3 src/phangorn.c | 453 ++++++++------- 13 files changed, 914 insertions(+), 924 deletions(-)
Author: Efthimios S. Motakis, Guy P. Nason, Piotr Fryzlewicz
Title: Variance Stabilization by Data-Driven Haar-Fisz (for
Microarrays)
Description: The package contains the normalizing and variance
stabilizing Data-Driven Haar-Fisz algorithm. Also contains
related algorithms for simulating from certain microarray gene
intensity models and evaluation of certain transformations.
Diff between DDHFm versions 1.0-2.1 dated 2009-02-23 and 1.0-3 dated 2009-11-27
DESCRIPTION | 25 ++++++++++++++----------- inst/doc/DDHFm.pdf |binary man/cDNAdata.Rd | 3 +-- 3 files changed, 15 insertions(+), 13 deletions(-)
Author: Paul Gilbert
Title: Set (Normal) Random Number Generator and Seed
Description: SetRNG provides utilities to help set and record the
setting of the seed and the uniform and normal generators used
when a random experiment is run. The utilities can be used in
other functions that do random experiments to simplify
recording and/or setting all the necessary information for
reproducibility. See the vignette and reference manual for
examples.
Diff between setRNG versions 2008.3-1 dated 2008-03-21 and 2009.11-1 dated 2009-11-27
DESCRIPTION | 22 ++++++++++++++++------ NEWS | 35 ++++++++++++++++++----------------- R/setRNG.R | 2 +- S |only inst/doc/setRNG.pdf |binary man/getRNG.Rd | 4 ++-- man/setRNG.Rd | 14 ++++++++++---- 7 files changed, 47 insertions(+), 30 deletions(-)
Author: Christophe Ambroise, Gilles Grasseau, Mark Hoebeke, Pierre
Latouche, Vincent Miele, Franck Picard
Title: Random graph clustering
Description: Routines for the analysis (unsupervised clustering) of
networks using MIXtures of Erdos-Renyi random graphs
Diff between mixer versions 1.0 dated 2009-11-19 and 1.1 dated 2009-11-27
DESCRIPTION | 6 +++--- NEWS | 5 ++++- inst/CITATION | 2 +- src/Makevars | 6 +++--- src/SparseMatrix.h | 4 +++- 5 files changed, 14 insertions(+), 9 deletions(-)
Author: lp_solve
Title: Interface to lp_solve 5.5.0.15
Description: The lpSolveAPI package provides an R interface to the
lp_solve library API - lp_solve is a Mixed Integer Linear
Programming (MILP) solver with support for pure linear, (mixed)
integer/binary, semi-continuous and special ordered sets (SOS)
models.
Diff between lpSolveAPI versions 5.5.0.15 dated 2009-09-28 and 5.5.0.15-1 dated 2009-11-27
DESCRIPTION | 10 +- inst/doc/lpSolveAPI.pdf |binary inst/include/myblas.h | 34 ++++----- src/Makevars | 8 +- src/RlpSolveLink.c | 71 +++++++++++-------- src/mmio.c | 107 ++++++++++++++--------------- src/myblas.c | 174 ++++++++++++++++++++++-------------------------- 7 files changed, 208 insertions(+), 196 deletions(-)
Author: Ulrike Groemping
Title: Full factorials, orthogonal arrays and base utilities for DoE
packages
Description: This package creates full factorial experimental designs
and designs based on orthogonal arrays for (industrial)
experiments. Additionally, it provides some utility functions
used also by other DoE packages.
Diff between DoE.base versions 0.9-8 dated 2009-11-26 and 0.9-10 dated 2009-11-27
DESCRIPTION | 8 ++++---- R/DesignAccessors.r | 6 +++++- inst/NEWS | 7 +++++++ 3 files changed, 16 insertions(+), 5 deletions(-)
Author: Tore Opsahl
Title: tnet: Software for Analysis of Weighted, Two-mode, and
Longitudinal networks
Description: R package to analyse weighted, two-mode, and longitudinal
networks.
Diff between tnet versions 0.1.2 dated 2009-09-18 and 0.1.3 dated 2009-11-26
tnet-0.1.2/tnet/R/clustering_w_barrat.R |only tnet-0.1.2/tnet/R/random_values.R |only tnet-0.1.2/tnet/man/clustering_w_barrat.Rd |only tnet-0.1.2/tnet/man/random_values.Rd |only tnet-0.1.3/tnet/DESCRIPTION | 10 +- tnet-0.1.3/tnet/R/as.tnet.R | 18 ++- tnet-0.1.3/tnet/R/betweenness_w.R | 21 +--- tnet-0.1.3/tnet/R/closeness_w.R | 33 ++---- tnet-0.1.3/tnet/R/clustering_tm.R | 1 tnet-0.1.3/tnet/R/clustering_w.R | 28 ++--- tnet-0.1.3/tnet/R/clustering_w_local.R |only tnet-0.1.3/tnet/R/degree_w.R | 28 ++--- tnet-0.1.3/tnet/R/dichotomise.R | 20 ++-- tnet-0.1.3/tnet/R/distance_wRBGL.R | 27 ++--- tnet-0.1.3/tnet/R/projecting_tm.R | 8 + tnet-0.1.3/tnet/R/rg_reshuffling_tm.R | 9 - tnet-0.1.3/tnet/R/rg_reshuffling_w.R | 21 ++-- tnet-0.1.3/tnet/R/rg_w.R | 13 +- tnet-0.1.3/tnet/R/shrink_to_weighted_network.R | 17 +-- tnet-0.1.3/tnet/R/small_world_test_tm.R |only tnet-0.1.3/tnet/R/small_world_test_w.R |only tnet-0.1.3/tnet/R/symmetrise.R | 32 +++--- tnet-0.1.3/tnet/R/weighted_richclub_tm.R | 12 +- tnet-0.1.3/tnet/R/weighted_richclub_w.R | 123 +++++++++++++------------ tnet-0.1.3/tnet/man/clustering_w_local.Rd |only tnet-0.1.3/tnet/man/small_world_test_tm.Rd |only tnet-0.1.3/tnet/man/small_world_test_w.Rd |only tnet-0.1.3/tnet/man/tnet-package.Rd | 2 tnet-0.1.3/tnet/man/weighted_richclub_w.Rd | 24 +--- 29 files changed, 220 insertions(+), 227 deletions(-)
Author: Roger Bivand
Title: Spatial dependence: weighting schemes, statistics and models
Description: A collection of functions to create spatial weights matrix
objects from polygon contiguities, from point patterns by
distance and tesselations, for summarising these objects, and
for permitting their use in spatial data analysis, including
regional aggregation by minimum spanning tree; a collection of
tests for spatial autocorrelation, including global Moran's I,
APLE, Geary's C, Hubert/Mantel general cross product statistic,
Empirical Bayes estimates and Assun��o/Reis Index, Getis/Ord G
and multicoloured join count statistics, local Moran's I and
Getis/Ord G, saddlepoint approximations and exact tests for
global and local Moran's I; and functions for estimating
spatial simultaneous autoregressive (SAR) lag and error models,
impact measures for lag models, weighted and unweighted SAR and
CAR spatial regression models, semi-parametric and Moran
eigenvector spatial filtering, GM SAR error models, and
generalized spatial two stage least squares models.
Diff between spdep versions 0.4-52 dated 2009-11-05 and 0.4-54 dated 2009-11-26
ChangeLog | 1297 +++++++++++++++++++++++++++++++++++++++++------------- DESCRIPTION | 8 NAMESPACE | 5 R/nb2listw.R | 6 inst/ChangeLog | 1297 +++++++++++++++++++++++++++++++++++++++++------------- inst/doc/CO69.pdf |binary inst/doc/sids.pdf | 1044 +++++++++++++++++++++---------------------- man/nb2lines.Rd | 2 8 files changed, 2513 insertions(+), 1146 deletions(-)
Author: Christiane Raemsch
Title: Estimation of attributable and partial attributable risks (AR
and PAR) and visualization of attributable risks from
case-control data
Description: Functions to estimate (partial) attributable risks from
case-control data with corresponding percentile or BCa
confidence intervals; Visualization of attributable riks
Diff between pARccs versions 0.1-1 dated 2008-10-15 and 0.2-1 dated 2009-11-26
DESCRIPTION | 29 +++--- NAMESPACE | 5 - R/AR_Plot.r |only R/AR_wC.r | 48 +++++++---- R/AR_woC.r | 29 +++++- R/AdjAR.R | 116 ++++++++++++++++++++++++--- R/Boot_CI.R | 231 +++++++++++++++++++++++++++++++++++++++--------------- R/Class_AR.r |only R/PAR.R | 17 +++ man/AR-class.Rd |only man/AR.rd | 12 +- man/AR_Plot.rd |only man/AdjAR.Rd | 17 +++ man/Boot-class.Rd |only man/Boot_CI.Rd | 34 ++++--- man/PAR-class.Rd |only man/PAR.Rd | 12 +- 17 files changed, 410 insertions(+), 140 deletions(-)
Author: Martin M�chler
Title: Normal (1-d) Mixture Models (S3 Classes and Methods)
Description: Onedimensional Normal Mixture Models Classes, for, e.g.,
density estimation or clustering algorithms research and
teaching; providing the widely used Marron-Wand densities, see
?MarronWand.
Diff between nor1mix versions 1.0-7 dated 2007-06-12 and 1.1-1 dated 2009-11-26
nor1mix-1.0-7/nor1mix/INDEX |only nor1mix-1.0-7/nor1mix/mle-ex-post.R |only nor1mix-1.1-1/nor1mix/ChangeLog | 91 +++++++ nor1mix-1.1-1/nor1mix/DESCRIPTION | 18 - nor1mix-1.1-1/nor1mix/NAMESPACE |only nor1mix-1.1-1/nor1mix/R/norMix.R | 395 ++++++++++++++++++++++++++++--- nor1mix-1.1-1/nor1mix/R/zMarrWand-dens.R | 16 + nor1mix-1.1-1/nor1mix/R/zzz.R | 154 +++++++++++- nor1mix-1.1-1/nor1mix/TODO |only nor1mix-1.1-1/nor1mix/man/MarronWand.Rd | 55 ++-- nor1mix-1.1-1/nor1mix/man/clus2norMix.Rd |only nor1mix-1.1-1/nor1mix/man/dnorMix.Rd | 23 + nor1mix-1.1-1/nor1mix/man/llnorMix.Rd |only nor1mix-1.1-1/nor1mix/man/norMix.Rd | 3 nor1mix-1.1-1/nor1mix/man/plot.norMix.Rd | 13 - nor1mix-1.1-1/nor1mix/man/pnorMix.Rd | 49 +++ nor1mix-1.1-1/nor1mix/man/rnorMix.Rd | 2 nor1mix-1.1-1/nor1mix/man/sort.norMix.Rd |only nor1mix-1.1-1/nor1mix/tests/MW.R | 10 nor1mix-1.1-1/nor1mix/tests/MW.Rout.save | 34 ++ nor1mix-1.1-1/nor1mix/tests/ex.R | 59 ++++ nor1mix-1.1-1/nor1mix/tests/par.R |only nor1mix-1.1-1/nor1mix/tests/randNM.R |only 23 files changed, 816 insertions(+), 106 deletions(-)
Author: Timothee Poisot
Title: Decimal log plotting in two and three dimensions
Description: Provides a range of function for 10-log plotting
Diff between log10 versions 0.0.3-05 dated 2009-11-22 and 0.1.0-01 dated 2009-11-26
DESCRIPTION | 10 +++++----- R/logplot.r | 18 ++++++++++++++++-- man/hcp3.Rd |only man/logfill.Rd | 2 +- man/loglm.Rd |only 5 files changed, 22 insertions(+), 8 deletions(-)
Author: Ulrike Groemping
Title: Fractional Factorial designs with 2-level factors
Description: This package creates regular and non-regular Fractional
Factorial designs. Furthermore, analysis tools for Fractional
Factorial designs with 2-level factors are offered (main
effects and interaction plots for all factors simultaneously,
cube plot for looking at the simultaneous effects of three
factors, full or half normal plot, alias structure in a more
readable format than with the built-in function alias). The
package is currently subject to intensive development. While
much of the intended functionality is already available, some
changes and improvements are still to be expected. Suggestions
are welcome.
Diff between FrF2 versions 1.0-1 dated 2009-11-18 and 1.0-2 dated 2009-11-26
DESCRIPTION | 8 ++++---- R/DanielPlot.R | 7 +++++-- R/FrF2.R | 4 +++- R/IAPlot.R | 7 +++++-- R/MEPlot.R | 7 +++++-- inst/NEWS | 8 +++++++- man/DanielPlot.Rd | 9 ++++++--- man/FrF2.Rd | 4 ++-- man/IAPlot.Rd | 7 +++++-- 9 files changed, 42 insertions(+), 19 deletions(-)
Author: Campo Elias Pardo
Title: Combination of Factorial Methods and Cluster Analysis
Description: Multivariate exploration of a data table with factorial
analysis and cluster methods.
Diff between FactoClass versions 1.0.1 dated 2009-07-21 and 1.0.3 dated 2009-11-26
FactoClass-1.0.1/FactoClass/R/stableclus.R |only FactoClass-1.0.1/FactoClass/man/stableclus.Rd |only FactoClass-1.0.1/FactoClass/src/kmnsw.f |only FactoClass-1.0.3/FactoClass/DESCRIPTION | 11 +++-- FactoClass-1.0.3/FactoClass/R/FactoClass.R | 4 +- FactoClass-1.0.3/FactoClass/R/kmeansW.R | 42 +++++++++++----------- FactoClass-1.0.3/FactoClass/R/plotFactoClass.R | 4 +- FactoClass-1.0.3/FactoClass/man/kmeansW.Rd | 19 ++++++--- FactoClass-1.0.3/FactoClass/man/plotFactoClass.Rd | 2 - FactoClass-1.0.3/FactoClass/src/kmeansw.cc |only FactoClass-1.0.3/FactoClass/src/kmeansw.h |only 11 files changed, 44 insertions(+), 38 deletions(-)
Author: Ulrike Groemping
Title: Full factorials, orthogonal arrays and base utilities for DoE
packages
Description: This package creates full factorial experimental designs
and designs based on orthogonal arrays for (industrial)
experiments. Additionally, it provides some utility functions
used also by other DoE packages.
Diff between DoE.base versions 0.9-7 dated 2009-11-05 and 0.9-8 dated 2009-11-26
DESCRIPTION | 8 - NAMESPACE | 2 R/DesignAccessors.r | 86 ++++++++++++++++--- R/export.design.R | 5 + R/formula.design.R | 13 ++ R/lm.design.R | 2 R/printandsummary.design.R | 25 ++++- inst/NEWS | 22 ++++ man/class-design.Rd | 70 +++++++++++---- tests/test_cross.Rout.save | 202 +++++++++++++++++++++++++++++++++++++-------- 10 files changed, 360 insertions(+), 75 deletions(-)
Author: James Carpenter
Title: Statistical methods to model and adjust for bias in
meta-analysis
Description: Copas selection model.
Diff between copas versions 0.6-2 dated 2009-04-15 and 0.6-3 dated 2009-11-26
ChangeLog |only DESCRIPTION | 8 ++++---- R/plot.copas.R | 3 ++- R/print.copas.R | 4 ++-- R/print.summary.copas.R | 4 ++++ R/summary.copas.R | 7 ++++--- man/plot.copas.Rd | 4 +++- man/print.copas.Rd | 14 +++++++++----- 8 files changed, 28 insertions(+), 16 deletions(-)
Author: Renaud Gaujoux
Title: Framework for Nonnegative Matrix Factorization (NMF) algorithms.
Description: This package provides a framework to perform Non-negative
Matrix Factorization (NMF). It implements a set of already
published algorithms and seeding methods, and provides a
framework to test and develop new algorithms.
Diff between NMF versions 0.2 dated 2009-11-23 and 0.2.2 dated 2009-11-26
DESCRIPTION | 6 inst/doc/NMF-vignette.Rnw | 8 inst/doc/NMF-vignette.pdf | 2366 +++++++++++++++++++++++----------------------- 3 files changed, 1222 insertions(+), 1158 deletions(-)
Author: Thomas Scheike with contributions from Torben Martinussen and
Jeremy Silver
Title: timereg package for Flexible regression models for survival
data.
Description: Programs for Martinussen and Scheike (2006), `Dynamic
Regression Models for Survival Data', Springer Verlag. Plus
more recent developments. Additive survival model,
semiparmetric proportional odds model, cumulative residuals,
excess risk models and more. Flexible competing risks
regression including GOF-tests. Two-stage frailty modelling.
Diff between timereg versions 1.2-5 dated 2009-07-31 and 1.2-7 dated 2009-11-26
DESCRIPTION | 14 +++++++------- R/additive-lasso.r | 8 ++++---- R/cox-aalen.r | 3 +-- R/mylars.r | 19 +++++++++---------- R/pls.cv.r | 5 +++++ R/predict-timereg.r | 37 +++++++++++++++++++++++++++---------- R/two-stage-reg.r | 42 ++++++++++++++++++++++++------------------ man/comp.risk.Rd | 2 +- man/surv-lars.Rd | 2 ++ man/two.stage.reg.Rd | 6 ++++-- src/aalen-test.c | 10 +++++----- src/breslow.c | 7 ++----- src/comprisk.c | 22 ++++++++++++++-------- src/dynadd.c | 4 +--- src/matrix.c | 2 +- src/matrix.h | 13 ------------- src/two-stage-reg.c | 28 ++++++++++++---------------- src/unifConfBandResampling.c | 2 +- 18 files changed, 120 insertions(+), 106 deletions(-)
Author: Christopher Jackson
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.
Diff between msm versions 0.9.4 dated 2009-11-13 and 0.9.5 dated 2009-11-26
ChangeLog | 8 ++++++++ DESCRIPTION | 8 ++++---- R/pearson.R | 6 +++--- inst/NEWS | 8 ++++++++ inst/doc/msm-manual.pdf |binary tests/pearson.R | 8 -------- 6 files changed, 23 insertions(+), 15 deletions(-)
Author: Matthew Vavrek
Title: Palaeoecological and Palaeogeographical Analysis Tools
Description: A set of analytical tools useful in analysing ecological
and geographical data sets, both ancient and modern. The
package includes functions for estimating species richness
(Chao 1 and 2, ACE, ICE, Jacknife), shared species/beta
diversity, species area curves and geographic distances and
areas.
Diff between fossil versions 0.2.1 dated 2009-04-14 and 0.2.2 dated 2009-11-26
DESCRIPTION | 15 +++++++-------- R/create.matrix.R | 3 ++- R/simpson.R | 11 +++++++---- inst/CITATION | 5 +++-- man/ace.Rd | 2 +- man/bray.curtis.Rd | 3 +-- man/create.lats.Rd | 8 +------- man/create.matrix.Rd | 16 +++++----------- man/dino.mst.Rd | 3 +-- man/earth.bear.Rd | 2 +- man/ebar.loc.Rd |only man/ebar.spp.Rd |only man/fossil-package.Rd | 31 ++++++------------------------- 13 files changed, 35 insertions(+), 64 deletions(-)
Author: David Hajage
Title: Export R objects to several markup languages
Description: Coerce R object to asciidoc, txt2tags, restructuredText or
org syntax. Package comes with a set of drivers for Sweave.
Diff between ascii versions 0.4 dated 2009-11-25 and 0.4-1 dated 2009-11-26
DESCRIPTION | 6 +++--- NAMESPACE | 2 ++ NEWS | 6 ++++++ R/asciiDescr.r | 8 ++++---- R/misc.r | 11 +++++------ man/ascii.Rd | 10 +++++----- 6 files changed, 25 insertions(+), 18 deletions(-)
More information about OligoSpecificitySystem at CRAN
Permanent link
Author: Ming-Huei Chen
Title: Genome-Wide Association analyses with Family data
Description: Functions to test genetic associations between SNPs and a
continuous/dichotomous trait using family data, and to make
genome-wide p-value plot and QQ plot.
Diff between GWAF versions 1.1 dated 2009-09-25 and 1.2 dated 2009-11-26
DESCRIPTION | 8 GWAF/CONTENTS | 8 GWAF/DESCRIPTION | 6 GWAF/INDEX | 4 GWAF/Meta/Rd.rds |binary GWAF/Meta/hsearch.rds |binary GWAF/Meta/package.rds |binary GWAF/R/GWAF.rdb |binary GWAF/R/GWAF.rdx |binary GWAF/doc/UsingGWAF.pdf | 281 +++++++++++++++++----------------- GWAF/help/AnIndex | 1 GWAF/help/GWAF-package | 23 +- GWAF/help/GWplot | 17 +- GWAF/help/auto |only GWAF/help/gee.lgst | 10 - GWAF/help/gee.lgst.batch | 48 +++-- GWAF/help/gee.lgst.batch.imputed | 16 + GWAF/help/gee.lgst.imputed | 6 GWAF/help/lme.batch | 46 +++-- GWAF/help/lme.batch.imputed | 16 + GWAF/html/00Index.html | 6 GWAF/html/GWAF-package.html | 14 - GWAF/html/GWplot.html | 11 - GWAF/html/auto.html |only GWAF/html/gee.lgst.batch.html | 40 +++- GWAF/html/gee.lgst.batch.imputed.html | 21 ++ GWAF/html/gee.lgst.html | 10 - GWAF/html/gee.lgst.imputed.html | 11 - GWAF/html/lme.batch.html | 32 ++- GWAF/html/lme.batch.imputed.html | 24 ++ GWAF/html/lmekin.html | 2 GWAF/html/qq.html | 2 GWAF/latex/GWAF-package.tex | 12 - GWAF/latex/GWplot.tex | 7 GWAF/latex/auto.tex |only GWAF/latex/gee.lgst.batch.imputed.tex | 11 - GWAF/latex/gee.lgst.batch.tex | 30 ++- GWAF/latex/gee.lgst.imputed.tex | 9 - GWAF/latex/gee.lgst.tex | 8 GWAF/latex/lme.batch.imputed.tex | 14 + GWAF/latex/lme.batch.tex | 22 +- GWAF/man/GWAF.Rd.gz |binary R/auto.R |only R/gee.lgst.R | 66 +++---- R/gee.lgst.batch.R | 30 ++- R/gee.lgst.batch.imputed.R | 31 +++ R/lme.R | 38 +++- R/lme.imputed.R | 38 +++- inst/doc/UsingGWAF.pdf | 281 +++++++++++++++++----------------- man/GWAF-package.Rd | 12 - man/GWplot.Rd | 7 man/auto.Rd |only man/gee.lgst.Rd | 8 man/gee.lgst.batch.Rd | 32 ++- man/gee.lgst.batch.imputed.Rd | 11 - man/gee.lgst.imputed.Rd | 9 - man/lme.batch.Rd | 157 +++++++++--------- man/lme.batch.imputed.Rd | 14 + 58 files changed, 866 insertions(+), 644 deletions(-)
Author: Brian Walters
Title: k-Nearest Neighbor Diagnostic Tools
Description: A suite of graphical diagnostic tools to evaluate kNN
classifications.
Diff between nnDiag versions 0.0-3 dated 2009-11-17 and 0.0-4 dated 2009-11-25
DESCRIPTION | 14 +++++++------- NAMESPACE | 4 ++-- R/knnvarfun.R |only man/LuceForgrp.Rd | 7 ++++++- man/LuceVolume.Rd | 7 ++++++- man/LuceVolume_subset.Rd | 7 ++++++- man/aoiMaker.Rd | 4 ++-- man/arealBias.Rd | 4 ++-- man/bias.Rd | 2 +- man/categorical.Rd | 2 +- man/extrap.Rd | 5 +++-- man/grouper.Rd | 2 +- man/knnvarfun.Rd |only man/nnDiag-package.Rd | 11 ++++++++--- man/outInflu.Rd | 2 +- man/rmse.Rd | 2 +- man/scedast.Rd | 2 +- src |only 18 files changed, 48 insertions(+), 27 deletions(-)
Author: K. Burkett
Title: Inference of trait associations with SNP haplotypes and other
attributes using the EM Algorithm
Description: The following R functions are used for inference of trait
associations with haplotypes and other covariates in
generalized linear models. The functions are developed
primarily for data collected in cohort or cross-sectional
studies. They can accommodate uncertain haplotype phase and
handle missing genotypes at some SNPs.
Diff between hapassoc versions 1.2-2 dated 2008-10-14 and 1.2-3 dated 2009-11-25
hapassoc-1.2-2/hapassoc/inst/doc/hapassoc.aux |only hapassoc-1.2-2/hapassoc/inst/doc/hapassoc.tex |only hapassoc-1.2-3/hapassoc/DESCRIPTION | 24 hapassoc-1.2-3/hapassoc/R/hapassoc.R | 4 hapassoc-1.2-3/hapassoc/inst/ChangeLog | 6 hapassoc-1.2-3/hapassoc/inst/doc/burkett_biblio.bib |only hapassoc-1.2-3/hapassoc/inst/doc/hapassoc.pdf | 955 ++++++++++---------- 7 files changed, 505 insertions(+), 484 deletions(-)
Author: David Ardia
Title: Bayesian Estimation of the GARCH(1,1) Model with Student-t
Innovations
Description: This package provides the bayesGARCH function which
performs the Bayesian estimation of the GARCH(1,1) model with
Student's t innovations.
Diff between bayesGARCH versions 1-00.04 dated 2009-05-11 and 1-00.05 dated 2009-11-25
DESCRIPTION | 8 ++++---- NEWS | 6 +++++- R/onload.R | 3 +-- inst/CITATION | 18 ++++++++++++++++-- man/bayesGARCH.Rd | 29 ++++++++++++++++------------- 5 files changed, 42 insertions(+), 22 deletions(-)
Author: David Hajage
Title: Export R objects to several markup languages
Description: Coerce R object to asciidoc, txt2tags, restructuredText or
org syntax. Package comes with a set of drivers for Sweave.
Diff between ascii versions 0.3.2 dated 2009-10-28 and 0.4 dated 2009-11-25
ascii-0.3.2/ascii/R/RweaveSphinx.r |only ascii-0.3.2/ascii/man/RweaveSphinx.Rd |only ascii-0.3.2/ascii/man/Sphinx.Rd |only ascii-0.4/ascii/DESCRIPTION | 10 ascii-0.4/ascii/NAMESPACE | 3 ascii-0.4/ascii/NEWS | 11 ascii-0.4/ascii/R/RweaveAsciidoc.r | 4 ascii-0.4/ascii/R/RweaveOrg.r | 2 ascii-0.4/ascii/R/RweaveReST.r |only ascii-0.4/ascii/R/RweaveT2t.r | 2 ascii-0.4/ascii/R/SweaveAscii.r | 4 ascii-0.4/ascii/R/asciiAnova.r | 72 ++++-- ascii-0.4/ascii/R/asciiDataFrame.r | 8 ascii-0.4/ascii/R/asciiDefault.r | 4 ascii-0.4/ascii/R/asciiDensity.r | 11 ascii-0.4/ascii/R/asciiDescr.r |only ascii-0.4/ascii/R/asciiGlm.r | 22 + ascii-0.4/ascii/R/asciiHtest.r | 11 ascii-0.4/ascii/R/asciiList.r | 4 ascii-0.4/ascii/R/asciiLm.r | 22 + ascii-0.4/ascii/R/asciiMatrix.r | 13 - ascii-0.4/ascii/R/asciiPrcomp.r | 26 +- ascii-0.4/ascii/R/asciiSurvival.r | 22 + ascii-0.4/ascii/R/asciiTable.r | 11 ascii-0.4/ascii/R/asciiTs.r | 11 ascii-0.4/ascii/R/asciiVector.r | 43 ++- ascii-0.4/ascii/R/misc.r | 20 - ascii-0.4/ascii/R/print.r | 21 + ascii-0.4/ascii/R/show.r | 383 +++++++++++++++++++++++++--------- ascii-0.4/ascii/TODO | 2 ascii-0.4/ascii/man/ReST.Rd |only ascii-0.4/ascii/man/RweaveReST.Rd |only ascii-0.4/ascii/man/ascii.Rd | 76 ++++-- ascii-0.4/ascii/man/print.ascii.Rd | 13 - 34 files changed, 594 insertions(+), 237 deletions(-)
Author: Micah Altman, Jeff Gill, Michael P. McDonald
Title: Tools for testing and improving accuracy of statistical results.
Description: This is a suite of tools designed to test and improve the
accuracy of statistical computation, including: Summarization
of the sensitivity of linear and non-linear models (lm, glm,
mle, nls) to measurement and numerical error; Sensitivity
analysis of dozens of models as run through Zelig; A
generalized cholesky method for correcting non-invertable
Hessians; Tests for the global optimality of non-linear
regression and maximum likelihood results; Tools for obtaining
true random numbers using entropy collected from the system
and/or entropy servers on the internet; A method for converting
floating point numbers to normalized fractions; Benchmark data
for checking the accuracy of basic distribution functions.
Diff between accuracy versions 1.33 dated 2009-10-30 and 1.34 dated 2009-11-25
CHANGELOG | 3 DESCRIPTION | 8 inst/doc/Rplots.pdf | 1200 +++++++++++----------------------- inst/doc/accuracy_vignette-plot1a.eps | 512 ++++++++------ inst/doc/accuracy_vignette-plot1a.pdf | 597 ++++++++++------ inst/doc/accuracy_vignette-plot2a.eps | 619 +---------------- inst/doc/accuracy_vignette-plot2a.pdf | 628 +---------------- inst/doc/accuracy_vignette.aux | 28 inst/doc/accuracy_vignette.log | 48 - inst/doc/accuracy_vignette.pdf |binary inst/doc/accuracy_vignette.tex | 129 +-- man/trueRandom.Rd | 2 12 files changed, 1230 insertions(+), 2544 deletions(-)
Author: Jon T. Schnute
Title: GUI Tools Made Easy: Interact with Models, Explore Data, Give
Dynamic Presentations
Description: PBS Modelling provides software to facilitate the design,
testing, and operation of computer models. It focuses
particularly on tools that make it easy to construct and edit a
customized graphical user interface (GUI). Although it depends
heavily on the R interface to the Tcl/Tk package, a user does
not need to know Tcl/Tk. The package contains examples that
illustrate models built with other R packages, including
PBSmapping, deSolve, PBSddesolve, and BRugs. It also serves as
a convenient prototype for building new R packages, along with
instructions and batch files to facilitate that process. The R
directory '.../library/PBSmodelling/doc' includes a complete
user guide PBSmodelling-UG.pdf. To use this package
effectively, please consult the guide.
Diff between PBSmodelling versions 2.50.162 dated 2009-10-20 and 2.51.168 dated 2009-11-25
DESCRIPTION | 12 ++++---- NAMESPACE | 1 R/presentTalk.r | 5 ++- R/supportFuns.r | 56 ++++++++++++++++++++++++++++----------- inst/PBStools/RmakePDF.bat | 5 ++- inst/doc/ChangeLog.txt | 6 ++++ inst/doc/PBSmodelling-UG.pdf |binary inst/doc/PBSmodellingIntro.pdf |binary inst/examples/runExamplesWin.txt | 2 - inst/examples/swisstalk.xml | 2 - man/showHelp.Rd | 24 +++++++++------- man/viewCode.Rd | 11 ++++++- 12 files changed, 86 insertions(+), 38 deletions(-)
Author: Alan T. Arnholt
Title: PROBABILITY and STATISTICS WITH R
Description: Data and functions for the book PROBABILITY and STATISTICS
WITH R.
Diff between PASWR versions 1.0 dated 2008-02-12 and 1.1 dated 2009-11-25
DESCRIPTION | 31 +++++++++++++++++-------------- R/CIsim.R | 2 +- R/Combinations.R | 2 +- R/EDA.R | 2 +- R/SIGN.test.R | 2 +- R/SRS.R | 2 +- R/bino.gen.R | 2 +- R/checking.plots.R | 2 +- R/interval.plot.R | 2 +- R/ksLdist.R | 2 +- R/ksdist.R | 2 +- R/normarea.R | 2 +- R/nsize.R | 2 +- R/ntester.R | 2 +- R/oneway.plots.R | 2 +- R/tsum.test.R | 2 +- R/twoway.plots.R | 2 +- R/wilcoxE.test.R | 2 +- R/z.test.R | 2 +- R/zsum.test.R | 2 +- data/Aggression.rda |binary data/Apple.rda |binary data/AptSize.rda |binary data/Baberuth.rda |binary data/Bac.rda |binary data/Battery.rda |binary data/Bodyfat.rda |binary data/Calculus.rda |binary data/Cars2004EU.rda |binary data/Chips.rda |binary data/CircuitDesigns.rda |binary data/CosAma.rda |binary data/Cows.rda |binary data/Depend.rda |only data/Drosophila.rda |binary data/EPIDURAL.rda |binary data/EPIDURALf.rda |binary data/EURD.rda |binary data/Engineer.rda |binary data/FCD.rda |binary data/Fertilize.rda |binary data/Formula1.rda |binary data/GD.rda |binary data/Grades.rda |binary data/Grocery.rda |binary data/HSwrestler.rda |binary data/HardWater.rda |only data/House.rda |binary data/Hubble.rda |binary data/InsurQuotes.rda |binary data/Kinder.rda |binary data/Leddiode.rda |binary data/LostR.rda |binary data/MilkCarton.rda |binary data/Phenyl.rda |binary data/Phone.rda |binary data/Rat.rda |binary data/Ratbp.rda |binary data/Refrigerator.rda |binary data/Roacheggs.rda |binary data/SBIQ.rda |binary data/SDS4.rda |binary data/Salinity.rda |binary data/Schizo.rda |binary data/Score.rda |binary data/SimDataST.rda |binary data/SimDataXT.rda |binary data/Soccer.rda |binary data/StatTemps.rda |binary data/Stschool.rda |binary data/Sundig.rda |binary data/SurfaceSpain.rda |binary data/Swimtimes.rda |binary data/TOE.rda |binary data/Tennis.rda |binary data/TestScores.rda |binary data/Tire.rda |binary data/TireWear.rda |binary data/Top20.rda |binary data/URLaddress.rda |binary data/WCST.rda |binary data/Wait.rda |binary data/Washer.rda |binary data/Water.rda |binary data/WeightGain.rda |only data/WheatSpain.rda |binary data/Wool.rda |binary data/biomass.rda |binary data/fagus.rda |binary data/food.rda |binary data/glucose.rda |binary data/janka.rda |only data/satfruit.rda |binary data/sunflower.rda |binary data/titanic3.rda |binary data/vit2005.rda |binary data/wheatUSA2004.rda |binary man/Aggression.Rd | 6 +++--- man/Apple.Rd | 8 ++++++++ man/AptSize.Rd | 6 ++---- man/Baberuth.Rd | 6 ++---- man/Bac.Rd | 5 ++--- man/Battery.Rd | 8 ++++---- man/Bodyfat.Rd | 4 +--- man/Calculus.Rd | 5 ++--- man/Cars2004EU.Rd | 4 +--- man/Chips.Rd | 16 ++++++++++------ man/CircuitDesigns.Rd | 4 ++++ man/CosAma.Rd | 5 +---- man/Cows.Rd | 4 +--- man/Depend.Rd |only man/Drosophila.Rd | 4 +--- man/EPIDURAL.Rd | 9 +++++---- man/EPIDURALf.Rd | 4 +--- man/EURD.Rd | 4 +++- man/Engineer.Rd | 6 +++--- man/FCD.Rd | 5 ++--- man/Fertilize.Rd | 5 ++--- man/Formula1.Rd | 5 ++--- man/GD.Rd | 16 ++++++++++++---- man/Grades.Rd | 7 ++++--- man/Grocery.Rd | 5 ++--- man/HSwrestler.Rd | 8 +++----- man/HardWater.Rd |only man/House.Rd | 6 ++---- man/Hubble.Rd | 11 ++++++----- man/InsurQuotes.Rd | 6 ++---- man/Kinder.Rd | 7 ++++--- man/Leddiode.Rd | 5 ++--- man/LostR.Rd | 4 +--- man/MilkCarton.Rd | 5 ++--- man/PASWR-package.Rd | 4 ++-- man/Phenyl.Rd | 5 ++--- man/Phone.Rd | 5 ++--- man/Rat.Rd | 5 ++--- man/Ratbp.Rd | 5 ++--- man/Refrigerator.Rd | 5 ++--- man/Roacheggs.Rd | 11 ++++++++--- man/SBIQ.Rd | 9 ++++----- man/SDS4.Rd | 4 +--- man/SIGN.test.Rd | 5 ++--- man/Salinity.Rd | 5 ++--- man/Schizo.Rd | 5 +++++ man/Score.Rd | 5 +---- man/SimDataST.Rd | 4 +--- man/SimDataXT.Rd | 4 +--- man/Soccer.Rd | 6 ++---- man/StatTemps.Rd | 4 +--- man/Stschool.Rd | 6 ++---- man/Sundig.Rd | 5 ++--- man/SurfaceSpain.Rd | 7 ++++--- man/Swimtimes.Rd | 6 ++---- man/TOE.Rd | 5 ++++- man/Tennis.Rd | 5 ++--- man/TestScores.Rd | 5 ++--- man/Tire.Rd | 4 +--- man/TireWear.Rd | 9 ++++----- man/Top20.Rd | 5 ++--- man/URLaddress.Rd | 4 +--- man/WCST.Rd | 4 +++- man/Wait.Rd | 5 ++--- man/Washer.Rd | 5 ++--- man/Water.Rd | 5 ++--- man/WeightGain.Rd |only man/WheatSpain.Rd | 5 ++--- man/Wool.Rd | 5 ++--- man/bino.gen.Rd | 1 - man/biomass.Rd | 4 +--- man/checking.plots.Rd | 7 +++---- man/fagus.Rd | 4 +--- man/food.Rd | 4 +--- man/glucose.Rd | 5 ++--- man/interval.plot.Rd | 1 - man/janka.Rd |only man/ksLdist.Rd | 1 - man/ksdist.Rd | 1 - man/oneway.plots.Rd | 6 ++---- man/satfruit.Rd | 7 ++++--- man/sunflower.Rd | 4 +--- man/titanic3.Rd | 6 ++---- man/tsum.test.Rd | 21 +++++++++++---------- man/twoway.plots.Rd | 2 +- man/vit2005.Rd | 12 ++++++------ man/wheatUSA2004.Rd | 7 +++---- man/wilcoxE.test.Rd | 6 +++--- man/z.test.Rd | 18 ++++++++++-------- man/zsum.test.Rd | 16 +++++++++++----- 187 files changed, 277 insertions(+), 309 deletions(-)
Author: John Maindonald and W. John Braun
Title: Data Analysis And Graphics data and functions
Description: various data sets used in examples and exercises in the
book Maindonald, J.H. and Braun, W.J. (2003, 2007) "Data
Analysis and Graphics Using R".
Diff between DAAG versions 1.00 dated 2009-08-23 and 1.01 dated 2009-11-25
DESCRIPTION | 8 ++++---- INDEX | 14 +++++++------- R/pause.R | 3 +-- R/qreference.R | 1 + 4 files changed, 13 insertions(+), 13 deletions(-)
Author: Andreas F. Hofmann, Karline Soetaert, Filip J.R. Meysman
Title: AquaEnv - an integrated development toolbox for aquatic chemical
model generation
Description: AquaEnv is an integrated development toolbox for aquatic
chemical model generation focused on (ocean) acidification and
CO2 air-water exchange. It contains all elements necessary to
model the pH, the related CO2 air-water exchange, as well as
aquatic acid-base chemistry in general for an arbitrary marine,
estuarine or freshwater system. Also chemical batches can be
modelled. Next to the routines necessary to calculate desired
information, AquaEnv also contains a suite of tools to
visualize this information. Furthermore, AquaEnv can not only
be used to build dynamic models of aquatic systems, but it can
also serve as a simple desktop tool for the experimental
aquatic chemist to generate and visualize all possible derived
information from a set of measurements with one single easy to
use R function. Additionally, the sensitivity of the system to
variations in the input variables can be visualized.
Diff between AquaEnv versions 0.8 dated 2009-11-18 and 0.8-1 dated 2009-11-25
DESCRIPTION | 10 R/aquaenv_private_DSApHfunctions.R | 292 inst/doc/AquaEnv-ConstantsAndFormulae.pdf | 5425 +++++----- inst/doc/AquaEnv-PrivateFunctions.pdf |binary inst/doc/AquaEnv.pdf |14858 ++++++++++++++---------------- inst/doc/AquaEnv.tex | 5854 +++++------ 6 files changed, 13152 insertions(+), 13287 deletions(-)
Author: Hsin-ya Lee
Title: data analysis of drug stability
Description: A menu-driven package for data analysis of drug stability
based on ICH guideline(such as estimation of shelf-life from a
3-batch profile.)
Diff between stab versions 0.0.5 dated 2008-11-04 and 0.0.6 dated 2009-11-24
DESCRIPTION | 27 ++++++++++++++++----------- R/MultipleAnalyze.r | 4 ++-- R/stabilitymenu.r | 2 +- R/zzz.R | 2 +- man/MultipleAnalyze.rd | 2 +- 5 files changed, 21 insertions(+), 16 deletions(-)
Author: Graham Williams
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.
Diff between rattle versions 2.5.3 dated 2009-11-06 and 2.5.6 dated 2009-11-24
DESCRIPTION | 8 R/cluster.R | 18 - R/data.R | 48 ++-- R/evaluate.R | 472 ++++++++++++++++++++++------------------- R/explore.R | 8 R/export.R | 12 - R/model.R | 135 +---------- R/nnet.R | 94 +------- R/projects.R | 6 R/rattle.R | 114 +++++---- R/rpart.R | 4 R/survival.R | 113 +++++---- R/zzz.R | 8 data/weather.RData |binary data/weatherCanberra.RData |binary data/weatherSydney.RData |binary inst/arff/weather.arff | 2 inst/arff/weatherCanberra.arff | 10 inst/arff/weatherSydney.arff | 8 inst/csv/weatherCanberra.csv | 8 inst/csv/weatherSydney.csv | 6 inst/etc/rattle.glade | 440 ++++++++++++-------------------------- man/internal.Rd | 22 + 23 files changed, 660 insertions(+), 876 deletions(-)
Author: Matthew Denwood
Title: Power calculations and Bayesian analysis of count distributions
and FECRT data using MCMC
Description: A set of functions to allow analysis of count data (such
as faecal egg count data) using Bayesian MCMC methods. Returns
information on the possible values for mean count, coefficient
of variation and zero inflation (true prevalence) present in
the data. A complete faecal egg count reduction test (FECRT)
model is implemented, which returns inference on the true
efficacy of the drug from the pre and post treatment data
provided, using non-parametric bootstrapping as well as using
Bayesian MCMC. Functions to perform power analyses for faecal
egg counts (including FECRT) are also provided. Requires Just
Another Gibbs Sampler (JAGS) for most functions (except power
analysis calculations), see:
http://www-fis.iarc.fr/~martyn/software/jags/.
Diff between bayescount versions 0.9.0-7 dated 2009-01-08 and 0.9.9-1 dated 2009-11-24
DESCRIPTION | 30 ++- NAMESPACE | 4 R/bayescount.R | 11 - R/bayescount.single.R | 40 +++- R/fec.power.R |only R/fecrt.R | 433 ++++++++++++++++++++++++---------------------- R/fecrt.power.R |only R/invisible.R | 104 +++++++++-- R/maximise.likelihood.R | 29 ++- R/run.model.R | 12 - R/zzz.R |only inst/CITATION | 20 +- inst/version_history.txt | 29 ++- man/bayescount.Rd | 6 man/bayescount.single.Rd | 2 man/fec.power.Rd |only man/fec.power.limits.Rd |only man/fecrt.Rd | 40 ++-- man/fecrt.power.Rd |only man/fecrt.power.limits.Rd |only man/run.model.Rd | 4 src |only 22 files changed, 476 insertions(+), 288 deletions(-)
Author: Enrico Glaab
Title: Generate 3D visualizations for data exploration on the web
Description: vrmlgen creates 3D scatter and bar plots, visualizations
of 3D meshes, parametric functions and height maps in
web-formats like the Virtual Reality Markup Language (VRML,
filetype .wrl) and the LiveGraphics3D format.
Diff between vrmlgen versions 1.2 dated 2009-11-12 and 1.3 dated 2009-11-24
DESCRIPTION | 6 - R/lbar.R | 68 ++++++++++++- R/lcloud.R | 133 +++++++++++++++++++++++--- R/lmesh.R | 92 +++++++++++++++--- R/vbar.R | 177 +++++++++++++++++++++++------------ R/vcloud.R | 255 +++++++++++++++++++++++++++------------------------ R/vmesh.R | 138 ++++++++++++++++++++++----- R/vrmlgen-internal.R | 29 +++++ man/lcloud.Rd | 13 +- man/lmesh.Rd | 10 +- man/vbar.Rd | 2 man/vcloud.Rd | 8 + man/vmesh.Rd | 14 ++ 13 files changed, 682 insertions(+), 263 deletions(-)
Author: Florian Jansen
Title: Functions to use vegetation databases (Turboveg) for vegetation
analyses in R
Description: Handling of vegetation data sets from Turboveg Databases.
Taxonomic valuation for German Taxonomical Standard List.
Diff between vegdata versions 0.1 dated 2009-11-11 and 0.1.1 dated 2009-11-24
vegdata-0.1.1/vegdata/DESCRIPTION | 6 vegdata-0.1.1/vegdata/R/freqtab.r | 21 vegdata-0.1.1/vegdata/R/tv.coverperc.r | 4 vegdata-0.1.1/vegdata/R/tv.home.r | 3 vegdata-0.1.1/vegdata/R/tv.metainfo.r |only vegdata-0.1.1/vegdata/R/tv.site.r | 4 vegdata-0.1.1/vegdata/R/tv.taxval.r | 114 vegdata-0.1.1/vegdata/R/tv.veg.r | 2 vegdata-0.1.1/vegdata/inst/CITATION | 4 vegdata-0.1.1/vegdata/inst/ChangeLog | 3 vegdata-0.1.1/vegdata/inst/doc/vegdata.bib | 43 vegdata-0.1.1/vegdata/inst/doc/vegdata.pdf |26955 +++++----- vegdata-0.1.1/vegdata/inst/doc/vegdata.rnw | 168 vegdata-0.1.1/vegdata/inst/extdata/Data/elbaue/metainfo.txt | 21 vegdata-0.1.1/vegdata/inst/extdata/Data/taxatest/metainfo.txt | 24 vegdata-0.1.1/vegdata/inst/extdata/Data/taxatest/tvabund.dbf |binary vegdata-0.1.1/vegdata/man/freqtab.rd | 3 vegdata-0.1.1/vegdata/man/tv.metainfo.rd |only vegdata-0.1.1/vegdata/man/tv.obs.rd | 10 vegdata-0.1.1/vegdata/man/tv.site.rd | 2 vegdata-0.1.1/vegdata/man/tv.taxval.rd | 41 vegdata-0.1.1/vegdata/man/tv.veg.rd | 2 vegdata-0.1/vegdata/R/metainfo.r |only vegdata-0.1/vegdata/man/metainfo.rd |only 24 files changed, 13766 insertions(+), 13664 deletions(-)
Author: Albart Coster
Title: Pedigree functions
Description: Pedigree related functions
Diff between pedigree versions 1.1 dated 2009-02-24 and 1.2 dated 2009-11-24
pedigree-1.1/pedigree/Read-and-delete-me |only pedigree-1.2/pedigree/DESCRIPTION | 10 +- pedigree-1.2/pedigree/NAMESPACE | 2 pedigree-1.2/pedigree/R/add.Inds.R | 5 - pedigree-1.2/pedigree/R/drivers.r | 26 ++++- pedigree-1.2/pedigree/man/countOff.Rd |only pedigree-1.2/pedigree/man/trimPed.Rd | 7 + pedigree-1.2/pedigree/src/Pedigree.cpp | 145 ++++++++++++++++++++++++------- pedigree-1.2/pedigree/src/Pedigree.h | 11 +- 9 files changed, 160 insertions(+), 46 deletions(-)
Author: Randy Bui, Ron N. Buliung, Tarmo K. Remmel
Title: A collection of functions for estimating centrographic statistcs
and computational geometries for spatial point patterns
Description: A collection of functions for computing centrographic
statistics (e.g., standard distance, standard deviation
ellipse, standard deviation box), and minimum convex polygons
(MCP) for observations taken at point locations. A tool is
also provided for converting geometric objects associated with
the centrographic statistics, and MCPs into ESRI Shapefiles.
Separate plotting functions have been developed for each
measure.
Diff between aspace versions 1.2 dated 2007-05-08 and 2.2 dated 2009-11-24
DESCRIPTION | 27 ++-- NAMESPACE | 2 R/calc_box.R |only R/calc_mcp.R | 72 ++++------ R/calc_sdd.R | 258 ++++++++++++++++++++------------------ R/calc_sde.R | 336 ++++++++++++++++++++++++++------------------------ R/distances.R | 4 R/ellipse3.R | 7 - R/plot_box.R |only R/plot_mcp.R |only R/plot_sdd.R |only R/plot_sde.R |only data/r.BOX.rda |only data/r.MCP.rda |only data/r.SDD.rda |only data/r.SDE.rda |only man/activities.Rd | 6 man/aspace.package.Rd | 16 +- man/calc_box.Rd |only man/calc_mcp.Rd | 29 +--- man/calc_sdd.Rd | 57 ++++---- man/calc_sde.Rd | 68 ++++------ man/ellipse3.Rd | 2 man/plot_box.Rd |only man/plot_mcp.Rd |only man/plot_sdd.Rd |only man/plot_sde.Rd |only man/r.BOX.Rd |only man/r.MCP.Rd |only man/r.SDD.Rd |only man/r.SDE.Rd |only man/wts.Rd | 2 32 files changed, 458 insertions(+), 428 deletions(-)
Author: Albart Coster, John Bastiaansen
Title: HaploSim
Description: Simulate haplotypes through meioses. Allows specification
of population parameters.
Diff between HaploSim versions 1.8 dated 2009-04-14 and 1.8.1 dated 2009-11-24
DESCRIPTION | 10 +++++----- R/SamplePedigree.R | 2 +- R/getAll.R | 33 +++++++++++++++++++++++++++++++++ 3 files changed, 39 insertions(+), 6 deletions(-)
Author: Markus Gesmann
Title: Mack-, Bootstrap and Munich-chain-ladder methods for insurance
claims reserving
Description: The package provides Mack-, Munich-, and Bootstrap
chain-ladder methods. These methods are typically used in
insurance claims reserving.
Diff between ChainLadder versions 0.1.2-11 dated 2009-03-28 and 0.1.2-13 dated 2009-11-24
ChainLadder-0.1.2-11/ChainLadder/data/M3IR5.Rdata |only ChainLadder-0.1.2-13/ChainLadder/DESCRIPTION | 14 ChainLadder-0.1.2-13/ChainLadder/NAMESPACE | 10 ChainLadder-0.1.2-13/ChainLadder/NEWS | 65 +- ChainLadder-0.1.2-13/ChainLadder/R/ChainLadder.R | 50 + ChainLadder-0.1.2-13/ChainLadder/R/MackChainLadderFunctions.R | 318 +++++++--- ChainLadder-0.1.2-13/ChainLadder/R/MunichChainLadderFunctions.R | 34 - ChainLadder-0.1.2-13/ChainLadder/R/Triangles.R |only ChainLadder-0.1.2-13/ChainLadder/THANKS | 6 ChainLadder-0.1.2-13/ChainLadder/data/ABC.RData |binary ChainLadder-0.1.2-13/ChainLadder/data/GenIns.RData |binary ChainLadder-0.1.2-13/ChainLadder/data/GenInsLong.RData |only ChainLadder-0.1.2-13/ChainLadder/data/M3IR5.RData |only ChainLadder-0.1.2-13/ChainLadder/data/MCLincurred.RData |binary ChainLadder-0.1.2-13/ChainLadder/data/MCLpaid.RData |binary ChainLadder-0.1.2-13/ChainLadder/data/Mortgage.RData |binary ChainLadder-0.1.2-13/ChainLadder/data/RAA.RData |binary ChainLadder-0.1.2-13/ChainLadder/data/qincurred.RData |binary ChainLadder-0.1.2-13/ChainLadder/data/qpaid.RData |binary ChainLadder-0.1.2-13/ChainLadder/inst/Experimental/doc |only ChainLadder-0.1.2-13/ChainLadder/inst/Images/MackLattice.png |only ChainLadder-0.1.2-13/ChainLadder/man/ABC.Rd | 3 ChainLadder-0.1.2-13/ChainLadder/man/BootChainLadder.Rd | 19 ChainLadder-0.1.2-13/ChainLadder/man/ChainLadder-package.Rd | 83 ++ ChainLadder-0.1.2-13/ChainLadder/man/GenIns.Rd | 21 ChainLadder-0.1.2-13/ChainLadder/man/M3IR5.Rd |only ChainLadder-0.1.2-13/ChainLadder/man/MCLpaid.Rd | 4 ChainLadder-0.1.2-13/ChainLadder/man/MackChainLadder.Rd | 170 +++-- ChainLadder-0.1.2-13/ChainLadder/man/Mortgage.Rd | 3 ChainLadder-0.1.2-13/ChainLadder/man/MunichChainLadder.Rd | 56 + ChainLadder-0.1.2-13/ChainLadder/man/RAA.Rd | 3 ChainLadder-0.1.2-13/ChainLadder/man/Triangles.Rd |only ChainLadder-0.1.2-13/ChainLadder/man/chainladder.Rd |only ChainLadder-0.1.2-13/ChainLadder/man/plot.BootChainLadder.Rd | 18 ChainLadder-0.1.2-13/ChainLadder/man/plot.MackChainLadder.Rd | 25 ChainLadder-0.1.2-13/ChainLadder/man/plot.MunichChainLadder.Rd | 15 ChainLadder-0.1.2-13/ChainLadder/man/predict.TriangleModel.Rd | 47 - ChainLadder-0.1.2-13/ChainLadder/man/qpaid.rd | 2 ChainLadder-0.1.2-13/ChainLadder/man/residuals.MackChainLadder.Rd | 2 ChainLadder-0.1.2-13/ChainLadder/man/summary.BootChainLadder.Rd | 2 ChainLadder-0.1.2-13/ChainLadder/man/summary.MackChainLadder.Rd | 8 ChainLadder-0.1.2-13/ChainLadder/man/summary.MunichChainLadder.Rd | 2 ChainLadder-0.1.2-13/ChainLadder/man/utilityfunctions.Rd |only 43 files changed, 695 insertions(+), 285 deletions(-)
Author: Thomas Hoffmann
Title: P2BAT
Description: This package provides data analysis via the pbat program,
and an alternative internal implementation of the power
calculations via simulation only. For analysis, this package
provides a frontend to the PBAT software, automatically reading
in the output from the pbat program and displaying the
corresponding figure when appropriate (i.e. PBAT-logrank). It
includes support for multiple processes and clusters. For
analysis, users must download PBAT (developed by Christoph
Lange) and accept it's license, available on the PBAT webpage.
Both the data analysis and power calculations have command line
and graphical interfaces using tcltk.
Diff between pbatR versions 2.1.5 dated 2009-06-18 and 2.2-0 dated 2009-11-23
DESCRIPTION | 14 ++--- R/clean.R | 17 +++--- R/createCommandfile.R | 3 - R/ped.R | 91 ++++++++++++++++++----------------- R/plot.pedigree.R |only R/power.R | 3 - R/powerConversions.R | 129 ++++++++++++++++++++++++++++++++++++++++++++++---- R/version.R | 6 +- man/pbat.clean.Rd | 3 - man/ped.Rd | 5 + 10 files changed, 196 insertions(+), 75 deletions(-)
Author: Vito M. R. Muggeo
Title: Modelling temperature effects using time series data
Description: Fits a Constrained Segmented Distributed Lag regression
model to epidemiological time series of mortality, temperature,
and other confounders.
Diff between modTempEff versions 1.3 dated 2009-11-22 and 1.4 dated 2009-11-23
DESCRIPTION | 8 ++++---- R/anova.modTempEff.R | 32 +++++++++++++++++++++++++++++++- R/print.modTempEff.R | 2 +- R/summary.modTempEff.R | 2 +- R/tempeff.R | 12 +++++++++--- data/dataset.rda |binary man/anova.modTempEff.Rd | 10 ++++++---- man/dataset.Rd | 8 +++++--- man/modTempEff-package.Rd | 4 ++-- 9 files changed, 59 insertions(+), 19 deletions(-)
Author: Timur V. Elzhov, Katharine M. Mullen
Title: R interface to the Levenberg-Marquardt nonlinear least-squares
algorithm found in MINPACK
Description: Provides R interface to lmder and lmdif from the MINPACK
library, for solving nonlinear least-squares problems by a
modification of the Levenberg-Marquardt algorithm.
Diff between minpack.lm versions 1.1-3 dated 2009-11-23 and 1.1-4 dated 2009-11-23
DESCRIPTION | 6 +++--- src/fcn_lmder.c | 7 +------ src/fcn_lmdif.c | 7 +------ src/nls_lm.c | 4 ++-- 4 files changed, 7 insertions(+), 17 deletions(-)
Author: Thomas Hoffmann
Title: Gene by Environment Interaction and Conditional Gene Tests for
Nuclear Families
Description: Does family-based gene by environment interaction tests,
joint gene, gene-environment interaction test, and a test of a
set of genes conditional on another set of genes.
Diff between fbati versions 0.6.2 dated 2009-03-11 and 0.7-1 dated 2009-11-23
DESCRIPTION | 8 - NAMESPACE | 3 R/REXP_joint.R | 6 R/cgFbatCode.R | 83 +++++++++- R/cgFbatRun.R | 35 ++++ R/fbatShell.R | 2 R/fbatcStrategyStep.R | 105 ++++++++----- R/fbatge.R |only R/fbatgeAll.R |only R/fbatgeInterface.R |only R/fbatmeev.R |only R/joint.R | 16 +- R/launchPad.R | 8 + R/merge.R | 21 +- man/fbatcStrategyStep.Rd | 2 man/fbatge.Rd |only man/fbatj.Rd | 4 man/fbatme.Rd |only man/nuclify.Rd | 7 src/RExportGen.cpp | 6 src/cgFbat.cpp | 235 +++++++++++++++++++++++++++--- src/fbatdist.cpp | 357 ++++++++++++++++++++++++++++++++++++++++++++++- src/fbatdist.h | 14 + src/fbatge.cpp |only src/fbatmeev.cpp |only src/fbatmeev.h |only src/joint.cpp | 191 +++++++++++++++++-------- src/joint.h | 2 src/nuclify.cpp | 15 + src/nuclify.h | 3 30 files changed, 952 insertions(+), 171 deletions(-)
Author: Karline Soetaert
Title: "A practical guide to ecological modelling - using R as a
simulation platform"
Description: Figures, data sets and examples from the book "A practical
guide to ecological modelling - using R as a simulation
platform" by Karline Soetaert and Peter MJ Herman (2009).
Springer. All figures from chapter x can be generated by
"demo(chapx)", where x = 1 to 11. The R-scripts of the model
examples discussed in the book are in subdirectory "examples",
ordered per chapter. Solutions to model projects are in the
same subdirectories.
Diff between ecolMod versions 1.2.1 dated 2009-02-20 and 1.2.2 dated 2009-11-23
ecolMod-1.2.1/ecolMod/inst/examples |only ecolMod-1.2.2/ecolMod/DESCRIPTION | 40 ++++++++++++++++++++------------ ecolMod-1.2.2/ecolMod/inst/doc |only ecolMod-1.2.2/ecolMod/man/ecolMod.Rd | 7 ++++- ecolMod-1.2.2/ecolMod/src/competition.f | 2 - 5 files changed, 31 insertions(+), 18 deletions(-)
Author: Karline Soetaert
Title: General solvers for initial value problems of ordinary
differential equations (ODE), partial differential equations
(PDE) and differential algebraic equations (DAE)
Description: Functions that solve initial value problems of a system of
first-order ordinary differential equations (ODE), of partial
differential equations (PDE) and of differential algebraic
equations (DAE). The functions provide an interface to the
FORTRAN functions lsoda, lsodar, lsode, lsodes of the ODEPACK
collection, to the FORTRAN functions dvode and daspk and a
C-implementation of solvers of the Runge-Kutta family with
fixed or variable time steps. The package contains routines
designed for solving ODEs resulting from 1-D, 2-D and 3-D
partial differential equations (PDE) that have been converted
to ODEs by numerical differencing.
Diff between deSolve versions 1.5 dated 2009-10-16 and 1.5-1 dated 2009-11-23
deSolve-1.5-1/deSolve/DESCRIPTION | 8 deSolve-1.5-1/deSolve/NAMESPACE | 7 deSolve-1.5-1/deSolve/R/Utilities.R | 2 deSolve-1.5-1/deSolve/R/diagnostics.R | 9 deSolve-1.5-1/deSolve/inst/CITATION |only deSolve-1.5-1/deSolve/inst/doc/compiledCode.pdf | 423 +++++++-------- deSolve-1.5-1/deSolve/inst/doc/deSolve.pdf | 648 +++++++++++------------ deSolve-1.5-1/deSolve/inst/doc/examples |only deSolve-1.5-1/deSolve/inst/doc/index.html | 2 deSolve-1.5-1/deSolve/inst/doc/source |only deSolve-1.5-1/deSolve/man/deSolve.Rd | 8 deSolve-1.5-1/deSolve/man/diagnostics.Rd | 54 - deSolve-1.5-1/deSolve/man/diagnostics.deSolve.Rd |only deSolve-1.5-1/deSolve/man/vode.Rd | 3 deSolve-1.5/deSolve/inst/dynload |only deSolve-1.5/deSolve/inst/examples |only deSolve-1.5/deSolve/inst/source |only 17 files changed, 585 insertions(+), 579 deletions(-)
Author: Paul Hiemstra
Title: Automatic interpolation package
Description: This package performs an automatic interpolation by
automatically estimating the variogram and then calling gstat.
Diff between automap versions 1.0-4 dated 2009-11-17 and 1.0-5 dated 2009-11-23
DESCRIPTION | 10 R/autoKrige.r | 6 R/autofitVariogram.r | 38 ++- SvnLog | 39 +++ man/autoKrige.rd | 7 man/autoKrige_cv.rd | 6 man/autofitVariogram.rd | 14 + man/compare.cv.rd | 6 tests/autoKrige.cv.Rout.save | 470 ------------------------------------------- tests/automap.R | 5 tests/automap.Rout.save | 23 +- 11 files changed, 119 insertions(+), 505 deletions(-)
Author: Emmanuel Paradis, Ben Bolker, Julien Claude, Hoa Sien Cuong,
Richard Desper, Benoit Durand, Julien Dutheil, Olivier Gascuel,
Gangolf Jobb, Christoph Heibl, Daniel Lawson, Vincent Lefort,
Pierre Legendre, Jim Lemon, Yvonnick Noel, Johan Nylander,
Rainer Opgen-Rhein, Korbinian Strimmer, Damien de Vienne
Title: Analyses of Phylogenetics and Evolution
Description: ape provides functions for reading, writing, plotting, and
manipulating phylogenetic trees, analyses of comparative data
in a phylogenetic framework, analyses of diversification and
macroevolution, computing distances from allelic and nucleotide
data, reading nucleotide sequences, and several tools such as
Mantel's test, computation of minimum spanning tree,
generalized skyline plots, estimation of absolute evolutionary
rates and clock-like trees using mean path lengths,
non-parametric rate smoothing and penalized likelihood.
Phylogeny estimation can be done with the NJ, BIONJ, and ME
methods.
Diff between ape versions 2.4 dated 2009-10-05 and 2.4-1 dated 2009-11-23
ChangeLog | 43 ++++++++++++++++++++++++++++++++++++++++++- DESCRIPTION | 8 ++++---- R/ace.R | 3 ++- R/ape-defunct.R | 23 ----------------------- R/as.phylo.R | 16 ++++++++-------- R/bind.tree.R | 9 +++++---- R/collapse.singles.R | 4 ++-- R/nj.R | 4 +++- R/plot.phylo.R | 27 ++++++++++----------------- R/read.nexus.R | 27 ++++++++++++++++++++++----- R/root.R | 10 +++++----- R/rtree.R | 9 ++++++--- R/vcv.phylo.R | 19 ++++++++++++++----- R/write.nexus.R | 10 ++++++---- inst/doc/MoranI.pdf |binary man/Initialize.corPhyl.Rd | 2 +- man/all.equal.phylo.Rd | 2 +- man/as.alignment.Rd | 2 +- man/as.phylo.Rd | 2 +- man/axisPhylo.Rd | 2 +- man/birthdeath.Rd | 2 +- man/compar.gee.Rd | 2 +- man/compute.brlen.Rd | 2 +- man/consensus.Rd | 2 +- man/corBrownian.Rd | 2 +- man/corGrafen.Rd | 2 +- man/corMartins.Rd | 2 +- man/identify.phylo.Rd | 2 +- man/is.monophyletic.Rd | 2 +- man/ltt.plot.Rd | 2 +- man/makeLabel.Rd | 2 +- man/mantel.test.Rd | 2 +- man/mst.Rd | 2 +- man/phymltest.Rd | 2 +- man/plot.ancestral.Rd | 2 +- man/plot.phylo.Rd | 2 +- man/print.phylo.Rd | 2 +- man/read.nexus.Rd | 18 +++++++++++++----- man/rtree.Rd | 12 +++++++----- man/skyline.Rd | 2 +- man/subtreeplot.Rd | 2 +- man/summary.phylo.Rd | 2 +- man/vcv.phylo.Rd | 42 +++++++++++++++++++++++++++++++----------- man/write.nexus.Rd | 2 +- man/zoom.Rd | 2 +- src/tree_build.c | 22 ++++++++-------------- 46 files changed, 215 insertions(+), 145 deletions(-)
Author: Jan Graffelman
Title: Graphical tests for Hardy-Weinberg equilibrium
Description: Package HardyWeinberg is a package for exploring
bi-allelic marker data. It focuses on the graphical
representation of the results of tests for Hardy-Weinberg
equlibrium in a ternary plot. Routines for several tests for
Hardy-Weinberg equilibrium are included in the package.
Diff between HardyWeinberg versions 1.3 dated 2009-03-27 and 1.4 dated 2009-11-23
DESCRIPTION | 10 NAMESPACE | 3 R/CompProbDown.R |only R/CompProbUp.R |only R/CritSam.R | 6 R/HWChisq.R | 66 R/HWChisqMat.R |only R/HWData.R | 72 R/HWExact.R | 142 R/HWExactMat.R |only R/HWTernaryPlot.R | 30 R/UniqueGenotypeCounts.R |only R/af.R |only R/cutoff.R |only R/maf.R |only inst/doc/HWTernaryPlots.pdf |only inst/doc/HardyWeinberg-009.eps |only inst/doc/HardyWeinberg-009.pdf |only inst/doc/HardyWeinberg.Snw | 149 inst/doc/HardyWeinberg.pdf |11305 +++++++++++++++++++++++++++++++---------- inst/doc/Rplots.pdf | 6355 +++++++++++++++-------- man/HWChisq.Rd | 7 man/HWChisqMat.Rd |only man/HWData.Rd | 22 man/HWExact.Rd | 44 man/HWExactMat.Rd |only man/HWTernaryPlot.Rd | 16 man/HardyWeinberg-package.Rd | 6 man/UniqueGenotypeCounts.Rd |only man/af.Rd |only man/maf.Rd |only 31 files changed, 13417 insertions(+), 4816 deletions(-)
Author: Bob Wheeler
Title: AlgDesign
Description: Algorithmic experimental designs. Calculates exact and
approximate theory experimental designs for D,A, and I
criteria. Very large designs may be created. Experimental
designs may be blocked or blocked designs created from a
candidate list, using several criteria. The blocking can be
done when whole and within plot factors interact.
Diff between AlgDesign versions 1.0-12 dated 2009-09-30 and 1.1-0 dated 2009-11-23
AlgDesign-1.0-12/AlgDesign/inst/doc/AlgDesign.dvi |only AlgDesign-1.1-0/AlgDesign/DESCRIPTION | 8 AlgDesign-1.1-0/AlgDesign/R/Utility.R | 256 ++++----- AlgDesign-1.1-0/AlgDesign/inst/doc/AlgDesign.Rnw |only AlgDesign-1.1-0/AlgDesign/inst/doc/AlgDesign.pdf |binary AlgDesign-1.1-0/AlgDesign/inst/doc/AlgDesignPaper.bib |only AlgDesign-1.1-0/AlgDesign/inst/doc/ConstrainedPlot.png |only AlgDesign-1.1-0/AlgDesign/man/Federov.Rd | 481 ++++++++--------- AlgDesign-1.1-0/AlgDesign/man/MonteOpt.Rd | 466 ++++++++-------- AlgDesign-1.1-0/AlgDesign/man/blockOpt.Rd | 5 10 files changed, 601 insertions(+), 615 deletions(-)
Author: Jonathan Harrington and others, IPS LMU Muenchen & IPDS CAU
Kiel
Title: Interface to the Emu Speech Database System
Description: Provides an interface to the Emu speech database system
and many special purpose functions for display and analysis of
speech data.
Diff between emu versions 4.1 dated 2009-09-08 and 4.2 dated 2009-11-23
DESCRIPTION | 8 ++++---- R/AAoptions.S | 16 ++++++++-------- R/emu.track.S | 38 ++++++++++++++++++++++++++++++-------- 3 files changed, 42 insertions(+), 20 deletions(-)
Author: Matthias Templ, Gerlinde Dinges, Alexander Kowarik, Bernhard
Meindl
Title: Teaching GUI - prototype
Description: Trainings-GUI
Diff between TGUITeaching versions 0.9.2 dated 2009-11-19 and 0.9.3 dated 2009-11-23
TGUITeaching-0.9.2/TGUITeaching/adminExercise.txt |only TGUITeaching-0.9.3/TGUITeaching/DESCRIPTION | 8 ++-- TGUITeaching-0.9.3/TGUITeaching/R/zzz.R | 40 ++++++++++++++-------- 3 files changed, 30 insertions(+), 18 deletions(-)
Author: Matthias Templ, Gerlinde Dinges, Alexander Kowarik, Bernhard
Meindl
Title: Teaching GUI - Core functionality
Description: Trainings-GUI
Diff between TGUICore versions 0.9.2 dated 2009-11-19 and 0.9.3 dated 2009-11-23
TGUICore-0.9.2/TGUICore/adminExercise.txt |only TGUICore-0.9.3/TGUICore/DESCRIPTION | 8 ++++---- TGUICore-0.9.3/TGUICore/R/ex_interactive_2_1.R | 10 +++++++--- TGUICore-0.9.3/TGUICore/R/zzz.R | 18 +++++++++++++----- 4 files changed, 24 insertions(+), 12 deletions(-)
Author: Kenneth Knoblauch and Laurence T. Maloney
Title: Maximum Likelihood Conjoint Measurement
Description: Conjoint measurement is a psychophysical procedure in
which stimulus pairs are presented that vary along 2 or more
dimensions and the observer is required to compare the stimuli
along one of them. This package contains functions to estimate
the contribution of the n scales to the judgment by a maximum
likelihood method under several hypotheses of how the
perceptual dimensions interact.
Diff between MLCM versions 0.0-6 dated 2009-10-05 and 0.0-7 dated 2009-11-23
DESCRIPTION | 8 ++++---- NAMESPACE | 2 ++ R/anova.mlcm.R | 22 ++++++++++++++++++++++ R/predict.mlcm.R |only inst/NEWS | 10 ++++++++++ inst/ToDo | 4 ---- man/anova.mlcm.Rd | 2 +- man/mlcm.Rd | 10 ++++------ man/predict.mlcm.Rd |only 9 files changed, 43 insertions(+), 15 deletions(-)
Author: Achim Zeileis, Gabor Grothendieck
Title: Z's ordered observations
Description: An S3 class with methods for totally ordered indexed
observations. It is particularly aimed at irregular time series
of numeric vectors/matrices and factors. zoo's key design goals
are independence of a particular index/date/time class and
consistency with ts and base R by providing methods to extend
standard generics.
Diff between zoo versions 1.6-1 dated 2009-11-19 and 1.6-2 dated 2009-11-23
DESCRIPTION | 8 ++++---- NEWS | 5 +++++ inst/doc/zoo-faq.Rnw | 2 +- inst/doc/zoo-faq.pdf | 10 +++++----- inst/doc/zoo-quickref.pdf | 14 +++++++------- inst/doc/zoo.pdf | 30 +++++++++++++++--------------- 6 files changed, 37 insertions(+), 32 deletions(-)
Author: Romain Francois
Title: Support for xterm256 escape sequences
Description: Support for xterm256 escape sequences, enabling R
functions to take advantage of foreground color, background
color, in capable terminals
Diff between xterm256 versions 0.0 dated 2009-04-20 and 0.1-2 dated 2009-11-23
DESCRIPTION | 13 ++++++------- NAMESPACE | 7 +++++-- NEWS |only R/highlight_renderer_xterm.R |only R/print.function.R |only R/style.R | 10 +++++++++- R/zzz.R | 12 ++++++------ man/print.function.Rd |only man/renderer_xterm.Rd |only man/style.Rd | 11 +++++++++-- man/xterm256-package.Rd | 4 ++-- 11 files changed, 37 insertions(+), 20 deletions(-)
Author: CHARLOTTE MAIA
Title: Object Oriented Statistical Programming
Description: A platform for, and collection of tools for, object
oriented statistical programming in R.
Diff between oosp versions 0.2.2 dated 2009-11-22 and 0.2.3 dated 2009-11-23
DESCRIPTION | 8 ++++---- inst/doc/oosp1.pdf |binary inst/doc/oosp1.rnw | 4 ++-- inst/doc/oosp2.pdf |binary inst/doc/oosp2.rnw | 4 ++-- inst/doc/oosp3.pdf |binary inst/doc/oosp3.rnw | 6 +++--- 7 files changed, 11 insertions(+), 11 deletions(-)
Author: Timur V. Elzhov, Katharine M. Mullen
Title: R interface to the Levenberg-Marquardt nonlinear least-squares
algorithm found in MINPACK
Description: Provides R interface to lmder and lmdif from the MINPACK
library, for solving nonlinear least-squares problems by a
modification of the Levenberg-Marquardt algorithm.
Diff between minpack.lm versions 1.1-1 dated 2008-05-25 and 1.1-3 dated 2009-11-23
minpack.lm-1.1-1/minpack.lm/R/zzz.R |only minpack.lm-1.1-3/minpack.lm/DESCRIPTION | 15 ++++++++++----- minpack.lm-1.1-3/minpack.lm/NAMESPACE | 1 + minpack.lm-1.1-3/minpack.lm/R/nls.lm.R | 3 ++- minpack.lm-1.1-3/minpack.lm/src/fcn_lmder.c | 6 ++++-- minpack.lm-1.1-3/minpack.lm/src/fcn_lmdif.c | 22 ++++++++++++---------- minpack.lm-1.1-3/minpack.lm/src/nls_lm.c | 12 +++++++++--- 7 files changed, 38 insertions(+), 21 deletions(-)
Author: S original by Venables & Ripley. R port by Brian Ripley
Title: Main Package of Venables and Ripley's MASS
Description: Functions and datasets to support Venables and Ripley,
'Modern Applied Statistics with S' (4th edition).
Diff between MASS versions 7.3-3 dated 2009-10-28 and 7.3-4 dated 2009-11-23
DESCRIPTION | 8 NAMESPACE | 1 R/glmmPQL.R | 3 R/polr.R | 37 ++++ R/rlm.R | 29 +-- inst/NEWS | 3 man/glmmPQL.Rd | 3 man/polr.Rd | 8 tests/Examples/MASS-Ex.Rout.save | 335 ++++++++++++++++++++------------------- 9 files changed, 246 insertions(+), 181 deletions(-)
Author: Angelos Markos
Title: A Tcl/Tk GUI for the functions in the ca package
Description: A Graphical User Interface (GUI) for computation and
visualization of simple, multiple and joint correspondence
analysis with the ca package.
Diff between caGUI versions 0.1-0 dated 2009-10-04 and 0.1-2 dated 2009-11-23
DESCRIPTION | 10 R/caGUI.r | 807 ++++++++++++++++++++++++++++++++++++++++++++++++----------- man/caGUI.Rd | 9 3 files changed, 671 insertions(+), 155 deletions(-)
Author: Andrew Gelman
Title: Data Analysis Using Regression and Multilevel/Hierarchical
Models
Description: R functions for processing lm, glm, mer and polr outputs.
Diff between arm versions 1.2-9.01 dated 2009-10-01 and 1.2-10 dated 2009-11-23
CHANGELOG | 4 ++++ DESCRIPTION | 8 +++----- NAMESPACE | 1 + man/invlogit.Rd | 6 ++++-- 4 files changed, 12 insertions(+), 7 deletions(-)
Author: Original code by many authors, notably Peter Rousseeuw and
Christophe Croux, see file 'Copyrights'; Valentin Todorov
Title: Basic Robust Statistics
Description: "Essential" Robust Statistics. The goal is to provide
tools allowing to analyze data with robust methods. This
includes regression methodology including model selections and
multivariate statistics where we strive to cover the book
"Robust Statistics, Theory and Methods" by Maronna, Martin and
Yohai; Wiley 2006.
Diff between robustbase versions 0.5-0 dated 2009-11-18 and 0.5-0-1 dated 2009-11-22
ChangeLog | 6 ++++++ DESCRIPTION | 8 ++++---- tests/mc-strict.R | 5 +++-- 3 files changed, 13 insertions(+), 6 deletions(-)
Author: Peter Langfelder
Title: Methods for detection of clusters in hierarchical clustering
dendrograms.
Description: Contains methods for detection of clusters in hierarchical
clustering dendrograms.
Diff between dynamicTreeCut versions 1.20 dated 2009-02-05 and 1.21 dated 2009-11-22
dynamicTreeCut-1.20/dynamicTreeCut/R/treeCut.R |only dynamicTreeCut-1.21/dynamicTreeCut/Changelog | 5 ++ dynamicTreeCut-1.21/dynamicTreeCut/DESCRIPTION | 23 ++++++---- dynamicTreeCut-1.21/dynamicTreeCut/R/TreeCut.R |only dynamicTreeCut-1.21/dynamicTreeCut/R/cutreeWrapper.R | 19 ++++++++ dynamicTreeCut-1.21/dynamicTreeCut/man/dynamicTreeCut-package.Rd | 5 +- dynamicTreeCut-1.21/dynamicTreeCut/man/merge2Clusters.Rd |only 7 files changed, 41 insertions(+), 11 deletions(-)
More information about dynamicTreeCut at CRAN
Permanent link
Author: Compiled by Adrian Trapletti
Title: Time series analysis and computational finance
Description: Package for time series analysis and computational finance
Diff between tseries versions 0.10-21 dated 2009-10-04 and 0.10-22 dated 2009-11-22
ChangeLog | 7 +++++++ DESCRIPTION | 8 ++++---- R/finance.R | 28 ++++++++++++++-------------- 3 files changed, 25 insertions(+), 18 deletions(-)
Author: S original by Trevor Hastie & Robert Tibshirani. R port by
Friedrich Leisch, Kurt Hornik and Brian D. Ripley.
Title: Mixture and flexible discriminant analysis
Description: Mixture and flexible discriminant analysis, multivariate
additive regression splines (MARS), BRUTO, ...
Diff between mda versions 0.3-4 dated 2009-01-04 and 0.3-5 dated 2009-11-22
mda-0.3-4/mda/R/zzz.R |only mda-0.3-5/mda/ChangeLog | 14 ++++++++++++++ mda-0.3-5/mda/DESCRIPTION | 12 +++++++----- mda-0.3-5/mda/R/mda.R | 2 -- mda-0.3-5/mda/man/bruto.Rd | 2 +- mda-0.3-5/mda/man/fda.Rd | 4 ++-- mda-0.3-5/mda/man/mars.Rd | 2 +- mda-0.3-5/mda/man/mda.Rd | 6 +++--- mda-0.3-5/mda/man/predict.fda.Rd | 2 +- mda-0.3-5/mda/man/predict.mda.Rd | 2 +- 10 files changed, 30 insertions(+), 16 deletions(-)
Author: Kurt Hornik, with contributions from Walter Boehm
Title: Cluster ensembles
Description: CLUster Ensembles
Diff between clue versions 0.3-32 dated 2009-10-18 and 0.3-33 dated 2009-11-22
DESCRIPTION | 8 ++++---- R/AAA.R | 5 +++++ R/consensus.R | 3 --- R/medoid.R | 20 ++++++++++---------- R/partition.R | 6 +++--- R/pclust.R | 46 +++++++++++++++++++++++----------------------- R/predict.R | 2 +- R/registration.R | 22 +++++++++++----------- R/sumt.R | 9 ++++----- R/ultrametric.R | 2 +- R/utilities.R | 12 +++++++++--- inst/doc/clue.pdf |binary 12 files changed, 71 insertions(+), 64 deletions(-)
Author: Friedrich Leisch and Andreas Weingessel and Kurt Hornik
Title: Generation of Artificial Binary Data
Description: Generation of correlated artificial binary data.
Diff between bindata versions 0.9-16 dated 2009-10-08 and 0.9-17 dated 2009-11-22
bindata-0.9-16/bindata/R/zzz.R |only bindata-0.9-17/bindata/DESCRIPTION | 8 ++++---- 2 files changed, 4 insertions(+), 4 deletions(-)
Author: Robert B. Gramacy
Title: Bayesian treed Gaussian process models
Description: Bayesian nonstationary, semiparametric nonlinear
regression and design by treed Gaussian processes with jumps to
the limiting linear model (LLM). Special cases also
implemented include Bayesian linear models, CART, treed linear
models, stationary separable and isotropic Gaussian processes.
Provides 1-d and 2-d plotting functions (with projection and
slice capabilities) and tree drawing, designed for
visualization of tgp-class output. Sensitivity analysis and
multi-resolution models are supported. Sequential experimental
design and adaptive sampling functions are also provided,
including ALM, ALC, and expected improvement. The latter
supports derivative-free optimization of noisy black-box
functions.
Diff between tgp versions 2.2-3 dated 2009-07-26 and 2.2-4 dated 2009-11-22
tgp-2.2-3/tgp/tgp_2.2-2.tar.gz |only tgp-2.2-4/tgp/._ChangeLog |binary tgp-2.2-4/tgp/._DESCRIPTION |binary tgp-2.2-4/tgp/._INDEX |binary tgp-2.2-4/tgp/._LICENSE |binary tgp-2.2-4/tgp/._R |binary tgp-2.2-4/tgp/._README |binary tgp-2.2-4/tgp/._data |binary tgp-2.2-4/tgp/._demo |binary tgp-2.2-4/tgp/._inst |binary tgp-2.2-4/tgp/._man |binary tgp-2.2-4/tgp/._src |binary tgp-2.2-4/tgp/._tgp_2.2-2.tar.gz |only tgp-2.2-4/tgp/ChangeLog | 14 ++++++++++++++ tgp-2.2-4/tgp/DESCRIPTION | 6 +++--- tgp-2.2-4/tgp/R/check.matrix.R | 4 ++-- tgp-2.2-4/tgp/R/predict.tgp.R | 2 +- tgp-2.2-4/tgp/R/tgp.R | 13 +++++++++++-- tgp-2.2-4/tgp/data/._exp2d.rda |binary tgp-2.2-4/tgp/inst/._.DS_Store |binary tgp-2.2-4/tgp/inst/._doc |binary tgp-2.2-4/tgp/man/interp.loess.Rd | 4 ++-- tgp-2.2-4/tgp/man/optim.tgp.Rd | 2 +- tgp-2.2-4/tgp/man/plot.tgp.Rd | 6 +++--- tgp-2.2-4/tgp/man/tgp.default.params.Rd | 8 +++++--- 25 files changed, 42 insertions(+), 17 deletions(-)
Author: Alberto Cassese, Marta Blangiardo
Title: Synthesizing List of Differentially Expressed Features
Description: The package performs two tests to evaluate if the
experiments are associated and returns a list of interesting
features common to all the experiments.
Diff between sdef versions 1.2 dated 2009-09-04 and 1.3 dated 2009-11-22
sdef-1.2/sdef/R/extractGenes.R.R |only sdef-1.2/sdef/R/extractGenes.T.R |only sdef-1.2/sdef/man/extractGenes.R.Rd |only sdef-1.2/sdef/man/extractGenes.T.Rd |only sdef-1.3/sdef/DESCRIPTION | 8 - sdef-1.3/sdef/R/Tmc.R | 25 +-- sdef-1.3/sdef/R/baymod.R | 35 ++--- sdef-1.3/sdef/R/createTable.R | 89 +++++++++++-- sdef-1.3/sdef/R/extractFeatures.R.R |only sdef-1.3/sdef/R/extractFeatures.T.R |only sdef-1.3/sdef/R/ratio.R | 48 +++---- sdef-1.3/sdef/R/sdef-internal.R |only sdef-1.3/sdef/data |only sdef-1.3/sdef/man/Liver.Muscle.Rd |only sdef-1.3/sdef/man/Tmc.Rd | 109 +--------------- sdef-1.3/sdef/man/baymod.Rd | 186 --------------------------- sdef-1.3/sdef/man/createTable.Rd | 78 +---------- sdef-1.3/sdef/man/extractFeatures.R.Rd |only sdef-1.3/sdef/man/extractFeatures.T.Rd |only sdef-1.3/sdef/man/ratio.Rd | 222 +-------------------------------- sdef-1.3/sdef/man/sdef-package.Rd | 6 sdef-1.3/sdef/man/simulation.Rd | 77 ----------- sdef-1.3/sdef/man/simulation.indep.Rd | 53 ------- 23 files changed, 172 insertions(+), 764 deletions(-)
Author: Romain Francois
Title: Detailed R source code parser
Description: detailed source code parser, based on the standard R
parser but organizing the information differently
Diff between parser versions 0.0-3 dated 2009-07-30 and 0.0-5 dated 2009-11-22
DESCRIPTION | 14 ++++++-------- NEWS |only R/parser.R | 36 ++++++++++++++++++++++++++++++++---- man/parser-package.Rd | 4 ++-- 4 files changed, 40 insertions(+), 14 deletions(-)
Author: CHARLOTTE MAIA
Title: Object Oriented Statistical Programming
Description: A platform for, and collection of tools for, object
oriented statistical programming in R.
Diff between oosp versions 0.1.0 dated 2009-08-20 and 0.2.2 dated 2009-11-22
oosp-0.1.0/oosp/R/component.r |only oosp-0.1.0/oosp/R/loop.r |only oosp-0.1.0/oosp/R/oosp.r |only oosp-0.1.0/oosp/man/equals.compenv.Rd |only oosp-0.1.0/oosp/man/is.hashed.Rd |only oosp-0.1.0/oosp/man/loop.Rd |only oosp-0.1.0/oosp/man/oospaslist.compenv.Rd |only oosp-0.1.0/oosp/man/oospbridges.Rd |only oosp-0.1.0/oosp/man/oospdefaults.Rd |only oosp-0.1.0/oosp/man/oospgenerics.Rd |only oosp-0.1.0/oosp/man/oospprint.compenv.Rd |only oosp-0.2.2/oosp/DESCRIPTION | 17 ++---- oosp-0.2.2/oosp/R/class.r |only oosp-0.2.2/oosp/R/compenv.r | 82 +++++++++--------------------- oosp-0.2.2/oosp/R/function.r | 30 +++------- oosp-0.2.2/oosp/R/generic.r | 28 ++++++++-- oosp-0.2.2/oosp/R/init.r |only oosp-0.2.2/oosp/R/method.r |only oosp-0.2.2/oosp/R/misc.r |only oosp-0.2.2/oosp/R/object.r | 39 +++++++++++++- oosp-0.2.2/oosp/R/pointer.r | 57 ++++++-------------- oosp-0.2.2/oosp/inst/doc/Makefile |only oosp-0.2.2/oosp/inst/doc/maia.sty |only oosp-0.2.2/oosp/inst/doc/oosp1.pdf |only oosp-0.2.2/oosp/inst/doc/oosp1.rnw |only oosp-0.2.2/oosp/inst/doc/oosp2.pdf |only oosp-0.2.2/oosp/inst/doc/oosp2.rnw |only oosp-0.2.2/oosp/inst/doc/oosp3.pdf |only oosp-0.2.2/oosp/inst/doc/oosp3.rnw |only oosp-0.2.2/oosp/man/as.r.default.Rd |only oosp-0.2.2/oosp/man/clone.compenv.Rd | 9 +-- oosp-0.2.2/oosp/man/collection.Rd |only oosp-0.2.2/oosp/man/compenv.Rd | 26 +++++---- oosp-0.2.2/oosp/man/component.Rd | 10 +-- oosp-0.2.2/oosp/man/datafile.Rd |only oosp-0.2.2/oosp/man/extend.Rd | 4 - oosp-0.2.2/oosp/man/freemethod.Rd |only oosp-0.2.2/oosp/man/function.Rd | 11 +--- oosp-0.2.2/oosp/man/is.cleancall.Rd |only oosp-0.2.2/oosp/man/list.to.compenv.Rd |only oosp-0.2.2/oosp/man/masks.Rd |only oosp-0.2.2/oosp/man/misc.Rd |only oosp-0.2.2/oosp/man/mobject.Rd |only oosp-0.2.2/oosp/man/newgenerics.Rd | 30 +++++----- oosp-0.2.2/oosp/man/object.Rd | 10 +-- oosp-0.2.2/oosp/man/pointer.Rd | 24 ++++---- oosp-0.2.2/oosp/man/preview.Rd |only oosp-0.2.2/oosp/man/print.compenv.Rd |only oosp-0.2.2/oosp/man/trim.Rd |only 49 files changed, 186 insertions(+), 191 deletions(-)
Author: Vito M. R. Muggeo
Title: Modelling temperature effects using time series data
Description: Fits a Constrained Segmented Distributed Lag regression
model to epidemiological time series of mortality, temperature,
and other confounders.
Diff between modTempEff versions 1.1 dated 2009-09-20 and 1.3 dated 2009-11-22
modTempEff-1.1/modTempEff/R/p.control.R |only modTempEff-1.1/modTempEff/R/temp.control.R |only modTempEff-1.1/modTempEff/man/p.control.Rd |only modTempEff-1.1/modTempEff/man/temp.control.Rd |only modTempEff-1.3/modTempEff/DESCRIPTION | 8 modTempEff-1.3/modTempEff/NAMESPACE | 8 modTempEff-1.3/modTempEff/R/anova.modTempEff.R |only modTempEff-1.3/modTempEff/R/coef.modTempEff.r |only modTempEff-1.3/modTempEff/R/csdl.R |only modTempEff-1.3/modTempEff/R/plot.modTempEff.R | 15 + modTempEff-1.3/modTempEff/R/print.modTempEff.R | 7 modTempEff-1.3/modTempEff/R/seas.R |only modTempEff-1.3/modTempEff/R/summary.modTempEff.R | 54 ++-- modTempEff-1.3/modTempEff/R/tempeff.R | 249 +++++++++++--------- modTempEff-1.3/modTempEff/R/tempeff.fit.R | 17 - modTempEff-1.3/modTempEff/man/anova.modTempEff.Rd |only modTempEff-1.3/modTempEff/man/coef.modTempEff.Rd |only modTempEff-1.3/modTempEff/man/csdl.Rd |only modTempEff-1.3/modTempEff/man/fit.control.Rd | 4 modTempEff-1.3/modTempEff/man/modTempEff-package.Rd | 24 + modTempEff-1.3/modTempEff/man/plot.modTempEff.Rd | 31 +- modTempEff-1.3/modTempEff/man/seas.Rd |only modTempEff-1.3/modTempEff/man/summary.modTempEff.Rd | 14 - modTempEff-1.3/modTempEff/man/tempeff.Rd | 78 ++++-- modTempEff-1.3/modTempEff/man/tempeff.fit.Rd | 8 25 files changed, 310 insertions(+), 207 deletions(-)
Author: Pavel N. Krivitsky
Title: Latent position and cluster models for statistical networks
Description: A package to fit and simulate latent position and cluster
models for statistical networks.
Diff between latentnet versions 2.2-2 dated 2009-10-28 and 2.2-3 dated 2009-11-22
ChangeLog | 3 ++ DESCRIPTION | 8 +++---- R/ergmm.probs.R | 2 - man/families.ergmm.Rd | 12 +++++----- man/gof.ergmm.Rd | 3 +- man/mcmc.diagnostics.ergmm.Rd | 3 +- man/plot.ergmm.Rd | 48 ++++++++++++++++++++---------------------- man/simulate.ergmm.Rd | 3 +- man/summary.ergmm.Rd | 3 +- tests/missing.R |only 10 files changed, 45 insertions(+), 40 deletions(-)
Author: Gabor Csardi
Title: Network analysis and visualization
Description: Routines for simple graphs and network analysis. igraph
can handle large graphs very well and provides functions for
generating random and regular graphs, graph visualization,
centrality indices and much more.
Diff between igraph versions 0.5.2-2 dated 2009-05-08 and 0.5.3 dated 2009-11-22
DESCRIPTION | 12 R/conversion.R | 15 R/socnet.R | 45 R/structural.properties.R | 43 R/structure.generators.R | 20 configure | 3109 ++++++++++++++++++++++---------------- man/aaa-igraph-package.Rd | 2 man/community.edge.betweenness.Rd | 2 man/constraint.Rd | 3 man/diameter.Rd | 20 man/graph.data.frame.Rd | 10 man/graph.laplacian.Rd | 3 man/graphNEL.Rd | 4 man/leading.eigenvector.Rd | 2 man/plot.common.Rd | 10 man/preference.game.Rd | 2 man/read.graph.Rd | 11 src/Makevars | 2 src/Makevars.win | 2 src/attributes.h | 4 src/bipartite.c | 2 src/bliss.cc | 4 src/bliss_bignum.hh | 8 src/bliss_defs.hh | 8 src/bliss_eqrefhash.cc | 4 src/bliss_eqrefhash.hh | 8 src/bliss_graph.cc | 4 src/bliss_graph.hh | 8 src/bliss_heap.cc | 4 src/bliss_heap.hh | 8 src/bliss_kqueue.hh | 8 src/bliss_kstack.hh | 8 src/bliss_orbit.cc | 4 src/bliss_orbit.hh | 8 src/bliss_partition.cc | 4 src/bliss_partition.hh | 8 src/bliss_timer.cc | 4 src/bliss_timer.hh | 8 src/bliss_utils.cc | 4 src/bliss_utils.hh | 8 src/centrality.c | 12 src/dqueue.pmt | 2 src/fast_community.c | 5 src/flow.c | 3 src/igraph.h | 8 src/pottsmodel_2.cpp | 9 src/rinterface.c | 32 src/structural_properties.c | 161 + src/vector.pmt | 6 src/vector_ptr.c | 18 src/walktrap.cpp | 6 src/walktrap_communities.cpp | 6 src/walktrap_communities.h | 6 src/walktrap_graph.cpp | 30 src/walktrap_graph.h | 5 src/walktrap_heap.cpp | 6 src/walktrap_heap.h | 6 57 files changed, 2410 insertions(+), 1354 deletions(-)
Author: Ulrike Groemping
Title: Inequality constrained inference in linear normal situations
Description: This package implements parameter estimation in normal
(linear) models under linear equality and inequality
constraints and implements normal likelihood ratio tests
involving inequality-constrained hypotheses. For
inequality-constrained linear models, averaging over R-squared
for different orderings of regressors is also included.
Diff between ic.infer versions 1.0-6 dated 2008-09-21 and 1.1 dated 2009-11-22
ic.infer-1.0-6/ic.infer/inst/doc |only ic.infer-1.1/ic.infer/DESCRIPTION | 33 +++++++++++++++--------- ic.infer-1.1/ic.infer/NAMESPACE | 5 ++- ic.infer-1.1/ic.infer/R/aaa.R |only ic.infer-1.1/ic.infer/R/contr.diff.R |only ic.infer-1.1/ic.infer/R/make.mon.ui.R |only ic.infer-1.1/ic.infer/data |only ic.infer-1.1/ic.infer/inst/NEWS |only ic.infer-1.1/ic.infer/man/bodyfat.Rd |only ic.infer-1.1/ic.infer/man/contr.diff.Rd |only ic.infer-1.1/ic.infer/man/grades.Rd |only ic.infer-1.1/ic.infer/man/ic.est.Rd | 7 +++-- ic.infer-1.1/ic.infer/man/ic.infer-package.rd | 19 ++++++++++++- ic.infer-1.1/ic.infer/man/ic.test.rd | 2 - ic.infer-1.1/ic.infer/man/ic.weights.rd | 2 - ic.infer-1.1/ic.infer/man/internal.functions.rd | 2 - ic.infer-1.1/ic.infer/man/make.mon.ui.rd |only ic.infer-1.1/ic.infer/man/or.relimp.rd | 2 - ic.infer-1.1/ic.infer/man/orlm.rd | 9 ++++-- 19 files changed, 56 insertions(+), 25 deletions(-)
Author: Jing Hua Zhao and colleagues with inputs from Kurt Hornik and
Brian Ripley
Title: Genetic analysis package
Description: It is designed as an integrated package for genetic data
analysis of both population and family data. Currently, it
contains functions for sample size calculations of both
population-based and family-based designs, classic twin models,
probability of familial disease aggregation, kinship
calculation, some statistics in linkage analysis, and
association analysis involving one or more genetic markers
including haplotype analysis with or without environmental
covariates.
Diff between gap versions 1.0-20 dated 2009-08-26 and 1.0-21 dated 2009-11-22
ChangeLog | 10 +++++++- DESCRIPTION | 8 +++--- NAMESPACE | 4 +-- R/abc.R |only R/mhtplot.R | 34 ++++++++++++++--------------- R/qqunif.R | 58 +++++++++++++++++++++++++++++++++++++++++++------- R/read.ms.output.R |only inst/doc/gap.pdf |binary inst/doc/ms |only man/abc.Rd |only man/gap-package.Rd | 4 ++- man/mhtplot.Rd | 8 ++++++ man/pbsize2.Rd | 4 +-- man/qqfun.Rd | 3 -- man/qqunif.Rd | 19 ++++++++++++---- man/read.ms.output.Rd |only 16 files changed, 109 insertions(+), 43 deletions(-)
Author: Mikis Stasinopoulos
Title: Generating and fitting truncated (gamlss.family) distributions
Description: This is an add on package to GAMLSS. The purpose of this
package is to allow users to defined truncated distributions in
GAMLSS models. The main function gen.trun() generates truncated
version of an existing GAMLSS family distribution.
Diff between gamlss.tr versions 3.0-1 dated 2009-10-14 and 3.1-0 dated 2009-11-22
DESCRIPTION | 8 ++++---- R/trun.d.R | 30 +++++++++++++++--------------- man/trun.d.Rd | 22 +++++++++++----------- 3 files changed, 30 insertions(+), 30 deletions(-)
Author: Mikis Stasinopoulos
Title: Fitting non linear parametric GAMLSS models
Description: This is an add on package to GAMLSS. It allows one extra
method for fitting GAMLSS models. The main function nlgamlss()
can fit any parametric (up to four parameter) GAMLSS
distribution.
Diff between gamlss.nl versions 3.0-1 dated 2009-10-14 and 3.1-0 dated 2009-11-22
DESCRIPTION | 8 ++++---- 1 file changed, 4 insertions(+), 4 deletions(-)
Author: Mikis Stasinopoulos
Title: A GAMLSS add on package for fitting mixture distributions
Description: The main purpose of this package is to allow fitting of
mixture distributions with GAMLSS models.
Diff between gamlss.mx versions 3.0-1 dated 2009-10-14 and 3.1-0 dated 2009-11-22
DESCRIPTION | 8 ++++---- 1 file changed, 4 insertions(+), 4 deletions(-)
Author: Mikis Stasinopoulos
Title: Distributions to be used for GAMLSS modelling.
Description: This package contains the distributions for GAMLSS
modelling.
Diff between gamlss.dist versions 3.0-1 dated 2009-10-14 and 3.1-0 dated 2009-11-22
DESCRIPTION | 8 ++++---- man/GB1.Rd | 6 +++--- man/GB2.Rd | 4 +++- 3 files changed, 10 insertions(+), 8 deletions(-)
Author: Mikis Stasinopoulos
Title: GAMLSS Data.
Description: Data for GAMLSS models.
Diff between gamlss.data versions 3.0-1 dated 2009-10-14 and 3.1-0 dated 2009-11-22
DESCRIPTION | 8 ++++---- data/acidity.r |only data/dbbmi.r |only data/tse.r |only data/vas5.r |only man/dbbmi.Rd |only man/tse.Rd |only man/vas5.Rd |only 8 files changed, 4 insertions(+), 4 deletions(-)
Author: Mikis Stasinopoulos
Title: Fitting an interval response variable using gamlss.family
distributions
Description: This is an add on package to GAMLSS. The purpose of this
package is to allow users to fit interval response variables in
GAMLSS models. The main function gen.cens() generates a
censored version of an existing GAMLSS family distribution.
Diff between gamlss.cens versions 3.0.1 dated 2009-10-14 and 3.1.0 dated 2009-11-22
DESCRIPTION | 8 ++++---- 1 file changed, 4 insertions(+), 4 deletions(-)
Author: Mikis Stasinopoulos
Title: Generalized Additive Models for Location Scale and Shape.
Description: The library for fitting GAMLSS models.
Diff between gamlss versions 3.0-1 dated 2009-10-14 and 3.1-0 dated 2009-11-22
DESCRIPTION | 8 ++++---- NAMESPACE | 3 ++- R/cy.R | 2 +- R/edf.R |only R/pb.R | 2 +- inst/doc/NEWS.txt | 19 +++++++++++++++++++ man/edf.Rd |only 7 files changed, 27 insertions(+), 7 deletions(-)
Author: S�ren H�jsgaard
Title: Graphical Independence Networks
Description: A package for probability propagation in graphical
independence networks, also known as probabilistic expert
systems (which includes Bayesian networks as a special case).
Diff between gRain versions 0.8.1 dated 2009-08-01 and 0.8.2 dated 2009-11-22
gRain-0.8.1/gRain/R/asxxx.R |only gRain-0.8.1/gRain/R/compile-grain2.R |only gRain-0.8.1/gRain/R/grain-main2.R |only gRain-0.8.2/gRain/ChangeLog | 6 ++ gRain-0.8.2/gRain/DESCRIPTION | 6 +- gRain-0.8.2/gRain/R/Finding.R | 60 ++++++++------------ gRain-0.8.2/gRain/R/SimulateArray.R | 8 +- gRain-0.8.2/gRain/R/compile-grain.R |only gRain-0.8.2/gRain/R/compileCPT.R | 34 ++++------- gRain-0.8.2/gRain/R/cptable.R | 85 +++-------------------------- gRain-0.8.2/gRain/R/display.R | 2 gRain-0.8.2/gRain/R/extractCPT.R | 19 ++++-- gRain-0.8.2/gRain/R/grain-main.R |only gRain-0.8.2/gRain/R/infoPrint.R |only gRain-0.8.2/gRain/R/loadSaveHuginNet.R | 33 ++++++----- gRain-0.8.2/gRain/R/methods.R | 14 ++-- gRain-0.8.2/gRain/R/potentialList.R | 28 ++------- gRain-0.8.2/gRain/R/propagate.R | 52 ++++------------- gRain-0.8.2/gRain/R/querygrain.R | 6 +- gRain-0.8.2/gRain/R/summary.R | 22 ++----- gRain-0.8.2/gRain/inst/doc/gRain-intro.pdf |binary gRain-0.8.2/gRain/man/compile.grain.Rd | 4 - gRain-0.8.2/gRain/man/compileCPT.Rd | 8 +- gRain-0.8.2/gRain/man/extractCPT.Rd | 4 - gRain-0.8.2/gRain/man/grain.Rd | 22 +++---- gRain-0.8.2/gRain/man/internal-gRain.Rd | 4 - gRain-0.8.2/gRain/man/loadSaveHuginNet.Rd | 10 +-- gRain-0.8.2/gRain/man/propagate.grain.Rd | 4 - gRain-0.8.2/gRain/man/querygrain.Rd | 3 - gRain-0.8.2/gRain/man/simulate.Rd | 2 30 files changed, 163 insertions(+), 273 deletions(-)
Author: Joseph Richards
Title: Diffusion map
Description: Implements diffusion map method of data parametrization,
including creation and visualization of diffusion map,
clustering with diffusion K-means and regression using adaptive
regression model.
Diff between diffusionMap versions 0.0-2 dated 2009-05-10 and 1.0-0 dated 2009-11-22
DESCRIPTION | 22 +++++++++++----------- NAMESPACE | 2 +- R/adapreg.R |only R/adapreg.m.R |only R/diffuse.R | 46 ++++++++++++++++++++++++++++++---------------- R/diffusionKmeans.R | 2 +- R/epsilonCompute.R | 3 ++- R/nystrom.R |only man/adapreg.Rd |only man/adapreg.m.Rd |only man/diffuse.Rd | 34 ++++++++++++++++++++++++---------- man/diffusionKmeans.Rd | 32 +++++++++++++++++++++++--------- man/distortionMin.Rd | 1 + man/epsilonCompute.Rd | 6 +++--- man/nystrom.Rd |only 15 files changed, 96 insertions(+), 52 deletions(-)
Author: Venkatraman E. Seshan
Title: Clinical Trial Design and Data Analysis Functions
Description: Utilities to make your clinical collaborations easier if
not fun.
Diff between clinfun versions 0.8.6 dated 2009-11-19 and 0.8.7 dated 2009-11-22
CHANGES | 4 ++++ DESCRIPTION | 6 +++--- R/pselect.R | 6 ++++-- 3 files changed, 11 insertions(+), 5 deletions(-)
Author: Ulrike Groemping
Title: R Commander Plugin for (industrial) Design of Experiments
Description: WARNING: This package is currently in beta status! The
package provides a platform-independent GUI for design of
experiments. It is implemented as a plugin to the R-Commander,
which is a more general graphical user interface for statistics
in R based on tcl/tk. DoE functionality can be accessed through
the menu Design that is added to the R-Commander menus.
Diff between RcmdrPlugin.DoE versions 0.6-6 dated 2009-10-26 and 0.6-7 dated 2009-11-22
DESCRIPTION | 8 ++++---- R/Menu.FrF2level.R | 2 +- R/Menu.bbd.r | 2 +- R/Menu.ccd.r | 2 +- R/Menu.fac.R | 2 +- R/Menu.lhs.R | 2 +- R/Menu.oa.R | 2 +- R/Menu.pb2level.R | 2 +- inst/NEWS | 6 ++++++ man/Menu.FrF2levelTabEstimable.Rd | 17 +++++++++++++++-- 10 files changed, 32 insertions(+), 13 deletions(-)
More information about RcmdrPlugin.DoE at CRAN
Permanent link
Author: Douglas Bates
Title: Sparse and Dense Matrix Classes and Methods
Description: Classes and methods for dense and sparse matrices and
operations on them using Lapack and SuiteSparse.
Diff between Matrix versions 0.999375-31 dated 2009-10-08 and 0.999375-32 dated 2009-11-22
ChangeLog | 97 + DESCRIPTION | 10 Done | 12 NAMESPACE | 1 R/AllClass.R | 51 R/Auxiliaries.R | 87 - R/Csparse.R | 10 R/Ops.R | 191 +- R/Tsparse.R | 43 R/abIndex.R |only R/ddenseMatrix.R | 2 R/dgCMatrix.R | 8 R/diagMatrix.R | 16 R/dspMatrix.R | 8 R/dsparseMatrix.R | 2 R/dsyMatrix.R | 14 R/dtpMatrix.R | 24 R/lsparseMatrix.R | 17 R/not.R | 6 R/products.R | 104 + R/sparseMatrix.R | 65 R/sparseVector.R | 92 - TODO | 18 data/CAex.R | 2 data/KNex.R | 2 data/USCounties.R | 2 inst/doc/Comparisons.pdf |binary inst/doc/Design-issues.pdf |binary inst/doc/Intro2Matrix.pdf | 3707 ++++++++++++++++++++++++++------------------- inst/doc/Introduction.pdf |binary inst/doc/sparseModels.pdf |binary inst/test-tools.R | 59 man/Matrix-class.Rd | 2 man/TsparseMatrix-class.Rd | 3 man/abIndex-class.Rd |only man/dMatrix-class.Rd | 8 man/dgCMatrix-class.Rd | 2 man/lu.Rd | 16 man/nMatrix-class.Rd | 1 man/printSpMatrix.Rd | 4 man/rleDiff-class.Rd |only man/sparseVector-class.Rd | 36 src/Csparse.c | 18 src/Mutils.c | 1 src/abIndex.c |only src/abIndex.h |only src/chm_common.c | 116 - src/dgCMatrix.c | 21 src/dgCMatrix.h | 2 src/dgeMatrix.c | 17 src/init.c | 8 src/scripts/SOURCES_C.mkf | 3 tests/Simple.R | 59 tests/abIndex-tsts.R |only tests/bind.Rout.save | 19 tests/group-methods.R | 12 tests/indexing.R | 12 tests/indexing.Rout.save | 80 tests/matprod.R | 15 tests/other-pkgs.R | 10 60 files changed, 3148 insertions(+), 1967 deletions(-)
Author: Michael Friendly, with contributions by Stephane Dray, Hadley
Wickham
Title: Data sets from the history of statistics and data visualization
Description: The HistData package provides a collection of small data
sets that are interesting and important in the history of
statistics and data visualization. The goal of the package is
to make these available, both for instructional use and for
historical research. Some of these present interesting
challenges for graphics or analysis in R.
Diff between HistData versions 0.6-4 dated 2009-11-13 and 0.6-5 dated 2009-11-22
DESCRIPTION | 10 +++++----- data/Dactyl.RData |only data/Fingerprints.RData |only data/Pyx.RData |only inst/ChangeLog | 10 ++++++++++ man/Arbuthnot.Rd | 6 ++++-- man/Dactyl.Rd |only man/DrinksWages.Rd | 5 +++-- man/Fingerprints.Rd |only man/HistData-package.Rd | 4 ++-- man/Jevons.Rd | 22 ++++++++++++++++++++++ man/Nightingale.Rd | 4 ++-- man/Pyx.Rd |only 13 files changed, 48 insertions(+), 13 deletions(-)
Author: Bendix Carstensen, Martyn Plummer, Esa Laara, Michael Hills et.
al.
Title: A package for statistical analysis in epidemiology.
Description: Functions for demographic and epidemiological analysis in
the Lexis diagram, i.e. register and cohort follow-up data,
including interval censored data and representation of
multistate data. Also some useful functions for tabulation and
plotting. Contains some epidemiological datasets.
Diff between Epi versions 1.1.7 dated 2009-09-30 and 1.1.9 dated 2009-11-22
CHANGES | 14 ++ DESCRIPTION | 10 - NAMESPACE | 3 R/apc.fit.R | 27 ++-- R/lexis.R | 37 ++++-- data/occup.R |only inst/doc/Follow-up.pdf | 270 ++++++++++++++++++++++++------------------------- inst/doc/Rplots.pdf | 30 ++--- man/occup.Rd |only man/plot.Lexis.Rd | 28 ++++- 10 files changed, 238 insertions(+), 181 deletions(-)
Author: Tom Price
Title: Time-frequency analysis of cycling cell luminescence data
Description: waveclock is an R function designed to assess the period
and amplitude of cycling cell luminescence data. The function
reconstructs the modal frequencies from a continuous wavelet
decomposition of the luminescence data using the 'crazy
climbers' algorithm described in "Practical Time-Frequency
Analysis: Gabor and Wavelet Transforms with an Implementation
in S", by Rene Carmona, Wen L. Hwang and Bruno Torresani,
Academic Press, 1998.
Diff between waveclock versions 1.0-3.1 dated 2009-02-23 and 1.0-4 dated 2009-11-20
CHANGES | 42 +++-- DESCRIPTION | 37 ++-- man/waveclock.Rd | 384 +++++++++++++++++++++++++------------------------- man/waveclock.auto.Rd | 62 ++++---- 4 files changed, 268 insertions(+), 257 deletions(-)
Author: Tom Price
Title: Titration analysis for mass spectrometry data
Description: GUI to analyze mass spectrometric data on the relative
abundance of two substances from a titration series.
Diff between titan versions 1.0-15.1 dated 2009-02-23 and 1.0-16 dated 2009-11-20
Changes | 19 +- DESCRIPTION | 28 ++- man/hypoxia.Rd | 64 ++++---- man/titan.Rd | 424 ++++++++++++++++++++++++++++----------------------------- 4 files changed, 270 insertions(+), 265 deletions(-)
Author: Edzer J. Pebesma
Title: classes and methods for spatial data
Description: A package that provides classes and methods for spatial
data. The classes document where the spatial location
information resides, for 2D or 3D data. Utility functions are
provided, e.g. for plotting data as maps, spatial selection, as
well as methods for retrieving coordinates, for subsetting,
print, summary, etc.
Diff between sp versions 0.9-44 dated 2009-09-18 and 0.9-47 dated 2009-11-20
.Rbuildindex.19095 |only ChangeLog | 59 DESCRIPTION | 10 INDEX | 4 NAMESPACE | 12 R/Spatial-methods.R | 5 R/SpatialLines-methods.R | 4 R/SpatialLinesDataFrame-methods.R | 4 R/SpatialPoints-methods.R | 5 R/SpatialPointsDataFrame-methods.R | 8 R/SpatialPolygons-methods.R | 5 R/SpatialPolygonsDataFrame-methods.R | 11 R/chfids.R |only R/flipSGDF.R |only R/image.R | 6 R/spplot.R | 14 inst/CITATION | 12 inst/ChangeLog | 59 inst/doc/sp.pdf | 3711 +++++++++++++++++------------------ man/bubble.Rd | 2 man/coordinates.Rd | 3 man/flip.Rd |only man/gridded-methods.Rd | 2 man/image.Rd | 3 man/spChFIDs-methods.Rd |only man/stack.Rd | 5 rlabs |only 27 files changed, 2043 insertions(+), 1901 deletions(-)
Author: S original by Berwin A. Turlach
Title: Functions to solve Quadratic Programming Problems.
Description: This package contains routines and documentation for
solving quadratic programming problems.
Diff between quadprog versions 1.4-11 dated 2007-07-13 and 1.4-12 dated 2009-11-20
ChangeLog | 8 ++ DESCRIPTION | 14 ++-- R/quadprog.R | 2 README | 18 ----- man/solve.QP.Rd | 83 ++++++++++++------------- man/solve.QP.compact.Rd | 159 ++++++++++++++++++++++++------------------------ 6 files changed, 140 insertions(+), 144 deletions(-)
Author: Tom Price
Title: Microarray CGH analysis using the Smith-Waterman algorithm
Description: Functions to analyze microarray comparative genome
hybridization data using the Smith-Waterman algorithm
Diff between cgh versions 1.0-6.1 dated 2009-02-23 and 1.0-7 dated 2009-11-20
CHANGES | 54 ++++++++++++++++-------------- DESCRIPTION | 27 ++++++++------- man/sw.perm.test.Rd | 91 +++++++++++++++++++++++++--------------------------- src/sw.c | 2 - 4 files changed, 90 insertions(+), 84 deletions(-)
Author: CHARLOTTE MAIA
Title: Random Time Variables
Description: An R package for conveniently representing, manipulating
and visualising realisations of random time variables. This
package is pending a major rewrite.
Diff between rtv versions 0.3.0 dated 2009-08-20 and 0.3.1 dated 2009-11-20
DESCRIPTION | 15 ++++++++------- inst/doc/rtv.pdf |binary inst/doc/rtv.rnw | 13 +++++++++---- 3 files changed, 17 insertions(+), 11 deletions(-)
Author: CHARLOTTE MAIA
Title: Random Return Variables
Description: An incomplete R package for working with random return
variables. The current package provides limited support for
formatting money. More features are planned for the future.
Diff between rrv versions 0.0.1 dated 2009-08-20 and 0.0.2 dated 2009-11-20
DESCRIPTION | 12 ++++++------ inst/doc/rrv.pdf |only inst/doc/rrv.rnw |only 3 files changed, 6 insertions(+), 6 deletions(-)
Author: Rajarshi Guha
Title: rpubchem - Interface to the PubChem Collection
Description: Access PubChem data (compounds, substance, assays).
Structural information is provided in the form of SMILES
strings. This package only provides access to a subset of the
precalculated data stored by PubChem. Bio-assay data can be
accessed to obtain descriptions as well as the actual data. It
is also possible to search for assay ID's by keyword. Currently
the main limitation is that only 1000 molecules can be
downloaded at a time from the PubChem servers
Diff between rpubchem versions 1.4.2 dated 2009-02-08 and 1.4.3 dated 2009-11-20
DESCRIPTION | 26 +++++++++++++++----------- R/bioassayQueries.R |only man/findaid.Rd | 2 +- man/getadesc.Rd | 2 +- man/getaidcid.Rd |only man/getassay.Rd | 2 +- man/getcid.Rd | 2 +- man/getcsid.Rd | 2 +- man/getsid.Rd | 2 +- 9 files changed, 21 insertions(+), 17 deletions(-)
Author: Hrishikesh D. Vinod
Title: Maximum Entropy Bootstrap for Time Series
Description: This package performs maximum entropy density based
dependent data bootstrap. An algorithm is provided to create a
population of time series (ensemble) without assuming
stationarity. The reference paper (Vinod, H.D., 2004) explains
how the algorithm satisfies the ergodic theorem and the central
limit theorem.
Diff between meboot versions 1.0-1 dated 2009-09-29 and 1.0-2 dated 2009-11-20
DESCRIPTION | 19 ++++++++++--------- NAMESPACE | 2 +- R/checkConv.R |only inst/doc/jss.bst |only inst/doc/jss.cls |only inst/doc/meboot.pdf |binary man/checkConv.Rd |only 7 files changed, 11 insertions(+), 10 deletions(-)
Author: Korbinian Strimmer.
Title: Estimation and Control of (Local) False Discovery Rates
Description: This package allows to estimate both tail area-based false
discovery rates (Fdr) as well as local false discovery rates
(fdr) for a variety of null models (p-values, z-scores,
correlation coefficients, t-scores). The proportion of null
values and the parameters of the null distribution are
adaptively estimated from the data. In addition, the package
contains functions for non-parametric density estimation
(Grenander estimator), for monotone regression (isotonic
regression and antitonic regression with weights), for
computing the greatest convex minorant (GCM) and the least
concave majorant (LCM), and for the half-normal and correlation
distributions.
Diff between fdrtool versions 1.2.5 dated 2008-07-07 and 1.2.6 dated 2009-11-20
fdrtool-1.2.5/fdrtool/CHANGES |only fdrtool-1.2.6/fdrtool/DESCRIPTION | 31 ++++++++++++++++++------------- fdrtool-1.2.6/fdrtool/NEWS |only fdrtool-1.2.6/fdrtool/R/censored.fit.R | 20 ++++++++++---------- fdrtool-1.2.6/fdrtool/R/nullmodel.R | 8 ++++---- fdrtool-1.2.6/fdrtool/man/fdrtool.Rd | 12 +++++++++--- 6 files changed, 41 insertions(+), 30 deletions(-)
Author: Peter Solymos
Title: Data Cloning and MCMC Tools for Maximum Likelihood Methods
Description: Low level functions for implementing maximum likelihood
estimating procedures for complex models using data cloning and
Bayesian Markov chain Monte Carlo methods with support for
JAGS, WinBUGS and OpenBUGS.
Diff between dclone versions 0.9-0 dated 2009-11-05 and 1.0-0 dated 2009-11-20
DESCRIPTION | 15 ++++---- HISTORY | 7 ++- NAMESPACE | 4 +- R/as.mcmc.list.bugs.R | 11 +++++- R/bugs.fit.R | 7 +++ R/confint.mcmc.list.dc.R | 8 ++++ R/dc.fit.R | 82 +++++---------------------------------------- R/dctable.default.R | 34 +++++++++++++++++- R/extractdctable.R |only R/extractdctable.default.R |only R/jags.fit.R | 5 ++ R/plot.dctable.R | 45 ++++++++++++++++++------ R/write.jags.model.R | 1 R/zzz.R | 12 +----- data/ovenbird.rda |binary man/coef.mcmc.list.Rd | 2 - man/dc.fit.Rd | 55 ++++++------------------------ man/dclone-package.Rd | 10 +++++ man/dclone.Rd | 8 +++- man/dctable.Rd |only man/errlines.Rd | 2 - man/jags.fit.Rd | 8 ++-- man/mcmcapply.Rd | 10 +---- man/ovenbird.Rd | 6 ++- man/regmod.Rd | 32 +++++++++++++++++ man/write.jags.model.Rd | 7 ++- 26 files changed, 197 insertions(+), 174 deletions(-)
Author: Christophe Ambroise, Gilles Grasseau, Mark Hoebeke, Pierre
Latouche, Vincent Miele, Franck Picard
Title: Random graph clustering
Description: Routines for the analysis (unsupervised clustering) of
networks using MIXtures of Erdos-Renyi random graphs
Diff between mixer versions 0.2 dated 2008-10-15 and 1.0 dated 2009-11-19
mixer-0.2/mixer/man/Gplot.Rd |only mixer-0.2/mixer/man/blog.Rd |only mixer-0.2/mixer/man/getAdjacencyMatrix-methods.Rd |only mixer-0.2/mixer/man/getAdjacencyMatrix.Rd |only mixer-0.2/mixer/man/getEdges-methods.Rd |only mixer-0.2/mixer/man/getEdges.Rd |only mixer-0.2/mixer/man/graph.affiliation.Rd |only mixer-0.2/mixer/man/initialize-methods.Rd |only mixer-0.2/mixer/man/macaque.Rd |only mixer-0.2/mixer/man/mixer.Rd |only mixer-0.2/mixer/man/plot.mixer.Rd |only mixer-0.2/mixer/man/spmgraph-class.Rd |only mixer-1.0/mixer/DESCRIPTION | 19 mixer-1.0/mixer/NAMESPACE | 13 mixer-1.0/mixer/NEWS |only mixer-1.0/mixer/R/Gplot-internals.R | 831 ++++++++++++++++++++-- mixer-1.0/mixer/R/Gplot.R | 598 ++++++++++++--- mixer-1.0/mixer/R/bayesianMixer.R | 157 ++-- mixer-1.0/mixer/R/init.R |only mixer-1.0/mixer/R/mixer.R | 362 +++++++-- mixer-1.0/mixer/inst/CITATION | 80 +- mixer-1.0/mixer/man/a_mixer.Rd |only mixer-1.0/mixer/man/b_graph.affiliation.Rd |only mixer-1.0/mixer/man/c_plot.mixer.Rd |only mixer-1.0/mixer/man/d_getModel.Rd |only mixer-1.0/mixer/man/d_getModel.mixer.Rd |only mixer-1.0/mixer/man/e_setSeed.Rd |only mixer-1.0/mixer/man/t_blog.Rd |only mixer-1.0/mixer/man/u_macaque.Rd |only mixer-1.0/mixer/src/Makevars | 17 mixer-1.0/mixer/src/SOCEm.h | 2 mixer-1.0/mixer/src/SparseMatrix.h | 2 mixer-1.0/mixer/src/VEstep_R.cc |only mixer-1.0/mixer/src/ermg_R.cc | 5 mixer-1.0/mixer/src/ermgo_R.cc | 7 mixer-1.0/mixer/src/init_ermg_R.cc | 7 mixer-1.0/mixer/src/matrix.cpp |only mixer-1.0/mixer/src/matrix.h |only mixer-1.0/mixer/src/util.h |only 39 files changed, 1734 insertions(+), 366 deletions(-)
Author: Venkatraman E. Seshan
Title: Clinical Trial Design and Data Analysis Functions
Description: Utilities to make your clinical collaborations easier if
not fun.
Diff between clinfun versions 0.8.5 dated 2009-07-18 and 0.8.6 dated 2009-11-19
CHANGES | 6 ++++++ DESCRIPTION | 8 ++++---- R/pselect.R | 18 ++++++++++-------- man/pselect.Rd | 11 +++++++---- 4 files changed, 27 insertions(+), 16 deletions(-)
Author: Karline Soetaert
Title: Datasets and tutorials for use in aquatic sciences
Description: Datasets and tutorials for use in the MArine, Riverine,
Estuarine, LAcustrine and Coastal sciences
Diff between marelacTeaching versions 1.0 dated 2009-09-07 and 1.1 dated 2009-11-19
marelacTeaching-1.0/marelacTeaching/R/addMarelacMenu.R |only marelacTeaching-1.0/marelacTeaching/R/sethelp.R |only marelacTeaching-1.0/marelacTeaching/inst/lecture |only marelacTeaching-1.0/marelacTeaching/man/addMarelacMenu.Rd |only marelacTeaching-1.0/marelacTeaching/man/sethelp.Rd |only marelacTeaching-1.1/marelacTeaching/DESCRIPTION | 11 marelacTeaching-1.1/marelacTeaching/NAMESPACE | 5 marelacTeaching-1.1/marelacTeaching/R/zzz.R | 4 marelacTeaching-1.1/marelacTeaching/inst/doc/Answers.pdf |binary marelacTeaching-1.1/marelacTeaching/inst/doc/UsingR.pdf | 1909 ++++++------- marelacTeaching-1.1/marelacTeaching/inst/doc/index.html | 4 marelacTeaching-1.1/marelacTeaching/inst/doc/lecture |only marelacTeaching-1.1/marelacTeaching/inst/doc/vignettes.bib | 349 +- marelacTeaching-1.1/marelacTeaching/man/marelacTeaching.Rd | 12 14 files changed, 1165 insertions(+), 1129 deletions(-)
More information about marelacTeaching at CRAN
Permanent link
Author: Edzer Pebesma
Title: procedures for automated interpolation
Description: A package that provides classes and methods for automated
spatial interpolation.
Diff between intamap versions 1.2-18 dated 2009-09-28 and 1.3-1 dated 2009-11-19
DESCRIPTION | 9 NAMESPACE | 2 R/init.R | 6 R/interpolate.R | 31 + R/pointKriging.R | 11 R/spCopPred.R | 771 +++++++++++++++++++++++------------------------- R/transGaussian.R | 2 man/bayesCopula.Rd | 5 man/getIntamapParams.Rd | 3 tests/interpolate.R | 2 10 files changed, 417 insertions(+), 425 deletions(-)
Author: Achim Zeileis, Gabor Grothendieck
Title: Z's ordered observations
Description: An S3 class with methods for totally ordered indexed
observations. It is particularly aimed at irregular time series
of numeric vectors/matrices and factors. zoo's key design goals
are independence of a particular index/date/time class and
consistency with ts and base R by providing methods to extend
standard generics.
Diff between zoo versions 1.6-0 dated 2009-11-17 and 1.6-1 dated 2009-11-19
DESCRIPTION | 8 NAMESPACE | 2 NEWS | 12 R/yearmon.R | 3 R/yearqtr.R | 3 inst/doc/zoo-faq.pdf | 10 inst/doc/zoo-quickref.pdf | 14 inst/doc/zoo-refcard.pdf |binary inst/doc/zoo.Rnw | 3 inst/doc/zoo.pdf | 823 ++++++++++++++++++++++------------------------ man/ORDER.Rd | 6 man/yearmon.Rd | 1 man/yearqtr.Rd | 1 man/zoo.Rd | 4 14 files changed, 454 insertions(+), 436 deletions(-)
Author: Richard D. Morey
Title: GUI implementing Bayesian working memory models
Description: A GUI R implementation of hierarchical Bayesian models of
working memory, used for analyzing change detection data.
Diff between WMCapacity versions 0.9 dated 2009-10-05 and 0.9.1 dated 2009-11-19
DESCRIPTION | 8 ++++---- R/WMCapacity.R | 2 +- R/WMCapacityGUI.R | 3 ++- R/output.R | 7 +++++-- man/WMCapacityGUI.Rd | 4 +++- 5 files changed, 15 insertions(+), 9 deletions(-)
Author: David Clifford, Glenn Stone
Title: Variable Penalty Dynamic Time Warping
Description: Variable Penalty Dynamic Time Warping for aligning GC-MS
chromatograms to a master signal and more. With the appropriate
penalty this method performs good alignment without altering
the shape of peaks in GC-MS data.
Diff between VPdtw versions 2.1-3 dated 2009-11-18 and 2.1-4 dated 2009-11-19
DESCRIPTION | 8 ++++---- R/VPdtw.R | 4 ++-- inst/CITATION | 2 +- src/matrix.cc | 12 ------------ src/matrix.h | 9 +++++++-- 5 files changed, 14 insertions(+), 21 deletions(-)
Author: Martin Maechler
Title: VLMC -- Variable Length Markov Chains
Description: Functions, Classes & Methods for estimation, prediction,
and simulation (bootstrap) of VLMC -- Variable Length Markov
Chain -- Models
Diff between VLMC versions 1.3-10 dated 2006-09-18 and 1.3-11 dated 2009-11-19
ChangeLog | 7 ++ DESCRIPTION | 17 ++--- R/vlmc.R | 4 - man/as.dendrogram.vlmc.Rd | 5 - man/simulate.vlmc.Rd | 2 tests/iid-cutoff.Rout.save | 153 ++++----------------------------------------- 6 files changed, 35 insertions(+), 153 deletions(-)
Author: Uwe Ligges
Title: Analysis of music
Description: Collection of tools to analyze music, handling wave files,
transcription, ...
Diff between tuneR versions 0.2-11 dated 2009-10-15 and 0.2-12 dated 2009-11-19
tuneR-0.2-11/tuneR/.project |only tuneR-0.2-12/tuneR/DESCRIPTION | 8 ++++---- tuneR-0.2-12/tuneR/R/readWave.R | 17 +++++++++++++---- tuneR-0.2-12/tuneR/R/writeWave.R | 12 +++++++++++- 4 files changed, 28 insertions(+), 9 deletions(-)
Author: Jeff Hallman
Title: Time Indexes and Time Indexed Series
Description: Functions and S3 classes for time indexes and time indexed
series, which are compatible with FAME frequencies.
Diff between tis versions 1.7 dated 2009-07-28 and 1.8 dated 2009-11-19
DESCRIPTION | 7 ++++--- NEWS | 5 +++++ R/fortify.tis.R | 22 ++++++++++++---------- man/fortify.tis.Rd | 22 ++++++++++++++-------- 4 files changed, 35 insertions(+), 21 deletions(-)
Author: Claus Dethlefsen, Soren Lundbye-Christensen and Anette Luther
Christensen
Title: State Space Models in R
Description: A glm-like formula language to define dynamic generalized
linear models (state space models). Includes functions for
Kalman filtering and smoothing. Estimation of variance matrices
can be perfomred using the EM algorithm in case of Gaussian
models. Read help(sspir) to get started.
Diff between sspir versions 0.2.7 dated 2009-08-10 and 0.2.8 dated 2009-11-19
CHANGES | 38 ++++++++++++++++++++++++++++++++++++++ DESCRIPTION | 8 ++++---- R/kfs.R | 11 +++++++---- 3 files changed, 49 insertions(+), 8 deletions(-)
Author: Patrick Mair, Eric Wu
Title: R/EQS Interface
Description: This package contains the function run.eqs() which calls
an EQS script file, executes the EQS estimation, and, finally,
imports the results as R objects. These two steps can be
performed separately: call.eqs() calls and executes EQS,
whereas read.eqs() imports existing EQS outputs as objects into
R.
Diff between REQS versions 0.8-4 dated 2009-08-30 and 0.8-5 dated 2009-11-19
DESCRIPTION | 8 ++++---- R/call.eqs.R | 7 ++++++- R/run.eqs.r | 6 +++--- man/call.eqs.rd | 2 +- man/run.eqs.rd | 2 +- 5 files changed, 15 insertions(+), 10 deletions(-)
Author: Simon Jackman, with contributions from Alex Tahk, Achim
Zeileis, Christina Maimone and Jim Fearon
Title: Political Science Computational Laboratory, Stanford University
Description: Bayesian analysis of item-response theory (IRT) models,
roll call analysis; computing highest density regions; maximum
likelihood estimation of zero-inflated and hurdle models for
count data; goodness-of-fit measures for GLMs; data sets used
in writing and teaching at the Political Science Computational
Laboratory; seats-votes curves.
Diff between pscl versions 1.03 dated 2009-01-27 and 1.03.2 dated 2009-11-19
pscl-1.03.2/pscl/COPYRIGHTS | 4 - pscl-1.03.2/pscl/DESCRIPTION | 22 +++-- pscl-1.03.2/pscl/HISTORY | 5 + pscl-1.03.2/pscl/R/hurdle.R | 44 ++++++++--- pscl-1.03.2/pscl/R/ideal.r | 20 +---- pscl-1.03.2/pscl/R/vuong.R | 127 ++++++++++++++++----------------- pscl-1.03.2/pscl/R/zeroinfl.R | 38 +++++++-- pscl-1.03.2/pscl/R/zzz.R |only pscl-1.03.2/pscl/inst/doc/countreg.Rnw | 2 pscl-1.03.2/pscl/inst/doc/countreg.pdf |binary pscl-1.03.2/pscl/man/bioChemists.Rd | 4 - pscl-1.03.2/pscl/man/hurdle.Rd | 1 pscl-1.03.2/pscl/man/ideal.Rd | 42 +++++----- pscl-1.03.2/pscl/man/zeroinfl.Rd | 2 pscl-1.03/pscl/inst/doc/auto |only 15 files changed, 174 insertions(+), 137 deletions(-)
Author: Harold C. Doran
Title: Miscellaneous Psychometric Analyses
Description: Miscellaneous functions for psychometric problems
Diff between MiscPsycho versions 1.4 dated 2009-03-10 and 1.5 dated 2009-11-19
MiscPsycho-1.4/MiscPsycho/R/alpha.Summary.R |only MiscPsycho-1.4/MiscPsycho/Read-and-delete-me |only MiscPsycho-1.4/MiscPsycho/inst/doc/stock_lord.pdf |only MiscPsycho-1.4/MiscPsycho/man/alpha.Summary.Rd |only MiscPsycho-1.4/MiscPsycho/man/fit.Stats.Rd |only MiscPsycho-1.4/MiscPsycho/man/pb.Rd |only MiscPsycho-1.4/MiscPsycho/man/piPlot.Rd |only MiscPsycho-1.5/MiscPsycho/DESCRIPTION | 26 +-- MiscPsycho-1.5/MiscPsycho/NAMESPACE |only MiscPsycho-1.5/MiscPsycho/R/SL.R | 20 -- MiscPsycho-1.5/MiscPsycho/R/SL.default.R |only MiscPsycho-1.5/MiscPsycho/R/SLderivs.R | 139 +++++++++--------- MiscPsycho-1.5/MiscPsycho/R/SSI.R |only MiscPsycho-1.5/MiscPsycho/R/SSI.default.R |only MiscPsycho-1.5/MiscPsycho/R/SSI.fit.R |only MiscPsycho-1.5/MiscPsycho/R/SSI.formula.R |only MiscPsycho-1.5/MiscPsycho/R/alpha.R | 10 - MiscPsycho-1.5/MiscPsycho/R/alpha.default.R |only MiscPsycho-1.5/MiscPsycho/R/alpha.fit.R |only MiscPsycho-1.5/MiscPsycho/R/alpha.formula.R |only MiscPsycho-1.5/MiscPsycho/R/cheat.R | 107 ------------- MiscPsycho-1.5/MiscPsycho/R/cheat.default.R |only MiscPsycho-1.5/MiscPsycho/R/cheat.fit.R |only MiscPsycho-1.5/MiscPsycho/R/cheat.formula.R |only MiscPsycho-1.5/MiscPsycho/R/choose.M.R | 2 MiscPsycho-1.5/MiscPsycho/R/class.acc.R | 2 MiscPsycho-1.5/MiscPsycho/R/classical.R | 8 - MiscPsycho-1.5/MiscPsycho/R/classical.default.R |only MiscPsycho-1.5/MiscPsycho/R/classical.formula.R |only MiscPsycho-1.5/MiscPsycho/R/irt.ability.R | 2 MiscPsycho-1.5/MiscPsycho/R/jml.R | 37 ---- MiscPsycho-1.5/MiscPsycho/R/jml.default.R |only MiscPsycho-1.5/MiscPsycho/R/jml.fit.R |only MiscPsycho-1.5/MiscPsycho/R/jml.formula.R |only MiscPsycho-1.5/MiscPsycho/R/pb.R | 2 MiscPsycho-1.5/MiscPsycho/R/piPlot.R | 2 MiscPsycho-1.5/MiscPsycho/R/plaus.val.R | 2 MiscPsycho-1.5/MiscPsycho/R/plot.jml.R |only MiscPsycho-1.5/MiscPsycho/R/posterior.R | 2 MiscPsycho-1.5/MiscPsycho/R/print.SL.R |only MiscPsycho-1.5/MiscPsycho/R/print.SSI.R |only MiscPsycho-1.5/MiscPsycho/R/print.alpha.R |only MiscPsycho-1.5/MiscPsycho/R/print.cheat.R |only MiscPsycho-1.5/MiscPsycho/R/print.classical.R |only MiscPsycho-1.5/MiscPsycho/R/print.jml.R |only MiscPsycho-1.5/MiscPsycho/R/print.scoreCon.R |only MiscPsycho-1.5/MiscPsycho/R/print.summary.SL.R |only MiscPsycho-1.5/MiscPsycho/R/print.summary.SSI.R |only MiscPsycho-1.5/MiscPsycho/R/print.summary.alpha.R |only MiscPsycho-1.5/MiscPsycho/R/print.summary.cheat.R |only MiscPsycho-1.5/MiscPsycho/R/print.summary.classical.R |only MiscPsycho-1.5/MiscPsycho/R/print.summary.jml.R |only MiscPsycho-1.5/MiscPsycho/R/print.summary.scoreCon.R |only MiscPsycho-1.5/MiscPsycho/R/scoreCon.R | 20 -- MiscPsycho-1.5/MiscPsycho/R/scoreCon.default.R |only MiscPsycho-1.5/MiscPsycho/R/scoreCon.fit.R |only MiscPsycho-1.5/MiscPsycho/R/simRasch.R | 2 MiscPsycho-1.5/MiscPsycho/R/stringMatch.R | 2 MiscPsycho-1.5/MiscPsycho/R/stringProbs.R | 2 MiscPsycho-1.5/MiscPsycho/R/summary.SL.R |only MiscPsycho-1.5/MiscPsycho/R/summary.SSI.R |only MiscPsycho-1.5/MiscPsycho/R/summary.alpha.R |only MiscPsycho-1.5/MiscPsycho/R/summary.cheat.R |only MiscPsycho-1.5/MiscPsycho/R/summary.classical.R |only MiscPsycho-1.5/MiscPsycho/R/summary.jml.R |only MiscPsycho-1.5/MiscPsycho/R/summary.scoreCon.R |only MiscPsycho-1.5/MiscPsycho/R/wrongProb.R |only MiscPsycho-1.5/MiscPsycho/R/wrongProb.default.R |only MiscPsycho-1.5/MiscPsycho/R/wrongProb.formula.R |only MiscPsycho-1.5/MiscPsycho/inst/doc/MP.Rnw |only MiscPsycho-1.5/MiscPsycho/inst/doc/MP.pdf |binary MiscPsycho-1.5/MiscPsycho/man/MiscPsycho-package.Rd | 33 +--- MiscPsycho-1.5/MiscPsycho/man/SL.Rd | 21 +- MiscPsycho-1.5/MiscPsycho/man/SSI.Rd |only MiscPsycho-1.5/MiscPsycho/man/alpha.Rd | 49 +++++- MiscPsycho-1.5/MiscPsycho/man/cheat.Rd | 81 ++++++++-- MiscPsycho-1.5/MiscPsycho/man/classical.Rd | 36 +++- MiscPsycho-1.5/MiscPsycho/man/jml.Rd | 79 +++++++--- MiscPsycho-1.5/MiscPsycho/man/posterior.Rd | 1 MiscPsycho-1.5/MiscPsycho/man/scoreCon.Rd | 38 +++- MiscPsycho-1.5/MiscPsycho/man/simRasch.Rd | 4 MiscPsycho-1.5/MiscPsycho/man/theta.max.Rd | 2 MiscPsycho-1.5/MiscPsycho/man/wrongProb.Rd |only 83 files changed, 361 insertions(+), 370 deletions(-)
Author: S scripts originally by Jan Beran
Title: Statistics for Long-Memory Processes (Jan Beran) -- Data and
Functions
Description: Datasets and Functionality from the textbook Jan Beran
(1994). Statistics for Long-Memory Processes; Chapman \& Hall.
Diff between longmemo versions 0.9-6 dated 2009-01-11 and 0.9-7 dated 2009-11-19
ChangeLog | 6 ++++++ DESCRIPTION | 17 ++++++++++------- man/specARIMA.Rd | 4 ++-- man/specFGN.Rd | 2 +- 4 files changed, 19 insertions(+), 10 deletions(-)
Author: Jeff Hallman
Title: Interface for FAME time series database
Description: Read and write FAME databases.
Diff between fame versions 2.6 dated 2009-04-14 and 2.7 dated 2009-11-19
DESCRIPTION | 9 +++-- NEWS | 8 +++++ R/fame.R | 79 ++++++++++++++++++++++++++++++---------------------- configure.win |only man/getfame.Rd | 16 +++++----- man/lowLevelFame.Rd | 15 ++++++--- man/osUtilities.Rd | 2 - src/Makevars.win | 15 +++++++-- src/chli.c | 76 +++++++++++++++++++++++++------------------------- 9 files changed, 127 insertions(+), 93 deletions(-)
Author: Achim Zeileis, Kurt Hornik
Title: CRAN Task Views
Description: Server-side and client-side tools for task views to
CRAN-style repositories
Diff between ctv versions 0.5-4 dated 2009-09-30 and 0.5-6 dated 2009-11-19
DESCRIPTION | 8 +- NEWS | 17 +++++ R/ctv-client.R | 6 + R/ctv-server.R | 1 inst/ctv/Bayesian.ctv | 15 +++- inst/ctv/ChemPhys.ctv | 7 +- inst/ctv/Cluster.ctv | 104 +++++++++++++++++++++++++++------- inst/ctv/Distributions.ctv | 31 +++++++--- inst/ctv/Econometrics.ctv | 23 +++---- inst/ctv/Environmetrics.ctv | 56 +++++++++++++----- inst/ctv/Finance.ctv | 18 +++-- inst/ctv/Genetics.ctv | 6 - inst/ctv/Graphics.ctv | 4 - inst/ctv/HighPerformanceComputing.ctv | 31 +++++----- inst/ctv/MachineLearning.ctv | 7 -- inst/ctv/MedicalImaging.ctv | 3 inst/ctv/Multivariate.ctv | 14 ++-- inst/ctv/Pharmacokinetics.ctv | 20 +++--- inst/ctv/Psychometrics.ctv | 16 +++-- inst/ctv/Robust.ctv | 6 - inst/ctv/SocialSciences.ctv | 23 +++++-- inst/ctv/Spatial.ctv | 25 ++++---- inst/ctv/Survival.ctv | 10 --- inst/ctv/TimeSeries.ctv | 26 +++++--- inst/ctv/gR.ctv | 10 --- inst/doc/ctv-howto.pdf |binary 26 files changed, 322 insertions(+), 165 deletions(-)
Author: Michael Friendly and John Fox
Title: Generalized Canonical Discriminant Analysis
Description: Functions for computing and graphing canonical
discriminant analyses.
Diff between candisc versions 0.5-15 dated 2009-06-14 and 0.5-16 dated 2009-11-19
DESCRIPTION | 12 ++++++------ demo |only man/candisc-package.Rd | 4 ++-- man/heplot.candisc.Rd | 14 ++++++++++++++ 4 files changed, 22 insertions(+), 8 deletions(-)
Author: Simon Wood
Title: GAMs with GCV/AIC/REML smoothness estimation and GAMMs by PQL
Description: Routines for GAMs and other generalized ridge regression
with multiple smoothing parameter selection by GCV, REML or
UBRE/AIC. Also GAMMs by REML or PQL. Includes a gam() function.
Diff between mgcv versions 1.5-6 dated 2009-09-12 and 1.6-0 dated 2009-11-18
DESCRIPTION | 10 ++-- NAMESPACE | 8 ++- R/bam.r |only R/gam.fit3.r | 126 +++++++++++++++++++++++++++++++-------------------- R/gamm.r | 2 R/mgcv.r | 110 ++++++++++++++++++++++---------------------- R/smooth.r | 6 +- changeLog | 37 ++++++++++++++ man/bam.Rd |only man/gam.Rd | 27 +++++++++- man/gam.fit3.Rd | 12 ++++ man/gam.models.Rd | 21 ++++++-- man/gam.selection.Rd | 6 +- man/gamObject.Rd | 6 ++ man/ls.size.Rd |only man/mgcv-package.Rd | 11 +++- man/rig.Rd |only man/summary.gam.Rd | 13 +---- po/R-de.po | 6 +- po/de.po | 6 +- 20 files changed, 264 insertions(+), 143 deletions(-)
Author: Simon Wood
Title: Generalized additive mixed models using mgcv and lme4
Description: Fit generalized additive mixed models via a version of
mgcv's gamm function, using lme4 for estimation via Fabian
Scheipl's trick.
Diff between gamm4 versions 0.0-1 dated 2009-09-07 and 0.0-2 dated 2009-11-18
DESCRIPTION | 6 +++--- R/gamm4.r | 6 +++++- changeLog |only 3 files changed, 8 insertions(+), 4 deletions(-)
Author: Martin Maechler and many others.
Title: Utilities from Seminar fuer Statistik ETH Zurich
Description: Useful utilities ['goodies'] from Seminar fuer Statistik
ETH Zurich, many ported from S-plus times.
Diff between sfsmisc versions 1.0-8 dated 2009-08-10 and 1.0-9 dated 2009-11-18
ChangeLog | 8 ++++++++ DESCRIPTION | 8 ++++---- R/TA.plot.R | 4 ++-- R/misc-goodies.R | 1 + inst/ChangeLog | 8 ++++++++ man/eaxis.Rd | 4 ++-- man/p.ts.Rd | 2 +- man/polyn.eval.Rd | 2 +- 8 files changed, 27 insertions(+), 10 deletions(-)
Author: Original code by many authors, notably Peter Rousseeuw and
Christophe Croux, see file 'Copyrights'; Valentin Todorov
Title: Basic Robust Statistics
Description: "Essential" Robust Statistics. The goal is to provide
tools allowing to analyze data with robust methods. This
includes regression methodology including model selections and
multivariate statistics where we strive to cover the book
"Robust Statistics, Theory and Methods" by Maronna, Martin and
Yohai; Wiley 2006.
Diff between robustbase versions 0.4-5 dated 2009-01-18 and 0.5-0 dated 2009-11-18
ChangeLog | 36 ++++++++ DESCRIPTION | 38 ++++---- Done | 3 R/anova-glmrob.R | 4 R/glmrob.R | 57 +++++++++---- R/glmrobMqle-DQD.R | 103 +++++++++++++++++++++++ R/glmrobMqle.R | 177 ++++++++++++++++++++++++++++++++++------- R/zzz.R | 9 -- TODO | 18 +--- data/wagnerGrowth.rda |only man/Qn.Rd | 2 man/Sn.Rd | 2 man/glmrob.Rd | 43 +++++++++ man/ltsReg.Rd | 2 man/pkg-internal.Rd | 4 man/wagnerGrowth.Rd |only tests/binom-ni-small.Rout.save | 19 ++-- tests/glmrob-1.R |only tests/glmrob-specials.R | 4 tests/mc-strict.R | 18 +++- tests/tmcd.R | 11 ++ tests/tmcd.Rout.save | 44 +++++++--- 22 files changed, 472 insertions(+), 122 deletions(-)
Author: Werner Stahel, Martin Maechler and potentially others
Title: eXperimental eXtraneous eXtraordinary ... Functionality for
Robust Statistics
Description: eXperimental eXtraneous eXtraordinary Functionality for
Robust Statistics
Diff between robustX versions 1.1-0 dated 2009-06-14 and 1.1-1 dated 2009-11-18
ChangeLog | 12 ++++++++---- DESCRIPTION | 8 ++++---- demo/00Index | 2 ++ demo/rbwheel_d.R |only demo/rbwheel_ics.R | 2 +- man/mvBACON.Rd | 2 +- stahel.mail_1 |only 7 files changed, 16 insertions(+), 10 deletions(-)
Author: Peter Baker
Title: Bayesian mixture models for marker dosage in autopolyploids
Description: Fits Bayesian mixture models to estimate marker dosage for
dominant markers on autopolyploids using JAGS (1.0 or greater).
May be used in conjunction with polySegratio for simulation
studies and comparison with standard methods
Diff between polySegratioMM versions 0.5-1 dated 2009-11-17 and 0.5-2 dated 2009-11-18
polySegratioMM-0.5-1/polySegratioMM/inst/doc/polySegratioMM-commands.pdf |only polySegratioMM-0.5-2/polySegratioMM/DESCRIPTION | 8 ++++---- polySegratioMM-0.5-2/polySegratioMM/inst/doc/polySegratioMM-overview.pdf |binary polySegratioMM-0.5-2/polySegratioMM/inst/doc/tmp/tmp-006.pdf | 4 ++-- polySegratioMM-0.5-2/polySegratioMM/inst/doc/tmp/tmp-009.pdf | 4 ++-- polySegratioMM-0.5-2/polySegratioMM/inst/doc/tmp/tmp-016.pdf | 4 ++-- polySegratioMM-0.5-2/polySegratioMM/inst/doc/tmp/tmp-017.pdf | 4 ++-- polySegratioMM-0.5-2/polySegratioMM/man/dosagesJagsMix.Rd | 3 ++- polySegratioMM-0.5-2/polySegratioMM/man/plotFitted.Rd | 6 +++--- polySegratioMM-0.5-2/polySegratioMM/man/polySegratioMM-package.Rd | 6 +++--- 10 files changed, 20 insertions(+), 19 deletions(-)
More information about polySegratioMM at CRAN
Permanent link
Author: Peter Baker
Title: Simulate and test marker dosage for dominant markers in
autopolyploids
Description: Perform classic chi-squared tests and Ripol et al(1999)
binomial confidence interval approach for autopolyploid
dominant markers. Also, dominant markers may be generated for
families of offspring where either one or both of the parents
possess the marker. Missing values and misclassified markers
may be generated at random.
Diff between polySegratio versions 0.2-1 dated 2009-11-17 and 0.2-2 dated 2009-11-18
DESCRIPTION | 8 TODO | 10 inst/doc/polySegratio-overview.pdf |binary inst/doc/tmp/tmp-007.eps | 250 ++++----- inst/doc/tmp/tmp-007.pdf | 268 +++++----- inst/doc/tmp/tmp-009.eps | 499 ++++++++----------- inst/doc/tmp/tmp-009.pdf | 503 +++++++++---------- inst/doc/tmp/tmp-010.eps | 934 ++++++++++++++++++----------------- inst/doc/tmp/tmp-010.pdf | 968 ++++++++++++++++++------------------- man/polySegratio-package.Rd | 7 man/simAutoCross.Rd | 2 11 files changed, 1700 insertions(+), 1749 deletions(-)
Author: Torsten Hothorn, Peter Buhlmann, Thomas Kneib, Matthias Schmid
and Benjamin Hofner
Title: Model-Based Boosting
Description: Functional gradient descent algorithms (boosting) for
optimizing general loss functions utilizing componentwise least
squares, either of parametric linear form or smoothing splines,
or regression trees as base learners for fitting generalized
linear, additive and interaction models to potentially
high-dimensional data.
Diff between mboost versions 1.1-3 dated 2009-09-23 and 1.1-4 dated 2009-11-18
mboost-1.1-3/mboost/R/AAA.R |only mboost-1.1-3/mboost/R/bbs2.R |only mboost-1.1-3/mboost/inst/doc/mboost_illustrations.bbl |only mboost-1.1-3/mboost/inst/doc/mboost_illustrations.blg |only mboost-1.1-4/mboost/DESCRIPTION | 8 - mboost-1.1-4/mboost/NEWS | 4 mboost-1.1-4/mboost/R/xsp.R | 58 ++++++++--- mboost-1.1-4/mboost/inst/CHANGES | 4 mboost-1.1-4/mboost/inst/doc/SurvivalEnsembles.pdf |binary mboost-1.1-4/mboost/inst/doc/mboost_illustrations.pdf |binary mboost-1.1-4/mboost/man/baselearners.Rd | 3 mboost-1.1-4/mboost/tests/Examples/mboost-Ex.Rout.save | 35 ++++--- mboost-1.1-4/mboost/tests/bugfixes.R | 71 ++++++++++---- mboost-1.1-4/mboost/tests/bugfixes.Rout.save | 73 ++++++++++----- mboost-1.1-4/mboost/tests/mboost_illustrations.Rout.save | 2 mboost-1.1-4/mboost/tests/regtest-blackboost.Rout.save | 2 mboost-1.1-4/mboost/tests/regtest-gamboost.Rout.save | 2 mboost-1.1-4/mboost/tests/regtest-glmboost.Rout.save | 2 mboost-1.1-4/mboost/tests/regtest-hatmatrix.Rout.save | 2 mboost-1.1-4/mboost/tests/setup.Rout.save | 2 20 files changed, 179 insertions(+), 89 deletions(-)
Author: Martin Maechler partly based on code from Robert Gentleman
Title: Construct Graphs of S4 Class Hierarchies
Description: Construct directed graphs of S4 class hierarchies and
visualize them. In general, these graphs typically are DAGs
(directed acyclic graphs), often simple trees in practice.
Diff between classGraph versions 0.7-2 dated 2009-04-15 and 0.7-3 dated 2009-11-18
ChangeLog | 6 ++++++ DESCRIPTION | 8 ++++---- man/mRagraph.Rd | 3 +-- 3 files changed, 11 insertions(+), 6 deletions(-)
Author: Andreas F. Hofmann, Karline Soetaert, Filip J.R. Meysman
Title: AquaEnv - an integrated development toolbox for aquatic chemical
model generation
Description: AquaEnv is an integrated development toolbox for aquatic
chemical model generation focused on (ocean) acidification and
CO2 air-water exchange. It contains all elements necessary to
model the pH, the related CO2 air-water exchange, as well as
aquatic acid-base chemistry in general for an arbitrary marine,
estuarine or freshwater system. Also chemical batches can be
modelled. Next to the routines necessary to calculate desired
information, AquaEnv also contains a suite of tools to
visualize this information. Furthermore, AquaEnv can not only
be used to build dynamic models of aquatic systems, but it can
also serve as a simple desktop tool for the experimental
aquatic chemist to generate and visualize all possible derived
information from a set of measurements with one single easy to
use R function. Additionally, the sensitivity of the system to
variations in the input variables can be visualized.
Diff between AquaEnv versions 0.7 dated 2009-03-31 and 0.8 dated 2009-11-18
AquaEnv-0.7/AquaEnv/man/Fugacity.Rd |only AquaEnv-0.8/AquaEnv/DESCRIPTION | 12 AquaEnv-0.8/AquaEnv/NAMESPACE | 2 AquaEnv-0.8/AquaEnv/R/aquaenv_private_DSApHfunctions.R | 22 AquaEnv-0.8/AquaEnv/R/aquaenv_private_Kfunctions.R | 348 AquaEnv-0.8/AquaEnv/R/aquaenv_private_auxilaryfunctions.R | 86 AquaEnv-0.8/AquaEnv/R/aquaenv_public_constants.R | 9 AquaEnv-0.8/AquaEnv/R/aquaenv_public_mainfunctions.R | 150 AquaEnv-0.8/AquaEnv/demo/basicfeatures.R | 20 AquaEnv-0.8/AquaEnv/demo/titration.R | 6 AquaEnv-0.8/AquaEnv/inst/CITATION | 16 AquaEnv-0.8/AquaEnv/inst/doc/AquaEnv-ConstantsAndFormulae.pdf | 6794 +- AquaEnv-0.8/AquaEnv/inst/doc/AquaEnv-ConstantsAndFormulae.tex | 90 AquaEnv-0.8/AquaEnv/inst/doc/AquaEnv-PrivateFunctions.pdf |binary AquaEnv-0.8/AquaEnv/inst/doc/AquaEnv.bib | 74 AquaEnv-0.8/AquaEnv/inst/doc/AquaEnv.pdf |32593 +++++----- AquaEnv-0.8/AquaEnv/inst/doc/AquaEnv.rnw | 55 AquaEnv-0.8/AquaEnv/inst/doc/AquaEnv.tex | 5849 - AquaEnv-0.8/AquaEnv/man/K_BOH3.Rd | 7 AquaEnv-0.8/AquaEnv/man/K_CO2.Rd | 16 AquaEnv-0.8/AquaEnv/man/K_H2PO4.Rd | 7 AquaEnv-0.8/AquaEnv/man/K_H2S.Rd | 7 AquaEnv-0.8/AquaEnv/man/K_H3PO4.Rd | 7 AquaEnv-0.8/AquaEnv/man/K_HCO3.Rd | 16 AquaEnv-0.8/AquaEnv/man/K_HF.Rd | 19 AquaEnv-0.8/AquaEnv/man/K_HPO4.Rd | 7 AquaEnv-0.8/AquaEnv/man/K_HSO4.Rd | 10 AquaEnv-0.8/AquaEnv/man/K_NH4.Rd | 7 AquaEnv-0.8/AquaEnv/man/K_SiOH4.Rd | 7 AquaEnv-0.8/AquaEnv/man/K_SiOOH3.Rd | 7 AquaEnv-0.8/AquaEnv/man/K_W.Rd | 7 AquaEnv-0.8/AquaEnv/man/aquaenv.Rd | 53 AquaEnv-0.8/AquaEnv/man/convert.Rd | 1 AquaEnv-0.8/AquaEnv/man/plot.aquaenv.Rd | 9 34 files changed, 23790 insertions(+), 22523 deletions(-)
Author: Seung W. Choi, with contributions from Laura E. Gibbons and
Paul K. Crane
Title: Logistic Regression Differential Item Functioning using IRT
Description: Analysis of Differential Item Functioning (DIF) for
dichotomous and polytomous items using an iterative hybrid of
(ordinal) logistic regression and item response theory (IRT).
Diff between lordif versions 0.1-3 dated 2009-11-05 and 0.1-4 dated 2009-11-18
DESCRIPTION | 8 ++++---- R/plotDIF.R | 18 +++++++++--------- man/lordif-package.Rd | 6 +++--- man/lordif.Rd | 2 +- man/montecarlo.Rd | 2 +- man/plotDIF.Rd | 5 +++-- man/plotMC.Rd | 3 +-- man/rundif.Rd | 2 +- man/runolr.Rd | 2 +- 9 files changed, 24 insertions(+), 24 deletions(-)
Author: Ulrike Groemping
Title: Fractional Factorial designs with 2-level factors
Description: This package creates regular and non-regular Fractional
Factorial designs. Furthermore, analysis tools for Fractional
Factorial designs with 2-level factors are offered (main
effects and interaction plots for all factors simultaneously,
cube plot for looking at the simultaneous effects of three
factors, full or half normal plot, alias structure in a more
readable format than with the built-in function alias). The
package is currently subject to intensive development. While
much of the intended functionality is already available, some
changes and improvements are still to be expected. Suggestions
are welcome.
Diff between FrF2 versions 1.0 dated 2009-10-08 and 1.0-1 dated 2009-11-18
DESCRIPTION | 8 ++++---- R/DanielPlot.R | 14 ++++++++++++-- inst/NEWS | 8 ++++++++ man/CatalogueAccessors.Rd | 16 ++++++++-------- 4 files changed, 32 insertions(+), 14 deletions(-)
Author: Achim Zeileis, Gabor Grothendieck
Title: Z's ordered observations
Description: An S3 class with methods for totally ordered indexed
observations. It is particularly aimed at irregular time series
of numeric vectors/matrices and factors. zoo's key design goals
are independence of a particular index/date/time class and
consistency with ts and base R by providing methods to extend
standard generics.
Diff between zoo versions 1.5-8 dated 2009-07-22 and 1.6-0 dated 2009-11-17
zoo-1.5-8/zoo/man/as.Date.ts.Rd |only zoo-1.6-0/zoo/COPYRIGHTS | 2 zoo-1.6-0/zoo/DESCRIPTION | 12 zoo-1.6-0/zoo/NAMESPACE | 6 zoo-1.6-0/zoo/NEWS | 28 zoo-1.6-0/zoo/R/aggregate.zoo.R | 4 zoo-1.6-0/zoo/R/as.Date.ts.R | 4 zoo-1.6-0/zoo/R/index.R | 2 zoo-1.6-0/zoo/R/merge.zoo.R | 27 zoo-1.6-0/zoo/R/na.locf.R | 2 zoo-1.6-0/zoo/R/plot.zoo.R | 60 zoo-1.6-0/zoo/R/read.zoo.R | 63 zoo-1.6-0/zoo/R/rollapply.R | 12 zoo-1.6-0/zoo/R/window.zoo.R | 20 zoo-1.6-0/zoo/R/xyplot.zoo.R | 8 zoo-1.6-0/zoo/R/yearmon.R | 6 zoo-1.6-0/zoo/R/yearqtr.R | 8 zoo-1.6-0/zoo/R/zoo.R | 13 zoo-1.6-0/zoo/R/zzz.R |only zoo-1.6-0/zoo/THANKS | 3 zoo-1.6-0/zoo/WISHLIST | 4 zoo-1.6-0/zoo/demo |only zoo-1.6-0/zoo/inst/doc/zoo-faq.R |only zoo-1.6-0/zoo/inst/doc/zoo-faq.Rnw | 109 + zoo-1.6-0/zoo/inst/doc/zoo-faq.pdf | 1532 +++++++++++---------- zoo-1.6-0/zoo/inst/doc/zoo-quickref.Rnw | 12 zoo-1.6-0/zoo/inst/doc/zoo-quickref.pdf | 569 ++++--- zoo-1.6-0/zoo/inst/doc/zoo.Rnw | 14 zoo-1.6-0/zoo/inst/doc/zoo.pdf | 2294 ++++++++++++++++---------------- zoo-1.6-0/zoo/man/aggregate.zoo.Rd | 10 zoo-1.6-0/zoo/man/as.zoo.Rd | 8 zoo-1.6-0/zoo/man/index.Rd | 4 zoo-1.6-0/zoo/man/lag.zoo.Rd | 2 zoo-1.6-0/zoo/man/merge.zoo.Rd | 18 zoo-1.6-0/zoo/man/na.locf.Rd | 9 zoo-1.6-0/zoo/man/plot.zoo.Rd | 57 zoo-1.6-0/zoo/man/read.zoo.Rd | 48 zoo-1.6-0/zoo/man/window.zoo.Rd | 13 zoo-1.6-0/zoo/man/xyplot.zoo.Rd | 2 zoo-1.6-0/zoo/man/yearmon.Rd | 2 zoo-1.6-0/zoo/man/zoo.Rd | 51 zoo-1.6-0/zoo/man/zooreg.Rd | 28 42 files changed, 2835 insertions(+), 2231 deletions(-)
Author: Thomas Lumley, Achim Zeileis
Title: Robust Covariance Matrix Estimators
Description: Model-robust standard error estimators for
cross-sectional, time series and longitudinal data.
Diff between sandwich versions 2.2-1 dated 2009-02-05 and 2.2-2 dated 2009-11-17
COPYRIGHTS | 2 +- DESCRIPTION | 12 +++++++----- NEWS | 5 +++++ R/estfun.R | 6 ++++-- inst/CITATION | 2 +- inst/doc/sandwich-OOP.pdf |binary inst/doc/sandwich.pdf |binary man/vcovHAC.Rd | 2 +- man/vcovHC.Rd | 2 +- man/weightsLumley.Rd | 2 +- 10 files changed, 21 insertions(+), 12 deletions(-)
Author: Torsten Hothorn, Achim Zeileis, Giovanni Millo, David Mitchell
Title: Testing Linear Regression Models
Description: A collection of tests, data sets and examples for
diagnostic checking in linear regression models.
Diff between lmtest versions 0.9-24 dated 2009-05-28 and 0.9-25 dated 2009-11-17
DESCRIPTION | 8 ++++---- NEWS | 5 +++++ inst/doc/lmtest-intro.pdf |binary man/Mandible.Rd | 4 ++-- man/USDistLag.Rd | 2 +- man/bondyield.Rd | 4 ++-- man/coeftest.Rd | 2 +- man/currencysubstitution.Rd | 6 +++--- man/hmctest.Rd | 2 +- man/jocci.Rd | 2 +- man/lrtest.Rd | 2 +- man/petest.Rd | 13 +++++++++++++ man/waldtest.Rd | 6 +++--- 13 files changed, 37 insertions(+), 19 deletions(-)
Author: Achim Zeileis, Ajay Shah, Ila Patnaik
Title: Exchange Rate Regime Analysis
Description: Exchange rate regression and structural change tools for
estimating, testing, dating, and monitoring (de facto) exchange
rate regimes.
Diff between fxregime versions 0.3-0 dated 2009-08-28 and 0.3-1 dated 2009-11-17
DESCRIPTION | 8 ++++---- NEWS | 5 +++++ inst/doc/CNY.pdf |binary inst/doc/INR.pdf |binary man/confint.fxregimes.Rd | 2 +- man/fxreturns.Rd | 2 +- man/refit.Rd | 12 ++++++------ 7 files changed, 17 insertions(+), 12 deletions(-)
Author: Josef Leydold and Wolfgang H\"ormann
Title: R interface to the UNU.RAN random variate generators
Description: Interface to the UNU.RAN library for Universal Non-Uniform
RANdom variate generators
Diff between Runuran versions 0.10.1 dated 2009-08-06 and 0.11.0 dated 2009-11-17
Runuran-0.10.1/Runuran/man/r-method.Rd |only Runuran-0.10.1/Runuran/man/unuran.distr.deprecated.Rd |only Runuran-0.10.1/Runuran/man/uqhinv.Rd |only Runuran-0.10.1/Runuran/man/urhitro.Rd |only Runuran-0.10.1/Runuran/man/urtdr.Rd |only Runuran-0.10.1/Runuran/src/Runuran_source.h |only Runuran-0.11.0/Runuran/DESCRIPTION | 15 Runuran-0.11.0/Runuran/NAMESPACE | 8 Runuran-0.11.0/Runuran/NEWS | 55 Runuran-0.11.0/Runuran/R/Runuran.R | 19 Runuran-0.11.0/Runuran/R/deprecated.R | 62 Runuran-0.11.0/Runuran/R/distributions.R | 320 Runuran-0.11.0/Runuran/R/universal.R | 109 Runuran-0.11.0/Runuran/R/unuran_cmv.R | 6 Runuran-0.11.0/Runuran/R/unuran_cont.R | 7 Runuran-0.11.0/Runuran/R/unuran_discr.R | 6 Runuran-0.11.0/Runuran/R/unuran_distr.R | 3 Runuran-0.11.0/Runuran/configure | 18 Runuran-0.11.0/Runuran/configure.ac | 13 Runuran-0.11.0/Runuran/inst/doc/Runuran.Rnw | 4 Runuran-0.11.0/Runuran/inst/doc/Runuran.pdf | 3445 +++++----- Runuran-0.11.0/Runuran/inst/doc/arvag.bib | 2 Runuran-0.11.0/Runuran/inst/doc/src/advanced.Rnw | 3 Runuran-0.11.0/Runuran/inst/doc/src/arvag.Rnw | 73 Runuran-0.11.0/Runuran/inst/doc/src/distributions.Rnw | 74 Runuran-0.11.0/Runuran/inst/doc/src/glossary.tex | 26 Runuran-0.11.0/Runuran/inst/doc/src/intro.Rnw | 21 Runuran-0.11.0/Runuran/inst/doc/src/specialgenerators.Rnw |only Runuran-0.11.0/Runuran/inst/doc/src/tab-distributions.tex | 64 Runuran-0.11.0/Runuran/inst/doc/src/tab-generators.tex |only Runuran-0.11.0/Runuran/inst/doc/src/version.tex | 2 Runuran-0.11.0/Runuran/man/Runuran-package.Rd | 202 Runuran-0.11.0/Runuran/man/Runuran.distributions.Rd |only Runuran-0.11.0/Runuran/man/Runuran.special.generators.Rd |only Runuran-0.11.0/Runuran/man/ars.new.Rd | 52 Runuran-0.11.0/Runuran/man/dari.new.Rd | 40 Runuran-0.11.0/Runuran/man/dau.new.Rd | 34 Runuran-0.11.0/Runuran/man/dgt.new.Rd | 33 Runuran-0.11.0/Runuran/man/hitro.new.Rd | 11 Runuran-0.11.0/Runuran/man/itdr.new.Rd | 50 Runuran-0.11.0/Runuran/man/pinv.new.Rd | 50 Runuran-0.11.0/Runuran/man/srou.new.Rd | 44 Runuran-0.11.0/Runuran/man/tdr.new.Rd | 55 Runuran-0.11.0/Runuran/man/ud.Rd |only Runuran-0.11.0/Runuran/man/udbeta.Rd |only Runuran-0.11.0/Runuran/man/udbinom.Rd |only Runuran-0.11.0/Runuran/man/udcauchy.Rd |only Runuran-0.11.0/Runuran/man/udchi.Rd |only Runuran-0.11.0/Runuran/man/udchisq.Rd |only Runuran-0.11.0/Runuran/man/udexp.Rd |only Runuran-0.11.0/Runuran/man/udf.Rd |only Runuran-0.11.0/Runuran/man/udfrechet.Rd |only Runuran-0.11.0/Runuran/man/udgamma.Rd |only Runuran-0.11.0/Runuran/man/udgeom.Rd |only Runuran-0.11.0/Runuran/man/udghyp.Rd |only Runuran-0.11.0/Runuran/man/udgig.Rd |only Runuran-0.11.0/Runuran/man/udgumbel.Rd |only Runuran-0.11.0/Runuran/man/udhyper.Rd |only Runuran-0.11.0/Runuran/man/udhyperbolic.Rd |only Runuran-0.11.0/Runuran/man/udig.Rd |only Runuran-0.11.0/Runuran/man/udlaplace.Rd |only Runuran-0.11.0/Runuran/man/udlnorm.Rd |only Runuran-0.11.0/Runuran/man/udlogarithmic.Rd |only Runuran-0.11.0/Runuran/man/udlogis.Rd |only Runuran-0.11.0/Runuran/man/udlomax.Rd |only Runuran-0.11.0/Runuran/man/udnbinom.Rd |only Runuran-0.11.0/Runuran/man/udnorm.Rd |only Runuran-0.11.0/Runuran/man/udpareto.Rd |only Runuran-0.11.0/Runuran/man/udpois.Rd |only Runuran-0.11.0/Runuran/man/udpowerexp.Rd |only Runuran-0.11.0/Runuran/man/udrayleigh.Rd |only Runuran-0.11.0/Runuran/man/udslash.Rd |only Runuran-0.11.0/Runuran/man/udt.Rd |only Runuran-0.11.0/Runuran/man/udweibull.Rd |only Runuran-0.11.0/Runuran/man/unuran-class.Rd | 10 Runuran-0.11.0/Runuran/man/unuran.cmv-class.Rd | 4 Runuran-0.11.0/Runuran/man/unuran.cmv.new.Rd | 8 Runuran-0.11.0/Runuran/man/unuran.cont-class.Rd | 4 Runuran-0.11.0/Runuran/man/unuran.cont.new.Rd | 15 Runuran-0.11.0/Runuran/man/unuran.details.Rd | 4 Runuran-0.11.0/Runuran/man/unuran.discr-class.Rd | 4 Runuran-0.11.0/Runuran/man/unuran.discr.new.Rd | 7 Runuran-0.11.0/Runuran/man/unuran.distr-class.Rd | 4 Runuran-0.11.0/Runuran/man/unuran.new.Rd | 2 Runuran-0.11.0/Runuran/man/unuran.packed-methods.Rd | 2 Runuran-0.11.0/Runuran/man/uq.Rd | 4 Runuran-0.11.0/Runuran/man/ur.Rd | 3 Runuran-0.11.0/Runuran/man/urbeta.Rd | 15 Runuran-0.11.0/Runuran/man/urbinom.Rd | 14 Runuran-0.11.0/Runuran/man/urburr.Rd | 11 Runuran-0.11.0/Runuran/man/urcauchy.Rd | 12 Runuran-0.11.0/Runuran/man/urchi.Rd | 11 Runuran-0.11.0/Runuran/man/urchisq.Rd | 12 Runuran-0.11.0/Runuran/man/urdgt.Rd | 5 Runuran-0.11.0/Runuran/man/urexp.Rd | 11 Runuran-0.11.0/Runuran/man/urextremeI.Rd | 13 Runuran-0.11.0/Runuran/man/urextremeII.Rd | 15 Runuran-0.11.0/Runuran/man/urf.Rd | 11 Runuran-0.11.0/Runuran/man/urgamma.Rd | 13 Runuran-0.11.0/Runuran/man/urgeom.Rd | 11 Runuran-0.11.0/Runuran/man/urgig.Rd | 11 Runuran-0.11.0/Runuran/man/urhyper.Rd | 13 Runuran-0.11.0/Runuran/man/urhyperbolic.Rd | 11 Runuran-0.11.0/Runuran/man/urlaplace.Rd | 11 Runuran-0.11.0/Runuran/man/urlnorm.Rd | 7 Runuran-0.11.0/Runuran/man/urlogarithmic.Rd | 10 Runuran-0.11.0/Runuran/man/urlogis.Rd | 12 Runuran-0.11.0/Runuran/man/urlomax.Rd | 11 Runuran-0.11.0/Runuran/man/urnbinom.Rd | 11 Runuran-0.11.0/Runuran/man/urnorm.Rd | 13 Runuran-0.11.0/Runuran/man/urpareto.Rd | 11 Runuran-0.11.0/Runuran/man/urplanck.Rd | 11 Runuran-0.11.0/Runuran/man/urpois.Rd | 13 Runuran-0.11.0/Runuran/man/urpowerexp.Rd | 11 Runuran-0.11.0/Runuran/man/urrayleigh.Rd | 11 Runuran-0.11.0/Runuran/man/urt.Rd | 7 Runuran-0.11.0/Runuran/man/urtriang.Rd | 15 Runuran-0.11.0/Runuran/man/urweibull.Rd | 12 Runuran-0.11.0/Runuran/man/vnrou.new.Rd | 10 Runuran-0.11.0/Runuran/src/Makevars.in | 4 Runuran-0.11.0/Runuran/src/README | 2 Runuran-0.11.0/Runuran/src/Runuran.c | 116 Runuran-0.11.0/Runuran/src/Runuran.h | 73 Runuran-0.11.0/Runuran/src/Runuran_distr.c | 195 Runuran-0.11.0/Runuran/src/Runuran_pinv.c | 4 Runuran-0.11.0/Runuran/src/config.h.in | 10 Runuran-0.11.0/Runuran/src/config.w32 | 12 Runuran-0.11.0/Runuran/src/distributions.c |only Runuran-0.11.0/Runuran/src/unuran-src/distributions/c_ghyp.c |only Runuran-0.11.0/Runuran/src/unuran-src/distributions/c_gig.c | 48 Runuran-0.11.0/Runuran/src/unuran-src/distributions/c_gig2.c |only Runuran-0.11.0/Runuran/src/unuran-src/distributions/c_hyperbolic.c |only Runuran-0.11.0/Runuran/src/unuran-src/distributions/c_ig.c |only Runuran-0.11.0/Runuran/src/unuran-src/distributions/c_lognormal.c | 24 Runuran-0.11.0/Runuran/src/unuran-src/distributions/c_slash.c | 14 Runuran-0.11.0/Runuran/src/unuran-src/distributions/unur_distributions.h | 4 Runuran-0.11.0/Runuran/src/unuran-src/distributions/unur_stddistr.h | 4 Runuran-0.11.0/Runuran/src/unuran-src/methods/ars.c | 36 Runuran-0.11.0/Runuran/src/unuran-src/methods/dari.c | 2 Runuran-0.11.0/Runuran/src/unuran-src/methods/hinv.c | 2 Runuran-0.11.0/Runuran/src/unuran-src/methods/ninv.c | 919 -- Runuran-0.11.0/Runuran/src/unuran-src/methods/ninv.h | 5 Runuran-0.11.0/Runuran/src/unuran-src/methods/ninv_debug.ch |only Runuran-0.11.0/Runuran/src/unuran-src/methods/ninv_info.ch |only Runuran-0.11.0/Runuran/src/unuran-src/methods/ninv_init.ch |only Runuran-0.11.0/Runuran/src/unuran-src/methods/ninv_newset.ch |only Runuran-0.11.0/Runuran/src/unuran-src/methods/ninv_newton.ch |only Runuran-0.11.0/Runuran/src/unuran-src/methods/ninv_regula.ch |only Runuran-0.11.0/Runuran/src/unuran-src/methods/ninv_sample.ch |only Runuran-0.11.0/Runuran/src/unuran-src/methods/ninv_struct.h | 6 Runuran-0.11.0/Runuran/src/unuran-src/methods/norta.c | 4 Runuran-0.11.0/Runuran/src/unuran-src/methods/pinv_prep.ch | 9 Runuran-0.11.0/Runuran/src/unuran-src/methods/pinv_sample.ch | 2 Runuran-0.11.0/Runuran/src/unuran-src/parser/parser.h | 2 Runuran-0.11.0/Runuran/src/unuran-src/parser/stringparser_lists.ch | 34 Runuran-0.11.0/Runuran/src/unuran-src/specfunct/besselK.c |only Runuran-0.11.0/Runuran/src/unuran-src/specfunct/unur_specfunct_source.h | 5 Runuran-0.11.0/Runuran/src/unuran-src/tests/inverror.c | 12 Runuran-0.11.0/Runuran/src/unuran-src/tests/timing.c | 127 Runuran-0.11.0/Runuran/src/unuran-src/tests/unuran_tests.h | 16 Runuran-0.11.0/Runuran/src/unuran-src/unur_Rmath.h |only Runuran-0.11.0/Runuran/src/unuran-src/unuran.h | 15 Runuran-0.11.0/Runuran/src/unuran-src/utils/stream.c | 7 Runuran-0.11.0/Runuran/src/unuran-src/utils/unur_fp.c | 24 Runuran-0.11.0/Runuran/tests/test_deprecated.R | 74 Runuran-0.11.0/Runuran/tests/test_distributions_cont.R | 8 Runuran-0.11.0/Runuran/tests/test_distributions_discr.R | 13 Runuran-0.11.0/Runuran/tests/test_routines.R | 54 Runuran-0.11.0/Runuran/tests/test_ud.R |only 169 files changed, 3895 insertions(+), 3353 deletions(-)
Author: Josef Leydold
Title: Streams of random numbers
Description: Unified object oriented interface for multiple independent
streams of random numbers from different sources.
Diff between rstream versions 1.2.3 dated 2009-01-08 and 1.2.4 dated 2009-11-17
DESCRIPTION | 11 +++++++---- NEWS | 4 ++++ man/rstream-package.Rd | 4 ++-- man/rstream.RNG.Rd | 2 +- man/rstream.lecuyer-class.Rd | 2 +- man/rstream.mrg32k3a-class.Rd | 2 +- man/rstream.runif-class.Rd | 4 ++-- 7 files changed, 18 insertions(+), 11 deletions(-)
Author: Robert B. Gramacy
Title: Estimation for multivariate normal and Student-t data with
monotone missingness
Description: Estimation of multivariate normal and student-t data of
arbitrary dimension where the pattern of missing data is
monotone. Through the use of parsimonious/shrinkage regressions
(plsr, pcr, lasso, ridge, etc.), where standard regressions
fail, the package can handle a nearly arbitrary amount of
missing data. The current version supports maximum likelihood
inference and a full Bayesian approach employing scale-mixtures
for the lasso (double-exponential) prior and Student-t errors.
Monotone data augmentation extends this Bayesian approach to
arbitrary missingness patterns. A fully functional standalone
interface to the Bayesian lasso (from Park & Casella) and ridge
regression with model selection via Reversible Jump, and
student-t errors (from Geweke) is also provided
Diff between monomvn versions 1.7-3 dated 2009-08-19 and 1.7-4 dated 2009-11-17
ChangeLog | 10 ++ DESCRIPTION | 8 - R/blasso.R | 19 ++- man/blasso.Rd | 11 +- man/bmonomvn.Rd | 4 man/monomvn-package.Rd | 2 man/monomvn.Rd | 4 src/blasso.cc | 235 +++++++++++++++++++++++++------------------------ src/blasso.h | 6 - 9 files changed, 165 insertions(+), 134 deletions(-)
Author: Fang Chang
Title: Clustering Method Based on Local Shrinking
Description: The package contains functions for automatically
estimating the number of clusters and getting the final cluster
partition without any input parameter except the stopping rule
for convergence. The package also provides functions to
evaluate and compare the performances of partitions of a data
set both numerically and graphically.
Diff between clues versions 0.3.2 dated 2009-03-17 and 0.3.9 dated 2009-11-17
clues-0.3.2/clues/R/clues.CH.R |only clues-0.3.2/clues/R/clues.sil.R |only clues-0.3.2/clues/data/Iris.R |only clues-0.3.2/clues/data/Ruspini.R |only clues-0.3.2/clues/data/iris.dat |only clues-0.3.2/clues/data/ruspini.dat |only clues-0.3.2/clues/man/Get.CH.Rd |only clues-0.3.2/clues/man/Get.Silhouette.Rd |only clues-0.3.2/clues/man/Iris.Rd |only clues-0.3.2/clues/man/Ruspini.Rd |only clues-0.3.2/clues/src/CH.f |only clues-0.3.2/clues/src/chooseK_CH3.f |only clues-0.3.2/clues/src/chooseK_sil3.f |only clues-0.3.2/clues/src/clustering2.f |only clues-0.3.2/clues/src/dmedian.f |only clues-0.3.2/clues/src/dsort.f |only clues-0.3.2/clues/src/sharpen2.f |only clues-0.3.2/clues/src/silhouette3.f |only clues-0.3.9/clues/DESCRIPTION | 14 - clues-0.3.9/clues/INDEX | 18 - clues-0.3.9/clues/NAMESPACE | 13 - clues-0.3.9/clues/R/adjustedRand.R | 98 ++++---- clues-0.3.9/clues/R/clues.R | 175 +++++++++----- clues-0.3.9/clues/R/clues_CH.R |only clues-0.3.9/clues/R/clues_sil.R |only clues-0.3.9/clues/R/clustering.R | 94 +++---- clues-0.3.9/clues/R/compClust.R | 142 +++++------ clues-0.3.9/clues/R/rankDist.R | 117 +++++---- clues-0.3.9/clues/R/shrinking.R | 69 ++--- clues-0.3.9/clues/R/view.R | 383 ++++++++++++++++++++++---------- clues-0.3.9/clues/data/Curve.R | 8 clues-0.3.9/clues/data/Maronna.R | 8 clues-0.3.9/clues/data/Ring.R | 8 clues-0.3.9/clues/data/Vowel.R | 8 clues-0.3.9/clues/inst |only clues-0.3.9/clues/man/Curve.Rd | 19 + clues-0.3.9/clues/man/Maronna.Rd | 23 + clues-0.3.9/clues/man/Ring.Rd | 21 + clues-0.3.9/clues/man/Vowel.Rd | 30 +- clues-0.3.9/clues/man/adjustedRand.Rd | 30 -- clues-0.3.9/clues/man/clues.Rd | 42 +-- clues-0.3.9/clues/man/clustering.Rd | 40 ++- clues-0.3.9/clues/man/compClust.Rd | 58 ++-- clues-0.3.9/clues/man/get_CH.Rd |only clues-0.3.9/clues/man/get_Silhouette.Rd |only clues-0.3.9/clues/man/plot.clues.Rd |only clues-0.3.9/clues/man/plotAvgCurves.Rd | 54 +++- clues-0.3.9/clues/man/plotClusters.Rd | 45 ++- clues-0.3.9/clues/man/plotCurves.Rd | 51 +++- clues-0.3.9/clues/man/print.clues.Rd |only clues-0.3.9/clues/man/shrinking.Rd | 21 - clues-0.3.9/clues/man/summary.clues.Rd |only clues-0.3.9/clues/src/CH.f95 |only clues-0.3.9/clues/src/adjustedRand.c | 170 +++++++------- clues-0.3.9/clues/src/chooseK.f95 |only clues-0.3.9/clues/src/clustering2.f95 |only clues-0.3.9/clues/src/dmedian.f95 |only clues-0.3.9/clues/src/dsort.f95 |only clues-0.3.9/clues/src/sharpen2.f95 |only clues-0.3.9/clues/src/silhouette3.f95 |only 60 files changed, 1061 insertions(+), 698 deletions(-)
More information about polySegratioMM at CRAN
Permanent link
Author: Brian Walters
Title: k-Nearest Neighbor Diagnostic Tools
Description: A suite of graphical diagnostic tools to evaluate kNN
classifications.
Diff between nnDiag versions 0.0-2 dated 2009-11-16 and 0.0-3 dated 2009-11-17
DESCRIPTION | 9 +++++---- 1 file changed, 5 insertions(+), 4 deletions(-)
Author: Daniel P Gaile
Title: Tool for sending interactive bioinformatic heatmaps with
tool-tip content.
Description: A tool for visualizing data
Diff between iGenomicViewer versions 2.4.4 dated 2009-10-29 and 2.4.6 dated 2009-11-17
DESCRIPTION | 9 ++- R/adfWrapper.R | 8 ++- R/convertLoc.R | 12 ++--- R/dfWrapper.R | 4 + R/marrayWrapper.R | 10 ++-- inst/doc/figure02.png |only inst/doc/figure03.png |only inst/doc/iGGV.Rnw | 80 ++++++++++++++++++++++++++++++++-- inst/doc/iGGV.dvi |binary inst/doc/iGGV.pdf |binary inst/doc/iGenomicViewer.Rnw | 102 ++++++++++++++++++++++++++++++++++++++++++++ inst/doc/iGenomicViewer.dvi |binary inst/doc/iGenomicViewer.pdf |binary 13 files changed, 203 insertions(+), 22 deletions(-)
More information about iGenomicViewer at CRAN
Permanent link
Author: Robin K. S. Hankin
Title: ecological drift under the UNTB
Description: A collection of utilities for biodiversity data. Includes
the simulation of ecological drift under Hubbell's Unified
Neutral Theory of Biodiversity, and the calculation of various
diagnostics such as Preston curves. Now includes functionality
provided by Francois Munoz and Andrea Manica.
Diff between untb versions 1.6-1 dated 2009-10-15 and 1.6-2 dated 2009-11-17
DESCRIPTION | 8 R/munoz.R | 2 inst/doc/untbpaper.pdf | 3293 ++++++++++++++++++++++++------------------------- 3 files changed, 1637 insertions(+), 1666 deletions(-)
Author: Nicole Kraemer, Juliane Schaefer
Title: Regularized estimation of partial correlation matrices
Description: The package estimates the matrix of partial correlations
based on different regularized regression methods: lasso,
adaptive lasso, PLS, and Ridge Regression.
Diff between parcor versions 0.2 dated 2009-11-12 and 0.2-1 dated 2009-11-17
DESCRIPTION | 8 ++++---- R/adalasso.R | 12 ++++++++---- R/mylars.R | 6 ++++-- R/ridge.cv.R | 6 ++++-- man/adalasso.Rd | 4 ++++ man/mylars.Rd | 6 +++++- man/parcor-package.Rd | 4 ++-- man/ridge.cv.Rd | 3 ++- 8 files changed, 33 insertions(+), 16 deletions(-)
Author: Paul Hiemstra
Title: Automatic interpolation package
Description: This package performs an automatic interpolation by
automatically estimating the variogram and then calling gstat.
Diff between automap versions 1.0-2 dated 2009-07-18 and 1.0-4 dated 2009-11-17
DESCRIPTION | 8 ++--- R/autoKrige.cv.r | 18 ++++++++++- R/autoKrige.r | 5 +++ R/autokrige.vgm.panel.r | 8 +++++ SvnLog | 65 +++++++++++++++++++++++++++++++++++++++++++ man/autoKrige.rd | 8 +---- man/autoKrige_cv.rd | 11 +++---- man/autofitVariogram.rd | 8 ++--- man/automapPlot.rd | 4 +- man/compare.cv.rd | 7 +--- man/plot.autoKrige.rd | 6 +-- man/posPredictionInterval.rd | 2 - 12 files changed, 119 insertions(+), 31 deletions(-)
Author: Peter K Dunn
Title: Tweedie exponential family models
Description: Maximum likelihood computations for Tweedie families.
Diff between tweedie versions 2.0.0 dated 2009-08-10 and 2.0.2 dated 2009-11-17
CHANGE.log | 11 +++++++++-- DESCRIPTION | 8 ++++---- R/tweedie.R | 25 ++++++++++++++++++++++++- man/AICtweedie.Rd |only man/tweedie-package.Rd | 4 ++-- man/tweedie.profile.Rd | 2 +- 6 files changed, 40 insertions(+), 10 deletions(-)
Author: Delphine Charif and Jean R. Lobry and Anamaria Necsulea and
Leonor Palmeira and Simon Penel
Title: Biological Sequences Retrieval and Analysis
Description: Exploratory data analysis and data visualization for
biological sequence (DNA and protein) data. Include also
utilities for sequence data management under the ACNUC system.
Diff between seqinr versions 2.0-6 dated 2009-10-18 and 2.0-7 dated 2009-11-17
seqinr-2.0-6/seqinr/inst/doc/seqinr_2_0-3.pdf |only seqinr-2.0-7/seqinr/DESCRIPTION | 10 seqinr-2.0-7/seqinr/R/comp.R | 13 seqinr-2.0-7/seqinr/R/trimSpace.R | 4 seqinr-2.0-7/seqinr/R/where.is.this.acc.R |only seqinr-2.0-7/seqinr/R/words.pos.R | 6 seqinr-2.0-7/seqinr/inst/doc/seqinr_2_0-7.pdf |only seqinr-2.0-7/seqinr/inst/doc/src/appendix/FAQ.rnw | 13 seqinr-2.0-7/seqinr/inst/doc/src/appendix/FAQ.tex | 42 +- seqinr-2.0-7/seqinr/inst/doc/src/appendix/releasenotes.rnw | 33 ++ seqinr-2.0-7/seqinr/inst/doc/src/appendix/releasenotes.tex | 76 ++++- seqinr-2.0-7/seqinr/inst/doc/src/config/book.bib | 8 seqinr-2.0-7/seqinr/inst/doc/src/figs/cover.pdf | 26 - seqinr-2.0-7/seqinr/inst/doc/src/frontmatter/cover.tex | 16 - seqinr-2.0-7/seqinr/inst/doc/src/frontmatter/licence.tex | 6 seqinr-2.0-7/seqinr/inst/doc/src/mainmatter/acnucsocket.tex | 59 ++-- seqinr-2.0-7/seqinr/inst/doc/src/mainmatter/dealseq.rnw | 65 ++-- seqinr-2.0-7/seqinr/inst/doc/src/mainmatter/dealseq.tex | 158 ++++------- seqinr-2.0-7/seqinr/inst/doc/src/mainmatter/extractseqs.tex | 60 ++-- seqinr-2.0-7/seqinr/inst/doc/src/mainmatter/getseqacnuc.rnw | 2 seqinr-2.0-7/seqinr/inst/doc/src/mainmatter/getseqacnuc.tex | 113 ++++--- seqinr-2.0-7/seqinr/inst/doc/src/mainmatter/getseqflat.tex | 31 +- seqinr-2.0-7/seqinr/inst/doc/src/mainmatter/introduction.tex | 38 +- seqinr-2.0-7/seqinr/inst/doc/src/mainmatter/multivariate.tex | 20 - seqinr-2.0-7/seqinr/inst/doc/src/mainmatter/nonparastats.rnw | 14 seqinr-2.0-7/seqinr/inst/doc/src/mainmatter/nonparastats.tex | 66 ++-- seqinr-2.0-7/seqinr/inst/doc/src/mainmatter/querylang.tex | 28 - seqinr-2.0-7/seqinr/inst/doc/src/tables/aacost.tex | 4 seqinr-2.0-7/seqinr/inst/doc/src/tables/dpqrtable.tex | 4 seqinr-2.0-7/seqinr/inst/doc/src/tables/toyaa.tex | 4 seqinr-2.0-7/seqinr/inst/doc/src/tables/toycodon.tex | 4 seqinr-2.0-7/seqinr/man/choosebank.Rd | 4 seqinr-2.0-7/seqinr/man/comp.Rd | 19 - seqinr-2.0-7/seqinr/man/uco.Rd | 21 + seqinr-2.0-7/seqinr/man/where.is.this.acc.Rd |only seqinr-2.0-7/seqinr/man/words.pos.Rd | 5 36 files changed, 543 insertions(+), 429 deletions(-)
Author: Valentin Rousson
Title: Simple Component Analysis
Description: Simple Component Analysis often provides much more
interpretable components than Principal Components (PCA)
without losing too much.
Diff between sca versions 0.8-6 dated 2009-02-09 and 0.8-7 dated 2009-11-17
ChangeLog | 6 ++++++ DESCRIPTION | 14 +++++++++----- R/aaa.R | 2 +- man/sca.Rd | 4 ++-- 4 files changed, 18 insertions(+), 8 deletions(-)
Author: Liviu Andronic
Title: Graphically export output to LaTeX or HTML
Description: The package helps users to graphically export Rcmdr output
to LaTeX or HTML code, via xtable() or Hmisc::latex(). The
plug-in was originally intended to facilitate exporting Rcmdr
output to formats other than ASCII text and to provide R
novices with an easy-to-use, easy-to-access reference on
exporting R objects to formats suited for printed output. The
package documentation contains several pointers on creating
reports, either by using conventional word processors or
LaTeX/LyX.
Diff between RcmdrPlugin.Export versions 0.2-2 dated 2009-10-14 and 0.3-0 dated 2009-11-17
RcmdrPlugin.Export-0.2-2/RcmdrPlugin.Export/R/xtable.Export.R |only RcmdrPlugin.Export-0.2-2/RcmdrPlugin.Export/inst/CHANGES |only RcmdrPlugin.Export-0.3-0/RcmdrPlugin.Export/DESCRIPTION | 28 - RcmdrPlugin.Export-0.3-0/RcmdrPlugin.Export/R/formatdfExport.R |only RcmdrPlugin.Export-0.3-0/RcmdrPlugin.Export/R/latexExport.R |only RcmdrPlugin.Export-0.3-0/RcmdrPlugin.Export/R/xtableExport.R |only RcmdrPlugin.Export-0.3-0/RcmdrPlugin.Export/inst/ChangeLog |only RcmdrPlugin.Export-0.3-0/RcmdrPlugin.Export/inst/LIMITATIONS | 8 RcmdrPlugin.Export-0.3-0/RcmdrPlugin.Export/inst/etc/menus.txt | 16 - RcmdrPlugin.Export-0.3-0/RcmdrPlugin.Export/man/.backups |only RcmdrPlugin.Export-0.3-0/RcmdrPlugin.Export/man/RcmdrPlugin.Export-package.Rd | 160 +++++----- RcmdrPlugin.Export-0.3-0/RcmdrPlugin.Export/man/formatdfExport.Rd |only RcmdrPlugin.Export-0.3-0/RcmdrPlugin.Export/man/latexExport.Rd |only RcmdrPlugin.Export-0.3-0/RcmdrPlugin.Export/man/utilities.Rd |only RcmdrPlugin.Export-0.3-0/RcmdrPlugin.Export/man/xtableExport.Rd | 99 ++---- 15 files changed, 153 insertions(+), 158 deletions(-)
More information about RcmdrPlugin.Export at CRAN
Permanent link
Author: Keyan Salari, Robert Tibshirani, Jonathan R. Pollack
Title: DR-Integrator
Description: Integrative analysis of DNA copy number and gene
expression data described in Salari et al 2009
Diff between DRI versions 1.0 dated 2009-08-05 and 1.1 dated 2009-11-17
DRI-1.0/DRI/man/dri.fix.missingvals.Rd |only DRI-1.1/DRI/DESCRIPTION | 11 ++++++----- DRI-1.1/DRI/NAMESPACE | 2 +- DRI-1.1/DRI/R/DRI-internal.R |only DRI-1.1/DRI/R/binary.fdr.search.R | 2 +- DRI-1.1/DRI/R/correlate.R | 2 +- DRI-1.1/DRI/R/drcorrelate.R | 2 +- DRI-1.1/DRI/R/drcorrelate.null.R | 2 +- DRI-1.1/DRI/R/dri.correlation.plot.R | 2 +- DRI-1.1/DRI/R/dri.fdrCutoff.R | 2 +- DRI-1.1/DRI/R/dri.fix.missingvals.R | 2 +- DRI-1.1/DRI/R/dri.heatmap.R | 2 +- DRI-1.1/DRI/R/dri.impute.R | 2 +- DRI-1.1/DRI/R/dri.merge.CNbyRNA.R |only DRI-1.1/DRI/R/dri.sig_genes.R | 6 +++--- DRI-1.1/DRI/R/dri.smooth.cghdata.R |only DRI-1.1/DRI/R/drsam.R | 2 +- DRI-1.1/DRI/R/drsam.null.R | 2 +- DRI-1.1/DRI/R/fdr.fast.R | 2 +- DRI-1.1/DRI/R/get.pi0.R | 2 +- DRI-1.1/DRI/R/observed_t.R | 2 +- DRI-1.1/DRI/R/permute.R | 2 +- DRI-1.1/DRI/R/permute_t.R | 2 +- DRI-1.1/DRI/R/runFusedLasso.R |only DRI-1.1/DRI/R/runningmean.R |only DRI-1.1/DRI/R/scale01.R | 2 +- DRI-1.1/DRI/R/sum.fp.R | 2 +- DRI-1.1/DRI/R/ttest.func.R | 2 +- DRI-1.1/DRI/R/varr.R | 2 +- DRI-1.1/DRI/man/DRI-package.Rd | 32 ++++++++++++++++++++------------ DRI-1.1/DRI/man/drcorrelate.Rd | 14 +++++++++----- DRI-1.1/DRI/man/drcorrelate.null.Rd | 14 +++++++++----- DRI-1.1/DRI/man/dri.correlation.plot.Rd | 17 +++++++++++------ DRI-1.1/DRI/man/dri.fdrCutoff.Rd | 25 ++++++++++++++++--------- DRI-1.1/DRI/man/dri.heatmap.Rd | 20 +++++++++++++------- DRI-1.1/DRI/man/dri.impute.Rd | 9 ++++----- DRI-1.1/DRI/man/dri.merge.CNbyRNA.Rd |only DRI-1.1/DRI/man/dri.sig_genes.Rd | 17 +++++++++++------ DRI-1.1/DRI/man/dri.smooth.cghdata.Rd |only DRI-1.1/DRI/man/drsam.Rd | 19 ++++++++++++------- DRI-1.1/DRI/man/drsam.null.Rd | 19 ++++++++++++------- DRI-1.1/DRI/man/mySampleData.Rd | 18 ++++++------------ DRI-1.1/DRI/man/runFusedLasso.Rd |only 43 files changed, 153 insertions(+), 110 deletions(-)
Author: James Honaker
Title: Amelia II: A Program for Missing Data
Description: Amelia II "multiply imputes" missing data in a single
cross-section (such as a survey), from a time series (like
variables collected for each year in a country), or from a
time-series-cross-sectional data set (such as collected by
years for each of several countries). Amelia II implements our
bootstrapping-based algorithm that gives essentially the same
answers as the standard IP or EMis approaches, is usually
considerably faster than existing approaches and can handle
many more variables. Unlike Amelia I and other statistically
rigorous imputation software, it virtually never crashes (but
please let us know if you find to the contrary!). The program
also generalizes existing approaches by allowing for trends in
time series across observations within a cross-sectional unit,
as well as priors that allow experts to incorporate beliefs
they have about the values of missing cells in their data.
Amelia II also includes useful diagnostics of the fit of
multiple imputation models. The program works from the R
command line or via a graphical user interface that does not
require users to know R.
Diff between Amelia versions 1.2-13 dated 2009-08-13 and 1.2-14 dated 2009-11-17
ChangeLog | 16 DESCRIPTION | 8 NEWS | 11 R/emb.r | 2 R/prep.r | 1 inst/doc/amelia.Rnw | 2 inst/doc/amelia.pdf | 6991 +++++++++++++++++++++------------------------------ inst/doc/copyRd.Rout | 4 inst/doc/index.shtml | 2 9 files changed, 2920 insertions(+), 4117 deletions(-)
Author: Hadley Wickham
Title: Make it easier to work with strings.
Description: stringr is a set of simple wrappers that make R's string
functions more consistent, simpler and easier to use. It does
this by ensuring that: function and argument names (and
positions) are consistent, all functions deal with NA's and
zero length character appropriately, and the output data
structures from each function matches the input data structures
of other functions.
Diff between stringr versions 0.1.10 dated 2009-11-09 and 0.2 dated 2009-11-16
stringr-0.1.10/stringr/R/basics.r |only stringr-0.1.10/stringr/R/regexp.r |only stringr-0.2/stringr/DESCRIPTION | 9 +++++---- stringr-0.2/stringr/NEWS |only stringr-0.2/stringr/R/detect.r |only stringr-0.2/stringr/R/dup.r |only stringr-0.2/stringr/R/extract.r |only stringr-0.2/stringr/R/join.r |only stringr-0.2/stringr/R/length.r |only stringr-0.2/stringr/R/locate.r |only stringr-0.2/stringr/R/match.r | 9 ++++++--- stringr-0.2/stringr/R/replace.r |only stringr-0.2/stringr/R/split.r |only stringr-0.2/stringr/R/sub.r |only stringr-0.2/stringr/TODO |only stringr-0.2/stringr/inst/doc/introduction.md |only stringr-0.2/stringr/man/str_detect.Rd | 4 ++-- stringr-0.2/stringr/man/str_dup.Rd | 4 ++-- stringr-0.2/stringr/man/str_join.Rd | 4 ++-- stringr-0.2/stringr/man/str_length.Rd | 4 ++-- stringr-0.2/stringr/man/str_match.Rd | 4 ++-- stringr-0.2/stringr/man/str_match_all.Rd | 4 ++-- stringr-0.2/stringr/man/str_pad.Rd | 4 ++-- stringr-0.2/stringr/man/str_split.Rd | 21 +++++++++++++++++---- stringr-0.2/stringr/man/str_split_fixed.Rd |only stringr-0.2/stringr/man/str_sub.Rd | 4 ++-- stringr-0.2/stringr/man/str_trim.Rd | 4 ++-- stringr-0.2/stringr/tests/test-length.r | 4 ++++ stringr-0.2/stringr/tests/test-match.r | 9 +++++++++ stringr-0.2/stringr/tests/test-split.r |only stringr-0.2/stringr/tests/test-sub.r | 12 ++++++++++++ 31 files changed, 71 insertions(+), 29 deletions(-)
Author: Brian Walters
Title: k-Nearest Neighbor Diagnostic Tools
Description: A suite of graphical diagnostic tools to evaluate kNN
classifications.
Diff between nnDiag versions 0.0-1 dated 2009-10-26 and 0.0-2 dated 2009-11-16
nnDiag-0.0-1/nnDiag/R/plotters.R |only nnDiag-0.0-1/nnDiag/R/printers.R |only nnDiag-0.0-1/nnDiag/data/FORGRP.tab |only nnDiag-0.0-1/nnDiag/data/VOLUME.tab |only nnDiag-0.0-1/nnDiag/data/VOLUMEnnIndex_k20.tab |only nnDiag-0.0-1/nnDiag/man/FORGRP.Rd |only nnDiag-0.0-1/nnDiag/man/VOLUME.Rd |only nnDiag-0.0-1/nnDiag/man/VOLUMEnnIndex_k20.Rd |only nnDiag-0.0-2/nnDiag/DESCRIPTION | 15 +++--- nnDiag-0.0-2/nnDiag/NAMESPACE | 10 +++- nnDiag-0.0-2/nnDiag/R/aoiMaker.R |only nnDiag-0.0-2/nnDiag/R/arealBias.R |only nnDiag-0.0-2/nnDiag/R/bias.R | 57 ++++++++++++++++++++++- nnDiag-0.0-2/nnDiag/R/categorical.R | 23 +++++++++ nnDiag-0.0-2/nnDiag/R/extrapolations.R |only nnDiag-0.0-2/nnDiag/R/grouper.R | 61 ++++++++++++++++++------- nnDiag-0.0-2/nnDiag/R/outInflu.R | 32 ++++++++++++- nnDiag-0.0-2/nnDiag/R/scedast.R | 40 ++++++++++++++-- nnDiag-0.0-2/nnDiag/data/LuceForgrp.tab |only nnDiag-0.0-2/nnDiag/data/LuceSubset_Mask.tif |only nnDiag-0.0-2/nnDiag/data/LuceSubset_Tcap.tif |only nnDiag-0.0-2/nnDiag/data/LuceSubset_Volume.tif |only nnDiag-0.0-2/nnDiag/data/LuceVolume.tab |only nnDiag-0.0-2/nnDiag/data/LuceVolume_indx.tab |only nnDiag-0.0-2/nnDiag/data/LuceVolume_subset.tab |only nnDiag-0.0-2/nnDiag/man/LuceForgrp.Rd |only nnDiag-0.0-2/nnDiag/man/LuceVolume.Rd |only nnDiag-0.0-2/nnDiag/man/LuceVolume_indx.Rd |only nnDiag-0.0-2/nnDiag/man/LuceVolume_subset.Rd |only nnDiag-0.0-2/nnDiag/man/aoiMaker.Rd |only nnDiag-0.0-2/nnDiag/man/arealBias.Rd |only nnDiag-0.0-2/nnDiag/man/bias.Rd | 44 ++++++++++-------- nnDiag-0.0-2/nnDiag/man/categorical.Rd | 18 +++---- nnDiag-0.0-2/nnDiag/man/extrap.Rd |only nnDiag-0.0-2/nnDiag/man/grouper.Rd | 33 +++++++------ nnDiag-0.0-2/nnDiag/man/nnDiag-package.Rd | 28 ----------- nnDiag-0.0-2/nnDiag/man/outInflu.Rd | 26 +++++----- nnDiag-0.0-2/nnDiag/man/rmse.Rd | 12 ++-- nnDiag-0.0-2/nnDiag/man/scedast.Rd | 25 ++++------ 39 files changed, 286 insertions(+), 138 deletions(-)
Author: Christian Roever, Nils Raabe, Karsten Luebke, Uwe Ligges, Gero
Szepannek, Marc Zentgraf
Title: Classification and visualization
Description: Miscellaneous functions for classification and
visualization developed at the Fakultaet Statistik, Technische
Universitaet Dortmund
Diff between klaR versions 0.6-0 dated 2009-09-22 and 0.6-1 dated 2009-11-16
Changes-ToDo | 8 +++----- DESCRIPTION | 8 ++++---- NAMESPACE | 3 ++- R/kmodes.R |only man/kmodes.Rd |only 5 files changed, 9 insertions(+), 10 deletions(-)
Author: Christian Hennig
Title: Fixed point clusters, clusterwise regression and discriminant
plots
Description: Fuzzy and crisp fixed point cluster analysis based on
Mahalanobis distance and linear regression fixed point
clusters. Semi-explorative, semi-model-based clustering
methods, operating on n*p data, do not need prespecification of
number of clusters, produce overlapping clusters. Symmetric and
asymmetric discriminant projections separate groups optimally,
used to visualize the separation of groupings, visual cluster
validation. Clusterwise linear regression by normal mixture
modeling. Cluster validation statistics for distance based
clustering including corrected Rand index. Clusterwise cluster
stability assessment. DBSCAN clustering. Interface functions
for many clustering methods implemented in R. Note that the use
of the package mclust (called by function prabclust) is
protected by a special license, see
http://www.stat.washington.edu/mclust/license.txt, particularly
point 6.
Diff between fpc versions 1.2-6 dated 2009-08-26 and 1.2-7 dated 2009-11-16
DESCRIPTION | 12 - R/rFace.R | 5 tests/examples.Rout.save | 473 +++++++++++++++++++++++------------------------ 3 files changed, 251 insertions(+), 239 deletions(-)
Author: E. Andres Houseman, Sc.D.
Title: Recursively Partitioned Mixture Model
Description: Recursively Partitioned Mixture Model for Beta and
Gaussian Mixtures. This is a model-based clustering algorithm
that returns a hierarchy of classes, similar to hierarchical
clustering, but also similar to finite mixture models.
Diff between RPMM versions 1.0 dated 2009-09-09 and 1.05 dated 2009-11-16
DESCRIPTION | 8 - R/betaRPMM.R | 4 R/gaussRPMM.R | 287 +++++++++++++++++++++++++++++----------------------------- 3 files changed, 154 insertions(+), 145 deletions(-)
Author: Ian Taylor, Ian Stewart, Tommy Garrison, Andre Punt, John
Wallace, and other contributors
Title: R code for Stock Synthesis
Description: Functions for reading output, plotting, exploring and
manipulating input files for Richard Methot's Stock Synthesis
fisheries stock assessment modeling platform.
Diff between r4ss versions 1.0 dated 2009-11-10 and 1.01 dated 2009-11-16
r4ss-1.0/r4ss/R/lines.sel.R |only r4ss-1.0/r4ss/man/lines.sel.Rd |only r4ss-1.01/r4ss/DESCRIPTION | 13 - r4ss-1.01/r4ss/R/SSv3_output.R | 19 ++ r4ss-1.01/r4ss/R/SSv3_plots.R | 229 ++++++++++++++++---------------- r4ss-1.01/r4ss/R/sel.line.R |only r4ss-1.01/r4ss/R/selfit.R | 8 - r4ss-1.01/r4ss/R/update_r4ss_files.R |only r4ss-1.01/r4ss/inst |only r4ss-1.01/r4ss/man/SS_changepars.Rd | 2 r4ss-1.01/r4ss/man/SS_profile.Rd | 27 +-- r4ss-1.01/r4ss/man/SS_recdevs.Rd | 8 - r4ss-1.01/r4ss/man/SSv3_FishGraph.Rd | 11 - r4ss-1.01/r4ss/man/SSv3_output.Rd | 16 +- r4ss-1.01/r4ss/man/SSv3_plotpars.Rd | 14 + r4ss-1.01/r4ss/man/SSv3_plots.Rd | 42 +++-- r4ss-1.01/r4ss/man/r4ss-package.Rd |only r4ss-1.01/r4ss/man/sel.line.Rd |only r4ss-1.01/r4ss/man/selfit.Rd | 9 - r4ss-1.01/r4ss/man/update_r4ss_files.Rd |only 20 files changed, 219 insertions(+), 179 deletions(-)
Author: Rolf Turner
Title: Delaunay Triangulation and Dirichlet (Voronoi) Tessellation.
Description: Calculates the Delaunay triangulation and the Dirichlet or
Voronoi tessellation (with respect to the entire plane) of a
planar point set.
Diff between deldir versions 0.0-9 dated 2009-11-04 and 0.0-10 dated 2009-11-16
deldir-0.0-10/deldir/ChangeLog | 7 +++++++ deldir-0.0-10/deldir/DESCRIPTION | 8 ++++---- deldir-0.0-10/deldir/R/First.R | 2 ++ deldir-0.0-10/deldir/R/deldir.R | 4 ++-- deldir-0.0-10/deldir/inst/ratfor.discarded |only deldir-0.0-10/deldir/man/deldir.Rd | 24 +++++++++++++++++------- deldir-0.0-9/deldir/inst/ratfor/inddup.r |only deldir-0.0-9/deldir/src/inddup.f |only 8 files changed, 32 insertions(+), 13 deletions(-)
Author: Roger Bivand
Title: Interface between GRASS 6 geographical information system and R
Description: Interpreted interface between GRASS 6 geographical
information system and R, based on starting R from within the
GRASS environment, or running free-standing R in a temporary
GRASS location; the package provides facilities for using all
GRASS commands from the R command line.
Diff between spgrass6 versions 0.6-11 dated 2009-10-30 and 0.6-12 dated 2009-11-15
ChangeLog | 8 ++- DESCRIPTION | 8 +-- R/bin_link.R | 110 ------------------------------------------ R/vect_link.R | 144 +++++++++++++++++++++++++++++++++++-------------------- R/xml1.R | 4 + inst/ChangeLog | 8 ++- man/readRAST6.Rd | 2 7 files changed, 118 insertions(+), 166 deletions(-)
Author: Aaron A. King, Edward L. Ionides, Carles Breto, Steve Ellner,
Bruce Kendall
Title: Statistical inference for partially observed Markov processes
Description: Inference methods for partially-observed Markov processes
Diff between pomp versions 0.25-4 dated 2009-09-22 and 0.25-7 dated 2009-11-15
DESCRIPTION | 14 ++--- NAMESPACE | 1 R/mif.R | 12 ++++ R/nlf.R | 6 +- R/slice.R | 15 +++++ inst/ChangeLog | 27 +++++++++ inst/doc/advanced_topics_in_pomp.pdf |binary inst/doc/intro_to_pomp.pdf |binary man/slice.Rd | 42 +++++++++++++-- man/sobol.Rd | 1 tests/ou2-mif.R | 22 ++++++++ tests/ou2-mif.Rout.save | 24 ++++++++ tests/ou2-nlf.R | 14 +++++ tests/ou2-nlf.Rout.save | 96 +++++++++++++++++++---------------- 14 files changed, 216 insertions(+), 58 deletions(-)
Author: Peter Solymos
Title: Multivariate Data Handling in Ecology and Biogeography
Description: A framework package aimed to provide standardized
computational environment for specialist work via object
classes to represent the data coded by samples, taxa and
segments (i.e. subpopulations, repeated measures). It supports
easy processing of the data along with cross tabulation and
relational data tables for samples and taxa. An object of class
`mefa' is a project specific compendium of the data and can be
easily used in further analyses. Methods are provided for
extraction, aggregation, conversion, plotting, summary and
reporting of `mefa' objects. Reports can be generated in plain
text or LaTeX format. Vignette contains worked examples.
Diff between mefa versions 3.1-3 dated 2009-10-15 and 3.1-4 dated 2009-11-15
DESCRIPTION | 10 +++++----- R/zzz.R | 2 +- inst/ChangeLog | 9 +++++++-- inst/doc/mefa.pdf |binary 4 files changed, 13 insertions(+), 8 deletions(-)
Author: code by Fionn Murtagh and R development team, modifications and
packaging by Peter Langfelder
Title: Implementation of optimal hierarchical clustering
Description: Implementation of optimal hierarchical clustering
Diff between flashClust versions 0.10 dated 2009-02-05 and 0.10-1 dated 2009-11-15
Changelog |only DESCRIPTION | 13 ++++++++----- R/murtagh.R | 3 +++ 3 files changed, 11 insertions(+), 5 deletions(-)
Author: Felix Kaminsky
Title: Estimates Output
Description: The function collection stores the estimates of several
models and formats it to a table of the form estimate starred
and std.err. below. The default output is LaTeX but output to
CSV for later editing in a spreadsheet tool is possible as
well. It works for linear models (lm) and panel models from the
"plm"-package (plm). The added "descsto" and "desctab" enable
you to export descriptive statistics of data-frames and single
variables to LaTeX and CSV.
Diff between estout versions 0.7-1 dated 2009-11-11 and 0.8-1 dated 2009-11-15
DESCRIPTION | 6 +- R/esttab.R | 172 ++++++++++++++++++++++++++++++++-------------------------- man/esttab.Rd | 9 ++- 3 files changed, 104 insertions(+), 83 deletions(-)
Author: Nils B. Weidmann
Title: CShapes Dataset and Utilities
Description: Package for CShapes, a GIS dataset of country boundaries
(1946-2008). Includes functions for data extraction and the
computation of weights matrices.
Diff between cshapes versions 0.1-1 dated 2009-08-13 and 0.1-2 dated 2009-11-15
DESCRIPTION | 8 ++++---- inst/java/cshapes.jar |binary inst/shp/changelog.txt |only inst/shp/cshapes.shp.xml |only inst/shp/readme.txt | 23 +++++++++++++++-------- man/cshapes-package.Rd | 10 +++++++++- man/cshapes2yearly.Rd | 4 ++-- man/cshp.Rd | 6 +++--- man/distmatrix.Rd | 9 +++++---- 9 files changed, 38 insertions(+), 22 deletions(-)
Author: Peter Gilbert, Ian McKeague, and Yanqing Sun
Title: Continuous mark-specific relative risks for two groups
Description: Estimation and testing of continuous mark-specific
relative risks in two groups as described in Gilbert, P.,
McKeague, I. and Sun, Y. (2008) The 2-sample problem for
failure rates depending on a continuous mark: an application to
vaccine efficacy. Biostatistics 9, 2, 263-276. This package
implements the methods presented in the paper for testing
mark-specific hazards ratios and for estimation of
mark-specific incidence ratios that are cumulative in time or
cumulative in both time and the continuous mark.
Diff between cmprskContin versions 1.3 dated 2009-08-28 and 1.5 dated 2009-11-15
DESCRIPTION | 8 ++++---- NEWS | 23 +++++++++++++++++++---- R/cmprsk.R | 18 +++++++++++++++--- man/cmprsk.Rd | 8 ++++---- man/cmprskContin-package.Rd | 4 ++-- man/plotCmprsk.Rd | 2 +- man/summaryCmprsk.Rd | 2 +- src/cmprskContin.f | 4 ++-- 8 files changed, 48 insertions(+), 21 deletions(-)
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
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.
Diff between seewave versions 1.5.5 dated 2009-06-26 and 1.5.6 dated 2009-11-13
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
Title: Data analysis in ecology
Description: Miscellaneous functions for analysis and display of
ecological and spatial data
Diff between pgirmess versions 1.4.1 dated 2009-11-08 and 1.4.2 dated 2009-11-13
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
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.
Diff between msm versions 0.9.3 dated 2009-08-26 and 0.9.4 dated 2009-11-13
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
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.
Diff between matrixStats versions 0.1.6 dated 2009-06-18 and 0.1.8 dated 2009-11-13
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
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.
Diff between vbmp versions 1.12.0 dated 2009-05-10 and 1.14.0 dated 2009-11-13
DESCRIPTION | 8 ++++---- data/BRCA12.RData |binary inst/doc/vbmp.pdf |binary 3 files changed, 4 insertions(+), 4 deletions(-)
Author: Jeff Gentry
Title: R based Twitter client
Description: Provides an interface to the Twitter web API
Diff between twitteR versions 0.1.2 dated 2009-10-20 and 0.1.3 dated 2009-11-13
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
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.
Diff between qvalue versions 1.18.0 dated 2009-05-10 and 1.20.0 dated 2009-11-13
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
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.
Diff between mvbutils versions 2.2.0 dated 2008-11-06 and 2.5.0 dated 2009-11-13
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
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).
Diff between hopach versions 2.4.0 dated 2009-05-10 and 2.6.0 dated 2009-11-13
DESCRIPTION | 6 inst/doc/hopach.pdf | 407 +++++++++++++++++++++++++++------------------------- 2 files changed, 217 insertions(+), 196 deletions(-)
Author: Dan Carr
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.
Diff between hexbin versions 1.18.0 dated 2009-05-10 and 1.20.0 dated 2009-11-13
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
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.
Diff between gene2pathway versions 1.2.0 dated 2009-05-10 and 1.4.0 dated 2009-11-13
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
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.
Diff between debug versions 1.2.0 dated 2008-10-27 and 1.2.1 dated 2009-11-13
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
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.
Diff between RLMM versions 1.6.0 dated 2009-05-10 and 1.8.0 dated 2009-11-13
DESCRIPTION | 10 - inst/doc/RLMM.pdf | 288 ++++++++++++++++++++++++++---------------------------- 2 files changed, 148 insertions(+), 150 deletions(-)
Author: Vince Carey
Title: An interface to the BOOST graph library
Description: A fairly extensive and comprehensive interface to the
graph algorithms contained in the BOOST library.
Diff between RBGL versions 1.20.0 dated 2009-05-10 and 1.22.0 dated 2009-11-13
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(-)
Author: Nicole Kraemer, Juliane Schaefer
Title: Regularized estimation of partial correlation matrices
Description: The package estimates the matrix of partial correlations
based on different regularized regression methods: lasso,
adaptive lasso, PLS, and Ridge Regression.
Diff between parcor versions 0.1 dated 2009-04-29 and 0.2 dated 2009-11-12
DESCRIPTION | 10 +++---- R/adalasso.R | 61 +++++++++++++++++++++++------------------------- R/mylars.R | 40 +++++++++++++++---------------- R/performance.pcor.R | 2 - man/Beta2parcor.Rd | 4 --- man/adalasso.Rd | 10 +++---- man/adalasso.net.Rd | 8 ++---- man/mylars.Rd | 24 +++++++++--------- man/parcor-package.Rd | 4 --- man/performance.pcor.Rd | 2 - man/pls.net.Rd | 12 +++------ man/ridge.cv.Rd | 10 +++---- man/ridge.net.Rd | 10 ++----- 13 files changed, 89 insertions(+), 108 deletions(-)
Author: Kenneth Knoblauch and Laurence T. Maloney, based in part on C
code written by Laurence T. Maloney and J. N. Yang
Title: Maximum Likelihood Difference Scaling
Description: Difference scaling is a method for scaling perceived
supra-threshold differences. The package contains functions
that allow the user to design and run a difference scaling
experiment, to fit the resulting data by maximum likelihood and
test the internal validity of the estimated scale.
Diff between MLDS versions 0.2-3 dated 2009-09-29 and 0.2-5 dated 2009-11-12
DESCRIPTION | 8 ++++---- inst/CITATION |only inst/NEWS | 6 ++++++ man/runQuadExperiment.Rd | 6 +++--- 4 files changed, 13 insertions(+), 7 deletions(-)
Author: Jarrod Hadfield
Title: MCMC Generalised Linear Mixed Models
Description: MCMC Generalised Linear Mixed Models
Diff between MCMCglmm versions 1.12 dated 2009-10-03 and 1.13 dated 2009-11-12
DESCRIPTION | 8 +- R/MCMCglmm.R | 143 +++++++++++++++++++++--------------------------- R/buildZ.R | 27 +++++++-- R/find.components.R | 8 ++ R/inverseA.R | 3 - R/posterior.mode.R | 9 +-- R/rbv.R | 1 inst/doc/Figures/TEST.R | 41 ++++++------- inst/doc/Tutorial.pdf |binary man/MCMCglmm.Rd | 11 +-- man/posterior.mode.Rd | 2 11 files changed, 126 insertions(+), 127 deletions(-)
Author: Gregory R. Warnes. Includes R source code and/or documentation
contributed by (in alphabetical order): Ben Bolker, Lodewijk
Bonebakker, Robert Gentleman, Wolfgang Huber Andy Liaw, Thomas
Lumley, Martin Maechler, Arni Magnusson, Steffen Moeller, Marc
Schwartz, Bill Venables
Title: Various R programming tools for plotting data
Description: Various R programming tools for plotting data
Diff between gplots versions 2.7.3 dated 2009-10-23 and 2.7.4 dated 2009-11-12
DESCRIPTION | 6 +++--- NEWS | 7 +++++++ R/plotmeans.R | 11 ++++++----- inst/NEWS | 7 +++++++ tests/plotmeans_nobars.R |only 5 files changed, 23 insertions(+), 8 deletions(-)
Author: J. O. Ramsay
Title: Functional Data Analysis
Description: These functions were developed to support functional data
analysis as described in Ramsay, J. O. and Silverman, B. W.
(2005) Functional Data Analysis. New York: Springer. They were
ported from earlier versions in Matlab and S-PLUS. An
introduction appears in Ramsay, J. O., Hooker, Giles, and
Graves, Spencer (2009) Functional Data Analysis with R and
Matlab (Springer). The package includes data sets and script
files working many examples including all but one of the 76
figures in this latter book.
Diff between fda versions 2.1.3 dated 2009-10-18 and 2.2.0 dated 2009-11-12
fda-2.1.3/fda/R/register.newfd.R |only fda-2.1.3/fda/R/use.proper.basis.R |only fda-2.1.3/fda/inst/Matlab/additions |only fda-2.1.3/fda/inst/Matlab/fdaM/@bibasis/@bibasis.zip |only fda-2.1.3/fda/inst/Matlab/fdaM/@bibasis/bibasis.asv |only fda-2.1.3/fda/inst/Matlab/fdaM/@bifdPar/@bifdPar.zip |only fda-2.1.3/fda/inst/Matlab/fdaM/@bifdPar/@fdPar.zip |only fda-2.1.3/fda/inst/scripts/fda-script-progress.xls |only fda-2.1.3/fda/inst/scripts/pda.fd.test.R |only fda-2.1.3/fda/man/register.newfd.rd |only fda-2.2.0/fda/DESCRIPTION | 10 fda-2.2.0/fda/R/Fperm.fd.R | 12 fda-2.2.0/fda/R/Fstat.fd.R | 5 fda-2.2.0/fda/R/basisfd.R | 52 +++ fda-2.2.0/fda/R/bifdPar.R |only fda-2.2.0/fda/R/eval.posfd.R | 2 fda-2.2.0/fda/R/fRegress.CV.R | 117 +++---- fda-2.2.0/fda/R/fRegress.R |only fda-2.2.0/fda/R/fRegress.stderr.R | 12 fda-2.2.0/fda/R/fRegressArgCheck.R |only fda-2.2.0/fda/R/fd.R | 272 ++++++++++++++--- fda-2.2.0/fda/R/linmod.R | 32 -- fda-2.2.0/fda/R/register.fd.R | 89 ++--- fda-2.2.0/fda/R/smooth.basis.R | 2 fda-2.2.0/fda/R/smooth.pos.R | 70 ++-- fda-2.2.0/fda/R/subscript.R | 4 fda-2.2.0/fda/R/varmx.R | 23 + fda-2.2.0/fda/R/varmx.pca.fd.R | 46 +- fda-2.2.0/fda/inst/Matlab/fdaM/@basis/basis.m | 26 + fda-2.2.0/fda/inst/Matlab/fdaM/@basis/getbasismatrix.m | 15 fda-2.2.0/fda/inst/Matlab/fdaM/@basis/getbasistype.m | 6 fda-2.2.0/fda/inst/Matlab/fdaM/@basis/getbasisvalues.m | 2 fda-2.2.0/fda/inst/Matlab/fdaM/@basis/times.m | 2 fda-2.2.0/fda/inst/Matlab/fdaM/@bifdPar/bifdPar.m | 52 +-- fda-2.2.0/fda/inst/Matlab/fdaM/@fd/mpower.m |only fda-2.2.0/fda/inst/Matlab/fdaM/@fd/power.m |only fda-2.2.0/fda/inst/Matlab/fdaM/Fperm_fd.m | 202 ++++++------ fda-2.2.0/fda/inst/Matlab/fdaM/Fstat_fd.m | 75 +--- fda-2.2.0/fda/inst/Matlab/fdaM/fRegress_CV.m | 141 ++++---- fda-2.2.0/fda/inst/Matlab/fdaM/smooth_basis.m | 166 ++-------- fda-2.2.0/fda/inst/Matlab/fdaM/tperm_fd.m | 206 ++++++------ fda-2.2.0/fda/inst/Matlab/fdaM/varmx.m | 53 +-- fda-2.2.0/fda/inst/Matlab/fdaM/varmx_pca.m | 8 fda-2.2.0/fda/inst/scripts/fdarm-ch01.R | 174 ++++++++-- fda-2.2.0/fda/inst/scripts/fdarm-ch01.m |only fda-2.2.0/fda/inst/scripts/fdarm-ch02.R | 81 ++++- fda-2.2.0/fda/inst/scripts/fdarm-ch03.R | 93 ++++- fda-2.2.0/fda/inst/scripts/fdarm-ch03.m |only fda-2.2.0/fda/inst/scripts/fdarm-ch04.R | 244 ++++++++++----- fda-2.2.0/fda/inst/scripts/fdarm-ch04.m |only fda-2.2.0/fda/inst/scripts/fdarm-ch05.R | 188 ++++++++++- fda-2.2.0/fda/inst/scripts/fdarm-ch05.m |only fda-2.2.0/fda/inst/scripts/fdarm-ch06.R | 158 +++++++-- fda-2.2.0/fda/inst/scripts/fdarm-ch06.m |only fda-2.2.0/fda/inst/scripts/fdarm-ch07.R | 109 ++++-- fda-2.2.0/fda/inst/scripts/fdarm-ch07.m |only fda-2.2.0/fda/inst/scripts/fdarm-ch08.R | 95 ++++- fda-2.2.0/fda/inst/scripts/fdarm-ch08.m |only fda-2.2.0/fda/inst/scripts/fdarm-ch09.R | 61 +++ fda-2.2.0/fda/inst/scripts/fdarm-ch09.m |only fda-2.2.0/fda/inst/scripts/fdarm-ch10.R | 259 +++++++++++----- fda-2.2.0/fda/inst/scripts/fdarm-ch10.m |only fda-2.2.0/fda/inst/scripts/fdarm-ch11.m |only fda-2.2.0/fda/man/bifdPar.Rd |only fda-2.2.0/fda/man/eval.posfd.Rd | 161 +++++----- fda-2.2.0/fda/man/fRegress.CV.Rd | 193 +++--------- fda-2.2.0/fda/man/fRegress.Rd | 7 fda-2.2.0/fda/man/fRegress.stderr.Rd | 149 ++++----- fda-2.2.0/fda/man/fda-internal.Rd | 2 fda-2.2.0/fda/man/linmod.Rd | 90 +++-- fda-2.2.0/fda/man/smooth.basis.Rd | 9 fda-2.2.0/fda/man/varmx.Rd | 85 ++--- 72 files changed, 2362 insertions(+), 1498 deletions(-)
Author: Enrico Glaab
Title: Generate 3D visualizations for data exploration on the web
Description: vrmlgen creates 3D scatter and bar plots, visualizations
of 3D meshes, parametric functions and height maps in
web-formats like the Virtual Reality Markup Language (VRML,
filetype .wrl) and the LiveGraphics3D format.
Diff between vrmlgen versions 1.1 dated 2009-10-12 and 1.2 dated 2009-11-12
DESCRIPTION | 18 +-- R/lbar.R | 90 ++++++++++++++--- R/lcloud.R | 247 +++++++++++++++++++++++++++++++++++++------------ R/lmesh.R |only R/vbar.R | 128 +++++++++++++++++++------ R/vcloud.R | 6 - R/vmesh.R |only man/lbar.Rd | 33 +++++- man/lcloud.Rd | 39 ++++++- man/lmesh.Rd |only man/vbar.Rd | 36 +++++-- man/vcloud.Rd | 32 ++++-- man/vmesh.Rd |only man/vrmlgen-package.Rd | 12 +- 14 files changed, 489 insertions(+), 152 deletions(-)
Author: D.J.J. Walvoort, D.J. Brus, and J.J. de Gruijter
Title: Spatial Coverage Sampling and Random Sampling from Compact
Geographical Strata
Description: Spatial coverage sampling and random sampling from compact
geographical strata created by k-means.
Diff between spcosa versions 0.1-5 dated 2009-09-09 and 0.2-0 dated 2009-11-12
DESCRIPTION | 16 NEWS | 8 R/method_stratify-SpatialPixels.R | 75 R/onLoad.R | 8 inst/doc/spcosa.pdf | 4371 ++++++++++++++++++-------------------- man/spcosa-package.Rd | 29 man/stratify-methods.Rd | 6 tests/unitTesting.html | 14 8 files changed, 2225 insertions(+), 2302 deletions(-)
Author: Tuomas Rajala
Title: Graphs for spatial point patterns
Description: Graphs, graph visualization and graph component
calculations, ment to be used as a tool in spatial point
pattern analysis. See package 'spatstat' for more info about
spatial point patterns.
Diff between spatgraphs versions 2.27 dated 2009-09-18 and 2.30 dated 2009-11-12
DESCRIPTION | 10 +++++----- R/edgelengths.R | 4 ++-- R/plot.R | 26 ++++++++++++++++++++------ R/spatgraph.R | 2 +- R/summary.R |only change.log | 11 +++++++++++ man/spatgraphs-other.Rd | 5 +++-- man/spatgraphs-package.Rd | 3 ++- man/spatgraphs-plot.sg.Rd | 1 + man/spatgraphs-sg.Rd | 3 +++ src/Graph.cpp | 6 +++--- src/dists.cpp | 2 +- 12 files changed, 52 insertions(+), 21 deletions(-)
Author: Peter Danenberg
Title: Literate Programming in R
Description: A Doxygen-like in-source documentation system for Rd,
collation, namespace and callgraphs.
Diff between roxygen versions 0.1 dated 2008-08-31 and 0.1-2 dated 2009-11-12
roxygen-0.1-2/roxygen/DESCRIPTION | 21 roxygen-0.1-2/roxygen/NAMESPACE | 5 roxygen-0.1-2/roxygen/R/Rd.R | 950 roxygen-0.1-2/roxygen/R/Rd2.R |only roxygen-0.1-2/roxygen/R/Rdapi.R |only roxygen-0.1-2/roxygen/R/Rdmerge.R |only roxygen-0.1-2/roxygen/R/Rdtank.R |only roxygen-0.1-2/roxygen/R/callgraph.R | 540 roxygen-0.1-2/roxygen/R/collate.R | 332 roxygen-0.1-2/roxygen/R/functional.R | 1 roxygen-0.1-2/roxygen/R/memoize.R |only roxygen-0.1-2/roxygen/R/namespace.R | 328 roxygen-0.1-2/roxygen/R/parse.R | 43 roxygen-0.1-2/roxygen/R/parseS4.R |only roxygen-0.1-2/roxygen/R/roclet.R | 8 roxygen-0.1-2/roxygen/R/roxygen.R | 2 roxygen-0.1-2/roxygen/R/roxygenize.R | 21 roxygen-0.1-2/roxygen/R/string.R | 336 roxygen-0.1-2/roxygen/README | 4 roxygen-0.1-2/roxygen/inst/doc/Compose-callgraph.pdf |binary roxygen-0.1-2/roxygen/inst/doc/GSoC-idea.tex |only roxygen-0.1-2/roxygen/inst/doc/helloRoxygen/DESCRIPTION | 22 roxygen-0.1-2/roxygen/inst/doc/helloRoxygen/man/helloRoxygen-package.Rd | 10 roxygen-0.1-2/roxygen/inst/doc/parse.file-callgraph.pdf |binary roxygen-0.1-2/roxygen/inst/doc/pseudoprime/DESCRIPTION | 26 roxygen-0.1-2/roxygen/inst/doc/pseudoprime/NAMESPACE | 2 roxygen-0.1-2/roxygen/inst/doc/pseudoprime/man/fermat.test.Rd | 32 roxygen-0.1-2/roxygen/inst/doc/pseudoprime/man/is.pseudoprime.Rd | 38 roxygen-0.1-2/roxygen/inst/doc/pseudoprime/man/pseudoprime-package.Rd | 50 roxygen-0.1-2/roxygen/inst/doc/roxygen-manual.pdf |13275 +++++----- roxygen-0.1-2/roxygen/inst/doc/roxygen.Rnw | 350 roxygen-0.1-2/roxygen/inst/doc/roxygen.aux | 40 roxygen-0.1-2/roxygen/inst/doc/roxygen.bbl | 26 roxygen-0.1-2/roxygen/inst/doc/roxygen.blg | 48 roxygen-0.1-2/roxygen/inst/doc/roxygen.log | 1277 roxygen-0.1-2/roxygen/inst/doc/roxygen.pdf |binary roxygen-0.1-2/roxygen/inst/doc/roxygen.tex | 357 roxygen-0.1-2/roxygen/inst/doc/roxygen.toc | 12 roxygen-0.1-2/roxygen/inst/doc/roxygenize-callgraph.pdf |binary roxygen-0.1-2/roxygen/man/assign.parent.Rd | 2 roxygen-0.1-2/roxygen/man/cat.description.Rd | 2 roxygen-0.1-2/roxygen/man/expression.from.partitum.Rd |only roxygen-0.1-2/roxygen/man/make.Rd.roclet.Rd | 20 roxygen-0.1-2/roxygen/man/make.Rd2.roclet.Rd |only roxygen-0.1-2/roxygen/man/make.callgraph.roclet.Rd | 2 roxygen-0.1-2/roxygen/man/make.collate.roclet.Rd | 2 roxygen-0.1-2/roxygen/man/make.namespace.roclet.Rd | 2 roxygen-0.1-2/roxygen/man/parse.ref.srcref.Rd | 8 roxygen-0.1-2/roxygen/man/roxygen-package.Rd | 2 roxygen-0.1-2/roxygen/man/roxygenize.Rd | 5 roxygen-0.1/roxygen/inst/doc/.build.timestamp |only roxygen-0.1/roxygen/inst/doc/helloRoxygen/Read-and-delete-me |only roxygen-0.1/roxygen/inst/doc/pseudoprime/inst/doc/fermat.test-callgraph.pdf |only roxygen-0.1/roxygen/sandbox |only 54 files changed, 9584 insertions(+), 8617 deletions(-)
Author: Nicole Kraemer
Title: Penalized Partial Least Squares
Description: This package contains linear and nonlinear regression
methods based on Partial Least Squares and Penalization
Techniques.
Diff between ppls versions 1.03 dated 2009-01-24 and 1.04 dated 2009-11-12
DESCRIPTION | 28 ++++++++++++++++------------ man/Penalty.matrix.Rd | 2 +- man/penalized.pls.cv.Rd | 3 +-- 3 files changed, 18 insertions(+), 15 deletions(-)
Author: Arthur Allignol
Title: Nelson-Aalen estimator of the cumulative hazard in multistate
models
Description: This package computes the Nelson-Aalen estimator of the
cumulative transition hazard for multistate models.
Diff between mvna versions 1.1-10 dated 2009-10-14 and 1.2 dated 2009-11-12
mvna-1.1-10/mvna/src/risk_set_mvna.cc |only mvna-1.2/mvna/ChangeLog | 43 ++++++++++++-- mvna-1.2/mvna/DESCRIPTION | 8 +- mvna-1.2/mvna/NAMESPACE | 4 + mvna-1.2/mvna/R/lines.mvna.R |only mvna-1.2/mvna/R/mvna.R | 41 +++++++++----- mvna-1.2/mvna/R/plot.mvna.R | 98 ++++++++++++++++++++-------------- mvna-1.2/mvna/R/predict.mvna.R | 54 ++++++++++-------- mvna-1.2/mvna/R/print.mvna.R | 39 ++++++------- mvna-1.2/mvna/R/print.summary.mvna.R |only mvna-1.2/mvna/R/summary.mvna.R |only mvna-1.2/mvna/R/xyplot.mvna.R | 85 +++++++++++------------------ mvna-1.2/mvna/man/abortion.Rd | 7 +- mvna-1.2/mvna/man/lines.mvna.Rd |only mvna-1.2/mvna/man/msmplot.Rd | 17 +++-- mvna-1.2/mvna/man/mvna.Rd | 39 ++++++------- mvna-1.2/mvna/man/plot.mvna.Rd | 53 +++++++++++------- mvna-1.2/mvna/man/predict.mvna.Rd | 42 +++++++++----- mvna-1.2/mvna/man/print.mvna.Rd | 15 ++--- mvna-1.2/mvna/man/sir.adm.Rd | 3 - mvna-1.2/mvna/man/sir.cont.Rd | 5 + mvna-1.2/mvna/man/summary.mvna.Rd |only mvna-1.2/mvna/man/xyplot.mvna.Rd | 46 ++++++++------- mvna-1.2/mvna/src/risk_set_mvna.c |only mvna-1.2/mvna/tests |only 25 files changed, 341 insertions(+), 258 deletions(-)
Author: Martin Elff
Title: Tools for Management of Survey Data, Graphics, Programming,
Statistics, and Simulation
Description: One of the aims of this package is to make life easier for
useRs who deal with survey data sets. It provides an
infrastructure for the management of survey data including
value labels, definable missing values, recoding of variables,
production of code books, and import of (subsets of) SPSS and
Stata files. Further, it provides functionality to produce
tables and data frames of arbitrary descriptive statistics and
(almost) publication-ready tables of regression model
estimates. Also some convenience tools for graphics,
programming, and simulation are provided.
Diff between memisc versions 0.95-22 dated 2009-10-15 and 0.95-23 dated 2009-11-12
DESCRIPTION | 8 +-- INDEX |only NEWS |only R/zzz.R | 86 +--------------------------------------- inst/doc/anes48.pdf |binary src/dta-for-R.c | 6 +- src/numeric_if_possible.c | 6 +- src/pspp-portableStream-for-R.c | 2 src/readfixed.c | 4 - 9 files changed, 16 insertions(+), 96 deletions(-)
Author: Arthur Allignol
Title: Empirical Transition Matrix
Description: Matrix of transition probabilities for any
time-inhomogeneous multistate model with finite state space
Diff between etm versions 0.4-6 dated 2009-09-03 and 0.4-7 dated 2009-11-12
ChangeLog | 81 ++++++++++++++++++++++++++++++------------------------ DESCRIPTION | 8 ++--- NAMESPACE | 1 R/lines.etm.R |only R/plot.etm.R | 80 ++++++++++++++++++++++++++++++++++------------------- R/xyplot.etm.R | 20 +++++++++---- man/lines.etm.Rd |only man/plot.etm.Rd | 17 ++++++++++- man/xyplot.etm.Rd | 10 ++---- 9 files changed, 134 insertions(+), 83 deletions(-)
Author: Yihui Xie
Title: Demonstrate Animations in Statistics
Description: This package consists of various functions for animations
in statistics, covering many areas such as probability theory,
mathematical statistics, multivariate statistics, nonparametric
statistics, sampling survey, linear models, time series,
computational statistics, data mining and machine learning.
These functions might be of help in teaching statistics and
data analysis.
Diff between animation versions 1.0-8 dated 2009-11-06 and 1.0-9 dated 2009-11-12
DESCRIPTION | 8 ++--- R/ani.options.R | 28 ++++++++++------- R/ani.start.R | 10 +++--- R/ani.stop.R | 16 +++++----- R/brownian.motion.R | 4 -- R/saveLatex.R |only R/saveMovie.R | 74 ++++++++++++++++++++++++++++++++++++++++++----- R/saveSWF.r | 4 +- R/write.rss.R | 12 +++---- R/zzz.R | 6 --- inst/NEWS | 66 +++++++++++++++++++++++++++++++++++------ man/BM.circle.Rd | 10 ++---- man/HuSpeech.Rd | 5 ++- man/Rosling.bubbles.Rd | 6 +-- man/ani.options.Rd | 19 ++++++------ man/ani.start.Rd | 2 - man/ani.stop.Rd | 2 - man/animation-package.Rd | 2 - man/bisection.method.Rd | 9 ++--- man/buffon.needle.Rd | 13 ++++---- man/clt.ani.Rd | 8 ++--- man/conf.int.Rd | 11 +++--- man/cv.ani.Rd | 13 ++++---- man/cv.nfeaturesLDA.Rd | 13 +++----- man/ecol.death.sim.Rd | 8 +++-- man/flip.coin.Rd | 10 +++--- man/g.brownian.motion.Rd | 6 +-- man/grad.desc.Rd | 8 ++--- man/highlight.def.Rd | 8 ++--- man/kfcv.Rd | 3 - man/kmeans.ani.Rd | 14 +++++--- man/knn.ani.Rd | 6 +-- man/least.squares.Rd | 15 +++++---- man/lln.ani.Rd | 6 +-- man/moving.block.Rd | 1 man/mwar.ani.Rd | 8 ++--- man/newton.method.Rd | 15 +++++---- man/pageview.Rd | 8 ++--- man/quincunx.Rd | 10 +++--- man/sample.cluster.Rd | 4 +- man/sample.simple.Rd | 5 +-- man/sample.strat.Rd | 2 - man/sample.system.Rd | 5 +-- man/saveLatex.Rd |only man/saveMovie.Rd | 10 +++--- man/saveSWF.Rd | 8 ++--- man/sim.qqnorm.Rd | 4 +- man/tidy.source.Rd | 7 +++- man/vi.grid.illusion.Rd | 8 +++-- man/vi.lilac.chaser.Rd | 6 +-- man/write.rss.Rd | 37 +++++++++++------------ tests |only 52 files changed, 341 insertions(+), 222 deletions(-)
Author: Erin Hodgess
Title: Rcmdr plugin for quality control course
Description: This package provides an Rcmdr "plug-in" based on the
Quality control class Stat 4300
Diff between RcmdrPlugin.qual versions 0.3.0 dated 2009-11-01 and 0.4.0 dated 2009-11-12
DESCRIPTION | 8 +++--- R/RcmdrPlugin.qual.R | 51 +++++++++++++++++++++++++++++++++++++++ inst/etc/menus.txt | 1 man/RcmdrPlugin.qual-internal.Rd | 1 4 files changed, 57 insertions(+), 4 deletions(-)
More information about RcmdrPlugin.qual at CRAN
Permanent link
Author: Reinhold Hatzinger, Patrick Mair, Norman Verhelst
Title: Rasch Sampler
Description: Sampling binary matrices with fixed margins
Diff between RaschSampler versions 0.8-2 dated 2009-08-19 and 0.8-3 dated 2009-11-12
DESCRIPTION | 8 ++++---- R/rserror.R | 4 ++-- data/xmplbig.rda |binary man/RaschSampler.package.Rd | 14 ++++++++++---- man/rsampler.Rd | 8 ++++---- man/xmpl.Rd | 4 ++-- src/RaschSampler.f90 | 18 ++++-------------- 7 files changed, 26 insertions(+), 30 deletions(-)
Author: Yu-Sung Su
Title: A Package for Running jags from R
Description: Using this package to call jags from R.
Diff between R2jags versions 0.01-26 dated 2009-10-13 and 0.01-27 dated 2009-11-12
CHANGELOG | 11 +++++++++++ DESCRIPTION | 8 ++++---- R/jags.R | 39 +++++++++++++++++++++++++++++++++------ R/jags.sims.R | 4 ++-- R/jags2.R | 26 +++++++++++++++++++++----- man/jags.Rd | 5 +++-- 6 files changed, 74 insertions(+), 19 deletions(-)
Author: Jarrod Hadfield
Title: ML and MCMC Methods for Pedigree Reconstruction and Analysis
Description: The primary aim of MasterBayes is to use MCMC techniques
to integrate over uncertainty in pedigree configurations
estimated from molecular markers and phenotypic data. Emphasis
is put on the marginal distribution of parameters that relate
the phenotypic data to the pedigree. All simulation is done in
compiled C++ for efficency.
Diff between MasterBayes versions 2.44 dated 2009-07-21 and 2.45 dated 2009-11-12
MasterBayes-2.44/MasterBayes/inst/doc/Tutorial.tex |only MasterBayes-2.45/MasterBayes/DESCRIPTION | 8 MasterBayes-2.45/MasterBayes/NAMESPACE | 4 MasterBayes-2.45/MasterBayes/R/ErrorCheck.R | 14 MasterBayes-2.45/MasterBayes/R/MCMCped.R | 31 MasterBayes-2.45/MasterBayes/R/MLE.popsize.R | 5 MasterBayes-2.45/MasterBayes/R/consensusG.R |only MasterBayes-2.45/MasterBayes/R/fillX.G.R | 9 MasterBayes-2.45/MasterBayes/R/getPost.R | 4 MasterBayes-2.45/MasterBayes/R/getXlist.R | 17 MasterBayes-2.45/MasterBayes/R/getsPandtP.R | 54 MasterBayes-2.45/MasterBayes/R/insertPed.R |only MasterBayes-2.45/MasterBayes/R/varPed.R | 105 MasterBayes-2.45/MasterBayes/inst/doc/Figures/Tutorial.Rnw | 8 MasterBayes-2.45/MasterBayes/inst/doc/Tutorial-006.eps | 27 MasterBayes-2.45/MasterBayes/inst/doc/Tutorial-006.pdf | 6 MasterBayes-2.45/MasterBayes/inst/doc/Tutorial-007.eps | 27 MasterBayes-2.45/MasterBayes/inst/doc/Tutorial-007.pdf | 6 MasterBayes-2.45/MasterBayes/inst/doc/Tutorial-008.eps | 43 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Author: Marc J. Mazerolle
Title: Model selection and multimodel inference based on (Q)AIC(c)
Description: This package includes functions to create model selection
tables based on Akaike's information criterion (AIC) and the
second-order AIC (AICc), as well as their quasi-likelihood
counterparts (QAIC, QAICc). Tables are printed with delta AIC
and Akaike weights. The package also includes functions to
conduct model averaging (multimodel inference) for a given
parameter of interest or predicted values. Other handy
functions enable the computation of relative variable
importance, evidence ratios, and confidence sets for the best
model. The present version works with linear models ('lm'
class), generalized linear models ('glm' class), linear mixed
models ('lme' class), multinomial and ordinal logistic
regressions ('multinom' and 'polr' classes).
Diff between AICcmodavg versions 1.03 dated 2009-10-22 and 1.04 dated 2009-11-12
DESCRIPTION | 8 ++-- R/aictab.R | 2 - R/confset.R | 2 - R/evidence.R | 2 - R/importance.R | 2 - R/modavg.R | 18 +++++---- R/modavg.glm.R | 90 ++++++++++++++++++++++++++++++++++++++++------ R/modavg.lme.R | 37 ++++++++++++++++-- R/modavg.mult.R | 76 ++++++++++++++++++++++++++++++-------- R/modavg.polr.R | 33 +++++++++++++--- R/modavgpred.R | 68 +++++++++++++++++++++++++++++++++- man/AICcmodavg-package.Rd | 20 +++++----- man/aictab.Rd | 18 ++++++--- man/confset.Rd | 8 +++- man/evidence.Rd | 5 +- man/importance.Rd | 4 ++ man/modavg.Rd | 28 +++++++++++--- man/modavgpred.Rd | 22 +++++++++-- 18 files changed, 360 insertions(+), 83 deletions(-)
Author: Evgenia Dimitriadou, Kurt Hornik, Friedrich Leisch, David
Meyer, and Andreas Weingessel
Title: Misc Functions of the Department of Statistics (e1071), TU Wien
Description: Functions for latent class analysis, short time Fourier
transform, fuzzy clustering, support vector machines, shortest
path computation, bagged clustering, naive Bayes classifier,
...
Diff between e1071 versions 1.5-20 dated 2009-10-19 and 1.5-21 dated 2009-11-11
e1071-1.5-20/e1071/inst/NEWS |only e1071-1.5-21/e1071/DESCRIPTION | 8 ++++---- e1071-1.5-21/e1071/NEWS | 4 ++++ e1071-1.5-21/e1071/R/svm.R | 19 ++++++++++--------- e1071-1.5-21/e1071/inst/doc/svmdoc.pdf |binary e1071-1.5-21/e1071/inst/doc/svmdoc.pdf.2.r3331 |only e1071-1.5-21/e1071/inst/doc/svmdoc.pdf.r3159 |only e1071-1.5-21/e1071/inst/doc/svmdoc.pdf.r3191 |only e1071-1.5-21/e1071/inst/doc/svmdoc.pdf.r3290 |only e1071-1.5-21/e1071/inst/doc/svmdoc.pdf.r3331 |only e1071-1.5-21/e1071/inst/doc/svmdoc.pdf.r3354 |only e1071-1.5-21/e1071/inst/doc/svmdoc.pdf.r3745 |only e1071-1.5-21/e1071/inst/doc/svmdoc.pdf.r3767 |only 13 files changed, 18 insertions(+), 13 deletions(-)
Author: Timothy H. Keitt
Title: Bindings for the Geospatial Data Abstraction Library
Description: Provides bindings to Frank Warmerdam's Geospatial Data
Abstraction Library (GDAL) (>= 1.3.1) and access to
projection/transformation operations from the PROJ.4 library.
The GDAL and PROJ.4 libraries are external to the package, and,
when installing the package from source, must be correctly
installed first. Both GDAL raster and OGR vector map data can
be imported into R, and GDAL raster data and OGR vector data
exported. Use is made of classes defined in the sp package.
Diff between rgdal versions 0.6-20 dated 2009-10-30 and 0.6-21 dated 2009-11-11
ChangeLog | 21 +++++++++++++++++++++ DESCRIPTION | 8 ++++---- R/AAA.R | 23 +++++++++++++---------- R/ogr_write.R | 22 +++++++++++++++++----- inst/ChangeLog | 21 +++++++++++++++++++++ man/writeOGR.Rd | 2 +- 6 files changed, 77 insertions(+), 20 deletions(-)
Author: Jim Lemon
Title: Pretty descriptive stats.
Description: Functions for conventionally formatted descriptive stats,
and to format R output as HTML.
Diff between prettyR versions 1.5 dated 2009-06-18 and 1.7 dated 2009-11-11
DESCRIPTION | 8 ++++---- NEWS |only R/htmlize.R | 13 ++++++++----- R/print.xtab.R | 27 ++++++++++++++++++++++----- R/xtab.R | 2 +- man/htmlize.Rd | 9 ++++++--- man/print.xtab.Rd | 20 +++++++++++++++----- man/xtab.Rd | 3 ++- 8 files changed, 58 insertions(+), 24 deletions(-)
Author: Tim Coelli, Arne Henningsen
Title: Stochastic Frontier Analysis
Description: Maximum Likelihood Estimation of Stochastic Frontier
Production and Cost Functions. Two specifications are
available: the error components specification with time-varying
efficiencies (Battese and Coelli, 1992) and a model
specification in which the firm effects are directly influenced
by a number of variables (Battese and Coelli, 1995).
Diff between frontier versions 0.995-8 dated 2009-10-18 and 0.996-0 dated 2009-11-11
DESCRIPTION | 9 INDEX | 2 NAMESPACE | 5 NEWS | 28 R/efficiencies.frontier.R | 18 R/frontierQuad.R | 8 R/logLik.frontier.R | 5 R/lrtest.frontier.R |only R/print.summary.frontier.R | 35 R/residuals.frontier.R | 18 R/sfa.R | 120 man/efficiencies.frontier.Rd | 5 man/frontier.Rd | 19 man/logLik.frontier.Rd | 5 man/lrtest.frontier.Rd |only man/summary.frontier.Rd | 7 src/front41.f | 171 tests/fail.R |only tests/fail.Rout.save |only tests/frontier41.Rout.save | 20 tests/frontierTest.R | 232 tests/frontierTest.Rout.save |32647 ++++++++++++++++++++++++------------------ tests/nestedModels.R | 20 tests/nestedModels.Rout.save | 70 tests/translogRay.R | 1 tests/translogRay.Rout.save | 306 tests/wrongSkewness.R |only tests/wrongSkewness.Rout.save |only 28 files changed, 19322 insertions(+), 14429 deletions(-)
Author: Hinda Haned
Title: Statistical tools for the interpretation of forensic DNA
mixtures
Description: Statistical methods and simulation tools for the
interpretation of forensic DNA mixtures
Diff between forensim versions 1.1-1 dated 2009-10-26 and 1.1-2 dated 2009-11-11
DESCRIPTION | 10 +++--- R/A2.simu.R | 6 +--- R/classes_constructors.R | 3 +- man/simufreqD.Rd | 2 - man/simupopD.Rd | 2 - src/recurs.c | 70 +++++++++++++++++++++++++++++++++++++---------- 6 files changed, 67 insertions(+), 26 deletions(-)
Author: Felix Kaminsky
Title: Estimates Output
Description: The function collection stores the estimates of several
models and formats it to a table of the form estimate starred
and std.err. below. The default output is LaTeX but output to
CSV for later editing in a spreadsheet tool is possible as
well. It works for linear models (lm) and panel models from the
"plm"-package (plm). The added "descsto" and "desctab" enable
you to export descriptive statistics of data-frames and single
variables to LaTeX and CSV.
Diff between estout versions 0.6-1 dated 2009-08-08 and 0.7-1 dated 2009-11-11
DESCRIPTION | 6 +- R/esttab.R | 173 +++++++++++++++++++++++++++++++++++----------------------- man/esttab.Rd | 14 +++- 3 files changed, 119 insertions(+), 74 deletions(-)
Author: Jouni Helske
Title: Multivariate Kalman filter and smoother, simulation smoother and
forecasting of state space models. State smoothing and
approximate likelihood of exponential family state space
models.
Description: Package KFAS provides functions for fast Kalman filtering,
state and disturbance smoothing, forecasting and simulation of
multivariate time-variant state space models. All functions can
use exact diffuse initialisation when distributions of some or
all elements of initial state vector are unknown. Filtering,
state smoothing and simulation functions use sequential
processing algorithm, which is faster than standard approach,
and it also allows singularity of prediction error variance
matrix. KFAS also contains function for approximation of
likelihood of exponential family state space models and
function for state smoothing of exponential family state space
models.
Diff between KFAS versions 0.4.6 dated 2009-10-22 and 0.4.7 dated 2009-11-11
DESCRIPTION | 23 ++++++++++++---------- NAMESPACE | 2 - R/KFAS.R | 54 +++++++++++++++++++++++++++++++--------------------- man/expflik.Rd | 38 ++++++++++++++++++++++++++++++++++++ man/expfsmoother.Rd |only man/ks.Rd | 1 6 files changed, 85 insertions(+), 33 deletions(-)
Author: Tomas Aragon
Title: Epidemiology Tools
Description: EpiTools: R Package for Epidemiologic Data and Graphics
Diff between epitools versions 0.5-3 dated 2009-04-15 and 0.5-4 dated 2009-11-11
DESCRIPTION | 8 ++++---- man/as.hour.Rd | 2 +- man/as.month.Rd | 2 +- man/as.week.Rd | 2 +- man/colorbrewer.Rd | 7 ------- man/epidate.Rd | 19 +------------------ man/julian2date.Rd | 2 +- 7 files changed, 9 insertions(+), 33 deletions(-)
Author: Hana Sevcikova
Title: R interface to RNG with multiple streams
Description: Provides an interface to the C implementation of the
random number generator with multiple independent streams
developed by L'Ecuyer et al (2002). The main purpose of this
package is to enable the use of this random number generator in
parallel R applications.
Diff between rlecuyer versions 0.2 dated 2009-01-23 and 0.3-1 dated 2009-11-10
DESCRIPTION | 19 +++++++++++++------ man/SetPackageSeed.Rd | 2 +- src/RngWrap.c | 4 +++- 3 files changed, 17 insertions(+), 8 deletions(-)
Author: Jon Clayden
Title: Basic functions for the TractoR (tractography with R) bundle
Description: The tractor.base package consists of functions for working
with magnetic resonance images. It can read and write image
files stored in Analyze, NIfTI and DICOM formats (DICOM support
is read only), generate images for use as regions of interest,
and manipulate and visualise images.
Diff between tractor.base versions 1.2.0 dated 2009-08-21 and 1.3.0 dated 2009-11-10
DESCRIPTION | 8 ++++---- R/bootstrap.R | 9 +++++++-- R/dicom.R | 16 +++++++++++----- R/internal.R | 20 +++++++++++--------- R/output.R | 2 +- R/png.R | 7 +++++-- R/viz.R | 24 +++++++++++++++--------- man/visualisation.Rd | 9 +++++---- 8 files changed, 59 insertions(+), 36 deletions(-)
Author: Adrian Baddeley
Title: Spatial Point Pattern analysis, model-fitting, simulation, tests
Description: A package for analysing spatial data, mainly Spatial Point
Patterns, including multitype/marked points and spatial
covariates, in any two-dimensional spatial region. Also
supports three-dimensional point patterns. Contains functions
for plotting spatial data, exploratory data analysis,
model-fitting, simulation, spatial sampling, model diagnostics,
and formal inference. Data types include point patterns, line
segment patterns, spatial windows, pixel images and
tessellations. Point process models can be fitted to point
pattern data. Cluster type models are fitted by the method of
minimum contrast. Very general Gibbs point process models can
be fitted to point pattern data using a function ppm similar to
lm or glm. Models may include dependence on covariates,
interpoint interaction and dependence on marks. Fitted models
can be simulated automatically. Also provides facilities for
formal inference (such as chi-squared tests) and model
diagnostics (including simulation envelopes, residuals,
residual plots and Q-Q plots).
Diff between spatstat versions 1.17-1 dated 2009-11-06 and 1.17-2 dated 2009-11-10
.Rbuildindex.12568 |only .Rbuildindex.17656 |only .Rbuildindex.9742 |only DESCRIPTION | 34 +- INDEX | 4 R/pp3.R | 45 +++ inst/doc/shapefiles.pdf | 673 ++++++++++++++++++++++++------------------------ man/F3est.Rd | 5 man/G3est.Rd | 5 man/K3est.Rd | 5 man/methods.box3.Rd | 9 man/methods.pp3.Rd | 24 + man/rpoispp.Rd | 7 man/rpoispp3.Rd |only man/runifpoint3.Rd |only man/spatstat-package.Rd | 5 src/areaint.c | 2 src/call3d.c | 22 - src/dgs.c | 2 src/diggra.c | 2 src/dist2.c | 2 src/f3.c | 13 src/g3.c | 21 - src/getcif.c | 31 -- src/geyer.c | 4 src/lookup.c | 12 src/methas.c | 8 src/methas.h | 2 src/sftcr.c | 5 src/straushm.c | 4 src/straussm.c | 4 31 files changed, 517 insertions(+), 433 deletions(-)
Author: Martyn Plummer
Title: Bayesian graphical models using MCMC
Description: Interface to the JAGS MCMC library
Diff between rjags versions 1.0.3-11 dated 2009-10-11 and 1.0.3-12 dated 2009-11-10
DESCRIPTION | 8 ++++---- NAMESPACE | 3 --- R/unix/progress.bar.R | 8 ++++---- 3 files changed, 8 insertions(+), 11 deletions(-)
Author: Matthias Gamer
Title: Various Coefficients of Interrater Reliability and Agreement
Description: Coefficients of Interrater Reliability and Agreement for
quantitative, ordinal and nominal data: ICC, Finn-Coefficient,
Robinson'A, Kendall's W, Cohen's Kappa, ...
Diff between irr versions 0.81 dated 2009-10-26 and 0.82 dated 2009-11-10
CHANGES | 3 +++ DESCRIPTION | 8 ++++---- R/icc.R | 12 ++++++------ R/print.icclist.R | 2 +- man/icc.Rd | 2 +- 5 files changed, 15 insertions(+), 12 deletions(-)
Author: Diethelm Wuertz and Yohan Chalabi with contribution from Michal
Miklovic, Chris Boudt, Pierre Chausse and others
Title: Rmetrics - Autoregressive Conditional Heteroskedastic Modelling
Description: Environment for teaching "Financial Engineering and
Computational Finance"
Diff between fGarch versions 2100.79 dated 2009-09-28 and 2110.80 dated 2009-11-10
ChangeLog | 2620 ++++++++++++++++++++++++++++++++++++++++++++++++++-- DESCRIPTION | 10 R/methods-predict.R | 18 3 files changed, 2544 insertions(+), 104 deletions(-)
Author: Dirk Eddelbuettel with contributions by Simon Urbanek and David
Reiss
Title: Rcpp R/C++ interface package
Description: R/C++ interface classes and examples The Rcpp library maps
data types betweeen R and C++, and includes support for R types
real, integer, character, vector, matrix, Date, datetime (i.e.
POSIXct) at microsecond resolution, data frame, and function.
It also supports calling R functions from C++. Several examples
are included.
Diff between Rcpp versions 0.6.7 dated 2009-11-08 and 0.6.8 dated 2009-11-10
DESCRIPTION | 8 - inst/ChangeLog | 10 ++ libRcpp.a |only src/Makevars | 16 ++- src/Makevars.win | 53 +++++++--- src/Rcpp.cpp | 250 --------------------------------------------------- src/Rcpp.h | 144 ----------------------------- src/RcppCommon.h |only src/RcppDate.cpp |only src/RcppDate.h |only src/RcppDatetime.cpp |only src/RcppDatetime.h |only src/RcppExample.cpp | 2 src/RcppList.cpp | 12 ++ src/RcppList.h | 23 ---- src/RcppParams.cpp |only src/RcppParams.h |only 17 files changed, 84 insertions(+), 434 deletions(-)
Author: Adam Glynn
Title: Estimation of Causal Effects with Generalized Additive Models
Description: This package implements various estimators for average
treatment effects---an inverse probability weighted (IPW)
estimator, an augmented inverse probability weighted (AIPW)
estimator, and a standard regression estimator---that make use
of generalized additive models for the treatment assignment
model and/or outcome model.
Diff between CausalGAM versions 0.1-1 dated 2009-11-08 and 0.1-2 dated 2009-11-10
DESCRIPTION | 8 ++++---- HISTORY | 2 +- R/zzz.R | 5 +---- 3 files changed, 6 insertions(+), 9 deletions(-)
Author: Max Kuhn. Contributions from Jed Wing, Steve Weston, Andre
Williams, Chris Keefer and Allan Engelhardt
Title: Classification and Regression Training
Description: Misc functions for training and plotting classification
and regression models
Diff between caret versions 4.27 dated 2009-11-05 and 4.30 dated 2009-11-09
caret-4.27/caret/inst/doc/caretMisc.tex |only caret-4.27/caret/inst/doc/caretSelection.tex |only caret-4.27/caret/inst/doc/caretTrain.tex |only caret-4.27/caret/inst/doc/caretVarImp.tex |only caret-4.30/caret/DESCRIPTION | 14 caret-4.30/caret/R/createGrid.R | 4 caret-4.30/caret/R/createModel.R | 50 + caret-4.30/caret/R/extractPrediction.R | 10 caret-4.30/caret/R/extractProb.R | 12 caret-4.30/caret/R/makeCubistFiles.R |only caret-4.30/caret/R/misc.R | 52 + caret-4.30/caret/R/plotClassProbs.R | 83 +- caret-4.30/caret/R/predictionFunction.R | 20 caret-4.30/caret/R/predictors.R | 7 caret-4.30/caret/R/probFunction.R | 20 caret-4.30/caret/R/selection.R | 5 caret-4.30/caret/R/train.default.R | 2 caret-4.30/caret/inst/CHANGES | 30 + caret-4.30/caret/inst/doc/caretMisc.pdf | 758 +++++++++++++-------------- caret-4.30/caret/inst/doc/caretSelection.pdf | 325 +++++------ caret-4.30/caret/inst/doc/caretTrain.Rnw | 17 caret-4.30/caret/inst/doc/caretTrain.pdf |binary caret-4.30/caret/inst/doc/caretVarImp.pdf | 199 +++---- caret-4.30/caret/man/extractPrediction.Rd | 1 caret-4.30/caret/man/plotClassProbs.Rd | 63 +- caret-4.30/caret/man/plsda.Rd | 13 caret-4.30/caret/man/train.Rd | 6 27 files changed, 958 insertions(+), 733 deletions(-)
Author: Michal Juraska
Title: Semiparametric efficient estimation for a two-sample treatment
effect
Description: The package performs estimation and testing of the
treatment effect in a 2-group randomized clinical trial with a
quantitative, dichotomous, or right-censored time-to-event
endpoint. The method improves efficiency by leveraging baseline
predictors of the endpoint. The inverse probability weighting
technique of Robins, Rotnitzky, and Zhao (JASA, 1994) is used
to provide unbiased estimation when the endpoint is missing at
random.
Diff between speff2trial versions 1.0.0 dated 2009-07-02 and 1.0.1 dated 2009-11-09
DESCRIPTION | 21 NAMESPACE | 7 R/print.summary.speffSurv.R |only R/speffSurv.R |only R/summary.speffSurv.R |only data/ACTG175.txt | 4280 ++++++++++++++++++++++---------------------- man/ACTG175.Rd | 25 man/speffSurv.Rd |only man/summaryspeffSurv.Rd |only 9 files changed, 2170 insertions(+), 2163 deletions(-)
Author: Han Lin Shang and Rob J Hyndman
Title: Rainbow plots, bagplots and boxplots for functional data
Description: Functions and datasets for functional data display and
outlier detection.
Diff between rainbow versions 1.5 dated 2009-10-08 and 1.6 dated 2009-11-09
CHANGELOG | 2 ++ DESCRIPTION | 8 ++++---- NAMESPACE | 3 ++- R/SVDplot.R |only man/SVDplot.Rd |only man/fboxplot.Rd | 3 +++ 6 files changed, 11 insertions(+), 5 deletions(-)
Author: Stephen Milborrow derived from mda:mars by Trevor Hastie and
Rob Tibshirani.
Title: Multivariate Adaptive Regression Spline Models
Description: Build regression models using the techniques in Friedman's
papers "Fast MARS" and "Multivariate Adaptive Regression
Splines". (The term "MARS" is copyrighted and thus not used in
the name of the package.)
Diff between earth versions 2.3-5 dated 2009-10-09 and 2.4-0 dated 2009-11-09
DESCRIPTION | 6 NEWS | 6 R/earth.R | 2 man/earth.Rd | 64 man/evimp.Rd | 16 man/format.earth.Rd | 34 man/mars.to.earth.Rd | 2 man/model.matrix.earth.Rd | 44 man/predict.earth.Rd | 2 man/summary.earth.Rd | 20 man/update.earth.Rd | 26 src/earth.c | 45 src/earth.h | 16 src/tests/test.earth.big.Rout.save | 61 src/tests/test.earth.cv.Rout.save | 743 +++--- src/tests/test.earth.full.R | 3 src/tests/test.earth.full.Rout.save | 3964 ++++++++++++++++++------------------ src/tests/test.earth.glm.Rout.save | 449 ++-- src/tests/test.earthc.out.save | 2861 +++++++++++++------------ src/tests/test.earthmain.out.save | 37 src/tests/test.plotd.R | 30 src/tests/test.plotd.Rout.save | 30 src/tests/test.plotmo.R | 14 src/tests/test.plotmo.Rout.save | 1553 +++++++------- tests/test.earth.Rout.save | 156 - 25 files changed, 5126 insertions(+), 5058 deletions(-)
Author: Ingmar Visser
Title: Dependent Mixture Models
Description: Fit (multigroup) mixtures of latent Markov models on mixed
categorical and continuous (timeseries) data
Diff between depmix versions 0.9.6 dated 2009-07-18 and 0.9.7 dated 2009-11-09
CHANGES | 6 ++++++ DESCRIPTION | 10 +++++----- README | 4 ++-- man/markovdata.Rd | 2 +- 4 files changed, 14 insertions(+), 8 deletions(-)
Author: Tianqing Liu, Nan Lin, Ningzhong Shi and Baoxue Zhang
Title: Order-restricted Information Criterion-based Clustering
Algorithm
Description: ORIClust is a user-friendly R-based software package for
gene clustering. Clusters are given by genes matched to
prespecified profiles across various ordered treatment groups.
It is particularly useful for analyzing data obtained from
short time-course or dose-response microarray experiments.
Diff between ORIClust versions 1.0-0 dated 2009-09-18 and 1.0-1 dated 2009-11-09
DESCRIPTION | 6 +++--- R/ORICC1.R | 27 +++++++++++++++++---------- R/ORICC2.R | 34 +++++++++++++++++++++++++--------- man/Breast.Rd | 2 +- man/ORICC1-package.Rd | 2 +- man/ORICC2-package.Rd | 2 +- man/complete.profile.Rd | 2 +- man/cyclical.max.min.Rd | 2 +- man/cyclical.min.max.Rd | 2 +- man/decreasing.Rd | 2 +- man/down.up.Rd | 2 +- man/flat.pattern.Rd | 2 +- man/increasing.Rd | 2 +- man/isodecre.Rd | 2 +- man/isoincre.Rd | 2 +- man/up.down.Rd | 2 +- 16 files changed, 58 insertions(+), 35 deletions(-)
Author: Klaus Nordhausen, Seija Sirkia, Hannu Oja, David E. Tyler
Title: Tools for Multivariate Nonparametrics
Description: Tools for multivariate nonparametrics, as location tests
based on marginal ranks, spatial median and spatial signs
computation, Hotelling's T-test, estimates of shape
Diff between ICSNP versions 1.0-5 dated 2009-09-12 and 1.0-6 dated 2009-11-09
DESCRIPTION | 8 ++++---- NAMESPACE | 2 +- R/HP.loc.test.R |only R/vdw.loc.R | 3 ++- data/LASERI.txt |only inst/CHANGES | 7 +++++++ man/HP.loc.test.Rd |only man/ICSNP-package.Rd | 4 ++-- man/LASERI.Rd |only man/pulmonary.Rd | 3 +++ 10 files changed, 19 insertions(+), 8 deletions(-)
Author: Steve Su
Title: Fitting Single and Mixture of Generalised Lambda Distributions
(RS and FMKL) using Discretised and Maximum Likelihood Methods
Description: The fitting algorithms considered in this package have two
major objectives. One is to provide a smoothing device to fit
distributions to data using the weight and unweighted
discretised approach based on the bin width of the histogram.
The other is to provide a definitive fit to the data set using
the maximum likelihood estimation. Diagnostics on goodness of
fit can be done via qqplots, KS-resample tests and comparing
mean, variance, skewness and kurtosis of the data with the
fitted distribution.
Diff between GLDEX versions 1.0.3.3 dated 2009-11-01 and 1.0.3.4 dated 2009-11-09
DESCRIPTION | 8 +++---- R/qqplot.gld.R | 31 +++++++++++++++++------------ R/qqplot.gld.bi.R | 53 ++++++++++++++++++++++++++++++++------------------- man/GLDEX.package.Rd | 4 +-- 4 files changed, 58 insertions(+), 38 deletions(-)
Author: Dongjun Chung
Title: Sparse Partial Least Squares (SPLS) Regression and
Classification
Description: This package provides functions for fitting a Sparse
Partial Least Squares Regression and Classification
Diff between spls versions 1.1-0 dated 2009-05-20 and 2.1-0 dated 2009-11-09
spls-1.1-0/spls/inst/doc/Rplots.pdf |only spls-2.1-0/spls/DESCRIPTION | 10 ++++----- spls-2.1-0/spls/R/cv.sgpls.R |only spls-2.1-0/spls/R/cv.sgpls.binary.R |only spls-2.1-0/spls/R/cv.sgpls.multi.R |only spls-2.1-0/spls/R/cv.split.R |only spls-2.1-0/spls/R/cv.splsda.R |only spls-2.1-0/spls/R/predict.sgpls.R |only spls-2.1-0/spls/R/predict.splsda.R |only spls-2.1-0/spls/R/print.sgpls.R |only spls-2.1-0/spls/R/print.splsda.R |only spls-2.1-0/spls/R/sgpls.R |only spls-2.1-0/spls/R/sgpls.binary.R |only spls-2.1-0/spls/R/sgpls.multi.R |only spls-2.1-0/spls/R/spls.R | 2 - spls-2.1-0/spls/R/splsda.R |only spls-2.1-0/spls/R/wpls.R |only spls-2.1-0/spls/data/filelist | 4 ++- spls-2.1-0/spls/data/lymphoma.RData |only spls-2.1-0/spls/data/prostate.RData |only spls-2.1-0/spls/inst/doc/spls-example.pdf |binary spls-2.1-0/spls/man/ci.spls.Rd | 32 +++++++++++++++--------------- spls-2.1-0/spls/man/coefplot.spls.Rd | 17 ++++++++------- spls-2.1-0/spls/man/correct.spls.Rd | 19 +++++++++-------- spls-2.1-0/spls/man/cv.sgpls.Rd |only spls-2.1-0/spls/man/cv.spls.Rd | 25 ++++++++++++----------- spls-2.1-0/spls/man/cv.splsda.Rd |only spls-2.1-0/spls/man/lymphoma.Rd |only spls-2.1-0/spls/man/mice.Rd | 13 +++++------- spls-2.1-0/spls/man/plot.spls.Rd | 7 +++--- spls-2.1-0/spls/man/predict.sgpls.Rd |only spls-2.1-0/spls/man/predict.spls.Rd | 9 ++++---- spls-2.1-0/spls/man/predict.splsda.Rd |only spls-2.1-0/spls/man/print.sgpls.Rd |only spls-2.1-0/spls/man/print.spls.Rd | 9 ++++---- spls-2.1-0/spls/man/print.splsda.Rd |only spls-2.1-0/spls/man/prostate.Rd |only spls-2.1-0/spls/man/sgpls.Rd |only spls-2.1-0/spls/man/spls-internal.Rd | 26 +++++++++++++++++++++++- spls-2.1-0/spls/man/spls.Rd | 23 +++++++++++---------- spls-2.1-0/spls/man/splsda.Rd |only spls-2.1-0/spls/man/yeast.Rd | 14 ++++++------- 42 files changed, 121 insertions(+), 89 deletions(-)
Author: S original by David James
Title: Chronological objects which can handle dates and times
Description: Chronological objects which can handle dates and times
Diff between chron versions 2.3-32 dated 2009-10-04 and 2.3-33 dated 2009-11-08
ChangeLog | 11 +++++++++++ DESCRIPTION | 8 ++++---- NAMESPACE | 3 +++ R/chron.R | 3 +++ R/dates.R | 4 ++++ R/times.R | 4 ++++ 6 files changed, 29 insertions(+), 4 deletions(-)
Author: originally written by Andrew Gelman
Title: Running WinBUGS and OpenBUGS from R / S-PLUS
Description: Using this package, it is possible to call a BUGS model,
summarize inferences and convergence in a table and graph, and
save the simulations in arrays for easy access in R / S-PLUS.
In S-PLUS, the openbugs functionality and the windows emulation
functionality is not yet available.
Diff between R2WinBUGS versions 2.1-15 dated 2009-11-05 and 2.1-16 dated 2009-11-08
DESCRIPTION | 8 ++++---- R/bugs.R | 2 +- R/write.model.R | 46 ++++++++++++++++++++++++++++++++++++---------- inst/NEWS | 3 +++ inst/doc/R2WinBUGS.pdf | 6 +++--- man/write.model.Rd | 6 ++++-- 6 files changed, 51 insertions(+), 20 deletions(-)
Author: David B. Dahl
Title: Export tables to LaTeX or HTML
Description: Coerce data to LaTeX and HTML tables
Diff between xtable versions 1.5-5 dated 2009-03-24 and 1.5-6 dated 2009-11-08
DESCRIPTION | 8 ++++---- NEWS |only R/print.xtable.R | 21 +++++++++++++++------ inst/doc/xtableGallery.pdf |binary 4 files changed, 19 insertions(+), 10 deletions(-)
Author: Patrick Giraudoux
Title: Data analysis in ecology
Description: Miscellaneous functions for analysis and display of
ecological and spatial data
Diff between pgirmess versions 1.4.0 dated 2009-09-13 and 1.4.1 dated 2009-11-08
pgirmess-1.4.0/pgirmess/R/distPolylines.R |only pgirmess-1.4.0/pgirmess/R/distTotshp.r |only pgirmess-1.4.0/pgirmess/R/valat.R |only pgirmess-1.4.0/pgirmess/R/write.arcGrid.R |only pgirmess-1.4.0/pgirmess/R/write.cl2grass.R |only pgirmess-1.4.0/pgirmess/R/write.kernel2points.R |only pgirmess-1.4.0/pgirmess/R/write.pts2grass.r |only pgirmess-1.4.0/pgirmess/man/distPolylines.rd |only pgirmess-1.4.0/pgirmess/man/distTotshp.rd |only pgirmess-1.4.0/pgirmess/man/valat.Rd |only pgirmess-1.4.0/pgirmess/man/write.arcGrid.Rd |only pgirmess-1.4.0/pgirmess/man/write.cl2grass.rd |only pgirmess-1.4.0/pgirmess/man/write.kernel2points.rd |only pgirmess-1.4.0/pgirmess/man/write.pts2grass.rd |only pgirmess-1.4.1/pgirmess/DESCRIPTION | 8 ++++---- pgirmess-1.4.1/pgirmess/R/gps2gpx.r |only pgirmess-1.4.1/pgirmess/R/readVista.r |only pgirmess-1.4.1/pgirmess/R/uploadGPS.r |only pgirmess-1.4.1/pgirmess/R/valchisq.R | 2 +- pgirmess-1.4.1/pgirmess/R/writeGPX.r |only pgirmess-1.4.1/pgirmess/man/distNode.rd | 3 +-- pgirmess-1.4.1/pgirmess/man/distSeg.rd | 5 +---- pgirmess-1.4.1/pgirmess/man/distTot.rd | 4 +--- pgirmess-1.4.1/pgirmess/man/gps2gpx.rd |only pgirmess-1.4.1/pgirmess/man/readVista.rd |only pgirmess-1.4.1/pgirmess/man/uploadGPS.rd |only pgirmess-1.4.1/pgirmess/man/valchisq.Rd | 8 ++++++-- pgirmess-1.4.1/pgirmess/man/writeGPX.rd |only 28 files changed, 14 insertions(+), 16 deletions(-)
Author: Paul Murrell and Richard Walton.
Title: Importing Vector Graphics
Description: Functions for converting, importing, and drawing
PostScript pictures in R plots.
Diff between grImport versions 0.4-4 dated 2009-09-18 and 0.4-5 dated 2009-11-08
DESCRIPTION | 6 R/PostScript2RGML.R | 11 inst/doc/import.pdf | 2291 ++++++++++++++++++++++----------------------- man/PictureStroke-class.Rd | 2 man/PostScriptTrace.Rd | 14 5 files changed, 1168 insertions(+), 1156 deletions(-)
Author: P. Filzmoser and K. Varmuza
Title: Multivariate Statistical Analysis in Chemometrics
Description: This package is the R companion to the book "Introduction
to Multivariate Statistical Analysis in Chemometrics" written
by K. Varmuza and P. Filzmoser (2009)
Diff between chemometrics versions 0.4 dated 2008-11-13 and 0.5 dated 2009-11-08
DESCRIPTION | 17 +++++++--- R/lassocoef.R | 2 - R/prm.R | 46 +++++++++++++++++++---------- R/prm_cv.R | 81 ++++++++++++++++++++++++++++------------------------ R/prm_dcv.R |only man/Moutlier.Rd | 2 - man/PAC.Rd | 4 +- man/Phenyl.Rd | 4 +- man/alr.Rd | 2 - man/ash.Rd | 6 +-- man/cereal.Rd | 4 +- man/chemometrics.Rd | 4 +- man/clr.Rd | 2 - man/clvalidity.Rd | 12 +++---- man/drawMahal.Rd | 2 - man/glass.Rd | 3 - man/glass.grp.Rd | 4 +- man/hyptis.Rd | 6 --- man/ilr.Rd | 2 - man/knnEval.Rd | 2 - man/lassoCV.Rd | 2 - man/lassocoef.Rd | 2 - man/lmCV.Rd | 2 - man/mvr_dcv.Rd | 2 - man/nipals.Rd | 2 - man/nnetEval.Rd | 2 - man/pcaCV.Rd | 2 - man/pcaDiagplot.Rd | 2 - man/pcaVarexpl.Rd | 2 - man/plotRidge.Rd | 2 - man/plotSEPmvr.Rd | 2 - man/plotcompmvr.Rd | 2 - man/plotpredmvr.Rd | 2 - man/plotprm.Rd | 2 - man/plotresmvr.Rd | 2 - man/plotsom.Rd | 2 - man/pls1_nipals.Rd | 2 - man/pls2_nipals.Rd | 2 - man/pls_eigen.Rd | 2 - man/prm.Rd | 9 ++++- man/prm_cv.Rd | 2 - man/prm_dcv.Rd |only man/ridgeCV.Rd | 2 - man/stepwise.Rd | 2 - man/svmEval.Rd | 2 - man/treeEval.Rd | 2 - 46 files changed, 143 insertions(+), 119 deletions(-)
Author: Dirk Eddelbuettel with contributions by Simon Urbanek and David
Reiss
Title: Rcpp R/C++ interface package
Description: R/C++ interface classes and examples The Rcpp library maps
data types betweeen R and C++, and includes support for R types
real, integer, character, vector, matrix, Date, datetime (i.e.
POSIXct) at microsecond resolution, data frame, and function.
It also supports calling R functions from C++. Several examples
are included.
Diff between Rcpp versions 0.6.6 dated 2009-08-04 and 0.6.7 dated 2009-11-08
Rcpp-0.6.6/Rcpp/inst/doc/html/RcppExample_8cpp-source.html |only Rcpp-0.6.6/Rcpp/inst/doc/html/RcppExample_8cpp_44dbfa080dcf3c7ed95e7d0b067276b3_cgraph.map |only Rcpp-0.6.6/Rcpp/inst/doc/html/RcppExample_8cpp_44dbfa080dcf3c7ed95e7d0b067276b3_cgraph.md5 |only Rcpp-0.6.6/Rcpp/inst/doc/html/RcppExample_8cpp_44dbfa080dcf3c7ed95e7d0b067276b3_cgraph.png |only Rcpp-0.6.6/Rcpp/inst/doc/html/RcppExample_8cpp_4d13d94df70a9a51d67cc6546eb2454f_cgraph.map |only Rcpp-0.6.6/Rcpp/inst/doc/html/RcppExample_8cpp_4d13d94df70a9a51d67cc6546eb2454f_cgraph.md5 |only Rcpp-0.6.6/Rcpp/inst/doc/html/RcppExample_8cpp_4d13d94df70a9a51d67cc6546eb2454f_cgraph.png |only Rcpp-0.6.6/Rcpp/inst/doc/html/RcppExample_8cpp_ecc07b10373d7134c6be02aaa652fc19_cgraph.map |only Rcpp-0.6.6/Rcpp/inst/doc/html/RcppExample_8cpp_ecc07b10373d7134c6be02aaa652fc19_cgraph.md5 |only Rcpp-0.6.6/Rcpp/inst/doc/html/RcppExample_8cpp_ecc07b10373d7134c6be02aaa652fc19_cgraph.png |only 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Rcpp-0.6.7/Rcpp/inst/doc/latex/classRcppResultSet_af6f50ca0a589fc12ef68c0406e83243b_cgraph.pdf |only Rcpp-0.6.7/Rcpp/inst/doc/latex/classRcppStringVector.tex | 98 Rcpp-0.6.7/Rcpp/inst/doc/latex/classRcppStringVectorView.tex | 74 Rcpp-0.6.7/Rcpp/inst/doc/latex/classRcppVector.tex | 106 Rcpp-0.6.7/Rcpp/inst/doc/latex/classRcppVectorView.tex | 76 Rcpp-0.6.7/Rcpp/inst/doc/latex/doxygen.sty | 304 ++ Rcpp-0.6.7/Rcpp/inst/doc/latex/files.tex | 6 Rcpp-0.6.7/Rcpp/inst/doc/latex/hierarchy.tex | 9 Rcpp-0.6.7/Rcpp/inst/doc/latex/refman.tex | 8 Rcpp-0.6.7/Rcpp/inst/doc/man/man3/ColDatum.3 | 68 Rcpp-0.6.7/Rcpp/inst/doc/man/man3/MyRListFunc.3 | 4 Rcpp-0.6.7/Rcpp/inst/doc/man/man3/MyRVectorFunc.3 | 4 Rcpp-0.6.7/Rcpp/inst/doc/man/man3/Rcpp.cpp.3 | 20 Rcpp-0.6.7/Rcpp/inst/doc/man/man3/Rcpp.h.3 | 10 Rcpp-0.6.7/Rcpp/inst/doc/man/man3/RcppDate.3 | 52 Rcpp-0.6.7/Rcpp/inst/doc/man/man3/RcppDateVector.3 | 16 Rcpp-0.6.7/Rcpp/inst/doc/man/man3/RcppDatetime.3 | 56 Rcpp-0.6.7/Rcpp/inst/doc/man/man3/RcppDatetimeVector.3 | 16 Rcpp-0.6.7/Rcpp/inst/doc/man/man3/RcppExample.cpp.3 | 2 Rcpp-0.6.7/Rcpp/inst/doc/man/man3/RcppFrame.3 | 22 Rcpp-0.6.7/Rcpp/inst/doc/man/man3/RcppFunction.3 | 44 Rcpp-0.6.7/Rcpp/inst/doc/man/man3/RcppList.3 |only Rcpp-0.6.7/Rcpp/inst/doc/man/man3/RcppList.cpp.3 |only Rcpp-0.6.7/Rcpp/inst/doc/man/man3/RcppList.h.3 |only Rcpp-0.6.7/Rcpp/inst/doc/man/man3/RcppMatrix.3 | 38 Rcpp-0.6.7/Rcpp/inst/doc/man/man3/RcppMatrixView.3 | 38 Rcpp-0.6.7/Rcpp/inst/doc/man/man3/RcppNumList.3 | 20 Rcpp-0.6.7/Rcpp/inst/doc/man/man3/RcppParams.3 | 10 Rcpp-0.6.7/Rcpp/inst/doc/man/man3/RcppResultSet.3 | 24 Rcpp-0.6.7/Rcpp/inst/doc/man/man3/RcppStringVector.3 | 18 Rcpp-0.6.7/Rcpp/inst/doc/man/man3/RcppStringVectorView.3 | 14 Rcpp-0.6.7/Rcpp/inst/doc/man/man3/RcppVector.3 | 14 Rcpp-0.6.7/Rcpp/inst/doc/man/man3/RcppVectorView.3 | 14 Rcpp-0.6.7/Rcpp/inst/examples |only Rcpp-0.6.7/Rcpp/man/RcppVector.Rd | 2 Rcpp-0.6.7/Rcpp/src/Makevars | 14 Rcpp-0.6.7/Rcpp/src/Rcpp.cpp | 5 Rcpp-0.6.7/Rcpp/src/Rcpp.h | 12 Rcpp-0.6.7/Rcpp/src/RcppList.cpp |only Rcpp-0.6.7/Rcpp/src/RcppList.h |only 741 files changed, 8928 insertions(+), 8145 deletions(-)
Author: P. Neytchev, P. Filzmoser, R. Patnaik, A. Eisl and R. Boubela
Title: Trimmed Maximum Likelihood Estimation
Description: TLE implements a general framework for robust fitting of
finite mixture models. Parameter estimation is performed using
the EM algorithm.
Diff between tlemix versions 0.0.6 dated 2009-07-02 and 0.0.7 dated 2009-11-08
DESCRIPTION | 10 inst/doc/references.bib | 2 inst/doc/tlemix-intro.pdf | 1457 ++++++++++++++++++++++++++-------------------- man/coefmclust.Rd | 2 4 files changed, 847 insertions(+), 624 deletions(-)
Author: Christian Hennig
Title: Functions for clustering of presence-absence and abundance data
Description: Distance-based parametric bootstrap tests for clustering,
mainly intended for presence-absence data and abundance data
(clustering of species distribution ranges). Jaccard,
Kulczynski, quantitative Kulczynski and geco distance measures,
clustering of presence-absence and abundance data, and nearest
neighbor based noise detection (R port of Byers and Raftery's
(1998) "NNclean"). Main functions are prabtest, abundtest (for
testing), prabclust (for clustering), prabinit (for preparing
the data) and NNclean (for noise detection). The help-pages for
prabtest, abundtest and prabclust contain simple standard
executions. Note that the use of the package mclust (called by
function prabclust) is protected by a special license, see
http://www.stat.washington.edu/mclust/license.txt, particularly
point 6.
Diff between prabclus versions 2.1-3 dated 2009-05-06 and 2.1-4 dated 2009-11-08
DESCRIPTION | 8 ++++---- R/abundfunctions.R | 8 ++++---- 2 files changed, 8 insertions(+), 8 deletions(-)
Author: Stefano Iacus
Title: CEM: Software for Coarsened Exact Matching
Description: This program implements the coarsened exact matching
algorithm (and many extensions) described in Stefano M. Iacus,
Gary King, and Giuseppe Porro, "Causal Inference Without
Balance Checking: Coarsened Exact Matching,"
http://gking.harvard.edu/files/abs/cem-plus-abs.shtml
Diff between cem versions 1.0.127 dated 2009-11-04 and 1.0.128 dated 2009-11-08
DESCRIPTION | 8 NAMESPACE | 3 R/L1profile.R | 36 R/imbspace.R |only R/imbspace.plot.R |only R/relax.cem.R | 46 - inst/doc/Rplots.pdf | 4 inst/doc/cem.Rnw | 2 inst/doc/cem.pdf | 2053 ++++++++++++++++++++++++-------------------------- inst/doc/coarsen1.pdf | 4 inst/doc/coarsen2.pdf | 4 inst/doc/copyRd.Rout | 2 inst/doc/index.shtml | 4 inst/doc/teff.pdf | 4 man/imbspace.Rd |only man/imbspace.plot.Rd |only man/relax.cem.Rd | 17 man/shift.cem.Rd | 2 18 files changed, 1095 insertions(+), 1094 deletions(-)
Author: David M. Schruth
Title: Generic Functions for R
Description: The caroline package is a collection of generic functions
useful for various applications.
Diff between caroline versions 0.1-3 dated 2009-10-28 and 0.1-6 dated 2009-11-08
caroline-0.1-3/caroline/man/plotRA.Rd |only caroline-0.1-6/caroline/DESCRIPTION | 10 - caroline-0.1-6/caroline/NAMESPACE |only caroline-0.1-6/caroline/R/plots.R | 228 ---------------------------------- caroline-0.1-6/caroline/R/system.R | 6 caroline-0.1-6/caroline/man/pies.Rd | 2 6 files changed, 13 insertions(+), 233 deletions(-)
Author: Robin Nunkesser
Title: R/FrEAK interface
Description: An R interface to a modified version of the Free
Evolutionary Algorithm Kit FrEAK. FrEAK is a toolkit written in
Java to design and analyze evolutionary algorithms. Both the R
interface and an extended version of FrEAK are contained in the
RFreak package. For more information on FrEAK see
http://sourceforge.net/projects/freak427/.
Diff between RFreak versions 0.2-5 dated 2009-01-27 and 0.2-6 dated 2009-11-08
DESCRIPTION | 15 R/functions.r | 32 + inst/java/resource/freak/gui/help/footnode.html | 2 inst/java/resource/freak/gui/help/index.html | 482 +++++++++++----------- inst/java/resource/freak/gui/help/node1.html | 4 inst/java/resource/freak/gui/help/node3.html | 268 ++++++------ inst/java/resource/freak/gui/help/node4.html | 284 ++++++------ inst/java/resource/freak/gui/help/node5.html | 186 ++++---- inst/java/resource/freak/gui/help/node7.html | 3 inst/java/resource/freak/gui/help/node8.html | 3 inst/java/resource/freak/gui/help/usersguide.html | 38 - man/FreakReturn-class.Rd | 6 man/GPAS-class.Rd | 2 13 files changed, 675 insertions(+), 650 deletions(-)
More information about MortalitySmooth at CRAN
Permanent link
Author: Vito M.R. Muggeo
Title: Segmented relationships in regression models
Description: Given a (generalized) linear model, segmented `updates'
the model by adding one or more segmented relationships.
Several variables with multiple breakpoints are allowed.
Diff between segmented versions 0.2-5 dated 2009-10-26 and 0.2-6 dated 2009-11-06
DESCRIPTION | 8 ++++---- R/broken.line.R | 5 +++-- R/confint.segmented.R | 12 ++++++++---- R/draw.history.R | 9 +-------- R/plot.segmented.R | 10 ++++++---- R/print.segmented.R | 6 +++--- R/print.summary.segmented.R | 21 +++++++++++++-------- R/segmented.lm.R | 1 + R/slope.R | 16 ++++++++++------ R/summary.segmented.R | 41 ++++++++++++++++++++++++++++++++++------- R/vcov.segmented.R |only man/broken.line.Rd | 4 ++-- man/confint.segmented.Rd | 19 ++++++++++--------- man/segmented-package.Rd | 6 ++++-- man/segmented.Rd | 17 ++++++++++------- man/slope.Rd | 32 +++++++++++++++++++++----------- man/summary.segmented.Rd | 39 ++++++++++++++++++++++++++++++++------- man/vcov.segmented.Rd |only 18 files changed, 162 insertions(+), 84 deletions(-)
Author: Graham Williams
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.
Diff between rattle versions 2.5.2 dated 2009-11-04 and 2.5.3 dated 2009-11-06
DESCRIPTION | 8 ++++---- NAMESPACE | 1 + R/cluster.R | 30 +++++++++++++++++------------- R/evaluate.R | 19 +++++++++++++++++-- R/execute.R | 10 +++++++++- R/hclust.R | 6 +++--- R/kmeans.R | 6 +++--- R/model.R | 2 +- R/rattle.R | 44 ++++++++++++++++++++++++++++++++++++-------- R/rpart.R | 4 ++-- R/survival.R | 49 +++++++++++++++++++++++++++++++++++++++++++------ R/textview.R | 26 ++++++++++++++++---------- R/transform.R | 5 +++-- inst/etc/rattle.glade | 49 +++++++++++++++++++++++++++++++++++-------------- man/internal.Rd | 2 ++ 15 files changed, 192 insertions(+), 69 deletions(-)
Author: Hein Putter, Liesbeth de Wreede, Marta Fiocco
Title: Data preparation, estimation and prediction in multi-state
models
Description: Functions for data preparation, descriptives, hazard
estimation and prediction with Aalen-Johansen or simulation in
competing risks and multi-state models
Diff between mstate versions 0.2.2 dated 2009-09-24 and 0.2.3 dated 2009-11-06
Changelog.txt | 13 DESCRIPTION | 10 NAMESPACE | 7 R/Cuminc.R | 8 R/events.R | 3 R/expandcovs.R | 10 R/msboot.R | 2 R/msfit.R | 11 R/msprep.R | 2 R/mssample.R | 2 R/plot.msfit.R |only R/plot.probtrans.R |only R/print.msdata.R |only R/probtrans.R | 7 R/redrank.R | 19 R/summary.msfit.R |only R/summary.probtrans.R |only R/transMat.R |only data/prothr.RData |binary inst/doc/Rplots.pdf |18346 +++++++++++++++++++++++++---------------------- inst/doc/Tutorial.Rnw | 266 inst/doc/Tutorial.pdf |binary inst/doc/agsm.bst |only man/Cuminc.Rd | 2 man/ebmt4.Rd | 2 man/events.Rd | 15 man/expandcovs.Rd | 15 man/msfit.Rd | 17 man/msprep.Rd | 8 man/mssample.Rd | 14 man/mstate-package.Rd | 4 man/plot.msfit.Rd |only man/plot.probtrans.Rd |only man/print.msdata.Rd |only man/probtrans.Rd | 15 man/redrank.Rd | 17 man/summary.msfit.Rd |only man/summary.probtrans.Rd |only man/trans.Rd | 29 39 files changed, 10226 insertions(+), 8618 deletions(-)
Author: Friedrich Leisch, with contributions by Evgenia Dimitriadou.
Title: Flexible Cluster Algorithms
Description: The main function kcca implements a general framework for
k-centroids cluster analysis supporting arbitrary distance
measures and centroid computation. Further cluster methods
include hard competitive learning, neural gas, and QT
clustering. There are numerous visualization methods for
cluster results (neighborhood graphs, convex cluster hulls,
barcharts of centroids, ...), and bootstrap methods for the
analysis of cluster stability.
Diff between flexclust versions 1.2-1 dated 2009-07-02 and 1.2-2 dated 2009-11-06
DESCRIPTION | 10 +-- NAMESPACE | 7 +- NEWS | 13 ++++ R/AAA-classes.R | 18 +++++- R/bootstrap.R | 19 ++++++ R/conversion.R | 42 ++++++++++++++- R/distances.R | 6 +- R/family.R |only R/info.R | 4 - R/kcca.R | 115 +----------------------------------------- R/tour.R | 78 ++++++++++++++++++++++++++++ R/utils.R | 2 inst/CITATION | 4 - man/barplot-methods.Rd | 4 - man/bootFlexclust.Rd | 6 +- man/conversion.Rd | 31 +++++++++-- man/distances.Rd | 4 + man/flexclustControl-class.Rd | 8 +- man/kcca.Rd | 4 - man/projAxes.Rd | 4 - man/propBarchart.Rd | 4 - man/qtclust.Rd | 7 +- man/randIndex.Rd | 13 +++- man/stepFlexclust.Rd | 13 ++++ man/stripes.Rd | 4 - tests/plots.R |only 26 files changed, 260 insertions(+), 160 deletions(-)
Author: Yihui Xie
Title: Demonstrate Animations in Statistics
Description: This package consists of various functions for animations
in statistics, covering many areas such as probability theory,
mathematical statistics, multivariate statistics, nonparametric
statistics, sampling survey, linear models, time series,
computational statistics, data mining and machine learning.
These functions might be of help in teaching statistics and
data analysis.
Diff between animation versions 1.0-7 dated 2009-11-02 and 1.0-8 dated 2009-11-06
DESCRIPTION | 10 +++++----- R/ecol.death.sim.R |only R/tidy.source.R | 2 +- inst/NEWS | 35 ++++++++++++++++++++++++++--------- man/HuSpeech.Rd | 2 +- man/animation-package.Rd | 2 +- man/ecol.death.sim.Rd |only 7 files changed, 34 insertions(+), 17 deletions(-)
Author: Marc Schwartz
Title: Cross-platform Perl based R function to create Excel 2003 (XLS)
files
Description: Cross-platform perl based R function to create Excel (XLS)
files from one or more data frames. Each data frame will be
written to a separate named worksheet in the Excel spreadsheet.
The worksheet name will be the name of the data frame it
contains or can be specified by the user.
Diff between WriteXLS versions 1.8.2 dated 2009-10-12 and 1.8.3 dated 2009-11-06
DESCRIPTION | 10 +++++----- R/testPerl.R | 17 +++++++++++------ 2 files changed, 16 insertions(+), 11 deletions(-)
Author: Peter Filzmoser and Barbara Steiger
Title: Statistical Analysis for Environmantel Data
Description: This package offers different possibilities to make
statistical analysis for Environmental Data.
Diff between StatDA versions 1.1 dated 2009-01-26 and 1.2 dated 2009-11-06
StatDA-1.1/StatDA/inst/doc/.build.timestamp |only StatDA-1.2/StatDA/DESCRIPTION | 14 ++++++++----- StatDA-1.2/StatDA/R/qqplot-das.R | 28 ++++++++++++++++++++------- StatDA-1.2/StatDA/data/AuNEW.rda |binary StatDA-1.2/StatDA/data/AuOLD.rda |binary StatDA-1.2/StatDA/data/CHorANADUP.rda |binary StatDA-1.2/StatDA/data/CHorFieldDUP.rda |binary StatDA-1.2/StatDA/data/CHorSTANDARD.rda |binary StatDA-1.2/StatDA/data/bhorizon.rda |binary StatDA-1.2/StatDA/data/bordersKola.rda |binary StatDA-1.2/StatDA/data/chorizon.rda |binary StatDA-1.2/StatDA/data/kola.background.rda |binary StatDA-1.2/StatDA/data/monch.rda |binary StatDA-1.2/StatDA/data/moss.rda |binary StatDA-1.2/StatDA/data/nizap.rda |binary StatDA-1.2/StatDA/data/ohorizon.rda |binary StatDA-1.2/StatDA/data/res.eyefit.As_C.rda |binary StatDA-1.2/StatDA/data/res.eyefit.As_C_m.rda |binary StatDA-1.2/StatDA/data/res.eyefit.AuNEW.rda |binary StatDA-1.2/StatDA/data/res.eyefit.Ca_C.rda |binary StatDA-1.2/StatDA/data/res.eyefit.Ca_O.rda |binary StatDA-1.2/StatDA/data/res.eyefit.Hg_O.rda |binary StatDA-1.2/StatDA/data/res.eyefit.Pb_O1.rda |binary StatDA-1.2/StatDA/data/res.eyefit.Pb_O2.rda |binary StatDA-1.2/StatDA/data/timetrend.rda |binary StatDA-1.2/StatDA/data/topsoil.rda |binary StatDA-1.2/StatDA/inst/doc/StatDA.pdf |binary StatDA-1.2/StatDA/man/concarea.Rd | 2 - StatDA-1.2/StatDA/man/qqplot.das.Rd | 5 +++- 29 files changed, 35 insertions(+), 14 deletions(-)
Author: David Meyer and Kurt Hornik (with contributions by Christian
Buchta)
Title: Sets, Generalized Sets, Customizable Sets and Intervals
Description: Data structures and basic operations for ordinary sets,
generalizations such as fuzzy sets, multisets, and fuzzy
multisets, customizable sets, and intervals.
Diff between sets versions 1.0 dated 2009-08-04 and 1.0-1 dated 2009-11-06
DESCRIPTION | 12 ++--- NAMESPACE | 88 +++++++++++++++++++++++++++++++++++++++++++ NEWS | 25 ++++++++++-- R/allEqual.R | 21 +++++----- R/cardinality.R | 18 ++++---- R/cartesian.R | 12 +++-- R/complement.R | 16 ++++--- R/converters.R | 37 ++++++------------ R/cset.R | 32 ++++++++++++--- R/cut.R | 38 +++++++++--------- R/element.R | 8 +-- R/extractors.R | 69 +++++++++++++++++----------------- R/fuzzyfuns.R | 2 R/fuzzyinference.R | 19 ++++----- R/fuzzylogic.R | 19 +++++---- R/gset.R | 79 +++++++++++++++++++++++---------------- R/intersection.R | 12 ++--- R/interval.R |only R/labels.R | 5 +- R/mean.R | 15 ++----- R/memberships.R | 32 ++++++++------- R/options.R | 2 R/plot.R | 26 +++++++----- R/power.R | 4 - R/predicates.R | 107 ++++++++++++++++++++++++++++++----------------------- R/product.R | 6 +- R/reduction.R | 10 ++-- R/rep.R | 4 - R/set.R | 14 +++++- R/similarity.R | 2 R/sumdiff.R | 6 +- R/summary.R | 33 +++++++++++----- R/tuple.R | 6 ++ R/union.R | 4 - R/utilities.R | 5 ++ inst/NEWS | 25 ++++++++++-- inst/doc/sets.pdf |binary man/cset.Rd | 30 +++++++------- man/gset.Rd | 30 +++++++------- man/interval.Rd |only 40 files changed, 550 insertions(+), 323 deletions(-)
Author: Adrian Baddeley
Title: Spatial Point Pattern analysis, model-fitting, simulation, tests
Description: A package for analysing spatial data, mainly Spatial Point
Patterns, including multitype/marked points and spatial
covariates, in any two-dimensional spatial region. Contains
functions for plotting spatial data, exploratory data analysis,
model-fitting, simulation, spatial sampling, model diagnostics,
and formal inference. Data types include point patterns, line
segment patterns, spatial windows, and pixel images. Point
process models can be fitted to point pattern data. Cluster
type models are fitted by the method of minimum contrast. Very
general Gibbs point process models can be fitted to point
pattern data using a function ppm similar to lm or glm. Models
may include dependence on covariates, interpoint interaction
and dependence on marks. Fitted models can be simulated
automatically. Also provides facilities for formal inference
(such as chi-squared tests) and model diagnostics (including
simulation envelopes, residuals, residual plots and Q-Q plots).
Diff between spatstat versions 1.17-0 dated 2009-10-22 and 1.17-1 dated 2009-11-06
spatstat-1.17-0/spatstat/man/eval.hyper.Rd |only spatstat-1.17-1/spatstat/.Rbuildindex.6632 |only spatstat-1.17-1/spatstat/.Rbuildindex.6913 |only spatstat-1.17-1/spatstat/DESCRIPTION | 17 spatstat-1.17-1/spatstat/INDEX | 30 spatstat-1.17-1/spatstat/R/Fest.S | 4 spatstat-1.17-1/spatstat/R/First.R | 2 spatstat-1.17-1/spatstat/R/discarea.R | 8 spatstat-1.17-1/spatstat/R/distbdry.S | 31 spatstat-1.17-1/spatstat/R/distmap.R | 8 spatstat-1.17-1/spatstat/R/fgk3.R |only spatstat-1.17-1/spatstat/R/fv.R | 5 spatstat-1.17-1/spatstat/R/hyperframe.R | 64 + spatstat-1.17-1/spatstat/R/images.R | 29 spatstat-1.17-1/spatstat/R/infline.R | 43 + spatstat-1.17-1/spatstat/R/morphology.R | 26 spatstat-1.17-1/spatstat/R/options.R | 127 ++- spatstat-1.17-1/spatstat/R/pairwise.S | 17 spatstat-1.17-1/spatstat/R/plot.owin.S | 45 - spatstat-1.17-1/spatstat/R/pp3.R |only spatstat-1.17-1/spatstat/R/ppx.R |only spatstat-1.17-1/spatstat/R/random.S | 47 - spatstat-1.17-1/spatstat/R/rmh.default.R | 220 ++++- spatstat-1.17-1/spatstat/R/rmhResolveTypes.R | 4 spatstat-1.17-1/spatstat/R/rmhcontrol.R | 117 ++- spatstat-1.17-1/spatstat/R/tess.R | 46 + spatstat-1.17-1/spatstat/R/util.S | 10 spatstat-1.17-1/spatstat/R/window.S | 7 spatstat-1.17-1/spatstat/R/wingeom.S | 133 ++- spatstat-1.17-1/spatstat/inst/doc/shapefiles.Rnw | 1 spatstat-1.17-1/spatstat/inst/doc/shapefiles.pdf | 845 +++++++--------------- spatstat-1.17-1/spatstat/man/F3est.Rd |only spatstat-1.17-1/spatstat/man/G3est.Rd |only spatstat-1.17-1/spatstat/man/K3est.Rd |only spatstat-1.17-1/spatstat/man/Kest.Rd | 7 spatstat-1.17-1/spatstat/man/PairPiece.Rd | 11 spatstat-1.17-1/spatstat/man/Pairwise.Rd | 49 + spatstat-1.17-1/spatstat/man/as.box3.Rd |only spatstat-1.17-1/spatstat/man/as.hyperframe.Rd |only spatstat-1.17-1/spatstat/man/as.hyperframe.ppx.Rd |only spatstat-1.17-1/spatstat/man/bdist.pixels.Rd | 19 spatstat-1.17-1/spatstat/man/bdist.points.Rd | 2 spatstat-1.17-1/spatstat/man/bdist.tiles.Rd |only spatstat-1.17-1/spatstat/man/border.Rd |only spatstat-1.17-1/spatstat/man/box3.Rd |only spatstat-1.17-1/spatstat/man/coords.Rd |only spatstat-1.17-1/spatstat/man/deprecated.Rd | 4 spatstat-1.17-1/spatstat/man/diameter.box3.Rd |only spatstat-1.17-1/spatstat/man/gpc2owin.Rd | 6 spatstat-1.17-1/spatstat/man/hist.im.Rd | 12 spatstat-1.17-1/spatstat/man/hyperframe.Rd | 16 spatstat-1.17-1/spatstat/man/internal.Rd | 28 spatstat-1.17-1/spatstat/man/intersect.owin.Rd | 22 spatstat-1.17-1/spatstat/man/methods.box3.Rd |only spatstat-1.17-1/spatstat/man/methods.pp3.Rd |only spatstat-1.17-1/spatstat/man/methods.ppx.Rd |only spatstat-1.17-1/spatstat/man/perimeter.Rd | 6 spatstat-1.17-1/spatstat/man/plot.hyperframe.Rd | 6 spatstat-1.17-1/spatstat/man/plot.owin.Rd | 2 spatstat-1.17-1/spatstat/man/plot.pp3.Rd |only spatstat-1.17-1/spatstat/man/pp3.Rd |only spatstat-1.17-1/spatstat/man/ppx.Rd |only spatstat-1.17-1/spatstat/man/rSSI.Rd | 9 spatstat-1.17-1/spatstat/man/rmh.default.Rd | 65 + spatstat-1.17-1/spatstat/man/rmhcontrol.Rd | 97 ++ spatstat-1.17-1/spatstat/man/spatstat-package.Rd | 59 + spatstat-1.17-1/spatstat/man/spatstat.options.Rd | 21 spatstat-1.17-1/spatstat/man/tess.Rd | 3 spatstat-1.17-1/spatstat/man/with.hyperframe.Rd |only spatstat-1.17-1/spatstat/src/call3d.c |only spatstat-1.17-1/spatstat/src/f3.c |only spatstat-1.17-1/spatstat/src/functable.h |only spatstat-1.17-1/spatstat/src/g3.c |only spatstat-1.17-1/spatstat/src/geom3.h |only spatstat-1.17-1/spatstat/src/k3.c |only spatstat-1.17-1/spatstat/src/methas.c | 34 spatstat-1.17-1/spatstat/src/methas.h | 2 spatstat-1.17-1/spatstat/src/sphefrac.c |only spatstat-1.17-1/spatstat/src/sphevol.c |only 79 files changed, 1510 insertions(+), 856 deletions(-)
Author: Andrej-Nikolai Spiess
Title: Modelling and analysis of real-time PCR data
Description: Model fitting, optimal model selection and calculation of
various features that are essential in the analysis of
quantitative real-time polymerase chain reaction (qPCR).
Diff between qpcR versions 1.2-2 dated 2009-09-21 and 1.2-3 dated 2009-11-06
DESCRIPTION | 6 ++-- NAMESPACE | 1 R/calib.r | 74 ++++++++++++++++++++++++++++++++---------------------- R/calib2.r | 13 +++++---- R/fitprob.r |only R/pcrGOF.R | 2 - data/batsch1.rda |only data/batsch2.rda |only data/batsch3.rda |only data/batsch4.rda |only data/batsch5.rda |only man/BIC.Rd | 2 - man/batschetal.rd |only man/calib.Rd | 10 +++++-- man/fitprob.rd |only man/pcrGOF.Rd | 1 16 files changed, 66 insertions(+), 43 deletions(-)
Author: Garrett M. Dancik
Title: Maximum Likelihood Estimates of Gaussian Processes
Description: Maximum likelihood Gaussian process modeling for
univariate and multi-dimensional outputs with diagnostic plots
and sensitivity analysis.
Diff between mlegp versions 2.2.6 dated 2009-03-08 and 3.1.0 dated 2009-11-06
mlegp-2.2.6/mlegp/R/ANOVAInteractionEffect.R |only mlegp-2.2.6/mlegp/R/ANOVAMainEffect.R |only mlegp-2.2.6/mlegp/R/FANOVADecomposition.R |only mlegp-2.2.6/mlegp/R/FANOVADecomposition.gp.R |only mlegp-2.2.6/mlegp/R/FANOVADecomposition.gp.list.R |only mlegp-2.2.6/mlegp/R/FunctionalVariance.R |only mlegp-2.2.6/mlegp/R/Integrate1DCor.R |only mlegp-2.2.6/mlegp/R/Integrate1DCorSquared.R |only mlegp-2.2.6/mlegp/R/IntegrateForVariance.R |only mlegp-2.2.6/mlegp/R/IntegrateInteractionEffectSquared.R |only mlegp-2.2.6/mlegp/R/IntegrateMainEffectSquared.R |only mlegp-2.2.6/mlegp/R/OverallMean.R |only mlegp-2.2.6/mlegp/R/calcMainEffect.R |only mlegp-2.2.6/mlegp/R/computeCorElement.R |only mlegp-2.2.6/mlegp/R/computeCorElementExcept.R |only mlegp-2.2.6/mlegp/R/createIntegratedCorMatrixExcept.R |only mlegp-2.2.6/mlegp/R/expectedMeanReg.R |only mlegp-2.2.6/mlegp/R/expectedMeanRegExcept.R |only mlegp-2.2.6/mlegp/R/nice.R |only mlegp-2.2.6/mlegp/R/plotInteractionEffect.R |only mlegp-2.2.6/mlegp/R/plotMainEffects.R |only mlegp-2.2.6/mlegp/R/plotMainEffects.gp.R |only mlegp-2.2.6/mlegp/R/plotMainEffects.gp.list.R |only mlegp-2.2.6/mlegp/R/plotMainEffectsUsingPCWeights.R |only mlegp-2.2.6/mlegp/inst/doc/Rplots.ps |only mlegp-2.2.6/mlegp/inst/doc/SA-005.pdf |only mlegp-2.2.6/mlegp/inst/doc/SA-007.pdf |only mlegp-2.2.6/mlegp/inst/doc/SA.Rnw |only mlegp-2.2.6/mlegp/inst/doc/SA.pdf |only mlegp-2.2.6/mlegp/inst/doc/SVD-004.pdf |only mlegp-2.2.6/mlegp/inst/doc/SVD-009.pdf |only mlegp-2.2.6/mlegp/inst/doc/SVD-012.pdf |only mlegp-2.2.6/mlegp/inst/doc/SVD.Rnw |only mlegp-2.2.6/mlegp/inst/doc/SVD.pdf |only mlegp-2.2.6/mlegp/inst/doc/gp.Rnw |only mlegp-2.2.6/mlegp/inst/doc/gp.pdf |only mlegp-2.2.6/mlegp/inst/doc/gp_ex-003.eps |only mlegp-2.2.6/mlegp/inst/doc/gp_ex-012.pdf |only mlegp-2.2.6/mlegp/inst/doc/gp_ex.Rnw |only mlegp-2.2.6/mlegp/inst/doc/gp_ex.pdf |only mlegp-2.2.6/mlegp/inst/doc/gp_ex.tex |only mlegp-2.2.6/mlegp/inst/doc/overview.Rnw |only mlegp-2.2.6/mlegp/inst/doc/overview.pdf |only mlegp-2.2.6/mlegp/inst/doc/play |only mlegp-2.2.6/mlegp/man/FANOVADecomposition.Rd |only mlegp-2.2.6/mlegp/man/FANOVAFunctions.Rd |only mlegp-2.2.6/mlegp/man/mlegp-sa-internal.Rd |only mlegp-2.2.6/mlegp/man/nice.Rd |only mlegp-2.2.6/mlegp/man/plotInteractionEffect.Rd |only mlegp-2.2.6/mlegp/man/plotMainEffects.Rd |only mlegp-3.1.0/mlegp/CHANGES | 5 mlegp-3.1.0/mlegp/DESCRIPTION | 28 - mlegp-3.1.0/mlegp/R/loadCLibAndAdapt.R | 28 - mlegp-3.1.0/mlegp/R/mlegp.R | 139 +++- mlegp-3.1.0/mlegp/R/mlegp2.R |only mlegp-3.1.0/mlegp/R/uniqueSummary.R |only mlegp-3.1.0/mlegp/inst/doc/Makefile | 56 +- mlegp-3.1.0/mlegp/inst/doc/Rplots.pdf |only mlegp-3.1.0/mlegp/inst/doc/gp_ex-003.pdf | 446 ++++++++-------- mlegp-3.1.0/mlegp/inst/doc/mlegp-003.pdf |only mlegp-3.1.0/mlegp/inst/doc/mlegp-018.pdf |only mlegp-3.1.0/mlegp/inst/doc/mlegp.Rnw | 270 +++++++++ mlegp-3.1.0/mlegp/inst/doc/mlegp.out |only mlegp-3.1.0/mlegp/inst/doc/mlegp.pdf |binary mlegp-3.1.0/mlegp/man/createGP.Rd | 2 mlegp-3.1.0/mlegp/man/createWindow.Rd | 2 mlegp-3.1.0/mlegp/man/is.gp.Rd | 2 mlegp-3.1.0/mlegp/man/mlegp.Rd | 40 + mlegp-3.1.0/mlegp/man/uniqueSummary.Rd |only mlegp-3.1.0/mlegp/src/fit_gp.h | 218 +++++-- mlegp-3.1.0/mlegp/src/gp.h | 15 mlegp-3.1.0/mlegp/src/matrix_vector.h | 34 + mlegp-3.1.0/mlegp/src/mlegp.c | 22 mlegp-3.1.0/mlegp/src/nelder_mead_min.c | 4 74 files changed, 928 insertions(+), 383 deletions(-)
Author: Dominick Samperi
Title: Rcpp R/C++ Object Mapping Library and Package Template
Description: The Rcpp class library enables C++ to speak the language
of R. The library maps the most commonly used R data structures
to C++ classes. This includes vectors, matrices, factors,
dates, data frames, time series, and functions. R can call C++
functions, and C++ objects can call R functions, and the
parameters and return values can be of any of the types just
mentioned. This package serves two roles: 1. it serves as a
demo package for Rcpp, and 2. it serves as a template for the
creation of new packages that use the Rcpp library (and also
for packages that do not). An important goal of the library is
to support the creation of high-performance packages that do
heavy computations on large data sets where a hybrid R/C++
strategy is the best fit. See the document RcppDoc.pdf for more
information. The R package Rcpp is a forked version of a
previous version of this software and is not discussed here.
Diff between RcppTemplate versions 6.0 dated 2009-11-03 and 6.1 dated 2009-11-06
DESCRIPTION | 13 +++++++------ RcppSrc/Rcpp.cpp | 2 +- inst/doc/RcppDoc.Rnw | 2 +- inst/doc/RcppDoc.pdf |binary 4 files changed, 9 insertions(+), 8 deletions(-)
Author: Yong ZANG
Title: Robust tests for case-control genetic association studies
Description: This package supplies several robust tests for
case-control genetic association studies. The tests contained
in this package are: allelic based test, Cochran-Armitage trend
test, maximin efficiency robust test, MAX3 test and genetic
model selection test. For each test, the corresponding R code
reports the test statistics and the associated p-value.
Diff between Rassoc versions 1.0 dated 2009-07-30 and 1.01 dated 2009-11-06
DESCRIPTION | 12 ++--- JSS487_revisionV2.pdf |only R/ABT.R | 56 +++++++++++++++++++---- R/CATT.R | 45 ++++++++++++++----- R/GMS.R | 118 +++++++++++++++++++++++++++++++++++--------------- R/MAX3.R | 113 ++++++++++++++++++++++++++++++++--------------- R/MERT.R | 57 +++++++++++++++++------- man/ABT.Rd | 30 +++--------- man/CATT.Rd | 27 +++-------- man/GMS.Rd | 93 +++++++++------------------------------ man/MAX3.Rd | 96 ++++++++++------------------------------ man/MERT.Rd | 27 +++-------- man/Rassoc-package.Rd | 6 +- man/caco.Rd | 16 ++---- 14 files changed, 367 insertions(+), 329 deletions(-)
Author: Roger Bivand
Title: Spatial dependence: weighting schemes, statistics and models
Description: A collection of functions to create spatial weights matrix
objects from polygon contiguities, from point patterns by
distance and tesselations, for summarising these objects, and
for permitting their use in spatial data analysis, including
regional aggregation by minimum spanning tree; a collection of
tests for spatial autocorrelation, including global Moran's I,
APLE, Geary's C, Hubert/Mantel general cross product statistic,
Empirical Bayes estimates and Assun��o/Reis Index, Getis/Ord G
and multicoloured join count statistics, local Moran's I and
Getis/Ord G, saddlepoint approximations and exact tests for
global and local Moran's I; and functions for estimating
spatial simultaneous autoregressive (SAR) lag and error models,
impact measures for lag models, weighted and unweighted SAR and
CAR spatial regression models, semi-parametric and Moran
eigenvector spatial filtering, GM SAR error models, and
generalized spatial two stage least squares models.
Diff between spdep versions 0.4-50 dated 2009-10-19 and 0.4-52 dated 2009-11-05
ChangeLog | 1287 ++++++++------------------------- DESCRIPTION | 10 R/error.spsarlm.R | 6 R/impacts.R | 129 +++ R/nblag.R | 2 R/read.gwt2nb.R | 22 R/tri2nb.R | 17 inst/ChangeLog | 1287 ++++++++------------------------- inst/doc/CO69.pdf |binary inst/doc/sids.pdf |binary inst/etc/shapes/columbusRegression.txt |only man/impacts.sarlm.Rd | 25 man/invIrM.Rd | 2 man/joincount.multi.Rd | 4 man/nb2blocknb.Rd | 2 man/read.gwt2nb.Rd | 8 man/tri2nb.Rd | 3 17 files changed, 841 insertions(+), 1963 deletions(-)
Author: Carsten F. Dormann and Bernd Gruber, with additional code from
Mariano Devoto, Jochen Fruend, Jose Iriondo and Diego Vazquez,
also based on C-code developed by Nils Bluethgen and by Miguel
Rodriguez-Girones.
Title: Visualising bipartite networks and calculating some ecological
indices.
Description: Bipartite provides functions to viualise webs and
calculate a series of indices commonly used to describe pattern
in ecological webs. It focusses on webs consisting of only two
trophic levels, e.g. pollination webs or predator-prey-webs.
Visualisation is important to get an idea of what we are
actually looking at, while the indices summarise different
aspects of the webs topology.
Diff between bipartite versions 1.02 dated 2009-09-12 and 1.03 dated 2009-11-05
bipartite-1.02/bipartite/Wishlist.txt |only bipartite-1.03/bipartite/.hg/branch.cache | 4 +- bipartite-1.03/bipartite/.hg/dirstate |binary bipartite-1.03/bipartite/.hg/store/00changelog.i |binary bipartite-1.03/bipartite/.hg/store/00manifest.i |binary bipartite-1.03/bipartite/.hg/store/data/_d_e_s_c_r_i_p_t_i_o_n.i |binary bipartite-1.03/bipartite/.hg/store/data/_r/_c.score._r.i |binary bipartite-1.03/bipartite/.hg/store/data/_r/_h2fun._r.i |binary bipartite-1.03/bipartite/.hg/store/data/_r/_p_a_c.r.i |only bipartite-1.03/bipartite/.hg/store/data/_r/bipartite-package._rd.i |binary bipartite-1.03/bipartite/.hg/store/data/_r/degreedistr._r.i |binary bipartite-1.03/bipartite/.hg/store/data/_r/dfun._r.i |binary bipartite-1.03/bipartite/.hg/store/data/_r/discrepancy.r.i |binary bipartite-1.03/bipartite/.hg/store/data/_r/nested.r.i |only bipartite-1.03/bipartite/.hg/store/data/_r/networklevel._r.i |binary bipartite-1.03/bipartite/.hg/store/data/_r/nullmodel.r.i |only bipartite-1.03/bipartite/.hg/store/data/_r/plotweb._r.i |binary bipartite-1.03/bipartite/.hg/store/data/_r/robustness.r.i |binary bipartite-1.03/bipartite/.hg/store/data/_r/slope.bipartite._r.i |binary bipartite-1.03/bipartite/.hg/store/data/_r/specieslevel._r.i |binary bipartite-1.03/bipartite/.hg/store/data/_wishlist.txt.i |binary bipartite-1.03/bipartite/.hg/store/data/man/_p_a_c.rd.i |only bipartite-1.03/bipartite/.hg/store/data/man/bipartite-package._rd.i |binary bipartite-1.03/bipartite/.hg/store/data/man/compart._rd.i |binary bipartite-1.03/bipartite/.hg/store/data/man/degreedistr._rd.i |binary bipartite-1.03/bipartite/.hg/store/data/man/dfun._rd.i |binary bipartite-1.03/bipartite/.hg/store/data/man/nested._rd.i |only bipartite-1.03/bipartite/.hg/store/data/man/networklevel._rd.i |binary bipartite-1.03/bipartite/.hg/store/data/man/nullmodel.rd.i |only bipartite-1.03/bipartite/.hg/store/data/man/plotweb._rd.i |binary bipartite-1.03/bipartite/.hg/store/data/man/specieslevel._rd.i |binary bipartite-1.03/bipartite/.hg/store/data/matrix.cpp.i |only bipartite-1.03/bipartite/.hg/store/data/src/bipartite.dll.d |binary bipartite-1.03/bipartite/.hg/store/data/src/bipartite.dll.i |binary bipartite-1.03/bipartite/.hg/store/data/src/bipartite__res.o.i |binary bipartite-1.03/bipartite/.hg/store/data/src/bmn5.o.i |binary bipartite-1.03/bipartite/.hg/store/undo |binary bipartite-1.03/bipartite/.hg/undo.dirstate |binary bipartite-1.03/bipartite/DESCRIPTION | 8 ++--- bipartite-1.03/bipartite/R/V.ratio.R | 11 ++++-- bipartite-1.03/bipartite/R/networklevel.R | 5 +-- bipartite-1.03/bipartite/man/bipartite-package.Rd | 12 +++++-- bipartite-1.03/bipartite/man/networklevel.Rd | 16 +++++++--- 43 files changed, 37 insertions(+), 19 deletions(-)
Author: Mario Hasler
Title: Simultaneous Comparisons for Multiple Endpoints
Description: Simultaneous tests and confidence intervals for one-way
experimental designs with one or many normally distributed,
primary response variables (endpoints). The procedure of Hasler
(2009) is applied for differences or ratios of means. Various
contrasts can be chosen, unbalanced sample sizes are allowed as
well as heterogeneous covariance matrices.
Diff between SimComp versions 1.4.2 dated 2009-10-22 and 1.4.3 dated 2009-11-05
DESCRIPTION | 9 +++++---- data |only man/SimCiDiff.Rd | 41 ++++++++++++++++++++++++++++------------- man/SimCiRat.Rd | 23 ++++++++++++++++++++--- man/SimComp-package.Rd | 44 ++++++++++++++++++++++++++++---------------- man/SimTestDiff.Rd | 22 +++++++++++++++++++--- man/SimTestRat.Rd | 22 +++++++++++++++++++--- man/coagulation.Rd |only 8 files changed, 119 insertions(+), 42 deletions(-)
Author: originally written by Andrew Gelman
Title: Running WinBUGS and OpenBUGS from R / S-PLUS
Description: Using this package, it is possible to call a BUGS model,
summarize inferences and convergence in a table and graph, and
save the simulations in arrays for easy access in R / S-PLUS.
In S-PLUS, the openbugs functionality and the windows emulation
functionality is not yet available.
Diff between R2WinBUGS versions 2.1-14 dated 2009-04-14 and 2.1-15 dated 2009-11-05
DESCRIPTION | 8 ++--- R/bugs.R | 3 +- R/bugs.script.R | 2 - R/bugs.update.settings.R | 64 ++++++++++++++++++++++++----------------------- R/openbugs.R | 3 +- R/write.model.R | 7 +++-- inst/NEWS | 7 +++++ inst/doc/R2WinBUGS.pdf | 6 ++-- man/openbugs.Rd | 3 +- 9 files changed, 59 insertions(+), 44 deletions(-)
Author: Yves Aragon, Thibault Laurent, Lauriane Robidou, Anne
Ruiz-Gazen, Christine Thomas-Agnan
Title: Interactive exploratory spatial data analysis
Description: GeoXp is a tool for researchers in spatial statistics,
spatial econometrics, geography, ecology etc allowing to link
dynamically statistical plots with elementary maps. This
coupling consists in the fact that the selection of a zone on
the map results in the automatic highlighting of the
corresponding points on the statistical graph or reversely the
selection of a portion of the graph results in the automatic
highlighting of the corresponding points on the map. GeoXp
includes tools from different areas of spatial statistics
including geostatistics as well as spatial econometrics and
point processes. Besides elementary plots like boxplots,
histograms or simple scatterplos, GeoXp also couples with maps
Moran scatterplots, variogram cloud, Lorentz Curves,...In order
to make the most of the multidimensionality of the data, GeoXp
includes some dimension reduction techniques such as PCA.
Diff between GeoXp versions 1.3 dated 2008-10-12 and 1.4 dated 2009-11-05
GeoXp-1.3/GeoXp/inst/doc/howusegeoxp.pdf |only GeoXp-1.3/GeoXp/inst/vectors |only GeoXp-1.3/GeoXp/man/choix.bubble.rd |only GeoXp-1.3/GeoXp/man/choix.couleur.rd |only GeoXp-1.3/GeoXp/man/choixvarfunc.rd |only GeoXp-1.4/GeoXp/DESCRIPTION | 44 ++++++++++---- GeoXp-1.4/GeoXp/R/angleplotmap.R | 6 +- GeoXp-1.4/GeoXp/R/barmap.R | 4 - GeoXp-1.4/GeoXp/R/barnbmap.r | 4 - GeoXp-1.4/GeoXp/R/boxplotmap.R | 4 - GeoXp-1.4/GeoXp/R/carte.R | 72 +++++++++++++++++++----- GeoXp-1.4/GeoXp/R/choix.bubble.r | 26 +++++++- GeoXp-1.4/GeoXp/R/clustermap.R | 4 - GeoXp-1.4/GeoXp/R/dbledensitymap.R | 6 +- GeoXp-1.4/GeoXp/R/dblehistomap.R | 4 - GeoXp-1.4/GeoXp/R/densitymap.R | 4 - GeoXp-1.4/GeoXp/R/driftmap.R | 2 GeoXp-1.4/GeoXp/R/ginimap.R | 4 - GeoXp-1.4/GeoXp/R/graphique.R | 58 ++++++++++++++++--- GeoXp-1.4/GeoXp/R/histnbmap.r | 4 - GeoXp-1.4/GeoXp/R/histobarmap.R | 4 - GeoXp-1.4/GeoXp/R/histomap.R | 4 - GeoXp-1.4/GeoXp/R/misolationmap.r |only GeoXp-1.4/GeoXp/R/moranplotmap.R | 6 +- GeoXp-1.4/GeoXp/R/mvariocloudmap.r |only GeoXp-1.4/GeoXp/R/neighbourmap.R | 4 - GeoXp-1.4/GeoXp/R/pcamap.R | 4 - GeoXp-1.4/GeoXp/R/plot3dmap.r | 4 - GeoXp-1.4/GeoXp/R/polyboxplotmap.R | 4 - GeoXp-1.4/GeoXp/R/scattermap.R | 4 - GeoXp-1.4/GeoXp/R/slider1.R | 5 + GeoXp-1.4/GeoXp/R/variocloudmap.R | 6 +- GeoXp-1.4/GeoXp/inst/doc/Fig1.ps |only GeoXp-1.4/GeoXp/inst/doc/Fig10.ps |only GeoXp-1.4/GeoXp/inst/doc/Fig11.ps |only GeoXp-1.4/GeoXp/inst/doc/Fig12.ps |only GeoXp-1.4/GeoXp/inst/doc/Fig13.ps |only GeoXp-1.4/GeoXp/inst/doc/Fig14.ps |only GeoXp-1.4/GeoXp/inst/doc/Fig15.ps |only GeoXp-1.4/GeoXp/inst/doc/Fig16.ps |only GeoXp-1.4/GeoXp/inst/doc/Fig17.ps |only GeoXp-1.4/GeoXp/inst/doc/Fig18.ps |only GeoXp-1.4/GeoXp/inst/doc/Fig19.ps |only GeoXp-1.4/GeoXp/inst/doc/Fig2.ps |only GeoXp-1.4/GeoXp/inst/doc/Fig20.ps |only GeoXp-1.4/GeoXp/inst/doc/Fig21.ps |only GeoXp-1.4/GeoXp/inst/doc/Fig22.ps |only GeoXp-1.4/GeoXp/inst/doc/Fig3.ps |only GeoXp-1.4/GeoXp/inst/doc/Fig4.ps |only GeoXp-1.4/GeoXp/inst/doc/Fig5.ps |only GeoXp-1.4/GeoXp/inst/doc/Fig6.ps |only GeoXp-1.4/GeoXp/inst/doc/Fig7.ps |only GeoXp-1.4/GeoXp/inst/doc/Fig8.ps |only GeoXp-1.4/GeoXp/inst/doc/Fig9.ps |only GeoXp-1.4/GeoXp/inst/doc/Sweave.sty |only GeoXp-1.4/GeoXp/inst/doc/presentation_geoxp.dvi |only GeoXp-1.4/GeoXp/inst/doc/presentation_geoxp.pdf |only GeoXp-1.4/GeoXp/inst/doc/presentation_geoxp.rnw |only GeoXp-1.4/GeoXp/inst/shapes |only GeoXp-1.4/GeoXp/man/GeoXp-package.Rd | 50 +++++++--------- GeoXp-1.4/GeoXp/man/angleplotmap.Rd | 46 +++++++-------- GeoXp-1.4/GeoXp/man/barmap.Rd | 23 +++---- GeoXp-1.4/GeoXp/man/barnbmap.rd | 19 +++--- GeoXp-1.4/GeoXp/man/boxplotmap.Rd | 23 +++---- GeoXp-1.4/GeoXp/man/carte.Rd | 20 +++--- GeoXp-1.4/GeoXp/man/choix.bubble.Rd |only GeoXp-1.4/GeoXp/man/choix.couleur.Rd |only GeoXp-1.4/GeoXp/man/choixvarfunc.Rd |only GeoXp-1.4/GeoXp/man/clustermap.Rd | 23 +++---- GeoXp-1.4/GeoXp/man/dbledensitymap.Rd | 29 +++++---- GeoXp-1.4/GeoXp/man/dblehistomap.Rd | 27 ++++----- GeoXp-1.4/GeoXp/man/densitymap.Rd | 31 +++++----- GeoXp-1.4/GeoXp/man/distchi2.Rd | 18 +++--- GeoXp-1.4/GeoXp/man/driftmap.Rd | 29 ++++----- GeoXp-1.4/GeoXp/man/genpca.Rd | 56 +++++++++--------- GeoXp-1.4/GeoXp/man/gini.Rd | 14 ++-- GeoXp-1.4/GeoXp/man/ginimap.Rd | 23 +++---- GeoXp-1.4/GeoXp/man/graphique.Rd | 14 ++-- GeoXp-1.4/GeoXp/man/histnbmap.rd | 21 +++---- GeoXp-1.4/GeoXp/man/histobarmap.Rd | 27 ++++----- GeoXp-1.4/GeoXp/man/histomap.Rd | 29 +++++---- GeoXp-1.4/GeoXp/man/immob.Rd | 4 - GeoXp-1.4/GeoXp/man/makeneighborsw.Rd | 32 +++++----- GeoXp-1.4/GeoXp/man/misolationmap.rd |only GeoXp-1.4/GeoXp/man/moranplotmap.Rd | 41 ++++++------- GeoXp-1.4/GeoXp/man/mvariocloudmap.rd |only GeoXp-1.4/GeoXp/man/neighbourmap.Rd | 28 +++++---- GeoXp-1.4/GeoXp/man/nonormmoran.Rd | 30 +++++----- GeoXp-1.4/GeoXp/man/normw.Rd | 10 +-- GeoXp-1.4/GeoXp/man/pcamap.Rd | 48 ++++++++-------- GeoXp-1.4/GeoXp/man/plot3dmap.rd | 30 +++++----- GeoXp-1.4/GeoXp/man/polyboxplotmap.Rd | 24 ++++---- GeoXp-1.4/GeoXp/man/polylist2list.Rd | 14 ++-- GeoXp-1.4/GeoXp/man/rotation.Rd | 16 ++--- GeoXp-1.4/GeoXp/man/scattermap.Rd | 34 +++++------ GeoXp-1.4/GeoXp/man/selectgraph.Rd | 4 - GeoXp-1.4/GeoXp/man/selectmap.Rd | 12 ++-- GeoXp-1.4/GeoXp/man/selectstat.Rd | 18 +++--- GeoXp-1.4/GeoXp/man/slider1.Rd | 2 GeoXp-1.4/GeoXp/man/slider2.Rd | 2 GeoXp-1.4/GeoXp/man/spdf2list.Rd | 18 ++---- GeoXp-1.4/GeoXp/man/variocloudmap.Rd | 54 +++++++++--------- 102 files changed, 671 insertions(+), 563 deletions(-)
Author: Ulrike Groemping
Title: Full factorials, orthogonal arrays and base utilities for DoE
packages
Description: This package creates full factorial experimental designs
and designs based on orthogonal arrays for (industrial)
experiments. Additionally, it provides some utility functions
used also by other DoE packages.
Diff between DoE.base versions 0.9-6 dated 2009-11-05 and 0.9-7 dated 2009-11-05
DESCRIPTION | 8 +++---- NAMESPACE | 2 - R/lm.design.R | 26 ++++------------------- inst/NEWS | 3 ++ man/lm.design.Rd | 17 +++++++++++++-- tests/test_qua.design.Rout.save | 45 ++++++++++++++++++---------------------- 6 files changed, 49 insertions(+), 52 deletions(-)
Author: Carla Moreira, Jacobo de U\eqn{\mbox{\textasciitilde}}{~}na-
\eqn{\mbox{\textasciitilde}}{'}Alvarez and Rosa Crujeiras
Title: Doubly truncated data analysis
Description: This package implements different algorithms for analyzing
randomly truncated data, one-sided and two-sided (i.e. doubly)
truncated data.
Diff between DTDA versions 1.1 dated 2009-09-21 and 1.2-0 dated 2009-11-05
DESCRIPTION | 9 R/efron.petrosian.R | 634 ++++++++++++++++- R/lynden.R | 764 ++++++++++++++++++++- R/shen.R | 1731 +++++++++++++++++++++++++++++++++++++++++-------- man/DTDA-package.Rd | 14 man/efron.petrosian.Rd | 14 man/lynden.Rd | 15 man/shen.Rd | 10 8 files changed, 2770 insertions(+), 421 deletions(-)
Author: Roger Koenker
Title: Quantile Regression
Description: Quantile regression and related methods.
Diff between quantreg versions 4.43 dated 2009-10-19 and 4.44 dated 2009-11-05
DESCRIPTION | 6 +++--- R/boot.R | 2 +- R/table.R | 2 +- inst/ChangeLog | 8 ++++++++ inst/doc/Rplots.pdf | 4 ++-- inst/doc/rq.pdf |binary 6 files changed, 15 insertions(+), 7 deletions(-)
Author: David Meyer and Christian Buchta
Title: Distance and Similarity Measures
Description: Provides an extensible framework for the effcient
calculation of auto- and cross-proximities, along with
implementations of the most popular ones.
Diff between proxy versions 0.4-4 dated 2009-10-13 and 0.4-5 dated 2009-11-05
DESCRIPTION | 8 ++++---- R/dissimilarities.R | 6 +++--- R/similarities.R | 10 +++++----- inst/doc/overview.pdf |binary 4 files changed, 12 insertions(+), 12 deletions(-)
Author: Dan Kelley
Title: Analysis of Oceanographic data
Description: Supports the analysis of Oceanographic data, including ADP
measurements, CTD measurements, sectional data, sea-level
timeseries, coastline files, etc. Provides functions for
calculating seawater properties such as potential temperature
and density, as well as derived properties such as buoyancy
frequency and dynamic height.
Diff between oce versions 0.1-79 dated 2009-10-26 and 0.1-80 dated 2009-11-05
DESCRIPTION | 8 NAMESPACE | 1 NEWS | 7 R/oce.R | 22 + R/section.R | 78 ++-- R/sun.R |only demo/TS.R | 5 inst/doc/oce.pdf | 789 +++++++++++++++++++++++-------------------------- man/adp.enu2other.Rd | 2 man/adv.enu2other.Rd | 7 man/oce.plot.sticks.Rd | 24 + man/plot.section.Rd | 2 man/sun.angle.Rd |only src/sunae.f |only 14 files changed, 486 insertions(+), 459 deletions(-)
Author: Seung W. Choi, with contributions from Laura E. Gibbons and
Paul K. Crane
Title: Logistic Regression Differential Item Functioning using IRT
Description: Analysis of Differential Item Functioning (DIF) for
dichotomous and polytomous items using an iterative hybrid of
(ordinal) logistic regression and item response theory (IRT).
Diff between lordif versions 0.1-2 dated 2009-10-14 and 0.1-3 dated 2009-11-05
DESCRIPTION | 8 ++++---- INDEX | 29 +++++++++++++++++++++++------ R/montecarlo.R | 26 +++++++++++++------------- R/plotDIF.R | 2 +- R/rundif.R | 8 ++++---- R/separate.R | 6 ++++-- data/Anxiety.rda |binary man/lordif-package.Rd | 4 ++-- 8 files changed, 51 insertions(+), 32 deletions(-)
Author: Christopher Brown
Title: Implements hash/associated arrays/dictionaries
Description: This package implements a data structure similar to hashes
in Perl and dictionaries in Python but with a purposefully R
flavor.
Diff between hash versions 1.0.2 dated 2009-10-12 and 1.0.3 dated 2009-11-05
ChangeLog | 6 ++++++ DESCRIPTION | 10 +++++----- R/format.R | 7 +++++-- R/values.R | 2 +- TODO | 5 +++-- man/hash-package.Rd | 6 +++--- 6 files changed, 23 insertions(+), 13 deletions(-)
Author: Daniel Adler
Title: memory-efficient storage of large data on disk and fast access
functions
Description: The ff package provides data structures that are stored on
disk but behave (almost) as if they were in RAM by
transparently mapping only a section (pagesize) in main memory
- the effective virtual memory consumption per ff object. ff
supports R's standard atomic data types 'double', 'logical',
'raw' and 'integer' and non-standard atomic types boolean (1
bit), quad (2 bit unsigned), nibble (4 bit unsigned), byte (1
byte signed with NAs), ubyte (1 byte unsigned), short (2 byte
signed with NAs), ushort (2 byte unsigned), single (4 byte
float with NAs). For example 'quad' allows efficient storage of
genomic data as an 'A','T','G','C' factor. The unsigned types
support 'circular' arithmetic. There is also support for
close-to-atomic types 'factor', 'ordered', 'POSIXct', 'Date'
and custom close-to-atomic types. ff not only has native
C-support for vectors, matrices and arrays with flexible
dimorder (major column-order, major row-order and
generalizations for arrays). There is also a ffdf class not
unlike data.frames and import/export filters for csv files. ff
objects store raw data in binary flat files in native encoding,
and complement this with metadata stored in R as physical and
virtual attributes. ff objects have well-defined hybrid copying
semantics, which gives rise to certain performance improvements
through virtualization. ff objects can be stored and reopened
across R sessions. ff files can be shared by multiple ff R
objects (using different data en/de-coding schemes) in the same
process or from multiple R processes to exploit parallelism. A
wide choice of finalizer options allows to work with
'permanent' files as well as creating/removing 'temporary' ff
files completely transparent to the user. On certain
OS/Filesystem combinations, creating the ff files works without
notable delay thanks to using sparse file allocation. Several
access optimization techniques such as Hybrid Index
Preprocessing and Virtualization are implemented to achieve
good performance even with large datasets, for example virtual
matrix transpose without touching a single byte on disk.
Further, to reduce disk I/O, 'logicals' and non-standard data
types get stored native and compact on binary flat files i.e.
logicals take up exactly 2 bits to represent TRUE, FALSE and
NA. Beyond basic access functions, the ff package also provides
compatibility functions that facilitate writing code for ff and
ram objects and support for batch processing on ff objects
(e.g. as.ram, as.ff, ffapply). ff interfaces closely with
functionality from package 'bit': chunked looping, fast bit
operations and coercions between different objects that can
store subscript information ('bit', 'bitwhich', ff 'boolean',
ri range index, hi hybrid index). This allows to work
interactively with selections of large datasets and quickly
modify selection criteria. Further high-performance
enhancements can be made available upon request.
Diff between ff versions 2.1-0 dated 2009-11-03 and 2.1-1 dated 2009-11-05
DESCRIPTION | 8 ++++---- R/ff.R | 5 +++++ man/filename.rd | 5 +++++ 3 files changed, 14 insertions(+), 4 deletions(-)
Author: Anthony Albano
Title: Traditional Methods for Test Score Equating
Description: The equate package contains functions for traditional
equating under both random groups and nonequivalent groups with
anchor test designs. Mean, linear, and equipercentile equating
are supported as are methods for univariate and bivariate
presmoothing of score distributions.
Diff between equate versions 0.1-0 dated 2009-11-01 and 0.1-1 dated 2009-11-05
equate-0.1-0/equate/R/var.freqtab.R |only equate-0.1-0/equate/man/print.equate.Rd |only equate-0.1-0/equate/man/var.freqtab.Rd |only equate-0.1-1/equate/COPYING |only equate-0.1-1/equate/DESCRIPTION | 30 +++++------- equate-0.1-1/equate/NAMESPACE | 4 - equate-0.1-1/equate/NEWS |only equate-0.1-1/equate/R/cov.freqtab.R |only equate-0.1-1/equate/R/equate.R | 32 +++++++------ equate-0.1-1/equate/R/equate.eq.R | 59 ++++++++++++------------- equate-0.1-1/equate/R/equate.ln.R | 35 ++++++++------ equate-0.1-1/equate/R/freqavg.R | 60 ++++++++++++------------- equate-0.1-1/equate/R/freqtab.R | 17 +++++-- equate-0.1-1/equate/R/fx.R | 8 +-- equate-0.1-1/equate/R/kurt.freqtab.R | 5 -- equate-0.1-1/equate/R/loglinear.R | 44 +++++++++--------- equate-0.1-1/equate/R/mean.freqtab.R | 2 equate-0.1-1/equate/R/px.R | 10 ++-- equate-0.1-1/equate/R/se.boot.R | 36 +++++++++++---- equate-0.1-1/equate/R/se.ln.R | 10 +--- equate-0.1-1/equate/R/skew.freqtab.R | 5 -- equate-0.1-1/equate/R/synthetic.R | 49 +++++++++++--------- equate-0.1-1/equate/man/ACTmath.Rd | 2 equate-0.1-1/equate/man/KBneat.Rd | 3 - equate-0.1-1/equate/man/casemod.Rd | 2 equate-0.1-1/equate/man/cov.freqtab.Rd |only equate-0.1-1/equate/man/equate.Rd | 75 +++++++++++++------------------- equate-0.1-1/equate/man/equate.eq.Rd | 44 ++++++------------ equate-0.1-1/equate/man/equate.ln.Rd | 40 +++++------------ equate-0.1-1/equate/man/freqavg.Rd | 15 ++---- equate-0.1-1/equate/man/freqbump.Rd | 10 +--- equate-0.1-1/equate/man/freqtab.Rd | 39 ++++++++++------ equate-0.1-1/equate/man/fx.Rd | 8 +-- equate-0.1-1/equate/man/kurt.freqtab.Rd | 10 +--- equate-0.1-1/equate/man/loglinear.Rd | 58 ++++++++++++++---------- equate-0.1-1/equate/man/mean.freqtab.Rd | 11 ++-- equate-0.1-1/equate/man/px.Rd | 8 +-- equate-0.1-1/equate/man/se.boot.Rd | 7 +- equate-0.1-1/equate/man/se.eq.Rd | 2 equate-0.1-1/equate/man/se.ln.Rd | 14 ++--- equate-0.1-1/equate/man/skew.freqtab.Rd | 8 +-- equate-0.1-1/equate/man/synthetic.Rd | 38 ++++------------ 42 files changed, 393 insertions(+), 407 deletions(-)
Author: Max Kuhn. Contributions from Jed Wing, Steve Weston, Andre
Williams, Chris Keefer and Allan Engelhardt
Title: Classification and Regression Training
Description: Misc functions for training and plotting classification
and regression models
Diff between caret versions 4.26 dated 2009-10-28 and 4.27 dated 2009-11-05
DESCRIPTION | 12 R/createGrid.R | 3 R/createModel.R | 22 + R/misc.R | 15 R/predictionFunction.R | 13 R/probFunction.R | 4 R/selection.R | 4 R/train.default.R | 2 inst/CHANGES | 7 inst/doc/caretMisc.pdf | 875 +++++++++++++++++++++----------------------- inst/doc/caretMisc.tex | 17 inst/doc/caretSelection.pdf | 664 ++++++++++++++++----------------- inst/doc/caretSelection.tex | 16 inst/doc/caretTrain.Rnw | 5 inst/doc/caretTrain.pdf |binary inst/doc/caretTrain.tex | 21 - inst/doc/caretVarImp.pdf |binary inst/doc/caretVarImp.tex | 16 man/train.Rd | 3 19 files changed, 877 insertions(+), 822 deletions(-)
Author: Gavin L. Simpson, Jari Oksanen
Title: Analogue and weighted averaging methods for palaeoecology
Description: Fits Modern Analogue Technique and Weighted Averaging
transfer function models for prediction of environmental data
from species data, and related methods used in palaeoecology.
Diff between analogue versions 0.6-21 dated 2009-11-03 and 0.6-22 dated 2009-11-05
DESCRIPTION | 10 +++++----- R/tran.R | 4 ++-- inst/ChangeLog | 6 ++++++ 3 files changed, 13 insertions(+), 7 deletions(-)
Author: Roger Koenker
Title: Sparse Linear Algebra
Description: Basic linear algebra for sparse matrices
Diff between SparseM versions 0.80 dated 2009-05-12 and 0.83 dated 2009-11-05
DESCRIPTION | 6 +++--- R/SparseM.R | 10 +++++----- inst/ChangeLog | 8 ++++++++ inst/doc/Rplots.pdf | 32 ++++++++++++++++---------------- inst/doc/SparseM.pdf |binary man/SparseM.ops.Rd | 4 +--- 6 files changed, 33 insertions(+), 27 deletions(-)
Author: Nathan S. Watson-Haigh
Title: PCIT algorithm - Partial Correlation Coefficient with
Information Theory
Description: This package provides the necessary functions for
performing the Partial Correlation coefficient with Information
Theory (PCIT) algorithm developed by Reverter and Chan (2008).
The PCIT algorithm identifies meaningful correlations to define
edges in a weighted network. The algorithm can be applied to
any correlation-based network including but not limited to gene
co-expression networks.
Diff between PCIT versions 1.01-1 dated 2009-08-28 and 1.02-1 dated 2009-11-05
DESCRIPTION | 14 + R/PCIT.R | 265 +++++++++++++++++++++++++++--------- R/internal.R | 33 ---- data/PCIT.rda |binary demo/00Index | 2 demo/PCIT.R | 30 ++-- man/PCIT-package.Rd | 10 - man/clusteringCoefficient.Rd | 16 +- man/clusteringCoefficientPercent.Rd | 16 +- man/data.Rd | 17 +- man/defineTasks.Rd | 57 ++++--- man/idx.Rd |only man/idxInvert.Rd |only man/maxMatrixSize.Rd |only man/pcit.Rd | 19 +- man/pcitMemoryRequirements.Rd |only man/plotCorCoeff.Rd | 34 +++- 17 files changed, 346 insertions(+), 167 deletions(-)
Author: Ulrike Groemping
Title: Full factorials, orthogonal arrays and base utilities for DoE
packages
Description: This package creates full factorial experimental designs
and designs based on orthogonal arrays for (industrial)
experiments. Additionally, it provides some utility functions
used also by other DoE packages.
Diff between DoE.base versions 0.9-5 dated 2009-11-03 and 0.9-6 dated 2009-11-05
DESCRIPTION | 8 +++---- NAMESPACE | 2 - R/lm.design.R | 26 ++++++++++++++++++----- inst/NEWS | 8 +++++++ man/lm.design.Rd | 17 +-------------- tests/test_qua.design.Rout.save | 45 +++++++++++++++++++++------------------- 6 files changed, 60 insertions(+), 46 deletions(-)
Author: Bill Morphet
Title: Functions For Circular Spatial Data
Description: The package is a collection of functions for color
continuous high resolution images of circular spatial data,
circular kriging, and simulation of circular random fields.
Diff between CircSpatial versions 1.0 dated 2009-09-21 and 1.0-1 dated 2009-11-05
CircSpatial-1.0-1/CircSpatial/DESCRIPTION | 14 +++++------ CircSpatial-1.0-1/CircSpatial/R/KrigCRF.R | 2 - CircSpatial-1.0-1/CircSpatial/inst/CHANGES |only CircSpatial-1.0-1/CircSpatial/inst/README |only CircSpatial-1.0-1/CircSpatial/man/CircDataimage.Rd | 19 ++++++++++++--- CircSpatial-1.0-1/CircSpatial/man/CircSpatial-package.Rd | 2 - CircSpatial-1.0/CircSpatial/README |only 7 files changed, 25 insertions(+), 12 deletions(-)
Author: Guido Schwarzer
Title: Meta-Analysis with R
Description: Fixed and random effects meta-analysis. Functions for
tests of bias, forest and funnel plot.
Diff between meta versions 1.1-3 dated 2009-10-30 and 1.1-4 dated 2009-11-04
ChangeLog | 41 ++++++++++++++++++++++++----- DESCRIPTION | 8 ++--- R/print.summary.meta.R | 60 +++++++++++++++++++++++++++---------------- R/summary.meta.R | 67 ++++++++++++++++++++++++++----------------------- man/forest.Rd | 8 +++++ man/metacr.Rd | 5 ++- man/metagen.Rd | 41 +++++++++++++++++++---------- man/print.meta.Rd | 41 ++++++++++++++++++++--------- 8 files changed, 174 insertions(+), 97 deletions(-)
Author: S. M. Barbosa
Title: Multivariate AutoRegressive analysis
Description: R functions for multivariate autoregressive analysis
Diff between mAr versions 1.1-1 dated 2007-04-13 and 1.1-2 dated 2009-11-04
DESCRIPTION | 8 +++++--- R/mAr.eig.R | 2 +- R/mAr.est.R | 2 +- R/mAr.pca.R | 4 ++-- R/mAr.sim.R | 2 +- data/pinkham.rda |binary data/sparrows.rda |binary data/waves.rda |binary man/mAr.est.Rd | 14 +++++++------- 9 files changed, 17 insertions(+), 15 deletions(-)
Author: Antonio Gasparrini and Ben Armstrong
Title: Distributed Lag Non-linear Models
Description: The package dlnm contains functions to specify basis and
cross-basis matrices in order to run distributed lag models and
their non-linear extension, then to predict and graph the
results for a fitted model.
Diff between dlnm versions 1.1.0 dated 2009-10-19 and 1.1.1 dated 2009-11-04
DESCRIPTION | 8 R/crosspred.R | 2 R/mkbasis.R | 4 inst/ChangeLog | 9 inst/doc/Rplots.pdf | 4 inst/doc/dlnmOverview.pdf | 944 +++++++++++++++++++++++----------------------- 6 files changed, 494 insertions(+), 477 deletions(-)
Author: Sergio Salvino Guirreri
Title: Modelling and estimation of the yield curve
Description: Modelling the yield curve with some parametric models. The
models implemented are: Nelson-Siegel, Diebold-Li and Svensson.
The package also includes the data of the term structure of
interest rate of Federal Reserve Bank and European Central
Bank.
Diff between YieldCurve versions 1.0 dated 2009-08-04 and 2.0 dated 2009-11-04
DESCRIPTION | 13 +++++++------ man/Srates.Rd | 12 ++++++------ man/YieldCurve-package.Rd | 10 ++++------ 3 files changed, 17 insertions(+), 18 deletions(-)
Author: Fortran code by H. Akima R port by Albrecht Gebhardt
Title: Interpolation of irregularly spaced data
Description: Linear or cubic spline interpolation for irregular gridded
data
Diff between akima versions 0.5-3 dated 2009-09-21 and 0.5-4 dated 2009-11-04
ChangeLog | 8 ++++---- DESCRIPTION | 6 +++--- man/akima.Rd | 23 +++++++++++------------ 3 files changed, 18 insertions(+), 19 deletions(-)
Author: Matthias Kohl
Title: Optimally robust influence curves for regression and scale
Description: functions for the determination of optimally robust
influence curves in case of linear regression with unknown
scale and standard normal distributed errors where the
regressor is random.
Diff between RobRex versions 0.6.1 dated 2009-02-28 and 0.7 dated 2009-11-04
DESCRIPTION | 36 ++++++++++++++++++++-------------- inst/NEWS | 51 ++++++++++++++++++++++++++++++++++++++++++++++++- inst/TOBEDONE |only inst/scripts/example.R |only tests |only 5 files changed, 71 insertions(+), 16 deletions(-)
Author: Matthias Kohl
Title: Optimally robust influence curves and estimators for location
and scale
Description: Functions for the determination of optimally robust
influence curves and estimators in case of normal location
and/or scale
Diff between RobLox versions 0.6.1 dated 2008-11-30 and 0.7 dated 2009-11-04
DESCRIPTION | 36 ++-- NAMESPACE | 3 R/colRoblox.R | 6 R/finiteSampleCorrection.R |only R/rlsOptIC_TuMad.R | 4 R/roblox.R | 363 ++++++++++++++++++++++++++++++------------ R/rowRoblox.R | 205 ++++++++++++++++++++--- R/sysdata.rda |binary inst/CITATION | 4 inst/NEWS | 50 +++++ inst/TOBEDONE |only man/0RobLox-package.Rd |only man/finiteSampleCorrection.Rd |only man/roblox.Rd | 28 ++- man/rowRoblox.Rd | 22 +- tests |only 16 files changed, 559 insertions(+), 162 deletions(-)
Author: Matthias Kohl, Peter Ruckdeschel
Title: Robust Asymptotic Statistics
Description: Base S4-classes and functions for robust asymptotic
statistics.
Diff between RobAStBase versions 0.1.5 dated 2009-01-13 and 0.7 dated 2009-11-04
DESCRIPTION | 35 - NAMESPACE | 20 R/AllClass.R | 62 + R/AllGeneric.R | 52 + R/AllPlot.R | 211 +++++- R/AllShow.R | 19 R/ContIC.R | 8 R/IC.R | 10 R/Neighborhood.R | 4 R/RobAStBaseOptions.R | 7 R/RobModel.R | 7 R/TotalVarIC.R | 19 R/Weights.R | 14 R/bALEstimate.R | 8 R/comparePlot.R | 354 +++++++++- R/generateICfct.R | 18 R/getBiasIC.R | 2 R/getRiskIC.R | 1 R/getboundedIC.R |only R/infoPlot.R | 386 +++++++++-- R/kStepEstimate.R |only R/kStepEstimator.R | 1172 ++++++++++++++++++++++-------------- R/kStepEstimatorStart.R |only R/locMEstimator.R | 6 R/masked.R |only R/oneStepEstimator.R | 496 +++++++-------- R/optIC.R | 9 R/qqplot.R |only inst/MASKING |only inst/NEWS | 206 ++++++ inst/TOBEDONE |only inst/doc |only man/0RobAStBase-package.Rd | 21 man/ALEstimate-class.Rd | 34 - man/BdStWeight-class.Rd | 8 man/BoundedWeight-class.Rd | 8 man/ContIC-class.Rd | 3 man/ContNeighborhood-class.Rd | 4 man/FixRobModel-class.Rd | 4 man/HampIC-class.Rd | 25 man/HampelWeight-class.Rd | 10 man/IC-class.Rd | 12 man/InfRobModel-class.Rd | 4 man/InfluenceCurve-class.Rd | 8 man/MEstimate-class.Rd | 18 man/Neighborhood-class.Rd | 8 man/OptionalInfluenceCurve-Class.Rd |only man/RobAStBaseMASK.Rd |only man/RobAStBaseOptions.Rd | 14 man/RobAStControl-class.Rd | 3 man/RobModel-class.Rd | 11 man/RobWeight-class.Rd | 4 man/TotalVarIC-class.Rd | 30 man/TotalVarNeighborhood-class.Rd | 4 man/UncondNeighborhood-class.Rd | 4 man/comparePlot.Rd | 118 +++ man/getBoundedIC.Rd |only man/getRiskIC.Rd | 2 man/infoPlot.Rd | 105 ++- man/internals-qqplot.Rd |only man/internals_ddPlot.Rd | 2 man/kStepEstimate-class.Rd | 100 ++- man/kStepEstimator.Rd | 120 ++- man/kStepEstimatorStart-methods.Rd |only man/locMEstimator.Rd | 3 man/masked-methods.Rd |only man/oneStepEstimator.Rd | 57 - man/plot-methods.Rd | 92 ++ man/qqplot.Rd |only tests |only 70 files changed, 2794 insertions(+), 1168 deletions(-)
Author: Matthias Kohl
Title: Optimally robust estimation for regression-type models
Description: Optimally robust estimation for regression-type models
using S4 classes and methods
Diff between ROptRegTS versions 0.6.1 dated 2009-02-28 and 0.7 dated 2009-11-04
DESCRIPTION | 34 ++++++++++++++++++++-------------- inst/NEWS | 35 +++++++++++++++++++++++++++++++++++ inst/TOBEDONE |only man/CondIC-class.Rd | 2 +- man/CondNeighborhood-class.Rd | 2 +- man/FixRobRegTypeModel-class.Rd | 2 +- man/InfRobRegTypeModel-class.Rd | 2 +- man/RegTypeFamily-class.Rd | 2 +- man/generateIC-methods.Rd | 2 +- man/getAsRiskRegTS.Rd | 2 +- man/getFiRiskRegTS.Rd | 2 +- man/getFixClipRegTS.Rd | 2 +- man/getIneffDiff-methods.Rd | 2 +- man/getInfCentRegTS.Rd | 2 +- man/getInfClipRegTS.Rd | 2 +- man/getInfGammaRegTS.Rd | 4 ++-- man/getInfStandRegTS.Rd | 2 +- man/leastFavorableRadius-methods.Rd | 2 +- man/optIC-methods.Rd | 2 +- man/radiusMinimaxIC-methods.Rd | 2 +- tests |only 21 files changed, 73 insertions(+), 32 deletions(-)
Author: Matthias Kohl
Title: Optimally robust estimation - old version
Description: Optimally robust estimation using S4 classes and methods.
Old version still needed for current versions of ROptRegTS and
RobRex.
Diff between ROptEstOld versions 0.5.2 dated 2009-02-28 and 0.7 dated 2009-11-04
ROptEstOld-0.5.2/ROptEstOld/R/DistrSymmList.R |only ROptEstOld-0.5.2/ROptEstOld/R/PosDefSymmMatrix.R |only ROptEstOld-0.5.2/ROptEstOld/man/DistrSymmList-class.Rd |only ROptEstOld-0.5.2/ROptEstOld/man/DistrSymmList.Rd |only ROptEstOld-0.5.2/ROptEstOld/man/DistributionSymmetry-class.Rd |only ROptEstOld-0.5.2/ROptEstOld/man/EllipticalSymmetry-class.Rd |only ROptEstOld-0.5.2/ROptEstOld/man/EllipticalSymmetry.Rd |only ROptEstOld-0.5.2/ROptEstOld/man/NoSymmetry-class.Rd |only ROptEstOld-0.5.2/ROptEstOld/man/NoSymmetry.Rd |only ROptEstOld-0.5.2/ROptEstOld/man/OptionalNumeric-class.Rd |only ROptEstOld-0.5.2/ROptEstOld/man/PosDefSymmMatrix-class.Rd |only ROptEstOld-0.5.2/ROptEstOld/man/PosDefSymmMatrix.Rd |only ROptEstOld-0.5.2/ROptEstOld/man/SphericalSymmetry-class.Rd |only ROptEstOld-0.5.2/ROptEstOld/man/SphericalSymmetry.Rd |only ROptEstOld-0.5.2/ROptEstOld/man/Symmetry-class.Rd |only ROptEstOld-0.7/ROptEstOld/DESCRIPTION | 33 +++--- ROptEstOld-0.7/ROptEstOld/NAMESPACE | 19 --- ROptEstOld-0.7/ROptEstOld/R/AllClass.R | 55 ---------- ROptEstOld-0.7/ROptEstOld/R/AllGeneric.R | 6 - ROptEstOld-0.7/ROptEstOld/R/AllShow.R | 7 - ROptEstOld-0.7/ROptEstOld/R/Symmetry.R | 17 --- ROptEstOld-0.7/ROptEstOld/inst |only ROptEstOld-0.7/ROptEstOld/man/EvenSymmetric.Rd | 2 ROptEstOld-0.7/ROptEstOld/man/FunctionSymmetry-class.Rd | 3 ROptEstOld-0.7/ROptEstOld/man/GammaFamily.Rd | 2 ROptEstOld-0.7/ROptEstOld/man/OddSymmetric.Rd | 2 ROptEstOld-0.7/ROptEstOld/man/TotalVarIC-class.Rd | 3 ROptEstOld-0.7/ROptEstOld/man/asUnOvShoot-class.Rd | 2 ROptEstOld-0.7/ROptEstOld/man/fiUnOvShoot-class.Rd | 2 29 files changed, 35 insertions(+), 118 deletions(-)
Author: Matthias Kohl, Peter Ruckdeschel
Title: Optimally robust estimation
Description: Optimally robust estimation in general smoothly
parameterized models using S4 classes and methods.
Diff between ROptEst versions 0.6.3 dated 2009-01-13 and 0.7 dated 2009-11-04
DESCRIPTION | 35 NAMESPACE | 4 R/AllGeneric.R | 5 R/LowerCaseMultivariate.R | 83 + R/cniperCont.R | 10 R/getAsRisk.R | 38 R/getFixRobIC_fiUnOvShoot.R | 2 R/getIneffDiff.R | 43 R/getInfCent.R | 50 R/getInfClip.R | 4 R/getInfGamma.R | 28 R/getInfLM.R |only R/getInfRobIC_asBias.R | 128 + R/getInfRobIC_asCov.R | 66 R/getInfRobIC_asGRisk.R | 855 +++++++++-- R/getInfRobIC_asHampel.R | 557 +++++-- R/getInfRobIC_asUnOvShoot.R | 5 R/getInfStand.R | 2 R/getInfV.R | 28 R/getModifyIC.R | 186 +- R/leastFavorableRadius.R | 61 R/optIC.R | 47 R/optRisk.R | 4 R/radiusMinimaxIC.R | 78 - R/roptest.R | 63 inst/NEWS | 188 ++ inst/TOBEDONE |only inst/scripts/BinomialModel.R | 2409 +++++++++++++++++++++++++++++++- inst/scripts/ExponentialScaleModel.R | 203 ++ inst/scripts/GammaModel.R | 56 inst/scripts/GumbelLocationModel.R | 2 inst/scripts/LognormalAndNormalModel.R | 8 inst/scripts/NormalLocationScaleModel.R | 82 + inst/scripts/PoissonModel.R | 15 man/0ROptEst-package.Rd | 26 man/getAsRisk.Rd | 148 + man/getFixRobIC.Rd | 3 man/getIneffDiff.Rd | 17 man/getInfCent.Rd | 19 man/getInfClip.Rd | 6 man/getInfGamma.Rd | 14 man/getInfRobIC.Rd | 119 + man/getInfStand.Rd | 6 man/getInfV.Rd | 6 man/getModifyIC.Rd | 51 man/getRiskIC.Rd | 2 man/getinfLM.Rd |only man/internals.Rd |only man/leastFavorableRadius.Rd | 14 man/minmaxBias.Rd | 32 man/optIC.Rd | 22 man/radiusMinimaxIC.Rd | 21 man/roptest.Rd | 72 tests |only 54 files changed, 5174 insertions(+), 749 deletions(-)
Author: Tony Plate
Title: Track Objects
Description: Stores objects in files on disk so that files are
automatically rewritten when objects are changed, and so that
objects are accessible but do not occupy memory until they are
accessed. Also tracks times when objects are created and
modified, and caches some basic characteristics of objects to
allow for fast summaries of objects.
Diff between trackObjs versions 0.8-3 dated 2009-02-20 and 0.8-6 dated 2009-11-04
trackObjs-0.8-3/trackObjs/man/trackObjs.Rd |only trackObjs-0.8-6/trackObjs/DESCRIPTION | 32 +++++++++++---------- trackObjs-0.8-6/trackObjs/NEWS | 7 +++- trackObjs-0.8-6/trackObjs/man/track.design.Rd | 6 +-- trackObjs-0.8-6/trackObjs/man/track.future.Rd | 2 - trackObjs-0.8-6/trackObjs/man/track.manage.Rd | 2 - trackObjs-0.8-6/trackObjs/man/track.options.Rd | 2 - trackObjs-0.8-6/trackObjs/man/track.rebuild.Rd | 2 - trackObjs-0.8-6/trackObjs/man/track.setup.Rd | 2 - trackObjs-0.8-6/trackObjs/man/track.status.Rd | 2 - trackObjs-0.8-6/trackObjs/man/track.summary.Rd | 2 - trackObjs-0.8-6/trackObjs/man/trackObjs-package.Rd |only 12 files changed, 33 insertions(+), 26 deletions(-)
Author: Graham Williams
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.
Diff between rattle versions 2.5.1 dated 2009-10-26 and 2.5.2 dated 2009-11-04
DESCRIPTION | 19 ++++++------ R/explore.R | 27 +++++++----------- R/export.R | 12 +++++--- R/model.R | 26 +++++++++-------- R/rattle.R | 17 +++-------- R/survival.R | 55 ++++++++++++++++++++++++++++++++++++ data/audit.RData |binary data/weather.RData |binary data/weatherCanberra.RData |binary data/weatherSydney.RData |binary inst/arff/weather.arff | 4 +- inst/arff/weatherCanberra.arff | 35 ++++++++++++++++++++++- inst/arff/weatherSydney.arff | 37 ++++++++++++++++++++++-- inst/csv/weatherCanberra.csv | 31 ++++++++++++++++++++ inst/csv/weatherSydney.csv | 31 ++++++++++++++++++++ inst/etc/rattle.glade | 61 ++++++++++++++++++++--------------------- man/internal.Rd | 2 + 17 files changed, 265 insertions(+), 92 deletions(-)
Author: Graham Williams, Michael Hahsler (arules), Zementis Inc, Hemant
Ishwaran, Udaya B. Kogalur, Rajarshi Guha
Title: Generate PMML for various models
Description: The Predictive Modelling Markup Language (PMML) is a
language for representing models, in an application independent
way. Such models can then be loaded into other applications
supporting PMML, including ADAPA from Zementis, Teradata
Warehouse Miner and IBM's DB2. The package provides a generic
pmml function to generate pmml for an object. Using a S3
generic function the approriate method for the class of the
supplied object is dispatched. The package currently supports
the export of PMML for linear regression, SVMs, rpart
classification trees, randomSurvivalForest forest models, and
kmeans clusters. This package is part of the Rattle toolkit.
Diff between pmml versions 1.2.19 dated 2009-10-26 and 1.2.20 dated 2009-11-04
DESCRIPTION | 8 ++++---- NAMESPACE | 1 + R/pmml.R | 5 +++-- R/pmml.coxph.R |only man/pmml.coxph.Rd |only 5 files changed, 8 insertions(+), 6 deletions(-)
Author: Rolf Turner
Title: Functions to fit mixtures of regressions.
Description: Fits mixtures of (possibly multivariate) regressions
(which has been described as doing ANCOVA when you don't know
the levels).
Diff between mixreg versions 0.0-2 dated 2006-09-12 and 0.0-3 dated 2009-11-04
mixreg-0.0-2/mixreg/aphids.dat |only mixreg-0.0-3/mixreg/ChangeLog |only mixreg-0.0-3/mixreg/DESCRIPTION | 18 ++++++++++-------- mixreg-0.0-3/mixreg/R/boot.sam.R | 4 ++-- mixreg-0.0-3/mixreg/inst/aphids.dat |only mixreg-0.0-3/mixreg/man/plot.cband.Rd | 2 +- mixreg-0.0-3/mixreg/man/plot.mresid.Rd | 2 +- 7 files changed, 14 insertions(+), 12 deletions(-)
Author: Rolf Turner
Title: Delaunay Triangulation and Dirichlet (Voronoi) Tessellation.
Description: Calculates the Delaunay triangulation and the Dirichlet or
Voronoi tessellation (with respect to the entire plane) of a
planar point set.
Diff between deldir versions 0.0-8 dated 2009-04-04 and 0.0-9 dated 2009-11-04
ChangeLog |only DESCRIPTION | 8 ++++---- INDEX | 1 + R/tile.centroids.R |only inst/READ_ME | 5 +++++ man/tile.centroids.Rd |only man/tile.list.Rd | 2 +- 7 files changed, 11 insertions(+), 5 deletions(-)
Author: Stefano Iacus
Title: CEM: Software for Coarsened Exact Matching
Description: This program implements the coarsened exact matching
algorithm (and many extensions) described in Stefano M. Iacus,
Gary King, and Giuseppe Porro, "Causal Inference Without
Balance Checking: Coarsened Exact Matching,"
http://gking.harvard.edu/files/abs/cem-plus-abs.shtml
Diff between cem versions 1.0.120 dated 2009-10-21 and 1.0.127 dated 2009-11-04
DESCRIPTION | 8 R/L1profile.R | 131 - R/cem.main.R | 2 R/imb.meas.R | 181 - inst/doc/Rplots.pdf | 50 inst/doc/cem.Rnw | 2 inst/doc/cem.pdf | 5676 ++++++++++++++++++-------------------------------- inst/doc/coarsen1.pdf | 28 inst/doc/coarsen2.pdf | 28 inst/doc/copyRd.Rout | 2 inst/doc/index.shtml | 4 inst/doc/teff.pdf | 38 man/L1.profile.Rd | 42 13 files changed, 2306 insertions(+), 3886 deletions(-)
Author: Tom Kincaid
Title: Spatial Survey Design and Analysis
Description: This group of functions implements algorithms required for
design and analysis of probability surveys such as those
utilized by the U.S. Environmental Protection Agency's
Environmental Monitoring and Assessment Program (EMAP).
Diff between spsurvey versions 2.0 dated 2008-06-20 and 2.1 dated 2009-11-03
spsurvey-2.0/spsurvey/inst/doc/00Index.html |only spsurvey-2.0/spsurvey/spsurvey_2.0.zip |only spsurvey-2.1/spsurvey/DESCRIPTION | 40 ++--- spsurvey-2.1/spsurvey/INDEX | 9 - spsurvey-2.1/spsurvey/R/albersgeod.r | 79 +++++----- spsurvey-2.1/spsurvey/R/cat.analysis.s | 5 spsurvey-2.1/spsurvey/R/category.est.s | 3 spsurvey-2.1/spsurvey/R/cdf.test.s | 8 - spsurvey-2.1/spsurvey/R/cont.analysis.s | 5 spsurvey-2.1/spsurvey/R/cont.cdfplot.s | 7 spsurvey-2.1/spsurvey/R/cont.cdftest.s | 9 - spsurvey-2.1/spsurvey/R/dframe.check.s | 186 +++++++++++++------------ spsurvey-2.1/spsurvey/R/dsgnsum.r | 117 ++++++++++++--- spsurvey-2.1/spsurvey/R/framesum.r | 3 spsurvey-2.1/spsurvey/R/geodalbers.r |only spsurvey-2.1/spsurvey/R/grts.r | 13 - spsurvey-2.1/spsurvey/R/input.check.s | 70 +++------ spsurvey-2.1/spsurvey/R/onLoad.r | 2 spsurvey-2.1/spsurvey/R/read.dbf.r | 11 + spsurvey-2.1/spsurvey/R/read.shape.r | 11 + spsurvey-2.1/spsurvey/R/relrisk.analysis.s | 15 +- spsurvey-2.1/spsurvey/R/spsurvey.analysis.s | 66 ++++---- spsurvey-2.1/spsurvey/R/total.est.s | 1 spsurvey-2.1/spsurvey/R/total.var.s | 3 spsurvey-2.1/spsurvey/R/write.dbf.r |only spsurvey-2.1/spsurvey/data/eco_l3_ut.s | 10 - spsurvey-2.1/spsurvey/data/luck-ash.s | 12 - spsurvey-2.1/spsurvey/data/reg1_lakes.s | 14 - spsurvey-2.1/spsurvey/demo/Area.R | 2 spsurvey-2.1/spsurvey/demo/Finite.R | 2 spsurvey-2.1/spsurvey/demo/Linear.R | 2 spsurvey-2.1/spsurvey/inst/doc/Area.Rnw |only spsurvey-2.1/spsurvey/inst/doc/Area.pdf |only spsurvey-2.1/spsurvey/inst/doc/CHANGES.pdf |binary spsurvey-2.1/spsurvey/inst/doc/Finite.Rnw |only spsurvey-2.1/spsurvey/inst/doc/Finite.pdf |only spsurvey-2.1/spsurvey/inst/doc/Linear.Rnw |only spsurvey-2.1/spsurvey/inst/doc/Linear.pdf |only spsurvey-2.1/spsurvey/inst/doc/README.pdf |binary spsurvey-2.1/spsurvey/inst/doc/Rplots.pdf |only spsurvey-2.1/spsurvey/inst/doc/UserGuide.pdf |binary spsurvey-2.1/spsurvey/inst/doc/eco_l3_ut.dbf |only spsurvey-2.1/spsurvey/inst/doc/eco_l3_ut.shp |only spsurvey-2.1/spsurvey/inst/doc/eco_l3_ut.shx |only spsurvey-2.1/spsurvey/inst/doc/luck_ash.dbf |only spsurvey-2.1/spsurvey/inst/doc/luck_ash.shp |only spsurvey-2.1/spsurvey/inst/doc/luck_ash.shx |only spsurvey-2.1/spsurvey/inst/doc/reg1_lakes.dbf |only spsurvey-2.1/spsurvey/inst/doc/reg1_lakes.shp |only spsurvey-2.1/spsurvey/inst/doc/reg1_lakes.shx |only spsurvey-2.1/spsurvey/man/albersgeod.Rd | 12 - spsurvey-2.1/spsurvey/man/cdf.decon.Rd | 2 spsurvey-2.1/spsurvey/man/cdf.est.Rd | 2 spsurvey-2.1/spsurvey/man/cdf.test.Rd | 3 spsurvey-2.1/spsurvey/man/cont.analysis.Rd | 2 spsurvey-2.1/spsurvey/man/framesum.Rd | 3 spsurvey-2.1/spsurvey/man/geodalbers.Rd |only spsurvey-2.1/spsurvey/man/grts.Rd | 9 - spsurvey-2.1/spsurvey/man/luck.ash.Rd | 2 spsurvey-2.1/spsurvey/man/spsurvey-internal.Rd | 3 spsurvey-2.1/spsurvey/man/spsurvey.analysis.Rd | 4 spsurvey-2.1/spsurvey/man/write.dbf.Rd |only spsurvey-2.1/spsurvey/src/init.c | 3 spsurvey-2.1/spsurvey/src/spsurvey.h | 1 64 files changed, 429 insertions(+), 322 deletions(-)
Author: Daniel Adler
Title: memory-efficient storage of large data on disk and fast access
functions
Description: The ff package provides data structures that are stored on
disk but behave (almost) as if they were in RAM by
transparently mapping only a section (pagesize) in main memory
- the effective virtual memory consumption per ff object. ff
supports R's standard atomic data types 'double', 'logical',
'raw' and 'integer' and non-standard atomic types boolean (1
bit), quad (2 bit unsigned), nibble (4 bit unsigned), byte (1
byte signed with NAs), ubyte (1 byte unsigned), short (2 byte
signed with NAs), ushort (2 byte unsigned), single (4 byte
float with NAs). For example 'quad' allows efficient storage of
genomic data as an 'A','T','G','C' factor. The unsigned types
support 'circular' arithmetic. There is also support for
close-to-atomic types 'factor', 'ordered', 'POSIXct', 'Date'
and custom close-to-atomic types. ff not only has native
C-support for vectors, matrices and arrays with flexible
dimorder (major column-order, major row-order and
generalizations for arrays). There is also a ffdf class not
unlike data.frames and import/export filters for csv files. ff
objects store raw data in binary flat files in native encoding,
and complement this with metadata stored in R as physical and
virtual attributes. ff objects have well-defined hybrid copying
semantics, which gives rise to certain performance improvements
through virtualization. ff objects can be stored and reopened
across R sessions. ff files can be shared by multiple ff R
objects (using different data en/de-coding schemes) in the same
process or from multiple R processes to exploit parallelism. A
wide choice of finalizer options allows to work with
'permanent' files as well as creating/removing 'temporary' ff
files completely transparent to the user. On certain
OS/Filesystem combinations, creating the ff files works without
notable delay thanks to using sparse file allocation. Several
access optimization techniques such as Hybrid Index
Preprocessing and Virtualization are implemented to achieve
good performance even with large datasets, for example virtual
matrix transpose without touching a single byte on disk.
Further, to reduce disk I/O, 'logicals' and non-standard data
types get stored native and compact on binary flat files i.e.
logicals take up exactly 2 bits to represent TRUE, FALSE and
NA. Beyond basic access functions, the ff package also provides
compatibility functions that facilitate writing code for ff and
ram objects and support for batch processing on ff objects
(e.g. as.ram, as.ff, ffapply). ff interfaces closely with
functionality from package 'bit': chunked looping, fast bit
operations and coercions between different objects that can
store subscript information ('bit', 'bitwhich', ff 'boolean',
ri range index, hi hybrid index). This allows to work
interactively with selections of large datasets and quickly
modify selection criteria. Further high-performance
enhancements can be made available upon request.
Diff between ff versions 2.0.1 dated 2009-04-16 and 2.1-0 dated 2009-11-03
ff-2.0.1/ff/ANNOUNCEMENT.txt |only ff-2.0.1/ff/man/bbatch.rd |only ff-2.0.1/ff/man/intrle.rd |only ff-2.0.1/ff/man/physical.rd |only ff-2.0.1/ff/man/repfromto.rd |only ff-2.0.1/ff/man/rlepack.rd |only ff-2.1-0/ff/ANNOUNCEMENT-2.0.txt |only ff-2.1-0/ff/ANNOUNCEMENT-2.1.txt |only ff-2.1-0/ff/DESCRIPTION | 108 +- ff-2.1-0/ff/LICENSE | 3 ff-2.1-0/ff/NAMESPACE | 260 ++++- ff-2.1-0/ff/NEWS |only ff-2.1-0/ff/R/array.R | 70 - ff-2.1-0/ff/R/as.ff.R | 6 ff-2.1-0/ff/R/ff.R | 1283 ++++++++++++++++++-------- ff-2.1-0/ff/R/ffapply.R | 143 -- ff-2.1-0/ff/R/ffbit.R |only ff-2.1-0/ff/R/ffcsv.R |only ff-2.1-0/ff/R/ffdf.R |only ff-2.1-0/ff/R/fffactor.R |only ff-2.1-0/ff/R/ffreturn.R | 4 ff-2.1-0/ff/R/fileresize.R |only ff-2.1-0/ff/R/fileutil.R |only ff-2.1-0/ff/R/generics.R | 112 ++ ff-2.1-0/ff/R/hi.R | 570 +++++------ ff-2.1-0/ff/R/util.R | 66 + ff-2.1-0/ff/R/vmode.R | 51 - ff-2.1-0/ff/R/vt.R | 8 ff-2.1-0/ff/R/zzz.R | 34 ff-2.1-0/ff/man/Extract.ff.rd | 11 ff-2.1-0/ff/man/Extract.ffdf.rd |only ff-2.1-0/ff/man/Forbidden_ffdf.rd |only ff-2.1-0/ff/man/Internal_ffdf.rd |only ff-2.1-0/ff/man/LimWarn.rd | 4 ff-2.1-0/ff/man/add.rd | 2 ff-2.1-0/ff/man/as.ff.bit.rd |only ff-2.1-0/ff/man/as.ff.rd | 6 ff-2.1-0/ff/man/as.ffdf.rd |only ff-2.1-0/ff/man/as.hi.rd | 26 ff-2.1-0/ff/man/as.integer.hi.rd | 6 ff-2.1-0/ff/man/chunk.ffdf.rd |only ff-2.1-0/ff/man/clone.ffdf.rd |only ff-2.1-0/ff/man/clone.rd | 48 ff-2.1-0/ff/man/close.ff.rd | 6 ff-2.1-0/ff/man/delete.rd | 14 ff-2.1-0/ff/man/dim.ff.rd | 42 ff-2.1-0/ff/man/dimnames.ff_array.rd | 5 ff-2.1-0/ff/man/dimnames.ffdf.rd |only ff-2.1-0/ff/man/ff.rd | 62 - ff-2.1-0/ff/man/ffapply.rd | 16 ff-2.1-0/ff/man/ffconform.rd | 2 ff-2.1-0/ff/man/ffdf.rd |only ff-2.1-0/ff/man/ffxtensions.rd | 5 ff-2.1-0/ff/man/file.resize.rd |only ff-2.1-0/ff/man/filename.rd | 59 + ff-2.1-0/ff/man/finalize.rd |only ff-2.1-0/ff/man/finalizer.rd |only ff-2.1-0/ff/man/geterror.ff.rd | 3 ff-2.1-0/ff/man/getset.ff.rd | 3 ff-2.1-0/ff/man/hi.rd | 14 ff-2.1-0/ff/man/hiparse.rd | 6 ff-2.1-0/ff/man/is.ff.rd | 2 ff-2.1-0/ff/man/is.ffdf.rd |only ff-2.1-0/ff/man/is.open.rd | 15 ff-2.1-0/ff/man/is.readonly.rd | 5 ff-2.1-0/ff/man/is.sorted.rd | 8 ff-2.1-0/ff/man/length.ff.rd | 21 ff-2.1-0/ff/man/length.ffdf.rd |only ff-2.1-0/ff/man/length.hi.rd | 18 ff-2.1-0/ff/man/levels.ff.rd | 10 ff-2.1-0/ff/man/maxlength.rd | 3 ff-2.1-0/ff/man/na.count.rd | 5 ff-2.1-0/ff/man/names.ff.rd | 5 ff-2.1-0/ff/man/nrowAssign.rd |only ff-2.1-0/ff/man/open.ff.rd | 14 ff-2.1-0/ff/man/physical.ff.rd |only ff-2.1-0/ff/man/physical.ffdf.rd |only ff-2.1-0/ff/man/print.ff.rd | 15 ff-2.1-0/ff/man/ramattribs.rd | 5 ff-2.1-0/ff/man/read.table.ffdf.rd |only ff-2.1-0/ff/man/readwrite.ff.rd | 3 ff-2.1-0/ff/man/repnam.rd |only ff-2.1-0/ff/man/sortLevels.rd |only ff-2.1-0/ff/man/splitPathFile.rd |only ff-2.1-0/ff/man/swap.rd | 5 ff-2.1-0/ff/man/update.ff.rd | 37 ff-2.1-0/ff/man/vecprint.rd | 2 ff-2.1-0/ff/man/vmode.ffdf.rd |only ff-2.1-0/ff/man/vmode.rd | 3 ff-2.1-0/ff/man/vt.rd | 8 ff-2.1-0/ff/man/vw.rd | 18 ff-2.1-0/ff/man/write.table.ffdf.rd |only ff-2.1-0/ff/prebuild.sh | 2 ff-2.1-0/ff/src/Array.hpp | 88 - ff-2.1-0/ff/src/FSInfo.hpp | 2 ff-2.1-0/ff/src/FSInfo_win32.cpp | 4 ff-2.1-0/ff/src/MMapFileMapping.cpp | 28 ff-2.1-0/ff/src/MMapFileMapping.hpp | 12 ff-2.1-0/ff/src/Win32FileMapping.cpp | 46 ff-2.1-0/ff/src/Win32FileMapping.hpp | 38 ff-2.1-0/ff/src/config.h | 7 ff-2.1-0/ff/src/r_ff.c | 149 --- ff-2.1-0/ff/src/r_ff.h | 3 ff-2.1-0/ff/src/r_ff_makevmodes.h | 26 ff-2.1-0/ff/src/r_file_resize.cpp |only ff-2.1-0/ff/src/r_file_resize.h |only ff-2.1-0/ff/src/utk_file_allocate_fseek.cpp | 8 ff-2.1-0/ff/src/utk_file_allocate_fseek.hpp | 2 ff-2.1-0/ff/src/utk_file_resize.cpp |only ff-2.1-0/ff/src/utk_file_resize.hpp |only ff-2.1-0/ff/src/utk_file_resize_ftruncate.hpp |only ff-2.1-0/ff/src/utk_file_resize_win32.hpp |only 112 files changed, 2293 insertions(+), 1382 deletions(-)
Author: Henrik Bengtsson
Title: Support package for aroma.affymetrix et al.
Description: This package is a private support package for
aroma.affymetrix et al. The methods and classes of this
package are independent of platform. Its API is in alpha and
beta stage.
Diff between aroma.core versions 1.2.0 dated 2009-09-10 and 1.3.1 dated 2009-11-03
aroma.core-1.2.0/aroma.core/R/Interface.R |only aroma.core-1.2.0/aroma.core/man/Interface.Rd |only aroma.core-1.3.1/aroma.core/DESCRIPTION | 24 ++++----- aroma.core-1.3.1/aroma.core/R/AromaCellPositionFile.R | 5 + aroma.core-1.3.1/aroma.core/R/AromaCellSequenceFile.R | 4 + aroma.core-1.3.1/aroma.core/R/AromaTransform.R | 4 - aroma.core-1.3.1/aroma.core/R/AromaUgpFile.R | 4 + aroma.core-1.3.1/aroma.core/R/AromaUnitCallSet.R | 4 - aroma.core-1.3.1/aroma.core/R/AromaUnitFracBCnBinarySet.R | 2 aroma.core-1.3.1/aroma.core/R/AromaUnitFracBCnBinarySet.exportFracBDiffSet.R | 2 aroma.core-1.3.1/aroma.core/R/AromaUnitGenotypeCallSet.R | 6 +- aroma.core-1.3.1/aroma.core/R/AromaUnitSignalBinaryFile.R | 5 + aroma.core-1.3.1/aroma.core/R/AromaUnitSignalBinarySet.R | 2 aroma.core-1.3.1/aroma.core/R/AromaUnitTotalCnBinarySet.R | 3 - aroma.core-1.3.1/aroma.core/R/AromaUnitTotalCnBinarySet.exportTotalCnRatioSet.R | 8 ++- aroma.core-1.3.1/aroma.core/R/RawGenomicSignals.R | 11 ++++ aroma.core-1.3.1/aroma.core/R/RawGenomicSignals.segmentByHaarSeg.R | 3 - aroma.core-1.3.1/aroma.core/R/SampleAnnotationFile.R | 7 ++ aroma.core-1.3.1/aroma.core/R/TextUnitNamesFile.R | 6 ++ aroma.core-1.3.1/aroma.core/R/UnitAnnotationDataFile.R | 2 aroma.core-1.3.1/aroma.core/R/fitGenotypeCone.matrix.R | 7 +- aroma.core-1.3.1/aroma.core/R/fitMultiDimensionalCone.matrix.R | 5 + aroma.core-1.3.1/aroma.core/incl/999.missingdocs.txt | 18 +++++- aroma.core-1.3.1/aroma.core/incl/RawGenomicSignals.SEG.Rex | 24 +++++---- aroma.core-1.3.1/aroma.core/inst/NEWS | 26 ++++++++++ aroma.core-1.3.1/aroma.core/man/AromaCellTabularBinaryFile.Rd | 19 ++++--- aroma.core-1.3.1/aroma.core/man/AromaMicroarrayDataFile.Rd | 13 +++-- aroma.core-1.3.1/aroma.core/man/AromaMicroarrayDataSet.Rd | 11 +++- aroma.core-1.3.1/aroma.core/man/AromaMicroarrayTabularBinaryFile.Rd | 17 ++++-- aroma.core-1.3.1/aroma.core/man/AromaTabularBinaryFile.Rd | 15 +++-- aroma.core-1.3.1/aroma.core/man/AromaTabularBinarySet.Rd | 13 +++-- aroma.core-1.3.1/aroma.core/man/AromaUnitCallFile.Rd | 21 +++++--- aroma.core-1.3.1/aroma.core/man/AromaUnitCallSet.Rd | 19 ++++--- aroma.core-1.3.1/aroma.core/man/AromaUnitFracBCnBinaryFile.Rd | 21 +++++--- aroma.core-1.3.1/aroma.core/man/AromaUnitFracBCnBinarySet.Rd | 17 ++++-- aroma.core-1.3.1/aroma.core/man/AromaUnitGenotypeCallFile.Rd | 23 +++++--- aroma.core-1.3.1/aroma.core/man/AromaUnitGenotypeCallSet.Rd | 23 +++++--- aroma.core-1.3.1/aroma.core/man/AromaUnitSignalBinaryFile.Rd | 17 ++++-- aroma.core-1.3.1/aroma.core/man/AromaUnitSignalBinarySet.Rd | 15 +++-- aroma.core-1.3.1/aroma.core/man/AromaUnitTabularBinaryFile.Rd | 19 ++++--- aroma.core-1.3.1/aroma.core/man/AromaUnitTotalCnBinaryFile.Rd | 21 +++++--- aroma.core-1.3.1/aroma.core/man/AromaUnitTotalCnBinarySet.Rd | 17 ++++-- aroma.core-1.3.1/aroma.core/man/AromaUnitTypesFile.Rd | 25 +++++---- aroma.core-1.3.1/aroma.core/man/Non-documented_objects.Rd | 14 +++-- aroma.core-1.3.1/aroma.core/man/RawAlleleBFractions.Rd | 2 aroma.core-1.3.1/aroma.core/man/RawCopyNumbers.Rd | 2 aroma.core-1.3.1/aroma.core/man/RawGenomicSignals.Rd | 1 aroma.core-1.3.1/aroma.core/man/RawMirroredAlleleBFractions.Rd | 2 aroma.core-1.3.1/aroma.core/man/RawSequenceReads.Rd | 2 aroma.core-1.3.1/aroma.core/man/SegmentedAlleleBFractions.Rd | 2 aroma.core-1.3.1/aroma.core/man/SegmentedCopyNumbers.Rd | 2 aroma.core-1.3.1/aroma.core/man/SegmentedGenomicSignalsInterface.Rd | 6 +- aroma.core-1.3.1/aroma.core/man/UnitAnnotationDataFile.Rd | 8 +-- aroma.core-1.3.1/aroma.core/man/UnitNamesFile.Rd | 4 - aroma.core-1.3.1/aroma.core/man/UnitTypesFile.Rd | 4 - aroma.core-1.3.1/aroma.core/man/fitGenotypeCone.matrix.Rd | 2 aroma.core-1.3.1/aroma.core/man/fitGenotypeConeBySfit.matrix.Rd | 5 + aroma.core-1.3.1/aroma.core/man/fitMultiDimensionalCone.matrix.Rd | 5 + aroma.core-1.3.1/aroma.core/man/getOutputDataSet.AromaTransform.Rd | 2 aroma.core-1.3.1/aroma.core/man/segmentByCBS.RawGenomicSignals.Rd | 26 +++++----- aroma.core-1.3.1/aroma.core/man/segmentByHaarSeg.RawGenomicSignals.Rd | 3 - 61 files changed, 394 insertions(+), 206 deletions(-)
Author: Ulrike Groemping
Title: Full factorials, orthogonal arrays and base utilities for DoE
packages
Description: This package creates full factorial experimental designs
and designs based on orthogonal arrays for (industrial)
experiments. Additionally, it provides some utility functions
used also by other DoE packages.
Diff between DoE.base versions 0.9-4 dated 2009-09-25 and 0.9-5 dated 2009-11-03
DESCRIPTION | 8 ++++---- NAMESPACE | 2 +- inst/NEWS | 8 +++++++- man/formula.design.Rd | 4 ++-- 4 files changed, 14 insertions(+), 8 deletions(-)
Author: Kellie J. Archer
Title: Ordinal classification tree functions
Description: This package contains functions that can be called in
conjunction with rpart for deriving a classification tree when
the response to be predicted is ordinal.
Diff between rpartOrdinal versions 1.0 dated 2009-07-18 and 1.1 dated 2009-11-03
DESCRIPTION | 8 ++++---- data/lowbwt.rda |binary man/loss.matrix.Rd | 11 +++++++---- man/lowbwt.Rd | 5 ++--- man/ordinal.Rd | 12 +++++------- man/rpartOrdinal-package.Rd | 2 +- man/twoing.Rd | 12 ++++-------- 7 files changed, 23 insertions(+), 27 deletions(-)
Author: G Grothendieck
Title: R interface to SymPy computer algebra system
Description: Access SymPy computer algebra system from R via Jython
Diff between rSymPy versions 0.1-2 dated 2009-01-11 and 0.1-4 dated 2009-11-03
rSymPy-0.1-2/rSymPy/inst/jython |only rSymPy-0.1-4/rSymPy/DESCRIPTION | 25 ++++++------- rSymPy-0.1-4/rSymPy/NEWS | 19 +++++++-- rSymPy-0.1-4/rSymPy/R/Sym.R |only rSymPy-0.1-4/rSymPy/R/sympy.R | 69 +++++++++++++++++++++++------------- rSymPy-0.1-4/rSymPy/inst/Lib |only rSymPy-0.1-4/rSymPy/inst/jython.jar |only rSymPy-0.1-4/rSymPy/inst/kopy.bat |only rSymPy-0.1-4/rSymPy/man/Sym.Rd |only rSymPy-0.1-4/rSymPy/man/sympy.Rd | 27 +++++++------- 10 files changed, 88 insertions(+), 52 deletions(-)
Author: Douglas Bates
Title: Data sets from Mixed-effects Models in S
Description: Data sets and sample analyses from Pinheiro and Bates,
"Mixed-effects Models in S and S-PLUS" (Springer, 2000).
Diff between MEMSS versions 0.3-5 dated 2009-02-11 and 0.3-6 dated 2009-11-03
DESCRIPTION | 16 ++++++++++------ man/CO2.Rd | 13 ++++++++----- 2 files changed, 18 insertions(+), 11 deletions(-)
Author: Florian Camphausen, Matthias Kohl, Peter Ruckdeschel, Thomas
Stabla
Title: Documentation for packages distr, distrEx, distrSim, distrTEst
Description: provides documentation in form of a common vignette to
packages distr, distrEx, distrMod, distrSim, distrTEst
Diff between distrDoc versions 2.1.1 dated 2009-07-03 and 2.2 dated 2009-11-03
distrDoc-2.1.1/distrDoc/inst/doc/Rplots.pdf |only distrDoc-2.1.1/distrDoc/inst/doc/distr.R |only distrDoc-2.2/distrDoc/DESCRIPTION | 21 distrDoc-2.2/distrDoc/R/distrDoc.R | 6 distrDoc-2.2/distrDoc/inst/NEWS | 19 distrDoc-2.2/distrDoc/inst/TOBEDONE |only distrDoc-2.2/distrDoc/inst/doc/distr.Rnw | 30 distrDoc-2.2/distrDoc/inst/doc/distr.pdf |33614 ++++++++++++------------- distrDoc-2.2/distrDoc/man/0distrDoc-package.Rd | 19 9 files changed, 16963 insertions(+), 16746 deletions(-)
Author: Matthias Kohl, Peter Ruckdeschel
Title: Implementation of random variables
Description: Implementation of random variables by means of S4 classes
and methods
Diff between RandVar versions 0.6.9 dated 2009-07-31 and 0.7 dated 2009-11-03
DESCRIPTION | 15 +++--- R/Expectation.R | 102 +++++++++++++++++++++--------------------- R/Matrixmult.R | 12 ++-- inst/NEWS | 56 +++++++++++++++++++++++ inst/TOBEDONE |only inst/doc/RandVar.Rnw | 4 - inst/doc/RandVar.pdf |binary man/0RandVar-package.Rd | 17 ++++--- man/EuclRandMatrix-class.Rd | 8 +-- man/EuclRandVarList-class.Rd | 6 +- man/EuclRandVariable-class.Rd | 8 +-- man/RandVariable-class.Rd | 6 +- man/RealRandVariable-class.Rd | 6 +- tests/Examples |only tests/tests.R | 1 tests/tests.Rout.save |only 16 files changed, 153 insertions(+), 88 deletions(-)
Author: Jeffrey A. Ryan, Josh M. Ulrich
Title: Extensible Time Series
Description: Provide for uniform handling of R's different time-based
data classes by extending zoo, maximizing native format
information preservation and allowing for user level
customization and extension, while simplifying cross-class
interoperability.
Diff between xts versions 0.6-8 dated 2009-10-14 and 0.6-9 dated 2009-11-03
DESCRIPTION | 8 NAMESPACE | 4 R/parse8601.R | 4 R/plot.R | 2 inst/doc/xts.pdf | 3023 +++++++++++++++++++++++++--------------------------- man/coredata.xts.Rd | 2 man/plot.xts.Rd | 7 man/xts-package.Rd | 1 src/coredata.c | 8 9 files changed, 1513 insertions(+), 1546 deletions(-)
Author: Spencer Graves, Sundar Dorai-Raj, and Romain Francois
Title: sos
Description: R related Search Engines
Diff between sos versions 1.1-5 dated 2009-10-01 and 1.1-7 dated 2009-11-03
DESCRIPTION | 8 ++++---- R/grepFn.R | 4 ++-- inst/doc/sos.pdf | 6 +++--- man/grepFn.Rd | 4 ++-- 4 files changed, 11 insertions(+), 11 deletions(-)
Author: Peter Ruckdeschel
Title: Utilities for start-up messages
Description: Utilities for start-up messages
Diff between startupmsg versions 0.6 dated 2009-04-15 and 0.7 dated 2009-11-03
DESCRIPTION | 15 ++++++++------- NAMESPACE | 2 +- R/startUpMessage.R | 6 ++++++ inst/NEWS | 16 ++++++++++++++++ inst/TOBEDONE |only man/StartupUtilities.Rd | 6 +++++- tests |only 7 files changed, 36 insertions(+), 9 deletions(-)
Author: Edzer J. Pebesma
Title: geostatistical modelling, prediction and simulation
Description: variogram modelling; simple, ordinary and universal point
or block (co)kriging, sequential Gaussian or indicator
(co)simulation; variogram and variogram map plotting utility
functions.
Diff between gstat versions 0.9-63 dated 2009-10-05 and 0.9-64 dated 2009-11-03
DESCRIPTION | 8 R/fit.lmc.R | 2 R/fit.variogram.reml.R | 3 R/gstat.R | 5 R/gstat.cv.R | 11 R/krige.cv.R | 8 R/predict.gstat.R | 3 R/variogram.default.R | 4 inst/doc/gstat.pdf |29116 +++++++++++++++++++++++++------------------------ man/gstat.Rd | 3 man/krige.cv.Rd | 12 man/variogram.Rd | 4 src/data.c | 6 src/data.h | 9 src/gls.c | 4 src/glvars.c | 10 src/lex.l | 3 src/lm.c | 2 src/nsearch.c | 19 src/s.c | 5 src/utils.c | 4 src/vario.c | 25 src/vario.h | 5 23 files changed, 14994 insertions(+), 14277 deletions(-)
Author: Ronja Foraita, Fabian Sobotka
Title: Validation of graphical models
Description: Simulate data sets given a dependence model, validate
graphical models using the bootstrap, find the best prediction
model using cross validation.
Diff between gmvalid versions 1.2 dated 2008-12-21 and 1.21 dated 2009-11-03
ChangeLog | 8 ++++++++ DESCRIPTION | 31 +++++++++++++++++-------------- inst |only man/unix/gmvalid-package.Rd | 7 ++++--- man/windows/gm.boot.mim.Rd | 2 +- man/windows/gm.cv.Rd | 2 +- man/windows/gm.mim.Rd | 2 +- man/windows/gmvalid-package.Rd | 11 ++++++----- 8 files changed, 38 insertions(+), 25 deletions(-)
Author: Han Lin Shang and Rob J Hyndman
Title: Functional data sets
Description: Functional data sets
Diff between fds versions 1.1 dated 2009-10-08 and 1.2 dated 2009-11-03
CHANGELOG | 8 +++++++- DESCRIPTION | 8 ++++---- R/hmdcountry.R |only R/hmdstatistic.R |only R/read.hmd.R | 52 +++++++++++++++++++++++++++++++++------------------- man/hmdcountry.Rd |only man/hmdstatistic.Rd |only man/read.hmd.Rd | 12 ++++++++---- 8 files changed, 52 insertions(+), 28 deletions(-)
Author: Diethelm Wuertz and many others, see the SOURCE file
Title: Exotic Option Valuation
Description: Environment for teaching "Financial Engineering and
Computational Finance"
Diff between fExoticOptions versions 2100.76 dated 2009-09-29 and 2110.77 dated 2009-11-03
ChangeLog | 379 +++++++++++++++++ DESCRIPTION | 10 R/AsianOptions.R | 480 +++++++++++----------- R/BarrierOptions.R | 726 ++++++++++++++++------------------ R/BinaryOptions.R | 76 +-- R/CurrencyTranslatedOptions.R | 561 +++++++++++++------------- R/LookbackOptions.R | 893 +++++++++++++++++++++--------------------- R/MultipleAssetsOptions.R | 138 +++--- R/MultipleExercisesOptions.R | 420 +++++++++---------- R/zzz.R | 26 - 10 files changed, 2036 insertions(+), 1673 deletions(-)
More information about fExoticOptions at CRAN
Permanent link
Author: Virasakdi Chongsuvivatwong
Title: Epidemiological calculator
Description: Functions making R easy for epidemiological calculation.
Diff between epicalc versions 2.9.2.8 dated 2009-10-16 and 2.10.0.0 dated 2009-11-03
DESCRIPTION | 8 ++++---- R/epicalc.R | 27 +++++++++++++++++---------- man/addMissingRecords.rd | 13 +++++++------ 3 files changed, 28 insertions(+), 20 deletions(-)
Author: Peter Ruckdeschel, Matthias Kohl, Anja Hueller, Eleonara Feist
Title: Extensions of package distr for teaching Stochastics/Statistics
in secondary school
Description: Extensions of package distr and some additional
functionality
Diff between distrTeach versions 2.1 dated 2009-04-15 and 2.2 dated 2009-11-03
DESCRIPTION | 17 +++++++++-------- demo/illustCLT.R | 1 + demo/illustLLN.R | 1 + inst/NEWS | 24 +++++++++++++++++++++++- inst/TOBEDONE |only man/0distrTeach-package.Rd | 42 ++++++++++++++++++++++++------------------ man/IllustLLN.Rd | 6 +++--- tests |only 8 files changed, 61 insertions(+), 30 deletions(-)
Author: Florian Camphausen, Matthias Kohl, Peter Ruckdeschel, Thomas
Stabla
Title: Estimation and Testing classes based on package distr
Description: Evaluation (S4-)classes based on package distr for
evaluating procedures (estimators/tests) at data/simulation in
a unified way.
Diff between distrTEst versions 2.1.1 dated 2009-07-31 and 2.2 dated 2009-11-03
distrTEst-2.1.1/distrTEst/man/distrTEstOptions.Rd |only distrTEst-2.2/distrTEst/DESCRIPTION | 19 +++++++++-------- distrTEst-2.2/distrTEst/inst/NEWS | 12 +++++++++++ distrTEst-2.2/distrTEst/inst/TOBEDONE |only distrTEst-2.2/distrTEst/man/0distrTEst-package.Rd | 24 ++++++++++++++-------- distrTEst-2.2/distrTEst/man/Evaluation-class.Rd | 12 +++++------ distrTEst-2.2/distrTEst/man/distrTEstoptions.Rd |only distrTEst-2.2/distrTEst/tests |only 8 files changed, 44 insertions(+), 23 deletions(-)
Author: Florian Camphausen, Matthias Kohl, Peter Ruckdeschel, Thomas
Stabla
Title: Simulation classes based on package distr
Description: Simulation (S4-)classes based on package distr
Diff between distrSim versions 2.1.1 dated 2009-07-31 and 2.2 dated 2009-11-03
distrSim-2.1.1/distrSim/man/distrSimOptions.Rd |only distrSim-2.2/distrSim/DESCRIPTION | 19 +++++++++-------- distrSim-2.2/distrSim/inst/NEWS | 17 +++++++++++++++ distrSim-2.2/distrSim/inst/TOBEDONE |only distrSim-2.2/distrSim/man/0distrSim-package.Rd | 26 +++++++++++++++--------- distrSim-2.2/distrSim/man/distrSimoptions.Rd |only distrSim-2.2/distrSim/man/print-methods.Rd | 2 - distrSim-2.2/distrSim/man/subsetting-methods.Rd | 2 - distrSim-2.2/distrSim/man/summary-methods.Rd | 14 ++++++------ distrSim-2.2/distrSim/man/versionmanagement.Rd | 2 - distrSim-2.2/distrSim/tests |only 11 files changed, 54 insertions(+), 28 deletions(-)
Author: Matthias Kohl, Peter Ruckdeschel
Title: Object orientated implementation of probability models
Description: Object orientated implementation of probability models
based on packages 'distr' and 'distrEx'
Diff between distrMod versions 2.1.1 dated 2009-07-31 and 2.2 dated 2009-11-03
distrMod-2.1.1/distrMod/R/DistrSymmList.R |only distrMod-2.1.1/distrMod/R/PosDefSymmMatrix.R |only distrMod-2.1.1/distrMod/R/solve.R |only distrMod-2.1.1/distrMod/R/sqrt.R |only distrMod-2.1.1/distrMod/man/DistrSymmList-class.Rd |only distrMod-2.1.1/distrMod/man/DistrSymmList.Rd |only distrMod-2.1.1/distrMod/man/DistributionSymmetry-class.Rd |only distrMod-2.1.1/distrMod/man/EllipticalSymmetry-class.Rd |only distrMod-2.1.1/distrMod/man/EllipticalSymmetry.Rd |only distrMod-2.1.1/distrMod/man/NoSymmetry-class.Rd |only distrMod-2.1.1/distrMod/man/NoSymmetry.Rd |only distrMod-2.1.1/distrMod/man/PosDefSymmMatrix-class.Rd |only distrMod-2.1.1/distrMod/man/PosDefSymmMatrix.Rd |only distrMod-2.1.1/distrMod/man/SphericalSymmetry-class.Rd |only distrMod-2.1.1/distrMod/man/SphericalSymmetry.Rd |only distrMod-2.1.1/distrMod/man/Symmetry-class.Rd |only distrMod-2.1.1/distrMod/man/solve-methods.Rd |only distrMod-2.1.1/distrMod/man/sqrt-methods.Rd |only distrMod-2.2/distrMod/DESCRIPTION | 19 - distrMod-2.2/distrMod/NAMESPACE | 22 - distrMod-2.2/distrMod/R/0distrModOptions.R | 3 distrMod-2.2/distrMod/R/0distrModUtils.R | 43 ++- distrMod-2.2/distrMod/R/AllClass.R | 104 ++----- distrMod-2.2/distrMod/R/AllGeneric.R | 21 - distrMod-2.2/distrMod/R/AllPlot.R | 11 distrMod-2.2/distrMod/R/AllShow.R | 56 ++-- distrMod-2.2/distrMod/R/Confint-class.R | 8 distrMod-2.2/distrMod/R/Estimate.R | 43 ++- distrMod-2.2/distrMod/R/Estimator.R | 6 distrMod-2.2/distrMod/R/Expectation.R | 12 distrMod-2.2/distrMod/R/L2ParamFamily.R | 25 - distrMod-2.2/distrMod/R/MCEstimate.R |only distrMod-2.2/distrMod/R/MCEstimator.R | 9 distrMod-2.2/distrMod/R/MDEstimator.R | 18 - distrMod-2.2/distrMod/R/MLEstimator.R | 5 distrMod-2.2/distrMod/R/ParamFamParameter.R | 49 ++- distrMod-2.2/distrMod/R/ParamFamily.R | 32 ++ distrMod-2.2/distrMod/R/ProbFamily.R | 2 distrMod-2.2/distrMod/R/SimpleL2ParamFamilies.R | 4 distrMod-2.2/distrMod/R/Symmetry.R | 16 - distrMod-2.2/distrMod/R/confint.R | 2 distrMod-2.2/distrMod/R/internalMleCalc.R | 21 + distrMod-2.2/distrMod/R/mleCalc-methods.R | 92 +++++- distrMod-2.2/distrMod/R/modifyModel.R | 2 distrMod-2.2/distrMod/R/qqplot.R |only distrMod-2.2/distrMod/R/setAs.R | 11 distrMod-2.2/distrMod/demo/modelExp3.R | 2 distrMod-2.2/distrMod/inst/MASKING | 10 distrMod-2.2/distrMod/inst/NEWS | 118 ++++++++ distrMod-2.2/distrMod/inst/TOBEDONE |only distrMod-2.2/distrMod/inst/scripts/BetaFam.R | 84 ++++++ distrMod-2.2/distrMod/inst/scripts/PoisFam.R | 75 +++++ distrMod-2.2/distrMod/inst/scripts/censoredPois.R | 135 +++++++++- distrMod-2.2/distrMod/inst/scripts/distrModExample.R |only distrMod-2.2/distrMod/inst/scripts/distrModExample1.R |only distrMod-2.2/distrMod/inst/scripts/example_CvMMDE.R | 104 +++++++ distrMod-2.2/distrMod/inst/scripts/examples2.R | 189 +++++++++++++- distrMod-2.2/distrMod/inst/scripts/modelExp3.R | 48 +++ distrMod-2.2/distrMod/man/0distrMod-package.Rd | 32 +- distrMod-2.2/distrMod/man/BiasType-class.Rd | 2 distrMod-2.2/distrMod/man/Confint-class.Rd | 33 +- distrMod-2.2/distrMod/man/Estimate-class.Rd | 149 +++++++---- distrMod-2.2/distrMod/man/Estimator.Rd | 3 distrMod-2.2/distrMod/man/EvenSymmetric-class.Rd | 4 distrMod-2.2/distrMod/man/EvenSymmetric.Rd | 2 distrMod-2.2/distrMod/man/FunSymmList-class.Rd | 2 distrMod-2.2/distrMod/man/FunctionSymmetry-class.Rd | 6 distrMod-2.2/distrMod/man/GammaFamily.Rd | 2 distrMod-2.2/distrMod/man/GumbelLocationFamily.Rd | 2 distrMod-2.2/distrMod/man/L2GroupFamily-class.Rd | 34 +- distrMod-2.2/distrMod/man/L2LocationFamily-class.Rd | 36 +- distrMod-2.2/distrMod/man/L2LocationScaleFamily-class.Rd | 36 +- distrMod-2.2/distrMod/man/L2ParamFamily-class.Rd | 44 +-- distrMod-2.2/distrMod/man/L2ScaleFamily-class.Rd | 36 +- distrMod-2.2/distrMod/man/MCEstimate-class.Rd | 52 ++- distrMod-2.2/distrMod/man/MCEstimator.Rd | 10 distrMod-2.2/distrMod/man/MDEstimator.Rd | 20 + distrMod-2.2/distrMod/man/MLEstimator.Rd | 5 distrMod-2.2/distrMod/man/NonSymmetric-class.Rd | 4 distrMod-2.2/distrMod/man/NormType-class.Rd | 4 distrMod-2.2/distrMod/man/OddSymmetric-class.Rd | 4 distrMod-2.2/distrMod/man/OddSymmetric.Rd | 2 distrMod-2.2/distrMod/man/ParamFamParameter-class.Rd | 10 distrMod-2.2/distrMod/man/ParamFamily-class.Rd | 18 - distrMod-2.2/distrMod/man/ProbFamily-class.Rd | 8 distrMod-2.2/distrMod/man/QFnorm-class.Rd | 6 distrMod-2.2/distrMod/man/RiskType-class.Rd | 2 distrMod-2.2/distrMod/man/asBias-class.Rd | 6 distrMod-2.2/distrMod/man/asCov-class.Rd | 2 distrMod-2.2/distrMod/man/asGRisk-class.Rd | 6 distrMod-2.2/distrMod/man/asHampel-class.Rd | 6 distrMod-2.2/distrMod/man/asMSE-class.Rd | 6 distrMod-2.2/distrMod/man/asRisk-class.Rd | 2 distrMod-2.2/distrMod/man/asRiskwithBias-class.Rd | 6 distrMod-2.2/distrMod/man/asSemivar-class.Rd | 13 distrMod-2.2/distrMod/man/asUnOvShoot-class.Rd | 8 distrMod-2.2/distrMod/man/asymmetricBias-class.Rd | 4 distrMod-2.2/distrMod/man/confint-methods.Rd | 2 distrMod-2.2/distrMod/man/distrModOptions.Rd | 13 distrMod-2.2/distrMod/man/fiBias-class.Rd | 2 distrMod-2.2/distrMod/man/fiCov-class.Rd | 2 distrMod-2.2/distrMod/man/fiHampel-class.Rd | 4 distrMod-2.2/distrMod/man/fiMSE-class.Rd | 2 distrMod-2.2/distrMod/man/fiRisk-class.Rd | 2 distrMod-2.2/distrMod/man/fiUnOvShoot-class.Rd | 6 distrMod-2.2/distrMod/man/internalClassUnions-class.Rd | 9 distrMod-2.2/distrMod/man/internals-qqplot.Rd |only distrMod-2.2/distrMod/man/internals.Rd | 12 distrMod-2.2/distrMod/man/meRes.Rd | 10 distrMod-2.2/distrMod/man/mleCalc-methods.Rd | 7 distrMod-2.2/distrMod/man/onesidedBias-class.Rd | 6 distrMod-2.2/distrMod/man/qqplot.Rd |only distrMod-2.2/distrMod/man/symmetricBias-class.Rd | 2 distrMod-2.2/distrMod/man/trAsCov-class.Rd | 2 distrMod-2.2/distrMod/man/trFiCov-class.Rd | 2 distrMod-2.2/distrMod/man/trafo-methods.Rd | 4 distrMod-2.2/distrMod/man/trafoEst.Rd | 4 distrMod-2.2/distrMod/tests |only 118 files changed, 1544 insertions(+), 575 deletions(-)
Author: Matthias Kohl, Peter Ruckdeschel
Title: Extensions of package distr
Description: Extensions of package distr and some additional
functionality
Diff between distrEx versions 2.1 dated 2009-04-15 and 2.2 dated 2009-11-03
DESCRIPTION | 17 +- NAMESPACE | 5 R/AllClass.R | 54 ++++++ R/AllInitialize.R | 70 ++++++++ R/ClippedMoments.R | 11 - R/ConvexContamination.R | 27 +++ R/DiscreteMVDistribution.R | 3 R/Expectation.R | 249 +++++++++++++++++++++++++++++--- R/Functionals.R | 75 ++++++++- R/GPareto.R |only R/KolmogorovDist.R | 34 +--- R/Kurtosis.R | 54 ++++++ R/Skewness.R | 42 +++++ demo/Prognose.R | 2 inst/NEWS | 87 +++++++++++ inst/TOBEDONE |only man/0distrEx-package.Rd | 22 +- man/AbscontCondDistribution-class.Rd | 32 ++-- man/Condition-class.Rd | 2 man/DiscreteCondDistribution-class.Rd | 34 ++-- man/DiscreteMVDistribution-class.Rd | 22 +- man/DiscreteMVDistribution.Rd | 12 + man/E.Rd | 66 ++++++++ man/EuclCondition-class.Rd | 4 man/GPareto-class.Rd |only man/GPareto.Rd |only man/GParetoParameter-class.Rd |only man/Gumbel-class.Rd | 32 ++-- man/GumbelParameter-class.Rd | 6 man/LMParameter-class.Rd | 8 - man/MultivariateDistribution-class.Rd | 24 ++- man/Pareto-class.Rd | 36 +++- man/Pareto.Rd | 2 man/ParetoParameter-class.Rd | 6 man/PrognCondition-class.Rd | 4 man/UnivariateCondDistribution-class.Rd | 26 ++- man/Var.Rd | 30 +++ man/distrExConstants.Rd | 4 man/distrExOptions.Rd | 2 tests |only 40 files changed, 915 insertions(+), 189 deletions(-)
Author: Florian Camphausen, Matthias Kohl, Peter Ruckdeschel, Thomas
Stabla
Title: Object orientated implementation of distributions
Description: Object orientated implementation of distributions
Diff between distr versions 2.1.3 dated 2009-07-03 and 2.2 dated 2009-11-03
distr-2.1.3/distr/inst/doc/Rplots.pdf |only distr-2.1.3/distr/man/ContDistribution-class.Rd |only distr-2.1.3/distr/man/ContDistribution.Rd |only distr-2.2/distr/DESCRIPTION | 16 + distr-2.2/distr/NAMESPACE | 13 + distr-2.2/distr/R/0distrOptions.R | 5 distr-2.2/distr/R/AllClasses.R | 135 ++++++++++++++- distr-2.2/distr/R/AllGenerics.R | 27 ++- distr-2.2/distr/R/AllInitialize.R | 34 ++- distr-2.2/distr/R/CompoundDistribution.R | 17 + distr-2.2/distr/R/ContDistribution.R | 158 ++++++++++++++---- distr-2.2/distr/R/Convpow.r | 15 + distr-2.2/distr/R/DiscreteDistribution.R | 154 ++++++++++++++--- distr-2.2/distr/R/DistrList.R | 31 +++ distr-2.2/distr/R/DistrSymmList.R |only distr-2.2/distr/R/Distribution.R | 12 + distr-2.2/distr/R/ExtraConvolutionMethods.R | 5 distr-2.2/distr/R/Huberize.R | 8 distr-2.2/distr/R/LaplaceDistribution.R | 6 distr-2.2/distr/R/LatticeDistribution.R | 65 +++++-- distr-2.2/distr/R/NormalDistribution.R | 17 + distr-2.2/distr/R/PosDefSymmMatrix.R |only distr-2.2/distr/R/Symmetry.R |only distr-2.2/distr/R/Truncate.R | 25 ++ distr-2.2/distr/R/UnivarLebDecDistribution.R | 11 + distr-2.2/distr/R/UnivarMixingDistribution.R | 54 ++++++ distr-2.2/distr/R/bAcDcLcDistribution.R | 29 ++- distr-2.2/distr/R/bAffLinUnivarLebDecDistribution.R | 15 + distr-2.2/distr/R/internalUtils.R | 4 distr-2.2/distr/R/internalUtils_LCD.R | 17 + distr-2.2/distr/R/internalUtils_trunc.R | 4 distr-2.2/distr/R/internals-qqplot.R |only distr-2.2/distr/R/print-show-methods.R | 8 distr-2.2/distr/R/qqbounds.R |only distr-2.2/distr/R/qqplot.R |only distr-2.2/distr/R/setIsRelations.R | 15 - distr-2.2/distr/R/solve.R |only distr-2.2/distr/R/sqrt.R |only distr-2.2/distr/inst/MASKING | 29 ++- distr-2.2/distr/inst/NEWS | 62 +++++++ distr-2.2/distr/inst/TOBEDONE |only distr-2.2/distr/inst/doc/newDistributions.Rnw | 14 - distr-2.2/distr/inst/doc/newDistributions.pdf |binary distr-2.2/distr/man/0distr-package.Rd | 134 ++++++++++----- distr-2.2/distr/man/AbscontDistribution-class.Rd |only distr-2.2/distr/man/AbscontDistribution.Rd |only distr-2.2/distr/man/Arcsine-class.Rd | 28 +-- distr-2.2/distr/man/Beta-class.Rd | 30 ++- distr-2.2/distr/man/BetaParameter-class.Rd | 8 distr-2.2/distr/man/Binom-class.Rd | 32 ++- distr-2.2/distr/man/BinomParameter-class.Rd | 6 distr-2.2/distr/man/Cauchy-class.Rd | 30 ++- distr-2.2/distr/man/CauchyParameter-class.Rd | 7 distr-2.2/distr/man/Chisq-class.Rd | 30 ++- distr-2.2/distr/man/ChisqParameter-class.Rd | 6 distr-2.2/distr/man/CompoundDistribution-class.Rd | 36 ++-- distr-2.2/distr/man/DExp-class.Rd | 30 ++- distr-2.2/distr/man/Dirac-class.Rd | 34 ++- distr-2.2/distr/man/DiracParameter-class.Rd | 4 distr-2.2/distr/man/DiscreteDistribution-class.Rd | 56 +++--- distr-2.2/distr/man/DiscreteDistribution.Rd | 22 +- distr-2.2/distr/man/DistrList-class.Rd | 2 distr-2.2/distr/man/DistrList.Rd | 11 - distr-2.2/distr/man/DistrSymmList-class.Rd |only distr-2.2/distr/man/DistrSymmList.Rd |only distr-2.2/distr/man/Distribution-class.Rd | 29 ++- distr-2.2/distr/man/DistributionSymmetry-class.Rd |only distr-2.2/distr/man/EllipticalSymmetry-class.Rd |only distr-2.2/distr/man/EllipticalSymmetry.Rd |only distr-2.2/distr/man/EuclideanSpace-class.Rd | 4 distr-2.2/distr/man/Exp-class.Rd | 24 ++ distr-2.2/distr/man/ExpOrGammaOrChisq-class.Rd | 3 distr-2.2/distr/man/ExpParameter-class.Rd | 4 distr-2.2/distr/man/FParameter-class.Rd | 9 - distr-2.2/distr/man/Fd-class.Rd | 32 ++- distr-2.2/distr/man/GammaParameter-class.Rd | 6 distr-2.2/distr/man/Gammad-class.Rd | 31 ++- distr-2.2/distr/man/Geom-class.Rd | 32 ++- distr-2.2/distr/man/GeomParameter-class.Rd | 4 distr-2.2/distr/man/Hyper-class.Rd | 34 ++- distr-2.2/distr/man/HyperParameter-class.Rd | 8 distr-2.2/distr/man/Integer-class.Rd | 4 distr-2.2/distr/man/Lattice-class.Rd | 8 distr-2.2/distr/man/LatticeDistribution-class.Rd | 40 ++-- distr-2.2/distr/man/LatticeDistribution.Rd | 25 +- distr-2.2/distr/man/Lnorm-class.Rd | 30 ++- distr-2.2/distr/man/LnormParameter-class.Rd | 6 distr-2.2/distr/man/Logis-class.Rd | 30 ++- distr-2.2/distr/man/LogisParameter-class.Rd | 6 distr-2.2/distr/man/Math-methods.Rd | 8 distr-2.2/distr/man/Naturals-class.Rd | 4 distr-2.2/distr/man/Nbinom-class.Rd | 32 ++- distr-2.2/distr/man/NbinomParameter-class.Rd | 6 distr-2.2/distr/man/NoSymmetry-class.Rd |only distr-2.2/distr/man/NoSymmetry.Rd |only distr-2.2/distr/man/Norm-class.Rd | 30 ++- distr-2.2/distr/man/NormParameter-class.Rd | 6 distr-2.2/distr/man/Parameter-class.Rd | 2 distr-2.2/distr/man/Pois-class.Rd | 32 ++- distr-2.2/distr/man/PoisParameter-class.Rd | 4 distr-2.2/distr/man/PosDefSymmMatrix-class.Rd |only distr-2.2/distr/man/PosDefSymmMatrix.Rd |only distr-2.2/distr/man/Reals-class.Rd | 4 distr-2.2/distr/man/SphericalSymmetry-class.Rd |only distr-2.2/distr/man/SphericalSymmetry.Rd |only distr-2.2/distr/man/Symmetry-class.Rd |only distr-2.2/distr/man/TParameter-class.Rd | 6 distr-2.2/distr/man/Td-class.Rd | 30 ++- distr-2.2/distr/man/UniNormParameter-class.Rd | 6 distr-2.2/distr/man/Unif-class.Rd | 26 +- distr-2.2/distr/man/UnifParameter-class.Rd | 6 distr-2.2/distr/man/UnivarDistrList-class.Rd | 2 distr-2.2/distr/man/UnivarDistrList.Rd | 10 - distr-2.2/distr/man/UnivarLebDecDistribution-class.Rd | 66 ++++--- distr-2.2/distr/man/UnivarMixingDistribution-class.Rd | 45 +++-- distr-2.2/distr/man/UnivarMixingDistribution.Rd | 2 distr-2.2/distr/man/UnivariateDistribution-class.Rd | 30 ++- distr-2.2/distr/man/Weibull-class.Rd | 30 ++- distr-2.2/distr/man/WeibullParameter-class.Rd | 6 distr-2.2/distr/man/distroptions.Rd | 12 + distr-2.2/distr/man/internalClassUnions-class.Rd |only distr-2.2/distr/man/internals-qqplot.Rd |only distr-2.2/distr/man/internals.Rd | 2 distr-2.2/distr/man/operators-methods.Rd | 2 distr-2.2/distr/man/options.Rd | 6 distr-2.2/distr/man/plot-methods.Rd | 20 +- distr-2.2/distr/man/qqbounds.Rd |only distr-2.2/distr/man/qqplot.Rd |only distr-2.2/distr/man/rSpace-class.Rd | 2 distr-2.2/distr/man/solve-methods.Rd |only distr-2.2/distr/man/sqrt-methods.Rd |only distr-2.2/distr/tests |only 132 files changed, 1630 insertions(+), 687 deletions(-)
Author: Pin T. Ng
Title: Constrained B-splines -- outdated 1999 version
Description: Qualitatively Constrained (Regression) Smoothing via
Linear Programming. OUTDATED version based on He & Ng (1999),
the modified "non-simplex" algorithm of Bartels and Conn
(1980).
Diff between cobs99 versions 0.9-7 dated 2007-10-09 and 0.9-8 dated 2009-11-03
ChangeLog | 8 ++++++++ DESCRIPTION | 22 ++++++++++++---------- man/cobs.Rd | 6 +++--- man/cobsOld.Rd | 7 +++---- man/predict.cobs.Rd | 3 --- man/qbsks.Rd | 2 -- tests/small-ex.Rout.save | 4 ++-- tests/spline-ex.Rout.save | 24 ++++++++++++------------ 8 files changed, 40 insertions(+), 36 deletions(-)
Author: Henrik Bengtsson
Title: Analysis of large Affymetrix microarray data sets
Description: This package implements classes for files and sets of
files for various Affymetrix file formats, e.g.
AffymetrixCdfFile, AffymetrixCelFile, and AffymetrixCelSet.
These are designed to be memory efficient but still being fast.
The idea is to keep all data on file and only read data into
memory when needed. Clever caching mechanisms are used to
minimize the overhead of data IO. All of the above is hidden
in the package API and for the developer (and the end user),
the data is queried as if it lives in memory. With this design
it is only the diskspace that limits what number of arrays can
be analyzed.
Diff between aroma.affymetrix versions 1.2.0 dated 2009-09-10 and 1.3.0 dated 2009-11-03
aroma.affymetrix-1.2.0/aroma.affymetrix/man/fromFiles.AffymetrixFileSet.Rd |only aroma.affymetrix-1.3.0/aroma.affymetrix/DESCRIPTION | 26 - aroma.affymetrix-1.3.0/aroma.affymetrix/R/AffymetrixCdfFile.R | 6 aroma.affymetrix-1.3.0/aroma.affymetrix/R/AffymetrixCelFile.R | 7 aroma.affymetrix-1.3.0/aroma.affymetrix/R/AffymetrixCelSet.R | 27 - aroma.affymetrix-1.3.0/aroma.affymetrix/R/AffymetrixCelSet.extractSnpFeatureSet.R |only aroma.affymetrix-1.3.0/aroma.affymetrix/R/AffymetrixCelSet.importFromDChip.R | 6 aroma.affymetrix-1.3.0/aroma.affymetrix/R/AffymetrixCelSet.xtras.R | 2 aroma.affymetrix-1.3.0/aroma.affymetrix/R/AffymetrixCelSetTuple.R | 2 aroma.affymetrix-1.3.0/aroma.affymetrix/R/AffymetrixCnChpFile.R | 6 aroma.affymetrix-1.3.0/aroma.affymetrix/R/AffymetrixCnChpSet.R | 11 aroma.affymetrix-1.3.0/aroma.affymetrix/R/AffymetrixCnChpSet.extras.R | 2 aroma.affymetrix-1.3.0/aroma.affymetrix/R/AffymetrixCsvFile.R | 6 aroma.affymetrix-1.3.0/aroma.affymetrix/R/AffymetrixFileSet.R | 12 aroma.affymetrix-1.3.0/aroma.affymetrix/R/AffymetrixProbeTabFile.R | 9 aroma.affymetrix-1.3.0/aroma.affymetrix/R/AffymetrixTsvFile.R | 5 aroma.affymetrix-1.3.0/aroma.affymetrix/R/AromaCellMatchScoreFile.R | 5 aroma.affymetrix-1.3.0/aroma.affymetrix/R/AromaCellSequenceFile.AFFX.R | 56 +++ aroma.affymetrix-1.3.0/aroma.affymetrix/R/AromaUfcFile.R | 7 aroma.affymetrix-1.3.0/aroma.affymetrix/R/AromaUflFile.R | 5 aroma.affymetrix-1.3.0/aroma.affymetrix/R/AromaUnitGcContentFile.R | 5 aroma.affymetrix-1.3.0/aroma.affymetrix/R/ChipEffectGroupMerge.R | 2 aroma.affymetrix-1.3.0/aroma.affymetrix/R/ChipEffectSet.R | 4 aroma.affymetrix-1.3.0/aroma.affymetrix/R/CnChipEffectSet.R | 4 aroma.affymetrix-1.3.0/aroma.affymetrix/R/CnChipEffectSet.importFromApt.R | 2 aroma.affymetrix-1.3.0/aroma.affymetrix/R/CnChipEffectSet.importFromDChip.R | 2 aroma.affymetrix-1.3.0/aroma.affymetrix/R/CnPlm.R | 4 aroma.affymetrix-1.3.0/aroma.affymetrix/R/CnagCfhFile.R | 7 aroma.affymetrix-1.3.0/aroma.affymetrix/R/CnagCfhSet.R | 24 - aroma.affymetrix-1.3.0/aroma.affymetrix/R/CrlmmModel.R | 6 aroma.affymetrix-1.3.0/aroma.affymetrix/R/CrlmmParametersSet.R | 6 aroma.affymetrix-1.3.0/aroma.affymetrix/R/DChipCdfBinFile.R | 1 aroma.affymetrix-1.3.0/aroma.affymetrix/R/DChipDcpFile.R | 6 aroma.affymetrix-1.3.0/aroma.affymetrix/R/DChipDcpSet.R | 11 aroma.affymetrix-1.3.0/aroma.affymetrix/R/DChipDcpSet.extras.R | 2 aroma.affymetrix-1.3.0/aroma.affymetrix/R/ExonChipEffectSet.R | 4 aroma.affymetrix-1.3.0/aroma.affymetrix/R/ExonRmaPlm.R | 12 aroma.affymetrix-1.3.0/aroma.affymetrix/R/FirmaSet.R | 4 aroma.affymetrix-1.3.0/aroma.affymetrix/R/PdInfo2Cdf.R | 162 ++++++---- aroma.affymetrix-1.3.0/aroma.affymetrix/R/ProbeLevelModel.calculateResiduals.R | 2 aroma.affymetrix-1.3.0/aroma.affymetrix/R/QualityAssessmentModel.R | 6 aroma.affymetrix-1.3.0/aroma.affymetrix/R/ResidualSet.R | 4 aroma.affymetrix-1.3.0/aroma.affymetrix/R/RmaPlm.R | 128 +++++-- aroma.affymetrix-1.3.0/aroma.affymetrix/R/SnpChipEffectSet.R | 4 aroma.affymetrix-1.3.0/aroma.affymetrix/R/SnpPlm.R | 6 aroma.affymetrix-1.3.0/aroma.affymetrix/R/Transform.R | 4 aroma.affymetrix-1.3.0/aroma.affymetrix/R/WeightsSet.R | 4 aroma.affymetrix-1.3.0/aroma.affymetrix/incl/999.missingdocs.txt | 18 + aroma.affymetrix-1.3.0/aroma.affymetrix/inst/CITATION | 2 aroma.affymetrix-1.3.0/aroma.affymetrix/inst/NEWS | 36 ++ aroma.affymetrix-1.3.0/aroma.affymetrix/inst/testScripts/replication/chipTypes/HG-U133_Plus_2/extractAffyBatch.R |only aroma.affymetrix-1.3.0/aroma.affymetrix/inst/testScripts/replication/chipTypes/Mapping50K_Hind240,Xba240/20091016,extractSnpFeatureSet.R |only aroma.affymetrix-1.3.0/aroma.affymetrix/inst/testScripts/system/chipTypes/GenomeWideSNP_6/test20090901,6.0,CRMAv2,ASCN,TumorBoost.R | 15 aroma.affymetrix-1.3.0/aroma.affymetrix/inst/testScripts/system/chipTypes/HuEx-1_0-st-v2/test20090927,gcrmabg.R |only aroma.affymetrix-1.3.0/aroma.affymetrix/inst/testScripts/system/chipTypes/HuGene-1_0-st-v1 |only aroma.affymetrix-1.3.0/aroma.affymetrix/man/AffymetrixCdfFile.Rd | 27 - aroma.affymetrix-1.3.0/aroma.affymetrix/man/AffymetrixCelFile.Rd | 21 - aroma.affymetrix-1.3.0/aroma.affymetrix/man/AffymetrixCelSet.Rd | 21 - aroma.affymetrix-1.3.0/aroma.affymetrix/man/AffymetrixCnChpSet.Rd | 22 - aroma.affymetrix-1.3.0/aroma.affymetrix/man/AffymetrixFile.Rd | 17 - aroma.affymetrix-1.3.0/aroma.affymetrix/man/AffymetrixFileSet.Rd | 18 - aroma.affymetrix-1.3.0/aroma.affymetrix/man/AffymetrixProbeTabFile.Rd | 19 - aroma.affymetrix-1.3.0/aroma.affymetrix/man/AromaChipTypeAnnotationFile.Rd | 19 - aroma.affymetrix-1.3.0/aroma.affymetrix/man/ChipEffectFile.Rd | 29 + aroma.affymetrix-1.3.0/aroma.affymetrix/man/ChipEffectSet.Rd | 25 - aroma.affymetrix-1.3.0/aroma.affymetrix/man/CnChipEffectFile.Rd | 31 + aroma.affymetrix-1.3.0/aroma.affymetrix/man/CnChipEffectSet.Rd | 33 +- aroma.affymetrix-1.3.0/aroma.affymetrix/man/CnPlm.Rd | 8 aroma.affymetrix-1.3.0/aroma.affymetrix/man/CnProbeAffinityFile.Rd | 31 + aroma.affymetrix-1.3.0/aroma.affymetrix/man/CnagCfhFile.Rd | 17 - aroma.affymetrix-1.3.0/aroma.affymetrix/man/CnagCfhSet.Rd | 15 aroma.affymetrix-1.3.0/aroma.affymetrix/man/CrlmmParametersFile.Rd | 21 - aroma.affymetrix-1.3.0/aroma.affymetrix/man/CrlmmParametersSet.Rd | 19 - aroma.affymetrix-1.3.0/aroma.affymetrix/man/DChipCdfBinFile.Rd | 23 - aroma.affymetrix-1.3.0/aroma.affymetrix/man/DChipDcpFile.Rd | 17 - aroma.affymetrix-1.3.0/aroma.affymetrix/man/DChipDcpSet.Rd | 22 - aroma.affymetrix-1.3.0/aroma.affymetrix/man/DChipGenomeInformation.Rd | 15 aroma.affymetrix-1.3.0/aroma.affymetrix/man/DChipSnpInformation.Rd | 15 aroma.affymetrix-1.3.0/aroma.affymetrix/man/ExonChipEffectFile.Rd | 29 + aroma.affymetrix-1.3.0/aroma.affymetrix/man/ExonChipEffectSet.Rd | 29 + aroma.affymetrix-1.3.0/aroma.affymetrix/man/ExonProbeAffinityFile.Rd | 29 + aroma.affymetrix-1.3.0/aroma.affymetrix/man/ExonRmaPlm.Rd | 14 aroma.affymetrix-1.3.0/aroma.affymetrix/man/FirmaFile.Rd | 27 - aroma.affymetrix-1.3.0/aroma.affymetrix/man/FirmaSet.Rd | 25 - aroma.affymetrix-1.3.0/aroma.affymetrix/man/GenomeInformation.Rd | 15 aroma.affymetrix-1.3.0/aroma.affymetrix/man/HetLogAddCnPlm.Rd | 4 aroma.affymetrix-1.3.0/aroma.affymetrix/man/HetLogAddPlm.Rd | 6 aroma.affymetrix-1.3.0/aroma.affymetrix/man/HetLogAddSnpPlm.Rd | 4 aroma.affymetrix-1.3.0/aroma.affymetrix/man/Model.Rd | 2 aroma.affymetrix-1.3.0/aroma.affymetrix/man/MultiArrayUnitModel.Rd | 2 aroma.affymetrix-1.3.0/aroma.affymetrix/man/Non-documented_objects.Rd | 29 + aroma.affymetrix-1.3.0/aroma.affymetrix/man/ParameterCelFile.Rd | 27 - aroma.affymetrix-1.3.0/aroma.affymetrix/man/ParameterCelSet.Rd | 23 - aroma.affymetrix-1.3.0/aroma.affymetrix/man/ProbeAffinityFile.Rd | 29 + aroma.affymetrix-1.3.0/aroma.affymetrix/man/ProbeLevelModel.Rd | 2 aroma.affymetrix-1.3.0/aroma.affymetrix/man/QualityAssessmentFile.Rd | 25 - aroma.affymetrix-1.3.0/aroma.affymetrix/man/QualityAssessmentSet.Rd | 23 - aroma.affymetrix-1.3.0/aroma.affymetrix/man/ResidualFile.Rd | 27 - aroma.affymetrix-1.3.0/aroma.affymetrix/man/ResidualSet.Rd | 23 - aroma.affymetrix-1.3.0/aroma.affymetrix/man/RmaCnPlm.Rd | 4 aroma.affymetrix-1.3.0/aroma.affymetrix/man/RmaPlm.Rd | 5 aroma.affymetrix-1.3.0/aroma.affymetrix/man/RmaSnpPlm.Rd | 4 aroma.affymetrix-1.3.0/aroma.affymetrix/man/SnpChipEffectFile.Rd | 31 + aroma.affymetrix-1.3.0/aroma.affymetrix/man/SnpChipEffectSet.Rd | 29 + aroma.affymetrix-1.3.0/aroma.affymetrix/man/SnpInformation.Rd | 15 aroma.affymetrix-1.3.0/aroma.affymetrix/man/SnpPlm.Rd | 12 aroma.affymetrix-1.3.0/aroma.affymetrix/man/SnpProbeAffinityFile.Rd | 31 + aroma.affymetrix-1.3.0/aroma.affymetrix/man/UgpGenomeInformation.Rd | 15 aroma.affymetrix-1.3.0/aroma.affymetrix/man/UnitModel.Rd | 2 aroma.affymetrix-1.3.0/aroma.affymetrix/man/WeightsFile.Rd | 27 - aroma.affymetrix-1.3.0/aroma.affymetrix/man/WeightsSet.Rd | 23 - aroma.affymetrix-1.3.0/aroma.affymetrix/man/byPath.AffymetrixFileSet.Rd |only aroma.affymetrix-1.3.0/aroma.affymetrix/man/getResiduals.QualityAssessmentModel.Rd | 2 aroma.affymetrix-1.3.0/aroma.affymetrix/man/importFromDChip.AffymetrixCelSet.Rd | 2 aroma.affymetrix-1.3.0/aroma.affymetrix/man/isDuplicated.AffymetrixCelSet.Rd | 14 aroma.affymetrix-1.3.0/aroma.affymetrix/man/isDuplicated.CnagCfhSet.Rd | 14 116 files changed, 1144 insertions(+), 662 deletions(-)
More information about aroma.affymetrix at CRAN
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Author: Gavin L. Simpson, Jari Oksanen
Title: Analogue and weighted averaging methods for palaeoecology
Description: Fits Modern Analogue Technique and Weighted Averaging
transfer function models for prediction of environmental data
from species data, and related methods used in palaeoecology.
Diff between analogue versions 0.6-8 dated 2009-05-07 and 0.6-21 dated 2009-11-03
DESCRIPTION | 10 +- R/Stratiplot.R | 41 +++++++- R/Stratiplot.formula.R | 14 +- R/deshrink.R |only R/deshrinkPred.R |only R/fixUpTol.R |only R/internal.R | 66 +++++++------ R/join.R | 119 ++++++++++++++++------- R/predict.wa.R | 235 ++++++++++++++++++++++++++++++----------------- R/roc.R | 28 ++++- R/tran.R | 42 ++++++-- R/wa.R | 63 ++++-------- R/wa.formula.R | 6 + R/zzz.R | 2 inst/ChangeLog | 121 +++++++++++++++++++++++- man/Stratiplot.Rd | 44 +++++--- man/analogue-internal.Rd | 11 +- man/deshrink.Rd |only man/join.Rd | 43 ++++++++ man/panel.Stratiplot.Rd | 2 man/roc.Rd | 18 +++ man/stdError.Rd | 2 man/tran.Rd | 60 ++++++++++-- man/wa.Rd | 19 ++- src |only 25 files changed, 679 insertions(+), 267 deletions(-)
Author: Daniel Chessel, Anne-Beatrice Dufour
Title: Analysis of Ecological Data : Exploratory and Euclidean methods
in Environmental sciences
Description: Multivariate data analysis and graphical display.
Diff between ade4 versions 1.4-11 dated 2009-04-04 and 1.4-13 dated 2009-11-03
ChangeLog | 97 ++++++++++++++++++++++++++++++++ DESCRIPTION | 11 +-- R/apqe.R |only R/area.plot.R | 2 R/dist.binary.R | 12 +++- R/dist.ktab.R |only R/dudi.R | 4 - R/kdisteuclid.R | 12 +--- R/mdpcoa.R |only R/newick2phylog.R | 41 ++++++------- R/originality.R | 135 ++++++++++++++++++++++++++++----------------- R/phylog.R | 18 +++--- R/plot.phylog.R | 8 +- R/pta.R | 6 +- data/macroloire.rda |only data/meaudret.rda |binary data/rhizobium.rda |only data/toxicity.rda |binary data/woangers.rda |only man/apqe.Rd |only man/dist.binary.Rd | 2 man/dist.ktab.Rd |only man/macroloire.Rd |only man/mdpcoa.Rd |only man/meau.Rd | 18 ++++-- man/meaudret.Rd | 17 ++++- man/multispati.Rd | 2 man/multispati.randtest.Rd | 2 man/multispati.rtest.Rd | 2 man/originality.Rd | 19 ++++-- man/rhizobium.Rd |only man/s.value.Rd | 2 man/scatter.dudi.Rd | 3 + man/toxicity.Rd | 6 +- man/variance.phylog.Rd | 2 man/woangers.Rd |only 36 files changed, 290 insertions(+), 131 deletions(-)
Author: Alexis Gabadinho
Title: Sequences and trajectories mining for social scientists
Description: This package is a toolbox for sequence manipulation,
description, rendering and more generally sequence data mining
in the field of social sciences. Though it is primarily
intended for analyzing state or event sequences that describe
life courses such as family formation histories or professional
careers its features apply indeed also to many other kinds of
categorical sequence data. It accepts as input many different
sequence representations and provides tools for translating
sequences from one format to another. It offers several
statistical functions for describing and rendering sequences,
for computing distances between sequences with different
metrics among which optimal matching, the longest common prefix
and the longest common subsequence, and simple functions for
extracting the most frequent subsequences and identifying the
most discriminating ones among them. A user's guide can be
found on TraMineR's web page.
Diff between TraMineR versions 1.4 dated 2009-08-06 and 1.4-1 dated 2009-11-03
TraMineR-1.4-1/TraMineR/DESCRIPTION | 8 TraMineR-1.4-1/TraMineR/NAMESPACE | 7 TraMineR-1.4-1/TraMineR/NEWS | 74 +++-- TraMineR-1.4-1/TraMineR/R/BIOSPELL_to_STS.R | 34 +- TraMineR-1.4-1/TraMineR/R/Levenshtein.R | 8 TraMineR-1.4-1/TraMineR/R/diss.rep-methods.R |only TraMineR-1.4-1/TraMineR/R/dissassoc.R | 12 TraMineR-1.4-1/TraMineR/R/dissmfac.R | 10 TraMineR-1.4-1/TraMineR/R/dissrep.R |only TraMineR-1.4-1/TraMineR/R/normdist.R | 5 TraMineR-1.4-1/TraMineR/R/plot.stslist.R | 20 + TraMineR-1.4-1/TraMineR/R/plot.stslist.rep.R | 12 TraMineR-1.4-1/TraMineR/R/seqdiff.R | 2 TraMineR-1.4-1/TraMineR/R/seqdist.R | 6 TraMineR-1.4-1/TraMineR/R/seqecmpgroup.R | 12 TraMineR-1.4-1/TraMineR/R/seqecreate.R | 225 +++++++++------- TraMineR-1.4-1/TraMineR/R/seqerules.R | 174 +++++------- TraMineR-1.4-1/TraMineR/R/seqplot.R | 8 TraMineR-1.4-1/TraMineR/R/seqrep.R | 259 ++----------------- TraMineR-1.4-1/TraMineR/R/stslist.rep-methods.R | 19 - TraMineR-1.4-1/TraMineR/R/subseqelist.R | 1 TraMineR-1.4-1/TraMineR/inst/doc |only TraMineR-1.4-1/TraMineR/man/alphabet.Rd | 74 ++--- TraMineR-1.4-1/TraMineR/man/biofam.Rd | 16 - TraMineR-1.4-1/TraMineR/man/cpal.Rd | 80 ++--- TraMineR-1.4-1/TraMineR/man/dissmfac.Rd | 7 TraMineR-1.4-1/TraMineR/man/dissrep.Rd |only TraMineR-1.4-1/TraMineR/man/mvad.Rd | 6 TraMineR-1.4-1/TraMineR/man/plot.subseqelistchisq.Rd | 6 TraMineR-1.4-1/TraMineR/man/seqST.Rd | 106 +++---- TraMineR-1.4-1/TraMineR/man/seqcomp.Rd | 64 ++-- TraMineR-1.4-1/TraMineR/man/seqdiff.Rd | 28 +- TraMineR-1.4-1/TraMineR/man/seqdistmc.Rd | 4 TraMineR-1.4-1/TraMineR/man/seqefsub.Rd | 2 TraMineR-1.4-1/TraMineR/man/seqgen.Rd | 50 +-- TraMineR-1.4-1/TraMineR/man/seqplot.Rd | 48 +-- TraMineR-1.4-1/TraMineR/man/seqrep.Rd | 106 +++++-- TraMineR-1.4-1/TraMineR/src/TraMineR.h | 7 TraMineR-1.4-1/TraMineR/src/distancefunctions.cpp | 9 TraMineR-1.4-1/TraMineR/src/eventseq.cpp | 11 TraMineR-1.4-1/TraMineR/src/eventseq.h | 22 + TraMineR-1.4-1/TraMineR/src/saltt.cpp | 2 TraMineR-1.4-1/TraMineR/src/seqedist.cpp | 225 ++++++++++++---- TraMineR-1.4-1/TraMineR/src/tmrsequence.cpp | 58 ++++ TraMineR-1.4/TraMineR/R/TSE_to_STS.R |only 45 files changed, 985 insertions(+), 842 deletions(-)
Author: Sergej Potapov
Title: Trees WIth eXtra splits
Description: Trees with extra splits
Diff between TWIX versions 0.2.6 dated 2008-11-28 and 0.2.10 dated 2009-11-03
TWIX-0.2.10/TWIX/DESCRIPTION | 22 - TWIX-0.2.10/TWIX/NAMESPACE | 9 TWIX-0.2.10/TWIX/R/bagg.boottwix.R | 6 TWIX-0.2.10/TWIX/R/boottwix.R | 119 ++++- TWIX-0.2.10/TWIX/R/get.splitvar.R | 2 TWIX-0.2.10/TWIX/R/get.tree.R | 77 +-- TWIX-0.2.10/TWIX/R/impor.R | 19 TWIX-0.2.10/TWIX/R/plot.twix.R | 215 ++++----- TWIX-0.2.10/TWIX/R/predict.bootwix.R | 66 ++- TWIX-0.2.10/TWIX/R/predict.bundl.R |only TWIX-0.2.10/TWIX/R/predict.twix.R | 14 TWIX-0.2.10/TWIX/R/print.padj.tree.R | 44 +- TWIX-0.2.10/TWIX/R/print.single.tree.R | 48 +- TWIX-0.2.10/TWIX/R/print.twix.R | 2 TWIX-0.2.10/TWIX/R/s_b.padj.R |only TWIX-0.2.10/TWIX/R/sp.bagg.R | 605 ++++++---------------------- TWIX-0.2.10/TWIX/R/sp.slave.R | 237 ++--------- TWIX-0.2.10/TWIX/R/splitt.cross.R |only TWIX-0.2.10/TWIX/R/splitt.deviance.R | 277 ++++++++---- TWIX-0.2.10/TWIX/R/splitt.padj.R | 16 TWIX-0.2.10/TWIX/R/trace.plot.R | 4 TWIX-0.2.10/TWIX/R/tuneTWIX.R | 321 ++++++++++++++ TWIX-0.2.10/TWIX/R/twix.R | 646 ++++++------------------------ TWIX-0.2.10/TWIX/R/utils.R |only TWIX-0.2.10/TWIX/man/Devplot.Rd | 4 TWIX-0.2.10/TWIX/man/bagg.default.Rd | 11 TWIX-0.2.10/TWIX/man/bootwix.Rd | 106 +++- TWIX-0.2.10/TWIX/man/deviance.twix.Rd | 2 TWIX-0.2.10/TWIX/man/export.Rd | 2 TWIX-0.2.10/TWIX/man/fullrks.Rd | 4 TWIX-0.2.10/TWIX/man/plot.twix.Rd | 9 TWIX-0.2.10/TWIX/man/predict.twix.Rd | 3 TWIX-0.2.10/TWIX/man/print.id.tree.Rd | 2 TWIX-0.2.10/TWIX/man/print.single.tree.Rd | 2 TWIX-0.2.10/TWIX/man/print.twix.Rd | 2 TWIX-0.2.10/TWIX/man/scree.plot.Rd | 2 TWIX-0.2.10/TWIX/man/splitt_dev.Rd |only TWIX-0.2.10/TWIX/man/splitt_padj.Rd | 6 TWIX-0.2.10/TWIX/man/summary.twix.Rd | 2 TWIX-0.2.10/TWIX/man/trace.plot.Rd | 4 TWIX-0.2.10/TWIX/man/tuneTWIX.Rd | 57 ++ TWIX-0.2.10/TWIX/man/twix.Rd | 83 +-- TWIX-0.2.10/TWIX/src/Devleaf.c | 30 - TWIX-0.2.10/TWIX/src/Devleaf.h | 2 TWIX-0.2.10/TWIX/src/important.c | 85 +-- TWIX-0.2.10/TWIX/src/maxstat.c | 134 +++--- TWIX-0.2.10/TWIX/src/maxstat.h |only TWIX-0.2.10/TWIX/src/pLausen94.c | 25 - TWIX-0.2.10/TWIX/src/pLausen94.h | 1 TWIX-0.2.10/TWIX/src/predict.c |only TWIX-0.2.10/TWIX/src/split-sum.c | 141 ++---- TWIX-0.2.10/TWIX/src/split-sum_cr.c | 122 ++--- TWIX-0.2.10/TWIX/src/split_boot.c |only TWIX-0.2.10/TWIX/src/split_boot.h |only TWIX-0.2.10/TWIX/src/split_cat.c | 243 ++++++----- TWIX-0.2.10/TWIX/src/split_cat.h |only TWIX-0.2.10/TWIX/src/split_cross.c | 132 +++--- TWIX-0.2.10/TWIX/src/split_int.c |only TWIX-0.2.10/TWIX/src/split_num.c |only TWIX-0.2.10/TWIX/src/split_rule.c | 457 +++++++++++++++++---- TWIX-0.2.10/TWIX/src/tw_table.c | 84 +-- TWIX-0.2.10/TWIX/src/tw_table.h | 3 TWIX-0.2.10/TWIX/src/utils.c | 204 +++++++++ TWIX-0.2.10/TWIX/src/utils.h | 14 TWIX-0.2.6/TWIX/R/nlogn.R |only TWIX-0.2.6/TWIX/R/predict.boot.R |only TWIX-0.2.6/TWIX/R/sb.padj.R |only TWIX-0.2.6/TWIX/clean.sh |only TWIX-0.2.6/TWIX/man/splitt.Rd |only TWIX-0.2.6/TWIX/src/pred.c |only TWIX-0.2.6/TWIX/src/split_single.c |only 71 files changed, 2458 insertions(+), 2269 deletions(-)
Author: Peter Ruckdeschel
Title: Utilities for Sweave together with TeX listings package
Description: provides utilities for defining R / Rd as
Tex-package-listings "language" and including R / Rd source
file (sniplets) copied from R-forge in its most recent version
(or another url) thereby avoiding inconsistencies between
vignette and documented source code
Diff between SweaveListingUtils versions 0.3.3 dated 2009-07-31 and 0.4 dated 2009-11-03
SweaveListingUtils-0.3.3/SweaveListingUtils/inst/try/try.Rtex.rnw |only SweaveListingUtils-0.3.3/SweaveListingUtils/inst/try/try.aux |only SweaveListingUtils-0.3.3/SweaveListingUtils/inst/try/try.log |only SweaveListingUtils-0.3.3/SweaveListingUtils/inst/try/try.nav |only SweaveListingUtils-0.3.3/SweaveListingUtils/inst/try/try.out |only SweaveListingUtils-0.3.3/SweaveListingUtils/inst/try/try.pdf |only SweaveListingUtils-0.3.3/SweaveListingUtils/inst/try/try.snm |only SweaveListingUtils-0.3.3/SweaveListingUtils/inst/try/try.toc |only SweaveListingUtils-0.3.3/SweaveListingUtils/inst/try/try.vrb |only SweaveListingUtils-0.4/SweaveListingUtils/DESCRIPTION | 17 SweaveListingUtils-0.4/SweaveListingUtils/NAMESPACE | 1 SweaveListingUtils-0.4/SweaveListingUtils/R/SweaveListingOptions.R | 10 SweaveListingUtils-0.4/SweaveListingUtils/R/SweaveListingUtils.R | 506 +++------ SweaveListingUtils-0.4/SweaveListingUtils/R/keywordsStyle.R | 47 SweaveListingUtils-0.4/SweaveListingUtils/R/lstset.R |only SweaveListingUtils-0.4/SweaveListingUtils/R/taglist.R |only SweaveListingUtils-0.4/SweaveListingUtils/inst/NEWS | 74 + SweaveListingUtils-0.4/SweaveListingUtils/inst/TOBEDONE |only SweaveListingUtils-0.4/SweaveListingUtils/inst/doc/AllClass.tex | 2 SweaveListingUtils-0.4/SweaveListingUtils/inst/doc/BinomParam.tex | 2 SweaveListingUtils-0.4/SweaveListingUtils/inst/doc/ExampleSweaveListingUtils.Rnw | 33 SweaveListingUtils-0.4/SweaveListingUtils/inst/doc/ExampleSweaveListingUtils.pdf |binary SweaveListingUtils-0.4/SweaveListingUtils/inst/doc/altPrep.tex | 2 SweaveListingUtils-0.4/SweaveListingUtils/inst/doc/locChange.tex | 2 SweaveListingUtils-0.4/SweaveListingUtils/inst/doc/preamble.tex | 4 SweaveListingUtils-0.4/SweaveListingUtils/inst/doc/preamble2.tex | 14 SweaveListingUtils-0.4/SweaveListingUtils/inst/doc/reqdistr.tex | 2 SweaveListingUtils-0.4/SweaveListingUtils/inst/try/algorithm2e.sty |only SweaveListingUtils-0.4/SweaveListingUtils/inst/try/fancyhdr.sty |only SweaveListingUtils-0.4/SweaveListingUtils/inst/try/lastpage.sty |only SweaveListingUtils-0.4/SweaveListingUtils/inst/try/test.Rnw |only SweaveListingUtils-0.4/SweaveListingUtils/inst/try/try.Rtex | 6 SweaveListingUtils-0.4/SweaveListingUtils/inst/try/try.tex | 555 ++++++++++ SweaveListingUtils-0.4/SweaveListingUtils/inst/try/try2.Rnw |only SweaveListingUtils-0.4/SweaveListingUtils/inst/try/try2.tex |only SweaveListingUtils-0.4/SweaveListingUtils/inst/try/try_Hausman.tex |only SweaveListingUtils-0.4/SweaveListingUtils/inst/try/try_Hausmann.Rnw |only SweaveListingUtils-0.4/SweaveListingUtils/man/0SweaveListingUtils-package.Rd | 44 SweaveListingUtils-0.4/SweaveListingUtils/man/SweaveListingOptions.Rd | 24 SweaveListingUtils-0.4/SweaveListingUtils/man/SweaveListingPreparations.Rd | 13 SweaveListingUtils-0.4/SweaveListingUtils/man/copySourceFromRForge.Rd | 8 SweaveListingUtils-0.4/SweaveListingUtils/man/library.Rd | 9 SweaveListingUtils-0.4/SweaveListingUtils/man/lstset.Rd | 67 - SweaveListingUtils-0.4/SweaveListingUtils/man/setToBeDefinedPkgs.Rd | 2 SweaveListingUtils-0.4/SweaveListingUtils/tests |only 45 files changed, 1029 insertions(+), 415 deletions(-)
More information about SweaveListingUtils at CRAN
Permanent link
Author: Dominick Samperi
Title: Demo Package for Rcpp R/C++ Object Mapping and Library
Description: The Rcpp class library enables C++ to speak the language
of R. The library maps the most commonly used R data structures
to C++ classes. This includes vectors, matrices, factors,
dates, data frames, time series, and functions. R can call C++
functions, and C++ objects can call R functions, and the
parameters and return values can be of any of the types just
mentioned. This package serves two roles: 1. it serves as a
demo package for Rcpp, and 2. it serves as a template for the
creation of new packages that use the Rcpp library (and also
for packages that do not). An important goal of the library is
to support the creation of high-performance packages that do
heavy computations on large data sets where a hybrid R/C++
strategy is the best fit. See the document RcppDoc.pdf for more
information.
Diff between RcppTemplate versions 5.2 dated 2006-11-28 and 6.0 dated 2009-11-03
RcppTemplate-5.2/RcppTemplate/INDEX |only RcppTemplate-5.2/RcppTemplate/R/RcppTemplateVersion.R |only RcppTemplate-5.2/RcppTemplate/RcppSrc/LICENSE-Rcpp.txt |only RcppTemplate-5.2/RcppTemplate/demo/ReadRcppAPI.R |only RcppTemplate-5.2/RcppTemplate/demo/SineCurve.R |only RcppTemplate-5.2/RcppTemplate/inst/doc/MakeWinBin.bat |only RcppTemplate-5.2/RcppTemplate/inst/doc/RcppAPI.Rnw |only RcppTemplate-5.2/RcppTemplate/inst/doc/RcppAPI.pdf |only RcppTemplate-5.2/RcppTemplate/man/RcppTemplateDemo.Rd |only RcppTemplate-5.2/RcppTemplate/man/RcppTemplateVersion.Rd |only RcppTemplate-5.2/RcppTemplate/src/Makefile.win |only RcppTemplate-6.0/RcppTemplate/.test |only RcppTemplate-6.0/RcppTemplate/DESCRIPTION | 34 RcppTemplate-6.0/RcppTemplate/NAMESPACE | 13 RcppTemplate-6.0/RcppTemplate/NEWS |only RcppTemplate-6.0/RcppTemplate/R/DateNum.R |only RcppTemplate-6.0/RcppTemplate/R/RcppDocs.R |only RcppTemplate-6.0/RcppTemplate/R/RcppExample.R | 9 RcppTemplate-6.0/RcppTemplate/R/zzz.R | 33 RcppTemplate-6.0/RcppTemplate/RcppSrc/Makefile | 9 RcppTemplate-6.0/RcppTemplate/RcppSrc/Makefile.win | 3 RcppTemplate-6.0/RcppTemplate/RcppSrc/Rcpp.cpp | 1637 +++- RcppTemplate-6.0/RcppTemplate/RcppSrc/Rcpp.hpp | 1121 ++- RcppTemplate-6.0/RcppTemplate/cleanup | 2 RcppTemplate-6.0/RcppTemplate/cleanup.win |only RcppTemplate-6.0/RcppTemplate/configure | 5118 ++++++++++---- RcppTemplate-6.0/RcppTemplate/configure.in | 39 RcppTemplate-6.0/RcppTemplate/configure.win | 12 RcppTemplate-6.0/RcppTemplate/demo/00Index | 3 RcppTemplate-6.0/RcppTemplate/demo/Peacock.R |only RcppTemplate-6.0/RcppTemplate/inst/LICENSE-Rcpp.txt | 27 RcppTemplate-6.0/RcppTemplate/inst/LICENSE.txt |only RcppTemplate-6.0/RcppTemplate/inst/datasets |only RcppTemplate-6.0/RcppTemplate/inst/doc/Makefile |only RcppTemplate-6.0/RcppTemplate/inst/doc/QuantLib |only RcppTemplate-6.0/RcppTemplate/inst/doc/QuickReference.txt |only RcppTemplate-6.0/RcppTemplate/inst/doc/RcppDoc.Rnw |only RcppTemplate-6.0/RcppTemplate/inst/doc/RcppDoc.pdf |only RcppTemplate-6.0/RcppTemplate/inst/images |only RcppTemplate-6.0/RcppTemplate/inst/libs |only RcppTemplate-6.0/RcppTemplate/libs |only RcppTemplate-6.0/RcppTemplate/man/DateNum.Rd |only RcppTemplate-6.0/RcppTemplate/man/RcppDocs.Rd |only RcppTemplate-6.0/RcppTemplate/man/RcppExample.Rd | 130 RcppTemplate-6.0/RcppTemplate/man/exam.Rd |only RcppTemplate-6.0/RcppTemplate/src/Makevars |only RcppTemplate-6.0/RcppTemplate/src/Makevars.in | 15 RcppTemplate-6.0/RcppTemplate/src/Makevars.win |only RcppTemplate-6.0/RcppTemplate/src/RcppExample.cpp | 794 +- RcppTemplate-6.0/RcppTemplate/src/config.hpp |only RcppTemplate-6.0/RcppTemplate/src/config.hpp.in |only 51 files changed, 6727 insertions(+), 2272 deletions(-)
Author: Henrik Bengtsson
Title: Easy handling of and access to files organized in structured
directories
Description: A file set refers to a set of files located in one or more
directories on the file system. This package provides classes
and methods to locate, setup, subset, navigate and iterative
suchs sets. The API is designed such that these classes can be
subsetted to provide for instance a richer API for special file
formats. Moreover, a specific name format is defined such that
filenames and directories can be considered to have fullnames
which consists of a name followed by comma-separated tags.
This adds additional flexibility to identify file sets and
individual files. NOTE: This package's API should be
considered to be in an beta stage. Its main purpose is
currently to support the aroma.* packages, where it is one of
the main core components; if you decide to build on top of this
package, please contact the author first.
Diff between R.filesets versions 0.5.3 dated 2009-08-14 and 0.6.5 dated 2009-11-03
R.filesets-0.5.3/R.filesets/man/fromFiles.GenericDataFileSet.Rd |only R.filesets-0.5.3/R.filesets/man/getFullName.GenericDataFile.Rd |only R.filesets-0.5.3/R.filesets/man/getFullName.GenericDataFileSet.Rd |only R.filesets-0.5.3/R.filesets/man/getName.GenericDataFile.Rd |only R.filesets-0.5.3/R.filesets/man/getName.GenericDataFileSet.Rd |only R.filesets-0.5.3/R.filesets/man/getTags.GenericDataFile.Rd |only R.filesets-0.5.3/R.filesets/man/getTags.GenericDataFileSet.Rd |only R.filesets-0.5.3/R.filesets/man/setTags.GenericDataFileSet.Rd |only R.filesets-0.6.5/R.filesets/DESCRIPTION | 16 R.filesets-0.6.5/R.filesets/R/999.NonDocumentedObjects.R | 2 R.filesets-0.6.5/R.filesets/R/FullNameInterface.R |only R.filesets-0.6.5/R.filesets/R/GenericDataFile.R | 242 ---- R.filesets-0.6.5/R.filesets/R/GenericDataFileSet.R | 530 +++------- R.filesets-0.6.5/R.filesets/R/GenericTabularFile.R | 16 R.filesets-0.6.5/R.filesets/R/TabularTextFile.R | 19 R.filesets-0.6.5/R.filesets/incl/999.missingdocs.txt |only R.filesets-0.6.5/R.filesets/incl/FullNameInterface.Rex |only R.filesets-0.6.5/R.filesets/inst/NEWS | 45 R.filesets-0.6.5/R.filesets/man/FullNameInterface.Rd |only R.filesets-0.6.5/R.filesets/man/GenericDataFile.Rd | 23 R.filesets-0.6.5/R.filesets/man/GenericDataFileSet.Rd | 21 R.filesets-0.6.5/R.filesets/man/GenericTabularFileSet.Rd | 13 R.filesets-0.6.5/R.filesets/man/Non-documented_objects.Rd | 69 + R.filesets-0.6.5/R.filesets/man/R.filesets-package.Rd | 2 R.filesets-0.6.5/R.filesets/man/TabularTextFileSet.Rd | 15 R.filesets-0.6.5/R.filesets/man/byPath.GenericDataFileSet.Rd |only R.filesets-0.6.5/R.filesets/man/getAlias.GenericDataFileSet.Rd | 2 R.filesets-0.6.5/R.filesets/man/getDefaultFullName.FullNameInterface.Rd |only R.filesets-0.6.5/R.filesets/man/getDefaultFullName.GenericDataFile.Rd |only R.filesets-0.6.5/R.filesets/man/getDefaultFullName.GenericDataFileSet.Rd |only R.filesets-0.6.5/R.filesets/man/getFullName.FullNameInterface.Rd |only R.filesets-0.6.5/R.filesets/man/getName.FullNameInterface.Rd |only R.filesets-0.6.5/R.filesets/man/getTags.FullNameInterface.Rd |only R.filesets-0.6.5/R.filesets/man/setAlias.GenericDataFileSet.Rd | 2 R.filesets-0.6.5/R.filesets/man/setTags.FullNameInterface.Rd |only 35 files changed, 422 insertions(+), 595 deletions(-)
Author: Ben Goodrich
Title: Factor Analysis in R
Description: This package estimates factor analysis models using a
genetic algorithm, which permits a general mechanism for
restricted optimization with arbitrary restrictions that are
chosen at run time with the help of a GUI. Importantly,
inequality restrictions can be imposed on functions of multiple
parameters, which provides a new avenues for testing and
generating theories with factor analysis models. This package
also includes an entirely new estimator of the common factor
analysis model called semi-exploratory factor analysis, which
is a general alternative to exploratory and confirmatory factor
analysis. Finally, this package integrates a lot of other
packages that estimate sample covariance matrices and thus
provides a lot of alternatives to the traditional sample
covariance calculation. Note that you need to have the Gtk run
time library installed on your system to use this package; see
the URL below for detailed installation instructions. Most
users would only need to understand the first twenty-four pages
of the PDF manual.
Diff between FAiR versions 0.4-4 dated 2009-01-12 and 0.4-5 dated 2009-11-03
DESCRIPTION | 35 + R/FAiR.R | 31 - inst/doc/FAiR.pdf | 889 +++++++++++++++++++++++------------------------- man/summary.FA-class.Rd | 1 4 files changed, 486 insertions(+), 470 deletions(-)
Author: Doug McIlroy. Packaged for R by Ray Brownrigg and Thomas P
Minka, transition to Plan 9 codebase by Roger Bivand.
Title: Map Projections
Description: Converts latitude/longitude into projected coordinates.
Diff between mapproj versions 1.1-7.2 dated 2008-08-06 and 1.1-8.2 dated 2009-11-03
mapproj-1.1-7.2/mapproj/src/doug |only mapproj-1.1-8.2/mapproj/DESCRIPTION | 23 +++++++------ mapproj-1.1-8.2/mapproj/LICENSE |only mapproj-1.1-8.2/mapproj/inst |only mapproj-1.1-8.2/mapproj/man/mapproject.Rd | 31 +++++++++++++++-- mapproj-1.1-8.2/mapproj/src/aitoff.c | 12 ++---- mapproj-1.1-8.2/mapproj/src/albers.c | 14 ++----- mapproj-1.1-8.2/mapproj/src/azequalarea.c | 9 +---- mapproj-1.1-8.2/mapproj/src/azequidist.c | 9 +---- mapproj-1.1-8.2/mapproj/src/bicentric.c | 9 +---- mapproj-1.1-8.2/mapproj/src/bonne.c | 11 +----- mapproj-1.1-8.2/mapproj/src/ccubrt.c | 9 +---- mapproj-1.1-8.2/mapproj/src/complex.c | 14 ++----- mapproj-1.1-8.2/mapproj/src/conic.c | 9 +---- mapproj-1.1-8.2/mapproj/src/cubrt.c | 9 +---- mapproj-1.1-8.2/mapproj/src/cuts.c | 22 +++++++----- mapproj-1.1-8.2/mapproj/src/cylequalarea.c | 9 +---- mapproj-1.1-8.2/mapproj/src/cylindrical.c | 9 +---- mapproj-1.1-8.2/mapproj/src/elco2.c | 9 +---- mapproj-1.1-8.2/mapproj/src/elliptic.c | 21 +++-------- mapproj-1.1-8.2/mapproj/src/fisheye.c | 9 +---- mapproj-1.1-8.2/mapproj/src/gall.c | 9 +---- mapproj-1.1-8.2/mapproj/src/gilbert.c | 12 ++---- mapproj-1.1-8.2/mapproj/src/guyou.c | 9 +---- mapproj-1.1-8.2/mapproj/src/harrison.c | 9 +---- mapproj-1.1-8.2/mapproj/src/hex.c | 51 +++++++++++++---------------- mapproj-1.1-8.2/mapproj/src/homing.c | 21 ++++++----- mapproj-1.1-8.2/mapproj/src/lagrange.c | 11 +----- mapproj-1.1-8.2/mapproj/src/lambert.c | 26 +++----------- mapproj-1.1-8.2/mapproj/src/laue.c | 9 +---- mapproj-1.1-8.2/mapproj/src/lune.c | 9 +---- mapproj-1.1-8.2/mapproj/src/map.h | 27 +++++++-------- mapproj-1.1-8.2/mapproj/src/mercator.c | 9 +---- mapproj-1.1-8.2/mapproj/src/mollweide.c | 9 +---- mapproj-1.1-8.2/mapproj/src/newyorker.c | 9 +---- mapproj-1.1-8.2/mapproj/src/orthographic.c | 11 +----- mapproj-1.1-8.2/mapproj/src/perspective.c | 21 ++++------- mapproj-1.1-8.2/mapproj/src/polyconic.c | 9 +---- mapproj-1.1-8.2/mapproj/src/rectangular.c | 9 +---- mapproj-1.1-8.2/mapproj/src/simpleconic.c | 9 +---- mapproj-1.1-8.2/mapproj/src/sinusoidal.c | 9 +---- mapproj-1.1-8.2/mapproj/src/tetra.c | 30 ++++++----------- mapproj-1.1-8.2/mapproj/src/trapezoidal.c | 9 +---- mapproj-1.1-8.2/mapproj/src/twocirc.c | 9 +---- mapproj-1.1-8.2/mapproj/src/zcoord.c | 36 +++++++++----------- 45 files changed, 225 insertions(+), 385 deletions(-)
Author: Paul Gilbert
Title: Time Frame coding kernel extensions
Description: Extensions and additional tframe utilities.
Diff between tframePlus versions 2009.10-1 dated 2009-10-18 and 2009.10-2 dated 2009-11-02
DESCRIPTION | 8 NEWS | 8 R/utils.R | 4 Rplots.pdf | 1433 +++++++++++++++++++++++------------------------- inst/doc/tframePlus.pdf |binary man/TSwriteXLS.Rd | 7 tests/perl.R |only 7 files changed, 716 insertions(+), 744 deletions(-)
Author: G. Jay Kerns
Title: Elementary Probability on Finite Sample Spaces
Description: This package provides a framework for performing
elementary probability calculations on finite sample spaces,
which may be represented by data frames or lists.
Functionality includes setting up sample spaces, counting
tools, defining probability spaces, performing set algebra,
calculating probability and conditional probability, tools for
simulation and checking the law of large numbers, adding random
variables, and finding marginal distributions. Characteristic
functions for all base R distributions are included.
Diff between prob versions 0.9-1 dated 2008-01-09 and 0.9-2 dated 2009-11-02
DESCRIPTION | 39 LICENSE |only NAMESPACE | 21 R/characteristicfunctions.r |only R/misc.r | 20 R/simulation.r | 14 inst/doc/charfunc.pdf |only inst/doc/charfunc.rnw |only inst/doc/prob.pdf | 1783 ++++++++++++++++++++++---------------------- man/CharFunc.Rd |only man/intersect.rd | 2 man/isin.rd | 2 man/prob-package.Rd | 10 man/setdiff.rd | 2 man/union.rd | 2 15 files changed, 993 insertions(+), 902 deletions(-)
Author: Yihui Xie
Title: Demonstrate Animations in Statistics
Description: This package consists of various functions for animations
in statistics, covering many areas such as probability theory,
mathematical statistics, multivariate statistics, nonparametric
statistics, sampling survey, linear models, time series,
computational statistics, data mining and machine learning.
These functions might be of help in teaching statistics and
data analysis.
Diff between animation versions 1.0-6 dated 2009-10-26 and 1.0-7 dated 2009-11-02
DESCRIPTION | 10 +++++----- R/ani.options.R | 2 +- R/ani.stop.R | 7 ++++--- R/moving.block.R |only data/HuSpeech.rda |only inst/NEWS | 43 ++++++++++++++++++++++++++++++------------- inst/js/ANI.css | 2 +- man/HuSpeech.Rd |only man/ani.options.Rd | 1 + man/animation-package.Rd | 2 +- man/moving.block.Rd |only 11 files changed, 43 insertions(+), 24 deletions(-)
Author: Henrik Bengtsson
Title: Various programming utilities
Description: This package provides utility classes and methods useful
when programming in R and developing R packages.
Diff between R.utils versions 1.2.2 dated 2009-10-18 and 1.2.4 dated 2009-11-02
R.utils-1.2.2/R.utils/R/beta |only R.utils-1.2.2/R.utils/R/devel |only R.utils-1.2.4/R.utils/DESCRIPTION | 12 ++---- R.utils-1.2.4/R.utils/R/Arguments.R | 45 +++++++++++++++++------ R.utils-1.2.4/R.utils/R/createLink.R | 6 ++- R.utils-1.2.4/R.utils/R/fileAccess.R | 18 +++++++-- R.utils-1.2.4/R.utils/R/findSourceTraceback.R |only R.utils-1.2.4/R.utils/R/readWindowsShortcut.R | 2 - R.utils-1.2.4/R.utils/R/saveObject.R | 39 ++++++++++++++++++- R.utils-1.2.4/R.utils/inst/NEWS | 18 +++++++++ R.utils-1.2.4/R.utils/man/GString.Rd | 2 - R.utils-1.2.4/R.utils/man/Sys.setenv.Rd |only R.utils-1.2.4/R.utils/man/fileAccess.Rd | 9 ++-- R.utils-1.2.4/R.utils/man/findSourceTraceback.Rd |only R.utils-1.2.4/R.utils/man/readWindowsShortcut.Rd | 2 - R.utils-1.2.4/R.utils/man/saveObject.Rd | 5 ++ 16 files changed, 125 insertions(+), 33 deletions(-)
Author: Henrik Bengtsson
Title: R object-oriented programming with or without references
Description: Methods and classes for object-oriented programming in R
with or without references. Large effort has been made on
making definition of methods as simple as possible with a
minimum of maintenance for package developers. The package has
been developed since 2001 and is now considered very stable.
This is a cross-platform package implemented in pure R that
defines standard S3 classes without any tricks.
Diff between R.oo versions 1.6.2 dated 2009-10-19 and 1.6.5 dated 2009-11-02
DESCRIPTION | 10 +-- R/050.Object.R | 46 ++++++++++++++++- R/Rdoc.R | 108 +++++++++++++++++++++++++++++------------- R/objectSize.environment.R |only inst/NEWS | 16 ++++++ man/BasicObject.Rd | 8 +-- man/Class.Rd | 4 - man/Object.Rd | 8 +-- man/objectSize.environment.Rd |only man/save.Object.Rd | 5 + 10 files changed, 153 insertions(+), 52 deletions(-)
Author: Henrik Bengtsson
Title: Read and write of MAT files together with R-to-Matlab
connectivity
Description: This package provides methods to read and write MAT files.
It also makes it possible to communicate (evaluate code, send
and retrieve objects etc.) with Matlab v6 or higher running
locally or on a remote host.
Diff between R.matlab versions 1.2.5 dated 2009-09-03 and 1.2.6 dated 2009-11-02
DESCRIPTION | 10 ++--- R/999.package.R | 19 ++++------ R/readMat.R | 88 +++++++++++++++++++++++++++++++++++++++++++----- inst/NEWS | 10 +++++ man/R.matlab-package.Rd | 19 ++++------ 5 files changed, 110 insertions(+), 36 deletions(-)
Author: Peng Dai
Title: Multivariate two-sample tests based on K-nearest-neighbors
Description: The package contains three multivariate two-sample tests
which are all based on k-nearest-neighbors. The testing
procedures are distribution free and are robust from balanced
designs to unbalanced designs.
Diff between MTSKNN versions 0.0-1 dated 2009-10-27 and 0.0-2 dated 2009-11-02
DESCRIPTION | 6 +++--- R/mtsknn.R | 2 +- R/mtsknn.eq.R | 27 ++++++++++++++------------- R/mtsknn.neq.R | 6 +++--- man/mtsknn.Rd | 14 +++++++------- man/mtsknn.eq.Rd | 6 +++--- man/mtsknn.neq.Rd | 7 ++++--- src/knn.cpp | 6 +++++- 8 files changed, 40 insertions(+), 34 deletions(-)
Author: Ian Fellows
Title: Deducer
Description: An intuitive, cross-platform graphical data analysis
system. It uses menus and dialogs to guide the user efficiently
through the data manipulation and analysis process, and has an
excel like spreadsheet for easy data frame visualization and
editing. Deducer works best when used with the Java based R GUI
JGR, but the dialogs can be called from the command line. Some
integration with the Windows Rgui has been done.
Diff between Deducer versions 0.1-0 dated 2009-08-02 and 0.2-0 dated 2009-11-02
Deducer-0.1-0/Deducer/R/sortData.R |only Deducer-0.1-0/Deducer/inst/deducer |only Deducer-0.1-0/Deducer/man/sortData.Rd |only Deducer-0.2-0/Deducer/DESCRIPTION | 18 ++++++++++++------ Deducer-0.2-0/Deducer/NEWS | 5 +++++ Deducer-0.2-0/Deducer/R/Deducer.R | 14 +++++++++----- Deducer-0.2-0/Deducer/R/sort.data.frame.R |only Deducer-0.2-0/Deducer/inst/java/deducer.jar |binary Deducer-0.2-0/Deducer/inst/javasrc |only Deducer-0.2-0/Deducer/man/sort.data.frame.Rd |only 10 files changed, 26 insertions(+), 11 deletions(-)
Author: Matthew Denwood
Title: Run Bayesian MCMC Models in the BUGS syntax from Within R
Description: A set of functions to allow any user specified model to be
run in JAGS from within R, returning the MCMC chains as R
objects. Includes functions to read external WinBUGS type
textfiles, and allows several ways of automatically specifying
model data from existing R objects or R functions. Also
includes functions to automatically calculate model run length,
autocorrealtion and Gelman Rubin statistic diagnostics for all
models to simplify the process of achieving chain convergence.
Designed for maximum compatibility with WinBUGS syntax,
although minor modification to existing .bug files will be
required. Requires Just Another Gibbs Sampler (JAGS) for most
functions, see: http://www-fis.iarc.fr/~martyn/software/jags/
Diff between runjags versions 0.9.5-1 dated 2009-10-15 and 0.9.5-2 dated 2009-11-01
DESCRIPTION | 8 ++++---- R/read.winbugs.R | 4 ++-- 2 files changed, 6 insertions(+), 6 deletions(-)
Author: Alex Couture-Beil
Title: JSON for R
Description: Converts R object into JSON objects and vice-versa
Diff between rjson versions 0.1.7 dated 2009-08-28 and 0.1.8 dated 2009-11-01
DESCRIPTION | 6 +++--- R/json.R | 8 ++++---- inst/doc/json_rpc_server.pdf |binary 3 files changed, 7 insertions(+), 7 deletions(-)
Author: Jeffrey A. Ryan
Title: Quantitative Financial Modelling Framework
Description: Specify, build, trade, and analyse quantitative financial
trading strategies
Diff between quantmod versions 0.3-12 dated 2009-10-03 and 0.3-13 dated 2009-11-01
DESCRIPTION | 8 ++++---- R/OHLC.transformations.R | 8 ++++---- R/addCLV.R | 2 +- R/addChaikin.R | 8 ++++---- R/addEMV.R | 4 ++-- R/addOBV.R | 4 ++-- R/axTicksByTime2.R |only R/newTA.R | 3 ++- man/OHLC.Transformations.Rd | 4 ++++ man/periodReturn.Rd | 2 -- 10 files changed, 23 insertions(+), 20 deletions(-)
Author: Rajarshi Guha
Title: Functions to operate on binary fingerprint data
Description: This package contains functions to manipulate binary
fingerprints of arbitrary length. A fingerprint is represented
by an object of S4 class 'fingerprint' which is internally
represented a vector of integers, such that each element
represents the position in the fingerprint that is set to 1.
The bitwise logical functions in R are overridden so that they
can be used directly with 'fingerprint' objects. A number of
distance metrics are also available (many contributed by
Michael Fadock). Fingerprints can be converted to Euclidean
vectors (i.e., points on the unit hypersphere) and can also be
folded using OR. Arbitrary fingerprint formats can be handled
via line handlers. Currently handlers are provided for CDK, MOE
and BCI fingerprint data.
Diff between fingerprint versions 3.1.2 dated 2009-02-23 and 3.2 dated 2009-11-01
DESCRIPTION | 31 ++++++++++++++++++------------- inst |only man/fingerprint.Rd | 3 +-- tests |only 4 files changed, 19 insertions(+), 15 deletions(-)
Author: A.I. McLeod and Changjiang Xu
Title: Best Subset GLM
Description: Best subset glm using AIC, BIC, EBIC, BICq or
Cross-Validation. For the normal case, the 'leaps' is used.
Otherwise, a slower exhaustive search. The 'xtable' package is
needed for vignette 'SimExperimentBICq.Rnw' accompanying this
package.
Diff between bestglm versions 0.14 dated 2009-10-19 and 0.20 dated 2009-11-01
bestglm-0.14/bestglm/R/oneSdRule.R |only bestglm-0.20/bestglm/DESCRIPTION | 8 bestglm-0.20/bestglm/R/CVHTF.R | 15 bestglm-0.20/bestglm/R/bestglm.R | 4 bestglm-0.20/bestglm/R/oneSd.R |only bestglm-0.20/bestglm/inst/doc/Rplots.pdf | 146 bestglm-0.20/bestglm/inst/doc/SimExperimentBICq.pdf | 252 - bestglm-0.20/bestglm/inst/doc/bestglm.Rnw | 210 - bestglm-0.20/bestglm/inst/doc/bestglm.pdf | 4111 +++++++++----------- bestglm-0.20/bestglm/man/CVDH.Rd | 7 bestglm-0.20/bestglm/man/CVHTF.Rd | 185 bestglm-0.20/bestglm/man/CVd.Rd | 150 bestglm-0.20/bestglm/man/Fires.Rd | 4 bestglm-0.20/bestglm/man/bestglm-package.Rd | 15 bestglm-0.20/bestglm/man/bestglm.Rd | 22 bestglm-0.20/bestglm/man/oneSdRule.Rd | 3 16 files changed, 2475 insertions(+), 2657 deletions(-)
Author: R by Martin Schlather
Title: Soil Physics Tools
Description: SWMS_2D interface
Diff between SoPhy versions 1.0.36 dated 2009-01-14 and 1.0.39 dated 2009-11-01
DESCRIPTION | 16 +++++++++++----- man/create.stones.Rd | 2 +- man/plotRGB.Rd | 2 +- man/plotWater.Rd | 2 +- man/quader.Rd | 3 ++- man/xswms2d.Rd | 4 ++-- src/Makevars | 2 +- 7 files changed, 19 insertions(+), 12 deletions(-)
Author: Erin Hodgess
Title: Rcmdr plugin for quality control course
Description: This package provides an Rcmdr "plug-in" based on the
Quality control class Stat 4300
Diff between RcmdrPlugin.qual versions 0.1.0 dated 2009-08-21 and 0.3.0 dated 2009-11-01
DESCRIPTION | 8 +-- R/RcmdrPlugin.qual.R | 87 ++++++++++++++++++++++++++++++++++++++- inst/etc/menus.txt | 35 ++++++++------- man/RcmdrPlugin.qual-internal.Rd | 7 ++- 4 files changed, 114 insertions(+), 23 deletions(-)
More information about RcmdrPlugin.qual at CRAN
Permanent link
Author: Martin Schlather
Title: Simulation and Analysis of Random Fields
Description: Simulation of Gaussian and extreme value random fields;
conditional simulation; kriging
Diff between RandomFields versions 1.3.40 dated 2009-07-01 and 1.3.41 dated 2009-11-01
DESCRIPTION | 6 +++--- man/RFparameters.Rd | 3 ++- 2 files changed, 5 insertions(+), 4 deletions(-)
Author: Martin Schlather
Title: Analysis of Marks of Marked Point Processes
Description: Non-parametric Analysis of the Marks of Marked Point
Processes
Diff between MarkedPointProcess versions 0.2.11 dated 2009-06-29 and 0.2.13 dated 2009-11-01
DESCRIPTION | 8 ++++---- NAMESPACE | 1 - R/srd.R | 12 ++++++++---- man/rfm.test.Rd | 2 +- 4 files changed, 13 insertions(+), 10 deletions(-)
More information about MarkedPointProcess at CRAN
Permanent link
Author: Steve Su
Title: Fitting Single and Mixture of Generalised Lambda Distributions
(RS and FMKL) using Discretised and Maximum Likelihood Methods
Description: The fitting algorithms considered in this package have two
major objectives. One is to provide a smoothing device to fit
distributions to data using the weight and unweighted
discretised approach based on the bin width of the histogram.
The other is to provide a definitive fit to the data set using
the maximum likelihood estimation. Diagnostics on goodness of
fit can be done via qqplots, KS-resample tests and comparing
mean, variance, skewness and kurtosis of the data with the
fitted distribution.
Diff between GLDEX versions 1.0.3.2 dated 2009-10-11 and 1.0.3.3 dated 2009-11-01
DESCRIPTION | 8 ++++---- R/fun.fmkl0.R | 5 +++-- man/GLDEX.package.Rd | 4 ++-- 3 files changed, 9 insertions(+), 8 deletions(-)
Author: Sundar Dorai-Raj and Spencer Graves
Title: R companion to "Curve and Surface Fitting with Splines"
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
Diff between DierckxSpline versions 1.1-3 dated 2009-04-16 and 1.1-4 dated 2009-11-01
DESCRIPTION | 9 ++++----- man/panel.dierckx.Rd | 6 +++--- 2 files changed, 7 insertions(+), 8 deletions(-)
More information about stockPortfolio at CRAN
Permanent link
Author: Holger Schwender, Arno Fritsch
Title: Analysis of High-Dimensional Categorical Data such as SNP Data
Description: Tools for the analysis of high-dimensional data
developed/implemented at the group "Statistical Complexity
Reduction In Molecular Epidemiology" (SCRIME). Main focus is on
SNP data. But most of the functions can also be applied to
other types of categorical data.
Diff between scrime versions 1.1.7 dated 2009-10-14 and 1.1.9 dated 2009-11-01
DESCRIPTION | 8 ++++---- R/recodeCount.R | 10 +++++----- inst/CHANGES | 12 ++++++++++++ man/rowHWEs.Rd | 5 ++--- 4 files changed, 23 insertions(+), 12 deletions(-)
Author: Rajarshi Guha
Title: rcdklib - CDK libraries packaged for R
Description: This package provides the CDK libraries for use in the R
environment. Given the size of the library itself, this package
is not expected to change very frequently. To make use of the
CDK within R, it is suggested that you use the rcdk package.
Note that it is possible to directly interact with the CDK
using rJava. However rcdk exposes functionality in a more
idiomatic way
Diff between rcdklibs versions 1.2.2 dated 2009-10-29 and 1.2.3 dated 2009-11-01
DESCRIPTION | 8 ++++---- inst/cont/cdk.jar |binary 2 files changed, 4 insertions(+), 4 deletions(-)
Author: Rajarshi Guha
Title: rcdk - Interface to the CDK Libraries
Description: This package allows the user to access functionality in
the CDK, a Java framework for cheminformatics. This allows the
user to load molecules, evaluate fingerprints, calculate
molecular descriptors and so on. In addition the CDK API allows
the user to view structures in 2D.
Diff between rcdk versions 2.9.4 dated 2009-08-24 and 2.9.6 dated 2009-11-01
DESCRIPTION | 8 R/atoms.R | 49 +- R/bonds.R | 23 - R/formula.R | 271 +++++++------ R/props.R | 45 +- R/rcdk.R | 4 R/visual.R | 4 inst/cont/rcdk.jar |binary inst/doc/rcdk.pdf | 928 +++++++++++++++++++++++------------------------ man/atomcontainer.Rd | 2 man/atoms.Rd | 2 man/evalatomicdesc.Rd | 2 man/evaldesc.Rd | 2 man/getatomdescnames.Rd | 2 man/getatoms.Rd | 2 man/getbonds.Rd | 2 man/getconatom.Rd | 2 man/getdesccat.Rd | 2 man/getdescnames.Rd | 2 man/getfp.Rd | 2 man/gethcount.Rd | 2 man/getisotopepattern.Rd | 2 man/getproperty.Rd | 2 man/getprops.Rd | 2 man/getsmiles.Rd | 2 man/getsmilesparser.Rd | 2 man/gettotalcharge.Rd | 2 man/props.Rd | 2 man/removehydrogens.Rd | 2 man/removeproperty.Rd | 2 man/setchargeformula.Rd | 2 man/setproperty.Rd | 2 man/viewmol2d.Rd | 2 man/viewtable.Rd | 2 man/writemols.Rd | 2 35 files changed, 731 insertions(+), 653 deletions(-)
Author: Simon Urbanek
Title: Low-level R to Java interface
Description: Low-level interface to Java VM very much like .C/.Call and
friends. Allows creation of objects, calling methods and
accessing fields.
Diff between rJava versions 0.8-0 dated 2009-10-28 and 0.8-1 dated 2009-11-01
DESCRIPTION | 4 +- NEWS | 11 +++++ R/arrays.R | 3 + R/call.R | 4 +- inst/javadoc/ArrayDimensionException.html | 2 - inst/javadoc/ArrayWrapper.html | 2 - inst/javadoc/ArrayWrapper_Test.html | 2 - inst/javadoc/FlatException.html | 2 - inst/javadoc/NotAnArrayException.html | 2 - inst/javadoc/NotComparableException.html | 2 - inst/javadoc/ObjectArrayException.html | 2 - inst/javadoc/PrimitiveArrayException.html | 2 - inst/javadoc/RJavaArrayIterator.html | 2 - inst/javadoc/RJavaArrayTools.ArrayDimensionMismatchException.html | 2 - inst/javadoc/RJavaArrayTools.html | 2 - inst/javadoc/RJavaArrayTools_Test.html | 2 - inst/javadoc/RJavaClassLoader.html | 2 - inst/javadoc/RJavaComparator.html | 2 - inst/javadoc/RJavaImport.html | 2 - inst/javadoc/RJavaTools.html | 2 - inst/javadoc/RJavaTools_Test.DummyNonStaticClass.html | 2 - inst/javadoc/RJavaTools_Test.TestException.html | 2 - inst/javadoc/RJavaTools_Test.html | 2 - inst/javadoc/RectangularArrayBuilder.html | 2 - inst/javadoc/RectangularArrayBuilder_Test.html | 2 - inst/javadoc/RectangularArrayExamples.html | 2 - inst/javadoc/RectangularArraySummary.html | 2 - inst/javadoc/TestException.html | 2 - inst/javadoc/allclasses-frame.html | 2 - inst/javadoc/allclasses-noframe.html | 2 - inst/javadoc/constant-values.html | 2 - inst/javadoc/deprecated-list.html | 2 - inst/javadoc/help-doc.html | 2 - inst/javadoc/index-all.html | 2 - inst/javadoc/index.html | 2 - inst/javadoc/overview-tree.html | 2 - inst/javadoc/package-frame.html | 2 - inst/javadoc/package-summary.html | 2 - inst/javadoc/package-tree.html | 2 - inst/javadoc/serialized-form.html | 2 - man/jcall.Rd | 2 - man/jrectRef-class.Rd | 4 +- src/otables.c | 2 + src/rJava.c | 19 ++++++++++ src/rJava.h | 2 - 45 files changed, 78 insertions(+), 45 deletions(-)
Author: Nicolai Meinshausen
Title: Node Harvest for regression and classification
Description: Node harvest is a simple interpretable tree-like estimator
for high-dimensional regression and classification. A few nodes
are selected from an initially large ensemble of nodes, each
associated with a positive weight. New observations can fall
into one or several nodes and predictions are the weighted
average response across all these groups. The package offers
visualization of the estimator. Predictions can return the
nodes a new observation fell into, along with the mean response
of training observations in each node, offering a simple
explanation of the prediction.
Diff between nodeHarvest versions 0.1 dated 2009-10-12 and 0.2 dated 2009-11-01
DESCRIPTION | 10 +++++----- R/makeRules.R | 8 +++++--- R/nodeHarvest.R | 8 ++++---- man/nodeHarvest.Rd | 4 ++++ man/plot.nodeHarvest.Rd | 5 +++-- man/predict.nodeHarvest.Rd | 2 +- 6 files changed, 22 insertions(+), 15 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 0.0-11 dated 2009-08-23 and 0.0-12 dated 2009-11-01
gWidgetsWWW-0.0-11/gWidgetsWWW/inst/doc/gWidgetsWWW.pdf.mine |only gWidgetsWWW-0.0-11/gWidgetsWWW/inst/doc/gWidgetsWWW.pdf.r100 |only gWidgetsWWW-0.0-11/gWidgetsWWW/inst/doc/gWidgetsWWW.pdf.r101 |only gWidgetsWWW-0.0-11/gWidgetsWWW/inst/test-ghtml.R |only gWidgetsWWW-0.0-11/gWidgetsWWW/inst/test-ghtml.html |only gWidgetsWWW-0.0-12/gWidgetsWWW/ChangeLog |only gWidgetsWWW-0.0-12/gWidgetsWWW/DESCRIPTION | 16 gWidgetsWWW-0.0-12/gWidgetsWWW/NEWS | 9 gWidgetsWWW-0.0-12/gWidgetsWWW/R/LocalVersion.R | 4 gWidgetsWWW-0.0-12/gWidgetsWWW/R/gslider.R | 3 gWidgetsWWW-0.0-12/gWidgetsWWW/inst/doc/gWidgetsWWW.pdf | 260 +++++------ gWidgetsWWW-0.0-12/gWidgetsWWW/man/gWidgetsWWW-package.Rd | 4 12 files changed, 159 insertions(+), 137 deletions(-)