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 1.1 dated 2009-08-19 and 1.2 dated 2009-09-04
DESCRIPTION | 15 +--- R/extractGenes.R.R | 12 +++ R/extractGenes.T.R | 12 ++- man/Tmc.Rd | 52 +++++++++----- man/baymod.Rd | 139 ++++++++++++++++++++++---------------- man/createTable.Rd | 36 ++++++--- man/designCount.Rd | 2 man/designMatrix.Rd | 11 +-- man/extractGenes.R.Rd | 117 +++++++++++++++++++------------- man/extractGenes.T.Rd | 53 +++++++++----- man/ratio.Rd | 174 +++++++++++++++++++++++++++++++----------------- man/sdef-package.Rd | 12 +-- man/simulation.Rd | 41 ++++++----- man/simulation.indep.Rd | 50 +++++++------ 14 files changed, 454 insertions(+), 272 deletions(-)
Author: Andy Bunn
Title: Dendrochronology Program Library in R
Description: This package contains functions for performing some
standard tree-ring analyses.
Diff between dplR versions 1.1.9 dated 2009-06-17 and 1.1.9.1 dated 2009-09-04
DESCRIPTION | 8 ++++---- NAMESPACE | 2 +- R/read.fh.R |only man/detrend.Rd | 3 ++- man/read.fh.rd |only 5 files changed, 7 insertions(+), 6 deletions(-)
Author: Bear F. Braumoeller
Diff between boolean versions 2.0-0 dated 2009-08-31 and 2.0-1 dated 2009-09-04
Title: Boolean Binary Response Models
Description: This package implements a partial-observability procedure
for testing Boolean hypotheses that generalizes the binary
response GLM.
DESCRIPTION | 8 ++++----
R/boolean.R | 5 ++++-
2 files changed, 8 insertions(+), 5 deletions(-)
Author: Martin Maechler
Title: R MPFR - Multiple Precision Floating-Point Reliable
Description: The package aims at providing S4 classes and methods for
arithmetic including transcendental ("special") functions for
arbitrary precision floating point numbers. To this end, it
interfaces to the LGPL'ed MPFR (Multiple Precision
Floating-Point Reliable) Library which itself is based on the
GMP (GNU Multiple Precision) Library.
Diff between Rmpfr versions 0.1-5 dated 2009-08-14 and 0.1-6 dated 2009-09-04
ChangeLog | 41 +++++++ DESCRIPTION | 11 + R/Math.R | 20 ++- R/array.R | 11 + R/as.R | 25 +++- R/mpfr.R | 268 ++++++++++++++++++++++++---------------------- R/special-fun.R | 8 + TODO | 28 ++++ man/atomicVector-class.Rd | 2 man/formatMpfr.Rd |only man/is.whole.Rd |only man/mpfr-class.Rd | 60 +++++++++- man/mpfr-utils.Rd | 15 ++ man/mpfr.Rd | 1 man/pmax.Rd | 6 - man/seqMpfr.Rd | 3 man/special-math.Rd | 24 +++- man/utils.Rd | 29 ++++ src/Ops.c | 1 src/Rmpfr_utils.h | 1 src/convert.c | 53 ++++++--- src/init.c | 2 src/utils.c | 1 tests/bit-repr.Rout.save | 10 - tests/create.R | 5 25 files changed, 436 insertions(+), 189 deletions(-)
Author: Marc J. Mazerolle
Diff between AICcmodavg versions 1.0 dated 2009-09-03 and 1.01 dated 2009-09-04
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 lm, glm, and lme object
classes.
DESCRIPTION | 8 +--
man/AICc.Rd | 7 +--
man/AICcmodavg-package.Rd | 4 -
man/aictab.Rd | 84 +++++++++++++++++++++---------------
man/c_hat.Rd | 25 ++++++----
man/confset.Rd | 86 +++++++++++++++++++++----------------
man/dry.frog.Rd | 3 -
man/evidence.Rd | 30 +++++++------
man/importance.Rd | 50 +++++++++++----------
man/modavg.Rd | 105 +++++++++++++++++++++++++++-------------------
man/modavgpred.Rd | 103 ++++++++++++++++++++++++---------------------
11 files changed, 290 insertions(+), 215 deletions(-)
Author: Jose Pinheiro
Diff between nlme versions 3.1-93 dated 2009-08-16 and 3.1-94 dated 2009-09-04
Title: Linear and Nonlinear Mixed Effects Models
Description: Fit and compare Gaussian linear and nonlinear
mixed-effects models.
ChangeLog | 6 ++++++
DESCRIPTION | 16 ++++++++--------
man/corExp.Rd | 2 +-
man/corGaus.Rd | 2 +-
man/corLin.Rd | 2 +-
man/corRatio.Rd | 2 +-
man/corSpatial.Rd | 2 +-
man/corSpher.Rd | 2 +-
man/glsControl.Rd | 2 +-
man/gnlsControl.Rd | 2 +-
man/lmeControl.Rd | 2 +-
man/pairs.compareFits.Rd | 4 ++--
man/pairs.lmList.Rd | 4 ++--
man/pairs.lme.Rd | 4 ++--
man/plot.ACF.Rd | 2 +-
man/plot.Variogram.Rd | 4 +---
man/plot.augPred.Rd | 2 +-
man/plot.gls.Rd | 6 +++---
man/plot.lmList.Rd | 4 ++--
man/plot.lme.Rd | 4 ++--
man/plot.nffGroupedData.Rd | 3 +--
man/plot.nfnGroupedData.Rd | 2 +-
man/plot.ranef.lmList.Rd | 9 ++++-----
tests/lmList.R |only
24 files changed, 45 insertions(+), 43 deletions(-)
Author: S original
Diff between boot versions 1.2-38 dated 2009-08-05 and 1.2-39 dated 2009-09-04
Title: Bootstrap R (S-Plus) Functions (Canty)
Description: functions and datasets for bootstrapping from the book
"Bootstrap Methods and Their Applications" by A. C. Davison and
D. V. Hinkley (1997, CUP).
ChangeLog | 6 +++++-
DESCRIPTION | 8 ++++----
man/catsM.Rd | 4 ++--
man/censboot.Rd | 2 +-
man/motor.Rd | 4 ++--
man/tsboot.Rd | 2 +-
tests/Examples/boot-Ex.Rout.save | 2 --
7 files changed, 15 insertions(+), 13 deletions(-)
Author: Wim de Leeuw
Title: SigWin-detector implementation in R
Description: Implementation of the SigWin-detector for the detection of
regions of increased or decreased gene expression (RIDGEs and
anti-RIDGES) in transcriptome maps and the presentation in so
called RIDGEOGRAMs as described by Marcia A. Inda et al. [BMC
Res Notes 2008; 1:63]
Diff between SigWinR versions 1.0 dated 2009-06-16 and 1.0.1 dated 2009-09-04
DESCRIPTION | 8 ++++---- R/RidgePlot.R | 6 +++--- R/RidgeogramPlot.R | 24 +++++++++++++++++++----- man/PosRidgeogram.Rd | 19 +++++++++++++++---- man/RidgePlot.Rd | 10 ++++++---- man/Ridgeogram.Rd | 5 +++-- man/RidgeogramPlot.Rd | 8 ++++---- man/Ridges.Rd | 15 ++++++++++----- man/SigWin.Rd | 2 +- man/SubRidgeogram.Rd | 5 +++-- man/rsigwin-package.Rd | 7 ++++--- 11 files changed, 72 insertions(+), 37 deletions(-)
Author: S original by Matt Wand. R port by Brian Ripley
Diff between KernSmooth versions 2.23-2 dated 2009-05-24 and 2.23-3 dated 2009-09-04
Title: Functions for kernel smoothing for Wand & Jones (1995)
Description: functions for kernel smoothing (and density estimation)
corresponding to the book: Wand, M.P. and Jones, M.C. (1995)
"Kernel Smoothing".
KernSmooth-2.23-2/KernSmooth/INDEX |only
KernSmooth-2.23-3/KernSmooth/DESCRIPTION | 8 ++++----
KernSmooth-2.23-3/KernSmooth/PORTING | 12 ++++++++++++
KernSmooth-2.23-3/KernSmooth/man/dpih.Rd | 8 +++-----
4 files changed, 19 insertions(+), 9 deletions(-)
Author: Christian Buchta, Kurt Hornik, Ingo Feinerer, David Meyer
Title: Text Analysis Utilities
Description: Utilities for text analysis
Diff between tau versions 0.0-2 dated 2009-08-31 and 0.0-3 dated 2009-09-04
CHANGELOG |only DESCRIPTION | 8 ++++---- NAMESPACE | 1 + R/encoding.R |only R/sysdata.rda |only R/translate.R | 20 ++++++-------------- man/encoding.Rd |only src/encoding.c |only tests |only 9 files changed, 11 insertions(+), 18 deletions(-)
Author: Thomas Petzoldt
Title: Simulation of ecological (and other) dynamic systems
Description: simecol is an object oriented framework to simulate
ecological (and other) dynamic systems. It can be used for
differential equations, individual-based (or agent-based) and
other models as well. The package helps to organize scenarios
(avoids copy and paste) and improves readability and usability
of code.
Diff between simecol versions 0.6-8 dated 2009-06-27 and 0.6-9 dated 2009-09-04
DESCRIPTION | 12 ++++++------ inst/doc/simecol-howtos.Rnw | 17 ++++++++--------- inst/doc/simecol-howtos.pdf |binary inst/doc/simecol-introduction.pdf |binary man/as.simObj.Rd | 2 +- man/iteration.Rd | 2 +- man/pcuseries.Rd | 2 +- 7 files changed, 17 insertions(+), 18 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 1.3 dated 2009-08-06 and 1.4 dated 2009-09-04
rainbow-1.3/rainbow/R/lines.sfts.R |only rainbow-1.3/rainbow/R/plot.sfts.R |only rainbow-1.3/rainbow/R/points.sfts.r |only rainbow-1.3/rainbow/man/lines.sfts.Rd |only rainbow-1.3/rainbow/man/plot.sfts.Rd |only rainbow-1.3/rainbow/man/points.sfts.Rd |only rainbow-1.3/rainbow/man/sfts.Rd |only rainbow-1.4/rainbow/CHANGELOG | 8 +++ rainbow-1.4/rainbow/DESCRIPTION | 8 +-- rainbow-1.4/rainbow/NAMESPACE | 6 -- rainbow-1.4/rainbow/R/Qn.r | 6 +- rainbow-1.4/rainbow/R/bbag.R | 10 ++-- rainbow-1.4/rainbow/R/compute.bagplot.r | 60 ++++++++++++------------- rainbow-1.4/rainbow/R/depth.FM.R | 8 +-- rainbow-1.4/rainbow/R/depth.RP.R | 12 ++--- rainbow-1.4/rainbow/R/depth.RPD.R | 9 +-- rainbow-1.4/rainbow/R/depth.mode.R | 10 +--- rainbow-1.4/rainbow/R/fbag.R | 15 ++---- rainbow-1.4/rainbow/R/fdepth.R | 2 rainbow-1.4/rainbow/R/fhdr.R | 38 +++++++-------- rainbow-1.4/rainbow/R/foutliers.R | 16 +++--- rainbow-1.4/rainbow/R/fts.R | 2 rainbow-1.4/rainbow/R/func.mean.R | 4 - rainbow-1.4/rainbow/R/func.med.RPD.R | 2 rainbow-1.4/rainbow/R/func.trimvar.RPD.R | 2 rainbow-1.4/rainbow/R/func.trimvar.mode.R | 2 rainbow-1.4/rainbow/R/func.var.R | 2 rainbow-1.4/rainbow/R/hossjercroux.r | 2 rainbow-1.4/rainbow/R/lines.fds.r | 22 ++++----- rainbow-1.4/rainbow/R/matrix.rank.r | 2 rainbow-1.4/rainbow/R/metri.p.r | 2 rainbow-1.4/rainbow/R/outliers.depth.pond.R | 8 +-- rainbow-1.4/rainbow/R/outliers.depth.trim.R | 13 ++--- rainbow-1.4/rainbow/R/outliers.lrt.R | 24 +++++----- rainbow-1.4/rainbow/R/outliers.thres.lrt.R | 24 +++++----- rainbow-1.4/rainbow/R/plot.bagplot.R | 38 +++++++-------- rainbow-1.4/rainbow/R/plot.fdepth.R | 3 - rainbow-1.4/rainbow/R/plot.fds.R | 31 ++++++------ rainbow-1.4/rainbow/R/points.fds.r | 24 +++++----- rainbow-1.4/rainbow/R/print.fds.R | 2 rainbow-1.4/rainbow/R/print.fts.R | 2 rainbow-1.4/rainbow/R/print.sfts.r | 2 rainbow-1.4/rainbow/R/quantile.outliers.pond.R | 14 ++--- rainbow-1.4/rainbow/R/quantile.outliers.trim.R | 14 ++--- rainbow-1.4/rainbow/R/rapca.R | 2 rainbow-1.4/rainbow/R/robout.R | 6 +- rainbow-1.4/rainbow/R/rstep.r | 4 - rainbow-1.4/rainbow/R/sfts.R | 56 ++++++++++++----------- rainbow-1.4/rainbow/data/ElNino.rda |binary rainbow-1.4/rainbow/man/Australiafertility.Rd | 2 rainbow-1.4/rainbow/man/ElNino.Rd | 2 rainbow-1.4/rainbow/man/Francemortality.Rd | 2 rainbow-1.4/rainbow/man/fboxplot.Rd | 2 rainbow-1.4/rainbow/man/fdepth.Rd | 2 rainbow-1.4/rainbow/man/fds.Rd | 16 ++++++ rainbow-1.4/rainbow/man/foutliers.Rd | 2 rainbow-1.4/rainbow/man/lines.fds.Rd | 2 rainbow-1.4/rainbow/man/plot.fds.Rd | 4 + rainbow-1.4/rainbow/man/points.fds.Rd | 2 59 files changed, 285 insertions(+), 268 deletions(-)
Author: Rolf Turner
Diff between Iso versions 0.0-6 dated 2008-11-28 and 0.0-7 dated 2009-09-04
Title: Functions to perform isotonic regression.
Description: Does linear order and unimodal order isotonic regression.
DESCRIPTION | 12 +++++++-----
NAMESPACE |only
R/First.R | 6 ++----
inst/change.log |only
4 files changed, 9 insertions(+), 9 deletions(-)
Author: Xiaoyong Sun
Title: Mapping between BioIDs
Description: facilitate mapping between different databases, integrate
various ID systems and provide a full view from gene level,
mRNA level and functional level regarding one specific ID. The
mapping system is based on NCBI and UniProt web service.
Diff between BioIDMapper versions 1.1 dated 2009-02-16 and 1.2 dated 2009-09-04
BioIDMapper-1.1/BioIDMapper/Rinst604863912 |only BioIDMapper-1.1/BioIDMapper/Rutils438456933 |only BioIDMapper-1.2/BioIDMapper/DESCRIPTION | 34 +++++++++-------- BioIDMapper-1.2/BioIDMapper/R/bio.convert.R | 2 - BioIDMapper-1.2/BioIDMapper/R/parse1.R | 29 +++++++++----- BioIDMapper-1.2/BioIDMapper/R/updateTerm.R | 2 - BioIDMapper-1.2/BioIDMapper/inst/doc/BioIDMapper.pdf |binary BioIDMapper-1.2/BioIDMapper/inst/doc/BioIDMapper.rnw | 8 ++-- BioIDMapper-1.2/BioIDMapper/inst/setup/BioIDMapper.xml | 2 - 9 files changed, 44 insertions(+), 33 deletions(-)