Author: Thomas Hoffmann
Diff between pbatR versions 2.1.5 dated 2009-06-18 and 2.2-0 dated 2009-11-23
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.
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
Diff between fbati versions 0.6.2 dated 2009-03-11 and 0.7-1 dated 2009-11-23
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.
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
Diff between ecolMod versions 1.2.1 dated 2009-02-20 and 1.2.2 dated 2009-11-23
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.
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
Diff between deSolve versions 1.5 dated 2009-10-16 and 1.5-1 dated 2009-11-23
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.
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
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
Diff between HardyWeinberg versions 1.3 dated 2009-03-27 and 1.4 dated 2009-11-23
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.
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
Diff between AlgDesign versions 1.0-12 dated 2009-09-30 and 1.1-0 dated 2009-11-23
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.
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
Diff between MASS versions 7.3-3 dated 2009-10-28 and 7.3-4 dated 2009-11-23
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).
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
Diff between caGUI versions 0.1-0 dated 2009-10-04 and 0.1-2 dated 2009-11-23
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.
DESCRIPTION | 10
R/caGUI.r | 807 ++++++++++++++++++++++++++++++++++++++++++++++++-----------
man/caGUI.Rd | 9
3 files changed, 671 insertions(+), 155 deletions(-)
Author: Andrew Gelman
Diff between arm versions 1.2-9.01 dated 2009-10-01 and 1.2-10 dated 2009-11-23
Title: Data Analysis Using Regression and Multilevel/Hierarchical
Models
Description: R functions for processing lm, glm, mer and polr outputs.
CHANGELOG | 4 ++++
DESCRIPTION | 8 +++-----
NAMESPACE | 1 +
man/invlogit.Rd | 6 ++++--
4 files changed, 12 insertions(+), 7 deletions(-)