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.
Diff between timereg versions 1.1-6 dated 2009-02-11 and 1.1-7 dated 2009-03-30
DESCRIPTION | 26 +++++++++++++++++--------- R/comprisk.r | 2 +- R/new.dynreg.r | 48 ++++++++++++++++++++++++------------------------ R/predict-timereg.r | 2 ++ data/mypbc.txt |only man/additive-lasso.Rd | 19 ++++++++----------- man/dynreg.Rd | 8 ++------ man/internal-addreg.Rd | 1 + man/krylow.pls.Rd | 16 +++++++--------- man/plot.dynreg.Rd | 2 +- man/surv-lars.Rd | 13 +++++++------ 11 files changed, 70 insertions(+), 67 deletions(-)
Author: Robin Nunkesser
Diff between rPorta versions 0.1-8 dated 2009-02-03 and 0.1-9 dated 2009-03-30
Title: R/PORTA interface
Description: An R interface to a modified version of PORTA. For more
information on PORTA see
http://www.zib.de/Optimization/Software/Porta/.
DESCRIPTION | 15 ++++++++++-----
src/printMethods.h | 2 +-
2 files changed, 11 insertions(+), 6 deletions(-)
Author: Lukas Meier
Title: Fitting user specified models with Group Lasso penalty
Description: Fits user specified (GLM-) models with Group Lasso penalty
Diff between grplasso versions 0.3-2 dated 2009-02-11 and 0.4-1 dated 2009-03-30
DESCRIPTION | 10 R/grplasso.R | 1191 +++++++++++++++++++++++---------------------- R/helpers.R | 512 +++++++++---------- R/zzz.R | 14 man/grplasso.Rd | 10 man/lambdamax.Rd | 7 tests/test_centerscaling.R |only tests/test_grplasso.R | 4 8 files changed, 907 insertions(+), 841 deletions(-)
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.
Diff between untb versions 1.3-3 dated 2009-01-20 and 1.4-2 dated 2009-03-30
DESCRIPTION | 21 ++++++++++++--------- inst |only 2 files changed, 12 insertions(+), 9 deletions(-)
Author: Robin K. S. Hankin
Title: create and investigate magic squares
Description: a collection of efficient, vectorized algorithms for the
creation and investigation of magic squares and hypercubes,
including a variety of functions for the manipulation and
analysis of arbitrarily dimensioned arrays. The package
includes methods for creating normal magic squares of any order
greater than 2. The ultimate intention is for the package to
be a computerized embodiment all magic square knowledge,
including direct numerical verification of properties of magic
squares (such as recent results on the determinant of
odd-ordered semimagic squares). Some antimagic functionality
is included. The package also serves as a rebuttal to the
often-heard comment "I thought R was just for statistics".
Diff between magic versions 1.4-3 dated 2009-01-22 and 1.4-4 dated 2009-03-30
magic-1.4-3/magic/inst/doc/magicpaper.tex |only magic-1.4-4/magic/DESCRIPTION | 30 ++++++++++++----------- magic-1.4-4/magic/inst/doc/magicpaper.pdf | 18 +++++++------- magic-1.4-4/magic/tests/aaa.R | 38 ++++++++++++++++++++---------- 4 files changed, 51 insertions(+), 35 deletions(-)
Author: Robin K. S. Hankin; qrng functions by Duncan Murdoch and
multimin by Andrew Clausen
Title: wrapper for the Gnu Scientific Library
Description: An R wrapper for the special functions and quasi random
number generators of the Gnu Scientific Library
(http://www.gnu.org/software/gsl/). See gsl-package.Rd for
details of overall package organization, and Misc.Rd for some
functions that are widely used in the package.
Diff between gsl versions 1.8-11 dated 2008-08-22 and 1.8-13 dated 2009-03-30
DESCRIPTION | 33 +++++++++++++++++---------------- man/Multimin.Rd | 2 ++ src/Makevars.win | 9 +++++++-- src/multimin.c | 10 ++++++++++ 4 files changed, 36 insertions(+), 18 deletions(-)
Author: Christopher Jackson
Title: Density strips and other methods for compactly illustrating
distributions
Description: Graphical methods for compactly illustrating probability
distributions, including density strips, density regions,
sectioned density plots and varying width strips.
Diff between denstrip versions 1.2 dated 2008-11-03 and 1.3 dated 2009-03-30
ChangeLog | 30 +++++++++++++++++++++++------- DESCRIPTION | 15 ++++++++++----- R/denstrip.R | 11 ++++++++--- inst/NEWS | 10 ++++++++++ man/cistrip.Rd | 14 ++++++++------ man/densregion.Rd | 7 +++++-- man/densregion.survfit.Rd | 6 +++--- man/denstrip.Rd | 2 +- man/denstrip.legend.Rd | 2 +- 9 files changed, 69 insertions(+), 28 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, the
population parameter theta based on various approaches,
nucleotide diversity, generalized skyline plots, estimation of
absolute evolutionary rates and clock-like trees using mean
path lengths, non-parametric rate smoothing and penalized
likelihood, classifying genes in trees using the
Klastorin-Misawa-Tajima approach. Phylogeny estimation can be
done with the NJ, BIONJ, and ME methods.
Diff between ape versions 2.2-4 dated 2009-02-09 and 2.3 dated 2009-03-30
ape-2.2-4/ape/data/xenarthra.R |only ape-2.2-4/ape/man/xenarthra.Rd |only ape-2.3/ape/ChangeLog | 43 ++++++++++++++++++++ ape-2.3/ape/DESCRIPTION | 41 ++++++++++--------- ape-2.3/ape/R/CDAM.global.R |only ape-2.3/ape/R/CDAM.post.R |only ape-2.3/ape/R/ace.R | 19 +++++---- ape-2.3/ape/R/drop.tip.R | 15 ++++--- ape-2.3/ape/R/is.ultrametric.R | 6 +- ape-2.3/ape/R/makeNodeLabel.R |only ape-2.3/ape/R/phymltest.R | 12 ++--- ape-2.3/ape/R/plot.phylo.R | 72 +++++++++++++++++------------------ ape-2.3/ape/R/read.tree.R | 27 ++++++++++--- ape-2.3/ape/R/write.tree.R | 80 +++++++++++++++++++++------------------ ape-2.3/ape/R/yule.time.R |only ape-2.3/ape/Thanks | 4 - ape-2.3/ape/data/mat3.RData |only ape-2.3/ape/data/mat5M3ID.RData |only ape-2.3/ape/data/mat5Mrand.RData |only ape-2.3/ape/data/woodmouse.R | 2 ape-2.3/ape/inst/doc/MoranI.pdf |binary ape-2.3/ape/man/CADM.global.Rd |only ape-2.3/ape/man/ace.Rd | 2 ape-2.3/ape/man/corGrafen.Rd | 2 ape-2.3/ape/man/corPagel.Rd | 6 +- ape-2.3/ape/man/makeNodeLabel.Rd |only ape-2.3/ape/man/mat3.Rd |only ape-2.3/ape/man/mat5M3ID.Rd |only ape-2.3/ape/man/mat5Mrand.Rd |only ape-2.3/ape/man/phymltest.Rd | 4 - ape-2.3/ape/man/plot.phylo.Rd | 14 +----- ape-2.3/ape/man/read.tree.Rd | 25 ++++++++---- ape-2.3/ape/man/rotate.Rd | 2 ape-2.3/ape/man/weight.taxo.Rd | 2 ape-2.3/ape/man/write.tree.Rd | 15 +++++-- ape-2.3/ape/man/yule.cov.Rd | 5 -- ape-2.3/ape/man/yule.time.Rd |only 37 files changed, 244 insertions(+), 154 deletions(-)