Author: Simon Wood
Diff between mgcv versions 1.5-6 dated 2009-09-12 and 1.6-0 dated 2009-11-18
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.
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
Diff between gamm4 versions 0.0-1 dated 2009-09-07 and 0.0-2 dated 2009-11-18
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.
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
Diff between robustbase versions 0.4-5 dated 2009-01-18 and 0.5-0 dated 2009-11-18
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.
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(-)