Author: Tom Price
Diff between waveclock versions 1.0-0 dated 2008-06-16 and 1.0-1 dated 2008-07-11
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.
CHANGES |only
DESCRIPTION | 6
R/my.crc.R |only
R/my.crcrec.R | 234 ++++++++--------
R/waveclock.R | 791 +++++++++++++++++++++++++++++--------------------------
data |only
man/U2OS.Rd |only
man/waveclock.Rd | 82 +++--
8 files changed, 596 insertions(+), 517 deletions(-)
Author: Bernhard Pfaff
Title: VAR Modelling
Description: Estimation, lag selection, diagnostic testing, forecasting, causality analysis, forecast error variance decomposition and impulse response functions of VAR models and estimation of SVAR/SVEC models.
Diff between vars versions 1.3-8 dated 2008-05-13 and 1.4-0 dated 2008-07-11
DESCRIPTION | 6 +++--- inst/CITATION |only inst/ChangeLog | 6 ++++++ inst/book-ex |only inst/doc |only 5 files changed, 9 insertions(+), 3 deletions(-)
Author: Bernhard Pfaff
Diff between urca versions 1.1-6 dated 2007-11-03 and 1.1-7 dated 2008-07-11
Title: Unit root and cointegration tests for time series data
Description: Unit root and cointegration tests encountered in applied
econometric analysis are implemented.
DESCRIPTION | 6 +++---
R/alrtest.R | 4 ++--
inst/CITATION | 12 +++++++-----
inst/ChangeLog | 6 ++++++
inst/book-ex |only
5 files changed, 18 insertions(+), 10 deletions(-)
Author: Gilles Pujol (this package was originally developped at Commissariat a
l'Energie Atomique CEA, Service d'Etudes et de Simulation du Comportement des
Combustibles CEA/DEN/CAD/DEC/SESC, France ; the author would like to thank :
Patrick Obry, Bertrand Iooss, Claire Cannamela and Frederic Michel).
Title: Sensitivity Analysis
Description: This package allows to perform sensitivity analyses within the R
environment. Implemented methods are : linear sensitivity analysis (SRC,
PCC, rank analysis), the screening method of Morris, the Sobol global
sensitivity indices (two methods of estimation), and the FAST method.
Diff between sensitivity versions 1.3-0 dated 2007-01-05 and 1.3-1 dated 2008-07-11
COPYRIGHT | 3 +-- DESCRIPTION | 8 ++++---- HISTORY | 1 + R/plot.R | 4 ++-- inst/doc/sensitivity_appendix.Rnw | 4 +++- inst/doc/sensitivity_appendix.pdf |binary inst/doc/stats.bib |only 7 files changed, 11 insertions(+), 9 deletions(-)
Author: David Firth with contributions from Heather Turner
Title: Relative Contribution of Effects in a Regression Model
Description: Functions to facilitate inference on the relative importance of predictors in a linear or generalized linear model, and a couple of useful Tcl/Tk widgets.
Diff between relimp versions 0.9-9 dated 2008-06-06 and 1.0-1 dated 2008-07-11
DESCRIPTION | 6 +++--- R/showData.R | 21 +++++++++++---------- 2 files changed, 14 insertions(+), 13 deletions(-)
Author: Douglas Bates
Diff between lme4 versions 0.999375-20 dated 2008-06-26 and 0.999375-21 dated 2008-07-11
Title: Linear mixed-effects models using S4 classes
Description: Fit linear and generalized linear mixed-effects models.
DESCRIPTION | 8 ++++----
inst/doc/Implementation.pdf |binary
inst/doc/PLSvGLS.pdf |binary
inst/doc/Theory.pdf |binary
4 files changed, 4 insertions(+), 4 deletions(-)
Author: Virasakdi Chongsuvivatwong
Diff between epicalc versions 2.7.1.1 dated 2008-07-08 and 2.7.1.2 dated 2008-07-11
Title: Epidemiological calculator
Description: Functions making R easy for epidemiological calculation.
DESCRIPTION | 6 +++---
data/VCT.rdata |binary
2 files changed, 3 insertions(+), 3 deletions(-)
Author: Andrew Gelman
Diff between arm versions 1.1-9 dated 2008-07-09 and 1.1-10 dated 2008-07-11
Title: Data Analysis Using Regression and Multilevel/Hierarchical Models
Description: R functions for processing lm, glm, mer and polr outputs.
CHANGELOG | 5 +++++
DESCRIPTION | 6 +++---
R/rescale.R | 19 ++++++++++++++-----
man/rescale.Rd | 2 +-
4 files changed, 23 insertions(+), 9 deletions(-)
Author: Emmanuel Paradis, Ben Bolker, Julien Claude, Hoa Sien Cuong,
Richard Desper, Benoit Durand, Julien Dutheil, Olivier Gascuel,
Gangolf Jobb, Christoph Heibl, Vincent Lefort, 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, ME, and ML methods.
Diff between ape versions 2.2 dated 2008-05-08 and 2.2-1 dated 2008-07-11
Changes | 53 ++++++++++++++++- DESCRIPTION | 6 - R/DNA.R | 23 +++++++ R/collapse.singles.R | 15 ++++ R/cophyloplot.R | 4 - R/dist.topo.R | 6 - R/makeLabel.R |only R/mlphylo.R | 10 +-- R/read.dna.R | 99 +++++++++++++++++--------------- R/read.nexus.R | 20 +++++- R/root.R | 32 +++++++++- R/sh.test.R | 8 +- R/unique.multiPhylo.R | 14 ++-- R/write.dna.R | 154 +++++++++++++++++++++----------------------------- Thanks | 4 - inst/doc/MoranI.pdf |binary man/bind.tree.Rd | 2 man/boot.phylo.Rd | 17 ++--- man/consensus.Rd | 2 man/cophyloplot.Rd | 2 man/corPagel.Rd | 2 man/del.gaps.Rd |only man/makeLabel.Rd |only man/read.dna.Rd | 27 ++++++-- man/write.dna.Rd | 30 +++++---- src/mlphylo.c | 123 ++++++++++++++------------------------- 26 files changed, 371 insertions(+), 282 deletions(-)
Author: Grant Izmirlian
Title: Power in a Group Sequential Design
Description: Tools to compute power in a group sequential design. SimPwrGSD C-kernel is a simulation routine that is similar in spirit to dssp2.f by Gu and Lai, but with major improvements. AsyPwrGSD has exactly the same range of application as SimPwrGSD but uses asymptotic methods and runs _much_ faster.
Diff between PwrGSD versions 1.1 dated 2008-05-14 and 1.15 dated 2008-07-11
DESCRIPTION | 4 R/PwrGSD.R | 37 inst/doc/GrpSeqBnds-vignette-1-incl-ex1-plot.eps |only inst/doc/GrpSeqBnds-vignette-1-incl-ex1-plot.pdf |only inst/doc/GrpSeqBnds-vignette-1-incl-ex2-plot.eps |only inst/doc/GrpSeqBnds-vignette-1-incl-ex2-plot.pdf |only inst/doc/GrpSeqBnds-vignette-1-incl-ex3-plot.eps |only inst/doc/GrpSeqBnds-vignette-1-incl-ex3-plot.pdf |only inst/doc/GrpSeqBnds-vignette-1-incl-ex4-plot.eps |only inst/doc/GrpSeqBnds-vignette-1-incl-ex4-plot.pdf |only inst/doc/GrpSeqBnds-vignette-1.Rnw | 1 inst/doc/GrpSeqBnds-vignette-1.log | 4 inst/doc/GrpSeqBnds-vignette-1.pdf |binary inst/doc/GrpSeqBnds-vignette-1.tex | 46 inst/doc/PwrGSD-vignette-1.Rnw | 2 inst/doc/PwrGSD-vignette-1.pdf |binary inst/doc/PwrGSD-vignette-1.tex |only inst/doc/Rplots.ps |42528 +++++++++++----------- inst/doc/cpd-PwrGSD-vignette-1-fig1-LanDemets.pdf | 4 inst/doc/cpd-PwrGSD-vignette-1-fig2-StochCurt.pdf | 4 inst/doc/cpd-PwrGSD-vignette-1.Rnw | 2 inst/doc/cpd-PwrGSD-vignette-1.log | 4 inst/doc/cpd-PwrGSD-vignette-1.pdf |binary inst/doc/cpd-PwrGSD-vignette-1.tex | 4 man/Ch1-PwrGSD.Rd | 10 man/Ch2-cpd.PwrGSD.Rd | 2 src/AsyPwrGSD.c | 10 27 files changed, 21336 insertions(+), 21326 deletions(-)
Author: Bjoern Bornkamp, Jose Pinheiro and Frank Bretz
Title: Design and Analysis of Dose-Finding Studies
Description: This package implements a methodology for the design and analysis of
dose-response studies that combines aspects of multiple comparison procedures
and modeling approaches (Bretz, Pinheiro and Branson, 2005, Biometrics 61, 738-748).
The package provides tools for the analysis of dose finding trials as well as a variety
of tools necessary to plan a trial to be conducted with the MCPMod methodology.
Diff between MCPMod versions 0.1-3 dated 2008-05-06 and 0.1-4 dated 2008-07-11
ChangeLog | 9 +++++++++ DESCRIPTION | 6 +++--- R/analysisMM.R | 31 ++++++++++++++++++++----------- man/MCPMod-package.Rd | 4 ++-- 4 files changed, 34 insertions(+), 16 deletions(-)
Author: Andreas Ruckstuhl, Thomas Unternaehrer, Rene Locher
Title: Utilities of Institute of Data Analyses and Process Design (www.idp.zhaw.ch)
Description: The IDPmisc package contains different high-level graphics functions for displaying large datasets, displaying circular data in a very flexible way, finding local maxima, brewing color ramps, drawing nice arrows, zooming 2D-plots, creating figures with differently colored margin and plot region. In addition, the package contains auxiliary functions for data manipulation like omitting observations with irregular values or selecting data by logical vectors, which include NAs. Other functions are especially useful in spectroscopy and analyses of environmental data: robust baseline fitting, finding peaks in spectra.
Diff between IDPmisc versions 0.9.5 dated 2007-10-03 and 0.9.7 dated 2008-07-11
IDPmisc-0.9.5/IDPmisc/man/ixyplot.Rd |only IDPmisc-0.9.5/IDPmisc/man/longts.plot.Rd |only IDPmisc-0.9.7/IDPmisc/ChangeLog | 32 +++ IDPmisc-0.9.7/IDPmisc/DESCRIPTION | 9 - IDPmisc-0.9.7/IDPmisc/NAMESPACE | 7 IDPmisc-0.9.7/IDPmisc/R/Image.R | 14 + IDPmisc-0.9.7/IDPmisc/R/iplot.R |only IDPmisc-0.9.7/IDPmisc/R/ixyplot.R | 165 +++----------------- IDPmisc-0.9.7/IDPmisc/R/longts.plot.R | 23 +- IDPmisc-0.9.7/IDPmisc/R/longtsPlot.R |only IDPmisc-0.9.7/IDPmisc/R/plot.onepage.R | 34 ++-- IDPmisc-0.9.7/IDPmisc/R/plot.page.R |only IDPmisc-0.9.7/IDPmisc/R/poster.plot.R | 8 IDPmisc-0.9.7/IDPmisc/R/showColors.R | 5 IDPmisc-0.9.7/IDPmisc/man/IDPmisc-package.Rd | 9 - IDPmisc-0.9.7/IDPmisc/man/Image.Rd | 11 - IDPmisc-0.9.7/IDPmisc/man/iplot.Rd |only IDPmisc-0.9.7/IDPmisc/man/ixyplot-deprecated.Rd |only IDPmisc-0.9.7/IDPmisc/man/longts.plot-deprecated.Rd |only IDPmisc-0.9.7/IDPmisc/man/longtsPlot.Rd |only IDPmisc-0.9.7/IDPmisc/man/pkg-internal.Rd | 18 +- IDPmisc-0.9.7/IDPmisc/man/rfbaseline.Rd | 2 22 files changed, 148 insertions(+), 189 deletions(-)
Author: Miika Ahdesmaki, Konstantinos Fokianos, and
Korbinian Strimmer.
Title: Identification of Periodically Expressed Genes
Description: The GeneCycle package implements the approaches of Wichert et al.
(2004), Ahdesmaki et al. (2005) and Ahdesmaki et al. (2007) for detecting periodically
expressed genes from gene expression time series data.
Diff between GeneCycle versions 1.0.4 dated 2008-06-03 and 1.1.0 dated 2008-07-11
GeneCycle-1.0.4/GeneCycle/COPYING |only GeneCycle-1.1.0/GeneCycle/CHANGES | 9 GeneCycle-1.1.0/GeneCycle/DESCRIPTION | 16 - GeneCycle-1.1.0/GeneCycle/LICENSE |only GeneCycle-1.1.0/GeneCycle/R/robust.g.test.R | 68 +++- GeneCycle-1.1.0/GeneCycle/R/robust.spectrum.R | 274 +++++++++++++++++--- GeneCycle-1.1.0/GeneCycle/man/GeneCycle-internal.Rd | 6 GeneCycle-1.1.0/GeneCycle/man/robust.g.test.Rd | 171 +++++++++--- 8 files changed, 442 insertions(+), 102 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 0.2-0 dated 2008-02-01 and 0.4-0 dated 2008-07-11
FAiR-0.2-0/FAiR/inst/doc/FAiR.aux |only FAiR-0.2-0/FAiR/inst/doc/FAiR.log |only FAiR-0.2-0/FAiR/inst/doc/FAiR.tex |only FAiR-0.2-0/FAiR/inst/doc/FAiR.toc |only FAiR-0.2-0/FAiR/inst/doc/screenshots |only FAiR-0.2-0/FAiR/man/FAiR-package.Rd |only FAiR-0.2-0/FAiR/man/Factanal.Rd |only FAiR-0.2-0/FAiR/man/Rotate.Rd |only FAiR-0.2-0/FAiR/man/classFA.Rd |only FAiR-0.2-0/FAiR/man/make_criteria.Rd |only FAiR-0.2-0/FAiR/man/make_restrictions.Rd |only FAiR-0.2-0/FAiR/tests/tests.R |only FAiR-0.4-0/FAiR/DESCRIPTION | 20 FAiR-0.4-0/FAiR/LICENSE |only FAiR-0.4-0/FAiR/NAMESPACE | 84 FAiR-0.4-0/FAiR/NEWS |only FAiR-0.4-0/FAiR/R/AllS4Generics.R |only FAiR-0.4-0/FAiR/R/Classes.R | 1629 ++ FAiR-0.4-0/FAiR/R/Criteria.R | 845 - FAiR-0.4-0/FAiR/R/FAiR.R | 723 - FAiR-0.4-0/FAiR/R/GPArotation.R |only FAiR-0.4-0/FAiR/R/GPLv3_or_later.R |only FAiR-0.4-0/FAiR/R/Menus.R | 2062 +-- FAiR-0.4-0/FAiR/R/S3methods.R | 258 FAiR-0.4-0/FAiR/R/S4methods.R | 5088 ++++--- FAiR-0.4-0/FAiR/R/TestStatistics.R |only FAiR-0.4-0/FAiR/R/Utils.R | 2915 +++- FAiR-0.4-0/FAiR/R/zzz.R | 61 FAiR-0.4-0/FAiR/inst/doc/FAiR.R |only FAiR-0.4-0/FAiR/inst/doc/FAiR.Rnw | 2257 ++- FAiR-0.4-0/FAiR/inst/doc/FAiR.dvi |binary FAiR-0.4-0/FAiR/inst/doc/FAiR.lyx | 8646 +++++++++---- FAiR-0.4-0/FAiR/inst/doc/FAiR.lyx.emergency |only FAiR-0.4-0/FAiR/inst/doc/FAiR.pdf |14617 +++++++++------------- FAiR-0.4-0/FAiR/inst/doc/FAiR.tex.backup | 1951 +- FAiR-0.4-0/FAiR/inst/doc/screenshots2 |only FAiR-0.4-0/FAiR/man/00FAiR-package.Rd |only FAiR-0.4-0/FAiR/man/01make_manifest.Rd |only FAiR-0.4-0/FAiR/man/02make_restrictions.Rd |only FAiR-0.4-0/FAiR/man/03Factanal.Rd |only FAiR-0.4-0/FAiR/man/04Rotate.Rd |only FAiR-0.4-0/FAiR/man/FAiR-internal.Rd |only FAiR-0.4-0/FAiR/man/GPA2FA.Rd |only FAiR-0.4-0/FAiR/man/S3methods.Rd | 159 FAiR-0.4-0/FAiR/man/S4methods.Rd | 216 FAiR-0.4-0/FAiR/man/create_FAobject.Rd |only FAiR-0.4-0/FAiR/man/equality_restriction-class.Rd |only FAiR-0.4-0/FAiR/man/loadings.Rd |only FAiR-0.4-0/FAiR/man/manifest-class.Rd |only FAiR-0.4-0/FAiR/man/mapping_rule.Rd |only FAiR-0.4-0/FAiR/man/model_comparison.Rd |only FAiR-0.4-0/FAiR/man/parameter-class.Rd |only FAiR-0.4-0/FAiR/man/read.cefa.Rd | 59 FAiR-0.4-0/FAiR/man/read.triangular.Rd |only FAiR-0.4-0/FAiR/man/restrictions-class.Rd | 306 FAiR-0.4-0/FAiR/man/restrictions2Mathomatic.Rd |only FAiR-0.4-0/FAiR/man/restrictions2RAM.Rd |only FAiR-0.4-0/FAiR/man/restrictions2draws.Rd |only FAiR-0.4-0/FAiR/man/restrictions2model.Rd |only FAiR-0.4-0/FAiR/man/summary.FA-class.Rd | 49 FAiR-0.4-0/FAiR/src |only FAiR-0.4-0/FAiR/tests/testsCFA.R |only FAiR-0.4-0/FAiR/tests/testsEFA.R |only FAiR-0.4-0/FAiR/tests/testsMANIFEST.R |only FAiR-0.4-0/FAiR/tests/testsMICRO.R |only FAiR-0.4-0/FAiR/tests/testsRESTRICTIONS.R |only FAiR-0.4-0/FAiR/tests/testsSEFA.R |only 67 files changed, 25364 insertions(+), 16581 deletions(-)
Author: David Firth
Title: Bradley-Terry models
Description: Specify and fit the Bradley-Terry model and structured versions
Diff between BradleyTerry versions 0.8-5 dated 2005-08-05 and 0.8-7 dated 2008-07-11
DESCRIPTION | 13 +++++++------ INDEX | 4 +++- R/BTm.R | 19 +++++++++---------- data/flatlizards.rda |only man/BTm.Rd | 13 ++++++------- man/flatlizards.Rd |only 6 files changed, 25 insertions(+), 24 deletions(-)