Author: Uwe Ligges
Diff between tuneR versions 0.2-10 dated 2009-03-29 and 0.2-11 dated 2009-10-15
Title: Analysis of music
Description: Collection of tools to analyze music, handling wave files,
transcription, ...
DESCRIPTION | 8 ++++----
man/WaveArith.Rd | 2 +-
man/plot.Rd | 2 +-
3 files changed, 6 insertions(+), 6 deletions(-)
Author: Uwe Ligges
Diff between scatterplot3d versions 0.3-28 dated 2009-05-28 and 0.3-29 dated 2009-10-15
Title: 3D Scatter Plot
Description: Plots a three dimensional (3D) point cloud.
CHANGES | 1 +
DESCRIPTION | 8 ++++----
R/scatterplot3d.R | 12 +++++++++---
inst/doc/s3d.pdf | 6 +++---
man/scatterplot3d.Rd | 4 +---
5 files changed, 18 insertions(+), 13 deletions(-)
Author: Matthew Denwood
Diff between runjags versions 0.9.4-2 dated 2009-05-28 and 0.9.5-1 dated 2009-10-15
Title: Run Bayesian MCMC Models in the BUGS syntax from Within R
Description: A set of functions to allow any user specified model to be
run in JAGS from within R, returning the MCMC chains as R
objects. Includes functions to read external WinBUGS type
textfiles, and allows several ways of automatically specifying
model data from existing R objects or R functions. Also
includes functions to automatically calculate model run length,
autocorrealtion and Gelman Rubin statistic diagnostics for all
models to simplify the process of achieving chain convergence.
Designed for maximum compatibility with WinBUGS syntax,
although minor modification to existing .bug files will be
required. Requires Just Another Gibbs Sampler (JAGS) for most
functions, see: http://www-fis.iarc.fr/~martyn/software/jags/
DESCRIPTION | 8 -
R/autorun.jags.R | 28 ++---
R/combine.mcmc.R | 2
R/invisible.R | 25 +---
R/read.winbugs.R | 244 ++++++++++++++++++++++++++++++++++++++++++++---
R/run.jags.R | 14 +-
inst/CITATION | 20 ++-
inst/version_history.txt | 25 ++++
man/autorun.jags.Rd | 3
man/autorun.jagsfile.Rd | 2
man/combine.mcmc.Rd | 4
man/read.winbugs.Rd | 4
man/run.jagsfile.Rd | 2
13 files changed, 309 insertions(+), 72 deletions(-)
Author: Fortran original by Leo Breiman and Adele Cutler, R port by
Andy Liaw and Matthew Wiener.
Title: Breiman and Cutler's random forests for classification and
regression
Description: Classification and regression based on a forest of trees
using random inputs.
Diff between randomForest versions 4.5-30 dated 2009-02-26 and 4.5-31 dated 2009-10-15
DESCRIPTION | 29 +- NAMESPACE | 1 R/margin.R | 48 ++- R/predict.randomForest.R | 43 +-- R/randomForest.default.R | 14 - inst/NEWS | 15 + man/MDSplot.Rd | 2 man/getTree.Rd | 8 man/margin.Rd | 29 +- man/predict.randomForest.Rd | 10 man/randomForest.Rd | 5 src/regTree.c | 268 ++++++++++----------- src/rf.c | 545 ++++++++++++++++++++++---------------------- src/rfutils.c | 65 ++--- 14 files changed, 569 insertions(+), 513 deletions(-)
Author: Jose Pinheiro
Diff between nlme versions 3.1-95 dated 2009-10-05 and 3.1-96 dated 2009-10-15
Title: Linear and Nonlinear Mixed Effects Models
Description: Fit and compare Gaussian linear and nonlinear
mixed-effects models.
ChangeLog | 5 +++++
DESCRIPTION | 8 ++++----
inst/po/de/LC_MESSAGES/R-nlme.mo |binary
inst/po/de/LC_MESSAGES/nlme.mo |binary
po/R-de.po | 31 ++++++++++++++-----------------
po/de.po | 6 +++---
6 files changed, 26 insertions(+), 24 deletions(-)
Author: Paulo J. Ribeiro Jr
Diff between geoR versions 1.6-25 dated 2009-02-19 and 1.6-27 dated 2009-10-15
Title: Analysis of geostatistical data
Description: Geostatistical analysis including traditional,
likelihood-based and Bayesian methods.
DESCRIPTION | 15 ++++++----
R/auxiliar.R | 66 ++++++++++++++++++++++++------------------------
R/corcov.R | 48 +++++++++-------------------------
R/geobayes.R | 33 +++++++++++-------------
R/geodata.R | 10 ++++---
R/likGRF.R | 19 ++++++-------
R/profiles.R | 2 -
R/variofit.R | 3 +-
inst/doc/CHANGES | 18 +++++++++++++
man/BoxCox.Rd | 2 -
man/boxcox.fit.Rd | 2 -
man/boxcox.geodata.Rd | 4 +-
man/ca20.Rd | 6 ++--
man/geoR-defunct.Rd | 2 -
man/image.kriging.Rd | 4 +-
man/krige.bayes.Rd | 18 ++-----------
man/krige.conv.Rd | 4 +-
man/pars.limits.Rd | 2 -
man/plot.geodata.Rd | 2 -
man/plot.krige.bayes.Rd | 4 +-
man/points.geodata.Rd | 7 ++---
man/soja98.Rd | 31 ++++++++++------------
man/summary.likGRF.Rd | 2 -
man/wo.Rd | 2 +
man/wrappers.Rd | 1
man/wrc.Rd | 1
man/xvalid.Rd | 2 +
27 files changed, 154 insertions(+), 156 deletions(-)
Author: John Fox
Diff between effects versions 2.0-9 dated 2009-10-14 and 2.0-10 dated 2009-10-15
Title: Effect Displays for Linear, Generalized Linear,
Multinomial-Logit, and Proportional-Odds Logit Models
Description: Graphical and tabular effect displays, e.g., of
interactions, for linear generalized linear, multinomial-logit,
and proportional-odds logit models.
DESCRIPTION | 13 ++---
R/effects.R | 69 ++++++++++------------------
R/utilities.R | 118 +++++++++++++++++++++++--------------------------
inst/CHANGES | 7 ++
man/effects-package.Rd | 12 +---
5 files changed, 96 insertions(+), 123 deletions(-)
Author: S original
Diff between boot versions 1.2-40 dated 2009-10-07 and 1.2-41 dated 2009-10-15
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 | 4 ++++
DESCRIPTION | 8 ++++----
inst/po/de/LC_MESSAGES/R-boot.mo |binary
inst/po/en@quot/LC_MESSAGES/R-boot.mo |binary
inst/po/ru/LC_MESSAGES/R-boot.mo |binary
po/R-boot.pot | 4 ++--
po/R-de.po | 7 +++----
po/R-en@quot.po | 6 +++---
po/R-ru.po | 23 ++++++++++-------------
9 files changed, 26 insertions(+), 26 deletions(-)
Author: Jonathan M. Lees
Title: Seismic Time Series Analysis Tools
Description: Multiple interactive codes to analyze seismic data, via,
spectrum analysis, wavelet transforms, particle motion,
hodograms.
Diff between RSEIS versions 2.1-6 dated 2009-06-02 and 2.2-0 dated 2009-10-15
RSEIS-2.1-6/RSEIS/R/spec.taper.R |only RSEIS-2.1-6/RSEIS/man/spec.taper.Rd |only RSEIS-2.2-0/RSEIS/DESCRIPTION | 8 RSEIS-2.2-0/RSEIS/R/ASCII.SEISN.R |only RSEIS-2.2-0/RSEIS/R/CHOP.SEISN.R | 2 RSEIS-2.2-0/RSEIS/R/DISPLACE.SEISN.R | 40 ++- RSEIS-2.2-0/RSEIS/R/DOsgram.R |only RSEIS-2.2-0/RSEIS/R/FILT.SEISN.R | 8 RSEIS-2.2-0/RSEIS/R/MTMgabor.R |only RSEIS-2.2-0/RSEIS/R/Mine.seis.R | 104 ++++++-- RSEIS-2.2-0/RSEIS/R/PICK.GEN.R | 395 ++++++++++++++++++++------------ RSEIS-2.2-0/RSEIS/R/SPECT.drive.R | 14 + RSEIS-2.2-0/RSEIS/R/VELOCITY.SEISN.R | 25 +- RSEIS-2.2-0/RSEIS/R/applytaper.R | 23 + RSEIS-2.2-0/RSEIS/R/doGABOR.AR.R |only RSEIS-2.2-0/RSEIS/R/doGABOR.MTM.R |only RSEIS-2.2-0/RSEIS/R/dowiggles.R |only RSEIS-2.2-0/RSEIS/R/evolAR.R | 2 RSEIS-2.2-0/RSEIS/R/evolMTM.R | 2 RSEIS-2.2-0/RSEIS/R/evolfft.R | 5 RSEIS-2.2-0/RSEIS/R/genrick.R |only RSEIS-2.2-0/RSEIS/R/infoDB.R |only RSEIS-2.2-0/RSEIS/R/markseis24.R |only RSEIS-2.2-0/RSEIS/R/plotarrivals.R |only RSEIS-2.2-0/RSEIS/R/plotevol.R | 11 RSEIS-2.2-0/RSEIS/R/rsspec.taper.R |only RSEIS-2.2-0/RSEIS/R/showdatetime.R | 3 RSEIS-2.2-0/RSEIS/R/sigconv.R |only RSEIS-2.2-0/RSEIS/R/sigconvGR.R |only RSEIS-2.2-0/RSEIS/R/symshot1.R |only RSEIS-2.2-0/RSEIS/R/trapz.R | 9 RSEIS-2.2-0/RSEIS/R/wiggleimage.R |only RSEIS-2.2-0/RSEIS/R/winmark.R | 123 ++++++++- RSEIS-2.2-0/RSEIS/R/winseis24.R | 8 RSEIS-2.2-0/RSEIS/demo/MTM.R | 2 RSEIS-2.2-0/RSEIS/inst/doc/hodo.pdf |binary RSEIS-2.2-0/RSEIS/inst/doc/rseis.pdf |binary RSEIS-2.2-0/RSEIS/man/ASCII.SEISN.Rd |only RSEIS-2.2-0/RSEIS/man/DISPLACE.SEISN.Rd | 2 RSEIS-2.2-0/RSEIS/man/DOsgram.Rd |only RSEIS-2.2-0/RSEIS/man/FILT.SEISN.Rd | 2 RSEIS-2.2-0/RSEIS/man/MTMgabor.Rd |only RSEIS-2.2-0/RSEIS/man/Mine.seis.Rd | 3 RSEIS-2.2-0/RSEIS/man/PICK.GEN.Rd | 33 ++ RSEIS-2.2-0/RSEIS/man/PLOT.MATN.Rd | 6 RSEIS-2.2-0/RSEIS/man/RSEIS-package.Rd | 6 RSEIS-2.2-0/RSEIS/man/VELOCITY.SEISN.Rd | 2 RSEIS-2.2-0/RSEIS/man/doGABOR.AR.Rd |only RSEIS-2.2-0/RSEIS/man/doGABOR.MTM.Rd |only RSEIS-2.2-0/RSEIS/man/dowiggles.Rd |only RSEIS-2.2-0/RSEIS/man/evolfft.Rd | 7 RSEIS-2.2-0/RSEIS/man/genrick.Rd |only RSEIS-2.2-0/RSEIS/man/infoDB.Rd |only RSEIS-2.2-0/RSEIS/man/markseis24.Rd |only RSEIS-2.2-0/RSEIS/man/pickseis24.Rd | 4 RSEIS-2.2-0/RSEIS/man/plotarrivals.Rd |only RSEIS-2.2-0/RSEIS/man/rsspec.taper.Rd |only RSEIS-2.2-0/RSEIS/man/sigconv.Rd |only RSEIS-2.2-0/RSEIS/man/sigconvGR.Rd |only RSEIS-2.2-0/RSEIS/man/symshot1.Rd |only RSEIS-2.2-0/RSEIS/man/wiggleimage.Rd |only RSEIS-2.2-0/RSEIS/man/winmark.Rd | 54 +++- RSEIS-2.2-0/RSEIS/man/winseis24.Rd | 8 63 files changed, 657 insertions(+), 254 deletions(-)
Author: Jonathan M. Lees
Title: Graphics for Spherical Distributions and Earthquake Focal
Mechanisms
Description: Graphics for statistics on a sphere, as applied to
geological fault data, crystalogaphy, earthquake focal
mechanisms, radiation patterns, ternary plots and
geographical/geological maps.
Diff between RFOC versions 1.0-5 dated 2009-01-26 and 1.0-6 dated 2009-10-15
DESCRIPTION | 14 ++++++++++---- inst/doc/focalmec.pdf |binary man/RFOC-package.Rd | 5 ++--- 3 files changed, 12 insertions(+), 7 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. Now includes functionality
provided by Francois Munoz and Andrea Manica.
Diff between untb versions 1.4-2 dated 2009-03-30 and 1.6-1 dated 2009-10-15
DESCRIPTION | 9 R/munoz.R |only R/sysdata.rda |binary R/untb.R | 204 +- data/caruso.R |only data/ghats.rda |only data/saunders.R | 16 inst/CITATION |only inst/doc/untbpaper.pdf | 3555 +++++++++++++++++++++----------------------- man/bci.Rd | 11 man/caruso.Rd |only man/ghats.Rd |only man/logS1.Rd | 8 man/logkda.Rd | 13 man/optimal.params.gst.Rd |only man/optimal.params.sloss.Rd |only man/optimal.prob.Rd | 2 man/saunders.Rd | 49 man/simpson.Rd | 50 man/untb.package.Rd | 14 20 files changed, 2018 insertions(+), 1913 deletions(-)
Author: M. Höhle with contributions from T. Correa, M. Hofmann, C.
Lang, M. Paul, A. Riebler, S. Steiner and V. Wimmer
Title: Modeling and monitoring discrete response time series
Description: A package implementing statistical methods for the
modeling and change-point detection in time series of counts,
proportions and categorical data. Focus is on outbreak
detection in count data time series originating from public
health surveillance of infectious diseases, but applications
could just as well originate from environmetrics, reliability
engineering, econometrics or social sciences. Currently the
package contains implementations typical outbreak detection
procedures such as Stroup et. al (1989), Farrington et al,
(1996), Rossi et al. (1999), Rogerson and Yamada (2001), a
Bayesian approach, negative binomial CUSUM methods and a
detector based on generalized likelihood ratios. Furthermore,
inference methods for the retrospective infectious disease
model in Held et al. (2005), Held et al. (2006) and Paul et al.
(2008) are provided. A novel CUSUM approach combining logistic
and multinomial logistic modelling is also included. The
package contains several real-world datasets, the ability to
simulate outbreak data, visualize the results of the monitoring
in temporal, spatial or spatio-temporal fashion.
Diff between surveillance versions 1.0-2 dated 2009-03-06 and 1.1-2 dated 2009-10-15
surveillance-1.0-2/surveillance/inst/doc/SurveillanceFlowchart.sxd |only surveillance-1.0-2/surveillance/inst/doc/flowchart.pdf |only surveillance-1.1-2/surveillance/DESCRIPTION | 49 + surveillance-1.1-2/surveillance/NEWS | 48 + surveillance-1.1-2/surveillance/R/AllClass.R | 6 surveillance-1.1-2/surveillance/R/AllGeneric.R | 78 ++ surveillance-1.1-2/surveillance/R/LRCUSUM.runlength.R |only surveillance-1.1-2/surveillance/R/algo_bayes.R | 6 surveillance-1.1-2/surveillance/R/algo_cdc.R | 8 surveillance-1.1-2/surveillance/R/algo_farrington.R | 135 +++- surveillance-1.1-2/surveillance/R/algo_glrnb.R | 17 surveillance-1.1-2/surveillance/R/algo_twins.R | 41 - surveillance-1.1-2/surveillance/R/catCUSUM.R |only surveillance-1.1-2/surveillance/R/pairedbinCUSUM.R |only surveillance-1.1-2/surveillance/R/plot_multi.R | 4 surveillance-1.1-2/surveillance/R/stcd.R |only surveillance-1.1-2/surveillance/R/sts.R | 315 ++++++---- surveillance-1.1-2/surveillance/R/wrap_univariate.R | 19 surveillance-1.1-2/surveillance/THANKS | 2 surveillance-1.1-2/surveillance/data/abattoir.RData |only surveillance-1.1-2/surveillance/data/deleval.RData |only surveillance-1.1-2/surveillance/data/momo.RData |only surveillance-1.1-2/surveillance/demo/00Index | 2 surveillance-1.1-2/surveillance/demo/biosurvbook.R |only surveillance-1.1-2/surveillance/demo/cost.R | 5 surveillance-1.1-2/surveillance/inst/CITATION | 36 - surveillance-1.1-2/surveillance/inst/doc/.Rresults |binary surveillance-1.1-2/surveillance/inst/doc/Rplots.pdf | 94 +- surveillance-1.1-2/surveillance/inst/doc/figs/vignette-002.eps | 2 surveillance-1.1-2/surveillance/inst/doc/figs/vignette-002.pdf | 26 surveillance-1.1-2/surveillance/inst/doc/figs/vignette-003.eps | 2 surveillance-1.1-2/surveillance/inst/doc/figs/vignette-003.pdf | 24 surveillance-1.1-2/surveillance/inst/doc/figs/vignette-004.eps | 2 surveillance-1.1-2/surveillance/inst/doc/figs/vignette-004.pdf | 26 surveillance-1.1-2/surveillance/inst/doc/figs/vignette-007.eps | 2 surveillance-1.1-2/surveillance/inst/doc/figs/vignette-007.pdf | 28 surveillance-1.1-2/surveillance/inst/doc/figs/vignette-020.eps | 2 surveillance-1.1-2/surveillance/inst/doc/figs/vignette-020.pdf | 26 surveillance-1.1-2/surveillance/inst/doc/figs/vignette-021.eps | 2 surveillance-1.1-2/surveillance/inst/doc/figs/vignette-021.pdf | 24 surveillance-1.1-2/surveillance/inst/doc/figs/vignette_glrnb-002.eps | 2 surveillance-1.1-2/surveillance/inst/doc/figs/vignette_glrnb-002.pdf | 26 surveillance-1.1-2/surveillance/inst/doc/figs/vignette_glrnb-004.eps | 2 surveillance-1.1-2/surveillance/inst/doc/figs/vignette_glrnb-004.pdf | 24 surveillance-1.1-2/surveillance/inst/doc/figs/vignette_glrnb-005.eps | 2 surveillance-1.1-2/surveillance/inst/doc/figs/vignette_glrnb-005.pdf | 26 surveillance-1.1-2/surveillance/inst/doc/figs/vignette_glrnb-012.eps | 2 surveillance-1.1-2/surveillance/inst/doc/figs/vignette_glrnb-012.pdf | 24 surveillance-1.1-2/surveillance/inst/doc/figs/vignette_glrnb-021.eps | 2 surveillance-1.1-2/surveillance/inst/doc/figs/vignette_glrnb-021.pdf | 26 surveillance-1.1-2/surveillance/inst/doc/figs/vignette_glrnb-023.eps | 2 surveillance-1.1-2/surveillance/inst/doc/figs/vignette_glrnb-023.pdf | 26 surveillance-1.1-2/surveillance/inst/doc/index.html | 44 - surveillance-1.1-2/surveillance/man/LRCUSUM.runlength.Rd |only surveillance-1.1-2/surveillance/man/abattoir.Rd |only surveillance-1.1-2/surveillance/man/algo.bayes.Rd | 4 surveillance-1.1-2/surveillance/man/algo.farrington.threshold.Rd | 10 surveillance-1.1-2/surveillance/man/algo.glrnb.Rd | 16 surveillance-1.1-2/surveillance/man/algo.glrpois.Rd | 8 surveillance-1.1-2/surveillance/man/algo.hhh.grid.Rd | 5 surveillance-1.1-2/surveillance/man/algo.hmm.Rd | 3 surveillance-1.1-2/surveillance/man/algo.twins.Rd | 12 surveillance-1.1-2/surveillance/man/categoricalCUSUM.Rd |only surveillance-1.1-2/surveillance/man/create.disProg.Rd | 5 surveillance-1.1-2/surveillance/man/deleval.Rd |only surveillance-1.1-2/surveillance/man/estimateGLRNbHook.Rd | 3 surveillance-1.1-2/surveillance/man/internal.Rd | 1 surveillance-1.1-2/surveillance/man/momo.Rd |only surveillance-1.1-2/surveillance/man/pairedbinCUSUM.Rd |only surveillance-1.1-2/surveillance/man/plot.survRes.Rd | 6 surveillance-1.1-2/surveillance/man/readData.Rd | 3 surveillance-1.1-2/surveillance/man/refvalIdxByDate.Rd |only surveillance-1.1-2/surveillance/man/stcd.Rd |only surveillance-1.1-2/surveillance/man/sts-class.Rd | 80 ++ surveillance-1.1-2/surveillance/man/stsDisp.Rd | 42 + surveillance-1.1-2/surveillance/man/stsSlots.Rd |only surveillance-1.1-2/surveillance/man/stsXtrct.Rd | 1 surveillance-1.1-2/surveillance/man/stsYear.Rd | 2 surveillance-1.1-2/surveillance/man/surveillance-package.Rd | 67 +- surveillance-1.1-2/surveillance/src/gsl_wrappers.h | 6 surveillance-1.1-2/surveillance/src/stcd-assuncaocorrea.cc |only surveillance-1.1-2/surveillance/src/stcd-assuncaocorrea.h |only surveillance-1.1-2/surveillance/src/twins.cc | 23 83 files changed, 1028 insertions(+), 508 deletions(-)
Author: Kaspar Rufibach
Diff between smoothtail versions 1.1.3 dated 2009-06-04 and 1.1.4 dated 2009-10-15
Title: Smooth Estimation of GPD Shape Parameter
Description: Given independent and identically distributed observations
X(1), ..., X(n) from a Generalized Pareto distribution with
shape parameter gamma in [-1,0], this package offers several
estimates to compute estimates of gamma. The estimates are
based on the principle of replacing the order statistics by
quantiles of a distribution function based on a log--concave
density function. This procedure is justified by the fact that
the GPD density is log--concave for gamma in [-1,0].
CHANGES | 4 ++++
DESCRIPTION | 8 ++++----
man/falk.Rd | 2 +-
man/falkMVUE.Rd | 2 +-
man/generalizedPick.Rd | 2 +-
man/lambdaGenPick.Rd | 2 +-
man/pickands.Rd | 2 +-
man/smoothtail-package.Rd | 6 +++---
8 files changed, 16 insertions(+), 12 deletions(-)
Author: Robin K. S. Hankin
Title: octonions and quaternions
Description: A collection of routines to manipulate and visualize
quaternions and octonions.
Diff between onion versions 1.2-2 dated 2009-01-20 and 1.2-3 dated 2009-10-15
onion-1.2-2/onion/inst/doc/jss.bst |only onion-1.2-2/onion/inst/doc/jss.cls |only onion-1.2-3/onion/DESCRIPTION | 23 ++++++++++++----------- onion-1.2-3/onion/inst/doc/onionpaper.Rnw | 4 ++-- onion-1.2-3/onion/inst/doc/onionpaper.pdf |binary onion-1.2-3/onion/man/Oil.Rd | 1 - onion-1.2-3/onion/man/onion-package.Rd | 2 +- 7 files changed, 15 insertions(+), 15 deletions(-)
Author: Kimihiro Noguchi
Diff between nparLD versions 1.0 dated 2009-09-18 and 1.1 dated 2009-10-15
Title: Nonparametric Analysis of Longitudinal Data in Factorial
Experiments
Description: The package "nparLD" is designed to perform nonparametric
analysis of longitudinal data in factorial experiments.
Longitudinal data are those which are collected from the same
subjects over time, and they frequently arise in biological
sciences. Nonparametric methods do not require assumptions on
distributions of parameters, and are applicable to a variety of
data types (continuous, discrete, purely ordinal, and
dichotomous). Such methods are also robust with respect to
outliers and for small sample sizes.
DESCRIPTION | 12 ++++++------
R/f1.ld.f2.R | 4 ++--
R/f2.ld.f1.R | 6 +++---
R/ld.ci.R | 4 ++--
R/ld.f1.R | 2 +-
R/ld.f2.R | 8 ++++----
man/f1.ld.f1.rd | 4 ++++
man/f1.ld.f2.rd | 4 ++++
man/f2.ld.f1.rd | 4 ++++
man/ld.f2.rd | 16 ++++++++++------
10 files changed, 40 insertions(+), 24 deletions(-)
Author: Robin K. S. Hankin
Title: multivariate polynomials
Description: Various utilities to manipulate multivariate polynomials
Diff between multipol versions 1.0-2 dated 2008-05-09 and 1.0-4 dated 2009-10-15
DESCRIPTION | 8 +++++--- inst |only man/ooom.Rd | 35 ++++++++++++++++++++++++++++++++--- 3 files changed, 37 insertions(+), 6 deletions(-)
Author: Martin Elff
Title: Tools for Management of Survey Data, Graphics, Programming,
Statistics, and Simulation
Description: One of the aims of this package is to make life easier for
useRs who deal with survey data sets. It provides an
infrastructure for the management of survey data including
value labels, definable missing values, recoding of variables,
production of code books, and import of (subsets of) SPSS and
Stata files. Further, it provides functionality to produce
tables and data frames of arbitrary descriptive statistics and
(almost) publication-ready tables of regression model
estimates. Also some convenience tools for graphics,
programming, and simulation are provided.
Diff between memisc versions 0.95-21 dated 2009-08-20 and 0.95-22 dated 2009-10-15
DESCRIPTION | 6 +++--- R/applyTemplate.R | 18 +++--------------- R/query.R | 4 ---- inst/NEWS | 4 ++++ inst/doc/anes48.pdf |binary 5 files changed, 10 insertions(+), 22 deletions(-)
Author: Peter Solymos
Title: Multivariate Data Handling in Ecology and Biogeography
Description: A framework package aimed to provide standardized
computational environment for specialist work via object
classes to represent the data coded by samples, taxa and
segments (i.e. subpopulations, repeated measures). It supports
easy processing of the data along with cross tabulation and
relational data tables for samples and taxa. An object of class
`mefa' is a project specific compendium of the data and can be
easily used in further analyses. Methods are provided for
extraction, aggregation, conversion, plotting, summary and
reporting of `mefa' objects. Reports can be generated in plain
text or LaTeX format. Vignette contains worked examples.
Diff between mefa versions 3.1-2 dated 2009-09-22 and 3.1-3 dated 2009-10-15
DESCRIPTION | 10 +++++----- NAMESPACE |only R/zzz.R | 18 +++++++++++++++--- inst/ChangeLog | 14 +++++++++++--- inst/doc/mefa.Rnw | 2 +- inst/doc/mefa.pdf |binary man/mefa.Rd | 2 +- 7 files changed, 33 insertions(+), 13 deletions(-)
Author: Michael Buecker
Title: Latent Class Discriminant Analysis
Description: Local Discrimination via Latent Class Models
Diff between lcda versions 0.1 dated 2009-03-25 and 0.2 dated 2009-10-15
DESCRIPTION | 6 +++--- man/cclcda.Rd | 6 +++--- man/cclcda2.Rd | 4 ++-- man/lcda.Rd | 6 +++--- man/predict.cclcda.Rd | 2 +- man/predict.cclcda2.Rd | 2 +- man/predict.lcda.Rd | 2 +- 7 files changed, 14 insertions(+), 14 deletions(-)
Author: Alexandros Karatzoglou, Alex Smola, Kurt Hornik
Title: Kernel-based Machine Learning Lab
Description: Kernel-based machine learning methods for classification,
regression, clustering, novelty detection, quantile regression
and dimensionality reduction. Among other methods kernlab
includes Support Vector Machines, Spectral Clustering, Kernel
PCA and a QP solver.
Diff between kernlab versions 0.9-8 dated 2008-09-28 and 0.9-9 dated 2009-10-15
DESCRIPTION | 19 +++++++++++-------- R/kcca.R | 3 ++- R/kernels.R | 10 +++++----- R/ksvm.R | 4 ++-- inst/doc/kernlab.Rnw | 12 ++++++------ man/as.kernelMatrix.Rd | 2 +- man/csi.Rd | 10 +++++----- man/gausspr.Rd | 4 ++-- man/inchol.Rd | 7 ++++--- man/income.Rd | 2 +- man/ipop-class.Rd | 9 +++++---- man/kcca.Rd | 4 ++-- man/kernelMatrix.Rd | 4 ++-- man/kfa-class.Rd | 2 +- man/kha-class.Rd | 8 ++++---- man/kha.Rd | 4 ++-- man/kkmeans.Rd | 2 +- man/kmmd-class.Rd | 8 ++++---- man/kpca-class.Rd | 8 ++++---- man/kpca.Rd | 2 +- man/kqr-class.Rd | 6 +++++- man/ksvm-class.Rd | 10 +++++----- man/ksvm.Rd | 6 +++--- man/lssvm-class.Rd | 10 ++++++---- man/lssvm.Rd | 7 +++---- man/onlearn-class.Rd | 2 +- man/prc-class.Rd | 6 +++--- man/rvm-class.Rd | 12 +++++++----- man/rvm.Rd | 5 ++--- man/sigest.Rd | 2 +- man/spam.Rd | 2 +- man/specc-class.Rd | 3 ++- man/specc.Rd | 2 +- man/stringdot.Rd | 4 ++-- man/ticdata.Rd | 4 ++-- man/vm-class.Rd | 4 ++-- src/esa.cpp | 2 +- 37 files changed, 112 insertions(+), 99 deletions(-)
Author: Jan de Leeuw, Kurt Hornik, Patrick Mair
Title: Active set and generalized PAVA for isotone optimization
Description: This package contains two main functions: gpava() for
solving general isotone regression problem using the
pool-adjacent-violators algorithm (PAVA). activeSet() provides
a framework of active set methods for isotone optimization
problems. Various loss functions are pre-spcified.
Diff between isotone versions 0.8-6 dated 2009-08-30 and 0.8-7 dated 2009-10-15
DESCRIPTION | 8 ++++---- R/gpava.R | 2 +- R/plot.gpava.R | 6 +++++- inst/doc/isotone.pdf |binary man/gpava.Rd | 1 + 5 files changed, 11 insertions(+), 6 deletions(-)
Author: Robert King
Diff between gld versions 1.8.3 dated 2007-10-11 and 1.8.4 dated 2009-10-15
Title: Estimation and use of the generalised (Tukey) lambda
distribution
Description: The generalised lambda distribution, or Tukey lambda
distribution, provides a wide variety of shapes with one
functional form. This package provides random numbers,
quantiles, probabilities, densities and plots. It also
includes an implementation of the starship estimation method
for the distribution.
Changelog | 4 ++++
DESCRIPTION | 27 ++++++++++++++++-----------
R/fxgld.R | 2 +-
R/methods.R |only
R/starship.R | 7 ++++++-
man/GeneralisedLambdaDistribution.Rd | 14 ++++++++------
man/StarshipClassDocs.Rd |only
man/plotgl.Rd | 4 ++--
man/starship.Rd | 30 +++++++++++++++++++++---------
man/starship.adaptivegrid.Rd | 4 ++--
man/starship.obj.Rd | 8 ++++----
11 files changed, 64 insertions(+), 36 deletions(-)
Author: Ole F. Christensen
Diff between geoRglm versions 0.8-25 dated 2009-04-15 and 0.8-26 dated 2009-10-15
Title: geoRglm - a package for generalised linear spatial models
Description: Functions for inference in generalised linear spatial
models. The posterior and predictive inference is based on
Markov chain Monte Carlo methods. Package geoRglm is an
extension to the package geoR, which must be installed first.
DESCRIPTION | 8 ++++----
inst/doc/geoRglmintro.pdf |binary
man/covariog.Rd | 2 +-
man/covariog.model.env.Rd | 2 +-
man/glsm.mcmc.Rd | 2 +-
man/likfit.glsm.Rd | 2 +-
man/proflik.glsm.Rd | 2 +-
man/summary.likGLSM.Rd | 6 +++---
8 files changed, 12 insertions(+), 12 deletions(-)
Author: Whit Armstrong
Diff between fts versions 0.7.5 dated 2008-07-16 and 0.7.6 dated 2009-10-15
Title: R interface to tslib (a time series library in c++)
Description: fast operations for time series objects
fts-0.7.5/fts/src/RAbstraction/Rutilities.cpp |only
fts-0.7.5/fts/src/tslib/tslib/date.policies/date.breaks.hpp |only
fts-0.7.5/fts/src/tslib/tslib/range.specifier/range.opp.hpp |only
fts-0.7.5/fts/src/tslib/tslib/ts.opps/ts.opps.predeclare.hpp |only
fts-0.7.5/fts/src/tslib/tslib/vector.transform/lag.hpp |only
fts-0.7.5/fts/src/tslib/tslib/vector.transform/lead.hpp |only
fts-0.7.6/fts/.gitignore | 3
fts-0.7.6/fts/.gitmodules | 6
fts-0.7.6/fts/DESCRIPTION | 8
fts-0.7.6/fts/NAMESPACE | 77 +
fts-0.7.6/fts/R/fts.R | 439 +++++++
fts-0.7.6/fts/man/as.fts.Rd | 4
fts-0.7.6/fts/man/frequency.convert.Rd | 6
fts-0.7.6/fts/man/fts.Rd | 8
fts-0.7.6/fts/man/indicators.Rd |only
fts-0.7.6/fts/man/intersect.all.Rd |only
fts-0.7.6/fts/man/lm.fts.Rd |only
fts-0.7.6/fts/man/read.write.fts.Rd | 8
fts-0.7.6/fts/src/R.tslib.backend/R.tseries.data.backend.hpp | 39
fts-0.7.6/fts/src/R.tslib.backend/R.tseries.object.convert.hpp | 12
fts-0.7.6/fts/src/RAbstraction/.gitignore |only
fts-0.7.6/fts/src/RAbstraction/R.backend.hpp |only
fts-0.7.6/fts/src/RAbstraction/Rmatrix.hpp |only
fts-0.7.6/fts/src/RAbstraction/Robject.hpp |only
fts-0.7.6/fts/src/RAbstraction/Rsexp.allocator.templates.hpp | 39
fts-0.7.6/fts/src/RAbstraction/Rtype.hpp | 60 -
fts-0.7.6/fts/src/RAbstraction/Rutilities.hpp | 61 -
fts-0.7.6/fts/src/RAbstraction/Rvector.hpp | 146 ++
fts-0.7.6/fts/src/analog.h |only
fts-0.7.6/fts/src/interface.cpp | 305 ++---
fts-0.7.6/fts/src/interface.h | 15
fts-0.7.6/fts/src/r.transform.template.h | 105 -
fts-0.7.6/fts/src/r.window.template.h | 106 +
fts-0.7.6/fts/src/tslib/test/Makefile | 2
fts-0.7.6/fts/src/tslib/test/test.cpp | 561 +++++++---
fts-0.7.6/fts/src/tslib/tslib/date.policies/date.partition.hpp |only
fts-0.7.6/fts/src/tslib/tslib/date.policies/posix.date.policy.hpp | 30
fts-0.7.6/fts/src/tslib/tslib/range.specifier/rangeSpecifier.hpp | 21
fts-0.7.6/fts/src/tslib/tslib/ts.opps/ifthenelse.hpp |only
fts-0.7.6/fts/src/tslib/tslib/ts.opps/ts.opps.hpp |only
fts-0.7.6/fts/src/tslib/tslib/ts.opps/ts.promotion.hpp |only
fts-0.7.6/fts/src/tslib/tslib/ts.opps/ts.scalar.opp.hpp | 127 +-
fts-0.7.6/fts/src/tslib/tslib/ts.opps/ts.ts.opp.hpp | 69 -
fts-0.7.6/fts/src/tslib/tslib/tseries.data.hpp | 13
fts-0.7.6/fts/src/tslib/tslib/tseries.hpp | 382 ++----
fts-0.7.6/fts/src/tslib/tslib/utils/breaks.hpp |only
fts-0.7.6/fts/src/tslib/tslib/utils/cbind.hpp |only
fts-0.7.6/fts/src/tslib/tslib/utils/window.apply.hpp | 22
fts-0.7.6/fts/src/tslib/tslib/utils/window.function.hpp | 18
fts-0.7.6/fts/src/tslib/tslib/utils/window.intersection.apply.hpp | 21
fts-0.7.6/fts/src/tslib/tslib/vector.summary.hpp | 5
fts-0.7.6/fts/src/tslib/tslib/vector.summary/close.hpp |only
fts-0.7.6/fts/src/tslib/tslib/vector.summary/contains.na.hpp |only
fts-0.7.6/fts/src/tslib/tslib/vector.summary/mean.hpp | 2
fts-0.7.6/fts/src/tslib/tslib/vector.summary/neg.sum.hpp |only
fts-0.7.6/fts/src/tslib/tslib/vector.summary/open.hpp |only
fts-0.7.6/fts/src/tslib/tslib/vector.summary/pos.sum.hpp |only
fts-0.7.6/fts/src/tslib/tslib/vector.summary/rsi.hpp |only
fts-0.7.6/fts/src/tslib/tslib/vector.summary/stdev.hpp | 2
fts-0.7.6/fts/src/tslib/tslib/vector.transform.hpp | 4
fts-0.7.6/fts/src/tslib/tslib/vector.transform/ema.hpp |only
fts-0.7.6/fts/src/tslib/tslib/vector.transform/ema.traits.hpp |only
fts-0.7.6/fts/src/tslib/tslib/vector.transform/fill.bwd.hpp | 2
63 files changed, 1879 insertions(+), 849 deletions(-)
Author: Robin K. S. Hankin
Title: Bayesian emulation of computer programs
Description: This package allows one to estimate the output of a
computer program, as a function of the input parameters,
without actually running it. The computer program is assumed to
be a Gaussian process, whose parameters are estimated using
Bayesian techniqes that give a PDF of expected program output.
This PDF is conditional on a ``training set'' of runs, each
consisting of a point in parameter space and the model output
at that point. The emphasis is on complex codes that take
weeks or months to run, and that have a large number of
undetermined input parameters; many climate prediction models
fall into this class. The emulator essentially determines
Bayesian a-postiori estimates of the PDF of the output of a
model, conditioned on results from previous runs and a
user-specified prior linear model. A working example is given
in the help page for function `interpolant', which should be
the users's first point of reference.
Diff between emulator versions 1.1-5 dated 2009-07-18 and 1.1-7 dated 2009-10-15
DESCRIPTION | 6 - inst/CITATION | 1 inst/doc/emulex.pdf | 242 +++++++++++++++++++++++------------------------ inst/doc/uncertainty.bib | 102 +++++++++++++++++++ man/betahat.fun.Rd | 2 man/corr.Rd | 6 - man/pad.Rd | 6 - man/regressor.basis.Rd | 2 man/scales.likelihood.Rd | 6 - 9 files changed, 238 insertions(+), 135 deletions(-)
Author: Lukasz Nieweglowski.
Diff between clv versions 0.3-1 dated 2009-02-17 and 0.3-2 dated 2009-10-15
Title: Cluster Validation Techniques
Description: Package contains most of the popular internal and external
cluster validation methods ready to use for the most of the
outputs produced by functions coming from package "cluster".
Package contains also functions and examples of usage for
cluster stability approach that might be applied to algorithms
implemented in "cluster" package as well as user defined
clustering algorithms.
DESCRIPTION | 19 ++++++++++++-------
README | 12 ++++++------
man/cluster_stability_usr.Rd | 2 +-
src/cluster_scatter.c | 2 +-
4 files changed, 20 insertions(+), 15 deletions(-)
Author: Robin K. S. Hankin
Title: Bayesian calibration of complex computer codes
Description: Performs Bayesian calibration of computer models as per
Kennedy and O'Hagan 2001. The package includes routines to
find the hyperparameters and parameters; see the help page for
stage1() for a worked example using the toy dataset. A
tutorial is provided in the calex.Rnw vignette; and a suite of
especially simple one dimensional examples appears in
inst/doc/one.dim/.
Diff between calibrator versions 1.1-6 dated 2009-07-23 and 1.1-7 dated 2009-10-15
DESCRIPTION | 6 inst/CITATION | 1 inst/doc/calex.pdf | 818 +++++++++++++++++++++++++++-------------------------- 3 files changed, 424 insertions(+), 401 deletions(-)
Author: Charles C. Berry
Diff between bqtl versions 1.0-24 dated 2009-01-12 and 1.0-25 dated 2009-10-15
Title: Bayesian QTL mapping toolkit
Description: QTL mapping toolkit for inbred crosses and recombinant
inbred lines. Includes maximum likelihood and Bayesian tools.
CHANGES | 3 +++
DESCRIPTION | 16 +++++++++-------
R/version.bqtl.R | 2 +-
man/linear.bayes.Rd | 3 +--
man/little.map.frame.Rd | 3 +--
man/make.loc.right.Rd | 3 ---
man/marker.levels.Rd | 4 ++--
7 files changed, 17 insertions(+), 17 deletions(-)
Author: Robin K. S. Hankin (R) and Luke G. West (C++)
Title: A generalization of Fisher's exact test
Description: A generalization of Fisher's exact test that allows for
structural zeros.
Diff between aylmer versions 1.0-3 dated 2009-01-20 and 1.0-4 dated 2009-10-15
aylmer-1.0-3/aylmer/inst/doc/jss.bst |only aylmer-1.0-3/aylmer/inst/doc/jss.cls |only aylmer-1.0-3/aylmer/inst/doc/jsslogo.jpg |only aylmer-1.0-4/aylmer/DESCRIPTION | 10 aylmer-1.0-4/aylmer/R/zzz.R | 9 aylmer-1.0-4/aylmer/inst/doc/fishervig.pdf | 3974 +++++++++++++---------------- aylmer-1.0-4/aylmer/man/allboards.Rd | 26 aylmer-1.0-4/aylmer/man/aylmer.test.Rd | 1 aylmer-1.0-4/aylmer/man/best.Rd | 16 aylmer-1.0-4/aylmer/man/randomprobs.Rd | 9 10 files changed, 1961 insertions(+), 2084 deletions(-)
Author: Rich FitzJohn & Ian Dickie
Title: TRFLP Analysis and Matching Package for R
Description: TRAMPR is an R package for matching terminal restriction
fragment length polymorphism (TRFLP) profiles between unknown
samples and a database of knowns. TRAMPR facilitates analysis
of many unknown profiles at once, and provides tools for
working directly with electrophoresis output through to
generating summaries suitable for community analyses with R's
rich set of statistical functions. TRAMPR also resolves the
issues of multiple TRFLP profiles within a species, and shared
TRFLP profiles across species.
Diff between TRAMPR versions 1.0-5 dated 2009-05-24 and 1.0-6 dated 2009-10-15
DESCRIPTION | 6 +++--- inst/CITATION | 7 ++++--- inst/doc/TRAMPRdemo.pdf |binary 3 files changed, 7 insertions(+), 6 deletions(-)
Author: Jeffrey A. Ryan
Title: R API to Oracle Berkeley DB
Description: Provides R Interface to Embedded Oracle Berkeley DB(tm)
Diff between RBerkeley versions 0.7-0 dated 2009-08-13 and 0.7-1 dated 2009-10-15
DESCRIPTION | 9 NAMESPACE | 1 R/db.R | 11 configure | 1563 +++++++++++++++++++++++++++++++++++++++++++-------- configure.in | 221 +++---- inst/INSTALL | 38 + inst/doc/DBIntro.pdf | 6 man/Databases.Rd | 1 src/Makevars | 16 src/Makevars.in | 16 src/db.c | 17 src/mkFlags.c | 8 12 files changed, 1546 insertions(+), 361 deletions(-)
Author: Robin K. S. Hankin
Title: The Davies quantile function
Description: The Davies quantile function and the Generalized Lambda
distribution
Diff between Davies versions 1.1-4 dated 2009-01-20 and 1.1-5 dated 2009-10-15
DESCRIPTION | 13 ++++++++----- R/parzfns.R | 2 +- inst/CITATION | 2 +- man/davies.moment.Rd | 24 ++++++++++++------------ man/expected.gld.Rd | 12 +++++++----- man/hypergeo.Rd | 10 +++++++--- man/ozturk.Rd | 9 +++++---- 7 files changed, 41 insertions(+), 31 deletions(-)
Author: Robin K. S. Hankin
Title: Bayesian Analysis of Computer Code Output (BACCO)
Description: The BACCO bundle of packages is replaced by the BACCO
package, which provides a vignette that illustrates the
constituent packages (emulator, approximator, calibrator) in
use.
Diff between BACCO versions 2.0-2 dated 2009-07-23 and 2.0-4 dated 2009-10-15
DESCRIPTION | 6 inst/CITATION |only inst/doc/both_papers.Rnw | 9 inst/doc/both_papers.pdf | 954 +++++++++++++++++++++++------------------------ 4 files changed, 479 insertions(+), 490 deletions(-)