Author: Tyler Kendall and Erik R. Thomas
Title: Vowel Manipulation, Normalization, and Plotting
Description: vowels is an R package for the manipulation,
normalization, and plotting of phonetic and sociophonetic vowel
formant data. vowels is the backend for the NORM website.
Diff between vowels versions 1.0-2 dated 2009-04-23 and 1.0-3 dated 2009-07-30
DESCRIPTION | 8 ++++---- R/vowels.R | 6 +++++- man/vowels-package.Rd | 4 ++-- 3 files changed, 11 insertions(+), 7 deletions(-)
Author: William Revelle
Diff between psych versions 1.0-77 dated 2009-07-27 and 1.0-78 dated 2009-07-30
Title: Procedures for Psychological, Psychometric, and Personality
Research
Description: A number of routines for personality, psychometrics and
experimental psychology. Functions are primarily for scale
construction using factor analysis, cluster analysis and
reliability analysis, although others provide basic descriptive
statistics. Functions for simulating particular item and test
structures are included. Several functions serve as a useful
front end for structural equation modeling. For more
information, see the personality-project.org/r webpage.
CHANGES | 12
DESCRIPTION | 8
R/ICLUST.cluster.R | 2
R/fa.R | 1
R/factor.stats.R | 6
R/principal.R | 2
inst/NEWS | 6
inst/doc/overview.pdf |13355 ++++++++++++++++++++++-----------------------
inst/doc/psych_for_sem.pdf | 1747 ++---
man/00.psych-package.Rd | 4
man/principal.Rd | 4
11 files changed, 7687 insertions(+), 7460 deletions(-)
Author: Luis Cayuela and Marcelino de la Cruz
Title: Functions to incorporate taxonomic uncertainty on multivariate
analyses of ecological data
Description: Permutational method to incorporate taxonomic uncertainty
and some functions to assess its effects on parameters of some
widely used multivariate methods in ecology
Diff between betaper versions 1.0-0 dated 2008-06-09 and 1.1-0 dated 2009-07-30
betaper-1.0-0/betaper/NAMESPACE |only betaper-1.0-0/betaper/R/betaper.R |only betaper-1.0-0/betaper/R/plot.betaper.R |only betaper-1.0-0/betaper/R/print.betaper.R |only betaper-1.0-0/betaper/man/betaper.Rd |only betaper-1.0-0/betaper/man/plot.betaper.Rd |only betaper-1.1-0/betaper/DESCRIPTION | 29 +++++++++++++---------- betaper-1.1-0/betaper/R/adonis.pertables.R |only betaper-1.1-0/betaper/R/cca.pertables.R |only betaper-1.1-0/betaper/R/mantel.pertables.R |only betaper-1.1-0/betaper/R/pertables.R |only betaper-1.1-0/betaper/R/plot.adonis.pertables.R |only betaper-1.1-0/betaper/R/plot.cca.pertables.R |only betaper-1.1-0/betaper/R/plot.mantel.pertables.R |only betaper-1.1-0/betaper/R/plot.rda.pertables.R |only betaper-1.1-0/betaper/R/print.adonis.pertables.R |only betaper-1.1-0/betaper/R/print.cca.pertables.R |only betaper-1.1-0/betaper/R/print.mantel.pertables.R |only betaper-1.1-0/betaper/R/print.pertables.R |only betaper-1.1-0/betaper/R/print.rda.pertables.R |only betaper-1.1-0/betaper/R/rda.pertables.R |only betaper-1.1-0/betaper/data/Amazonia.rda |binary betaper-1.1-0/betaper/data/HCP.coords.rda |binary betaper-1.1-0/betaper/data/HCP.rda |binary betaper-1.1-0/betaper/data/soils.rda |binary betaper-1.1-0/betaper/man/adonis.pertables.Rd |only betaper-1.1-0/betaper/man/cca.pertables.Rd |only betaper-1.1-0/betaper/man/mantel.pertables.Rd |only betaper-1.1-0/betaper/man/pertables.Rd |only betaper-1.1-0/betaper/man/rda.pertables.Rd |only 30 files changed, 17 insertions(+), 12 deletions(-)
Author: Kurt Hornik
Title: Harvest Metadata Using OAI-PMH v2.0
Description: Harvest metadata using the Open Archives Initiative
Protocol for Metadata Harvesting (OAI-PMH) version 2.0.
Diff between OAIHarvester versions 0.0-3 dated 2009-03-14 and 0.0-4 dated 2009-07-30
DESCRIPTION | 8 ++++---- R/pmh.R | 3 +++ inst/doc/oaih.Rnw | 13 ++++++++----- inst/doc/oaih.bib | 8 ++++++++ inst/doc/oaih.pdf |binary 5 files changed, 23 insertions(+), 9 deletions(-)
Author: Marie Morfin and David Makowski
Title: Model selection uncertainty and model mixing
Description: Implement different types of model mixing and model
selection methods for linear or logistic models.
Diff between MMIX versions 1.0 dated 2009-07-24 and 1.1 dated 2009-07-30
DESCRIPTION | 10 ++++----- R/aucCV.r | 51 ++++++++++++++++++++++--------------------------- R/bmaBic.r | 37 ++++++++++++++++++----------------- R/mixAic.r | 36 +++++++++++++++++----------------- R/pmseCV.r | 17 +++++++++------- R/print.MMIX.r | 7 ++---- man/MMIX-package.Rd | 6 ++--- man/arms.Rd | 2 - man/bootFreq.Rd | 11 +++------- man/pmseCV.Rd | 5 +++- man/print.MMIXclass.Rd | 6 ++--- man/stepSel.Rd | 6 ++--- man/varSelec.Rd | 2 - 13 files changed, 97 insertions(+), 99 deletions(-)
Author: Jon Wakefield
Diff between HWEBayes versions 1.1 dated 2009-07-22 and 1.2 dated 2009-07-30
Title: Bayesian investigation of Hardy-Weinberg Equilibrium via
estimation and testing.
Description: Estimation and testing of HWE using Bayesian methods.
Three models are currently considered: HWE, a model
parameterized in terms of the allele frequencies and a single
inbreeding coefficient f, and the saturated model. Testing is
based on Bayes factors.
DESCRIPTION | 6 +++---
inst/doc/HWEBayes-Guide.Snw |only
inst/doc/HWEBayes-Guide.pdf |binary
3 files changed, 3 insertions(+), 3 deletions(-)
Author: Brian Ripley
Diff between tree versions 1.0-26 dated 2007-07-28 and 1.0-27 dated 2009-07-30
Title: Classification and regression trees
Description: Classification and Regression Trees.
ChangeLog | 9 +
DESCRIPTION | 11 +-
R/grow.q | 22 ++--
R/plot.tree.sequence.q | 10 +-
R/treefix.R | 50 +++++-----
R/treemisc.R | 163 +++++++++++++++++-----------------
inst/po/en@quot/LC_MESSAGES/R-tree.mo |binary
inst/po/en@quot/LC_MESSAGES/tree.mo |binary
man/na.tree.replace.Rd | 4
man/tile.tree.Rd | 10 +-
man/tree.control.Rd | 6 -
po/R-en@quot.po | 9 +
po/R-tree.pot | 10 +-
po/en@quot.po | 16 +--
po/tree.pot | 8 -
src/treefix.c | 8 +
tests/Examples |only
17 files changed, 179 insertions(+), 157 deletions(-)
Author: Mark Bravington, Karen Martien, Dave Gregovich
Title: Testing of Spatial Structure Methods
Description: Provides a framework under which methods of detecting and
managing genetic spatial structure in populations can be
tested.
Diff between tossm versions 1.2 dated 2009-03-06 and 1.3 dated 2009-07-30
tossm-1.2/tossm/NAMESPACE |only tossm-1.2/tossm/R/sysdata.rda |only tossm-1.3/tossm/DESCRIPTION | 31 ++++++++++-------- tossm-1.3/tossm/R/CLA.R | 13 +++++-- tossm-1.3/tossm/R/TOSSM.utils.R | 27 +++++++++++++++ tossm-1.3/tossm/R/Voronoi.funcs.R |only tossm-1.3/tossm/R/def.depleter.R | 3 + tossm-1.3/tossm/R/def.genetic.sampler.R | 17 ++------- tossm-1.3/tossm/R/get.n.in.ss.R |only tossm-1.3/tossm/R/humpbackism.R | 4 +- tossm-1.3/tossm/R/hyptest.network.BSA.R | 24 +++++++++++--- tossm-1.3/tossm/R/hyptest.seq.BSA.R | 2 - tossm-1.3/tossm/R/new.harvest.R | 32 +++++++++++------- tossm-1.3/tossm/R/run.tossm.R | 41 +++++++++++++----------- tossm-1.3/tossm/R/wombsoft.BSA.R | 12 +++---- tossm-1.3/tossm/R/zzz.R |only tossm-1.3/tossm/data/sysdata.rda |only tossm-1.3/tossm/inst/TOSSM_dataset_handbook.pdf |binary tossm-1.3/tossm/inst/TOSSM_users_guide.pdf |binary tossm-1.3/tossm/man/def.genetic.sampler.Rd | 5 +- tossm-1.3/tossm/man/hyptest.network.BSA.Rd | 12 ++++--- tossm-1.3/tossm/man/run.tossm.Rd | 6 +-- tossm-1.3/tossm/man/tossm-internal.Rd |only tossm-1.3/tossm/src/CLC-D.f | 5 +- tossm-1.3/tossm/src/MANAGE-D.f | 24 ++++++++++---- 25 files changed, 164 insertions(+), 94 deletions(-)
Author: Valentin Todorov
Diff between rrcov versions 0.5-01 dated 2009-03-05 and 0.5-02 dated 2009-07-30
Title: Scalable Robust Estimators with High Breakdown Point
Description: Robust Location and Scatter Estimation and Robust
Multivariate Analysis with High Breakdown Point.
ChangeLog | 6 +
DESCRIPTION | 27 ++--
NAMESPACE | 2
R/AllClasses.R | 117 +++++++++----------
R/CovRobust.R | 32 ++---
R/Pca.R | 196 ++++++++++++++++++++++++--------
R/PcaClassic.R | 36 +++---
R/PcaHubert.R | 262 ++++++++++++++++++++++----------------------
R/Wilks.test.R | 172 +++++++++++++++++-----------
inst/doc/UML.pdf |binary
man/CovControlMcd-class.Rd | 45 ++++---
man/CovControlMest-class.Rd | 29 ++--
man/CovControlMve-class.Rd | 35 +++--
man/CovControlOgk-class.Rd | 43 ++++---
man/CovControlSde-class.Rd | 41 +++---
man/CovControlSest-class.Rd | 43 ++++---
man/CovMcd-class.Rd | 84 ++++++--------
man/CovMcd.Rd | 32 ++---
man/CovMest-class.Rd | 36 ++----
man/CovMve-class.Rd | 81 ++++++-------
man/CovOgk-class.Rd | 50 +++-----
man/CovRobust-class.Rd | 29 ++--
man/CovRobust.Rd | 46 ++++---
man/CovSde-class.Rd | 34 ++---
man/CovSest-class.Rd | 42 ++-----
man/CovSest.Rd | 74 ++++++------
man/Pca-class.Rd | 5
man/PcaCov-class.Rd | 43 ++-----
man/PcaGrid-class.Rd | 39 ++----
man/PcaHubert-class.Rd | 49 +++-----
man/PcaHubert.Rd | 6 -
man/PcaLocantore-class.Rd | 45 ++-----
man/PcaProj-class.Rd | 39 ++----
man/Wilks.test.Rd | 18 ++-
man/biplot.Rd |only
man/estimate-methods.Rd | 10 -
tests/thubert.Rout.save | 4
tests/tlda.Rout.save | 4
tests/tmcd4.Rout.save | 4
tests/tmest.Rout.save | 4
tests/tmest4.Rout.save | 4
tests/tmve4.Rout.save | 4
tests/togk4.Rout.save | 4
tests/tqda.Rout.save | 4
tests/tsde.Rout.save | 4
tests/tsest.Rout.save | 4
46 files changed, 978 insertions(+), 910 deletions(-)
Author: Romain Francois
Diff between parser versions 0.0-2 dated 2009-07-27 and 0.0-3 dated 2009-07-30
Title: Detailed R source code parser
Description: detailed source code parser, based on the standard R
parser but organizing the information differently
parser-0.0-2/parser/data/symbols.txt |only
parser-0.0-3/parser/DESCRIPTION | 11 ++++++-----
parser-0.0-3/parser/NAMESPACE | 2 +-
parser-0.0-3/parser/R/parser.R | 9 ++++-----
parser-0.0-3/parser/R/zzz.R | 2 +-
parser-0.0-3/parser/data/grammar_symbols.txt |only
parser-0.0-3/parser/inst/example |only
parser-0.0-3/parser/man/grammar.symbols.Rd | 7 ++++---
parser-0.0-3/parser/man/parser.Rd | 15 ++++-----------
parser-0.0-3/parser/man/symbols.Rd | 8 ++++----
10 files changed, 24 insertions(+), 30 deletions(-)
Author: Vincent J Carey. Ported to R by Thomas Lumley (versions 3.13
and 4.4) and Brian Ripley
Diff between gee versions 4.13-13 dated 2007-06-19 and 4.13-14 dated 2009-07-30
Title: Generalized Estimation Equation solver
Description: Generalized Estimation Equation solver
ChangeLog |only
DESCRIPTION | 16 ++++++++++------
man/gee.Rd | 4 ++--
tests/Examples |only
4 files changed, 12 insertions(+), 8 deletions(-)
Author: Virasakdi Chongsuvivatwong
Diff between epicalc versions 2.9.1.3 dated 2009-07-26 and 2.9.1.4 dated 2009-07-30
Title: Epidemiological calculator
Description: Functions making R easy for epidemiological calculation.
DESCRIPTION | 8 +--
R/epicalc.R | 130 ++++++++++++++++++++++++++++++++++--------------------------
man/VCT.rd | 4 -
3 files changed, 80 insertions(+), 62 deletions(-)
Author: Antonio Gasparrini and Ben Armstrong
Title: Distributed Lag Non-linear Models
Description: The package dlnm contains functions to specify basis and
cross-basis matrices in order to run distributed lag models and
their non-linear extension, then to predict and graph the
results for a fitted model.
Diff between dlnm versions 0.2.1 dated 2009-07-18 and 0.3.0 dated 2009-07-30
DESCRIPTION | 8 R/crossplot.R | 24 R/mkbasis.R | 47 R/mklagbasis.R | 1 inst/dlnmChangeLog | 34 inst/doc/Rplots.pdf |47088 +++++++++++++++++++++++++++++++------------ inst/doc/dlnmOverview.Rnw | 124 inst/doc/dlnmOverview.pdf |50073 +++++++++++++++++++++++++++++++++------------- man/crossbasis.Rd | 20 man/crossplot.Rd | 14 man/crosspred.Rd | 4 11 files changed, 70948 insertions(+), 26489 deletions(-)
Author: Jun Yan
Diff between copula versions 0.8-9 dated 2009-07-24 and 0.8-10 dated 2009-07-30
Title: Multivariate dependence with copulas
Description: Classes (S4) of commonly used copulas including elliptical
(normal and t), Archimedean (Clayton, Gumbel, Frank, and
Ali-Mikhail-Haq), extreme value (Gumbel, Husler-Reiss,
Galambos, and t-EV), and other families (Plackett and
Farlie-Gumbel-Morgenstern). Methods for density, distribution,
random number generation, bivariate dependence measures,
perspective and contour plots. Functions for fitting copula
models with variance estimate. Independence tests among random
variables and random vectors. Serial independence tests for
univariate and multivariate continuous time series.
Goodness-of-fit tests for copulas based on multipliers and on
the parametric bootstrap.
ChangeLog | 7 +++++++
DESCRIPTION | 8 ++++----
R/claytonCopula.R | 2 +-
3 files changed, 12 insertions(+), 5 deletions(-)
Author: Joshua Ulrich
Title: Technical Trading Rules
Description: Functions and data to construct technical trading rules
with R.
Diff between TTR versions 0.2 dated 2009-02-11 and 0.20-0 dated 2009-07-30
CHANGES | 78 +++++---------------- DESCRIPTION | 17 ++-- NAMESPACE | 2 R/GMMA.R |only R/KST.R | 15 +++- R/MACD.R | 13 ++- R/RSI.R | 7 + R/TRIX.R | 21 +++-- R/WebData.R | 72 +++++-------------- R/adjRatios.R |only R/envelopes.R |only R/runFun.R | 137 ++++++++++++++++++++++--------------- R/stochastics.R | 50 ++++++++++--- R/volatility.R | 45 +++++++++--- R/zzz.R | 6 - man/ADX.Rd | 5 - man/ATR.Rd | 2 man/CCI.Rd | 7 + man/CLV.Rd | 2 man/CMF.Rd | 2 man/CMO.Rd | 2 man/DPO.Rd | 2 man/DonchianChannel.Rd | 2 man/EMV.Rd | 2 man/GMMA.Rd |only man/KST.Rd | 5 + man/MACD.Rd | 5 - man/MFI.Rd | 2 man/MovingAverages.Rd | 2 man/OBV.Rd | 2 man/RSI.Rd | 2 man/SAR.Rd | 2 man/TDI.Rd | 6 - man/TRIX.Rd | 6 + man/TTR.Rd | 8 +- man/TTRtools.Rd | 2 man/VHF.Rd | 9 +- man/WPR.Rd | 2 man/WebData.Rd | 2 man/ZigZag.Rd | 2 man/adjRatios.Rd |only man/aroon.Rd | 5 - man/bollingerBands.Rd | 2 man/chaikinAD.Rd | 2 man/chaikinVolatility.Rd | 2 man/changes.Rd | 2 man/runFun.Rd | 30 ++++---- man/stochastics.Rd | 16 +++- man/volatility.Rd | 28 +++++-- man/williamsAD.Rd | 2 src/adjRatios.c |only src/runFun.f | 37 +++++---- tests/unitTests/runit.TTR.runFun.R | 2 53 files changed, 391 insertions(+), 283 deletions(-)
Author: Markus Loecher
Diff between ReadImages versions 0.1.3 dated 2009-07-27 and 0.1.3.1 dated 2009-07-30
Title: Image Reading Module for R
Description: This package provides functions for reading JPEG and PNG
files. This package requires libjpeg
DESCRIPTION | 6 +++---
man/ReadImages-package.Rd | 2 +-
src/Makevars.win |only
3 files changed, 4 insertions(+), 4 deletions(-)
Author: Douglas Bates
Diff between Matrix versions 0.999375-29 dated 2009-06-11 and 0.999375-30 dated 2009-07-30
Title: Sparse and Dense Matrix Classes and Methods
Description: Classes and methods for dense and sparse matrices and
operations on them using Lapack and SuiteSparse.
ChangeLog | 92 +++++++
DESCRIPTION | 8
NAMESPACE | 16 -
R/Auxiliaries.R | 20 +
R/CHMfactor.R | 44 +++
R/Csparse.R | 10
R/Matrix.R | 23 +
R/Tsparse.R | 2
R/bind2.R | 2
R/diagMatrix.R | 65 +++--
R/dsCMatrix.R | 4
R/ldenseMatrix.R | 6
R/rankMatrix.R | 2
R/spModels.R |only
R/sparseMatrix.R | 115 +--------
R/zzz.R | 4
TODO | 2
inst/doc/Comparisons.pdf |binary
inst/doc/Design-issues.pdf |binary
inst/doc/Intro2Matrix.pdf | 417 +++++++++++++++++-----------------
inst/doc/Introduction.pdf |binary
inst/doc/fullpage.sty |only
inst/doc/sparseModels.pdf |binary
inst/po/de/LC_MESSAGES/Matrix.mo |binary
inst/po/de/LC_MESSAGES/R-Matrix.mo |binary
inst/po/en@quot/LC_MESSAGES/Matrix.mo |binary
inst/test-tools.R | 60 ++++
man/BunchKaufman-methods.Rd | 8
man/CHMfactor-class.Rd | 34 +-
man/Cholesky-class.Rd | 39 ++-
man/Cholesky.Rd | 18 +
man/contrast.Rd |only
man/diagonalMatrix-class.Rd | 16 -
man/qr-methods.Rd | 8
man/sparse.model.matrix.Rd |only
man/sparseQR-class.Rd | 33 +-
po/Matrix.pot | 61 ++--
po/R-de.po | 5
po/de.po | 130 ++++------
po/en@quot.po | 63 ++---
src/CHMfactor.c | 14 +
src/CHMfactor.h | 1
src/chm_common.c | 25 +-
src/dsCMatrix.c | 37 ++-
src/init.c | 1
tests/Simple.R | 2
tests/factorizing.R | 107 ++++++++
tests/indexing.R | 13 -
tests/indexing.Rout.save | 33 ++
tests/spModel.matrix.R |only
50 files changed, 976 insertions(+), 564 deletions(-)
Author: Andrew D. Martin
Diff between MCMCpack versions 1.0-2 dated 2009-07-18 and 1.0-3 dated 2009-07-30
Title: Markov chain Monte Carlo (MCMC) Package
Description: This package contains functions to perform Bayesian
inference using posterior simulation for a number of
statistical models. Most simulation is done in compiled C++
written in the Scythe Statistical Library Version 1.0.2. All
models return coda mcmc objects that can then be summarized
using the coda package. MCMCpack also contains some useful
utility functions, including some additional density functions
and pseudo-random number generators for statistical
distributions, a general purpose Metropolis sampling algorithm,
and tools for visualization.
DESCRIPTION | 8 +-
HISTORY | 6 +
NAMESPACE | 1
R/MCMCquantreg.R |only
man/MCMCirtHier1d.Rd | 4 -
man/MCMCquantreg.Rd |only
src/MCMCfcds.h | 172 ++++++++++++++++++++++++++++++++++++++++++++++++++-
src/MCMCmedreg.cc |only
src/MCMCquantreg.cc |only
9 files changed, 180 insertions(+), 11 deletions(-)