Title: Bayesian chronologies via compound Poisson-Gamma processes.
Diff between Bchron versions 3.0 dated 2009-12-09 and 3.1 dated 2010-01-14
Description: This package takes dating information to produce joint
chronological reconstructions for age-depth data. The package
allows for: radiocarbon and non-radiocarbon depths, thickness
errors, outlying dates, multiple calibration curves, and event
prediction. It also produces some pretty pictures, and writes
all output to files to allow for further analysis (eg
palaeoclimate reconstruction). There is a menu system for
users, as well as a command line interface for advanced and/or
batch processing. Latest version contains IntCal09 data.
Author: Andrew Parnell
Maintainer: Andrew Parnell
Bchron-3.0/Bchron/inst/CalCurve/IntCal04.14c |only
Bchron-3.0/Bchron/inst/CalCurve/IntCal04.bch |only
Bchron-3.0/Bchron/inst/CalCurve/marine04.14c |only
Bchron-3.0/Bchron/inst/CalCurve/marine04.bch |only
Bchron-3.1/Bchron/DESCRIPTION | 8 ++++----
Bchron-3.1/Bchron/R/Bchroncreatecalcurve.R | 2 +-
Bchron-3.1/Bchron/R/Bchronload.R | 4 +++-
Bchron-3.1/Bchron/R/Bchronplot.R | 1 +
Bchron-3.1/Bchron/R/Bchronplotevent.R | 2 ++
Bchron-3.1/Bchron/R/Bchronpredictdepth.R |only
Bchron-3.1/Bchron/R/Bchronproxyplot.R | 25 +++++++++++++++++--------
Bchron-3.1/Bchron/inst/CalCurve/intcal09.14c |only
Bchron-3.1/Bchron/inst/CalCurve/intcal09.bch |only
Bchron-3.1/Bchron/inst/CalCurve/marine09.14c |only
Bchron-3.1/Bchron/inst/CalCurve/marine09.bch |only
Bchron-3.1/Bchron/man/Bchron-package.Rd | 2 +-
Bchron-3.1/Bchron/man/Bchronload.Rd | 2 +-
Bchron-3.1/Bchron/man/Bchronmenu.Rd | 3 ++-
Bchron-3.1/Bchron/man/Bchronproxyplot.Rd | 14 ++++++++++----
19 files changed, 42 insertions(+), 21 deletions(-)
Title: Foreach parallel adaptor for the Rmpi package
Diff between doMPI versions 0.1-3 dated 2009-12-09 and 0.1-4 dated 2010-01-14
Description: Provides a parallel backend for the %dopar% function using
the Rmpi package.
Author: Steve Weston
Maintainer: Steve Weston
DESCRIPTION | 10 +++++---
NAMESPACE | 2 -
NEWS | 9 ++++++-
R/doMPI.R | 38 +++++++++++++++++++++++++++++--
R/master.R | 55 +++++++++++++++++++++++++++++-----------------
R/mpiworkers.R | 15 ++++++++++--
inst/benchmarks/rforest.R |only
inst/doc/doMPI.Rnw | 2 -
inst/doc/doMPI.pdf |binary
inst/examples/arima.R |only
inst/examples/nested.R |only
inst/examples/pi2.R |only
inst/examples/rforest.R |only
man/doMPI-package.Rd | 10 ++++++++
man/getDoMpiCluster.Rd |only
15 files changed, 108 insertions(+), 33 deletions(-)
Title: Computation of functional similarities between GO terms and gene
products; GO enrichement analysis
Diff between GOSim versions 1.2 dated 2009-09-10 and 1.2.1.0 dated 2010-01-14
Description: This package implements several functions useful for
computing similarities between GO terms and gene products based
on their GO annotation. Moreover it allows for computing a GO
enrichment analysis
Author: Holger Froehlich
Maintainer: Holger Froehlich
GOSim-1.2.1.0/GOSim/DESCRIPTION | 12
GOSim-1.2.1.0/GOSim/R/geneSimilarity.R | 13
GOSim-1.2.1.0/GOSim/R/termSimilarity.R | 1
GOSim-1.2.1.0/GOSim/data/ICsBPhumanall.rda |binary
GOSim-1.2.1.0/GOSim/data/ICsCChumanall.rda |binary
GOSim-1.2.1.0/GOSim/data/ICsMFhumanall.rda |binary
GOSim-1.2.1.0/GOSim/inst/doc/GOSim.pdf | 3424 ++++++++++++++--------------
GOSim-1.2.1.0/GOSim/man/IC.Rd | 36
GOSim-1.2.1.0/GOSim/man/selectPrototypes.Rd | 2
GOSim-1.2/GOSim/.Rd2dvi18631 |only
10 files changed, 1758 insertions(+), 1730 deletions(-)
Title: Survival Regression with Smoothed Error Distribution
Diff between smoothSurv versions 0.5-1 dated 2009-06-25 and 0.6 dated 2010-01-14
Description: This package contains primarily a function to fit a
regression model with possibly right, left or interval censored
observations and with the error distrbution expressed as a
mixture of G-splines. Core part of the computation is done in
compiled C++ written using the Scythe Statistical Libary
Version 0.3.
Author: Arnost Komarek
Maintainer: Arnost Komarek
CHANGES | 4 ++++
DESCRIPTION | 8 ++++----
R/estimTdiff.R | 30 ++++++++++++++++++------------
3 files changed, 26 insertions(+), 16 deletions(-)
Title: Estimation for multivariate normal and Student-t data with
monotone missingness
Diff between monomvn versions 1.7-4 dated 2009-11-17 and 1.8 dated 2010-01-14
Description: Estimation of multivariate normal and student-t data of
arbitrary dimension where the pattern of missing data is
monotone. Through the use of parsimonious/shrinkage regressions
(plsr, pcr, lasso, ridge, etc.), where standard regressions
fail, the package can handle a nearly arbitrary amount of
missing data. The current version supports maximum likelihood
inference and a full Bayesian approach employing scale-mixtures
for the lasso (double-exponential) and Normal-Gamma priors, and
Student-t errors. Monotone data augmentation extends this
Bayesian approach to arbitrary missingness patterns. A fully
functional standalone interface to the Bayesian lasso (from
Park & Casella), Normal-Gamma (from Griffin & Brown), and ridge
regression with model selection via Reversible Jump, and
student-t errors (from Geweke) is also provided
Author: Robert B. Gramacy
Maintainer: Robert B. Gramacy
.Rbuildindex.20799 |only
ChangeLog | 7
DESCRIPTION | 17 +-
R/blasso.R | 10 +
R/blasso.s3.R | 32 +++-
R/bmonomvn.R | 14 +
R/bmonomvn.traces.R | 12 +
R/util.R | 18 ++
man/blasso.Rd | 19 ++
man/blasso.s3.Rd | 7
man/bmonomvn.Rd | 36 ++--
man/monomvn-internal.Rd | 1
man/monomvn-package.Rd | 6
src/blasso.cc | 350 ++++++++++++++++++++++++++++++++----------------
src/blasso.h | 44 +++---
src/bmonomvn.cc | 18 +-
src/bmonomvn.h | 1
src/nu.c | 14 -
src/rgig.c |only
src/rgig.h |only
src/solve.QP.f | 11 +
21 files changed, 421 insertions(+), 196 deletions(-)
Title: Multivariate Imputation by Chained Equations
Diff between mice versions 2.1 dated 2009-09-18 and 2.2 dated 2010-01-14
Description: Multiple Imputation using Fully Conditional Specification
Author: Stef van Buuren
Maintainer: Stef van Buuren
.vmGUIprefs.RData |only
DESCRIPTION | 8 ++--
NAMESPACE | 1
R/mice.R | 96 ++++++++++++++++++++++++++++++++++++++-------------
R/zzz.R | 6 +--
inst/CITATION | 6 +--
inst/NEWS | 8 +++-
man/mice-internal.Rd | 7 +++
8 files changed, 97 insertions(+), 35 deletions(-)
Title: Bayesian Analysis in Extreme Value Theory
Diff between evdbayes versions 1.0-7 dated 2008-07-05 and 1.0-8 dated 2010-01-14
Description: Provides functions for the bayesian analysis of extreme
value models, using MCMC methods.
Author: Alec Stephenson and Mathieu Ribatet.
Maintainer: Mathieu Ribatet
DESCRIPTION | 24 +++++++++++++-----------
inst/doc/evdbayesGuide.pdf |binary
man/posterior.mix.Rd | 4 ++--
3 files changed, 15 insertions(+), 13 deletions(-)
Title: Dendrochronology Program Library in R
Diff between dplR versions 1.2.3 dated 2010-01-05 and 1.2.4 dated 2010-01-14
Description: This package contains functions for performing some
standard tree-ring analyses.
Author: Andy Bunn
Maintainer: Andy Bunn
DESCRIPTION | 8 ++++----
R/spag.plot.R | 4 ++--
man/cms.Rd | 2 +-
man/ffcsaps.Rd | 2 +-
man/rcs.Rd | 2 +-
man/spag.plot.Rd | 2 +-
6 files changed, 10 insertions(+), 10 deletions(-)
Title: Collection of methods to detect dichotomous differential item
functioning (DIF) in psychometrics
Diff between difR versions 2.0 dated 2009-12-20 and 2.1 dated 2010-01-14
Description: The difR package contains several traditional methods to
detect DIF in dichotomously scored items. Both uniform and
non-uniform DIF effects can be detected, with methods relying
upon item response models or not. Some methods deal with more
than one focal group.
Author: Sebastien Beland (UQAM), David Magis (U Liege) and Gilles
Raiche (UQAM)
Maintainer: David Magis
DESCRIPTION | 11
NEWS | 22
R/difGenLogistic.R | 2
R/difLogistic.r | 2
R/difMH.r | 2
R/difStd.r | 2
inst/CITATION |only
inst/doc/Rd2.pdf | 3516 +++++++++++++++++++++++------------------------
man/LRT.Rd | 2
man/Logistik.rd | 2
man/breslowDay.rd | 4
man/dichoDif.rd | 2
man/difBD.rd | 4
man/difGMH.rd | 2
man/difGenLogistic.rd | 2
man/difGenLord.rd | 2
man/difLRT.rd | 2
man/difLogistic.rd | 2
man/difLord.rd | 2
man/difMH.rd | 2
man/difRaju.rd | 2
man/difStd.rd | 2
man/genDichoDif.rd | 2
man/genLogistik.rd | 2
man/genMantelHaenszel.rd | 2
man/mantelHaenszel.rd | 2
man/selectDif.rd | 2
man/selectGenDif.rd | 2
man/stdPDIF.rd | 2
29 files changed, 1806 insertions(+), 1797 deletions(-)
Title: CCMN and other noRMalizatioN methods for metabolomics data
Diff between crmn versions 0.0.12 dated 2010-01-08 and 0.0.14 dated 2010-01-14
Description: Implements the Cross-contribution Compensating Multiple
standard Normalization (CCMN) method and other normalization
algorithms.
Author: Henning Redestig
Maintainer: Henning Redestig
DESCRIPTION | 6
NAMESPACE | 4
NEWS | 19
R/crmn-package.R | 4
R/generic.R | 19
R/misc.R | 75 +
R/norm.R | 27
inst/doc/auto/crmn.el | 3
inst/doc/crmn.Rnw | 16
inst/doc/crmn.pdf | 1982 +++++++++++++++++++++++-------------------------
man/analytes.Rd | 2
man/analytes_eset.Rd | 12
man/analytes_other.Rd | 5
man/crmn.Rd | 2
man/dropunusedlevels.Rd | 2
man/makeX.Rd | 2
man/makeX_eset.Rd | 4
man/makeX_other.Rd | 2
man/method.Rd | 2
man/mexprs.Rd | 2
man/mexprs_bla.Rd | 2
man/mix.Rd | 2
man/model.Rd | 2
man/normFit.Rd | 2
man/normPred.Rd | 4
man/normalize.Rd | 6
man/pcaMuffle.Rd | 2
man/plot.nFit.Rd | 2
man/sFit.Rd | 2
man/set_mexprs.Rd | 2
man/show.Rd | 2
man/show_nfit.Rd | 2
man/standards.Rd | 2
man/standardsFit.Rd | 6
man/standardsPred.Rd | 2
man/standards_eset.Rd | 11
man/standards_other.Rd | 2
man/weightnorm.Rd | 2
38 files changed, 1110 insertions(+), 1135 deletions(-)
Title: Efficient Estimation of Covariance and (Partial) Correlation
Diff between corpcor versions 1.5.4 dated 2009-12-16 and 1.5.5 dated 2010-01-14
Description: This package implements a James-Stein-type shrinkage
estimator for the covariance matrix, with separate shrinkage
for variances and correlations. The details of the method are
explained in Sch\"afer and Strimmer (2005) and Opgen-Rhein and
Strimmer (2007). The approach is both computationally as well
as statistically very efficient, it is applicable to "small n,
large p" data, and always returns a positive definite and
well-conditioned covariance matrix. In addition to inferring
the covariance matrix the package also provides shrinkage
estimators for partial correlations, partial variances, and
regression coefficients. The inverse of the covariance and
correlation matrix can be efficiently computed, and as well as
any arbitrary power of the shrinkage correlation matrix.
Furthermore, functions are available for fast singular value
decomposition, for computing the pseudoinverse, and for
checking the rank and positive definiteness of a matrix.
Author: Juliane Schaefer, Rainer Opgen-Rhein, and Korbinian Strimmer.
Maintainer: Korbinian Strimmer
corpcor-1.5.4/corpcor/R/zzz.R |only
corpcor-1.5.4/corpcor/src |only
corpcor-1.5.5/corpcor/DESCRIPTION | 8 +-
corpcor-1.5.5/corpcor/NEWS | 14 ++++
corpcor-1.5.5/corpcor/R/mpower.R | 7 +-
corpcor-1.5.5/corpcor/R/powcor.shrink.R | 9 ++-
corpcor-1.5.5/corpcor/R/pvt.get.lambda.R |only
corpcor-1.5.5/corpcor/R/shrink.internal.R | 77 --------------------------
corpcor-1.5.5/corpcor/man/corpcor-internal.Rd | 4 +
corpcor-1.5.5/corpcor/man/invcov.shrink.Rd | 6 --
corpcor-1.5.5/corpcor/man/powcor.shrink.Rd | 6 --
11 files changed, 33 insertions(+), 98 deletions(-)
Title: Data Analysis Using Regression and Multilevel/Hierarchical
Models
Diff between arm versions 1.3-01 dated 2010-01-08 and 1.3-02 dated 2010-01-14
Description: R functions for processing lm, glm, mer and polr outputs.
Author: Andrew Gelman
Maintainer: Yu-Sung Su
CHANGELOG | 5
DESCRIPTION | 8
R/bayesglm.R | 1546 ++++++++++++++++++++++++++---------------------------------
R/coefplot.R | 1
4 files changed, 695 insertions(+), 865 deletions(-)
Title: Modelling Spatial Extremes
Diff between SpatialExtremes versions 1.5-0 dated 2009-12-30 and 1.5-1 dated 2010-01-14
More information about SpatialExtremes at CRAN
Description: This package proposes several approaches for spatial
extremes modelling.
Author: Mathieu Ribatet
Maintainer: Mathieu Ribatet
ChangeLog | 76
DESCRIPTION | 10
NEWS | 8
R/fitcovmat.R | 2
R/madogram.R | 45
R/plots.R | 9
R/standardErrors.R | 62
R/swiss.R |only
R/utils.R | 4
data |only
inst/doc/SpatialExtremesGuide.pdf | 4916 +++++++++++++++++++-------------------
man/condmap.Rd | 2
man/map.Rd | 2
man/rainfall.Rd |only
man/swiss.Rd |only
man/swissalt.Rd |only
src/gpdproc.c |only
src/madogram.c | 8
src/standardErrors.c | 40
src/utils.c | 46
src/weightedStandardErrors.c | 42
21 files changed, 2712 insertions(+), 2560 deletions(-)
Permanent link
Title: SAGA Geoprocessing and Terrain Analysis in R
Diff between RSAGA versions 0.9-1 dated 2007-11-11 and 0.9-6 dated 2010-01-14
Description: RSAGA provides access to geocomputing and terrain analysis
functions of SAGA from within R by running the command line
version of SAGA. In addition, several R functions for handling
and manipulating ASCII grids are provided, including a flexible
framework for applying local functions (including predict
methods of fitted models) or focal functions to multiple grids.
SAGA is available under GPL via
http://sourceforge.net/projects/saga-gis/.
Author: Alexander Brenning
Maintainer: Alexander Brenning
DESCRIPTION | 17 -
R/RSAGA-core.R | 139 +++++----
R/RSAGA-modules.R | 500 ++++++++++++++++++++++++++++++---
R/gridtools.R | 495 ++++++++++++++++++++++++++++++--
configure | 2
man/RSAGA-package.Rd | 30 -
man/focal.function.Rd | 16 -
man/grid.predict.Rd |only
man/multi.focal.function.Rd |only
man/pick.from.points.Rd | 18 -
man/read.ascii.grid.Rd | 14
man/rsaga.add.grid.values.to.points.Rd |only
man/rsaga.close.gaps.Rd | 15
man/rsaga.env.Rd | 48 +--
man/rsaga.esri.wrapper.Rd | 9
man/rsaga.geoprocessor.Rd | 7
man/rsaga.grid.calculus.Rd |only
man/rsaga.grid.to.points.Rd |only
man/rsaga.html.help.Rd | 7
man/rsaga.import.gdal.Rd |only
man/rsaga.inverse.distance.Rd |only
man/rsaga.ordinary.kriging.Rd |only
man/rsaga.parallel.processing.Rd | 3
man/rsaga.target.Rd |only
man/rsaga.wetness.index.Rd |only
25 files changed, 1123 insertions(+), 197 deletions(-)
Title: Regional Frequency Analysis
Diff between RFA versions 0.0-8 dated 2008-07-05 and 0.0-9 dated 2010-01-14
Description: Several function to perform a Regional Frequency Analysis
Author: Mathieu Ribatet
Maintainer: Mathieu Ribatet
DESCRIPTION | 10 ++++++----
man/graphics.Rd | 2 +-
man/lmomreg.Rd | 2 +-
man/maxWind.Rd | 2 +-
man/northCascades.Rd | 2 +-
man/reganalysis.Rd | 2 +-
man/regdist.Rd | 6 +++---
man/region.Rd | 2 +-
man/samlmu.Rd | 2 +-
9 files changed, 16 insertions(+), 14 deletions(-)
Title: Multiple comparisons using normal approximation
Diff between MCPAN versions 1.1-9 dated 2009-10-13 and 1.1-10 dated 2010-01-14
Description: Multiple contrast tests and simultaneous confidence
intervals based on normal approximation. With implementations
for binomial proportions in a 2xk setting (risk difference and
odds ratio), poly-3-adjusted tumour rates, and multiple
comparisons of biodiversity indices. Approximative power
calculation for multiple contrast tests of binomial
proportions.
Author: Frank Schaarschmidt, Daniel Gerhard, Martin Sill
Maintainer: Frank Schaarschmidt
DESCRIPTION | 8 +-
R/plotCI.R | 185 +++++++++++++++++++++++++++++++++------------------------
man/plotCI.Rd | 2
man/plotCII.Rd | 11 ---
man/poly3ci.Rd | 4 -
5 files changed, 120 insertions(+), 90 deletions(-)
Title: Full factorials, orthogonal arrays and base utilities for DoE
packages
Diff between DoE.base versions 0.9-11 dated 2010-01-03 and 0.9-14 dated 2010-01-14
Description: This package creates full factorial experimental designs
and designs based on orthogonal arrays for (industrial)
experiments. Additionally, it provides some utility functions
used also by other DoE packages.
Author: Ulrike Groemping
Maintainer: Ulrike Groemping
DESCRIPTION | 8 +++----
NAMESPACE | 1
R/fac.design.R | 14 +++++++++---
R/oa.design.R | 7 ++++--
R/plot.design.R | 48 ++++++++++++++++++++++++++++++--------------
R/show.oas.R |only
inst/NEWS | 16 ++++++++++++++
man/class-design-methods.Rd | 20 +++++++++++++++++-
man/show.oas.Rd |only
9 files changed, 88 insertions(+), 26 deletions(-)
Title: Analyzing survival data
Diff between p3state.msm versions 1.0 dated 2009-07-18 and 1.1 dated 2010-01-14
Description: Analyzing survival data from illness-death model
Author: Luis Meira-Machado and Javier Roca-Pardinas
Maintainer: Luis Felipe Meira-Machado
p3state.msm-1.0/p3state.msm/R/p11LIDA.R |only
p3state.msm-1.0/p3state.msm/R/p12LIDA.R |only
p3state.msm-1.0/p3state.msm/R/p22LIDA.R |only
p3state.msm-1.0/p3state.msm/Read-and-delete-me |only
p3state.msm-1.0/p3state.msm/man/p11LIDA.Rd |only
p3state.msm-1.0/p3state.msm/man/p12LIDA.Rd |only
p3state.msm-1.0/p3state.msm/man/p22LIDA.Rd |only
p3state.msm-1.0/p3state.msm/p3statemsmLAST.txt |only
p3state.msm-1.1/p3state.msm/DESCRIPTION | 8
p3state.msm-1.1/p3state.msm/R/Biv.R | 35 +-
p3state.msm-1.1/p3state.msm/R/data.creation.reg.R | 172 +++++-----
p3state.msm-1.1/p3state.msm/R/p3state.R | 270 +++++++++------
p3state.msm-1.1/p3state.msm/R/pLIDA.R |only
p3state.msm-1.1/p3state.msm/R/plot.p3state.R | 290 ++++++++++------
p3state.msm-1.1/p3state.msm/R/summary.p3state.R | 377 ++++++++++++----------
p3state.msm-1.1/p3state.msm/man/pLIDA.Rd |only
p3state.msm-1.1/p3state.msm/man/plot.p3state.Rd | 17
17 files changed, 676 insertions(+), 493 deletions(-)
Title: Fit, Simulate and Diagnose Exponential-Family Models for
Networks
Diff between ergm versions 2.2-1 dated 2009-03-08 and 2.2-2 dated 2010-01-14
Description: An integrated set of tools to analyze and simulate
networks based on exponential-family random graph models
(ERGM). "ergm" is a part of the "statnet" suite of packages for
network analysis. For a list of functions type:
help(package='ergm')
Author: Mark S. Handcock
Maintainer: David R. Hunter
ergm-2.2-1/ergm/examples |only
ergm-2.2-2/ergm/DESCRIPTION | 31 ++++++++++++++++-----------
ergm-2.2-2/ergm/LICENSE | 3 +-
ergm-2.2-2/ergm/R/ergm.pl.R | 1
ergm-2.2-2/ergm/man/ergm-terms.Rd | 10 ++++----
ergm-2.2-2/ergm/man/mcmc.diagnostics.ergm.Rd | 16 ++++++-------
6 files changed, 34 insertions(+), 27 deletions(-)
Title: Bayesian clustering using spike-and-slab hierarchical model,
suitable for clustering high-dimensional data.
Diff between bclust versions 1.0 dated 2009-08-04 and 1.1 dated 2010-01-14
Description: The package builds a dendrogram with log posterior as a
natural distance defined by the model. It is also capable to
computing Bayesian discrimination probabilities equivalent to
the implemented Bayesian clustering. Spike-and-Slab models are
adopted in a way to be able to produce an importance measure
for clustering and discriminant variables. The method works
properly for data with small sample size and high dimensions.
The model parameter estimation maybe difficult, depending on
data structure and the chosen distribution family.
Author: Vahid PARTOVI NIA and Anthony C. DAVISON
Maintainer: Vahid PARTOVI NIA
DESCRIPTION | 8 ++++----
R/bclust.R | 18 +++++++++---------
man/bdiscrim.Rd | 16 ++++++++--------
src/ClusteringvsGAL05.c | 9 ---------
4 files changed, 21 insertions(+), 30 deletions(-)