Title: World Development Indicators (World Bank)
Diff between WDI versions 0.1.4 dated 2011-03-20 and 2.0 dated 2012-06-19
Description: Search, extract and format data from the World Bank's
World Development Indicators
Author: Vincent Arel-Bundock
Maintainer: Vincent Arel-Bundock
WDI-0.1.4/WDI/data/extra2010.rda |only
WDI-0.1.4/WDI/data/series2010.rda |only
WDI-0.1.4/WDI/man/extra2010.Rd |only
WDI-0.1.4/WDI/man/series2010.Rd |only
WDI-2.0/WDI/DESCRIPTION | 24 ++---
WDI-2.0/WDI/MD5 |only
WDI-2.0/WDI/NAMESPACE |only
WDI-2.0/WDI/NEWS |only
WDI-2.0/WDI/R/WDI-package.R |only
WDI-2.0/WDI/R/WDI.R | 176 +++++++++++++++++++++++++-------------
WDI-2.0/WDI/R/WDI_data.R |only
WDI-2.0/WDI/README.md |only
WDI-2.0/WDI/data/WDI_data.RData |only
WDI-2.0/WDI/man/WDI-package.Rd |only
WDI-2.0/WDI/man/WDI.Rd | 47 +++++-----
WDI-2.0/WDI/man/WDI_data.Rd |only
WDI-2.0/WDI/man/WDIcache.Rd |only
WDI-2.0/WDI/man/WDIsearch.Rd | 42 +++++----
18 files changed, 181 insertions(+), 108 deletions(-)
Title: R Code for MARK Analysis
Diff between RMark versions 2.1.1 dated 2012-05-05 and 2.1.3 dated 2012-06-19
Description: This package provides an interface to the software package
MARK developed by Gary White. MARK is freely available at
(http://www.phidot.org/software/mark/download/) but is not open
source.
Author: Jeff Laake
Maintainer: Jeff Laake
DESCRIPTION | 17 ++-
MD5 | 180 ++++++++++++++++++++---------------------
NAMESPACE | 5 +
NEWS | 38 ++++++++
R/PIMS.R | 4
R/RMark-package.R | 118 +++++++++++++-------------
R/TransitionMatrix.R | 90 ++++++++++++++++++--
R/add.design.data.R | 4
R/adjust.chat.R | 3
R/adjust.parameter.count.R | 4
R/compute.design.data.R | 12 +-
R/convert.inp.r | 4
R/covariate.predictions.r | 10 +-
R/create.mark.mcmc.R |only
R/create.model.list.R | 7 -
R/deltamethod.r | 4
R/export.MARK.r | 8 -
R/export.chdata.R | 2
R/export.model.r | 2
R/extract.mark.output.R | 7 -
R/get.link.R | 2
R/get.real.R | 2
R/import.chdata.R | 4
R/make.mark.model.R | 108 +++++++++++++++++-------
R/mark.R | 6 -
R/mark.wrapper.parallel.r | 2
R/merge.design.covariates.r | 3
R/model.average.list.r | 4
R/model.average.marklist.R | 6 -
R/model.table.R | 11 +-
R/popan.r | 4
R/process.data.R | 2
R/release.gof.R | 8 -
R/rerun.mark.R | 52 +++++------
R/run.mark.model.R | 51 +++++------
R/splitCH.r |only
R/summary.mark.R | 2
R/utility.r | 4
R/var.components.R | 4
R/var.components.reml.r | 4
R/zzz.R | 121 +++++++++++++++++++++------
inst/MarkModels.pdf |binary
inst/README.txt | 23 ++---
inst/parameters.txt | 2
man/Blackduck.Rd | 2
man/Donovan.7.Rd | 4
man/Donovan.8.Rd | 6 -
man/IELogitNormalMR.Rd | 2
man/LogitNormalMR.Rd | 2
man/NicholsMSOccupancy.Rd | 2
man/PIMS.Rd | 2
man/PoissonMR.Rd | 4
man/Poisson_twoMR.Rd | 4
man/RDOccupancy.Rd | 3
man/RDSalamander.Rd | 8 +
man/TransitionMatrix.Rd | 60 +++++++++++--
man/add.design.data.Rd | 2
man/adjust.parameter.count.Rd | 2
man/adjust.value.Rd | 2
man/convert.inp.Rd | 2
man/covariate.predictions.Rd | 6 -
man/crdms.Rd | 8 +
man/create.mark.mcmc.Rd |only
man/create.model.list.Rd | 2
man/deltamethod.special.Rd | 2
man/dipper.Rd | 2
man/edwards.eberhardt.Rd | 2
man/example.data.Rd | 2
man/export.MARK.Rd | 6 -
man/export.chdata.Rd | 2
man/export.model.Rd | 2
man/extract.indices.Rd | 2
man/import.chdata.Rd | 2
man/killdeer.Rd | 8 +
man/make.mark.model.Rd | 10 ++
man/mallard.Rd | 2
man/mark.Rd | 9 +-
man/mark.wrapper.parallel.Rd | 2
man/merge_design.covariates.Rd | 2
man/model.average.list.Rd | 2
man/model.average.marklist.Rd | 2
man/model.table.Rd | 2
man/mstrata.Rd | 4
man/popan.derived.Rd | 2
man/release.gof.Rd | 6 -
man/rerun.mark.Rd | 50 +++++------
man/robust.Rd | 14 +--
man/run.mark.model.Rd | 2
man/salamander.Rd | 2
man/splitCH.Rd |only
man/var.components.Rd | 2
man/var.components.reml.Rd | 2
man/weta.Rd | 3
93 files changed, 794 insertions(+), 421 deletions(-)
Title: CUR decomposition package
Diff between rCUR versions 1.1 dated 2012-03-12 and 1.2 dated 2012-06-19
Description: Functions and objects for CUR matrix decomposition.
Author: Andras Bodor, Norbert Solymosi
Maintainer: Andras Bodor
ChangeLog |only
DESCRIPTION | 6 +++---
MD5 | 29 +++++++++++++++--------------
R/rCUR.R | 16 ++++++++++------
man/CUR.Rd | 7 ++++++-
man/CURobj-class.Rd | 5 +++++
man/STTa.Rd | 5 +++++
man/STTm.Rd | 5 +++++
man/getC.rd | 5 +++++
man/getError.rd | 5 +++++
man/getR.rd | 5 +++++
man/getU.rd | 5 +++++
man/leverage.Rd | 5 +++++
man/plotLeverage.Rd | 5 +++++
man/rCUR-package.Rd | 7 ++++++-
man/topLeverage.Rd | 5 +++++
16 files changed, 90 insertions(+), 25 deletions(-)
Title: Tools for working with URLs and HTTP
Diff between httr versions 0.1 dated 2012-05-06 and 0.1.1 dated 2012-06-19
Description: Provides useful tools for working with HTTP connections.
Is a simplified wrapper built on top of RCurl. It is much much
less configurable but because it only attempts to encompass the
most common operations it is also much much simpler.
Author: Hadley Wickham
Maintainer: Hadley Wickham
DESCRIPTION | 6 +++---
MD5 | 31 ++++++++++++++++---------------
NAMESPACE | 32 ++++++++++++++++----------------
NEWS |only
R/authenticate.r | 3 +++
R/config.r | 10 ++++++++--
R/proxy.r | 4 +---
README.md | 4 ++--
inst/tests/test-config.r | 21 +++++++++++++--------
man/authenticate.Rd | 4 +++-
man/oauth1.0_token.Rd | 5 ++---
man/oauth2.0_token.Rd | 5 ++---
man/oauth_app.Rd | 4 ++--
man/oauth_endpoint.Rd | 5 ++---
man/sign_ouath1.0.Rd | 7 +++----
man/sign_ouath2.0.Rd | 7 +++----
man/use_proxy.Rd | 4 +---
17 files changed, 80 insertions(+), 72 deletions(-)
Title: Tools to make developing R code easier
Diff between devtools versions 0.6 dated 2012-02-28 and 0.7 dated 2012-06-19
Description: Collection of package development tools
Author: Hadley Wickham
Maintainer: Hadley Wickham
devtools-0.6/devtools/R/utils.r |only
devtools-0.6/devtools/man/with_locale.Rd |only
devtools-0.7/devtools/DESCRIPTION | 29 ++---
devtools-0.7/devtools/MD5 | 100 +++++++++++--------
devtools-0.7/devtools/NAMESPACE | 35 +++++-
devtools-0.7/devtools/NEWS | 88 ++++++++++++++++
devtools-0.7/devtools/R/build.r | 4
devtools-0.7/devtools/R/check-cran.r |only
devtools-0.7/devtools/R/check.r | 48 ++-------
devtools-0.7/devtools/R/decompress.r | 2
devtools-0.7/devtools/R/dependencies.r |only
devtools-0.7/devtools/R/devel-mode.r | 2
devtools-0.7/devtools/R/document.r | 10 +
devtools-0.7/devtools/R/install-bitbucket.r |only
devtools-0.7/devtools/R/install-github.r | 7 -
devtools-0.7/devtools/R/install-gitorious.r | 7 -
devtools-0.7/devtools/R/install-url.r | 31 +++--
devtools-0.7/devtools/R/install-version.r | 4
devtools-0.7/devtools/R/install.r | 48 +++++++--
devtools-0.7/devtools/R/load-code.r | 30 +++--
devtools-0.7/devtools/R/load-data.r | 2
devtools-0.7/devtools/R/package-env.r | 6 -
devtools-0.7/devtools/R/package.r | 16 +--
devtools-0.7/devtools/R/path.r |only
devtools-0.7/devtools/R/release.r | 42 ++++++-
devtools-0.7/devtools/R/run-examples.r | 2
devtools-0.7/devtools/R/run-source.r | 19 ++-
devtools-0.7/devtools/R/system.r | 19 +--
devtools-0.7/devtools/R/test.r | 6 -
devtools-0.7/devtools/R/with.r |only
devtools-0.7/devtools/R/zzz.r | 78 +++++++++++---
devtools-0.7/devtools/inst/tests/collate-absent |only
devtools-0.7/devtools/inst/tests/collate-extra |only
devtools-0.7/devtools/inst/tests/collate-missing |only
devtools-0.7/devtools/inst/tests/test-load-collate.r |only
devtools-0.7/devtools/man/as.package.Rd | 2
devtools-0.7/devtools/man/build_win.Rd | 4
devtools-0.7/devtools/man/check.Rd | 14 ++
devtools-0.7/devtools/man/check_cran.Rd | 31 +++++
devtools-0.7/devtools/man/dev_mode.Rd | 2
devtools-0.7/devtools/man/install.Rd | 19 ++-
devtools-0.7/devtools/man/install_bitbucket.Rd |only
devtools-0.7/devtools/man/install_github.Rd | 10 +
devtools-0.7/devtools/man/install_gitorious.Rd | 8 +
devtools-0.7/devtools/man/install_url.Rd | 12 +-
devtools-0.7/devtools/man/install_version.Rd | 16 ++-
devtools-0.7/devtools/man/on_path.Rd |only
devtools-0.7/devtools/man/path.Rd |only
devtools-0.7/devtools/man/release.Rd | 14 ++
devtools-0.7/devtools/man/revdep.Rd |only
devtools-0.7/devtools/man/run_examples.Rd | 2
devtools-0.7/devtools/man/show_rd.Rd | 8 +
devtools-0.7/devtools/man/source_gist.Rd | 4
devtools-0.7/devtools/man/test.Rd | 6 -
devtools-0.7/devtools/man/with_debug.Rd |only
devtools-0.7/devtools/man/with_something.Rd |only
devtools-0.7/devtools/tests |only
57 files changed, 559 insertions(+), 228 deletions(-)
Title: Sparse Discriminant Analysis
Diff between sparseLDA versions 0.1-5 dated 2009-03-03 and 0.1-6 dated 2012-06-19
Description: Performs sparse linear discriminant analysis for gaussians
and mixture of gaussians models.
Author: Line Clemmensen
Maintainer: Line Clemmensen
DESCRIPTION | 27 +-
MD5 |only
R/sda.R | 421 +++++++++++++++++++++++++---------------------
R/smda.R | 211 +++++++++++++----------
data/penicilliumYES.RData |binary
man/sda.Rd | 21 +-
man/smda.Rd | 10 -
7 files changed, 395 insertions(+), 295 deletions(-)
Title: Generalized Method of Moments and Generalized Empirical
Likelihood
Diff between gmm versions 1.4-1 dated 2012-05-30 and 1.4-2 dated 2012-06-19
Description: It is a complete suite to estimate models based on moment
conditions. It includes the two step Generalized method of
moments (GMM) of Hansen(1982), the iterated GMM and continuous
updated estimator (CUE) of Hansen-Eaton-Yaron(1996) and several
methods that belong to the Generalized Empirical Likelihood
(GEL) family of estimators, as presented by Smith(1997),
Kitamura(1997), Newey-Smith(2004) and Anatolyev(2005).
Author: Pierre Chausse
Maintainer: Pierre Chausse
DESCRIPTION | 10 +++++-----
MD5 | 12 ++++++------
NEWS | 5 +++++
R/Methods.gel.R | 26 +++++++++++++++++++++-----
R/getModel.R | 7 +++++--
R/momentEstim.R | 6 +++---
inst/doc/gmm_with_R.pdf |binary
7 files changed, 45 insertions(+), 21 deletions(-)
Title: Implement tour methods in pure R code
Diff between tourr versions 0.5.1 dated 2012-03-20 and 0.5.2 dated 2012-06-19
Description: Implements geodesic interpolation and basis generation
functions that allow you to create new tour methods from R.
Author: Dianne Cook
Maintainer: Hadley Wickham
DESCRIPTION | 6 +++---
MD5 | 18 +++++++++---------
NAMESPACE | 1 +
NEWS | 11 +++++++++++
R/display-density.r | 6 +++---
R/geodesic-path.r | 2 +-
R/interesting-indices.r | 10 ++++++++--
R/linear-algebra.r | 8 ++++----
R/search-better.r | 2 +-
R/tour-guided.r | 3 ++-
10 files changed, 43 insertions(+), 24 deletions(-)
Title: L1 (lasso and fused lasso) and L2 (ridge) penalized estimation
in GLMs and in the Cox model
Diff between penalized versions 0.9-39 dated 2012-04-29 and 0.9-40 dated 2012-06-19
Description: A package for fitting possibly high dimensional penalized
regression models. The penalty structure can be any combination
of an L1 penalty (lasso), an L2 penalty (ridge) and a
positivity constraint on the regression coefficients. The
supported regression models are linear, logistic and poisson
regression and the Cox Proportional Hazards model.
Cross-validation routines allow optimization of the tuning
parameters.
Author: Jelle Goeman
Maintainer: Jelle Goeman
DESCRIPTION | 15
MD5 | 31 -
R/checkinput.R | 71 +++-
R/core.R | 817 +++++++++++++++++++++++++++++++++++++++++++++++-
R/cvl.R | 133 ++++---
R/penalized.R | 30 +
R/penfit.R | 9
inst/CITATION | 2
inst/doc/penalized.Rnw | 136 +++++--
inst/doc/penalized.bib |only
inst/doc/penalized.pdf |binary
man/cvl.Rd | 63 +--
man/penalized.Rd | 26 -
man/plotpath.Rd | 2
man/predict.Rd | 2
vignettes/penalized.Rnw | 144 ++++++--
vignettes/penalized.bib | 18 +
17 files changed, 1284 insertions(+), 215 deletions(-)
Title: Coercion routines for network data objects in R
Diff between intergraph versions 1.1-0 dated 2011-09-20 and 1.2-0 dated 2012-06-19
Description: R world provides several packages for working with network
data. This package supplements that functionality by providing
methods for converting network data objects between classes
defined in other packages. Currently supported classes:
network, igraph0. This version is compatible with legacy
version of igraph (prior to 0.6, renamed to igraph0). Future
versions of 'intergraph' will be compatible with new igraph API
(0.6 or later).
Author: Michal Bojanowski
Maintainer: Michal Bojanowski
intergraph-1.1-0/intergraph/inst/SVNREV |only
intergraph-1.2-0/intergraph/DESCRIPTION | 21 ++--
intergraph-1.2-0/intergraph/MD5 | 44 +++++-----
intergraph-1.2-0/intergraph/R/as.igraph.R | 8 -
intergraph-1.2-0/intergraph/R/as.matrix.igraph.R | 4
intergraph-1.2-0/intergraph/R/as.network.R | 15 +--
intergraph-1.2-0/intergraph/R/asDF.R | 4
intergraph-1.2-0/intergraph/R/dumpAttr.R | 12 +-
intergraph-1.2-0/intergraph/R/s3common.R | 6 -
intergraph-1.2-0/intergraph/data/exIgraph.rda |binary
intergraph-1.2-0/intergraph/data/exIgraph2.rda |binary
intergraph-1.2-0/intergraph/data/exNetwork.rda |binary
intergraph-1.2-0/intergraph/data/exNetwork2.rda |binary
intergraph-1.2-0/intergraph/inst/CITATION | 6 -
intergraph-1.2-0/intergraph/inst/utests/runit.as.igraph.data.frame.R | 4
intergraph-1.2-0/intergraph/inst/utests/runit.as.igraph.network.R | 2
intergraph-1.2-0/intergraph/inst/utests/runit.as.network.igraph.R | 2
intergraph-1.2-0/intergraph/inst/utests/runit.bug1926.R |only
intergraph-1.2-0/intergraph/man/as.igraph.Rd | 6 -
intergraph-1.2-0/intergraph/man/as.matrix.igraph.Rd | 4
intergraph-1.2-0/intergraph/man/as.network.Rd | 4
intergraph-1.2-0/intergraph/man/asDF.Rd | 2
intergraph-1.2-0/intergraph/man/exNetwork.Rd | 28 +++---
intergraph-1.2-0/intergraph/man/intergraph-package.Rd | 17 ++-
24 files changed, 101 insertions(+), 88 deletions(-)
Title: Distributed Lag Non-linear Models
Diff between dlnm versions 1.6.2 dated 2012-04-19 and 1.6.3 dated 2012-06-19
Description: The package dlnm contains functions to specify and run
distributed lag linear and non-linear models.
Author: Antonio Gasparrini and Ben Armstrong
Maintainer: Antonio Gasparrini
DESCRIPTION | 8 +-
MD5 | 32 +++++------
R/crossbasis.R | 2
R/crosspred.R | 78 +++++++++++++++++++--------
R/crossreduce.R | 26 +++++++--
R/internal.R | 8 +-
R/onebasis.R | 3 -
inst/ChangeLog | 132 +++++++++++++++++++++++++++-------------------
inst/doc/dlnmOverview.Rnw | 132 ++++++++++++++++++++++------------------------
inst/doc/dlnmOverview.pdf |binary
man/crossbasis.Rd | 8 +-
man/crosspred.Rd | 45 ++++++++-------
man/crossreduce.Rd | 32 +++++------
man/dlnm-package.Rd | 4 -
man/onebasis.Rd | 12 ++--
man/plot.crosspred.Rd | 20 +++---
man/plot.crossreduce.Rd | 16 ++---
17 files changed, 316 insertions(+), 242 deletions(-)
Title: Bayesian Survival Regression with Flexible Error and Random
Effects Distributions
Diff between bayesSurv versions 0.6-2 dated 2010-01-03 and 1.0-1 dated 2012-06-19
Description: Later
Author: Arnošt Komárek
Maintainer: Arnošt Komárek
bayesSurv-0.6-2/bayesSurv/data/cgd.R |only
bayesSurv-0.6-2/bayesSurv/data/cgd.dat |only
bayesSurv-0.6-2/bayesSurv/data/tandmob2.R |only
bayesSurv-0.6-2/bayesSurv/data/tandmob2.dat |only
bayesSurv-0.6-2/bayesSurv/data/tandmobRoos.R |only
bayesSurv-0.6-2/bayesSurv/data/tandmobRoos.dat |only
bayesSurv-0.6-2/bayesSurv/inst/doc/ex-cgd.pdf |only
bayesSurv-0.6-2/bayesSurv/inst/doc/ex-eortc.pdf |only
bayesSurv-0.6-2/bayesSurv/inst/doc/ex-tandmobCS.pdf |only
bayesSurv-0.6-2/bayesSurv/inst/doc/ex-tandmobMixture.pdf |only
bayesSurv-0.6-2/bayesSurv/inst/doc/ex-tandmobPA.pdf |only
bayesSurv-1.0-1/bayesSurv/CHANGES | 3
bayesSurv-1.0-1/bayesSurv/DESCRIPTION | 15 -
bayesSurv-1.0-1/bayesSurv/MD5 |only
bayesSurv-1.0-1/bayesSurv/NAMESPACE |only
bayesSurv-1.0-1/bayesSurv/R/files2coda.R | 2
bayesSurv-1.0-1/bayesSurv/R/zzz.R | 15 +
bayesSurv-1.0-1/bayesSurv/data/cgd.RData |only
bayesSurv-1.0-1/bayesSurv/data/tandmob2.RData |only
bayesSurv-1.0-1/bayesSurv/data/tandmobRoos.RData |only
bayesSurv-1.0-1/bayesSurv/inst/CITATION |only
bayesSurv-1.0-1/bayesSurv/inst/doc/index.html | 10 -
bayesSurv-1.0-1/bayesSurv/man/bayesBisurvreg.Rd | 21 +-
bayesSurv-1.0-1/bayesSurv/man/bayesBisurvreg.help.Rd | 2
bayesSurv-1.0-1/bayesSurv/man/bayesDensity.Rd | 14 +
bayesSurv-1.0-1/bayesSurv/man/bayesGspline.Rd | 25 +-
bayesSurv-1.0-1/bayesSurv/man/bayesHistogram.Rd | 15 -
bayesSurv-1.0-1/bayesSurv/man/bayesHistogram.help.Rd | 2
bayesSurv-1.0-1/bayesSurv/man/bayessurvreg.help.Rd | 2
bayesSurv-1.0-1/bayesSurv/man/bayessurvreg1.Rd | 18 +-
bayesSurv-1.0-1/bayesSurv/man/bayessurvreg1.files2init.Rd | 2
bayesSurv-1.0-1/bayesSurv/man/bayessurvreg1.help.Rd | 2
bayesSurv-1.0-1/bayesSurv/man/bayessurvreg2.Rd | 21 +-
bayesSurv-1.0-1/bayesSurv/man/bayessurvreg2.help.Rd | 2
bayesSurv-1.0-1/bayesSurv/man/bayessurvreg3.Rd | 21 +-
bayesSurv-1.0-1/bayesSurv/man/bayessurvreg3.help.Rd | 2
bayesSurv-1.0-1/bayesSurv/man/credible.region.Rd | 2
bayesSurv-1.0-1/bayesSurv/man/densplot2.Rd | 2
bayesSurv-1.0-1/bayesSurv/man/files.Gspline.Rd | 2
bayesSurv-1.0-1/bayesSurv/man/files2coda.Rd | 2
bayesSurv-1.0-1/bayesSurv/man/give.init.Rd | 2
bayesSurv-1.0-1/bayesSurv/man/give.summary.Rd | 2
bayesSurv-1.0-1/bayesSurv/man/marginal.bayesGspline.Rd | 9 -
bayesSurv-1.0-1/bayesSurv/man/plot.bayesDensity.Rd | 2
bayesSurv-1.0-1/bayesSurv/man/plot.bayesGspline.Rd | 2
bayesSurv-1.0-1/bayesSurv/man/plot.marginal.bayesGspline.Rd | 2
bayesSurv-1.0-1/bayesSurv/man/predictive.Rd | 14 +
bayesSurv-1.0-1/bayesSurv/man/predictive2.Rd | 25 +-
bayesSurv-1.0-1/bayesSurv/man/print.bayesDensity.Rd | 2
bayesSurv-1.0-1/bayesSurv/man/rMVNorm.Rd | 2
bayesSurv-1.0-1/bayesSurv/man/rWishart.Rd | 2
bayesSurv-1.0-1/bayesSurv/man/sampleCovMat.Rd | 2
bayesSurv-1.0-1/bayesSurv/man/sampled.kendall.tau.Rd | 9 -
bayesSurv-1.0-1/bayesSurv/man/scanFN.Rd | 2
bayesSurv-1.0-1/bayesSurv/man/simult.pvalue.Rd | 2
bayesSurv-1.0-1/bayesSurv/man/tandmob2.Rd | 15 -
bayesSurv-1.0-1/bayesSurv/man/tandmobRoos.Rd | 8
bayesSurv-1.0-1/bayesSurv/man/traceplot2.Rd | 2
bayesSurv-1.0-1/bayesSurv/man/vecr2matr.Rd | 2
bayesSurv-1.0-1/bayesSurv/src/AK_Error.h | 17 +
bayesSurv-1.0-1/bayesSurv/src/MHblocks.cpp | 105 ++++++++----
bayesSurv-1.0-1/bayesSurv/src/arms.cpp | 25 ++
bayesSurv-1.0-1/bayesSurv/src/bayessurvreg1.cpp | 2
bayesSurv-1.0-1/bayesSurv/src/bayessurvreg1.h | 4
bayesSurv-1.0-1/bayesSurv/src/bblocks.cpp | 69 +++++--
bayesSurv-1.0-1/bayesSurv/src/covMatrix.cpp | 32 ++-
bayesSurv-1.0-1/bayesSurv/src/templatefun.cpp | 7
67 files changed, 349 insertions(+), 220 deletions(-)
Title: A package for Graphical Markov Models
Diff between ggm versions 1.99-3 dated 2012-06-14 and 1.99-5 dated 2012-06-19
Description: Functions for analyzing and fitting Graphical Markov
models
Author: Giovanni M. Marchetti, Mathias Drton, Kayvan Sadeghi
Maintainer: Giovanni M. Marchetti
ggm-1.99-3/ggm/misc |only
ggm-1.99-5/ggm/DESCRIPTION | 11 ++++++-----
ggm-1.99-5/ggm/MD5 | 20 +++++---------------
ggm-1.99-5/ggm/NAMESPACE | 3 ++-
ggm-1.99-5/ggm/R/functions.R | 5 +++--
ggm-1.99-5/ggm/R/kayvan.R | 4 ++--
ggm-1.99-5/ggm/man/isAcyclic.Rd | 2 +-
7 files changed, 19 insertions(+), 26 deletions(-)
Title: Rich Text Format (RTF) Output
Diff between rtf versions 0.4-4 dated 2012-05-12 and 0.4-6 dated 2012-06-19
Description: A set of R functions to output Rich Text Format (RTF)
files with high resolution tables and graphics that may be
edited with a standard word processor such as Microsoft Word.
Author: Michael E. Schaffer
Maintainer: Michael E. Schaffer
DESCRIPTION | 10 +--
LICENSE | 2
MD5 | 47 ++++++++-------
NEWS | 10 +++
R/rtf.R | 137 ++++++++++++++++++++++++++++++++++++++------
inst |only
man/addHeader.RTF.Rd | 3
man/addNewLine.RTF.Rd | 3
man/addPageBreak.RTF.Rd | 4 -
man/addParagraph.RTF.Rd | 3
man/addPlot.RTF.Rd | 3
man/addPng.RTF.Rd | 3
man/addSessionInfo.RTF.Rd | 3
man/addTable.RTF.Rd | 3
man/addText.RTF.Rd | 3
man/addTrellisObject.RTF.Rd | 3
man/decreaseIndent.RTF.Rd | 3
man/done.RTF.Rd | 8 ++
man/endParagraph.RTF.Rd | 3
man/increaseIndent.RTF.Rd | 3
man/setFontSize.RTF.Rd | 3
man/startParagraph.RTF.Rd | 3
man/view.RTF.Rd | 3
tests/tests.R | 4 +
vignettes |only
25 files changed, 203 insertions(+), 64 deletions(-)
Title: Parametric Time Warping
Diff between ptw versions 1.0-1 dated 2010-11-17 and 1.0-2 dated 2012-06-19
Description: Parametric Time Warping aligns patterns, i.e. it aims to
put corresponding features at the same locations. The algorithm
searches for an optimal polynomial describing the warping. It
is possible to align one sample to a reference, several samples
to the same reference, or several samples to several
references. One can choose between calculating individual
warpings, or one global warping for a set of samples and one
reference. Two optimization criteria are implemented: RMS (Root
Mean Square error) and WCC (Weighted Cross Correlation).
Author: Jan Gerretzen
Maintainer: Tom Bloemberg
ptw-1.0-1/ptw/R/zzz.R |only
ptw-1.0-1/ptw/demo/warpdemo.r |only
ptw-1.0-2/ptw/DESCRIPTION | 8 ++++----
ptw-1.0-2/ptw/MD5 |only
ptw-1.0-2/ptw/NAMESPACE |only
ptw-1.0-2/ptw/R/select.traces.R | 2 +-
ptw-1.0-2/ptw/data/datalist |only
ptw-1.0-2/ptw/demo/00Index | 4 +++-
ptw-1.0-2/ptw/demo/demo1.R |only
ptw-1.0-2/ptw/demo/demo2.R |only
ptw-1.0-2/ptw/demo/demo3.R |only
ptw-1.0-2/ptw/src/smth.c | 1 -
12 files changed, 8 insertions(+), 7 deletions(-)
Title: Community Ecology Package
Diff between vegan versions 2.0-3 dated 2012-03-03 and 2.0-4 dated 2012-06-19
Description: Ordination methods, diversity analysis and other functions
for community and vegetation ecologists.
Author: Jari Oksanen, F. Guillaume Blanchet, Roeland Kindt, Pierre
Legendre, Peter R. Minchin, R. B. O'Hara, Gavin L. Simpson,
Peter Solymos, M. Henry H. Stevens, Helene Wagner
Maintainer: Jari Oksanen
DESCRIPTION | 8 +-
MD5 | 137 +++++++++++++++++++++-------------------
NAMESPACE | 9 ++
R/adipart.R | 111 ---------------------------------
R/adipart.default.R |only
R/adipart.formula.R |only
R/anova.prc.R | 2
R/betadisper.R | 10 ++
R/bioenv.default.R | 13 +++
R/centroids.cca.R | 1
R/checkSelect.R |only
R/clamtest.R | 5 -
R/hiersimu.R | 95 ----------------------------
R/hiersimu.default.R |only
R/hiersimu.formula.R |only
R/metaMDS.R | 5 +
R/monoMDS.R | 2
R/msoplot.R | 41 +++++-------
R/multipart.R | 138 -----------------------------------------
R/multipart.default.R |only
R/multipart.formula.R |only
R/ordiellipse.R | 9 +-
R/ordihull.R | 38 +++++++++--
R/ordilabel.R | 4 -
R/ordiplot3d.R | 42 ++++++++++++
R/ordipointlabel.R | 12 +++
R/plot.envfit.R | 17 +++--
R/plot.prc.R | 4 -
R/points.cca.R | 18 ++---
R/points.decorana.R | 2
R/points.metaMDS.R | 4 -
R/points.ordiplot.R | 4 -
R/predict.cca.R | 12 ++-
R/print.adipart.R | 6 +
R/print.metaMDS.R | 8 +-
R/rrarefy.R | 4 +
R/simper.R | 4 -
R/text.cca.R | 18 ++---
R/text.decorana.R | 2
R/text.metaMDS.R | 8 +-
R/text.ordiplot.R | 6 -
inst/ChangeLog | 57 +++++++++++++++--
inst/NEWS.Rd | 98 ++++++++++++++++++++++++++++-
inst/doc/FAQ-vegan.pdf |binary
inst/doc/FAQ-vegan.texi | 47 ++++++++++----
inst/doc/NEWS.html | 144 ++++++++++++++++++++++++++++++++++++++-----
inst/doc/decision-vegan.Rnw | 2
inst/doc/decision-vegan.pdf |binary
inst/doc/decision-vegan.tex | 20 ++---
inst/doc/diversity-vegan.pdf |binary
inst/doc/diversity-vegan.tex | 67 +++++++++-----------
inst/doc/intro-vegan.Rnw | 2
inst/doc/intro-vegan.pdf |binary
inst/doc/intro-vegan.tex | 36 +++++-----
man/adipart.Rd | 28 +++++++-
man/adonis.Rd | 16 ++++
man/anosim.Rd | 19 ++++-
man/anova.cca.Rd | 2
man/betadisper.Rd | 42 ++++++++++--
man/bioenv.Rd | 7 +-
man/decostand.Rd | 4 -
man/envfit.Rd | 11 ++-
man/metaMDS.Rd | 4 -
man/monoMDS.Rd | 5 +
man/mrpp.Rd | 137 +++++++++++++++++++++-------------------
man/mso.Rd | 3
man/multipart.Rd | 15 ++++
man/ordihull.Rd | 31 +++++----
man/ordiplot3d.Rd | 44 ++++++++++---
man/ordipointlabel.Rd | 8 ++
man/predict.cca.Rd | 30 +++++---
man/pyrifos.Rd | 2
man/simper.Rd | 13 +++
73 files changed, 975 insertions(+), 718 deletions(-)
Title: QuACN: Quantitative Analysis of Complex Networks
Diff between QuACN versions 1.3.4 dated 2011-10-18 and 1.6 dated 2012-06-19
Description: Quantitative Analysis of Complex Networks. This package
offers a set of topological network measures to analyze complex
Networks structurally.
Author: Laurin Mueller, Michael Schutte, Karl Kugler, Matthias Dehmer
Maintainer: Laurin Mueller
QuACN-1.3.4/QuACN/R/informationTheoreticGCM.R |only
QuACN-1.3.4/QuACN/inst/doc/QuACN.Rnw.backup |only
QuACN-1.3.4/QuACN/inst/doc/Sweave.sty |only
QuACN-1.6/QuACN/DESCRIPTION | 11
QuACN-1.6/QuACN/MD5 | 71 ++-
QuACN-1.6/QuACN/R/bonchev3.R |only
QuACN-1.6/QuACN/R/bondOrderID.R | 2
QuACN-1.6/QuACN/R/calculateDescriptors.R | 63 +++
QuACN-1.6/QuACN/R/distanceCodes.R |only
QuACN-1.6/QuACN/R/distanceDegreeCompactness.R |only
QuACN-1.6/QuACN/R/distanceDegreeEquality.R |only
QuACN-1.6/QuACN/R/distanceDegreeMIC.R |only
QuACN-1.6/QuACN/R/edgeDataMatrix.R | 4
QuACN-1.6/QuACN/R/edgeEqualityMIC.R |only
QuACN-1.6/QuACN/R/edgeMagnitudeMIC.R |only
QuACN-1.6/QuACN/R/edgesNoDupls.R | 2
QuACN-1.6/QuACN/R/getLabels.R | 31 +
QuACN-1.6/QuACN/R/graphDistanceComplexity.R |only
QuACN-1.6/QuACN/R/graphVertexComplexity.R | 4
QuACN-1.6/QuACN/R/huXuID.R | 4
QuACN-1.6/QuACN/R/infoTheoretic.R |only
QuACN-1.6/QuACN/R/infoTheoreticGCM.R |only
QuACN-1.6/QuACN/R/infoTheoreticLabeled.R |only
QuACN-1.6/QuACN/R/infoTheoreticSum.R |only
QuACN-1.6/QuACN/R/informationBondIndex.R |only
QuACN-1.6/QuACN/R/informationLayerIndex.R |only
QuACN-1.6/QuACN/R/layerMatrix.R |only
QuACN-1.6/QuACN/R/localClusteringCoeff.R | 2
QuACN-1.6/QuACN/R/nodeDataVector.R | 19 -
QuACN-1.6/QuACN/R/symmetryIndex.R |only
QuACN-1.6/QuACN/data |only
QuACN-1.6/QuACN/inst/doc/QuACN.Rnw | 420 +++++++++++++++++++----
QuACN-1.6/QuACN/inst/doc/QuACN.bib | 70 +++
QuACN-1.6/QuACN/inst/doc/QuACN.pdf |binary
QuACN-1.6/QuACN/inst/doc/logo.jpg |only
QuACN-1.6/QuACN/man/bonchev3.Rd |only
QuACN-1.6/QuACN/man/bondOrderID.Rd | 8
QuACN-1.6/QuACN/man/calculateDescriptors.Rd | 24 +
QuACN-1.6/QuACN/man/chemicalElements.Rd |only
QuACN-1.6/QuACN/man/distanceDegreeCompactness.Rd |only
QuACN-1.6/QuACN/man/distanceDegreeEquality.Rd |only
QuACN-1.6/QuACN/man/distanceDegreeMIC.Rd |only
QuACN-1.6/QuACN/man/edgeEqualityMIC.Rd |only
QuACN-1.6/QuACN/man/edgeMagnitudeMIC.Rd |only
QuACN-1.6/QuACN/man/graphDistanceComplexity.Rd |only
QuACN-1.6/QuACN/man/huXuID.Rd | 10
QuACN-1.6/QuACN/man/infoTheoreticGCM.Rd | 5
QuACN-1.6/QuACN/man/infoTheoreticLabeledE.Rd |only
QuACN-1.6/QuACN/man/infoTheoreticLabeledV1.Rd |only
QuACN-1.6/QuACN/man/infoTheoreticLabeledV2.Rd |only
QuACN-1.6/QuACN/man/infoTheoreticSum.Rd |only
QuACN-1.6/QuACN/man/informationBondIndex.Rd |only
QuACN-1.6/QuACN/man/informationLayerIndex.Rd |only
QuACN-1.6/QuACN/man/layerMatrix.Rd |only
QuACN-1.6/QuACN/man/symmetryIndex.Rd |only
55 files changed, 623 insertions(+), 127 deletions(-)
Title: Model selection uncertainty and model mixing
Diff between MMIX versions 1.1 dated 2009-07-30 and 1.2 dated 2012-06-19
Description: Implement different types of model mixing and model
selection methods for linear or logistic models.
Author: Marie Morfin and David Makowski
Maintainer:
DESCRIPTION | 8 ++++----
MD5 |only
NAMESPACE |only
R/arms.r | 2 +-
R/bootFreq.r | 3 ++-
inst |only
man/MMIX-package.Rd | 4 ++--
7 files changed, 9 insertions(+), 8 deletions(-)
Title: Mixture of methods including mixtures
Diff between mixAK versions 2.2 dated 2011-12-20 and 2.4 dated 2012-06-19
Description: This package contains a mixture of statistical methods
including the MCMC methods to analyze normal mixtures
Author: Arnošt Komárek
Maintainer: Arnošt Komárek
mixAK-2.2/mixAK/inst/doc/Faithful.pdf |only
mixAK-2.2/mixAK/inst/doc/Galaxy.pdf |only
mixAK-2.2/mixAK/inst/doc/Komarek-NMix-supplement.pdf |only
mixAK-2.2/mixAK/inst/doc/PBCseq.pdf |only
mixAK-2.2/mixAK/inst/doc/Tandmob.pdf |only
mixAK-2.2/mixAK/inst/doc/img |only
mixAK-2.4/mixAK/DESCRIPTION | 11
mixAK-2.4/mixAK/MD5 | 110 ++----
mixAK-2.4/mixAK/NAMESPACE | 2
mixAK-2.4/mixAK/NEWS | 3
mixAK-2.4/mixAK/R/GLMM_MCMC.R | 57 +--
mixAK-2.4/mixAK/R/GLMM_MCMCinit.b.R | 33 +
mixAK-2.4/mixAK/R/GLMM_MCMCprior.b.R | 101 +++--
mixAK-2.4/mixAK/R/GLMM_MCMCwrapper.R | 26 -
mixAK-2.4/mixAK/R/NMixRelabel.GLMM_MCMC.R | 84 ++--
mixAK-2.4/mixAK/R/dMVT.R |only
mixAK-2.4/mixAK/R/fitted.GLMM_MCMC.R | 237 +++++++++++--
mixAK-2.4/mixAK/R/plotProfiles.R | 34 +
mixAK-2.4/mixAK/data/Acidity.rda |binary
mixAK-2.4/mixAK/data/Enzyme.rda |binary
mixAK-2.4/mixAK/data/Galaxy.rda |binary
mixAK-2.4/mixAK/inst/CITATION | 4
mixAK-2.4/mixAK/inst/doc/Faithful.R | 6
mixAK-2.4/mixAK/inst/doc/Galaxy.R | 6
mixAK-2.4/mixAK/inst/doc/PBCseq.R | 6
mixAK-2.4/mixAK/inst/doc/Tandmob.R | 6
mixAK-2.4/mixAK/inst/doc/arnost02.css | 8
mixAK-2.4/mixAK/inst/doc/bodybg.jpg |only
mixAK-2.4/mixAK/inst/doc/index.html | 14
mixAK-2.4/mixAK/inst/doc/menuhover.jpg |only
mixAK-2.4/mixAK/man/GLMMMCMC.Rd | 62 ++-
mixAK-2.4/mixAK/man/MVT.Rd | 26 -
mixAK-2.4/mixAK/man/NMixMCMC.Rd | 8
mixAK-2.4/mixAK/man/NMixPredDensJoint2.Rd | 5
mixAK-2.4/mixAK/man/NMixPredDensMarg.Rd | 5
mixAK-2.4/mixAK/man/NMixRelabel.Rd | 5
mixAK-2.4/mixAK/man/fitted.GLMMMCMC.Rd | 9
mixAK-2.4/mixAK/man/plot.NMixPredDensJoint2.Rd | 5
mixAK-2.4/mixAK/man/plot.NMixPredDensMarg.Rd | 5
mixAK-2.4/mixAK/man/plotProfiles.Rd | 6
mixAK-2.4/mixAK/src/AK_BLAS.h | 122 ++++++
mixAK-2.4/mixAK/src/AK_LAPACK.cpp | 20 +
mixAK-2.4/mixAK/src/AK_LAPACK.h | 24 +
mixAK-2.4/mixAK/src/Dist_MVT.cpp | 179 +++++++++-
mixAK-2.4/mixAK/src/Dist_MVT.h | 125 ++++++-
mixAK-2.4/mixAK/src/GLMM.h | 5
mixAK-2.4/mixAK/src/GLMM_Deviance.cpp | 339 +++++++++++++++----
mixAK-2.4/mixAK/src/GLMM_Deviance.h | 22 -
mixAK-2.4/mixAK/src/GLMM_MCMC.cpp | 108 ++++--
mixAK-2.4/mixAK/src/GLMM_MCMC.h | 45 +-
mixAK-2.4/mixAK/src/GLMM_NMixRelabel.cpp | 31 +
mixAK-2.4/mixAK/src/GLMM_NMixRelabel.h | 8
mixAK-2.4/mixAK/src/GLMM_PED.cpp | 55 ++-
mixAK-2.4/mixAK/src/GLMM_PED.h | 14
mixAK-2.4/mixAK/src/MCMC_loglik_Zwork1_stres.cpp | 137 +++++++
mixAK-2.4/mixAK/src/MCMC_loglik_Zwork1_stres.h | 33 +
mixAK-2.4/mixAK/src/NMix.h | 6
mixAK-2.4/mixAK/src/NMix_MCMC.cpp | 11
mixAK-2.4/mixAK/src/NMix_Utils.cpp | 137 ++++++-
mixAK-2.4/mixAK/src/NMix_Utils.h | 90 ++++-
60 files changed, 1931 insertions(+), 464 deletions(-)
Previous versions (as known to CRANberries) which should be available via the Archive link are:
2011-12-05 0.3.1
2011-12-02 0.3.0
2010-12-07 0.2-5
2010-11-19 0.2-3
2010-08-01 0.2-2
2010-06-04 0.2-1
2010-06-01 0.2-0
2010-05-28 0.1-9
2010-05-22 0.1-8
2010-02-15 0.1-7
2009-11-22 0.1-3
Previous versions (as known to CRANberries) which should be available via the Archive link are:
2011-10-23 0.0-14
2010-11-29 0.0-13
2010-05-31 0.0-10
2010-02-12 0.0-8
2010-02-12 0.0-9
2009-12-13 0.0-6
2009-12-13 0.0-7
2009-11-22 0.0-5
2009-07-30 0.0-3
2009-07-27 0.0-2
Previous versions (as known to CRANberries) which should be available via the Archive link are:
2009-11-23 0.1-2
2009-04-20 0.0
Title: Weighted Correlation Network Analysis
Diff between WGCNA versions 1.20 dated 2012-04-24 and 1.22 dated 2012-06-19
Description: Functions necessary to perform Weighted Correlation
Network Analysis
Author: Peter Langfelder
Maintainer: Peter Langfelder
Changelog | 43 +++++++++++++++++++++++++
DESCRIPTION | 8 ++--
MD5 | 23 +++++++------
R/Functions-modColor.R | 77 ++++++++++++++++++++++------------------------
R/Functions.R | 17 +---------
R/blockwiseModulesC.R | 16 +--------
R/corFunctions.R | 6 ---
R/internalConstants.R |only
R/modulePreservation.R | 66 +++++++++++++++++++++++----------------
R/userListEnrichment.R | 6 +--
man/WGCNA-package.Rd | 4 +-
man/modulePreservation.Rd | 4 ++
src/networkFunctions.c | 2 -
13 files changed, 151 insertions(+), 121 deletions(-)
Title: Unsupervised and Supervised methods of Propensity Score
Adjustment for Bias
Diff between USPS versions 1.2-1 dated 2011-12-27 and 1.2-2 dated 2012-06-19
Description: Unsupervised PS Methods define Local Treatment Differences
(LTDs) within numerous Clusters of patients well-matched on
their pre-treatment X-characteristics and display the resulting
distribution of local effect-size estimates across Clusters. I
now prefer to call this form of Nonparametric Preprocessing of
observational outcomes Local Control; it uses patient blocking
/ matching concepts so as to rely only on a simple model
(Nested ANOVA, treatment within cluster) that becomes more and
more relastic as Clusters become small and numerous. In sharp
contrast, the Supervised PS Methods provided here attempt to
estimate unknow true Propensities with parametric models that
can be quite wrong and unrealistic. PS estimates always need
to be Validated; there is usually no guarantee that such
estimatres actually block patients with similar
X-characteristics together, like true propensities do.
Author: Bob Obenchain
Maintainer: Bob Obenchain
DESCRIPTION | 31 ++++++++++++++++++++-----------
MD5 | 12 ++++++------
R/USPS.R | 20 ++++++++++----------
data/lindner.rda |binary
demo/abcix.R | 3 ---
inst/doc/USPSinR.pdf |binary
man/USPS-package.Rd | 2 +-
7 files changed, 37 insertions(+), 31 deletions(-)
Title: sos
Diff between sos versions 1.3-1 dated 2011-07-06 and 1.3-4 dated 2012-06-19
Description: Search contributed R packages, sort by package
Author: Spencer Graves, Sundar Dorai-Raj, and Romain Francois
Maintainer: Spencer Graves
sos-1.3-1/sos/inst/doc/RJournal.sty |only
sos-1.3-4/sos/DESCRIPTION | 12 +-
sos-1.3-4/sos/MD5 |only
sos-1.3-4/sos/NAMESPACE |only
sos-1.3-4/sos/R/PackageSum2.R | 51 ++++-----
sos-1.3-4/sos/R/back2ForwardSlash.R |only
sos-1.3-4/sos/R/findFn.R | 5
sos-1.3-4/sos/R/writeFindFn2xls.R | 179 +++++++++++++++++++--------------
sos-1.3-4/sos/inst/doc/sos.pdf |binary
sos-1.3-4/sos/inst/tests |only
sos-1.3-4/sos/man/back2ForwardSlash.Rd |only
sos-1.3-4/sos/man/writeFindFn2xls.Rd | 13 --
sos-1.3-4/sos/vignettes |only
13 files changed, 140 insertions(+), 120 deletions(-)
Title: Regression Estimation and Presentation
Diff between rockchalk versions 1.6 dated 2012-06-12 and 1.6.2 dated 2012-06-19
Description: A collection of functions for ease of presentation and
interpretation of regression analysis. These functions are
developed in response to student requests that have arisen in
our regression course. For regression diagnostics, see
mcDiagnose, getDeltaRsquare, meanCenter or residualCenter. See
the outreg function for a way to generate LaTeX tables of
regression models. For nice, easy to use pictures, see
plotSlopes, plotCurves, plotPlane for graphs. There are some
functions for re-organization of data, especially useful might
be combineLevels for re-coding factors. The vignette
"rockchalk" offers a fairly broad survey. The package title
"rockchalk" refers to the expression, "Rock Chalk Jayhawk, Go
K.U.".
Author: Paul E. Johnson
Maintainer: Paul E. Johnson
DESCRIPTION | 8
MD5 | 20
R/meanCenter.R | 14
inst/doc/Rchaeology.Rnw | 674 +++++++++++++-----
inst/doc/Rchaeology.pdf |binary
inst/doc/rockchalk.pdf |binary
vignettes/Rchaeology.R | 90 +-
vignettes/Rchaeology.Rnw | 674 +++++++++++++-----
vignettes/Rchaeology.lyx | 1697 +++++++++++++++++++++++++++++++++++++----------
vignettes/rockchalk.R | 2
vignettes/rockchalk.bib | 74 +-
11 files changed, 2447 insertions(+), 806 deletions(-)