Tue, 22 May 2012

Package iterLap updated to version 1.1-2 with previous version 1.1-1 dated 2011-11-13

Title: Approximate probability densities by iterated Laplace Approximations
Description: The iterLap (iterated Laplace approximation) algorithm approximates a general (possibly non-normalized) probability density on R^p, by repeated Laplace approximations to the difference between current approximation and true density (on log scale). The final approximation is a mixture of multivariate normal distributions and might be used for example as a proposal distribution for importance sampling (eg in Bayesian applications). The algorithm can be seen as a computational generalization of the Laplace approximation suitable for skew or multimodal densities.
Author: Bjoern Bornkamp
Maintainer: Bjoern Bornkamp

Diff between iterLap versions 1.1-1 dated 2011-11-13 and 1.1-2 dated 2012-05-22

 DESCRIPTION            |   28 +++++++++++++++-------------
 MD5                    |   12 ++++++------
 R/iterLap.R            |   13 ++-----------
 inst/CITATION          |    6 +++---
 man/GRApprox.Rd        |    2 +-
 man/iterLap-package.Rd |    6 +++---
 man/iterLap.Rd         |    2 +-
 7 files changed, 31 insertions(+), 38 deletions(-)

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Package doRNG updated to version 1.3 with previous version 1.2.6 dated 2012-04-17

Title: Generic Reproducible Parallel Backend for foreach Loops
Description: This package provides functions to perform reproducible parallel foreach loops, using independent random streams as generated by L'Ecuyer's combined multiple-recursive generator [L'Ecuyer (1999)]. It enables to easily convert standard %dopar% loops into fully reproducible loops, independently of the number of workers, the task scheduling strategy, or the chosen parallel environment and associated foreach backend.
Author: Renaud Gaujoux
Maintainer: Renaud Gaujoux

Diff between doRNG versions 1.2.6 dated 2012-04-17 and 1.3 dated 2012-05-22

 doRNG-1.2.6/doRNG/vignettes/Rpackages.bib     |only
 doRNG-1.3/doRNG/DESCRIPTION                   |    7 ++++---
 doRNG-1.3/doRNG/MD5                           |   23 +++++++++++------------
 doRNG-1.3/doRNG/NAMESPACE                     |    5 +++--
 doRNG-1.3/doRNG/R/doRNG-package.R             |    1 +
 doRNG-1.3/doRNG/R/doRNG.R                     |    1 +
 doRNG-1.3/doRNG/inst/doc/doRNG-unitTests.Rnw  |   18 +++++++++---------
 doRNG-1.3/doRNG/inst/doc/doRNG-unitTests.pdf  |binary
 doRNG-1.3/doRNG/inst/doc/doRNG.pdf            |binary
 doRNG-1.3/doRNG/man/RNGseq.Rd                 |    2 ++
 doRNG-1.3/doRNG/man/doRNG.Rd                  |    6 +++++-
 doRNG-1.3/doRNG/vignettes/doRNG-unitTests.Rnw |   18 +++++++++---------
 doRNG-1.3/doRNG/vignettes/src/doRNG.Rnw       |    7 +++++++
 13 files changed, 52 insertions(+), 36 deletions(-)

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Package rtape updated to version 2.1 with previous version 2.0 dated 2012-04-25

Title: Manage and manipulate large collections of R objects stored as tape-like files
Description: Storing huge data in RData format causes problems because of the nessesity to load the whole file to the memory in order to access and manipulate objects inside such file; rtape is a simple solution to this problem. The package contains serveral wrappers of R built-in serialize/unserialize mechanism allowing user to quickly append objects to a tape-like file and later iterate over them requiring only one copy of each stored object to reside in memory a time.
Author: Miron B. Kursa
Maintainer: Miron B. Kursa

Diff between rtape versions 2.0 dated 2012-04-25 and 2.1 dated 2012-05-22

 rtape-2.0/rtape/man/rtape_apply.Rd     |only
 rtape-2.1/rtape/DESCRIPTION            |    8 ++++----
 rtape-2.1/rtape/MD5                    |   27 ++++++++++++++-------------
 rtape-2.1/rtape/R/rtapeAdd.R           |    2 +-
 rtape-2.1/rtape/R/rtapeLapply.R        |    2 +-
 rtape-2.1/rtape/R/rtape_apply.R        |    2 +-
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 rtape-2.1/rtape/inst/NEWS              |    4 ++++
 rtape-2.1/rtape/man/guessFileFormat.Rd |    7 +++++--
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 rtape-2.1/rtape/man/rtapeAdd.Rd        |    9 ++++++---
 rtape-2.1/rtape/man/rtapeAsList.Rd     |    7 +++++--
 rtape-2.1/rtape/man/rtapeFilter.Rd     |    7 +++++--
 rtape-2.1/rtape/man/rtapeLapply.Rd     |    7 +++++--
 rtape-2.1/rtape/man/rtapeRerecord.Rd   |    9 ++++++---
 16 files changed, 62 insertions(+), 37 deletions(-)

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Package RForcecom updated to version 0.2 with previous version 0.1 dated 2012-03-05

Title: RForcecom provides the connection to Force.com (Salesforce.com) from R.
Description: RForcecom provides the connection to Force.com and Salesforce.com from R.
Author: Takekatsu Hiramura
Maintainer: Takekatsu Hiramura

Diff between RForcecom versions 0.1 dated 2012-03-05 and 0.2 dated 2012-05-22

 DESCRIPTION                         |   12 ++++----
 MD5                                 |   34 +++++++++++++-----------
 NAMESPACE                           |    2 +
 R/rforcecom.api.R                   |   11 ++++++++
 R/rforcecom.create.R                |   49 ++++++++++++++++++++++++++++++------
 R/rforcecom.delete.R                |   24 +++++++++++++++--
 R/rforcecom.getServerTimestamp.R    |only
 R/rforcecom.login.R                 |   20 ++++++++++++--
 R/rforcecom.query.R                 |   24 ++++++++++++++---
 R/rforcecom.retrieve.R              |    4 ++
 R/rforcecom.search.R                |   24 +++++++++++++++--
 R/rforcecom.update.R                |   28 ++++++++++++++++++--
 R/rforcecom.upsert.R                |   28 ++++++++++++++++++--
 man/RForcecom-package.Rd            |    4 ++
 man/rforcecom.api.Rd                |    3 ++
 man/rforcecom.create.Rd             |    2 -
 man/rforcecom.getServerTimestamp.Rd |only
 man/rforcecom.update.Rd             |    2 -
 man/rforcecom.upsert.Rd             |    4 +-
 19 files changed, 222 insertions(+), 53 deletions(-)

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Package SPARQL updated to version 1.9 with previous version 1.7 dated 2011-11-03

Title: SPARQL client
Description: Use SPARQL to pose SELECT or UPDATE queries to an end-point.
Author: Willem Robert van Hage and Tomi Kauppinen , with contributions from Christopher Davis and Jesper Hoeksema
Maintainer: Willem Robert van Hage and Tomi Kauppinen

Diff between SPARQL versions 1.7 dated 2011-11-03 and 1.9 dated 2012-05-22

 DESCRIPTION           |   16 +-
 MD5                   |   11 +
 NAMESPACE             |only
 R/SPARQL.R            |  302 ++++++++++++++++++++++++++++++--------------------
 man/SPARQL-package.Rd |   34 +++++
 man/SPARQL.Rd         |   33 ++++-
 man/get_value.Rd      |only
 man/interpret_type.Rd |only
 8 files changed, 259 insertions(+), 137 deletions(-)

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Package changepoint updated to version 0.7 with previous version 0.6.1 dated 2012-05-13

Title: An R package for changepoint analysis
Description: Implements various mainstream and specialised changepoint methods for finding single and multiple changepoints within data. Many popular non-parametric and frequentist methods are included. The cpt.mean, cpt.var, cpt.meanvar functions should be your first point of call.
Author: Rebecca Killick , Idris A. Eckley
Maintainer: Rebecca Killick

Diff between changepoint versions 0.6.1 dated 2012-05-13 and 0.7 dated 2012-05-22

 changepoint-0.6.1/changepoint/R/multiple.nonparametric.r       |only
 changepoint-0.6.1/changepoint/R/multiple.norm.r                |only
 changepoint-0.7/changepoint/DESCRIPTION                        |    6 
 changepoint-0.7/changepoint/MD5                                |   37 +-
 changepoint-0.7/changepoint/NAMESPACE                          |   12 
 changepoint-0.7/changepoint/NEWS                               |    4 
 changepoint-0.7/changepoint/R/cpt.R                            |   17 
 changepoint-0.7/changepoint/R/cpt.class.R                      |   25 +
 changepoint-0.7/changepoint/R/decision.R                       |    2 
 changepoint-0.7/changepoint/R/gamma.R                          |    7 
 changepoint-0.7/changepoint/R/multiple.nonparametric.R         |only
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 changepoint-0.7/changepoint/man/changepoint-package.Rd         |    2 
 changepoint-0.7/changepoint/man/cpt.meanvar.Rd                 |    4 
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 changepoint-0.7/changepoint/man/segneigh.meanvar.poisson.Rd    |only
 changepoint-0.7/changepoint/man/single.meanvar.exp.Rd          |    2 
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 changepoint-0.7/changepoint/man/single.meanvar.poisson.Rd      |only
 changepoint-0.7/changepoint/man/single.meanvar.poisson.calc.Rd |only
 changepoint-0.7/changepoint/src/PELT.c                         |  179 +++++++++-
 25 files changed, 268 insertions(+), 35 deletions(-)

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Package ror updated to version 0.8 with previous version 0.6.1 dated 2011-12-31

Title: Robust Ordinal Regression MCDA library
Description: An R package for computing both exact- and stochastic robust ordinal regression and maximal vectors.
Author: Tommi Tervonen
Maintainer: Tommi Tervonen

Diff between ror versions 0.6.1 dated 2011-12-31 and 0.8 dated 2012-05-22

 ror-0.6.1/ror/inst/java/libror-0.4.1-jar-with-dependencies.jar |only
 ror-0.8/ror/DESCRIPTION                                        |   11 +-
 ror-0.8/ror/MD5                                                |   20 ++--
 ror-0.8/ror/NAMESPACE                                          |    4 
 ror-0.8/ror/R/commonsmath-utagms.R                             |    4 
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 ror-0.8/ror/R/ror_common.R                                     |    8 -
 ror-0.8/ror/R/rorsmaa.R                                        |   48 +---------
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 ror-0.8/ror/man/rejection.Rd                                   |only
 ror-0.8/ror/man/ror-package.Rd                                 |    7 +
 15 files changed, 39 insertions(+), 63 deletions(-)

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Package caMassClass (with last version 1.9) was removed from CRAN

Previous versions (as known to CRANberries) which should be available via the Archive link are:

2010-12-09 1.9
2009-12-13 1.8
2009-10-11 1.7
2007-02-01 1.6

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Package egarch (with last version 1.0.0) was removed from CRAN

Previous versions (as known to CRANberries) which should be available via the Archive link are:

2010-10-19 1.0.0

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Package pkDACLASS (with last version 1.0) was removed from CRAN

Previous versions (as known to CRANberries) which should be available via the Archive link are:

2011-01-15 1.0

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Package spatialprobit updated to version 0.9-2 with previous version 0.9-1 dated 2012-02-19

Title: Spatial Probit Models
Description: Bayesian Estimation of Spatial Probit Models
Author: Stefan Wilhelm and Miguel Godinho de Matos
Maintainer: Stefan Wilhelm

Diff between spatialprobit versions 0.9-1 dated 2012-02-19 and 0.9-2 dated 2012-05-22

 DESCRIPTION            |    8 +-
 MD5                    |    9 +-
 NAMESPACE              |    9 +-
 NEWS                   |    4 +
 R/SpatialProbit-MCMC.R |  161 ++++++++++++++++++++++++++++++++++++++++++-------
 man/c.sarprobit.Rd     |only
 6 files changed, 159 insertions(+), 32 deletions(-)

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Package maxent updated to version 1.3.2 with previous version 1.3.1 dated 2011-12-22

Title: Low-memory Multinomial Logistic Regression with Support for Text Classification
Description: maxent is an R package with tools for low-memory multinomial logistic regression, also known as maximum entropy. The focus of this maximum entropy classifier is to minimize memory consumption on very large datasets, particularly sparse document-term matrices represented by the tm package. The classifier is based on an efficient C++ implementation written by Dr. Yoshimasa Tsuruoka.
Author: Timothy P. Jurka, Yoshimasa Tsuruoka
Maintainer: Timothy P. Jurka

Diff between maxent versions 1.3.1 dated 2011-12-22 and 1.3.2 dated 2012-05-22

 ChangeLog        |    5 +++++
 DESCRIPTION      |   18 ++++++++++++------
 MD5              |    8 ++++----
 src/Makevars     |    2 +-
 src/Makevars.win |    2 +-
 5 files changed, 23 insertions(+), 12 deletions(-)

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New package dataframe with initial version 2.5
Package: dataframe
Type: Package
Title: Fast data frames
Version: 2.5
Date: 2012-05-20
Author: Tim Hesterberg
Maintainer: Tim Hesterberg
Depends: R (>= 2.15.0)
Suggests: splus2R
Enhances: chron
Description: This contains versions of standard data frame functions in R, modified to avoid making extra copies of inputs. This is faster, particularly for large data.
License: GPL-2
LazyLoad: no
ByteCompile: yes
Packaged: 2012-05-21 20:28:04 UTC; rocket
Repository: CRAN
Date/Publication: 2012-05-22 05:54:50

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Package CDVine updated to version 1.1-7 with previous version 1.1-6 dated 2012-05-14

Title: Statistical inference of C- and D-vine copulas
Description: This package provides functions for statistical inference of canonical vine (C-vine) and D-vine copulas. It contains tools for bivariate exploratory data analysis and for bivariate as well as vine copula selection. Models can be estimated either sequentially or by joint maximum likelihood estimation. Sampling algorithms and plotting methods are also included. Data is assumed to lie in the unit hypercube (so-called copula data).
Author: Ulf Schepsmeier, Eike Christian Brechmann
Maintainer: Ulf Schepsmeier, Eike Christian Brechmann

Diff between CDVine versions 1.1-6 dated 2012-05-14 and 1.1-7 dated 2012-05-22

 CDVine.pdf                  |binary
 DESCRIPTION                 |    8 ++++----
 MD5                         |   20 ++++++++++----------
 R/BiCopSelect.r             |    9 +++++----
 inst/ChangeLog              |    9 +++++++++
 inst/doc/CDVine-package.pdf |binary
 man/BiCopChiPlot.Rd         |    2 +-
 man/BiCopKPlot.Rd           |    2 +-
 man/BiCopLambda.Rd          |    4 ++--
 man/BiCopPar2Tau.Rd         |    4 ++--
 man/CDVine-package.Rd       |    4 ++--
 11 files changed, 36 insertions(+), 26 deletions(-)

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New package CpGassoc with initial version 1.00
Package: CpGassoc
Type: Package
Title: Association between Methylation and a phenotype of interest
Version: 1.00
Date: 2012-05-10
Author: Barfield, R., Conneely, K., Kilaru,V
Maintainer: R Barfield
Description: CpGassoc is designed to test for association between methylation at CpG sites across the genome and a phenotype of interest, adjusting for any relevant covariates. The package can perform standard analyses of large datasets very quickly with no need to impute the data. It can also handle mixed effects models with chip or batch entering the model as a random intercept. CpGassoc also includes tools to apply quality control filters, perform permutation tests, and create QQ plots, manhattan plots, and scatterplots for individual CpG sites.
Depends: R (>= 2.10), nlme
Suggests: qvalue
License: GPL (>= 2)
Packaged: 2012-05-21 19:11:49 UTC; rbarfield
Repository: CRAN
Date/Publication: 2012-05-22 05:54:48

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