Mon, 20 Aug 2012

Package rgdal updated to version 0.7-16 with previous version 0.7-15 dated 2012-08-20

Title: Bindings for the Geospatial Data Abstraction Library
Description: Provides bindings to Frank Warmerdam's Geospatial Data Abstraction Library (GDAL) (>= 1.6.0) and access to projection/transformation operations from the PROJ.4 library. The GDAL and PROJ.4 libraries are external to the package, and, when installing the package from source, must be correctly installed first. Both GDAL raster and OGR vector map data can be imported into R, and GDAL raster data and OGR vector data exported. Use is made of classes defined in the sp package. Windows and Mac Intel OS X binaries (including GDAL, PROJ.4 and Expat) are provided on CRAN.
Author: Timothy H. Keitt , Roger Bivand , Edzer Pebesma , Barry Rowlingson
Maintainer: Roger Bivand

Diff between rgdal versions 0.7-15 dated 2012-08-20 and 0.7-16 dated 2012-08-20

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Package softclassval updated to version 0.99-20120820 with previous version 0.5-20120202 dated 2012-02-02

Title: Soft classification performance measures
Description: Extension of sensitivity, specificity, positive and negative predictive value to continuous predicted and reference memberships in [0, 1]
Author: C. Beleites
Maintainer: C. Beleites

Diff between softclassval versions 0.5-20120202 dated 2012-02-02 and 0.99-20120820 dated 2012-08-20

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Package longitudinalData updated to version 2.1 with previous version 2.0 dated 2012-03-28

Title: Longitudinal Data
Description: Tools for longitudinal data and joint longitudinal data (used by packages kml and kml3d).
Author: Christophe Genolini [cre, aut]
Maintainer: Christophe Genolini

Diff between longitudinalData versions 2.0 dated 2012-03-28 and 2.1 dated 2012-08-20

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Package kml3d updated to version 2.1 with previous version 2.0 dated 2012-03-28

Title: K-means for joint Longitudinal data
Description: KmL3D is an implementation of k-means specifically design to cluster joint trajectories (longitudinal data on several variable-trajectories). Like KmL, it provides facilities to deal with missing value, compute several quality criterion (Calinski and Harabatz, Ray and Turie, Davies and Bouldin, BIC,...) and propose a graphical interface for choosing the 'best' number of clusters. In addition, the 3D graph representing the mean joint-trajectories of each cluster can be exported through LaTeX in a 3D dynamic rotating PDF graph.
Author: Christophe Genolini [cre, aut], Bruno Falissard [ctb], Jean-Baptiste Pingault [ctb]
Maintainer: Christophe Genolini

Diff between kml3d versions 2.0 dated 2012-03-28 and 2.1 dated 2012-08-20

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Package kml updated to version 2.1 with previous version 2.0 dated 2012-03-28

Title: K-means for Longitudinal data
Description: KmL is an implementation of k-means specifically design to cluster longitudinal data. It provides facilities to deal with missing value, compute several quality criterion (Calinski and Harabatz, Ray and Turie, Davies and Bouldin, BIC, ...) and propose a graphical interface for choosing the 'best' number of clusters.
Author: Christophe Genolini [cre, aut], Bruno Falissard [ctb]
Maintainer: Christophe Genolini

Diff between kml versions 2.0 dated 2012-03-28 and 2.1 dated 2012-08-20

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Package tnet updated to version 3.0.8 with previous version 3.0.7 dated 2012-07-10

Title: tnet: Software for Analysis of Weighted, Two-mode, and Longitudinal networks
Description: R package for analyzing weighted, two-mode, and longitudinal networks.
Author: Tore Opsahl
Maintainer: Tore Opsahl

Diff between tnet versions 3.0.7 dated 2012-07-10 and 3.0.8 dated 2012-08-20

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Package quantchem updated to version 0.13 with previous version 0.12-1 dated 2007-04-11

Title: Quantitative chemical analysis: calibration and evaluation of results
Description: Statistical evaluation of calibration curves by different regression techniques: ordinary, weighted, robust (up to 4th order polynomial). Log-log and Box-Cox transform, estimation of optimal power and weighting scheme. Tests for heteroscedascity and normality of residuals. Different kinds of plots commonly used in illustrating calibrations. Easy "inverse prediction" of concentration by given responses and statistical evaluation of results (comparison of precision and accuracy by common tests).
Author: Lukasz Komsta
Maintainer: Lukasz Komsta

Diff between quantchem versions 0.12-1 dated 2007-04-11 and 0.13 dated 2012-08-20

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Package VBLPCM updated to version 2.2 with previous version 2.1 dated 2012-07-10

Title: Variational Bayes Latent Position Cluster Model for networks.
Description: A package to fit and simulate latent position and cluster models for statistical networks using a Variational Bayes approximation.
Author: Michael Salter-Townshend
Maintainer: Michael Salter-Townshend

Diff between VBLPCM versions 2.1 dated 2012-07-10 and 2.2 dated 2012-08-20

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Package POT updated to version 1.1-2 with previous version 1.1-1 dated 2011-06-22

Title: Generalized Pareto Distribution and Peaks Over Threshold
Description: Some functions useful to perform a Peak Over Threshold analysis in univariate and bivariate cases. A user's guide is available.
Author: Mathieu Ribatet
Maintainer: Mathieu Ribatet

Diff between POT versions 1.1-1 dated 2011-06-22 and 1.1-2 dated 2012-08-20

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New package ppstat with initial version 0.8.1
Package: ppstat
Type: Package
Title: Point Process Statistics
Version: 0.8.1
Date: 2012-05-16
Author: Niels Richard Hansen .
Maintainer: Niels Richard Hansen
Depends: R (>= 2.14.1), processdata (>= 0.8), reshape2, ggplot2 (>= 0.9.0), methods, igraph
Imports: stats, splines, Matrix, parallel
Suggests: RUnit, glmnet, MatrixModels
Description: This package implements statistical methods for one-dimensional marked point process models.
License: GPL (>= 2)
URL: http://www.math.ku.dk/~richard/ppstat
LazyLoad: yes
Packaged: 2012-08-20 10:47:04 UTC; Niels
Repository: CRAN
Date/Publication: 2012-08-20 12:29:03

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Package stpp updated to version 1.0 with previous version 0.3 dated 2012-06-05

Title: Space-Time Point Pattern simulation, visualisation and analysis
Description: A package for analysing, simulating and displaying space-time point patterns
Author: Edith Gabriel, Peter J Diggle, stan function by Barry Rowlingson
Maintainer: Edith Gabriel

Diff between stpp versions 0.3 dated 2012-06-05 and 1.0 dated 2012-08-20

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Package RWekajars updated to version 3.7.7-1 with previous version 3.7.5-1 dated 2011-11-30

Title: R/Weka interface jars
Description: External jars required for package RWeka.
Author: Kurt Hornik
Maintainer: Kurt Hornik

Diff between RWekajars versions 3.7.5-1 dated 2011-11-30 and 3.7.7-1 dated 2012-08-20

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Package RWeka updated to version 0.4-12 with previous version 0.4-11 dated 2012-02-21

Title: R/Weka interface
Description: An R interface to Weka (Version 3.7.7). Weka is a collection of machine learning algorithms for data mining tasks written in Java, containing tools for data pre-processing, classification, regression, clustering, association rules, and visualization. Package RWeka contains the interface code, the Weka jar is in a separate package RWekajars. For more information on Weka see http://www.cs.waikato.ac.nz/~ml/weka/.
Author: Kurt Hornik, with contributions from Christian Buchta, Torsten Hothorn, Alexandros Karatzoglou, David Meyer, and Achim Zeileis
Maintainer: Kurt Hornik

Diff between RWeka versions 0.4-11 dated 2012-02-21 and 0.4-12 dated 2012-08-20

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Package partitionMap (with last version 0.4) was removed from CRAN

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

2012-03-20 0.4
2010-11-29 0.2
2010-11-22 0.1

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Package ppstat (with last version 0.8) was removed from CRAN

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

2012-03-09 0.8
2010-10-20 0.7

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Package COZIGAM (with last version 2.0-3) was removed from CRAN

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

2010-07-24 2.0-3
2009-07-21 2.0-2
2009-02-25 2.0-1
2009-01-11 2.0-0
2008-08-14 1.0-3
2008-06-25 1.0-2
2008-03-21 1.0-1

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Package logitnorm (with last version 0.8.26) was removed from CRAN

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

2012-04-16 0.8.26

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Package surveillance updated to version 1.4-2 with previous version 1.4-1 dated 2012-07-26

Title: Temporal and Spatio-Temporal Modeling and Monitoring of Epidemic Phenomena
Description: A package implementing statistical methods for the modeling and change-point detection in time series of counts, proportions and categorical data, as well as for the modeling of continuous-time epidemic phenomena, e.g. discrete-space setups such as the spatially enriched Susceptible-Exposed-Infectious-Recovered (SEIR) models for surveillance data, or continuous-space point process data such as the occurrence of disease or earthquakes. Main 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 of 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), Paul et al (2008) and Paul and Held (2011) are provided. A novel CUSUM approach combining logistic and multinomial logistic modelling is also included. Continuous self-exciting spatio-temporal point processes are modeled through additive-multiplicative conditional intensities as described in Höhle (2009) ("twinSIR", discrete space) and Meyer et al (2012) ("twinstim", continuous space). 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.
Author: M. Höhle, S. Meyer and M. Paul with contributions from T. Correa, M. Hofmann, C. Lang, A. Riebler, D. Sabanés Bové, S. Steiner, M. Virtanen and V. Wimmer. A few code segments are modified versions of code by The R Core Team (available under GPL-2).
Maintainer: Michael Höhle

Diff between surveillance versions 1.4-1 dated 2012-07-26 and 1.4-2 dated 2012-08-20

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Package st updated to version 1.1.8 with previous version 1.1.7 dated 2012-01-22

Title: Shrinkage t Statistic and CAT Score
Description: This package implements the "shrinkage t" statistic introduced in Opgen-Rhein and Strimmer (2007) and a shrinkage estimate of the "correlation-adjusted t-score" (CAT score) described in Zuber and Strimmer (2009). It also offers a convenient interface to a number of other regularized t-statistics commonly employed in high-dimensional case-control studies.
Author: Rainer Opgen-Rhein, Verena Zuber, and Korbinian Strimmer.
Maintainer: Korbinian Strimmer

Diff between st versions 1.1.7 dated 2012-01-22 and 1.1.8 dated 2012-08-20

 DESCRIPTION      |   10 +++++-----
 MD5              |   20 ++++++++++----------
 NEWS             |    6 ++++++
 R/cst.R          |    6 +++---
 R/efront.R       |    6 +++---
 R/lait.R         |    8 ++++----
 R/samL1.R        |    8 ++++----
 R/shrinkcat.R    |    6 +++---
 R/shrinkt.R      |    8 ++++----
 R/studentt.R     |    8 ++++----
 man/lait.stat.Rd |    4 ++--
 11 files changed, 48 insertions(+), 42 deletions(-)

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Package sda updated to version 1.2.2 with previous version 1.2.1 dated 2012-01-22

Title: Shrinkage Discriminant Analysis and CAT Score Variable Selection
Description: This package provides an efficient framework for high-dimensional linear and diagonal discriminant analysis with variable selection. The classifier is trained using James-Stein-type shrinkage estimators and predictor variables are ranked using CAT scores (correlation-adjusted t-scores). Variable selection error is controlled using false non-discovery rates or higher criticism scores.
Author: Miika Ahdesmaki, Verena Zuber, and Korbinian Strimmer
Maintainer: Korbinian Strimmer

Diff between sda versions 1.2.1 dated 2012-01-22 and 1.2.2 dated 2012-08-20

 sda-1.2.1/sda/R/pvt.hcobj.R       |only
 sda-1.2.2/sda/DESCRIPTION         |   10 ++---
 sda-1.2.2/sda/MD5                 |   21 +++++------
 sda-1.2.2/sda/NEWS                |   12 ++++++
 sda-1.2.2/sda/R/catscore.R        |   56 ++++++++++++------------------
 sda-1.2.2/sda/R/centroids.R       |   70 ++++++++++++++++++++++++++++----------
 sda-1.2.2/sda/R/sda.R             |   17 ++++-----
 sda-1.2.2/sda/R/sda.ranking.R     |    8 ++--
 sda-1.2.2/sda/man/catscore.Rd     |   15 +++++---
 sda-1.2.2/sda/man/centroids.Rd    |   22 +++++------
 sda-1.2.2/sda/man/sda-internal.Rd |    2 -
 sda-1.2.2/sda/man/sda.package.Rd  |    2 -
 12 files changed, 136 insertions(+), 99 deletions(-)

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Package Rmpi updated to version 0.6-1 with previous version 0.6-0 dated 2012-08-08

Title: Interface (Wrapper) to MPI (Message-Passing Interface)
Description: Rmpi provides an interface (wrapper) to MPI APIs. It also provides interactive R slave environment.
Author: Hao Yu
Maintainer: Hao Yu

Diff between Rmpi versions 0.6-0 dated 2012-08-08 and 0.6-1 dated 2012-08-20

 Rmpi-0.6-0/Rmpi/inst/Rslaves.bat         |only
 Rmpi-0.6-0/Rmpi/inst/Rslaves32.bat       |only
 Rmpi-0.6-0/Rmpi/inst/Rslaves64.bat       |only
 Rmpi-0.6-0/Rmpi/inst/sleep.c             |only
 Rmpi-0.6-1/Rmpi/DESCRIPTION              |    8 +-
 Rmpi-0.6-1/Rmpi/INDEX                    |   19 ++--
 Rmpi-0.6-1/Rmpi/MD5                      |   40 ++++------
 Rmpi-0.6-1/Rmpi/R/Rcoll.R                |  122 +++++++++++++++++--------------
 Rmpi-0.6-1/Rmpi/R/Rmpi.R                 |   17 +++-
 Rmpi-0.6-1/Rmpi/R/Rng.R                  |    2 
 Rmpi-0.6-1/Rmpi/R/Rparutilities.R        |   89 +++++++++++-----------
 Rmpi-0.6-1/Rmpi/R/zzz.R                  |   27 ++----
 Rmpi-0.6-1/Rmpi/inst/Rprofile            |   24 ++++--
 Rmpi-0.6-1/Rmpi/inst/Rslaves32.cmd       |only
 Rmpi-0.6-1/Rmpi/inst/Rslaves64.cmd       |only
 Rmpi-0.6-1/Rmpi/inst/slavedaemon.R       |    6 +
 Rmpi-0.6-1/Rmpi/man/internal.Rd          |   11 --
 Rmpi-0.6-1/Rmpi/man/mpi.apply.Rd         |    2 
 Rmpi-0.6-1/Rmpi/man/mpi.bcast.cmd.Rd     |   25 ++++--
 Rmpi-0.6-1/Rmpi/man/mpi.iapply.Rd        |   16 ++--
 Rmpi-0.6-1/Rmpi/man/mpi.parSim.Rd        |    1 
 Rmpi-0.6-1/Rmpi/man/mpi.spawn.Rslaves.Rd |   17 ++--
 Rmpi-0.6-1/Rmpi/src/Makevars.win         |    5 +
 Rmpi-0.6-1/Rmpi/src/Rmpi.c               |   10 +-
 24 files changed, 241 insertions(+), 200 deletions(-)

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Package rgdal updated to version 0.7-15 with previous version 0.7-12 dated 2012-06-23

Title: Bindings for the Geospatial Data Abstraction Library
Description: Provides bindings to Frank Warmerdam's Geospatial Data Abstraction Library (GDAL) (>= 1.6.0) and access to projection/transformation operations from the PROJ.4 library. The GDAL and PROJ.4 libraries are external to the package, and, when installing the package from source, must be correctly installed first. Both GDAL raster and OGR vector map data can be imported into R, and GDAL raster data and OGR vector data exported. Use is made of classes defined in the sp package. Windows and Mac Intel OS X binaries (including GDAL, PROJ.4 and Expat) are provided on CRAN.
Author: Timothy H. Keitt , Roger Bivand , Edzer Pebesma , Barry Rowlingson
Maintainer: Roger Bivand

Diff between rgdal versions 0.7-12 dated 2012-06-23 and 0.7-15 dated 2012-08-20

 ChangeLog                          |   38 
 DESCRIPTION                        |    8 
 MD5                                |   36 
 NAMESPACE                          |    2 
 R/AAA.R                            |    5 
 R/gdal.R                           |    4 
 R/ogr_write.R                      |   11 
 R/project.R                        |   80 
 configure                          | 5372 +++++++++++++++++++------------------
 configure.ac                       |    2 
 inst/ChangeLog                     |   38 
 man/GDALDriver-class.Rd            |    7 
 man/GDALReadOnlyDataset-methods.Rd |    2 
 man/SpatialGDAL-class.Rd           |    2 
 man/project.Rd                     |   12 
 man/readGDAL.Rd                    |    2 
 man/spTransform-methods.Rd         |   18 
 src/gdal-bindings.cpp              |   23 
 src/projectit.cpp                  |   11 
 19 files changed, 3141 insertions(+), 2532 deletions(-)

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