Wed, 10 Sep 2014

New package saery with initial version 1.0
Package: saery
Type: Package
Title: Small Area Estimation for Rao and Yu Model
Version: 1.0
Date: 2014-09-10
Author: Maria Dolores Esteban Lefler, Domingo Morales Gonzalez, Agustin Perez Martin
Maintainer: Agustin Perez Martin
Description: A complete set of functions to calculate several EBLUP (Empirical Best Linear Unbiased Predictor) estimators and their mean squared errors. All estimators are based on an area-level linear mixed model introduced by Rao and Yu in 1994 (see documentation). The REML method is used for fitting this model.
License: GPL-2
LazyData: true
Packaged: 2014-09-10 20:48:45 UTC; agus
NeedsCompilation: no
Repository: CRAN
Date/Publication: 2014-09-10 23:18:02

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Package RcmdrPlugin.IPSUR updated to version 0.2-1 with previous version 0.2-0 dated 2014-08-29

Title: An IPSUR Plugin for the R Commander
Description: This package is an R Commander plugin that accompanies IPSUR, an Introduction to Probability and Statistics Using R.
Author: G. Jay Kerns [aut, cre], Theophilus Boye [ctb], Tyler Drombosky [ctb]
Maintainer: G. Jay Kerns

Diff between RcmdrPlugin.IPSUR versions 0.2-0 dated 2014-08-29 and 0.2-1 dated 2014-09-10

 DESCRIPTION                      |    8 ++++----
 MD5                              |    6 +++---
 inst/etc/menus.txt               |   36 ++++++++++++++++++------------------
 man/RcmdrPlugin.IPSUR-package.Rd |    6 +++---
 4 files changed, 28 insertions(+), 28 deletions(-)

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Package glmmLasso updated to version 1.3.2 with previous version 1.3.1 dated 2014-07-10

Title: Variable selection for generalized linear mixed models by L1-penalized estimation
Description: Variable selection for generalized linear mixed models by L1-penalized estimation
Author: Andreas Groll
Maintainer: Andreas Groll

Diff between glmmLasso versions 1.3.1 dated 2014-07-10 and 1.3.2 dated 2014-09-10

 DESCRIPTION                        |    8 
 MD5                                |   18 
 R/glmmLasso.r                      |  896 ++++++++++++++++++-------------------
 R/glmm_final.r                     |    9 
 R/glmm_final.smooth.r              |    6 
 R/glmm_final_multi_random.r        |    6 
 R/glmm_final_multi_random_smooth.r |   14 
 R/logLik.glmmLasso.r               |    8 
 demo/glmmLasso-soccer.r            |   49 +-
 man/glmmLasso.rd                   |   38 -
 10 files changed, 521 insertions(+), 531 deletions(-)

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Package cgam updated to version 1.2 with previous version 1.1 dated 2014-04-16

Title: Constrained Generalized Additive Model
Description: In this package, a constrained generalized additive model is fitted by the cgam routine. Given a set of predictors with or without shape or order restrictions, the maximum likelihood estimator for the constrained generalized additive model is found using an iteratively re-weighted cone projection algorithm. The cone information criterion (CIC) may be used to select the best combination of variables and shapes. This package depends on the R package coneproj.
Author: Mary C. Meyer and Xiyue Liao
Maintainer: Xiyue Liao

Diff between cgam versions 1.1 dated 2014-04-16 and 1.2 dated 2014-09-10

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 NAMESPACE          |    2 
 R/cgam.R           | 1894 ++++++++++++++++++++++++++++++++++++++++++++---------
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 27 files changed, 1793 insertions(+), 414 deletions(-)

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Package segmented updated to version 0.5-0.0 with previous version 0.4-0.0 dated 2014-07-11

Title: Segmented relationships in regression models with breakpoints/changepoints estimation
Description: Given a regression model, segmented `updates' the model by adding one or more segmented relationships. Several variables with multiple breakpoints are allowed.
Author: Vito M. R. Muggeo [aut, cre]
Maintainer: Vito M. R. Muggeo

Diff between segmented versions 0.4-0.0 dated 2014-07-11 and 0.5-0.0 dated 2014-09-10

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 segmented-0.5-0.0/segmented/MD5                      |   45 +++++++++----------
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 segmented-0.5-0.0/segmented/NEWS                     |   13 +++++
 segmented-0.5-0.0/segmented/R/confint.segmented.R    |    2 
 segmented-0.5-0.0/segmented/R/davies.test.r          |    4 -
 segmented-0.5-0.0/segmented/R/intercept.r            |    5 --
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 segmented-0.5-0.0/segmented/R/slope.R                |   28 +++++++----
 segmented-0.5-0.0/segmented/R/summary.segmented.R    |   18 +++++++
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 segmented-0.5-0.0/segmented/man/davies.test.Rd       |   35 ++++++++------
 segmented-0.5-0.0/segmented/man/seg.control.Rd       |   12 ++++-
 segmented-0.5-0.0/segmented/man/seg.lm.fit.Rd        |   25 ++++++++--
 segmented-0.5-0.0/segmented/man/segmented-package.Rd |   12 +++--
 segmented-0.5-0.0/segmented/man/segmented.Rd         |   42 +++++++++++++++--
 26 files changed, 234 insertions(+), 84 deletions(-)

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Package GGMselect updated to version 0.1-9 with previous version 0.1-8 dated 2013-12-12

Title: Gaussian Graphs Models selection
Description: GGMselect is a package dedicated to graph estimation in Gaussian Graphical Models. The main functions return the adjacency matrix of an undirected graph estimated from a data matrix.
Author: Annie Bouvier, Christophe Giraud, Sylvie Huet, Verzelen N.
Maintainer: Annie Bouvier

Diff between GGMselect versions 0.1-8 dated 2013-12-12 and 0.1-9 dated 2014-09-10

 DESCRIPTION               |    8 ++---
 MD5                       |   57 +++++++++++++++++++++---------------------
 NAMESPACE                 |    2 +
 NEWS                      |   17 ++++++++++--
 R/MyFamily.R              |   13 +++++----
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 inst/doc/Notice.pdf       |binary
 man/GGMselect-package.Rd  |   14 +++++-----
 man/selectQE.Rd           |   14 +++++-----
 src/Makevars              |    5 ++-
 src/boucle.f              |    2 -
 src/critQE.c              |    5 ++-
 tests/bsch.Rout.save      |    8 ++---
 tests/penInf.Rout.save    |    8 ++---
 tests/raj.Rout.save       |   54 ++++++++++++++++++++--------------------
 tests/sh9.2012.Rout.save  |    8 ++---
 tests/shPUR.Rout.save     |    8 ++---
 tests/test1Fast.Rout.save |    8 ++---
 tests/test1QE.Rout.save   |   44 ++++++++++++++++----------------
 tests/test2Fast.Rout.save |    8 ++---
 tests/test2QE.Rout.save   |   26 +++++++++----------
 tests/test3Fast.Rout.save |    8 ++---
 tests/test3QE.Rout.save   |   62 +++++++++++++++++++++++-----------------------
 tests/test4Fast.R         |    2 -
 tests/test4Fast.Rout.save |   10 +++----
 tests/test4QE.Rout.save   |   38 ++++++++++++++--------------
 tests/test5Fast.Rout.save |    8 ++---
 tests/test6Fast.Rout.save |    8 ++---
 tests/test7Fast.Rout.save |    8 ++---
 tests/testMyFam.Rout.save |    8 ++---
 30 files changed, 239 insertions(+), 222 deletions(-)

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New package Ohmage with initial version 2.11-4
Package: Ohmage
Type: Package
Title: R Client for Ohmage 2 server
Version: 2.11-4
Date: 2014-09-10
Author: Jeroen Ooms
Maintainer: Jeroen Ooms
Description: R Client for Ohmage 2 server. Implements basic R functions to retrieve and process data.
License: GPL
Depends: R (>= 2.14), stats, methods
Imports: RCurl, RJSONIO
Suggests: XML
Packaged: 2014-09-10 13:00:58 UTC; jeroen
NeedsCompilation: no
Repository: CRAN
Date/Publication: 2014-09-10 15:14:12

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Package caTools updated to version 1.17.1 with previous version 1.17 dated 2014-04-21

Title: Tools: moving window statistics, GIF, Base64, ROC AUC, etc.
Description: Contains several basic utility functions including: moving (rolling, running) window statistic functions, read/write for GIF and ENVI binary files, fast calculation of AUC, LogitBoost classifier, base64 encoder/decoder, round-off-error-free sum and cumsum, etc.
Author: Jarek Tuszynski
Maintainer: Harutyun Khachatryan

Diff between caTools versions 1.17 dated 2014-04-21 and 1.17.1 dated 2014-09-10

 DESCRIPTION  |   10 ++---
 MD5          |    6 +--
 R/runfunc.R  |  103 +++++++++++++++++++++++++++++------------------------------
 R/sumexact.R |   10 ++---
 4 files changed, 63 insertions(+), 66 deletions(-)

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Package pkgKitten updated to version 0.1.1 with previous version 0.1.0 dated 2014-06-13

Title: Create Simple Packages Which Do Not Upset R CMD check
Description: Provides a function kitten() which create cute little packages which pass R CMD check. This sets it apart from package.skeleton() which it calls, and which leaves imperfect files behind. As this is not exactly helpful for beginners, kitten() offers an alternative.
Author: Dirk Eddelbuettel
Maintainer: Dirk Eddelbuettel

Diff between pkgKitten versions 0.1.0 dated 2014-06-13 and 0.1.1 dated 2014-09-10

 ChangeLog                         |   13 +++++++++
 DESCRIPTION                       |   20 +++++++-------
 MD5                               |   12 ++++----
 NAMESPACE                         |    3 +-
 R/pkgKitten.R                     |   54 ++++++++++++++++++++++++++++----------
 inst/NEWS.Rd                      |only
 man/kitten.Rd                     |    4 +-
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 8 files changed, 75 insertions(+), 31 deletions(-)

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New package ForwardSearch with initial version 1.0
Package: ForwardSearch
Type: Package
Title: Forward Search using asymptotic theory
Version: 1.0
Date: 2014-09-10
Author: Bent Nielsen
Maintainer: Bent Nielsen
URL: http://users.ox.ac.uk/~nuff0078/
Description: Forward Search analysis of time series regressions. Implements the asymptotic theory developed in Johansen and Nielsen (2013, 2014).
License: GPL-3
Depends: robustbase
Packaged: 2014-09-10 11:19:57 UTC; Nielsen
NeedsCompilation: no
Repository: CRAN
Date/Publication: 2014-09-10 13:56:09

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Package sjPlot updated to version 1.5 with previous version 1.4.3 dated 2014-08-14

Title: sjPlot - data visualization for statistics in social science
Description: Collection of several plotting / table output functions for visualizing data and utility functions.
Author: Daniel L├╝decke
Maintainer: Daniel Luedecke

Diff between sjPlot versions 1.4.3 dated 2014-08-14 and 1.5 dated 2014-09-10

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 sjPlot-1.5/sjPlot/R/sjPlotLikert.R             |   28 
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 sjPlot-1.5/sjPlot/R/sjPlotPropTable.R          |   32 
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 sjPlot-1.5/sjPlot/R/sjPlotStackFrequencies.R   |   38 
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 sjPlot-1.5/sjPlot/R/sjTabPropTable.R           | 1558 +++++++++---------
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New package RImpala with initial version 0.1.4
Package: RImpala
Version: 0.1.4
Date: 2014-09-10
Title: R and Impala
Author: Vijay Raajaa, Austin Chungath Vincent, Sachin Sudarshana, Vikas Raguttahalli
Maintainer: Vijay Raajaa
Contact: Austin Chungath Vincent ,Vikas Raguttahalli , Sachin Sudarshana
Description: RImpala facilitates the connection and execution of distributed queries using Cloudera Impala, which is a massively parallel processing (MPP) SQL query engine that runs natively in Apache Hadoop. Impala supports jdbc integration which RImpala utilizes to establish the connection between R and Impala.
Depends: R (>= 2.7.0), rJava (>= 0.5-0)
SystemRequirements: Java (>= 1.5)
License: GPL-3
Packaged: 2014-09-10 08:47:33 UTC; root
NeedsCompilation: no
Repository: CRAN
Date/Publication: 2014-09-10 11:43:20

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New package RDML with initial version 0.4-2
Package: RDML
Type: Package
Title: Importing real-time thermo cycler (qPCR) data from RDML format files
Version: 0.4-2
LazyData: true
Date: 2014-09-10
Description: Imports real-time thermo cycler (qPCR) data from RDML format files and transforms to the appropriate formats of the 'qpcR' and 'chipPCR' packages.
Authors@R: c( person("Konstantin A.", "Blagodatskikh", email = "k.blag@yandex.ru", role = c("cre", "aut")), person("Stefan", "Roediger", email = "stefan.roedigier@hs-lausitz.de", role = "aut"), person("Michal", "Burdukiewicz", email = "michalburdukiewicz@gmail.com", role = "aut"))
License: GPL (>= 2)
URL: https://github.com/kablag/RDML
Depends: XML (>= 3.98-1.1)
Imports: chipPCR (>= 0.0.8-1)
Suggests: qpcR (>= 1.3-9)
Packaged: 2014-09-10 08:55:14 UTC; kablag
Author: Konstantin A. Blagodatskikh [cre, aut], Stefan Roediger [aut], Michal Burdukiewicz [aut]
Maintainer: Konstantin A. Blagodatskikh
NeedsCompilation: no
Repository: CRAN
Date/Publication: 2014-09-10 11:38:16

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Package catR updated to version 3.2 with previous version 3.1 dated 2014-06-04

Title: Procedures to generate IRT adaptive tests (CAT)
Description: The catR package allows the generation of response patterns under computerized adaptive testing (CAT) framework, with the choice of several starting rules, next item selection routines, stopping rules and ability estimators. Control methods for item exposure and content balancing are also included.
Author: David Magis (U Liege, Belgium), Gilles Raiche (UQAM, Canada), Juan Ramon Barrada (U Zaragoza, Spain)
Maintainer: David Magis

Diff between catR versions 3.1 dated 2014-06-04 and 3.2 dated 2014-09-10

 DESCRIPTION       |    8 
 MD5               |   12 -
 NEWS              |   36 +++
 R/MEI.R           |    2 
 R/eapEst.R        |    2 
 R/genPolyMatrix.R |    2 
 R/randomCAT.R     |  523 +++++++++++++++++++++++++++++-------------------------
 7 files changed, 336 insertions(+), 249 deletions(-)

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Package synbreed updated to version 0.10-2 with previous version 0.10-1 dated 2014-09-02

Title: Framework for the analysis of genomic prediction data using R
Description: The package was developed within the Synbreed project for synergistic plant and animal breeding (www.synbreed.tum.de). It contains a collection of functions required for genomic prediction in both plant and animal breeding. This covers data processing, data visualization and analysis. All functions are embedded within the framework of a single, unified data object. The implementation is flexible with respect to a wide range of data formats. This research was funded by the German Federal Ministry of Education and Research (BMBF) within the AgroClustEr Synbreed - Synergistic plant and animal breeding (FKZ 0315528A).
Author: Valentin Wimmer, Hans-Juergen Auinger, Theresa Albrecht, Chris-Carolin Schoen with contributions by Larry Schaeffer, Malena Erbe, Ulrike Ober, Christian Reimer, Yvonne Badke and Peter VandeHaar
Maintainer: Valentin Wimmer

Diff between synbreed versions 0.10-1 dated 2014-09-02 and 0.10-2 dated 2014-09-10

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Package dismo updated to version 1.0-5 with previous version 0.9-3 dated 2013-12-15

Title: Species distribution modeling
Description: Functions for species distribution modeling, that is, predicting entire geographic distributions form occurrences at a number of sites.
Author: Robert J. Hijmans, Steven Phillips, John Leathwick and Jane Elith
Maintainer: Robert J. Hijmans

Diff between dismo versions 0.9-3 dated 2013-12-15 and 1.0-5 dated 2014-09-10

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Package bstats (with last version 1.1-11-5) was removed from CRAN

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

2014-05-04 1.1-11-5
2014-01-23 1.1-11-4
2013-11-26 1.1-11-1
2013-09-08 1.1-9-8
2013-08-07 1.1-8-8
2011-12-04 1.0-12-3
2011-11-18 1.0-11-17
2011-11-15 1.0-2
2011-11-10 1.0-1
2011-11-02 0.01-4

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Package Sim.DiffProc updated to version 2.9 with previous version 2.8 dated 2014-08-19

Title: Simulation of Diffusion Processes
Description: The package Sim.DiffProc is an object created in R environment for simulation and modeling of stochastic differential equations (SDE's) the type Ito and Stratonovich. This package contains many objects, the numerical methods to find the solutions to SDE's (1, 2 and 3-dim), with a possibility for simulates a flows trajectories,with good accuracy. Many theoretical problems on the SDE's have become the object of practical research, as statistical analysis and simulation of solution of SDE's, enabled many searchers in different domains to use these equations to modeling and to analyse practical problems, in financial and actuarial modeling and other areas of application, for example modelling and simulate of dispersion in shallow water using the attractive center (Boukhetala K, 1996). We hope that the package presented here and the updated survey on the subject might be of help for practitioners, postgraduate and PhD students, and researchers in the field who might want to implement new methods.
Author: Arsalane Chouaib Guidoum, Kamal Boukhetala
Maintainer: Arsalane Chouaib Guidoum

Diff between Sim.DiffProc versions 2.8 dated 2014-08-19 and 2.9 dated 2014-09-10

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Package mmcm updated to version 1.2-5 with previous version 1.2-4 dated 2013-01-20

Title: Modified Maximum Contrast Method
Description: This package provides an implementation of modified maximum contrast methods and the maximum contrast method. This version supports functions mmcm.mvt, mcm.mvt that gives P-value by using randomized quasi-Monte Carlo method from pmvt function of package mvtnorm, and mmcm.resamp that gives P-value by using the permutation method.
Author: Kengo NAGASHIMA and Yasunori SATO
Maintainer: Kengo NAGASHIMA

Diff between mmcm versions 1.2-4 dated 2013-01-20 and 1.2-5 dated 2014-09-10

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Package isotone updated to version 1.0-2 with previous version 1.0-1 dated 2011-01-23

Title: Active set and generalized PAVA for isotone optimization
Description: Contains two main functions: gpava() for solving general isotone regression problem using the pool-adjacent-violators algorithm (PAVA). activeSet() provides a framework of active set methods for isotone optimization problems with arbitrary order restrictions. Various types of loss functions are pre-specified.
Author: Patrick Mair [aut, cre], Jan De Leeuw [aut], Kurt Hornik [aut]
Maintainer: Patrick Mair

Diff between isotone versions 1.0-1 dated 2011-01-23 and 1.0-2 dated 2014-09-10

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Package hwriter updated to version 1.3.2 with previous version 1.3.1 dated 2014-08-23

Title: HTML Writer - Outputs R objects in HTML format
Description: Easy-to-use and versatile functions to output R objects in HTML format
Author: Gregoire Pau
Maintainer: Gregoire Pau

Diff between hwriter versions 1.3.1 dated 2014-08-23 and 1.3.2 dated 2014-09-10

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Package dunn.test updated to version 1.2.0 with previous version 1.1.0 dated 2014-08-24

Title: Dunn's test of multiple comparisons using rank sums
Description: dunn.test computes Dunn's test (1964) for stochastic dominance and reports the results among multiple pairwise comparisons after a Kruskal-Wallis test for stochastic dominance among k groups (Kruskal and Wallis, 1952). The interpretation of stochastic dominance requires an assumption that the CDF of one group does not cross the CDF of the other. dunn.test makes k(k-1)/2 multiple pairwise comparisons based on Dunn's z-test-statistic approximations to the actual rank statistics. The null hypothesis for each pairwise comparison is that the probability of observing a randomly selected value from the first group that is larger than a randomly selected value from the second group equals one half; this null hypothesis corresponds to that of the Wilcoxon-Mann-Whitney rank-sum test. Like the rank-sum test, if the data can be assumed to be continuous, and the distributions are assumed identical except for a difference in location, Dunn's test may be understood as a test for median difference. dunn.test accounts for tied ranks.
Author: Alexis Dinno
Maintainer: Alexis Dinno

Diff between dunn.test versions 1.1.0 dated 2014-08-24 and 1.2.0 dated 2014-09-10

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