Tue, 30 Sep 2014

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

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

2014-09-29 0.4

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Package rgl updated to version 0.94.1143 with previous version 0.94.1131 dated 2014-09-08

Title: 3D visualization device system (OpenGL)
Description: Provides medium to high level functions for 3D interactive graphics, including functions modelled on base graphics (plot3d(), etc.) as well as functions for constructing representations of geometric objects (cube3d(), etc.). Output may be on screen using OpenGL, or to various standard 3D file formats including WebGL, PLY, OBJ, STL as well as 2D image formats, including PNG, Postscript, SVG, PGF.
Author: Daniel Adler , Duncan Murdoch , and others (see README)
Maintainer: Duncan Murdoch

Diff between rgl versions 0.94.1131 dated 2014-09-08 and 0.94.1143 dated 2014-09-30

 DESCRIPTION             |   10 
 MD5                     |   57 
 NAMESPACE               |    2 
 R/persp3d.R             |   71 
 R/plot3d.R              |    2 
 R/webGL.R               | 3578 +++++++++++++++++++++++-------------------------
 inst/NEWS               |   11 
 man/persp3d.Rd          |   17 
 man/persp3d.function.Rd |only
 man/plot3d.Rd           |    1 
 man/subscene3d.Rd       |    4 
 src/Background.cpp      |    2 
 src/NULLgui.cpp         |    6 
 src/Texture.cpp         |  227 +--
 src/Viewpoint.cpp       |   17 
 src/Viewpoint.h         |    6 
 src/callbacks.cpp       |    8 
 src/device.cpp          |    3 
 src/geom.cpp            |   31 
 src/geom.h              |    1 
 src/glgui.cpp           |   11 
 src/gui.cpp             |   26 
 src/gui.h               |    5 
 src/par3d.cpp           |   56 
 src/rglmath.cpp         |   39 
 src/rglmath.h           |    7 
 src/rglview.cpp         |   14 
 src/rglview.h           |    3 
 src/subscene.cpp        |   84 -
 src/subscene.h          |   12 
 30 files changed, 2231 insertions(+), 2080 deletions(-)

More information about rgl at CRAN
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Package pipeR updated to version 0.5 with previous version 0.4-2 dated 2014-08-22

Title: Pipe operator and function
Description: Provides Pipe operator and function based on syntax which support to pipe value to first-argument of a function, to dot in expression, by formula as lambda expression, for side-effect, and with assignment. The set of syntax is designed to make the pipeline highly readable.
Author: Kun Ren
Maintainer: Kun Ren

Diff between pipeR versions 0.4-2 dated 2014-08-22 and 0.5 dated 2014-09-30

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 pipeR-0.5/pipeR/NAMESPACE                                      |    4 
 pipeR-0.5/pipeR/NEWS                                           |   14 
 pipeR-0.5/pipeR/R/functions.R                                  |  149 +++---
 pipeR-0.5/pipeR/R/pipe.R                                       |  193 ++++---
 pipeR-0.5/pipeR/R/pipeR.R                                      |  115 ++++
 pipeR-0.5/pipeR/R/utils.R                                      |   19 
 pipeR-0.5/pipeR/README.md                                      |  242 ++++++----
 pipeR-0.5/pipeR/inst/doc/Examples.R                            |    1 
 pipeR-0.5/pipeR/inst/doc/Examples.html                         |   60 ++
 pipeR-0.5/pipeR/inst/doc/Introduction.html                     |  185 ++++---
 pipeR-0.5/pipeR/inst/doc/Performance.R                         |   50 --
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 pipeR-0.5/pipeR/tests/testthat/test1-operator.R                |  108 ++++
 pipeR-0.5/pipeR/tests/testthat/test2-Pipe.R                    |   69 ++
 24 files changed, 1011 insertions(+), 561 deletions(-)

More information about pipeR at CRAN
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Package rbamtools updated to version 2.10.0 with previous version 2.9.14 dated 2014-07-29

Title: An R package for reading and writing BAM (Binary alignment) files.
Description: This package provides an interface to functions of the 'SAMtools' C-Library by Heng Li.
Author: Wolfgang Kaisers
Maintainer: Wolfgang Kaisers

Diff between rbamtools versions 2.9.14 dated 2014-07-29 and 2.10.0 dated 2014-09-30

 rbamtools-2.10.0/rbamtools/ChangeLog                    |   15 
 rbamtools-2.10.0/rbamtools/DESCRIPTION                  |    9 
 rbamtools-2.10.0/rbamtools/MD5                          |  110 +-
 rbamtools-2.10.0/rbamtools/NAMESPACE                    |    6 
 rbamtools-2.10.0/rbamtools/NEWS                         |   27 
 rbamtools-2.10.0/rbamtools/R/rbamtools.r                |  842 ++++++++++++----
 rbamtools-2.10.0/rbamtools/inst/doc/rbamtools.R         |   14 
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 58 files changed, 2528 insertions(+), 950 deletions(-)

More information about rbamtools at CRAN
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Package protViz updated to version 0.2.9 with previous version 0.2.06 dated 2014-09-18

Title: Visualizing and Analyzing Mass Spectrometry Related Data in Proteomics
Description: This R package helps with quality checks, visualizations and analysis of mass spectrometry data, coming from proteomics experiments. The package is developed, tested and used at the Functional Genomics Center Zurich. We use this package mainly for prototyping, teaching, and having fun with proteomics data. But it can also be used to do data analysis for small scale data sets.
Author: Christian Panse , Jonas Grossmann , Simon Barkow-Oesterreicher
Maintainer: Christian Panse

Diff between protViz versions 0.2.06 dated 2014-09-18 and 0.2.9 dated 2014-09-30

 DESCRIPTION                    |   10 ++--
 MD5                            |   48 ++++++++++----------
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 26 files changed, 159 insertions(+), 84 deletions(-)

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Package NPBayesImpute updated to version 0.3 with previous version 0.2 dated 2014-09-04

Title: Non-parametric Bayesian Multiple Imputation for Categorical Data
Description: These routines create multiple imputations of missing at random categorical data, with or without structural zeros. Imputations are based on Dirichlet process mixtures of multinomial distributions, which is a non-parametric Bayesian modeling approach that allows for flexible joint modeling.
Author: Quanli Wang, Daniel Manrique-Vallier, Jerome P. Reiter and Jingchen Hu
Maintainer: Quanli Wang

Diff between NPBayesImpute versions 0.2 dated 2014-09-04 and 0.3 dated 2014-09-30

 DESCRIPTION    |    6 +++---
 MD5            |    4 ++--
 R/ArrayUtils.R |   41 ++++++++++++++++++++++++++++++++++++-----
 3 files changed, 41 insertions(+), 10 deletions(-)

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Package lavaan updated to version 0.5-17 with previous version 0.5-16 dated 2014-03-07

Title: Latent Variable Analysis
Description: Fit a variety of latent variable models, including confirmatory factor analysis, structural equation modeling and latent growth curve models.
Author: Yves Rosseel [aut, cre], Daniel Oberski [ctb], Jarrett Byrnes [ctb], Leonard Vanbrabant [ctb], Victoria Savalei [ctb], Ed Merkle [ctb], Michael Hallquist [ctb], Mijke Rhemtulla [ctb], Myrsini Katsikatsou [ctb], Mariska Barendse [ctb]
Maintainer: Yves Rosseel

Diff between lavaan versions 0.5-16 dated 2014-03-07 and 0.5-17 dated 2014-09-30

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More information about lavaan at CRAN
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Package rcicr updated to version 0.2.4 with previous version 0.2.1 dated 2014-07-31

Title: Reverse correlation image classification toolbox
Description: Functions to generate stimuli and analyze data of reverse correlation image classification experiments.
Author: Ron Dotsch
Maintainer: Ron Dotsch

Diff between rcicr versions 0.2.1 dated 2014-07-31 and 0.2.4 dated 2014-09-30

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More information about rcicr at CRAN
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Package PowerTOST updated to version 1.2-01 with previous version 1.1-13 dated 2014-08-12

Title: Power and Sample size based on two one-sided t-tests (TOST) for (bio)equivalence studies
Description: Contains functions to calculate power and sample size for various study designs used for bioequivalence studies. See function known.designs() for study designs covered. Moreover the package contains functions for power and sample size based on 'expected' power in case of uncertain (estimated) variability. ----- Added are functions for the power and sample size for the ratio of two means with normally distributed data on the original scale (based on Fieller's confidence ('fiducial') interval). ----- Contains further functions for power and sample size calculations based on non-inferiority t-test. This is not a TOST procedure but eventually useful if the question of 'non-superiority' must be evaluated. The power and sample size calculations based on non-inferiority test may also performed via 'expected' power in case of uncertain (estimated) variability. ----- Contains functions power.scABEL() and sampleN.scABEL() to calculate power and sample size for the BE decision via scaled (widened) BE acceptance limits based on simulations. Contains further functions power.RSABE() and sampleN.RSABE() to calculate power and sample size for the BE decision via reference scaled ABE criterion according to the FDA procedure based on simulations. Contains further functions power.NTIDFDA() and sampleN.NTIDFDA() to calculate power and sample size for the BE decision via the FDA procedure for NTID's based on simulations. ----- Contains functions for power analysis of a sample size plan for ABE (pa.ABE()), scaled ABE (pa.scABE()) and scaled ABE for NTID's (pa.NTIDFDA()) analysing power if deviating from assumptions of the plan. ----- Contains further functions for power calculations / samplesize estimation for dose proportionality studies using the Power model.
Author: Detlew Labes [aut, cre], Helmut Schuetz [aut]
Maintainer: Detlew Labes

Diff between PowerTOST versions 1.1-13 dated 2014-08-12 and 1.2-01 dated 2014-09-30

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 PowerTOST-1.2-01/PowerTOST/NEWS                                            |   15 ++
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Package gvcm.cat updated to version 1.7 with previous version 1.6 dated 2013-11-14

Title: Regularized Categorical Effects/Categorical Effect Modifiers/Continuous/Smooth effects in GLMs
Description: Generalized structured regression models with regularized categorical effects, categorical effect modifiers, continuous effects and smooth effects.
Author: Margret Oelker
Maintainer: Margret Oelker

Diff between gvcm.cat versions 1.6 dated 2013-11-14 and 1.7 dated 2014-09-30

 DESCRIPTION          |   12 ++++++------
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Package CINID updated to version 1.1 with previous version 1.0 dated 2013-10-11

Title: Curculionidae INstar IDentification
Description: This package provides functions to compute a method for identifying the instar of Curculionid larvae from the observed distribution of the headcapsule size of mature larvae.
Author: Aurelie Siberchicot, Adrien Merville, Marie-Claude Bel-Venner and Samuel Venner
Maintainer: Aurelie Siberchicot

Diff between CINID versions 1.0 dated 2013-10-11 and 1.1 dated 2014-09-30

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More information about CINID at CRAN
Permanent link

Package ASMap updated to version 0.3-1 with previous version 0.3 dated 2014-09-24

Title: Linkage map construction using the MSTmap algorithm
Description: Functions for (A)ccurate and (S)peedy linkage map construction, manipulation and diagnosis of Doubled Haploid, Backcross and Recombinant Inbred R/qtl objects. This includes extremely fast linkage map clustering and optimal marker ordering using MSTmap (see Wu et al.,2008).
Author: Julian Taylor , David Butler .
Maintainer: Julian Taylor

Diff between ASMap versions 0.3 dated 2014-09-24 and 0.3-1 dated 2014-09-30

 DESCRIPTION |   10 +++++-----
 MD5         |    4 ++--
 R/mstmap9.R |   10 ++++++----
 3 files changed, 13 insertions(+), 11 deletions(-)

More information about ASMap at CRAN
Permanent link

Package faisalconjoint (with last version 1.10) was removed from CRAN

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

2012-07-04 1.10
2012-02-23 1.0

Permanent link
Package shiny updated to version 0.10.2 with previous version 0.10.1 dated 2014-07-26

Title: Web Application Framework for R
Description: Shiny makes it incredibly easy to build interactive web applications with R. Automatic "reactive" binding between inputs and outputs and extensive pre-built widgets make it possible to build beautiful, responsive, and powerful applications with minimal effort.
Author: RStudio, Inc.
Maintainer: Winston Chang

Diff between shiny versions 0.10.1 dated 2014-07-26 and 0.10.2 dated 2014-09-30

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 shiny-0.10.2/shiny/NEWS                                                    |   45 +
 shiny-0.10.2/shiny/R/app.R                                                 |  113 ++-
 shiny-0.10.2/shiny/R/bootstrap.R                                           |   17 
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 shiny-0.10.2/shiny/R/fileupload.R                                          |   39 -
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Package RHive updated to version 2.0-0.2 with previous version 2.0-0.1 dated 2014-08-27

Title: R and Hive
Description: RHive is an R extension facilitating distributed computing via HIVE query. It provides an easy to use HQL like SQL and R objects and functions in HQL.
Author: NexR
Maintainer: Bruce Shin

Diff between RHive versions 2.0-0.1 dated 2014-08-27 and 2.0-0.2 dated 2014-09-30

 DESCRIPTION |   10 +++++-----
 MD5         |    2 +-
 2 files changed, 6 insertions(+), 6 deletions(-)

More information about RHive at CRAN
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New package mdsdt with initial version 1.0
Package: mdsdt
Version: 1.0
Date: 2014-09-27
Title: Functions for Analysis of Data with General Recognition Theory
Author: Robert X.D. Hawkins , Joe Houpt , Noah Silbert , Leslie Blaha , Thomas D. Wickens
Maintainer: Robert X.D. Hawkins
Depends: R (>= 1.8.0), ellipse, mnormt, polycor
Description: This package contains a series of tools associated with General Recognition Theory (Townsend & Ashby, 1986), including Gaussian model fitting of 4x4 and more general confusion matrices, associated plotting and model comparison tools, and tests of marginal response invariance and report independence.
License: GPL (>= 2)
Collate: 'grt-data.R' 'grt_base.R'
Packaged: 2014-09-30 02:49:43 UTC; hawkrobe
NeedsCompilation: no
Repository: CRAN
Date/Publication: 2014-09-30 07:50:30

More information about mdsdt at CRAN
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Package mco updated to version 1.0-15 with previous version 1.0-14 dated 2014-09-21

Title: Multiple Criteria Optimization Algorithms and Related Functions
Description: Functions for multiple criteria optimization using genetic algorithms and related test problems
Author: Olaf Mersmann [aut, cre], Heike Trautmann [ctb], Detlef Steuer [ctb], Bernd Bischl [ctb], Kalyanmoy Deb [cph]
Maintainer: Olaf Mersmann

Diff between mco versions 1.0-14 dated 2014-09-21 and 1.0-15 dated 2014-09-30

 DESCRIPTION           |   10 ++++----
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More information about mco at CRAN
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Package MASS updated to version 7.3-35 with previous version 7.3-34 dated 2014-08-21

Title: Support Functions and Datasets for Venables and Ripley's MASS
Description: Functions and datasets to support Venables and Ripley, 'Modern Applied Statistics with S' (4th edition, 2002).
Author: Brian Ripley [aut, cre, cph], Bill Venables [ctb], Douglas M. Bates [ctb], Kurt Hornik [trl] (partial port ca 1998), Albrecht Gebhardt [trl] (partial port ca 1998), David Firth [ctb]
Maintainer: Brian Ripley

Diff between MASS versions 7.3-34 dated 2014-08-21 and 7.3-35 dated 2014-09-30

 DESCRIPTION                      |   10 +-
 MD5                              |   10 +-
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 6 files changed, 115 insertions(+), 119 deletions(-)

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Package boot updated to version 1.3-13 with previous version 1.3-11 dated 2014-03-28

Title: Bootstrap Functions (originally by Angelo Canty for S)
Description: functions and datasets for bootstrapping from the book "Bootstrap Methods and Their Applications" by A. C. Davison and D. V. Hinkley (1997, CUP).
Author: Angelo Canty [aut], Brian Ripley [aut, trl, cre] (author of parallel support)
Maintainer: Brian Ripley

Diff between boot versions 1.3-11 dated 2014-03-28 and 1.3-13 dated 2014-09-30

 ChangeLog                             |    8 +++++
 DESCRIPTION                           |    8 ++---
 MD5                                   |   14 ++++-----
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 8 files changed, 56 insertions(+), 32 deletions(-)

More information about boot at CRAN
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Built and running on Debian GNU/Linux using R, littler and blosxom. Styled with Bootstrap.