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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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

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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

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More information about shiny at CRAN
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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

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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

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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 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

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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

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Permanent link

Mon, 29 Sep 2014

New package repra with initial version 0.4
Package: repra
Title: Renewable Energy Probability Resource Assessment Tool (REPRA)
Version: 0.4
Date: 2014-09-29
Author: Eduardo Ibanez
Maintainer: Eduardo Ibanez
Description: This package includes methods to calculate resource adequacy metrics in power systems. These methods are based in the notion of loss-of-load probability (LOLP) and include the treatment of conventional and variable renewable generators.
License: MIT + file LICENSE
Depends: R(>= 3.1.0)
Imports: data.table, dplyr, Rcpp, reshape2, ggplot2, assertthat
Suggests: testthat, knitr
LinkingTo: Rcpp (>= 0.11.1)
VignetteBuilder: knitr
LazyData: TRUE
Packaged: 2014-09-29 21:02:43 UTC; eibanez
NeedsCompilation: yes
Repository: CRAN
Date/Publication: 2014-09-30 00:03:48

More information about repra at CRAN
Permanent link

Package log4r updated to version 0.2 with previous version 0.1-4 dated 2012-03-01

Title: A simple logging system for R, based on log4j.
Description: logr4 provides an object-oriented logging system that uses an API roughly equivalent to log4j and its related variants.
Author: John Myles White [aut, cph], Kenton White [ctb], Kirill Müller [ctb, cre]
Maintainer: Kirill Müller

Diff between log4r versions 0.1-4 dated 2012-03-01 and 0.2 dated 2014-09-29

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Permanent link

Package GPFDA updated to version 2.2 with previous version 2.1 dated 2014-05-29

Title: Apply Gaussian Process in Functional data analysis
Description: Use functional regression as the mean structure and Gaussian Process as the covariance structure.
Author: Jian Qing Shi, Yafeng Cheng
Maintainer: Yafeng Cheng

Diff between GPFDA versions 2.1 dated 2014-05-29 and 2.2 dated 2014-09-29

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Package DoE.wrapper updated to version 0.8-10 with previous version 0.8-9 dated 2013-09-13

Title: Wrapper package for design of experiments functionality
Description: This package creates various kinds of designs for (industrial) experiments. It uses, and sometimes enhances, design generation routines from other packages. So far, response surface designs from package rsm, latin hypercube samples from packages lhs and DiceDesign, and D-optimal designs from package AlgDesign have been implemented.
Author: Ulrike Groemping [aut, cre], Lenth Russ [ctb]
Maintainer: Ulrike Groemping

Diff between DoE.wrapper versions 0.8-9 dated 2013-09-13 and 0.8-10 dated 2014-09-29

 DESCRIPTION              |    8 ++++----
 MD5                      |    8 ++++----
 inst/NEWS                |    5 +++++
 man/Dopt.design.Rd       |    5 +++--
 tests/bbd.test.Rout.save |   28 ++++++++++++++--------------
 5 files changed, 30 insertions(+), 24 deletions(-)

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Package DoE.base updated to version 0.26-3 with previous version 0.26-2 dated 2014-08-16

Title: Full factorials, orthogonal arrays and base utilities for DoE packages
Description: This package creates full factorial experimental designs and designs based on orthogonal arrays for (industrial) experiments. Additionally, it provides some utility functions used also by other DoE packages.
Author: Ulrike Groemping [aut, cre], Boyko Amarov [ctb], Hongquan Xu [ctb]
Maintainer: Ulrike Groemping

Diff between DoE.base versions 0.26-2 dated 2014-08-16 and 0.26-3 dated 2014-09-29

 DESCRIPTION          |    8 ++++----
 MD5                  |   12 +++++++-----
 NAMESPACE            |    2 +-
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 8 files changed, 21 insertions(+), 14 deletions(-)

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Package ScottKnott updated to version 1.2-5 with previous version 1.2-4 dated 2013-11-28

Title: The ScottKnott Clustering Algorithm
Description: Division of an ANOVA experiment treatment means into homogeneous distinct groups using the clustering method of Scott & Knott
Author: Enio Jelihovschi Jos Cludio Faria Ivan Bezerra Allaman
Maintainer: Ivan Bezerra Allaman

Diff between ScottKnott versions 1.2-4 dated 2013-11-28 and 1.2-5 dated 2014-09-29

 ChangeLog                 |  102 ++---
 DESCRIPTION               |   10 
 INDEX                     |   42 +-
 MD5                       |   39 +-
 NAMESPACE                 |   20 -
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 R/SK.R                    |   10 
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 R/plot.SK.R               |  220 +++++------
 R/summary.SK.R            |   78 ++--
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 demo/00Index              |   14 
 inst/CITATION             |   47 +-
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 21 files changed, 1129 insertions(+), 1117 deletions(-)

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New package rjstat with initial version 0.2
Package: rjstat
Type: Package
Title: Read and write JSON-stat data sets
Version: 0.2
Date: 2014-08-16
Author: Aaron Schumacher , Håkon Malmedal
Maintainer: Aaron Schumacher
Description: Read and write the JSON-stat format (http://json-stat.org) to and from (lists of) R data frames. Not all features are supported, especially the extensive metadata features of JSON-stat.
License: MIT + file LICENSE
Encoding: UTF-8
URL: https://github.com/ajschumacher/rjstat
BugReports: https://github.com/ajschumacher/rjstat/issues
Imports: jsonlite (>= 0.9.8), assertthat
Suggests: testthat (>= 0.8), reshape (>= 0.7)
Packaged: 2014-09-29 13:40:28 UTC; hmalmedal
NeedsCompilation: no
Repository: CRAN
Date/Publication: 2014-09-29 23:06:22

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New package gender with initial version 0.4.1
Package: gender
Type: Package
Title: Gender: predict gender from names using historical data
Version: 0.4.1
Authors@R: c(person("Lincoln", "Mullen", role = c("aut", "cre"), email = "lincoln@lincolnmullen.com"), person("Cameron", "Blevins", role = "ctb"), person("Ben", "Schmidt", role = "ctb"))
Description: Encodes gender based on names and dates of birth, using either the Social Security Administration's data set of first names by year of birth or Census Bureau data from 1789 to 1940, both from the United States of America. By using these data sets instead of lists of male and female names, this package is able to more accurately guess the gender of a name, and it is able to report the probability that a name was male or female.
URL: https://github.com/ropensci/gender
Depends: R (>= 3.0.0), utils, stats
Imports: devtools(>= 1.5), dplyr (>= 0.2), httr (>= 0.4), jsonlite (>= 0.9.10)
Suggests: ggplot2, knitr, magrittr, testthat
LazyData: yes
License: MIT + file LICENSE
VignetteBuilder: knitr
BugReports: https://github.com/ropensci/gender/issues
Packaged: 2014-09-29 15:17:37 UTC; lmullen
Author: Lincoln Mullen [aut, cre], Cameron Blevins [ctb], Ben Schmidt [ctb]
Maintainer: Lincoln Mullen
NeedsCompilation: no
Repository: CRAN
Date/Publication: 2014-09-29 23:04:09

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Package dendsort updated to version 0.3.2 with previous version 0.3.1 dated 2014-09-27

Title: Modular Leaf Ordering Methods for Dendrogram Nodes
Description: This package includes functions to optimize ordering of nodes in a dendrogram, without affecting the meaning of the dendrogram. A dendrogram can be sorted based on the average distance of subtrees, or based on the smallest distance value. These sorting methods improve readability and interpretability of tree structure, especially for tasks such as comparison of different distance measures or linkage types and identification of tight clusters and outliers. As a result, it also introduces more meaningful reordering for a coupled heatmap visualization.
Author: Ryo Sakai
Maintainer: Ryo Sakai

Diff between dendsort versions 0.3.1 dated 2014-09-27 and 0.3.2 dated 2014-09-29

 DESCRIPTION             |   10 +++----
 MD5                     |   34 +++++++++++++-------------
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 18 files changed, 49 insertions(+), 89 deletions(-)

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New package atmcmc with initial version 1.0
Package: atmcmc
Type: Package
Title: Automatically Tuned Markov Chain Monte Carlo
Version: 1.0
Date: 2014-09-16
Author: Jinyoung Yang
Maintainer: Jinyoung Yang
Description: Uses adaptive diagnostics to tune and run a random walk Metropolis MCMC algorithm, to converge to a specified target distribution and estimate means of functionals.
License: GPL (>= 2)
Packaged: 2014-09-29 20:01:29 UTC; 1
NeedsCompilation: no
Repository: CRAN
Date/Publication: 2014-09-29 23:00:15

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New package sprint with initial version 1.0.7
Package: sprint
Title: Simple Parallel R INTerface
Version: 1.0.7
Date: 2014-09-24
Author: University of Edinburgh SPRINT Team
Copyright: University of Edinburgh
Maintainer: Eilidh Troup
Contact: University of Edinburgh SPRINT Team
Depends: R (>= 2.9.2), rlecuyer, ff (>= 2.1-1), randomForest
Suggests: cluster, stringdist, RUnit, Matrix, SparseM, multtest, Biostrings, ShortRead, golubEsets, RankProd
Imports: boot, e1071
SystemRequirements: MPI(>= 2.0)
Description: SPRINT (Simple Parallel R INTerface) is a parallel framework for R. It provides a High Performance Computing (HPC) harness which allows R scripts to run on HPC clusters. SPRINT contains a library of selected R functions that have been parallelized. Functions are named after the original R function with the added prefix 'p', i.e. the parallel version of cor() in SPRINT is called pcor(). Call to the parallel R functions are included directly in standard R scripts. SPRINT contains functions for correlation (pcor), partitioning around medoids (ppam), apply (papply), permutation testing (pmaxT), bootstrapping (pboot), random forest (prandomForest), rank product (pRP) and hamming distance (pstringdistmatrix).
License: GPL (>= 3)
URL: http://www.r-sprint.org
Repository: CRAN
Packaged: 2014-09-29 12:12:34 UTC; eilidhtroup
Date/Publication: 2014-09-29 18:03:00
NeedsCompilation: yes

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Package signal.hsmm updated to version 1.1 with previous version 1.0 dated 2014-08-07

Title: Predict Presence of Signal Peptides
Description: Predicts presence of signal peptides in eukaryotic protein using hidden semi-Markov models. The implemented algorithm can be accessed both from command line and GUI.
Author: Michal Burdukiewicz [cre, aut], Piotr Sobczyk [aut]
Maintainer: Michal Burdukiewicz

Diff between signal.hsmm versions 1.0 dated 2014-08-07 and 1.1 dated 2014-09-29

 signal.hsmm-1.0/signal.hsmm/R/durationViterbi.R                   |only
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 signal.hsmm-1.1/signal.hsmm/R/find_nhc.R                          |  135 +--
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 signal.hsmm-1.1/signal.hsmm/R/read_txt.R                          |   74 +-
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Package magicaxis updated to version 1.9.3 with previous version 1.9 dated 2014-07-16

Title: Pretty scientific plotting with minor-tick and log minor-tick support
Description: Functions to make useful (and pretty) plots for scientific plotting. Additional plotting features are added for base plotting, with particular emphasis on making attractive log axis plots.
Author: Aaron Robotham
Maintainer: Aaron Robotham

Diff between magicaxis versions 1.9 dated 2014-07-16 and 1.9.3 dated 2014-09-29

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 13 files changed, 181 insertions(+), 82 deletions(-)

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Package hierfstat updated to version 0.04-14 with previous version 0.04-10 dated 2013-04-10

Title: Estimation and tests of hierarchical F-statistics
Description: This R package allows the estimation of hierarchical F-statistics from haploid or diploid genetic data with any numbers of levels in the hierarchy, following the algorithm of Yang (Evolution, 1998, 52(4):950-956). Functions are also given to test via randomisations the significance of each F and variance components, using the likelihood-ratio statistics G -see Goudet etal (Genetics, 1996, 144(4): 1933-1940)
Author: Jerome Goudet
Maintainer: Jerome Goudet

Diff between hierfstat versions 0.04-10 dated 2013-04-10 and 0.04-14 dated 2014-09-29

 CHANGES                |   11 +++++++
 DESCRIPTION            |   16 +++-------
 MD5                    |   32 +++++++++++----------
 NAMESPACE              |   29 +++++++++++++------
 R/beta.R               |    6 ++--
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 man/boot.ppfst.rd      |    4 +-
 man/indpca.rd          |    3 +-
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 18 files changed, 157 insertions(+), 117 deletions(-)

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Package httpRequest updated to version 0.0.10 with previous version 0.0.9 dated 2012-12-04

Title: Basic HTTP Request
Description: HTTP Request protocols. Implements the GET, POST and multipart POST request.
Author: Eryk Witold Wolski, Andreas Westfeld
Maintainer: Andreas Westfeld

Diff between httpRequest versions 0.0.9 dated 2012-12-04 and 0.0.10 dated 2014-09-29

 DESCRIPTION             |   12 +++---
 MD5                     |    6 +--
 R/httpRequest.R         |   92 ++++++++++++++++++++++--------------------------
 man/simplePostToHost.Rd |   21 +++++++---
 4 files changed, 67 insertions(+), 64 deletions(-)

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Package gapmap updated to version 0.0.2 with previous version 0.0.1 dated 2014-09-11

Title: Functions for Drawing Gapped Cluster Heatmap with ggplot2
Description: The gap encodes the distance between clusters and improves interpretation of cluster heatmaps. The gaps can be of the same distance based on a height threshold to cut the dendrogram. Another option is to vary the size of gaps based on the distance between clusters.
Author: Ryo Sakai
Maintainer: Ryo Sakai

Diff between gapmap versions 0.0.1 dated 2014-09-11 and 0.0.2 dated 2014-09-29

 DESCRIPTION                  |   10 +++----
 MD5                          |   22 ++++++++--------
 R/gap_dendrogram.R           |    2 -
 R/gapmap.R                   |    6 ++--
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 inst/doc/simple_example.Rmd  |   22 ++++++++--------
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 inst/doc/tcga_example.R      |   25 ++++++++++++++++--
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 vignettes/tcga_example.Rmd   |   47 +++++++++++++++++++++++++++++-----
 12 files changed, 220 insertions(+), 85 deletions(-)

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Package FeedbackTS updated to version 1.2 with previous version 1.1 dated 2014-07-03

Title: Analysis of Feedback in Time Series
Description: Analysis of fragmented time directionality to investigate feedback in time series. Tools provided by the package allow the analysis of feedback for a single time series and the analysis of feedback for a set of time series collected across a spatial domain.
Author: Samuel Soubeyrand, Cindy E. Morris, E. Keith Bigg
Maintainer: Samuel Soubeyrand

Diff between FeedbackTS versions 1.1 dated 2014-07-03 and 1.2 dated 2014-09-29

 DESCRIPTION                     |   10 +++++-----
 MD5                             |   12 ++++++------
 NAMESPACE                       |    1 +
 man/FeedbackTS-package.Rd       |    4 ++--
 man/KDD-class.Rd                |   20 ++++++++++++--------
 man/KDD.yearly.average-class.Rd |    6 +++---
 man/KT.output-class.Rd          |   10 +++++-----
 7 files changed, 34 insertions(+), 29 deletions(-)

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New package EffectStars with initial version 1.5
Package: EffectStars
Type: Package
Title: Visualization of Categorical Response Models
Version: 1.5
Date: 2014-09-29
Depends: VGAM
Author: Gunther Schauberger
Maintainer: Gunther Schauberger
Description: The package provides functions to visualize regression models with categorical response. The effects of the covariates are plotted with star plots in order to allow for an optical impression of the fitted model.
License: GPL-2
LazyLoad: yes
Packaged: 2014-09-29 13:30:38 UTC; schaubergerg
NeedsCompilation: no
Repository: CRAN
Date/Publication: 2014-09-29 18:02:57

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Package corpcor updated to version 1.6.7 with previous version 1.6.6 dated 2013-05-15

Title: Efficient Estimation of Covariance and (Partial) Correlation
Description: This package implements a James-Stein-type shrinkage estimator for the covariance matrix, with separate shrinkage for variances and correlations. The details of the method are explained in Sch\"afer and Strimmer (2005) and Opgen-Rhein and Strimmer (2007). The approach is both computationally as well as statistically very efficient, it is applicable to "small n, large p" data, and always returns a positive definite and well-conditioned covariance matrix. In addition to inferring the covariance matrix the package also provides shrinkage estimators for partial correlations and partial variances. The inverse of the covariance and correlation matrix can be efficiently computed, as well as any arbitrary power of the shrinkage correlation matrix. Furthermore, functions are available for fast singular value decomposition, for computing the pseudoinverse, and for checking the rank and positive definiteness of a matrix.
Author: Juliane Sch\"afer, Rainer Opgen-Rhein, Verena Zuber, Miika Ahdesm\"aki, A. Pedro Duarte Silva, and Korbinian Strimmer.
Maintainer: Korbinian Strimmer

Diff between corpcor versions 1.6.6 dated 2013-05-15 and 1.6.7 dated 2014-09-29

 DESCRIPTION |   45 +++++++++++++++++++++------------------------
 MD5         |    4 ++--
 NEWS        |    7 +++++++
 3 files changed, 30 insertions(+), 26 deletions(-)

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Package aLFQ updated to version 1.3.2 with previous version 1.3.1 dated 2014-02-27

Title: An R-package for estimating absolute protein quantities from label-free LC-MS/MS proteomics data
Description: Determination of absolute protein quantities is necessary for multiple applications, such as mechanistic modeling of biological systems. Quantitative liquid chromatography tandem mass spectrometry (LC-MS/MS) proteomics can measure relative protein abundance on a system-wide scale. To estimate absolute quantitative information using these relative abundance measurements requires additional information such as heavy-labeled references of known concentration. Multiple methods have been using different references and strategies; some are easily available whereas others require more effort on the users end. Hence, we believe the field might benefit from making some of these methods available under an automated framework, which also facilitates validation of the chosen strategy. We have implemented the most commonly used absolute label-free protein abundance estimation methods for LC-MS/MS modes quantifying on either MS1-, MS2-levels or spectral counts together with validation algorithms to enable automated data analysis and error estimation. Specifically, we used Monte-carlo cross-validation and bootstrapping for model selection and imputation of proteome-wide absolute protein quantity estimation. Our open-source software is written in the statistical programming language R and validated and demonstrated on a synthetic sample.
Author: aLFQ: George Rosenberger, Hannes Roest, Christina Ludwig. AAindex: Barry Grant.
Maintainer: George Rosenberger

Diff between aLFQ versions 1.3.1 dated 2014-02-27 and 1.3.2 dated 2014-09-29

 DESCRIPTION                      |   13 +++++++------
 MD5                              |   17 +++++++++--------
 NAMESPACE                        |    9 ++++++++-
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 10 files changed, 33 insertions(+), 57 deletions(-)

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Package yuima updated to version 1.0.36 with previous version 1.0.30 dated 2014-09-17

Title: The YUIMA Project package for SDEs
Description: Simulation and Inference for Stochastic Differential Equations
Author: YUIMA Project Team
Maintainer: Stefano M. Iacus

Diff between yuima versions 1.0.30 dated 2014-09-17 and 1.0.36 dated 2014-09-29

 DESCRIPTION                |    8 +-
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Package soiltexture updated to version 1.2.19 with previous version 1.2.13 dated 2014-01-14

Title: Functions for soil texture plot, classification and transformation
Description: "The Soil Texture Wizard" is a set of R functions designed to produce texture triangles (also called texture plots, texture diagrams, texture ternary plots), classify and transform soil textures data. These functions virtually allows to plot any soil texture triangle / classification into any triangle geometry (isosceles, right-angled triangles, etc.). This set of function is expected to be useful to people using soil textures data from different soil texture classification or different particle size systems. Several texture triangles are predefined: USDA; FAO (which is also the triangle for the soil map of Europe); Aisne (France); GEPPA (France); German triangles "Bodenkundliche Kartieranleitung 1994", "SEA 1974" and "TGL 1985"; Soil Survey of England and Wales; Australian triangle; Belgian triangle; Canadian triangle; ISSS triangle; Romanian triangle; Polish triangle.
Author: Julien MOEYS , contributions from Wei Shangguan.
Maintainer: Julien MOEYS

Diff between soiltexture versions 1.2.13 dated 2014-01-14 and 1.2.19 dated 2014-09-29

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New package rFDSN with initial version 0.0.0
Package: rFDSN
Type: Package
Title: Get Seismic Data from the International Federation of Digital Seismograph Networks
Description: This package facilitates searching for and downloading seismic time series in miniSEED format (a minimalist version of the Standard for the Exchange of Earthquake Data) from International Federation of Digital Seismograph Networks repositories. This package can also be used to gather information about seismic networks (stations, channels, locations, etc) and find historical earthquake data (origins, magnitudes, etc).
Version: 0.0.0
Date: 2014-09-28
Authors@R: c(person(given="Daniel C.",family="Bowman", role=c("aut", "cre"), email="daniel.bowman@unc.edu"))
Depends: R (>= 3.1.1), XML (>= 3.98.1.1)
Enhances: RSEIS (>= 3.3.3)
License: GPL (>= 3)
Packaged: 2014-09-29 12:44:12 UTC; bowman
Maintainer: Daniel C. Bowman
Author: Daniel C. Bowman [aut, cre]
NeedsCompilation: no
Repository: CRAN
Date/Publication: 2014-09-29 15:10:04

More information about rFDSN at CRAN
Permanent link

Package LSAfun updated to version 0.3.2 with previous version 0.3.1 dated 2014-07-07

Title: Applied Latent Semantic Analysis (LSA) functions
Description: This package provides functions that allow for convenient working with Latent Semantic Analysis. For actually building an LSA space, use the package 'lsa'.
Author: Fritz Guenther [aut, cre]
Maintainer: Fritz Guenther

Diff between LSAfun versions 0.3.1 dated 2014-07-07 and 0.3.2 dated 2014-09-29

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 DESCRIPTION           |    8 ++++----
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More information about LSAfun at CRAN
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Package ggdendro updated to version 0.1-15 with previous version 0.1-14 dated 2013-09-03

Title: Tools for extracting dendrogram and tree diagram plot data for use with ggplot2
Description: This is a set of tools for dendrograms and tree plots using ggplot2. The ggplot2 philosophy is to clearly separate data from the presentation. Unfortunately the plot method for dendrograms plots directly to a plot device without exposing the data. The ggdendro package resolves this by making available functions that extract the dendrogram plot data.
Author: Andrie de Vries [aut, cre], Brian D. Ripley [aut] (author of package tree)
Maintainer: Andrie de Vries

Diff between ggdendro versions 0.1-14 dated 2013-09-03 and 0.1-15 dated 2014-09-29

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Package fSRM updated to version 0.6 with previous version 0.3.5 dated 2014-05-13

Title: Social Relations Analyses with roles ("Family SRM")
Description: The package computes Social Relations Analysis with roles ("Family SRM"), using a structural equation modeling approach. Groups ranging from three members up to an unlimited number of members are supported and the mean structure can be computed. Means and variances can be compared between different groups of families and between roles.
Author: Felix Schönbrodt, Lara Stas, Tom Loeys
Maintainer: Felix Schönbrodt

Diff between fSRM versions 0.3.5 dated 2014-05-13 and 0.6 dated 2014-09-29

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More information about fSRM at CRAN
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Package fscaret updated to version 0.8.6.2 with previous version 0.8.5.7 dated 2014-08-28

Title: Automated caret feature selection
Description: Automated feature selection using variety of models provided by caret package
Author: Jakub Szlek , acknowledgments to Aleksander Mendyk, contributions from stackoverflow and r-help@r-project.org mailing list community. Acknowledgments: This work was funded by Poland-Singapore bilateral cooperation project no 2/3/POL-SIN/2012.
Maintainer: Jakub Szlek

Diff between fscaret versions 0.8.5.7 dated 2014-08-28 and 0.8.6.2 dated 2014-09-29

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Package FLSSS updated to version 2.0 with previous version 1.0 dated 2014-05-29

Title: Fixed Size Subset Sum Solution
Description: Solve an approximate Subset Sum Problem by introducing a recursive compression algorithm
Author: Charlie Wusuo Liu
Maintainer: Charlie Wusuo Liu

Diff between FLSSS versions 1.0 dated 2014-05-29 and 2.0 dated 2014-09-29

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New package activity with initial version 1.0
Package: activity
Title: Animal Activity Statistics
Version: 1.0
Date: 24/09/14
Author: Marcus Rowcliffe
Maintainer: Marcus Rowcliffe
Description: Provides functions to fit kernel density functions to animal activity time data; plot activity distributions; quantify overall levels of activity; statistically compare activity metrics through bootstrapping; and evaluate variation in linear variables with time (or other circular variables).
License: GPL-3
Depends: methods
Imports: circular, overlap, pbapply,
LazyData: true
Packaged: 2014-09-29 11:45:26 UTC; Rowcliffe.M
NeedsCompilation: no
Repository: CRAN
Date/Publication: 2014-09-29 15:07:49

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Package Rcpp updated to version 0.11.3 with previous version 0.11.2 dated 2014-06-08

Title: Seamless R and C++ Integration
Description: The Rcpp package provides R functions as well as C++ classes which offer a seamless integration of R and C++. Many R data types and objects can be mapped back and forth to C++ equivalents which facilitates both writing of new code as well as easier integration of third-party libraries. Documentation about Rcpp is provided by several vignettes included in this package, via the Rcpp Gallery site at http://gallery.rcpp.org, the paper by Eddelbuettel and Francois (2011, JSS), and the book by Eddelbuettel (2013, Springer); see 'citation("Rcpp")' for details on these last two.
Author: Dirk Eddelbuettel, Romain Francois, JJ Allaire, Kevin Ushey, Douglas Bates, and John Chambers
Maintainer: Dirk Eddelbuettel

Diff between Rcpp versions 0.11.2 dated 2014-06-08 and 0.11.3 dated 2014-09-29

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Package nleqslv updated to version 2.5 with previous version 2.4 dated 2014-08-09

Title: Solve systems of non linear equations
Description: Solve a system of non linear equations using a Broyden or a Newton method with a choice of global strategies such as line search and trust region. There are options for using a numerical or user supplied Jacobian and for specifying that a numerical Jacobian is banded.
Author: Berend Hasselman
Maintainer: Berend Hasselman

Diff between nleqslv versions 2.4 dated 2014-08-09 and 2.5 dated 2014-09-29

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More information about nleqslv at CRAN
Permanent link

New package robustDA with initial version 1.0
Package: robustDA
Type: Package
Title: Robust Mixture Discriminant Analysis
Version: 1.0
Date: 2014-09-26
Author: Charles Bouveyron & Stephane Girard
Maintainer: Charles Bouveyron
Depends: MASS, mclust, Rsolnp
Description: Robust mixture discriminant analysis (RMDA, Bouveyron & Girard, 2009) allows to build a robust supervised classifier from learning data with label noise. The idea of the proposed method is to confront an unsupervised modeling of the data with the supervised information carried by the labels of the learning data in order to detect inconsistencies. The method is able afterward to build a robust classifier taking into account the detected inconsistencies into the labels.
License: GPL-2
Packaged: 2014-09-28 17:32:50 UTC; charles
NeedsCompilation: no
Repository: CRAN
Date/Publication: 2014-09-29 07:27:55

More information about robustDA at CRAN
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Package RcmdrPlugin.EZR updated to version 1.26 with previous version 1.25 dated 2014-08-19

Title: R Commander Plug-in for the EZR (Easy R) Package
Description: EZR (Easy R) adds a variety of statistical functions, including survival analyses, ROC analyses, metaanalyses, sample size calculation, and so on, to the R commander. EZR enables point-and-click easy access to statistical functions, especially for medical statistics. EZR is platform-independent and runs on Windows, Mac OS X, and UNIX. Its complete manual is available only in Japanese (Chugai Igakusha, ISBN-10: 4498109007), but an report that introduced the investigation of EZR was published in Bone Marrow Transplantation (Nature Publishing Group) as an Open article. This report can be used as a simple manual. It can be freely downloaded from the journal website as shown below.
Author: Yoshinobu Kanda
Maintainer: Yoshinobu Kanda

Diff between RcmdrPlugin.EZR versions 1.25 dated 2014-08-19 and 1.26 dated 2014-09-29

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More information about RcmdrPlugin.EZR at CRAN
Permanent link

Package chipPCR updated to version 0.0.8-3 with previous version 0.0.8-1 dated 2014-08-26

Title: Toolkit of helper functions to pre-process amplification data
Description: The chipPCR package is a toolkit of functions to pre-process amplification curve data. Amplification data can be obtained from conventional PCR reactions or isothermal amplification reactions. The package contains functions to normalize and baseline amplification curves, a routine to detect the start of an amplification reaction, several smoothers for amplification data, a function to distinguish positive and negative amplification reactions and a function to determine the amplification efficiency. The smoothers are based on LOWESS, moving average, cubic splines, Savitzky-Golay and others. In addition the first approximate approximate derivative maximum (FDM) and second approximate derivative maximum (SDM) can be calculated by a 5-point-stencil as quantification points from real-time amplification curves. chipPCR contains data sets of experimental nucleic acid amplification systems including the VideoScan HCU and a capillary convective PCR (ccPCR) system. The amplification data were generated by helicase dependent amplification (HDA) or polymerase chain reaction (PCR) under various temperature conditions. As detection system intercalating dyes (EvaGreen, SYBR Green) and hydrolysis probes (TaqMan) were used. The latest source code is available via: https://github.com/michbur/chipPCR
Author: Stefan Roediger [cre, aut], Michal Burdukiewicz [aut]
Maintainer: Stefan Roediger

Diff between chipPCR versions 0.0.8-1 dated 2014-08-26 and 0.0.8-3 dated 2014-09-29

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More information about chipPCR at CRAN
Permanent link

New package blocksdesign with initial version 1.0
Package: blocksdesign
Type: Package
Title: Nested block designs for unstructured treatments
Version: 1.0
Date: 2014-09-16
Author: R. N. Edmondson
Maintainer: Rodney Edmondson
Description: Nested block designs for unstructured treatment sets where blocks can be repeatedly nested and treatments can have different levels of replication. Blocks strata are optimized hierarchically with each set of nested blocks optimized within the levels of the preceding set. Block sizes are equal if the number of blocks exactly divides the number of plots, otherwise they differ by at most one plot. The design output is a data table giving a randomised allocation of treatments to blocks together with a plan table showing treatments in blocks and a set of blocks-by-treatments incidence matrices, one for each blocks stratum.
License: GPL (>= 2)
URL: http://www.expdesigns.co.uk
Suggests: knitr
VignetteBuilder: knitr
Imports: crossdes
Packaged: 2014-09-28 18:51:17 UTC; rne
NeedsCompilation: no
Repository: CRAN
Date/Publication: 2014-09-29 07:23:52

More information about blocksdesign at CRAN
Permanent link

Sun, 28 Sep 2014

Package readMzXmlData updated to version 2.8 with previous version 2.7 dated 2013-07-03

Title: Reads Mass Spectrometry Data in mzXML Format
Description: Functions for reading mass spectrometry data in mzXML format.
Author: Sebastian Gibb [aut, cre]
Maintainer: Sebastian Gibb

Diff between readMzXmlData versions 2.7 dated 2013-07-03 and 2.8 dated 2014-09-28

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More information about readMzXmlData at CRAN
Permanent link

Package LARF updated to version 1.2 with previous version 1.1 dated 2013-09-12

Title: Local Average Response Functions for Instrumental Variable Estimation of Treatment Effects
Description: Provides instrumental variable estimation of treatment effects when both the endogenous treatment and its instrument are binary. Applicable to both binary and continuous outcomes.
Author: Weihua An and Xuefu Wang, Indiana University Bloomington
Maintainer: Weihua An

Diff between LARF versions 1.1 dated 2013-09-12 and 1.2 dated 2014-09-28

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More information about LARF at CRAN
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Package expands updated to version 1.5 with previous version 1.4 dated 2014-03-02

Title: ExPANdS
Description: Expanding Ploidy and Allele Frequency on Nested Subpopulations (ExPANdS) characterizes coexisting subpopulations in a tumor using copy number and allele frequencies derived from exome- or whole genome sequencing input data (http://www.ncbi.nlm.nih.gov/pubmed/24177718). The model amplifies the statistical power to detect coexisting genotypes, by exploiting run-specific tradeoffs between depth of coverage and breadth of coverage. ExPANdS predicts the number of clonal expansions, the size of the resulting subpopulations in the tumor bulk, the mutations specific to each subpopulation and tumor purity. The main function runExPANdS provides the complete functionality needed to predict coexisting subpopulations from single nucleotide variations (SNVs) and associated copy numbers. The robustness of the subpopulation predictions by ExPANdS increases with the number of mutations provided. It is recommended that at least 200 mutations are used as an input to obtain stable results. Updates include: (1) Additional optional parameter "min_CellFreq" provided for function runExPANdS, specifying the minimum cellular prevalence of mutations to be included for subpopulation predictions.(2) Filtered loci with high-level amplifications, according to max_PM setting. This reduces unnecessary processing time, as assignment of mutations within amplified regions to subpopulations is not successful. (3) Additional function "buildMultiSamplePhylo" available, which integrates the subpopulations predicted in multiple, geographically distinct tumor samples into one common phylogeny.
Author: Noemi Andor
Maintainer: Noemi Andor

Diff between expands versions 1.4 dated 2014-03-02 and 1.5 dated 2014-09-28

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More information about expands at CRAN
Permanent link

Package sweidnumbr updated to version 0.2 with previous version 0.1.1 dated 2014-09-06

Title: Handling of Swedish Identity Numbers
Description: Structural handling of identity numbers used in the Swedish administration such as personal identity numbers ('personnummer') and organizational identity numbers ('organisationsnummer').
Author: Mans Magnusson
Maintainer: Mans Magnusson

Diff between sweidnumbr versions 0.1.1 dated 2014-09-06 and 0.2 dated 2014-09-28

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More information about sweidnumbr at CRAN
Permanent link

Package pdfetch updated to version 0.1.6 with previous version 0.1.5 dated 2014-08-10

Title: Fetch economic and financial time series data from public sources
Description: A package for downloading economic and financial time series from public sources.
Author: Abiel Reinhart
Maintainer: Abiel Reinhart

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More information about pdfetch at CRAN
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New package neural with initial version 1.4.2.2
Package: neural
Version: 1.4.2.2
Title: Neural Networks
Author: Adam Nagy
Maintainer: Billy Aung Myint
Description: RBF and MLP neural networks with graphical user interface
License: GPL (>= 2)
Repository: CRAN
Packaged: 2014-09-28 13:32:07 UTC; billy
NeedsCompilation: no
Date/Publication: 2014-09-28 18:26:46

More information about neural at CRAN
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Package microbenchmark updated to version 1.4-2 with previous version 1.3-0 dated 2013-02-20

Title: Accurate Timing Functions
Description: Provides infrastructure to accurately measure and compare the execution time of R expressions.
Author: Olaf Mersmann [aut, cre], Claudia Beleites [ctb], Rainer Hurling [ctb], Ari Friedman [ctb]
Maintainer: Olaf Mersmann

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 34 files changed, 742 insertions(+), 534 deletions(-)

More information about microbenchmark at CRAN
Permanent link

Package meboot updated to version 1.4-5 with previous version 1.4-3 dated 2014-03-26

Title: Maximum Entropy Bootstrap for Time Series
Description: This package performs maximum entropy density based dependent data bootstrap. An algorithm is provided to create a population of time series (ensemble) without assuming stationarity. The reference paper (Vinod, H.D., 2004) explains how the algorithm satisfies the ergodic theorem and the central limit theorem.
Author: Hrishikesh D. Vinod and Javier López-de-Lacalle
Maintainer: Javier López-de-Lacalle

Diff between meboot versions 1.4-3 dated 2014-03-26 and 1.4-5 dated 2014-09-28

 meboot-1.4-3/meboot/R/slider.mts.R      |only
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 meboot-1.4-5/meboot/NAMESPACE           |    2 +-
 meboot-1.4-5/meboot/R/expand.sd.R       |   29 +++++++++++++++++++++++------
 meboot-1.4-5/meboot/R/flexMeboot.R      |    4 ++--
 meboot-1.4-5/meboot/R/meboot.R          |    2 +-
 meboot-1.4-5/meboot/inst/doc/meboot.pdf |binary
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 10 files changed, 41 insertions(+), 28 deletions(-)

More information about meboot at CRAN
Permanent link

Package mc2d updated to version 0.1-15 with previous version 0.1-14 dated 2013-10-16

Title: Tools for Two-Dimensional Monte-Carlo Simulations
Description: Various distributions and utilities to ease the use of R to build and study Two-Dimensional Monte-Carlo simulations
Author: Regis Pouillot [aut, cre], Marie-Laure Delignette-Muller [ctb], Jean-Baptiste Denis [ctb]
Maintainer: Regis Pouillot

Diff between mc2d versions 0.1-14 dated 2013-10-16 and 0.1-15 dated 2014-09-28

 DESCRIPTION        |   12 ++++++------
 MD5                |   10 +++++-----
 R/mcstoc.R         |   40 +++++++++++++++++++++++++---------------
 build/vignette.rds |binary
 data/ec.rda        |binary
 inst/NEWS          |    7 +++++++
 6 files changed, 43 insertions(+), 26 deletions(-)

More information about mc2d at CRAN
Permanent link

Package lm.beta updated to version 1.5 with previous version 1.0 dated 2014-07-20

Title: Add Standardized Regression Coefficients to lm-Objects
Description: Adds standardized regression coefficients to objects created by lm. Also extends the S3 methods print, summary and coef with additional boolean argument standardized.
Author: Stefan Behrendt [aut, cre]
Maintainer: Stefan Behrendt

Diff between lm.beta versions 1.0 dated 2014-07-20 and 1.5 dated 2014-09-28

 DESCRIPTION            |   15 ++++++++-------
 MD5                    |   21 +++++++++++----------
 NEWS                   |only
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 R/lm.beta.R            |    4 +---
 R/print.lm.beta.R      |    6 +++---
 R/summary.lm.beta.R    |    2 +-
 man/coef.lm.beta.Rd    |   10 ++++++----
 man/lm.beta-package.Rd |   26 ++++++++++++++++++--------
 man/lm.beta.Rd         |   26 ++++++++++++++++++--------
 man/print.lm.beta.Rd   |   10 ++++++----
 man/summary.lm.beta.Rd |   12 +++++++-----
 12 files changed, 81 insertions(+), 55 deletions(-)

More information about lm.beta at CRAN
Permanent link

Package DoseFinding updated to version 0.9-12 with previous version 0.9-11 dated 2014-02-11

Title: Planning and Analyzing Dose Finding experiments
Description: The DoseFinding package provides functions for the design and analysis of dose-finding experiments (with focus on pharmaceutical Phase II clinical trials). It provides functions for: multiple contrast tests, fitting non-linear dose-response models (using Bayesian and non-Bayesian estimation), calculating optimal designs and an implementation of the MCPMod methodology.
Author: Bjoern Bornkamp, Jose Pinheiro, Frank Bretz
Maintainer: Bjoern Bornkamp

Diff between DoseFinding versions 0.9-11 dated 2014-02-11 and 0.9-12 dated 2014-09-28

 ChangeLog                  |   10 +++++++
 DESCRIPTION                |   12 ++++----
 MD5                        |   52 +++++++++++++++++++-------------------
 R/Mods.R                   |    6 ++--
 R/bFitMod.R                |    4 ++
 R/optContr.R               |    9 ++++--
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 R/planMod.R                |    4 +-
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 tests/testgFit.R           |    4 --
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 tests/testsFitting.R       |    2 -
 tests/testsMCPMod.R        |    3 --
 tests/testsMCT.R           |    6 ++--
 tests/testsoptContr.R      |    6 ++--
 tests/testsplotDRMod.R     |    2 -
 tests/testssampSize.R      |    2 -
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 27 files changed, 199 insertions(+), 86 deletions(-)

More information about DoseFinding at CRAN
Permanent link

New package ecoretriever with initial version 0.1
Package: ecoretriever
Title: R Interface to the EcoData Retriever
Description: Provides an R interface to the EcoData Retriever (http://ecodataretriever.org/) via the EcoData Retriever's command line interface. The EcoData Retriever automates the tasks of finding, downloading, and cleaning ecological datasets, and then stores them in a local database.
Version: 0.1
Date: 2014-09-07
Authors@R: c(person("Daniel", "McGlinn", role = c("aut", "cre"), email = "danmcglinn@gmail.com"), person("Ethan", "White", role = "aut", email = "ethan@weecology.org"))
BugReports: https://github.com/ropensci/ecoretriever/issues
URL: https://github.com/ropensci/ecoretriever/
Depends: R (>= 3.0.0)
SystemRequirements: EcoData Retriever (>= 1.6)
License: MIT + file LICENSE
LazyData: true
Packaged: 2014-09-28 14:46:23 UTC; danmcglinn
Author: Daniel McGlinn [aut, cre], Ethan White [aut]
Maintainer: Daniel McGlinn
NeedsCompilation: no
Repository: CRAN
Date/Publication: 2014-09-28 18:18:03

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Package HotDeckImputation updated to version 1.0.0 with previous version 0.1.0 dated 2013-08-12

Title: Hot Deck Imputation Methods for Missing Data.
Description: This package provides hot deck imputation methods to resolve missing data.
Author: Dieter William Joenssen [aut, cre, cph]
Maintainer: Dieter William Joenssen

Diff between HotDeckImputation versions 0.1.0 dated 2013-08-12 and 1.0.0 dated 2014-09-28

 DESCRIPTION                      |   17 ++--
 MD5                              |   26 ++++---
 NAMESPACE                        |    4 -
 NEWS                             |    5 +
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 17 files changed, 171 insertions(+), 150 deletions(-)

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Permanent link

Sat, 27 Sep 2014

Package dendsort updated to version 0.3.1 with previous version 0.2.1 dated 2014-06-17

Title: Modular Leaf Orering Methods for Dendrogram Nodes
Description: This package includes functions to optimize ordering of nodes in a dendrogram, without affecting the meaning of the dendrogram. A dendrogram can be sorted based on the average distance of subtrees, or based on the smallest distance value. These sorting methods improve readability and interpretability of tree structure, especially for tasks such as comparison of different distance measures or linkage types and identification of tight clusters and outliers. As a result, it also introduces more meaningful reordering for a coupled heatmap visualization.
Author: Ryo Sakai
Maintainer: Ryo Sakai

Diff between dendsort versions 0.2.1 dated 2014-06-17 and 0.3.1 dated 2014-09-27

 DESCRIPTION             |   15 +++++++++------
 MD5                     |   42 +++++++++++++++++++++++++-----------------
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Package mrds updated to version 2.1.10 with previous version 2.1.8 dated 2014-09-15

Title: Mark-Recapture Distance Sampling (mrds)
Description: This package implements mark-recapture distance sampling methods as described in D.L. Borchers, W. Zucchini and Fewster, R.M. (1988), "Mark-recapture models for line transect surveys", Biometrics 54: 1207-1220. and Laake, J.L. (1999) "Distance sampling with independent observers: Reducing bias from heterogeneity by weakening the conditional independence assumption." in Amstrup, G.W., Garner, S.C., Laake, J.L., Manly, B.F.J., McDonald, L.L. and Robertson, D.G. (eds) "Marine mammal survey and assessment methods", Balkema, Rotterdam: 137-148 and Borchers, D.L., Laake, J.L., Southwell, C. and Paxton, C.L.G. "Accommodating unmodelled heterogeneity in double-observer distance sampling surveys". 2006. Biometrics 62:372-378.)
Author: Jeff Laake , David Borchers , Len Thomas , David Miller and Jon Bishop
Maintainer: David Miller

Diff between mrds versions 2.1.8 dated 2014-09-15 and 2.1.10 dated 2014-09-27

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More information about mrds at CRAN
Permanent link

New package MetFns with initial version 1.0
Package: MetFns
Type: Package
Title: Analysis of Visual Meteor Data
Version: 1.0
Date: 2014-09-16
Author: Kristina Veljkovic
Maintainer: Kristina Veljkovic
Description: Functions for selection of visual meteor data, calculations of Zenithal Hourly Rate (ZHR) and population index, graphics of ZHR and magnitude distribution
License: GPL-2 | GPL-3
Depends: astroFns, plotrix, graphics, R (>= 2.10)
Packaged: 2014-09-27 12:44:17 UTC; Kiki Moreau
NeedsCompilation: no
Repository: CRAN
Date/Publication: 2014-09-27 16:04:27

More information about MetFns at CRAN
Permanent link

Package readBrukerFlexData updated to version 1.8 with previous version 1.7 dated 2013-08-10

Title: Reads mass spectrometry data in Bruker *flex format
Description: Reads data files acquired by MALDI-TOF MS on Bruker Daltonics machines of the *flex series.
Author: Sebastian Gibb [aut, cre]
Maintainer: Sebastian Gibb

Diff between readBrukerFlexData versions 1.7 dated 2013-08-10 and 1.8 dated 2014-09-27

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Package eHOF updated to version 1.5 with previous version 1.4 dated 2014-04-23

Title: Extended and enhanced Hierarchical Logistic Regression models (so called Huisman-Olff-Fresco models).
Description: Hierarchical logistic species response curves along one-dimensional gradients including no response, monotone, plateau, unimodal and bimodal models.
Author: Florian Jansen, Jari Oksanen
Maintainer: Florian Jansen

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Package trustOptim updated to version 0.8.4.1 with previous version 0.8.3 dated 2013-12-08

Title: Trust region nonlinear optimization, efficient for sparse Hessians
Description: Trust region algorithm for nonlinear optimization. In addition to being more stable and robust than optim, this package includes methods that are scalable and efficient (in terms of both speed and memory usage) when the Hessian is sparse.
Author: Michael Braun
Maintainer: Michael Braun

Diff between trustOptim versions 0.8.3 dated 2013-12-08 and 0.8.4.1 dated 2014-09-27

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Package RVAideMemoire updated to version 0.9-40 with previous version 0.9-39 dated 2014-09-18

Title: Diverse basic statistical and graphical functions
Description: This package contains diverse more or less complicated functions, written to simplify user's life: simplifications of existing functions, basic but not implemented tests, easy-to-use tools, bridges between functions of different packages... All functions are presented in the French book 'Aide-memoire de statistique appliquee a la biologie', written by the same author and available on CRAN.
Author: Maxime Herv
Maintainer: Maxime Herv

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Package propagate updated to version 1.0-4 with previous version 1.0-3 dated 2014-03-03

Title: Propagation of Uncertainty
Description: Propagation of uncertainty using higher-order Taylor expansion and Monte Carlo simulation.
Author: Andrej-Nikolai Spiess
Maintainer: Andrej-Nikolai Spiess

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Package hglm updated to version 2.0-9 with previous version 2.0-8 dated 2014-07-23

Title: Hierarchical Generalized Linear Models
Description: The hglm package is used to fit hierarchical generalized linear models. It can be used for linear mixed models and generalized linear mixed models with random effects for a variety of links and a variety of distributions for both the outcomes and the random effects. Fixed effects can also be fitted in the dispersion part of the mean model.
Author: Xia Shen, Moudud Alam, Lars Ronnegard
Maintainer: Xia Shen

Diff between hglm versions 2.0-8 dated 2014-07-23 and 2.0-9 dated 2014-09-27

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Package BrailleR updated to version 0.11 with previous version 0.9 dated 2014-06-27

Title: Improved access for blind useRs
Description: Blind useRs do not have access to the graphical output from R without printing the content of graph windows to an embosser of some kind. This is not as immediate as is required for efficient access to statistical output. The functions here are created so that blind people can make even better use of R.
Author: A. Jonathan R. Godfrey [aut, cre], Greg Snow [ctb], Paul Murrell [ctb], Yihui Xie [ctb]
Maintainer: A. Jonathan R. Godfrey

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Package Rcmdr updated to version 2.1-2 with previous version 2.1-1 dated 2014-09-04

Title: R Commander
Description: A platform-independent basic-statistics GUI (graphical user interface) for R, based on the tcltk package.
Author: John Fox [aut, cre], Milan Bouchet-Valat [aut], Liviu Andronic [ctb], Michael Ash [ctb], Theophilius Boye [ctb], Stefano Calza [ctb], Andy Chang [ctb], Philippe Grosjean [ctb], Richard Heiberger [ctb], Kosar Karimi Pour [ctb], G. Jay Kerns [ctb], Renaud Lancelot [ctb], Matthieu Lesnoff [ctb], Uwe Ligges [ctb], Samir Messad [ctb], Martin Maechler [ctb], Robert Muenchen [ctb], Duncan Murdoch [ctb], Erich Neuwirth [ctb], Dan Putler [ctb], Brian Ripley [ctb], Miroslav Ristic [ctb], Peter Wolf [ctb], Kevin Wright [ctb]
Maintainer: John Fox

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Package oro.pet updated to version 0.2.3 with previous version 0.2.1 dated 2012-07-20

Title: Rigorous - Positron Emission Tomography
Description: Image analysis techniques for positron emission tomography (PET) that form part of the Rigorous Analytics bundle.
Author: Brandon Whitcher
Maintainer: Brandon Whitcher

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Package jsonlite updated to version 0.9.12 with previous version 0.9.11 dated 2014-09-04

Title: A Robust, High Performance JSON Parser and Generator for R
Description: A fast JSON parser and generator optimized for statistical data and the web. Started out as a fork of RJSONIO, but has been completely rewritten in recent versions. The package offers flexible, robust, high performance tools for working with JSON in R and is particularly powerful for building pipelines and interacting with web APIs. The parser implementation is based on the mapping described in the vignette of the package (Ooms, 2014). In addition to drop-in replacements for toJSON and fromJSON, jsonlite contains functions to stream, validate, and prettify JSON data, and many unit tests to verify that all edge cases are encoded and decoded consistently for use with dynamic data in systems and applications.
Author: Jeroen Ooms, Duncan Temple Lang, Lloyd Hilaiel
Maintainer: Jeroen Ooms

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Fri, 26 Sep 2014

Package mime updated to version 0.2 with previous version 0.1.2 dated 2014-07-25

Title: Map filenames to MIME types
Description: This package guesses the MIME type from a filename extension using the data derived from /etc/mime.types in UNIX-type systems.
Author: Jeffrey Horner [ctb], Yihui Xie [aut, cre]
Maintainer: Yihui Xie

Diff between mime versions 0.1.2 dated 2014-07-25 and 0.2 dated 2014-09-26

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Package alr4 updated to version 1.0.5 with previous version 1.0.3 dated 2013-10-11

Title: Data to accompany Applied Linear Regression 4rd edition
Description: This package is a companion to the textbook S. Weisberg (2014), "Applied Linear Regression," 4rd edition, Wiley. It includes all the data sets discussed in the book and one function to access the textbook's website. This package depends on the car package. Many data files in this package are included in the alr3 package as well, so only one of them should be loaded.
Author: Sanford Weisberg
Maintainer: Sanford Weisberg

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New package oc with initial version 0.95
Package: oc
Version: 0.95
Date: 2014-09-25
Title: OC Roll Call Analysis Software.
Author: Keith Poole , Jeffrey Lewis , James Lo and Royce Carroll
Maintainer: James Lo
Depends: R (>= 2.3.1), pscl (>= 0.59)
Description: Estimates Optimal Classification scores from roll call votes supplied though a 'rollcall' object from package 'pscl'.
License: GPL-2
Repository: CRAN
Date/Publication: 2014-09-26 19:05:36
Packaged: 2014-09-25 23:15:49 UTC; jameslo
NeedsCompilation: yes

More information about oc at CRAN
Permanent link

Package lmSupport updated to version 2.9.1 with previous version 2.09 dated 2014-09-04

Title: Support for Linear Models
Description: Accompanies Markus Brauer, Bas Rokers, and John Curtin's two-course graduate series in General, Generalized, and Multi-level Linear Models (PSY 610/710).
Author: John Curtin
Maintainer: John Curtin

Diff between lmSupport versions 2.09 dated 2014-09-04 and 2.9.1 dated 2014-09-26

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Package jSonarR updated to version 1.1.1 with previous version 1.1 dated 2014-09-03

Title: jSonar Analytics Platform API for R
Description: This package enables users to access MongoDB by running queries and returning their results in R data frames. Usually, data in MongoDB is only available in the form of a JSON document. jSonarR uses data processing and conversion capabilities in the jSonar Analytics Platform and the JSON Studio Gateway (http://www.jsonstudio.com), to convert it to a tabular format which is easy to use with existing R packages.
Author: jSonar Inc.
Maintainer: Dylan McCall

Diff between jSonarR versions 1.1 dated 2014-09-03 and 1.1.1 dated 2014-09-26

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New package Guerry with initial version 1.6-1
Package: Guerry
Type: Package
Title: Maps, data and methods related to Guerry (1833) "Moral Statistics of France"
Version: 1.6-1
Date: 2014-09-26
Authors@R: c(person(given = "Michael", family = "Friendly", role=c("aut", "cre"), email="friendly@yorku.ca"), person(given = "Stephane", family = "Dray", role="aut"))
Author: Michael Friendly [aut, cre], Stephane Dray [aut]
Maintainer: Michael Friendly
Encoding: latin1
Depends: R (>= 2.10)
Suggests: sp, shapefiles, spdep, ade4, maptools
Description: This package comprises maps of France in 1830, multivariate data from A.-M. Guerry and others, and statistical and graphic methods related to Guerry's "Moral Statistics of France". The goal is to facilitate the exploration and development of statistical and graphic methods for multivariate data in a geo-spatial context of historical interest.
License: GPL
URL: http://guerry.r-forge.r-project.org/
LazyLoad: yes
LazyData: yes
Repository: CRAN
Repository/R-Forge/Project: guerry
Repository/R-Forge/Revision: 25
Repository/R-Forge/DateTimeStamp: 2014-09-26 12:11:25
Date/Publication: 2014-09-26 19:03:40
Packaged: 2014-09-26 12:50:09 UTC; rforge
NeedsCompilation: no

More information about Guerry at CRAN
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Package glcm updated to version 1.0 with previous version 0.3.2 dated 2014-07-30

Title: Calculate textures from grey-level co-occurrence matrices (GLCMs) in R
Description: Enables calculation of image textures derived from grey-level co-occurrence matrices (GLCMs) in R. Supports processing images that cannot fit in memory.
Author: Alex Zvoleff [aut, cre]
Maintainer: Alex Zvoleff

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Package cape updated to version 1.3 with previous version 1.2 dated 2013-08-03

Title: Combined analysis of pleiotropy and epistasis
Description: This package combines complementary information across multiple related phenotypes to infer directed epistatic interactions between genetic markers. The analysis in this package can be applied to a variety of engineered and natural populations.
Author: Anna L. Tyler, Wei Lu, Justin J. Hendrick, Vivek M. Philip, and Greg W. Carter
Maintainer: Anna L. Tyler

Diff between cape versions 1.2 dated 2013-08-03 and 1.3 dated 2014-09-26

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Package aplpack updated to version 1.3.0 with previous version 1.2.9 dated 2013-11-05

Title: Another Plot PACKage: stem.leaf, bagplot, faces, spin3R, plotsummary, plothulls, and some slider functions
Description: set of functions for drawing some special plots: stem.leaf plots a stem and leaf plot, stem.leaf.backback plots back-to-back versions of stem and leafs, bagplot plots a bagplot, skyline.hist plots several histgramm in one plot of a one dimensional data set, plotsummary plots a graphical summary of a data set with one or more variables, plothulls plots sequentially hulls of a bivariate data set, faces plots chernoff faces, spin3R for an inspection of a 3-dim point cloud, slider functions for interactive graphics.
Author: Hans Peter Wolf, Uni Bielefeld
Maintainer: Hans Peter Wolf

Diff between aplpack versions 1.2.9 dated 2013-11-05 and 1.3.0 dated 2014-09-26

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New package GenWin with initial version 0.1
Package: GenWin
Title: Spline Based Window Boundaries for Genomic Analyses
Version: 0.1
Date: 9/25/2014
Author: Timothy M. Beissinger
Maintainer: Timothy M. Beissinger
Description: Defines window or bin boundaries for the analysis of genomic data. Boundaries are based on the inflection points of a cubic smoothing spline fitted to the raw data. Along with defining boundaries, a technique to evaluate results obtained from unequally-sized windows is provided. Applications are particularly pertinent for, though not limited to, genome scans for selection based on variability between populations (e.g. using Wright's fixations index, Fst, which measures variability in subpopulations relative to the total population).
Depends: R (>= 3.1.1)
Imports: pspline
License: MIT + file LICENSE
LazyData: true
Packaged: 2014-09-26 13:33:03 UTC; beissinger
NeedsCompilation: no
Repository: CRAN
Date/Publication: 2014-09-26 16:51:09

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Package GENLIB updated to version 1.0.1 with previous version 1.0 dated 2014-09-22

Title: Genealogical Data Analysis
Description: Genealogical data analysis including descriptive statistics (e.g., kinship and inbreeding coefficients) and gene-dropping simulations.
Author: Louis Houde [aut], Jean-Francois Lefebvre [aut], Valery Roy-Lagace [aut], Sebastien Lemieux [aut], Michael J. Fromberger [ctb], Marie-Helene Roy-Gagnon [cre]
Maintainer: Marie-Helene Roy-Gagnon

Diff between GENLIB versions 1.0 dated 2014-09-22 and 1.0.1 dated 2014-09-26

 GENLIB-1.0.1/GENLIB/DESCRIPTION            |   27 +++++++----
 GENLIB-1.0.1/GENLIB/MD5                    |   71 +++++++++++++----------------
 GENLIB-1.0.1/GENLIB/R/fonctionsBase.R      |    2 
 GENLIB-1.0.1/GENLIB/data/geneaJi.rda       |binary
 GENLIB-1.0.1/GENLIB/data/pop140.rda        |binary
 GENLIB-1.0.1/GENLIB/man/GenlibR-package.Rd |    2 
 GENLIB-1.0.1/GENLIB/man/gen.f.Rd           |   10 ++--
 GENLIB-1.0.1/GENLIB/man/gen.fCI.Rd         |    3 -
 GENLIB-1.0.1/GENLIB/man/gen.findMRCA.Rd    |   26 +++-------
 GENLIB-1.0.1/GENLIB/man/gen.phi.Rd         |   12 ----
 GENLIB-1.0.1/GENLIB/man/gen.phiCI.Rd       |   12 ++--
 GENLIB-1.0.1/GENLIB/man/gen.phiMean.Rd     |    9 ++-
 GENLIB-1.0.1/GENLIB/man/gen.phiOver.Rd     |   10 ++--
 GENLIB-1.0.1/GENLIB/src/apparentement.cpp  |   10 ++--
 GENLIB-1.0.1/GENLIB/src/apparentement.h    |    2 
 GENLIB-1.0.1/GENLIB/src/base.h             |    2 
 GENLIB-1.0.1/GENLIB/src/congen.cpp         |    4 -
 GENLIB-1.0.1/GENLIB/src/consanguinite.cpp  |   14 ++---
 GENLIB-1.0.1/GENLIB/src/fondateur.cpp      |   47 +++++++++----------
 GENLIB-1.0.1/GENLIB/src/fondateur.h        |    2 
 GENLIB-1.0.1/GENLIB/src/genphi.cpp         |   21 ++++----
 GENLIB-1.0.1/GENLIB/src/hal.cpp            |    8 +--
 GENLIB-1.0.1/GENLIB/src/hal.h              |    4 +
 GENLIB-1.0.1/GENLIB/src/hashtable.h        |    4 -
 GENLIB-1.0.1/GENLIB/src/interface.cpp      |   26 ++++------
 GENLIB-1.0.1/GENLIB/src/md5.cpp            |    2 
 GENLIB-1.0.1/GENLIB/src/mpi-types.h        |    2 
 GENLIB-1.0.1/GENLIB/src/mpi.c              |    6 +-
 GENLIB-1.0.1/GENLIB/src/outilanal.cpp      |    2 
 GENLIB-1.0.1/GENLIB/src/outils.cpp         |    7 +-
 GENLIB-1.0.1/GENLIB/src/outilsalloc.h      |    7 +-
 GENLIB-1.0.1/GENLIB/src/probsimul.cpp      |   18 ++++---
 GENLIB-1.0.1/GENLIB/src/userInterface.cpp  |   10 ++--
 GENLIB-1.0/GENLIB/src/RInside.h            |only
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 GENLIB-1.0/GENLIB/src/RInsideEnvVars.h     |only
 GENLIB-1.0/GENLIB/src/crtdbg.h             |only
 GENLIB-1.0/GENLIB/src/crtdbg_s.h           |only
 40 files changed, 186 insertions(+), 196 deletions(-)

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Package copBasic updated to version 1.6.0 with previous version 1.5.4 dated 2013-05-10

Title: Basic Theoretical Copula, Empirical Copula, and Various Utility Functions
Description: The package implements extensive functions for copula computations and related mathematical operations oriented around the oft cited and fundamental copula theory described by Nelson (2006). The lower (W), upper (M), product (P), PSP, and Plackett (with parameter estimation) copulas are provided. Individual copula functional support is intentionally limited to keep the package focused on an API to general copula theory. Expressions available for an arbitrary copula include the diagonal of a copula, the survival copula, the dual of a copula, and co-copula. Level curves (sets) are available. Horizontal and vertical copula sections and derivatives of such sections also are supported. The numerical derivatives of a copula are provided as well as inverses, and thus functions for copula simulation also are supported. Composition of copulas is provided: (1) composition of a single copula using two composition parameters, (2) composition of two copulas using two composition parameters, (3) composition of two copulas using four composition parameters, and (4) composite copula random variates. Characteristics of copulas include Kendall Tau, Spearman Rho, Gini Gamma, Blomqvist Beta, and Schweizer-Wolff Sigma. Logical evaluators of positively/negatively quadrant dependency, left-tail decreasing, and right-tail increasing also are available. Quantile and median regression for V with respect to U and U with respect to V is available. Empirical copulas (EC) are supported. ECs are dependent on gridded data structures for which generation capability is provided. The derivatives of the EC grid are computable. Also, the inverses of the derivatives, which are the conditional QDFs of copula sections also are computable. Median and quantile regression of an EC also is supported along with support for EC simulation of V conditional on U.
Author: William Asquith
Maintainer: William Asquith

Diff between copBasic versions 1.5.4 dated 2013-05-10 and 1.6.0 dated 2014-09-26

 ChangeLog                         |   55 +++++-
 DESCRIPTION                       |   60 +------
 MD5                               |  217 +++++++++++++------------
 NAMESPACE                         |    9 +
 R/COP.R                           |    4 
 R/EMPIRcop.R                      |   62 +++++--
 R/EMPIRgrid.R                     |   25 +-
 R/EMPIRgridderinv.R               |    6 
 R/EMPIRgridderinv2.R              |    6 
 R/EMPIRqua.regress.R              |   12 -
 R/EMPIRqua.regress2.R             |   12 -
 R/EMPIRsim.R                      |    6 
 R/M.R                             |   15 +
 R/P.R                             |   17 +
 R/PSP.R                           |   16 +
 R/W.R                             |   17 +
 R/asCOP.R                         |only
 R/coCOP.R                         |    5 
 R/derCOP.R                        |   38 +++-
 R/derCOP2.R                       |   37 +++-
 R/diagCOP.R                       |    8 
 R/duCOP.R                         |    4 
 R/giniCOP.R                       |   16 -
 R/gridCOP.R                       |only
 R/hoefCOP.R                       |only
 R/isCOP.LTD.R                     |   30 +--
 R/isCOP.PQD.R                     |only
 R/isCOP.RTI.R                     |   30 +--
 R/isCOP.radsym.R                  |only
 R/level.curvesCOP.R               |   52 +++++-
 R/level.curvesCOP2.R              |only
 R/level.setCOP.R                  |only
 R/level.setCOP2.R                 |only
 R/med.regressCOP.R                |    5 
 R/med.regressCOP2.R               |    5 
 R/qua.regressCOP.R                |   28 +--
 R/qua.regressCOP.draw.R           |   18 --
 R/qua.regressCOP2.R               |   28 +--
 R/rhoCOP.R                        |   50 ++++-
 R/sectionCOP.R                    |   54 +-----
 R/simCOP.R                        |   36 ++--
 R/simCOPmicro.R                   |    8 
 R/simcomposite3COP.R              |    6 
 R/simcompositeCOP.R               |    8 
 R/surCOP.R                        |    4 
 R/surfuncCOP.R                    |only
 R/taildepCOP.R                    |   45 ++---
 R/tauCOP.R                        |   54 ++++--
 R/wolfCOP.R                       |   30 ++-
 man/COP.Rd                        |   43 +----
 man/COPinv.Rd                     |   45 +----
 man/COPinv2.Rd                    |   27 +--
 man/EMPIRcop.Rd                   |  119 +++++++------
 man/EMPIRcopdf.Rd                 |   41 +---
 man/EMPIRgrid.Rd                  |  197 ++++++++++++-----------
 man/EMPIRgridder.Rd               |   47 ++---
 man/EMPIRgridder2.Rd              |   65 -------
 man/EMPIRgridderinv.Rd            |  123 ++++++--------
 man/EMPIRgridderinv2.Rd           |   14 -
 man/EMPIRmed.regress.Rd           |   13 -
 man/EMPIRmed.regress2.Rd          |   11 -
 man/EMPIRqua.regress.Rd           |  324 ++++++++++++++++----------------------
 man/EMPIRqua.regress2.Rd          |   24 +-
 man/EMPIRsim.Rd                   |   48 ++---
 man/EMPIRsimv.Rd                  |   78 +++++----
 man/M.Rd                          |   23 +-
 man/N4212cop.Rd                   |   31 +--
 man/P.Rd                          |   19 +-
 man/PLACKETTcop.Rd                |   33 +--
 man/PLACKETTpar.Rd                |   39 +---
 man/PLACKETTsim.Rd                |   25 +-
 man/PSP.Rd                        |   21 +-
 man/PlackettPlackettABKGtest.Rd   |   83 +++------
 man/PlackettPlackettNP.Rd         |  118 +++++--------
 man/ReineckeWell266.Rd            |   14 -
 man/ReineckeWells.Rd              |   12 -
 man/W.Rd                          |   23 +-
 man/asCOP.Rd                      |only
 man/blomCOP.Rd                    |   24 +-
 man/coCOP.Rd                      |   64 +++----
 man/composite1COP.Rd              |   49 ++---
 man/composite2COP.Rd              |   93 ++++++----
 man/composite3COP.Rd              |   98 +++++------
 man/copBasic-package.Rd           |only
 man/derCOP.Rd                     |   82 ++++-----
 man/derCOP2.Rd                    |   74 ++++----
 man/derCOPinv.Rd                  |   69 +++-----
 man/derCOPinv2.Rd                 |   68 +++----
 man/diagCOP.Rd                    |   30 +--
 man/duCOP.Rd                      |   48 +++--
 man/giniCOP.Rd                    |   62 ++++---
 man/gridCOP.Rd                    |only
 man/hoefCOP.Rd                    |only
 man/isCOP.LTD.Rd                  |   53 ++----
 man/isCOP.PQD.Rd                  |only
 man/isCOP.RTI.Rd                  |   57 ++----
 man/isCOP.radsym.Rd               |only
 man/lcomoms2.ABKGcop2parameter.Rd |   60 +++----
 man/lcomoms2.ABcop2parameter.Rd   |   62 +++----
 man/level.curvesCOP.Rd            |   32 ++-
 man/level.curvesCOP2.Rd           |only
 man/level.setCOP.Rd               |only
 man/level.setCOP2.Rd              |only
 man/med.regressCOP.Rd             |   63 +++----
 man/med.regressCOP2.Rd            |   34 +--
 man/qua.regressCOP.Rd             |  109 ++++--------
 man/qua.regressCOP.draw.Rd        |   24 +-
 man/qua.regressCOP2.Rd            |   58 +-----
 man/rhoCOP.Rd                     |   66 +++----
 man/sectionCOP.Rd                 |  121 +++++++-------
 man/simCOP.Rd                     |   48 ++---
 man/simCOPmicro.Rd                |   30 +--
 man/simcomposite3COP.Rd           |   86 ++++------
 man/simcompositeCOP.Rd            |   56 +++---
 man/surCOP.Rd                     |   65 +++----
 man/surfuncCOP.Rd                 |only
 man/taildepCOP.Rd                 |   92 +++++-----
 man/tauCOP.Rd                     |  130 ++++++---------
 man/wolfCOP.Rd                    |   74 ++++++--
 119 files changed, 2429 insertions(+), 2450 deletions(-)

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Package snpEnrichment updated to version 1.5-0 with previous version 1.4-1 dated 2014-09-11

Title: SNPs enrichment analysis
Description: Implements classes and methods for large scale SNP enrichment analysis (e.g. SNPs associated with genes expression in a GWAS signal)
Author: Mickael Canouil [aut, cre], Loic Yengo [ctb]
Maintainer: Mickael Canouil

Diff between snpEnrichment versions 1.4-1 dated 2014-09-11 and 1.5-0 dated 2014-09-26

 ChangeLog                    |   18 ++++++++++++++++
 DESCRIPTION                  |   10 ++++-----
 MD5                          |   22 +++++++++++---------
 R/Global.R                   |    6 +++--
 R/enrichment.R               |    3 ++
 README.md                    |only
 inst/example.R               |only
 man/Enrichment-class.Rd      |    4 +--
 man/compareEnrichment.Rd     |   13 +++++++-----
 man/excludeSNP-methods.Rd    |    7 ++++--
 man/readEnrichment.Rd        |    3 --
 man/snpEnrichment-package.Rd |   46 ++++++++++++++++++++++++-------------------
 man/writeLD.Rd               |    2 -
 13 files changed, 84 insertions(+), 50 deletions(-)

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Package iC10TrainingData updated to version 1.0.1 with previous version 1.0.0 dated 2014-06-18

Title: Training datasets for iC10 package.
Description: Training datasets for iC10; which implements the classifier described in the paper 'Genome-driven integrated classification of breast cancer validated in over 7,500 samples' (Ali HR et al., Genome Biology 2014). It uses copy number and/or expression form breast cancer data, trains a pamr classifier (Tibshirani et al.) with the features available and predicts the iC10 group. Genomic annotation for the training dataset has been obtained from Mark Dunning's lluminaHumanv3.db package.
Author: Oscar M Rueda
Maintainer: Oscar M. Rueda

Diff between iC10TrainingData versions 1.0.0 dated 2014-06-18 and 1.0.1 dated 2014-09-26

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

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Package iC10 updated to version 1.1.1 with previous version 1.0.2 dated 2014-06-19

Title: A copy number and expression-based classifier for breast tumours.
Description: iC10 implements the classifier described in the paper 'Genome-driven integrated classification of breast cancer validated in over 7,500 samples' (Ali HR et al., Genome Biology 2014). It uses copy number and/or expression form breast cancer data, trains a pamr classifier (Tibshirani et al.) with the features available and predicts the iC10 group.
Author: Oscar M Rueda
Maintainer: Oscar M. Rueda

Diff between iC10 versions 1.0.2 dated 2014-06-19 and 1.1.1 dated 2014-09-26

 DESCRIPTION              |   12 +++++-----
 MD5                      |   30 +++++++++++++--------------
 NAMESPACE                |    2 -
 NEWS                     |    5 ++++
 R/getCNfeatures.R        |    4 +--
 R/goodnessOfFit.R        |    2 -
 R/normalizeFeatures.R    |   52 ++++++++++++++++++++++++++++-------------------
 man/compare.Rd           |    6 +++--
 man/goodnessOfFit.Rd     |    8 ++++---
 man/iC10-package.Rd      |    4 ++-
 man/iC10.Rd              |    6 +++--
 man/matchFeatures.Rd     |   13 ++++++++---
 man/normalizeFeatures.Rd |   23 +++++---------------
 man/plot.iC10.Rd         |   18 +++++++++-------
 man/print.iC10.Rd        |    4 ++-
 man/summary.iC10.Rd      |    8 ++++---
 16 files changed, 111 insertions(+), 86 deletions(-)

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Package postCP (with last version 1.7.2) was removed from CRAN

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

2013-12-11 1.7.2
2013-07-01 1.7.0
2013-04-04 1.6.4
2013-01-31 1.6.3
2012-12-21 1.6.2
2012-10-26 1.6.1
2012-10-23 1.6.0
2012-02-15 1.05
2012-02-10 1.0

Permanent link
Package CONORData (with last version 1.0.2) was removed from CRAN

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

2012-10-02 1.0.2

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Package CONOR (with last version 1.0.2) was removed from CRAN

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

2013-05-06 1.0.2

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Package MAT updated to version 2.0 with previous version 0.1-3 dated 2011-01-26

Title: Multidimensional Adaptive Testing
Description: Simulate Multidimensional Adaptive Testing
Author: Seung W. Choi and David R. King
Maintainer: Seung W. Choi

Diff between MAT versions 0.1-3 dated 2011-01-26 and 2.0 dated 2014-09-26

 MAT-0.1-3/MAT/R/calcFI.R        |only
 MAT-0.1-3/MAT/R/calcHessian.R   |only
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 MAT-0.1-3/MAT/R/score.R         |only
 MAT-0.1-3/MAT/R/score_1.R       |only
 MAT-2.0/MAT/DESCRIPTION         |   19 +--
 MAT-2.0/MAT/MD5                 |only
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 MAT-2.0/MAT/R/MAT.R             |  246 ++++++++++++++++++++--------------------
 MAT-2.0/MAT/R/RcppExports.R     |only
 MAT-2.0/MAT/man/MAT-internal.Rd |only
 MAT-2.0/MAT/man/MAT-package.Rd  |    4 
 MAT-2.0/MAT/man/MAT.Rd          |    3 
 MAT-2.0/MAT/man/sample.ipar.Rd  |    2 
 MAT-2.0/MAT/man/simM3PL.Rd      |    2 
 MAT-2.0/MAT/src                 |only
 18 files changed, 147 insertions(+), 134 deletions(-)

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New package ADDT with initial version 1.0
Package: ADDT
Type: Package
Title: A Package for Analysis of Accelerated Destructive Degradation Test Data
Version: 1.0
Date: 2014-09-23
Author: Yili Hong, Yimeng Xie, and Caleb King
Maintainer: Yili Hong
Description: Accelerated destructive degradation tests (ADDT) are often used to collect necessary data for assessing the long-term properties of polymeric materials. Based on the collected data, a thermal index (TI) is estimated. The TI can be useful for material rating and comparison. This package performs the least squares (LS) and maximum likelihood (ML) procedures for estimating TI for polymeric materials. The LS approach is a two-step approach that is currently used in industrial standards, while the ML procedure is widely used in the statistical literature. The ML approach allows one to do statistical inference such as quantifying uncertainties in estimation, hypothesis testing, and predictions. Two publicly available datasets are provided to allow users to experiment and practice with the functions.
License: GPL-2
Packaged: 2014-09-25 23:57:12 UTC; Yili Hong
NeedsCompilation: no
Repository: CRAN
Date/Publication: 2014-09-26 07:55:35

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