Fri, 30 May 2014

New package transport with initial version 0.6-1
Package: transport
Type: Package
Title: Optimal transport in various forms
Version: 0.6-1
Date: 2014-05-30
Author: Dominic Schuhmacher with substantial contributions of code by Bjoern Baehre and Carsten Gottschlich
Maintainer: Dominic Schuhmacher
Depends: R (>= 3.0.0), utils, grDevices, graphics, stats
Description: Solve optimal transport problems in statistics. Compute Wasserstein metrics (a.k.a. Kantorovitch, Fortet--Mourier, Mallows, Earth Mover's, or minimal L_p metrics), return the corresponding transference plans, and display them graphically. Objects that can be compared include grey-scale images, point patterns, and mass vectors.
License: GPL (>= 2)
URL: http://www.dominic.schuhmacher.name
LazyData: yes
Packaged: 2014-05-30 20:11:11 UTC; schumi
NeedsCompilation: yes
Repository: CRAN
Date/Publication: 2014-05-31 01:29:01

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Package ripa updated to version 2.0-2 with previous version 2.0-1 dated 2014-05-14

Title: R Image Processing and Analysis
Description: A package including various functions for image processing and analysis. With this package is possible to process and analyse RGB, LAN (multispectral) and AVIRIS (hyperspectral) images. This packages also provides functions for reading JPEG files, extracted from the archived 'rimage' package.
Author: Talita Perciano [aut, cre], Alejandro C Frery [ctb]
Maintainer: Talita Perciano

Diff between ripa versions 2.0-1 dated 2014-05-14 and 2.0-2 dated 2014-05-30

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Package rplotengine updated to version 1.0-5 with previous version 1.0-3 dated 2012-11-03

Title: R as a plotting engine
Description: This package is intended for using R as a plotting engine either by custom applications, or from a small script launched from the system console, or even within the R console. Two ASCII text files are necessary: (1) The graph parameters file, which name is passed to the function 'rplotengine()'. The user can specify the titles, choose the type of the graph, graph output formats (e.g. png, eps), proportion of the X-axis and Y-axis, position of the legend, whether to show or not a grid at the background, etc. (2) The data to be plotted, which name is specified as a parameter ('data_filename') in the previous file. This data file has a tabulated format, with a single character (e.g. tab) between each column, and a headers line located in the first row. Optionally, the file could include data columns for showing confidence intervals.
Author: Pedro-Pablo Garrido Abenza [aut, cre]
Maintainer: Pedro-Pablo Garrido Abenza

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Package qdapDictionaries updated to version 1.0.1 with previous version 0.0.4 dated 2014-04-24

Title: Dictionaries and word lists for the qdap package.
Description: This package is a collection of dictionaries and word lists for use with the qdap package.
Author: Tyler Rinker
Maintainer: Tyler Rinker

Diff between qdapDictionaries versions 0.0.4 dated 2014-04-24 and 1.0.1 dated 2014-05-30

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New package IsoCI with initial version 1.0
Package: IsoCI
Type: Package
Title: Transformed and bootstrap confidence intervals for current status data
Version: 1.0
Date: 2014-05-30
Author: Byeong Yeob Choi, Jason P. Fine and M. Alan Brookhart
Maintainer: Byeong Yeob Choi
Description: This packages calculated transformed Wald-type confidence intervals, bootstrap confidence intervals, bootstrap-Wald confidence intervals for current status data
Depends: R(>= 2.13.1), KernSmooth
License: GPL (>= 2)
Packaged: 2014-05-30 20:13:18 UTC; bychoi
NeedsCompilation: no
Repository: CRAN
Date/Publication: 2014-05-31 01:42:26

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Package birch (with last version 1.2-3) was removed from CRAN

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

2012-05-04 1.2-3
2012-04-30 1.2-2
2012-03-30 1.2-1
2011-09-16 1.2
2008-02-27 1.1-3
2008-02-24 1.1-2

Permanent link
Package pipeR (with last version 0.2-3) was removed from CRAN

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

2014-05-30 0.2-3

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Package steepness (with last version 0.2-1) was removed from CRAN

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

2014-05-22 0.2-1

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Package RcmdrPlugin.steepness (with last version 0.3-1) was removed from CRAN

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

2014-05-22 0.3-1

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Package HiDimDA (with last version 0.2-1) was removed from CRAN

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

2012-07-08 0.2-1
2012-06-29 0.2-0
2011-06-15 0.1-1
2011-04-26 0.1-0

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Package TBEST updated to version 3.0 with previous version 1.4 dated 2014-02-24

Title: Tree Branches Evaluated Statistically for Tightness
Description: Our method introduces mathematically well-defined measures for tightness of branches in a hierarchical tree. Statistical significance of the findings is determined, for all branches of the tree, by performing permutation tests, optionally with generalized Pareto p-value estimation.
Author: Guoli Sun, Alex Krasnitz
Maintainer: Guoli Sun

Diff between TBEST versions 1.4 dated 2014-02-24 and 3.0 dated 2014-05-30

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Package SensitivityCaseControl updated to version 2.1 with previous version 1.0 dated 2012-11-08

Title: Sensitivity Analysis for Case-Control Studies
Description: This package performs sensitivity analysis for case-control studies in which some cases may meet a more narrow definition of being a case compared to other cases which only meet a broad definition. The sensitivity analyses are described in Small, Cheng, Halloran and Rosenbaum (2013, "Case Definition and Sensitivity Analysis", Journal of the American Statistical Association, 1457-1468). The functions sens.analysis.mh and sens.analysis.aberrant.rank provide sensitivity analyses based on the Mantel-Haenszel test statistic and aberrant rank test statistic as described in Rosenbaum (1991, "Sensitivity Analysis for Matched Case Control Studies", Biometrics); see also Section 1 of Small et al. The function adaptive.case.test provides adaptive inferences as described in Section 5 of Small et al. The function adaptive.noether.brown provides a sensitivity analysis for a matched cohort study based on an adaptive test. The other functions in the package are internal functions.
Author: Dylan Small
Maintainer: Dylan Small

Diff between SensitivityCaseControl versions 1.0 dated 2012-11-08 and 2.1 dated 2014-05-30

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New package qcr with initial version 0.1-18
Package: qcr
Type: Package
Title: Quality control and reliability
Version: 0.1-18
Date: 2014-05-30
Author: Miguel Flores , Salvador Naya , Ruben Fernandez
Maintainer: Miguel Flores
Depends: R (>= 1.8.0), qcc
Suggests: IQCC
Description: This package allows to generate Shewhart-type charts and to obtain numerical results of interest to the quality control of a process (involving continuous, attribute or count data). This package provides basic functionality for univariable and multivariable quality control analysis, including: xbar, xbar-one, S, R, ewna, cusum, mewna, mcusum and T2 charts.
License: GPL (>= 2)
LazyData: yes
Packaged: 2014-05-30 18:10:15 UTC; MIGUEL FLORES
NeedsCompilation: no
Repository: CRAN
Date/Publication: 2014-05-30 21:11:18

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New package pipeR with initial version 0.2-3
Package: pipeR
Type: Package
Title: Pipeline operators for R
Description: Provides operators for chaining commands with various forward-piping mechanisms: first-argument piping, free piping, and lambda piping.
Version: 0.2-3
Date: 2014-05-28
Author: Kun Ren
Maintainer: Kun Ren
Suggests: dplyr
Enhances: magrittr
License: MIT
Packaged: 2014-05-30 16:05:32 UTC; Ken
NeedsCompilation: no
Repository: CRAN
Date/Publication: 2014-05-30 21:11:16

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Package OjaNP updated to version 0.9-7 with previous version 0.9-6 dated 2013-03-20

Title: Multivariate Methods Based on the Oja Median and Related Concepts
Description: The package provides functions for the Oja median, Oja signs and ranks and methods based upon them.
Author: Daniel Fischer, Jyrki Möttönen, Klaus Nordhausen, Daniel Vogel
Maintainer: Klaus Nordhausen

Diff between OjaNP versions 0.9-6 dated 2013-03-20 and 0.9-7 dated 2014-05-30

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Package mstate updated to version 0.2.7 with previous version 0.2.6 dated 2011-01-03

Title: Data preparation, estimation and prediction in multi-state models
Description: Functions for data preparation, descriptives, hazard estimation and prediction with Aalen-Johansen or simulation in competing risks and multi-state models
Author: Hein Putter, Liesbeth de Wreede, Marta Fiocco
Maintainer: Hein Putter

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Package IBDsim updated to version 0.9-4 with previous version 0.9-3 dated 2014-05-29

Title: Simulation of chromosomal regions shared by family members.
Description: R package for simulation of IBD sharing among family members. Using sex specific recombination rates from the Decode map (2010) of the human genome, phased chromosomes are simulated for all pedigree members, either by unconditional 'gene dropping' or conditional on a specified IBD pattern. Regions compatible with the query IBD pattern (possibly different from the conditional pattern) are subsequently detected and summarized.
Author: Magnus Dehli Vigeland
Maintainer: Magnus Dehli Vigeland

Diff between IBDsim versions 0.9-3 dated 2014-05-29 and 0.9-4 dated 2014-05-30

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Package stm updated to version 0.6.16 with previous version 0.6.12 dated 2014-05-14

Title: Estimation of the Structural Topic Model
Description: The Structural Topic Model (STM) allows researchers to estimate topic models with document-level covariates. The package also includes tools for model selection, visualization, and estimation of topic-covariate regressions.
Author: Margaret E. Roberts, Brandon M. Stewart and Dustin Tingley
Maintainer: Brandon Stewart

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Package sirt updated to version 0.45-23 with previous version 0.44-48 dated 2014-04-27

Title: Supplementary Item Response Theory Models
Description: Supplementary item response theory models to complement existing functions in R.
Author: Alexander Robitzsch
Maintainer: Alexander Robitzsch

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Package R2jags updated to version 0.04-02 with previous version 0.04-01 dated 2014-02-26

Title: A Package for Running jags from R
Description: Using this package to call jags from R.
Author: Yu-Sung Su , Masanao Yajima ,
Maintainer: Yu-Sung Su

Diff between R2jags versions 0.04-01 dated 2014-02-26 and 0.04-02 dated 2014-05-30

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Package geomorph updated to version 2.1 with previous version 2.0.1 dated 2014-04-18

Title: Geometric morphometric analyses of 2d/3d landmark data
Description: Read, manipulate, and digitize landmark data, generate shape variables via Procrustes analysis for points, curves and surfaces, perform shape analyses, and provide graphical depictions of shapes and patterns of shape variation
Author: Dean Adams, Michael Collyer, Erik Otarola-Castillo, Emma Sherratt
Maintainer: Dean Adams

Diff between geomorph versions 2.0.1 dated 2014-04-18 and 2.1 dated 2014-05-30

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Package stsm updated to version 1.3 with previous version 1.2 dated 2014-01-27

Title: Structural Time Series Models
Description: This package provides algorithms to fit structural time series models by maximum likelihood.
Author: Javier López-de-Lacalle
Maintainer: Javier López-de-Lacalle

Diff between stsm versions 1.2 dated 2014-01-27 and 1.3 dated 2014-05-30

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Package sparr updated to version 0.3-5 with previous version 0.3-4 dated 2013-12-10

Title: The sparr package: SPAtial Relative Risk
Description: Provides functions to estimate kernel-smoothed relative risk functions and perform subsequent inference.
Author: T.M. Davies, M.L. Hazelton and J.C. Marshall
Maintainer: Tilman M. Davies

Diff between sparr versions 0.3-4 dated 2013-12-10 and 0.3-5 dated 2014-05-30

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Package party updated to version 1.0-14 with previous version 1.0-13 dated 2014-02-01

Title: A Laboratory for Recursive Partytioning
Description: A computational toolbox for recursive partitioning. The core of the package is ctree(), an implementation of conditional inference trees which embed tree-structured regression models into a well defined theory of conditional inference procedures. This non-parametric class of regression trees is applicable to all kinds of regression problems, including nominal, ordinal, numeric, censored as well as multivariate response variables and arbitrary measurement scales of the covariates. Based on conditional inference trees, cforest() provides an implementation of Breiman's random forests. The function mob() implements an algorithm for recursive partitioning based on parametric models (e.g. linear models, GLMs or survival regression) employing parameter instability tests for split selection. Extensible functionality for visualizing tree-structured regression models is available.
Author: Torsten Hothorn [aut, cre], Kurt Hornik [aut], Carolin Strobl [aut], Achim Zeileis [aut]
Maintainer: Torsten Hothorn

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Package NbClust updated to version 2.0 with previous version 1.4 dated 2013-08-17

Title: NbClust package for determining the best number of clusters
Description: NbClust package provides 30 indices for determining the optimal number of clusters in a dataset.
Author: Malika Charrad and Nadia Ghazzali and Veronique Boiteau and Azam Niknafs
Maintainer: Malika Charrad

Diff between NbClust versions 1.4 dated 2013-08-17 and 2.0 dated 2014-05-30

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New package NormPsy with initial version 1.0.1
Package: NormPsy
Type: Package
Title: Normalisation of psychometric tests
Version: 1.0.1
Date: 2014-05-28
Author: Cecile Proust-Lima, Viviane Philipps
Maintainer: Cecile Proust-Lima
Description: This package provides functions for normalizing psychometric test scores. The normalization aims at correcting the metrological properties of the psychometric tests such as the ceiling and floor effects and the curvilinearity (unequal interval scaling). The package also provides functions to compute and plot predictions in the natural scale of the psychometric test from the estimates of a linear mixed model estimated on the normalized scores.
License: GPL
Depends: R (>= 2.9.0)
Imports: lcmm (>= 1.6.4)
Packaged: 2014-05-30 08:49:11 UTC; vp3
NeedsCompilation: yes
Repository: CRAN
Date/Publication: 2014-05-30 16:22:15

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Package mvSLOUCH updated to version 1.1.1 with previous version 1.1 dated 2013-12-27

Title: MultiVariate Stochastic Linear Ornstein-Uhlenbeck models for phylogenetic Comparative hypotHeses
Description: Fits multivariate Ornstein-Uhlenbeck types of models to continues trait data from species related by a common evolutionary history.
Author: Krzysztof Bartoszek
Maintainer: Krzysztof Bartoszek

Diff between mvSLOUCH versions 1.1 dated 2013-12-27 and 1.1.1 dated 2014-05-30

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Package interventionalDBN updated to version 1.2.2 with previous version 1.2.1 dated 2014-05-29

Title: Interventional Inference for Dynamic Bayesian Networks
Description: This package allows a dynamic Bayesian network to be inferred from microarray timecourse data with interventions (inhibitors).
Author: Simon Spencer
Maintainer: Simon Spencer

Diff between interventionalDBN versions 1.2.1 dated 2014-05-29 and 1.2.2 dated 2014-05-30

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Package RSGHB updated to version 1.0.2 with previous version 1.0.1 dated 2013-04-10

Title: Functions for Hierarchical Bayesian Estimation: A Flexible Approach
Description: This package can be used to estimate models using a hierarchical Bayesian framework. The flexibility comes in allowing the user to specify the likelihood function directly instead of assuming predetermined model structures. Types of models that can be estimated with this code include the family of discrete choice models (Multinomial Logit, Mixed Logit, Nested Logit, Error Components Logit and Latent Class) as well ordered response models like ordered probit and ordered logit. In addition, the package allows for flexibility in specifying parameters as either fixed (non-varying across individuals) or random with continuous distributions. Parameter distributions supported include normal, positive/negative log-normal, positive/negative censored normal, and the Johnson SB distribution. Kenneth Train's Matlab and Gauss code for doing hierarchical Bayesian estimation has served as the basis for a few of the functions included in this package. These Matlab/Gauss functions have been rewritten to be optimized within R. Considerable code has been added to increase the flexibility and usability of the code base. Train's original Gauss and Matlab code can be found here: http://elsa.berkeley.edu/Software/abstracts/train1006mxlhb.html See Train's chapter on HB in Discrete Choice with Simulation here: http://elsa.berkeley.edu/books/choice2.html; and his paper on using HB with non-normal distributions here: http://elsa.berkeley.edu/~train/trainsonnier.pdf
Author: Jeff Dumont , Jeff Keller , Chase Carpenter
Maintainer: Jeff Dumont

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New package rsdepth with initial version 0.1-4
Package: rsdepth
Type: Package
Title: Ray Shooting Depth (i.e. RS Depth) functions for bivariate analysis
Version: 0.1-4
Date: 2014-05-29
Author: Nabil Mustafa , Saurabh Ray , Mudassir Shabbir .
Maintainer: Mudassir Shabbir
Description: Ray Shooting Depth functions are provided for bivariate analysis.
Depends: R (>= 2.4.0)
License: GPL-2
Packaged: 2014-05-30 08:07:57 UTC; mudassir
NeedsCompilation: yes
Repository: CRAN
Date/Publication: 2014-05-30 10:21:11

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Package mcprofile updated to version 0.2-0 with previous version 0.1-7 dated 2013-09-10

Title: Multiple Contrast Profiles
Description: Calculation of signed root deviance profiles for linear combinations of parameters in a generalized linear model. Multiple tests and simultaneous confidence intervals are provided.
Author: Daniel Gerhard
Maintainer: Daniel Gerhard

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Package wsrf updated to version 1.4.0 with previous version 1.3.0 dated 2014-02-09

Title: Weighted Subspace Random Forest
Description: The wsrf package is a parallel implementation of the Weighted Subspace Random Forest algorithm proposed (wsrf). A novel variable weighting method is used for variable subspace selection in place of the traditional approach of random variable sampling. This new approach is particularly useful in building models for high dimensional data---often consisting of thousands of variables. Parallel computation is used to take advantage of multi-core machines and clusters of machines to build random forest models from high dimensional data with reduced elapsed times.
Author: Qinghan Meng [aut], He Zhao [aut, cre], Graham Williams [aut], Junchao Lv [ctb]
Maintainer: He Zhao

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Package swirl updated to version 2.2.9 with previous version 2.2.6 dated 2014-05-10

Title: Statistics with Interactive R Learning
Description: swirl turns the R console into an interactive learning environment. Users receive immediate feedback as they are guided through self-paced lessons in data science and R programming.
Author: Nick Carchedi [aut, cre], Bill Bauer [aut], Gina Grdina [aut], Sean Kross [aut]
Maintainer: Nick Carchedi

Diff between swirl versions 2.2.6 dated 2014-05-10 and 2.2.9 dated 2014-05-30

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Package glmmLasso updated to version 1.3.0 with previous version 1.2.2 dated 2013-11-18

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

Diff between glmmLasso versions 1.2.2 dated 2013-11-18 and 1.3.0 dated 2014-05-30

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