Fri, 28 Mar 2014

Package InterVA4 updated to version 1.2 with previous version 1.1 dated 2014-02-05

Title: Replicate and analyse InterVA4
Description: The package provides an R version of the InterVA4 software for coding cause of death from verbal autopsies. It also provides simple graphical representation of individual and population level statistics.
Author: Zehang Li, Tyler McCormick, Sam Clark
Maintainer: Zehang Li

Diff between InterVA4 versions 1.1 dated 2014-02-05 and 1.2 dated 2014-03-28

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New package pdmod with initial version 1.0
Package: pdmod
Type: Package
Title: Proximal/distal modeling framework for Pavlovian conditioning phenomena
Version: 1.0
Date: 2014-03-28
Author: Chloe Bracis
Maintainer: Chloe Bracis
Imports: mco,stats
Depends:
Suggests: RUnit
Description: This package provides a model of Pavlovian conditioning phenomena, such as response extinction and spontaneous recovery, and partial reinforcement extinction effects. Competing proximal and distal reward predictions, computed using fast and slow learning rates, combine according to their uncertainties and the recency of information. The resulting mean prediction drives the response rate.
License: GPL (>= 2)
Packaged: 2014-03-28 17:22:36 UTC; chloe
NeedsCompilation: yes
Repository: CRAN
Date/Publication: 2014-03-28 19:37:19

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Package SpatialVx updated to version 0.2-0 with previous version 0.1-9 dated 2014-01-30

Title: Spatial Forecast Verification
Description: Functions to perform spatial forecast verification
Author: Eric Gilleland
Maintainer: Eric Gilleland

Diff between SpatialVx versions 0.1-9 dated 2014-01-30 and 0.2-0 dated 2014-03-28

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Package questionr updated to version 0.4 with previous version 0.3.1 dated 2013-12-02

Title: Functions to make surveys processing easier.
Description: This package provides some convenience functions to make the processing and analysis of surveys easier.
Author: Julien Barnier [aut, cre], François Briatte [aut], Joseph Larmarange [aut]
Maintainer: Julien Barnier

Diff between questionr versions 0.3.1 dated 2013-12-02 and 0.4 dated 2014-03-28

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Package nat updated to version 1.4.5 with previous version 1.0.1 dated 2014-02-07

Title: nat: NeuroAnatomy Toolbox for Analysis of 3D Image Data
Description: This package is a reboot of the AnalysisSuite (https://github.com/jefferis/AnalysisSuite) bundle of R code that I have been using for a number of years to analyse and visualise 3D biological image data, especially traced neurons. AnalysisSuite is most easily installed using the nat.as package presently available at https://github.com/jefferis/nat.as. The nat package is considerably cleaner but currently provides only a subset of the full functionality of nat.as / AnalysisSuite. nat can read and write 3D images in NRRD and Amira formats and read surfaces in Amira's hxsurf format. Traced neurons can be imported from and written to SWC and Amira LineSet and SkeletonGraph formats. These data can then be visualised in 3D via rgl, manipulated including applying calculated registrations, e.g. using the CMTK registration suite, and analysed. The package also has a simple representation for neurons that have been subjected to a 3D skeletonisation but not formally traced; this allows morphological comparison between neurons including searches and clustering.
Author: Greg Jefferis with contributions from Ashley Manton
Maintainer: Greg Jefferis

Diff between nat versions 1.0.1 dated 2014-02-07 and 1.4.5 dated 2014-03-28

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New package MMMS with initial version 0.1
Package: MMMS
Type: Package
Title: Multi-Marker Molecular Signature for Treatment-specific Subgroup Identification
Version: 0.1
Date: 2014-03-18
Author: Lin Li, Tobias Guennel,Scott Marshall, Leo Wang-Kit Cheung
Maintainer: Lin Li
Description: The package implements a multi-marker molecular signature (MMMS) approach for treatment-specific subgroup identification.
Reference: Lin Li, Tobias Guennel,Scott Marshall, Leo Wang-Kit Cheung (2014) A multi-marker molecular signature approach for treatment-specific subgroup identification with survival outcomes. The Pharmacogenomics Journal, http://dx.doi.org/10.1038/tpj.2014.9
License: GPL-3
Depends: survival, glmnet
Packaged: 2014-03-28 15:22:29 UTC; lli
NeedsCompilation: no
Repository: CRAN
Date/Publication: 2014-03-28 17:27:21

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New package gfcanalysis with initial version 1.1
Package: gfcanalysis
Version: 1.1
Date: 2014-03-28
Title: Tools for working with Hansen et al. 2013 Global Forest Change dataset
Authors@R: c(person("Alex", "Zvoleff", email="azvoleff@conservation.org", role=c("aut", "cre")))
Maintainer: Alex Zvoleff
Depends: R (>= 2.10.0), raster, methods
Imports: rgdal, geosphere, RCurl, rgeos, plyr, ggplot2, grid, sp, stringr, animation, rasterVis
Enhances: snow
Description: The gfcanalysis package supports analyses using the Global Forest Change dataset released by Hansen et al. 2013. gfcanalysis was written by the Tropical Ecology Assessment and Monitoring (TEAM) Network (http://www.teamnetwork.org). For additional details on the Global Forest Change dataset, see: Hansen, M. et al. 2013. "High-Resolution Global Maps of 21st-Century Forest Cover Change." Science 342 (15 November): 850-53. Data available on-line from: http://earthenginepartners.appspot.com/science-2013-global-forest
License: GPL (>= 3)
URL: http://azvoleff.com/gfcanalysis
BugReports: https://github.com/azvoleff/gfcanalysis/issues
LazyData: true
Packaged: 2014-03-28 15:19:41 UTC; azvoleff
Author: Alex Zvoleff [aut, cre]
NeedsCompilation: no
Repository: CRAN
Date/Publication: 2014-03-28 17:27:23

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Package egcm updated to version 1.0.2 with previous version 1.0.1 dated 2014-01-30

Title: Engle-Granger cointegration models
Description: This package provides an easy-to-use implementation of the Engle-Granger two-step procedure for identifying pairs of cointegrated series. It is geared towards the analysis of pairs of securities. Summary and plot functions are provided, and the package is able to fetch closing prices of securities from Yahoo. A variety of unit root tests are supported, and an improved unit root test is included.
Author: Matthew Clegg
Maintainer: Matthew Clegg

Diff between egcm versions 1.0.1 dated 2014-01-30 and 1.0.2 dated 2014-03-28

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Package fanovaGraph updated to version 1.4.7 with previous version 1.4.6 dated 2014-02-27

Title: Building Kriging models from FANOVA graphs
Description: Estimation and plotting of a function's FANOVA graph to identify the interaction structure and fitting, prediction and simulation of a kriging model modified by the identified structure. The interactive function plotManipulate can only be run on the RStudio IDE with RStudio's package manipulate loaded. RStudio is freely available (www.rstudio.org), and includes package manipulate. The equivalent function plotTk bases on CRAN Repository packages only.
Author: Jana Fruth, Thomas Muehlenstaedt, Olivier Roustant, Malte Jastrow
Maintainer: Jana Fruth

Diff between fanovaGraph versions 1.4.6 dated 2014-02-27 and 1.4.7 dated 2014-03-28

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Package iterpc (with last version 0.2) was removed from CRAN

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

2014-03-28 0.2

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Package simMSM updated to version 1.0.1 with previous version 1.0 dated 2013-06-05

Title: Simulation of event histories based on nonlinear hazard rate functions and potentially nonlinear covariate effects.
Description: This package provides R functions for simulation of event histories with nonlinear baseline hazard rate functions and nonlinear covariate effects using inversion sampling on all-cause hazard rate functions.
Author: Holger Reulen
Maintainer: Holger Reulen

Diff between simMSM versions 1.0 dated 2013-06-05 and 1.0.1 dated 2014-03-28

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Package R2MLwiN updated to version 0.2-0 with previous version 0.1-9 dated 2014-03-10

Title: Running MLwiN from within R
Description: R2MLwiN is an R command interface to the MLwiN multilevel modelling software package, allowing users to fit multilevel models using MLwiN from within the R environment.
Author: Zhengzheng Zhang [aut, cre], Chris Charlton [aut], Richard Parker [aut], George Leckie [aut], William Browne [aut]
Maintainer: Zhengzheng Zhang

Diff between R2MLwiN versions 0.1-9 dated 2014-03-10 and 0.2-0 dated 2014-03-28

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Package pks updated to version 0.3-0 with previous version 0.2-1 dated 2013-06-10

Title: Probabilistic Knowledge Structures
Description: Fitting and testing probabilistic knowledge structures, especially the basic local independence model (BLIM, Doignon & Flamagne, 1999), using the minimum discrepancy maximum likelihood (MDML) method.
Author: Florian Wickelmaier [cre, aut], Juergen Heller [aut], Pasquale Anselmi [ctb]
Maintainer: Florian Wickelmaier

Diff between pks versions 0.2-1 dated 2013-06-10 and 0.3-0 dated 2014-03-28

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New package invGauss with initial version 1.1
Package: invGauss
Type: Package
Title: Threshold regression that fits the (randomized drift) inverse Gaussian distribution to survival data.
Version: 1.1
Date: 2014-03-29
Author: Hakon K. Gjessing
Maintainer: Hakon K. Gjessing
Depends: survival
Imports: optimx
Description: invGauss fits the (randomized drift) inverse Gaussian distribution to survival data. The model is described in Aalen OO, Borgan O, Gjessing HK. Survival and Event History Analysis. A Process Point of View. Springer, 2008. It is based on describing time to event as the barrier hitting time of a Wiener process, where drift towards the barrier has been randomized with a Gaussian distribution. The model allows covariates to influence starting values of the Wiener process and/or average drift towards a barrier, with a user-defined choice of link functions.
License: GPL (>= 2)
URL: http://www.uib.no/smis/gjessing/projects/invgauss/
Packaged: 2014-03-28 12:41:01 UTC; hkgjess
NeedsCompilation: no
Repository: CRAN
Date/Publication: 2014-03-28 14:06:47

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New package GraphPCA with initial version 1.0
Package: GraphPCA
Type: Package
Title: GraphPCA, Graphical tools of histogram PCA
Version: 1.0
Depends: R (>= 2.15.1)
Imports: ggplot2, FactoMineR, scatterplot3d, scales,
Date: 2014-03-21
Author: Brahim Brahim and Sun Makosso-Kallyth
Maintainer: Brahim Brahim
Description: This package implements a histogram principal components analysis. It provides numerical and graphical tools to deal with big data.
License: GPL (>= 2)
Packaged: 2014-03-28 12:18:15 UTC; PSA
NeedsCompilation: no
Repository: CRAN
Date/Publication: 2014-03-28 13:53:47

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Package clickstream updated to version 1.1.0 with previous version 1.0 dated 2014-02-28

Title: Analyzes clickstreams based on Markov chains
Description: This package allows modeling clickstreams with Markov chains. It supports to model clickstreams as zero-order, first-order or higher-order Markov chains.
Author: Michael Scholz
Maintainer: Michael Scholz

Diff between clickstream versions 1.0 dated 2014-02-28 and 1.1.0 dated 2014-03-28

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Package hsphase updated to version 1.2.6 with previous version 1.2.5 dated 2014-02-21

Title: Phasing and imputation of half-sib families using SNP data
Description: Identification of recombination events, haplotype reconstruction, sire imputation and pedigree reconstruction using half-sib family SNP data
Author: Mohammad Ferdosi , Cedric Gondro
Maintainer: Mohammad Ferdosi

Diff between hsphase versions 1.2.5 dated 2014-02-21 and 1.2.6 dated 2014-03-28

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Package EMA updated to version 1.4.4 with previous version 1.4.3 dated 2013-08-05

Title: Easy Microarray data Analysis
Description: We propose both a clear analysis strategy and a selection of tools to investigate microarray gene expression data. The most usual and relevant existing R functions were discussed, validated and gathered in an easy-to-use R package (EMA) devoted to gene expression microarray analysis. These functions were improved for ease of use, enhanced visualisation and better interpretation of results.
Author: Nicolas Servant, Eleonore Gravier, Pierre Gestraud, Cecile Laurent, Caroline Paccard, Anne Biton, Jonas Mandel, Bernard Asselain, Emmanuel Barillot, Philippe Hupe
Maintainer: Pierre Gestraud

Diff between EMA versions 1.4.3 dated 2013-08-05 and 1.4.4 dated 2014-03-28

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Package aCRM updated to version 0.1.1 with previous version 0.1.0 dated 2013-03-25

Title: Convenience functions for analytical Customer Relationship Management
Description: Convenience functions for data preparation and modeling often used in aCRM.
Author: Dirk Van den Poel, Michel Ballings, Andrey Volkov, Jeroen D'haen, Michiel Van Herwegen
Maintainer: Michel Ballings

Diff between aCRM versions 0.1.0 dated 2013-03-25 and 0.1.1 dated 2014-03-28

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Package spatial updated to version 7.3-8 with previous version 7.3-7 dated 2013-07-01

Title: Functions for Kriging and Point Pattern Analysis
Description: Functions for kriging and point pattern analysis.
Author: Brian Ripley [aut, cre, cph], Roger Bivand [ctb], William Venables [cph]
Maintainer: Brian Ripley

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Package rpart updated to version 4.1-8 with previous version 4.1-7 dated 2014-03-24

Title: Recursive Partitioning and Regression Trees
Description: Recursive partitioning for classification, regression and survival trees. An implementation of most of the functionality of the 1984 book by Breiman, Friedman, Olshen and Stone.
Author: Terry Therneau [aut], Beth Atkinson [aut], Brian Ripley [aut, trl, cre] (author of initial R port)
Maintainer: Brian Ripley

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Package nnet updated to version 7.3-8 with previous version 7.3-7 dated 2013-07-01

Title: Feed-forward Neural Networks and Multinomial Log-Linear Models
Description: Software for feed-forward neural networks with a single hidden layer, and for multinomial log-linear models.
Author: Brian Ripley [aut, cre, cph], William Venables [cph]
Maintainer: Brian Ripley

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Package nlme updated to version 3.1-116 with previous version 3.1-115 dated 2014-03-09

Title: Linear and Nonlinear Mixed Effects Models
Description: Fit and compare Gaussian linear and nonlinear mixed-effects models.
Author: José Pinheiro [aut] (S version), Douglas Bates [aut] (up to 2007), Saikat DebRoy [ctb] (up to 2002), Deepayan Sarkar [ctb] (up to 2005), EISPACK authors [ctb] (src/rs.f), R-core [aut, cre]
Maintainer: R-core

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Package MASS updated to version 7.3-31 with previous version 7.3-30 dated 2014-03-08

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

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Package KernSmooth updated to version 2.23-12 with previous version 2.23-11 dated 2014-03-24

Title: Functions for kernel smoothing for Wand & Jones (1995)
Description: functions for kernel smoothing (and density estimation) corresponding to the book: Wand, M.P. and Jones, M.C. (1995) "Kernel Smoothing".
Author: Matt Wand [aut], Brian Ripley [trl, cre, ctb] (R port and updates)
Maintainer: Brian Ripley

Diff between KernSmooth versions 2.23-11 dated 2014-03-24 and 2.23-12 dated 2014-03-28

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Package foreign updated to version 0.8-61 with previous version 0.8-60 dated 2014-03-24

Title: Read Data Stored by Minitab, S, SAS, SPSS, Stata, Systat, Weka, dBase, ...
Description: Functions for reading and writing data stored by some versions of Epi Info, Minitab, S, SAS, SPSS, Stata, Systat and Weka and for reading and writing some dBase files.
Author: R Core Team [aut, cph, cre], Roger Bivand [ctb, cph], Vincent J. Carey [ctb, cph], Saikat DebRoy [ctb, cph], Stephen Eglen [ctb, cph], Rajarshi Guha [ctb, cph], Nicholas Lewin-Koh [ctb, cph], Mark Myatt [ctb, cph], Ben Pfaff [ctb], Brian Quistorff [ctb], Frank Warmerdam [ctb, cph], Stephen Weigand [ctb, cph], Free Software Foundation, Inc. [cph]
Maintainer: R Core Team

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Package class updated to version 7.3-10 with previous version 7.3-9 dated 2013-08-21

Title: Functions for Classification
Description: Various functions for classification.
Author: Brian Ripley [aut, cre, cph], William Venables [cph]
Maintainer: Brian Ripley

Diff between class versions 7.3-9 dated 2013-08-21 and 7.3-10 dated 2014-03-28

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Package boot updated to version 1.3-11 with previous version 1.3-10 dated 2014-03-08

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 1.3-10 dated 2014-03-08 and 1.3-11 dated 2014-03-28

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Package SparseTSCGM (with last version 2.0) was removed from CRAN

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

2014-01-31 2.0
2013-05-24 1.0

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Package Rcmdr updated to version 2.0-4 with previous version 2.0-3 dated 2014-01-16

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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New package NHMMfdr with initial version 1.0.6
Package: NHMMfdr
Type: Package
Title: Compute FDR under dependence using NHMM
Version: 1.0.6
Date: 2013-03-04
Author: Pei Fen Kuan
Maintainer: Pei Fen Kuan
Depends: R (>= 2.10.0), MASS, locfdr
Description: The NHMMfdr package implements the non-homogeneous Hidden Markov Model based FDR control as described in Kuan et al., 2011 for multiple comparison adjustment under dependence. It allows for prior information to be incorporated in the model to improve detection of significant tests.
License: GPL (>= 2)
LazyLoad: yes
Packaged: 2014-03-28 01:56:25 UTC; peifenkuan
NeedsCompilation: yes
Repository: CRAN
Date/Publication: 2014-03-28 07:18:34

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Package FinTS updated to version 0.4-5 with previous version 0.4-4 dated 2009-12-16

Title: Companion to Tsay (2005) Analysis of Financial Time Series
Description: R companion to Tsay (2005) Analysis of Financial Time Series, 2nd ed. (Wiley). Includes data sets, functions and script files required to work some of the examples. Version 0.3-x includes R objects for all data files used in the text and script files to recreate most of the analyses in chapters 1-3 and 9 plus parts of chapters 4 and 11.
Author: Spencer Graves
Maintainer: Spencer Graves

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Package ddalpha updated to version 1.0.6 with previous version 1.0.5 dated 2014-03-16

Title: DDalpha-classifier, depth-calculating methods and associated functions
Description: Contains methods for depth classification based on the \eqn{\alpha}-procedure and for calculation of statistical depths
Author: Oleksii Pokotylo [aut, cre], Pavlo Mozharovskyi [aut]
Maintainer: Oleksii Pokotylo

Diff between ddalpha versions 1.0.5 dated 2014-03-16 and 1.0.6 dated 2014-03-28

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