Package markovchain updated to version 0.0.9.5 with previous version 0.0.9 dated 2014-04-19

Title: A package to handle and analyse discrete Markov chains
Description: A package for easily handling discrete Markov chains
Author: Giorgio Alfredo Spedicato
Maintainer: Giorgio Alfredo Spedicato

Diff between markovchain versions 0.0.9 dated 2014-04-19 and 0.0.9.5 dated 2014-06-20

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New package funreg with initial version 1.1
Package: funreg
Type: Package
Title: funreg (Functional Regression for Irregularly Timed Data)
Version: 1.1
Date: 2014-06-12
Authors@R: c(person("John", "Dziak", role = c("aut", "cre"), email = "jjd264@psu.edu"), person("Mariya", "Shiyko", role = "aut", email = "M.Shiyko@neu.edu"))
Depends: R (>= 2.15.0)
Imports: MASS, mgcv, mvtnorm, splines
Copyright: The Pennsylvania State University and Northeastern University
Description: This package performs functional regression, and some related approaches, for intensive longitudinal data (see Walls & Schafer, 2006) which is not necessarily observed on an equally spaced grid of times. The approach generally follows the ideas of Goldsmith, Bobb, Crainiceanu, Caffo, and Reich (2011) and the approach taken in their sample code, but with some modifications to make it more feasible to use with long rather than wide, non-rectangular longitudinal datasets with unequal and potentially random measurement times. It also allows easy plotting of the correlation between the smoothed covariate and the outcome as a function of time, which can add additional insights on how to interpret a functional regression. Additionally, it also provides several permutation tests for the significance of the functional predictor. The heuristic interpretation of ``time'' is used to describe the index of the functional predictor, but the same methods can equally be used for another unidimensional continuous index, such as space along a north-south axis. The development of this package was part of a research project supported by Award R03 CA171809-01 from the National Cancer Institute and Award P50 DA010075 from the National Institute on Drug Abuse. The content is solely the responsibility of the authors and does not necessarily represent the official views of the National Institute on Drug Abuse, the National Cancer Institute, or the National Institutes of Health.
License: GPL (>= 2)
LazyData: true
Packaged: 2014-06-20 22:20:03 UTC; admin_jjd264
Author: John Dziak [aut, cre], Mariya Shiyko [aut]
Maintainer: John Dziak
NeedsCompilation: no
Repository: CRAN
Date/Publication: 2014-06-21 01:11:39

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Package permGPU updated to version 0.14.4 with previous version 0.14.3 dated 2012-12-27

Title: permPGU: Using GPUs in Statistical Genomics
Description: This R extension package can be used to carry out permutation resampling inference in the context of RNA microarray studies
Author: Ivo D. Shterev, Sin-Ho Jung, Stephen L. George and Kouros Owzar
Maintainer: Ivo D. Shterev

Diff between permGPU versions 0.14.3 dated 2012-12-27 and 0.14.4 dated 2014-06-20

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Package usl updated to version 1.3.1 with previous version 1.3.0 dated 2014-06-02

Title: Analyze system scalability with the Universal Scalability Law
Description: The Universal Scalability Law is a model to predict hardware and software scalability. It uses system capacity as a function of load to forecast the scalability for the system.
Author: Neil J. Gunther [aut], Stefan Moeding [aut, cre]
Maintainer: Stefan Moeding

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Package MPSEM updated to version 0.2-5 with previous version 0.2-3 dated 2014-03-19

Title: Modeling Phylogenetic Signals using Eigenvector Maps
Description: Computational tools to represent phylogenetic signals using adapted eigenvector maps.
Author: Guillaume Guenard, with contribution from Pierre Legendre
Maintainer: Guillaume Guenard

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Package pawacc updated to version 1.2 with previous version 1.1 dated 2013-11-13

Title: Physical activity with accelerometers
Description: Process, format and store accelerometer data
Author: Marco Geraci
Maintainer: Marco Geraci

Diff between pawacc versions 1.1 dated 2013-11-13 and 1.2 dated 2014-06-20

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Package bayesSurv updated to version 2.3 with previous version 2.1-1 dated 2013-06-11

Title: Bayesian Survival Regression with Flexible Error and Random Effects Distributions
Description: Later
Author: Arnošt Komárek
Maintainer: Arnošt Komárek

Diff between bayesSurv versions 2.1-1 dated 2013-06-11 and 2.3 dated 2014-06-20

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Package nadiv updated to version 2.13.2 with previous version 2.13 dated 2014-06-16

Title: Functions to construct (non)additive genetic relatedness matrices and facilitate animal model analyses
Description: Constructs (non)additive genetic relationship matrices, and their inverses, from a pedigree to be used in linear mixed effect models (A.K.A. the 'animal model'). Also includes other functions to facilitate the use of animal models. Some functions have been created to be used in conjunction with the R package for ASReml software, which can be obtained upon purchase from VSN international ().
Author: Matthew Wolak
Maintainer: Matthew Wolak

Diff between nadiv versions 2.13 dated 2014-06-16 and 2.13.2 dated 2014-06-20

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New package hypergea with initial version 0.99.4
Package: hypergea
Type: Package
Title: Hypergeometric tests
Version: 0.99.4
Date: 2014-06-16
Author: Markus Boenn
Maintainer: Markus Boenn
Description: Package to perform (exact) hypergeometric tests on IxJ and 2x2x2 contingency tables using parallelised C code
License: GPL (>= 2)
Depends: R (>= 3.0.0)
Imports:
SystemRequirements: OpenMP (>=3.0)
Packaged: 2014-06-20 11:06:13 UTC; boenn
NeedsCompilation: yes
Repository: CRAN
Date/Publication: 2014-06-20 13:22:32

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Package Bergm updated to version 2.7 with previous version 2.6 dated 2013-05-07

Title: Bayesian analysis for exponential random graph models
Description: Set of tools to analyse Bayesian exponential random graph models
Author: Alberto Caimo and Nial Friel
Maintainer: Alberto Caimo

Diff between Bergm versions 2.6 dated 2013-05-07 and 2.7 dated 2014-06-20

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Package SSDforR updated to version 1.4.5 with previous version 1.4.4 dated 2014-05-05

Title: SSD for R to analyze single system data
Description: Package to visually and statistically analyze single system data
Author: Charles Auerbach,PHD Wendy Zeitlin Schudrich,PHD Wurzweiler School of Social Work
Maintainer: Charles Auerbach

Diff between SSDforR versions 1.4.4 dated 2014-05-05 and 1.4.5 dated 2014-06-20

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Package sheldusr (with last version 0.1) was removed from CRAN

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

2013-11-14 0.1

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New package parallelMCMCcombine with initial version 1.0
Package: parallelMCMCcombine
Type: Package
Title: Methods for combining independent subset Markov chain Monte Carlo (MCMC) posterior samples to estimate a posterior density given the full data set
Version: 1.0
Date: 2014-06-12
Author: Alexey Miroshnikov, Erin Conlon
Maintainer: Alexey Miroshnikov
Description: Recent Bayesian Markov chain Monto Carlo (MCMC) methods have been developed for big data sets that are too large to be analyzed using traditional statistical methods. These methods partition the data into non-overlapping subsets, and perform parallel independent Bayesian MCMC analyses on the data subsets, creating independent subposterior samples for each data subset. These independent subposterior samples are combined through four functions in this package, including averaging across subset samples, weighted averaging across subsets samples, and kernel smoothing across subset samples. The four functions assume the user has previously run the Bayesian analysis and has produced the independent subposterior samples outside of the package; the functions use as input the array of subposterior samples. The methods have been demonstrated to be useful for Bayesian MCMC models including Bayesian logistic regression, Bayesian Gaussian mixture models and Bayesian hierarchical Poisson-Gamma models. The methods are appropriate for Bayesian hierarchical models with hyperparameters, as long as data values in a single level of the hierarchy are not split into subsets.
Depends: mvtnorm
License: GPL (>= 2)
Packaged: 2014-06-19 18:45:42 UTC; Alexey
NeedsCompilation: no
Repository: CRAN
Date/Publication: 2014-06-20 08:03:26

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Package lpSolve updated to version 5.6.9 with previous version 5.6.8 dated 2014-04-29

Title: Interface to Lp_solve v. 5.5 to solve linear/integer programs
Description: Lp_solve is freely available (under LGPL 2) software for solving linear, integer and mixed integer programs. In this implementation we supply a "wrapper" function in C and some R functions that solve general linear/integer problems, assignment problems, and transportation problems. This version calls lp_solve version 5.5.
Author: Michel Berkelaar and others
Maintainer: Samuel E. Buttrey

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Package gplots updated to version 2.14.0 with previous version 2.13.0 dated 2014-04-05

Title: Various R programming tools for plotting data
Description: Various R programming tools for plotting data
Author: Gregory R. Warnes, Ben Bolker, Lodewijk Bonebakker, Robert Gentleman, Wolfgang Huber Andy Liaw, Thomas Lumley, Martin Maechler, Arni Magnusson, Steffen Moeller, Marc Schwartz, Bill Venables
Maintainer: Gregory R. Warnes

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