Wed, 11 Dec 2013

Package survSNP updated to version 0.21-6 with previous version 0.21-5 dated 2012-08-06

Title: Power and Sample Size Calculations for SNP Association Studies with Censored Time to Event Outcomes
Description: This package can be used to conduct asymptotic and empirical power and sample size calculations for SNP association studies with right censored time to event outcomes
Author: Kouros Owzar, Zhiguo Li, Nancy Cox, Sin-Ho Jung and Chanhee Yi
Maintainer: Kouros Owzar

Diff between survSNP versions 0.21-5 dated 2012-08-06 and 0.21-6 dated 2013-12-11

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Package sealasso updated to version 0.1-2 with previous version 0.1-1 dated 2013-09-08

Title: Standard Error Adjusted Adaptive Lasso
Description: Standard error adjusted adaptive lasso (SEA-lasso) is a version of the adaptive lasso, which incorporates OLS standard error to the L1 penalty weight. This method is intended for variable selection under linear regression settings (n > p). This new weight assignment strategy is especially useful when the collinearity of the design matrix is a concern.
Author: Wei Qian
Maintainer: Wei Qian

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Package SBSA updated to version 0.2.1 with previous version 0.2.0 dated 2012-03-16

Title: Simplified Bayesian Sensitivity Analysis
Description: Simplified Bayesian Sensitivity Analysis
Author: Davor Cubranic and Paul Gustafson
Maintainer: Davor Cubranic

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Package QTLRel updated to version 0.2-14 with previous version 0.2-12 dated 2012-11-15

Title: Tools for mapping of quantitative traits of genetically related individuals and calculating identity coefficients from a pedigree
Description: This software provides tools for quantitative trait mapping in populations such as advanced intercross lines where relatedness among individuals should not be ignored. It can estimate background genetic variance components, impute missing genotypes, simulate genotypes, perform a genome scan for putative quantitative trait loci (QTL), and plot mapping results. It also has functions to calculate identity coefficients from pedigrees, especially suitable for pedigrees that consist of a large number of generations, or estimate identity coefficients from genotypic data in certain circumstances.
Author: Riyan Cheng
Maintainer: Riyan Cheng

Diff between QTLRel versions 0.2-12 dated 2012-11-15 and 0.2-14 dated 2013-12-11

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New package npbr with initial version 1.0
Package: npbr
Type: Package
Title: Nonparametric boundary regression
Version: 1.0
Date: 2013-11-26
Author: Abdelaati Daouia , Thibault Laurent , Hohsuk Noh
Maintainer: Thibault Laurent
Depends: R (>= 2.9.1), splines, graphics, Rglpk, Benchmarking
Description: This package provides functions for the best known approaches to nonparametric boundary estimation. The selected methods are concerned with empirical, smooth, unconstrained as well as restricted estimates under both separate and multiple shape constraints. The package also allows for Monte Carlo comparisons among these different estimation procedures, illustrating the simulation experiments by Daouia, Noh and Park (2013), Data envelope fitting with constrained polynomial splines, TSE Working Paper, http://www.tse-fr.eu/images/doc/wp/etrie/wp_tse_449.pdf
License: GPL (>= 2)
Packaged: 2013-12-11 18:26:26 UTC; laurent
NeedsCompilation: no
Repository: CRAN
Date/Publication: 2013-12-12 01:35:35

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New package mmeta with initial version 2.0
Package: mmeta
Type: Package
Title: Multivariate Meta-Analysis Using Sarmanov Beta Prior Distributions
Version: 2.0
Date: 2013-12-3
Author: Sheng Luo, Yong Chen, Xiao Su, Haitao Chu
Maintainer: Xiao Su
Description: This package implements a novel bivariate meta-analysis using Sarmanov beta prior distributions.
Depends: R (>= 2.10.0)
Imports: aod,xtable,HI
License: GPL (>= 2)
LazyLoad: no
Packaged: 2013-12-11 20:15:36 UTC; xsu
NeedsCompilation: yes
Repository: CRAN
Date/Publication: 2013-12-12 01:31:53

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Package mleur updated to version 1.0-6 with previous version 1.0-5 dated 2012-09-22

Title: Maximum likelihood unit root test
Description: Provides functions for unit root testing using MLE method
Author: A. I. McLeod, Hao Yu and Ying Zhang
Maintainer: Ian McLeod

Diff between mleur versions 1.0-5 dated 2012-09-22 and 1.0-6 dated 2013-12-11

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New package languageR with initial version 1.4.1
Package: languageR
Type: Package
Title: Data sets and functions with "Analyzing Linguistic Data: A practical introduction to statistics".
Version: 1.4.1
Date: 2013-12-9
Author: R. H. Baayen
Maintainer: R. H. Baayen
Description: Data sets exemplifying statistical methods, and some facilitatory utility functions used in "Analyzing Linguistic Data: A practical introduction to statistics using R", Cambridge University Press, 2008.
LazyData: yes
License: GPL (>= 2)
Depends: R(>= 3.0.2)
Suggests: cluster, e1071, rms, Hmisc, MASS, rpart, lattice, zipfR, lme4, multcomp, lmerTest, optimx
Imports: methods
Packaged: 2013-12-11 18:47:42 UTC; harald
Repository: CRAN
Date/Publication: 2013-12-12 01:27:42
NeedsCompilation: no

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Package HistogramTools updated to version 0.3 with previous version 0.2 dated 2013-10-03

Title: Utility Functions for R Histograms
Description: This package provides a number of utility functions useful for manipulating large histograms. This includes methods to trim, subset, merge buckets, merge histograms, convert to CDF, and calculate information loss due to binning. It also provides a protocol buffer representations of the default R histogram class to allow histograms over large data sets to be computed and manipulated in a MapReduce environment.
Author: Murray Stokely
Maintainer: Murray Stokely

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Package dmt updated to version 0.8.20 with previous version 0.8.10 dated 2012-05-30

Title: Dependency Modeling Toolkit
Description: Probabilistic dependency modeling toolkit.
Author: Leo Lahti and Olli-Pekka Huovilainen
Maintainer: Leo Lahti

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New package dfexplore with initial version 0.2
Package: dfexplore
Type: Package
Title: Explore data.frames by plotting NA and classes of each variable
Version: 0.2
Date: 2013-12-06
Author: Joris Muller
Maintainer: Joris Muller
Description: Quickly and graphicaly show NA and classes of each variable and each observation of a data.frame. The aim is to show pattern of NA
License: GPL
Depends: ggplot2, methods
URL: http://blog.chmilblick.fr
Encoding: UTF-8
Packaged: 2013-12-11 20:25:50 UTC; joris
NeedsCompilation: no
Repository: CRAN
Date/Publication: 2013-12-12 01:38:32

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New package chipPCR with initial version 0.0.5
Package: chipPCR
Type: Package
Title: Toolkit of helper functions to pre-process amplification data
Version: 0.0.5
Date: 2013-12-12
Author: Stefan Roediger, Michal Burdukiewicz
Maintainer: Stefan Roediger
Description: The chipPCR package is a toolkit of helper functions to pre-process amplification data. Amplification data can be obtained from classical PCR reactions or isothermal amplification reactions. The package contains functions to normalize amplification, a simple routine to detect the start of an amplification reaction and several smoothers for amplification data. The smoothers are based on LOWESS, moving average, cubic splines, Savitzky-Golay and others. In addition contains the chipPCR package data sets of experimental nucleic acid amplification systems including the VideoScan HCU and a capillary convective PCR 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.
License: GPL-3
Depends: R (>= 3.0.0)
Imports: outliers, robustbase, signal
Packaged: 2013-12-12 00:06:52 UTC; tux
NeedsCompilation: no
Repository: CRAN
Date/Publication: 2013-12-12 01:51:15

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Package sphet updated to version 1.5 with previous version 1.4 dated 2013-06-21

Title: Estimation of spatial autoregressive models with and without heteroskedastic innovations
Description: Generalized Method of Moment estimation of Cliff-Ord-type spatial autoregressive models with and without heteroskedastic innovations
Author: Gianfranco Piras
Maintainer: Gianfranco Piras

Diff between sphet versions 1.4 dated 2013-06-21 and 1.5 dated 2013-12-11

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Package smfsb updated to version 1.1 with previous version 1.0 dated 2011-10-26

Title: SMfSB 2e: Stochastic Modelling for Systems Biology, second edition
Description: This package contains code and data for modelling and simulation of stochastic kinetic biochemical network models. It contains the code and data associated with the second edition of the book Stochastic Modelling for Systems Biology, published by Chapman & Hall/CRC Press, November 2011.
Author: Darren Wilkinson
Maintainer: Darren Wilkinson

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Package grImport updated to version 0.9-0 with previous version 0.8-4 dated 2012-02-15

Title: Importing Vector Graphics
Description: Functions for converting, importing, and drawing PostScript pictures in R plots.
Author: Paul Murrell [aut, cre], Richard Walton [aut], Simon Potter [ctb]
Maintainer: Paul Murrell

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New package aidar with initial version 1.0.0
Package: aidar
Title: Tools for reading AIDA (http://aida.freehep.org/) files into R
Description: Read objects from the AIDA file and make them available as dataframes in R
Version: 1.0.0
Author: Andreas Pfeiffer
Maintainer: Andreas Pfeiffer
License: LGPL (>= 2)
Suggests: testthat
Depends: XML
Packaged: 2013-12-11 17:12:21 UTC; ap
NeedsCompilation: no
Repository: CRAN
Date/Publication: 2013-12-11 21:05:22

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Package TInPosition updated to version 0.13.6 with previous version 0.10.4 dated 2013-06-15

Title: Inference tests for TExPosition
Description: Non-parametric resampling-based inference tests for TExPosition.
Author: Derek Beaton, Jenny Rieck, Herve Abdi
Maintainer: Derek Beaton

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Package rspear updated to version 0.1-2 with previous version 0.1-1 dated 2013-09-09

Title: Calculate SPEARpesticide in R (http://www.systemecology.eu/SPEAR/index.php)
Description: Calculate SPEARpesticide in R (http://www.systemecology.eu/SPEAR/index.php)
Author: Eduard Szoecs
Maintainer: Eduard Szoecs

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Package prob updated to version 0.9-5 with previous version 0.9-2 dated 2009-11-02

Title: Elementary Probability on Finite Sample Spaces
Description: This package provides a framework for performing elementary probability calculations on finite sample spaces, which may be represented by data frames or lists. Functionality includes setting up sample spaces, counting tools, defining probability spaces, performing set algebra, calculating probability and conditional probability, tools for simulation and checking the law of large numbers, adding random variables, and finding marginal distributions. Characteristic functions for all base R distributions are included.
Author: G. Jay Kerns [aut, cre, cph]
Maintainer: G. Jay Kerns

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Package pgs updated to version 0.4-0 with previous version 0.3-0 dated 2010-02-09

Title: Precision of Geometric Sampling
Description: Computation of mean squared errors of stereological predictors.
Author: Kien Kieu , Marianne Mora
Maintainer: Kien Kieu

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Package kernelPop updated to version 1.0.2 with previous version 1.0.0 dated 2013-11-27

Title: Spatially explicit population genetic simulations
Description: This package creates a individual-based population genetic simulation. Individuals have spatial coordinates, dispersal governed by mixtures of Weibull and normal pdfs. It is discrete-time. It can be arbitrarily complex given enough known or assumed demographic characteristics. Simulates diploid and haploid inheritance. Allows the development of null distributions of genotypes for complex demographic scenarios. This version includes some approximations for pollen (male gamete) dispersal.
Author: Allan Strand and James Niehaus
Maintainer: Allan Strand

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Package genlasso updated to version 1.1 with previous version 1.0 dated 2012-08-19

Title: Path algorithm for generalized lasso problems
Description: This package computes the solution path for generalized lasso problems. Important use cases are the fused lasso over an arbitrary graph, and trend fitting of any given polynomial order. Specialized implementations for the latter two subproblems are given to improve stability and speed.
Author: Ryan J. Tibshirani, Taylor B. Arnold
Maintainer: Taylor Arnold

Diff between genlasso versions 1.0 dated 2012-08-19 and 1.1 dated 2013-12-11

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Package etable updated to version 1.2.0 with previous version 1.0.8 dated 2013-02-22

Title: Easy Table
Description: A table function for descriptive statistics in tabular format, using variables in a data.frame. You can create simple or highly customized tables.
Author: Andreas Schulz
Maintainer: Andreas Schulz

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Package diffractometry updated to version 0.1-8 with previous version 0.1-7 dated 2013-06-17

Title: Baseline identification and peak decomposition for x-ray diffractograms
Description: Residual-based baseline identification and peak decomposition for x-ray diffractograms as introduced in Davies/Gather/Mergel/Meise/Mildenberger (2008).
Author: P.L. Davies, U. Gather, M. Meise, D.Mergel, T. Mildenberger. Additional Code by T. Bernholt and T. Hofmeister
Maintainer: T. Mildenberger

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Package TExPosition updated to version 2.6.10 with previous version 2.0.2 dated 2013-06-15

Title: Two-table ExPosition
Description: TExPosition is an extension of ExPosition for two table analyses, specifically, discriminant analyses.
Author: Derek Beaton, Jenny Rieck, Cherise R. Chin Fatt, Herve Abdi
Maintainer: Derek Beaton

Diff between TExPosition versions 2.0.2 dated 2013-06-15 and 2.6.10 dated 2013-12-11

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Package mvngGrAd updated to version 0.1.3 with previous version 0.1.2 dated 2011-10-12

Title: Software for moving grid adjustment in plant breeding field trials
Description: Package for moving grid adjustment in plant breeding field trials.
Author: Frank Technow
Maintainer: Frank Technow

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Package mvmeta updated to version 0.3.5 with previous version 0.3.4 dated 2013-01-23

Title: Multivariate and univariate meta-analysis and meta-regression
Description: The package mvmeta consists of a collection of functions to perform fixed and random-effects multivariate and univariate meta-analysis and meta-regression in R.
Author: Antonio Gasparrini
Maintainer: Antonio Gasparrini

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Package miscFuncs updated to version 1.2-3 with previous version 1.2-2 dated 2013-05-21

Title: Miscellaneous Useful Functions
Description: LaTeX tables, Kalman filter, web scraping, development tools, relative risk, odds ratio
Author: Benjamin M. Taylor
Maintainer: Benjamin M. Taylor

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Package MCDA updated to version 0.0.3 with previous version 0.0.1 dated 2013-11-29

Title: MCDA
Description: The MCDA package for the R statistical software allows you to use MCDA methods and functions in R.
Author: Patrick Meyer, S├ębastien Bigaret.
Maintainer: Patrick Meyer

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Package InPosition updated to version 0.12.7 with previous version 0.10.4 dated 2013-06-15

Title: Inference Tests for ExPosition
Description: Non-parametric resampling-based inference tests for ExPosition.
Author: Derek Beaton, Joseph Dunlop, Herve Abdi
Maintainer: Derek Beaton

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Package ExomeDepth updated to version 0.9.8 with previous version 0.9.7 dated 2012-12-11

Title: Calls CNV from exome sequence data
Description: Calls copy number variants (CNVs) from targeted sequence data
Author: Vincent Plagnol
Maintainer: Vincent Plagnol

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Package dtw updated to version 1.17-1 with previous version 1.16 dated 2013-05-28

Title: Dynamic time warping algorithms
Description: A comprehensive implementation of dynamic time warping (DTW) algorithms in R. DTW computes the optimal (least cumulative distance) alignment between points of two time series. Common DTW variants covered include local (slope) and global (window) constraints, subsequence matches, arbitrary distance definitions, normalizations, minimum variance matching, and so on. Provides cumulative distances, alignments, specialized plot styles, etc.
Author: Toni Giorgino ,
Maintainer: Toni Giorgino

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Package DoE.base updated to version 0.25-3 with previous version 0.25-2 dated 2013-08-26

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 0.25-2 dated 2013-08-26 and 0.25-3 dated 2013-12-11

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Package clusterCrit updated to version 1.2.3 with previous version 1.2.2 dated 2013-06-15

Title: Clustering Indices
Description: compute clustering validation indices
Author: Bernard Desgraupes (University of Paris Ouest - Lab Modal'X)
Maintainer: Bernard Desgraupes

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Package pvar updated to version 1.0.9 with previous version 1.0.6 dated 2012-09-28

Title: p-variation, calculation and application
Description: The calculation of p-variation of the finite sample data
Author: Vygantas Butkus
Maintainer: Vygantas Butkus

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Package mlogitBMA updated to version 0.1-6 with previous version 0.1-5 dated 2012-02-22

Title: Bayesian Model Averaging for Multinomial Logit Models
Description: Provides a modified function bic.glm of the BMA package that can be applied to multinomial logit (MNL) data. The data is converted to binary logit using the Begg & Gray approximation. The package also contains functions for maximum likelihood estimation of MNL.
Author: Hana Sevcikova, Adrian Raftery
Maintainer: Hana Sevcikova

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Package gmm updated to version 1.5-0 with previous version 1.4-5 dated 2013-01-11

Title: Generalized Method of Moments and Generalized Empirical Likelihood
Description: It is a complete suite to estimate models based on moment conditions. It includes the two step Generalized method of moments (GMM) of Hansen(1982), the iterated GMM and continuous updated estimator (CUE) of Hansen-Eaton-Yaron(1996) and several methods that belong to the Generalized Empirical Likelihood (GEL) family of estimators, as presented by Smith(1997), Kitamura(1997), Newey-Smith(2004) and Anatolyev(2005).
Author: Pierre Chausse
Maintainer: Pierre Chausse

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Package wle updated to version 0.9-9 with previous version 0.9-7 dated 2012-10-16

Title: Weighted Likelihood Estimation
Description: Approach to the robustness via Weighted Likelihood.
Author: Claudio Agostinelli , SLATEC Common Mathematical Library
Maintainer: Claudio Agostinelli

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Package depmixS4 updated to version 1.3-1 with previous version 1.3-0 dated 2013-09-18

Title: Dependent Mixture Models - Hidden Markov Models of GLMs and Other Distributions in S4
Description: Fit latent (hidden) Markov models on mixed categorical and continuous (timeseries) data, otherwise known as dependent mixture models
Author: Ingmar Visser , Maarten Speekenbrink
Maintainer: Ingmar Visser

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Package simPopulation updated to version 0.4.1 with previous version 0.4.0 dated 2012-02-12

Title: Simulation of synthetic populations for surveys based on sample data
Description: Simulate populations for surveys based on sample data with special application to EU-SILC.
Author: Andreas Alfons [aut, cre], Stefan Kraft [aut]
Maintainer: Andreas Alfons

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Package simFrame updated to version 0.5.1 with previous version 0.5.0 dated 2012-01-02

Title: Simulation framework
Description: A general framework for statistical simulation.
Author: Andreas Alfons [aut, cre]
Maintainer: Andreas Alfons

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Package selectiongain updated to version 2.0.29 with previous version 2.0.28 dated 2013-10-22

Title: A tool for calculation and optimization of the expected gain from multi-stage selection
Description: Multi-stage selection is practiced in numerous fields of life and social sciences and particularly in breeding. A special characteristic of multi-stage selection is that candidates are evaluated in successive stages with increasing intensity and effort, and only a fraction of the superior candidates is selected and promoted to the next stage. For the optimum design of such selection programs, the selection gain plays a crucial role. It can be calculated by integration of a truncated multivariate normal (MVN) distribution. While mathematical formulas for calculating the selection gain and the variance among selected candidates were developed long time ago, solutions for numerical calculation were not available. This package can also be used for optimizing multi-stage selection programs for a given total budget and different costs of evaluating the candidates in each stage.
Author: Xuefei Mi, H. Friedrich Utz, Albrecht E. Melchinger (Project contact person: Melchinger@uni-hohenheim.de )
Maintainer: Xuefei Mi

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Package rhosp updated to version 1.05 with previous version 1.04 dated 2009-02-10

Title: Side effect risks in hospital : simulation and estimation
Description: Evaluating risk (that a patient arises a side effect) during hospitalization is the main purpose of this package. Several methods (Parametric, non parametric and De Vielder estimation) to estimate the risk constant (R) are implemented in this package. There are also functions to simulate the different models of this issue in order to quantify the previous estimators. It is necessary to read at least the first six pages of the report to understand the topic.
Author: Christophe Dutang and Julie Barthes
Maintainer: Christophe Dutang

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Package QCA updated to version 1.1-1 with previous version 1.1-0 dated 2013-11-01

Title: A Package for Qualitative Comparative Analysis
Description: This package provides functions for performing Qualitative Comparative Analysis (csQCA, tQCA, mvQCA and fsQCA).
Author: Adrian Dusa [aut, cre], Alrik Thiem [aut]
Maintainer: Adrian Dusa

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Package DataFrameConstr (with last version 1.1-2) was removed from CRAN

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

2013-03-20 1.1-2
2013-03-19 1.1-0

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Package SOAR updated to version 0.99-11 with previous version 0.99-10 dated 2012-01-14

Title: Memory management in R by delayed assignments
Description: Allows objects to be stored on disc and automatically recalled into memory, as required, by delayed assignment.
Author: Bill Venables, based on original code by David Brahm
Maintainer: Bill Venables

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New package rpartitions with initial version 0.1
Package: rpartitions
Title: Code for integer partitioning
Description: Provides algorithims for randomly sampling a feasible set defined by a given total and number of elements using integer partitioning.
Version: 0.1
Author: Ken Locey, Daniel McGlinn
Maintainer: Daniel McGlinn
Depends: R (>= 2.15.1), hash
Suggests: testthat (>= 0.2)
NeedsCompilation: yes
Repository: CRAN
URL: https://github.com/klocey/partitions
License: MIT
LazyData: true
Collate: 'rpartitions.R' 'rpartitions-package.r'
Packaged: 2013-12-11 04:02:10 UTC; adminwhite
Date/Publication: 2013-12-11 07:34:59

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Package random updated to version 0.2.2 with previous version 0.2.1 dated 2009-08-13

Title: True random numbers using random.org
Description: This package provides an interface to the true random number service provided by the random.org website created by Mads Haahr. The random.org web service samples atmospheric noise via radio tuned to an unused broadcasting frequency together with a skew correction algorithm due to John von Neumann. More background is available in the included vignette based on an essay by Mads Haahr. In its current form, the package offers functions to retrieve random integers, randomized sequences and random strings.
Author: Dirk Eddelbuettel
Maintainer: Dirk Eddelbuettel

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Package postCP updated to version 1.7.2 with previous version 1.7.0 dated 2013-07-01

Title: A package to estimate posterior probabilities and perform model selection in change-point models using constrained HMM.
Description: The functions are used for change-point problems, after an initial set of change-points within the data has already been obtained. The function postCP obtains estimates of posterior probabilities of change-point and hidden states for each observation, and confidence intervals for the positions of the change-point. The function postCPsample obtains random samples of sets of change-points using the output of the postCP function. Model selection may be performed using function postCPmodelsel through criteria obtained from function postCPcrit.
Author: Gregory Nuel and The Minh Luong
Maintainer: The Minh Luong

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Package OUwie updated to version 1.37 with previous version 1.36 dated 2013-11-22

Title: Analysis of evolutionary rates in an OU framework
Description: Calculates and compares rate differences of continuous character evolution under Brownian motion and a new set of Ornstein-Uhlenbeck-based Hansen models that allow the strength of selection and stochastic motion to vary across selective regimes.
Author: Jeremy M. Beaulieu , Brian O'Meara
Maintainer: Jeremy Beaulieu

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Package mugnet updated to version 1.02.0 with previous version 1.01.3 dated 2013-02-26

Title: Mixture of Gaussian Bayesian Network Model
Description: A package that models continuous multivariate data via directional acyclic graphs and provides inference based on the frequentist approach
Author: Nikolay Balov
Maintainer: Nikolay Balov

Diff between mugnet versions 1.01.3 dated 2013-02-26 and 1.02.0 dated 2013-12-11

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Package catnet updated to version 1.14.3 with previous version 1.14.2 dated 2013-07-31

Title: Categorical Bayesian Network Inference
Description: A package that handles discrete Bayesian network models and provides inference using the frequentist approach
Author: Nikolay Balov, Peter Salzman
Maintainer: Nikolay Balov

Diff between catnet versions 1.14.2 dated 2013-07-31 and 1.14.3 dated 2013-12-11

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