Tue, 03 Dec 2013

Package multgee updated to version 1.4 with previous version 1.3 dated 2013-06-21

Title: GEE Solver for Correlated Nominal or Ordinal Multinomial Responses
Description: GEE solver for correlated nominal or ordinal multinomial responses using a local odds ratios parameterization.
Author: Anestis Touloumis
Maintainer: Anestis Touloumis

Diff between multgee versions 1.3 dated 2013-06-21 and 1.4 dated 2013-12-03

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 inst/CITATION          |    8 +++++---
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 man/nomLORgee.Rd       |   22 +++++++++++-----------
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Package Boruta updated to version 3.0.0 with previous version 2.1.0 dated 2013-04-25

Title: A wrapper algorithm for all-relevant feature selection
Description: Boruta is an all-relevant feature selection wrapper algorithm. It finds relevant features by comparing original attributes' importance with importance achievable at random, estimated using their permuted copies.
Author: Miron Bartosz Kursa [aut, cre], Witold Remigiusz Rudnicki [aut]
Maintainer: Miron Bartosz Kursa

Diff between Boruta versions 2.1.0 dated 2013-04-25 and 3.0.0 dated 2013-12-03

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Package structSSI updated to version 1.0.5 with previous version 1.0.4 dated 2013-08-13

Title: Multiple Testing for Hypotheses with Hierarchical or Group Structure
Description: Performs multiple testing corrections that take specific structure of hypotheses into account.
Author: Kris Sankaran
Maintainer: Kris Sankaran

Diff between structSSI versions 1.0.4 dated 2013-08-13 and 1.0.5 dated 2013-12-03

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 16 files changed, 137 insertions(+), 148 deletions(-)

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Package rtfbs updated to version 0.3 with previous version 0.2 dated 2012-03-30

Title: R Transcription Factor Binding Site identification tool
Description: RTFBS identifies and scores possible Transcription Factor Binding Sites and allows for FDR analysis and pruning. It supports splitting of sequences based on size or a specified GFF, grouping by G+C content, and specification of Markov model order. The heavy lifting is done in C while all results are made available via R.
Author: Nicholas Peterson, Andre Martins, Melissa Hubisz, and Adam Siepel
Maintainer: Melissa Hubisz

Diff between rtfbs versions 0.2 dated 2012-03-30 and 0.3 dated 2013-12-03

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Package RJDBC updated to version 0.2-2 with previous version 0.2-1 dated 2012-12-02

Title: Provides access to databases through the JDBC interface
Description: RJDBC is an implementation of R's DBI interface using JDBC as a back-end. This allows R to connect to any DBMS that has a JDBC driver.
Author: Simon Urbanek
Maintainer: Simon Urbanek

Diff between RJDBC versions 0.2-1 dated 2012-12-02 and 0.2-2 dated 2013-12-03

 DESCRIPTION                   |   10 ++---
 MD5                           |   15 ++++----
 NAMESPACE                     |    4 +-
 NEWS                          |   12 ++++++
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 9 files changed, 107 insertions(+), 26 deletions(-)

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Package rJava updated to version 0.9-5 with previous version 0.9-4 dated 2013-03-12

Title: Low-level R to Java interface
Description: Low-level interface to Java VM very much like .C/.Call and friends. Allows creation of objects, calling methods and accessing fields.
Author: Simon Urbanek
Maintainer: Simon Urbanek

Diff between rJava versions 0.9-4 dated 2013-03-12 and 0.9-5 dated 2013-12-03

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Package RCassandra updated to version 0.1-3 with previous version 0.1-2.1 dated 2013-03-23

Title: R/Cassandra interface
Description: This packages provides a direct interface (without the use of Java) to the most basic functionality of Apache Cassanda such as login, updates and queries.
Author: Simon Urbanek
Maintainer: Simon Urbanek

Diff between RCassandra versions 0.1-2.1 dated 2013-03-23 and 0.1-3 dated 2013-12-03

 DESCRIPTION      |   12 +++---
 MD5              |    8 ++--
 NEWS             |    9 ++++
 man/RC.insert.Rd |   33 ++++++++++++----
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 5 files changed, 131 insertions(+), 41 deletions(-)

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Package png updated to version 0.1-7 with previous version 0.1-6 dated 2013-08-02

Title: Read and write PNG images
Description: This package provides an easy and simple way to read, write and display bitmap images stored in the PNG format. It can read and write both files and in-memory raw vectors.
Author: Simon Urbanek
Maintainer: Simon Urbanek

Diff between png versions 0.1-6 dated 2013-08-02 and 0.1-7 dated 2013-12-03

 DESCRIPTION |    6 +++---
 MD5         |    6 +++---
 NEWS        |    4 ++++
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 4 files changed, 15 insertions(+), 11 deletions(-)

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Package netClass updated to version 1.2.1 with previous version 1.2 dated 2013-09-18

Title: netClass: An R Package for Network-Based Biomarker Discovery
Description: netClass is an R package for network-based feature (gene) selection for biomarkers discovery via integrating biological information. This package adapts the following 5 algorithms for classifying and predicting gene expression data using prior knowledge: 1) average gene expression of pathway (aep); 2) pathway activities classification (PAC); 3) Hub network Classification (hubc); 4) filter via top ranked genes (FrSVM); 5) network smoothed t-statistic (stSVM).
Author: Yupeng Cun
Maintainer: Yupeng Cun

Diff between netClass versions 1.2 dated 2013-09-18 and 1.2.1 dated 2013-12-03

 DESCRIPTION   |    8 ++++----
 MD5           |    5 +++--
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Package iplots updated to version 1.1-7 with previous version 1.1-6 dated 2013-07-30

Title: iPlots - interactive graphics for R
Description: Interactive plots for R
Author: Simon Urbanek , Tobias Wichtrey
Maintainer: Simon Urbanek

Diff between iplots versions 1.1-6 dated 2013-07-30 and 1.1-7 dated 2013-12-03

 DESCRIPTION          |    6 +-
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 NAMESPACE            |    1 
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Package ecodist updated to version 1.2.9 with previous version 1.2.7 dated 2012-03-22

Title: Dissimilarity-based functions for ecological analysis
Description: Dissimilarity-based analysis functions including ordination and Mantel test functions, intended for use with spatial and community data.
Author: Sarah Goslee and Dean Urban
Maintainer: Sarah Goslee

Diff between ecodist versions 1.2.7 dated 2012-03-22 and 1.2.9 dated 2013-12-03

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Package Cairo updated to version 1.5-3 with previous version 1.5-2 dated 2012-11-05

Title: R graphics device using cairo graphics library for creating high-quality bitmap (PNG, JPEG, TIFF), vector (PDF, SVG, PostScript) and display (X11 and Win32) output.
Description: This package provides a Cairo graphics device that can be use to create high-quality vector (PDF, PostScript and SVG) and bitmap output (PNG,JPEG,TIFF), and high-quality rendering in displays (X11 and Win32). Since it uses the same back-end for all output, copying across formats is WYSIWYG. Files are created without the dependence on X11 or other external programs. This device supports alpha channel (semi-transparent drawing) and resulting images can contain transparent and semi-transparent regions. It is ideal for use in server environments (file output) and as a replacement for other devices that don't have Cairo's capabilities such as alpha support or anti-aliasing. Backends are modular such that any subset of backends is supported.
Author: Simon Urbanek , Jeffrey Horner
Maintainer: Simon Urbanek

Diff between Cairo versions 1.5-2 dated 2012-11-05 and 1.5-3 dated 2013-12-03

 DESCRIPTION   |   24 ---
 MD5           |   12 -
 NEWS          |    6 
 R/zzz.R       |    8 -
 configure     |  363 +++++++++++++++++++++++++++++++---------------------------
 src/cairogd.c |    9 +
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 7 files changed, 224 insertions(+), 200 deletions(-)

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Package wppExplorer updated to version 1.1-2 with previous version 1.1-1 dated 2013-10-09

Title: Explorer of World Population Prospects
Description: A shiny interface for exploring data in wpp2008-wpp2012 packages.
Author: Hana Sevcikova
Maintainer: Hana Sevcikova

Diff between wppExplorer versions 1.1-1 dated 2013-10-09 and 1.1-2 dated 2013-12-03

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Package weirs updated to version 0.23 with previous version 0.21 dated 2010-10-05

Title: A Hydraulics Package to Compute Open-Channel Flow over Weirs
Description: This hydraulics package provides computational support for flow over weirs, such as sharp-crested, broad-crested, and embankments. Initially, the package supports broad- and sharp-crested weirs.
Author: William Asquith
Maintainer: William Asquith

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Package randomizationInference updated to version 1.0.1 with previous version 1.0.0 dated 2013-09-10

Title: Flexible Randomization-Based Inference
Description: The 'randomizationInference' package allows the user to conduct randomization-based inference for a wide variety of experimental scenarios. The package leverages a potential outcomes framework to output randomization-based p-values and null intervals for any estimand of interest, according to the specified null and alternative hypotheses. The package also creates visualizations of randomization distributions and can test multiple test statistics simultaneously.
Author: Joseph J. Lee and Tirthankar Dasgupta
Maintainer: Joseph J. Lee

Diff between randomizationInference versions 1.0.0 dated 2013-09-10 and 1.0.1 dated 2013-12-03

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Package mefa updated to version 3.2-5 with previous version 3.2-4 dated 2013-10-07

Title: Multivariate Data Handling in Ecology and Biogeography
Description: A framework package aimed to provide standardized computational environment for specialist work via object classes to represent the data coded by samples, taxa and segments (i.e. subpopulations, repeated measures). It supports easy processing of the data along with cross tabulation and relational data tables for samples and taxa. An object of class `mefa' is a project specific compendium of the data and can be easily used in further analyses. Methods are provided for extraction, aggregation, conversion, plotting, summary and reporting of `mefa' objects. Reports can be generated in plain text or LaTeX format. Vignette contains worked examples.
Author: Peter Solymos
Maintainer: Peter Solymos

Diff between mefa versions 3.2-4 dated 2013-10-07 and 3.2-5 dated 2013-12-03

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Package LogicReg updated to version 1.5.5 with previous version 1.5.4 dated 2013-04-26

Title: Logic Regression
Description: Routines for Logic Regression
Author: Charles Kooperberg and Ingo Ruczinski
Maintainer: Charles Kooperberg

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Package lmomco updated to version 1.7.9 with previous version 1.7.8 dated 2013-07-05

Title: L-moments, Censored L-moments, Trimmed L-moments, L-comoments, and Many Distributions
Description: The package provides a comparatively comprehensive implementation of the theory of L-moments. Implementations for L-moment and probability-weighted moment (PWM) estimation, and parameter estimation for numerous familiar and not-so-familiar distributions are provided. L-moment estimation for the same distributions from parameters. L-moments are linear functions of order statistics and are linearly related to PWMs. L-moments are analogous to product moments; however, L-moments have many advantages including unbiasedness, robustness, and consistency. L-moments can outperform maximum likelihood for small to moderate samples. The lmomco package historically was originally oriented around circa 1996-FORTRAN algorithms by Hosking, and the nomenclature parallels those of the Hosking library. The Hosking algorithms later became available in the lmom package. However, vast extensions, components, concepts, L-moment curiosities, and research topics are added to aid and expand the breadth of L-moment applications. Such extensions the Sen weighted mean, Gini mean difference, plotting positions, and conditional probability adjustments. L-moment ratio diagrams are supported. Computations of L-moments for right-tail and left-tail censoring by known or unknown censoring threshold (via Hosking) and also by indicator variable (via Wang et al.) also are available. Asymmetric trimmed L-moments are supported as are numerical integration dynamically compute trajectories of select TL-moment ratios for the construction of TL-moment ratio diagrams. L-moments have been extended into multivariate space; the sample L-comoments are implemented and might have considerable application in copula theory because L-comoments measure asymmetric association and higher comoments or comovements of variables. The package supports exact analytical boot-strap estimates of order statistics, L-moments, and variances-covariances of L-moments. The package provides the Harri-Coble Tau34-squared Test for Normality using sample L-skew and L-kurtosis. Support for the following distributions, with moment type shown as "L" (L-moments) or "TL" (trimmed L-moments) and additional support for right-tail censoring ([RC]) include, is available: Asymmetric Exponential Power (L), Cauchy (TL), Eta-Mu (L), Exponential (L), Gamma (L), Generalized Extreme Value (L), Generalized Lambda (L & TL), Generalized Logistic (L), Generalized Normal (L), Generalized Pareto (L[RC] & TL), Gumbel (L), Kappa (L), Kappa-Mu (L), Kumaraswamy (L), Laplace (L), Normal (L), 3-parameter log-Normal (L), Pearson Type III (L), Rayleigh (L), Reverse Gumbel (L[RC]), Rice/Rician (L), Truncated Exponential (L), Wakeby (L), and Weibull (L).
Author: William Asquith
Maintainer: William Asquith

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New package clere with initial version 1.0
Package: clere
Type: Package
Title: CLERE methodology for simultaneous variables clustering and regression.
Version: 1.0
Date: 2013-11-21
Authors@R: c(person("Loic", "Yengo", role = c("aut", "cre"), email = "loic.yengo@gmail.com"), person("Mickael", "Canouil", role = "ctb", email = "mickael.canouil@good.ibl.fr"))
Description: This package implements the CLERE methodology for simultaneous variables clustering and regression.
License: GPL (>= 2)
Depends: Rcpp (>= 0.10.3), methods
Suggests: grid, ggplot2
LinkingTo: Rcpp
Collate: 'fit.clere.R' 'Clere.R' 'sClere-Class.R'
Packaged: 2013-12-03 18:20:18 UTC; root
Author: Loic Yengo [aut, cre], Mickael Canouil [ctb]
Maintainer: Loic Yengo
NeedsCompilation: yes
Repository: CRAN
Date/Publication: 2013-12-03 20:12:20

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Package bayesPop updated to version 4.2-2 with previous version 4.2-1 dated 2013-10-10

Title: Probabilistic Population Projection
Description: The package allows to generate population projections for all countries of the world using several probabilistic components, such as total fertility rate (TFR) and life expectancy.
Author: Hana Sevcikova, Adrian Raftery
Maintainer: Hana Sevcikova

Diff between bayesPop versions 4.2-1 dated 2013-10-10 and 4.2-2 dated 2013-12-03

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Package smacof updated to version 1.2-3 with previous version 1.2-1 dated 2011-11-29

Title: SMACOF for Multidimensional Scaling.
Description: This package provides the following approaches of multidimensional scaling (MDS) based on stress minimization by means of majorization (smacof): Simple smacof on symmetric dissimilarity matrices, smacof for rectangular matrices (unfolding models), smacof with constraints on the configuration, three-way smacof for individual differences (including constraints for idioscal, indscal, and identity), and spherical smacof (primal and dual algorithm). Each of these approaches is implemented in a metric and nonmetric manner including primary, secondary, and tertiary approaches for tie handling. Jackknife and permutation tests are included as well.
Author: Jan de Leeuw, Patrick Mair
Maintainer: Jan de Leeuw

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Package sgr updated to version 1.0.3 with previous version 1.0.2 dated 2013-08-17

Title: Sample Generation by Replacement
Description: The library for Sample Generation by Replacement simulations. The package can be used to perform fake data analysis according to the sample generation by replacement approach. It includes functions for making simple inferences about discrete/ordinal fake data. The package allows to study the implications of fake data for empirical results.
Author: Massimiliano Pastore & Luigi Lombardi
Maintainer: Massimiliano Pastore

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Package ESPRESSO updated to version 2.0 with previous version 1.1 dated 2011-12-19

Title: Power Analysis and Sample Size Calculation
Description: The package allows for the Estimation of Sample-size and Power by Exploring Simulated Study Outcomes. WE ARE AWARE A BUG ON THE LAST VERSION OF THE TOOL AND I WORKING TO SORT IT OUT. A NEW VERSION WILL BE AVAILABLE BY THE END OF DECEMBER 2013. WE ARE ALSO WORKING ON A WEB-BASED INTERFACE WHICH THAT WILL BE AVAILABLE AT www.espresso-research.org
Author: A. Gaye & Burton P.
Maintainer: Amadou Gaye

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Package BoolNet updated to version 1.62 with previous version 1.61 dated 2013-03-20

Title: Generation, reconstruction, simulation and analysis of synchronous, asynchronous, and probabilistic Boolean networks
Description: Provides methods to reconstruct and generate synchronous, asynchronous, and probabilistic Boolean networks, and to analyze and visualize attractors in Boolean networks
Author: Christoph Müssel, Martin Hopfensitz, Dao Zhou, Hans Kestler
Maintainer: Hans Kestler

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Package ClustOfVar updated to version 0.8 with previous version 0.7 dated 2012-09-19

Title: Clustering of variables
Description: Cluster analysis of a set of variables. Variables can be quantitative, qualitative or a mixture of both.
Author: Marie Chavent and Vanessa Kuentz and Benoit Liquet and Jerome Saracco
Maintainer: Marie Chavent

Diff between ClustOfVar versions 0.7 dated 2012-09-19 and 0.8 dated 2013-12-03

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Package WhopGenome updated to version 0.8.2 with previous version 0.8.1 dated 2013-11-19

Title: High-speed processing of whole-genome VCF-format variation data, FASTA-format sequence data and several alignments formats.
Description: WhopGenome's provides very fast access to whole genome, population scale variation data from VCF files and sequence data from FASTA-formatted files. It also reads in alignments from FASTA, Phylip, MAF and other file formats. Provides easy-to-use interfaces to genome annotation from UCSC and Bioconductor and gene ontology data from AmiGO and is capable to read, modify and write PLINK .PED-format pedigree files.
Author: Ulrich Wittelsbuerger
Maintainer: Ulrich Wittelsbuerger

Diff between WhopGenome versions 0.8.1 dated 2013-11-19 and 0.8.2 dated 2013-12-03

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Package RImpala updated to version 0.1.1 with previous version 0.1.0 dated 2013-11-27

Title: RImpala
Description: A package to connect and run queries on Cloudera Impala (thanks to Mu Sigma)
Author: Austin Chungath Vincent, Sachin Sudarshana, Vikas Raguttahalli
Maintainer: Austin Chungath Vincent

Diff between RImpala versions 0.1.0 dated 2013-11-27 and 0.1.1 dated 2013-12-03

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New package seasonal with initial version 0.20.2
Package: seasonal
SystemRequirements: Binary executables of X-13ARIMA-SEATS (installation details included)
Type: Package
Title: R interface to X-13ARIMA-SEATS
Version: 0.20.2
Date: 2013-12-02
Author: Christoph Sax
Maintainer: Christoph Sax
Description: seasonal is an easy-to-use R-interface to X-13ARIMA-SEATS, a seasonal adjustment software developed by the United States Census Bureau. X-13ARIMA-SEATS combines and extends the capabilities of the older X-12ARIMA (developed by the Census Bureau) and the TRAMO-SEATS (developed by the Bank of Spain) software packages. For installation details, see the vignette.
Imports: stringr
Enhances: manipulate
License: GPL-3
Collate: 'parse.R' 'plot.R' 'seas.R' 'outlier.R' 'inspect.R' 'static.R' 'read_data.R' 'read_est.R' 'read_mdl.R' 'summary.R' 'extractors.R' 'default.methods.R' 'read_lks.R' 'startup.R' 'seasonal-package.R'
BugReports: https://github.com/christophsax/seasonal
Packaged: 2013-12-03 10:41:48 UTC; christophsax
NeedsCompilation: no
Repository: CRAN
Date/Publication: 2013-12-03 13:30:38

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Package Interpol.T updated to version 2.1.1 with previous version 2.1 dated 2012-08-03

Title: Hourly interpolation of multiple temperature daily series
Description: Hourly interpolation of daily minimum and maximum temperature series. Carries out interpolation on multiple series ad once. Requires some hourly series for calibration (alternatively can use default calibration table).
Author: Emanuele Eccel & Emanuele Cordano
Maintainer: Emanuele Eccel

Diff between Interpol.T versions 2.1 dated 2012-08-03 and 2.1.1 dated 2013-12-03

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Package catR updated to version 2.6 with previous version 2.5 dated 2013-02-07

Title: Procedures to generate IRT adaptive tests (CAT)
Description: The catR package allows the generation of response patterns under computerized adaptive testing (CAT) framework, with the choice of several starting rules, next item selection routines, stopping rules and ability estimators. Control methods for item exposure and content balancing are also included.
Author: David Magis (U Liege, Belgium), Gilles Raiche (UQAM, Canada)
Maintainer: David Magis

Diff between catR versions 2.5 dated 2013-02-07 and 2.6 dated 2013-12-03

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Package lfe updated to version 1.6-1161 with previous version 1.5-1118 dated 2013-11-12

Title: Linear Group Fixed Effects
Description: Transforms away factors with many levels prior to doing an OLS. Useful for estimating linear models with multiple group fixed effects, and for estimating linear models which uses factors as pure control variables.
Author: Simen Gaure, Ragnar Frisch Centre for Economic Research
Maintainer: Simen Gaure

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Package DEMEtics updated to version 0.8-7 with previous version 0.8-5 dated 2012-02-26

Title: Evaluating the genetic differentiation between populations based on Gst and D values.
Description: This package allows to calculate the fixation index Gst (Nei, 1973) and the differentiation index D (Jost, 2008) pairwise between or averaged over several populations. P-values, stating the significance of differentiation, and 95 percent confidence intervals can be estimated using bootstrap resamplings. In the case that more than two populations are compared pairwise, the p-values are adjusted by bonferroni correction and in several other ways due to the multiple comparison from one data set.
Author: Alexander Jueterbock, Philipp Kraemer, Gabriele Gerlach and Jana Deppermann
Maintainer: Alexander Jueterbock

Diff between DEMEtics versions 0.8-5 dated 2012-02-26 and 0.8-7 dated 2013-12-03

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Package pedgene updated to version 1.3 with previous version 1.2 dated 2013-11-18

Title: Gene-level statistics for Pedigree Data
Description: Gene-level association tests with disease status for pedigree data: kernel and burden association statistics.
Author: Dan Schaid and Jason Sinnwell
Maintainer: Jason Sinnwell

Diff between pedgene versions 1.2 dated 2013-11-18 and 1.3 dated 2013-12-03

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Package lmeNBBayes updated to version 1.1 with previous version 1.0 dated 2013-04-16

Title: Sample from the posterior of the negative binomial mixed-effect regression model. The random effect is modeled with DP mixture of beta distributions.
Description: This package contains a gibbs sampler to sample from the posterior distribution of the negative binomial mixed-effect regression model. For the distribution of subject-specific random intercept, user can choose a beta distribution or an infinite mixture of beta distributions. For the safety monitoring, subject-specific conditional probability indices can be computed. For details, see Kondo,Y. and Zhao, Y. A Flexible Mixed Effect Negative Binomial Regression for Detecting Abrupt Increase in MRI Lesion Counts in Multiple Sclerosis Patients.
Author: Yumi Kondo
Maintainer: Yumi Kondo

Diff between lmeNBBayes versions 1.0 dated 2013-04-16 and 1.1 dated 2013-12-03

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Package lmeNB updated to version 1.1 with previous version 1.0 dated 2013-04-16

Title: Fit negative binomial mixed-effect regression model.
Description: Fit negative binomial mixed-effect regression model. For the distribution of subject-specific random intercept, a gamma or log-normal distributions or semi-parametric procedure are allowed. For the safety monitoring, subject-specific conditional probability index can be computed. For details, see Zhao, Y., Li, D.K.B., Petkau, J.A., Riddehough, A. & Traboulsee, A. Detection of unusual increases in MRI lesion counts in multiple sclerosis patients.
Author: Zhao, Y. and Kondo, Y.
Maintainer: Yumi Kondo

Diff between lmeNB versions 1.0 dated 2013-04-16 and 1.1 dated 2013-12-03

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Package GLDEX updated to version 1.0.4.5 with previous version 1.0.4.4 dated 2012-10-24

Title: Fitting Single and Mixture of Generalised Lambda Distributions (RS and FMKL) using Various Methods
Description: The fitting algorithms considered in this package have two major objectives. One is to provide a smoothing device to fit distributions to data using the weight and unweighted discretised approach based on the bin width of the histogram. The other is to provide a definitive fit to the data set using the maximum likelihood and quantile matching estimation. Other methods such as moment matching, starship method, L moment matching are also provided. Diagnostics on goodness of fit can be done via qqplots, KS-resample tests and comparing mean, variance, skewness and kurtosis of the data with the fitted distribution.
Author: Steve Su, with contributions from: Diethelm Wuertz, Martin Maechler and Rmetrics core team members for low discrepancy algorithm, Juha Karvanen for L moments codes, Robert King for gld C codes and starship codes, Benjamin Dean for corrections and input in ks.gof code and R core team for histsu function.
Maintainer: Steve Su

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Package gemtc updated to version 0.5-2 with previous version 0.5-1 dated 2013-10-30

Title: GeMTC network meta-analysis
Description: An R package for performing network meta-analyses (mixed treatment comparisons).
Author: Gert van Valkenhoef, Joel Kuiper
Maintainer: Gert van Valkenhoef

Diff between gemtc versions 0.5-1 dated 2013-10-30 and 0.5-2 dated 2013-12-03

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Package cheddar updated to version 0.1-624 with previous version 0.1-622 dated 2013-03-21

Title: Analysis and visualisation of ecological communities
Description: Cheddar provides a flexible, extendable representation of an ecological community and a range of functions for analysis and visualisation, focusing on food web, body mass and numerical abundance data. It also allows inter-web comparisons such as examining changes in community structure over environmental, temporal or spatial gradients.
Author: Lawrence Hudson with contributions from Dan Reuman and Rob Emerson
Maintainer: Lawrence Hudson

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Package ADM3 updated to version 1.3 with previous version 1.2 dated 2013-07-15

Title: An Interpretation of the ADM method - automated detection algorithm.
Description: Robust change point detection using ADM3 algorithm.
Author: Tomas William Fitzgerald
Maintainer: Tom Fitzgerald

Diff between ADM3 versions 1.2 dated 2013-07-15 and 1.3 dated 2013-12-03

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 4 files changed, 7 insertions(+), 6 deletions(-)

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Package adk (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:

2011-06-19 1.0-2
2011-05-21 1.0-1
2008-01-23 1.0

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Package EstSimPDMP (with last version 1.1) was removed from CRAN

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

2012-04-10 1.1

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Package sifds (with last version 0.9-1) was removed from CRAN

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

2010-08-23 0.9-1
2010-04-02 0.9

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Package charlson (with last version 1.0) was removed from CRAN

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

2010-08-12 1.0

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Package seqMeta updated to version 1.3 with previous version 1.2 dated 2013-09-09

Title: An R package for meta-analyzing region-based tests of rare DNA variants
Description: Computes necessary information to meta analyze region-based tests for rare genetic variants (e.g. SKAT, T1) in individual studies, and performs meta analysis.
Author: Arend Voorman, Jennifer Brody, Han Chen, Thomas Lumley
Maintainer: Arend Voorman

Diff between seqMeta versions 1.2 dated 2013-09-09 and 1.3 dated 2013-12-03

 DESCRIPTION           |    8 
 MD5                   |   24 +-
 NAMESPACE             |    2 
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 inst/doc/seqMeta.pdf  |binary
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Package RcmdrPlugin.BCA updated to version 0.9-7 with previous version 0.9-6 dated 2013-07-15

Title: Rcmdr Plug-In for Business and Customer Analytics
Description: This package provides an Rcmdr "plug-in" to accompany the book Customer and Business Analytics: Applied Data Mining for Business Decision Making Using R by Daniel S. Putler and Robert E. Krider.
Author: Dan Putler
Maintainer: Dan Putler

Diff between RcmdrPlugin.BCA versions 0.9-6 dated 2013-07-15 and 0.9-7 dated 2013-12-03

 DESCRIPTION         |    8 ++++----
 MD5                 |    6 +++---
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 R/RcmdrPlugin.BCA.R |   17 +++++++++--------
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New package jsonlite with initial version 0.9.0
Package: jsonlite
Version: 0.9.0
Title: Convert R objects to JSON and vice versa
License: Apache License (== 2.0)
NeedsCompilation: yes
Depends: methods
Author: Jeroen Ooms, Duncan Temple Lang
URL: http://github.com/jeroenooms/jsonlite#readme
BugReports: http://github.com/jeroenooms/jsonlite/issues
Maintainer: Jeroen Ooms
VignetteBuilder: knitr
Description: This package is a fork of the RJSONIO package by Duncan Temple Lang. It builds on the parser from RJSONIO, but implements a different mapping between R objects and JSON strings. The C code in this package is mostly from Temple Lang, the R code has been rewritten from scratch. In addition to drop-in replacements for fromJSON and toJSON, the package has functions to serialize objects. Furthermore, the package contains a lot of unit tests to make sure that all edge cases are encoded and decoded consistently for use with dynamic data in systems and applications.
Suggests: testthat, knitr, reshape2, httr
Packaged: 2013-12-02 17:58:25 UTC; jeroen
Repository: CRAN
Date/Publication: 2013-12-03 08:23:02

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Package digest updated to version 0.6.4 with previous version 0.6.3 dated 2013-02-16

Title: Create cryptographic hash digests of R objects
Description: The digest package provides a function 'digest()' for the creation of hash digests of arbitrary R objects (using the md5, sha-1, sha-256 and crc32 algorithms) permitting easy comparison of R language objects, as well as a function 'hmac()' to create hash-based message authentication code. The md5 algorithm by Ron Rivest is specified in RFC 1321, the sha-1 and sha-256 algorithms are specified in FIPS-180-1 and FIPS-180-2, and the crc32 algorithm is described in ftp://ftp.rocksoft.com/cliens/rocksoft/papers/crc_v3.txt. For md5, sha-1, sha-256 and aes, this package uses a small standalone implementations that were provided by Christophe Devine. For crc32, code from the zlib library is used. For sha-512, an implementation by Aaron D. Gifford is used. Please note that this package is not meant to be deployed for cryptographic purposes for which more comprehensive (and widely tested) libraries such as OpenSSL should be used.
Author: Dirk Eddelbuettel with contributions by Antoine Lucas, Jarek Tuszynski, Henrik Bengtsson, Simon Urbanek, Mario Frasca, Bryan Lewis, Murray Stokely, Hannes Muehleisen and Duncan Murdoch.
Maintainer: Dirk Eddelbuettel

Diff between digest versions 0.6.3 dated 2013-02-16 and 0.6.4 dated 2013-12-03

 ChangeLog     |    7 +++++++
 DESCRIPTION   |   48 ++++++++++++++++++++++++------------------------
 MD5           |   10 +++++-----
 man/digest.Rd |   11 +++++++----
 man/hmac.Rd   |    6 ++++--
 src/sha2.h    |   13 +++++++++++++
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Package aspect updated to version 1.0-2 with previous version 1.0-0 dated 2010-01-02

Title: Aspects of Multivariables
Description: This package consists of two main functions: The first function is corAspect() performs optimal scaling by maximizing an aspect (i.e. a target function such as the sum of eigenvalues, sum of squared correlations, squared multiple correlations, etc.) of the corresponding correlation matrix. The second function is lineals() performs optimal scaling by minimization a non-correlational aspect based on pairwise correlations and correlation ratios. The resulting correlation matrix and category scores can be used for further multivariate methods such as SEM. A platform including related PsychoR packages is provided on R-Forge.
Author: Jan de Leeuw, Kurt Hornik, Patrick Mair
Maintainer: Jan de Leeuw

Diff between aspect versions 1.0-0 dated 2010-01-02 and 1.0-2 dated 2013-12-03

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Package anacor updated to version 1.0-4 with previous version 1.0-2 dated 2013-04-05

Title: Simple and Canonical Correspondence Analysis.
Description: This package performs simple and canonical CA (covariates on rows/columns) on a two-way frequency table (with missings) by means of SVD. Different scaling methods (standard, centroid, Benzecri, Goodman) as well as various plots including confidence ellipsoids are provided.
Author: Jan de Leeuw, Patrick Mair
Maintainer: Jan de Leeuw

Diff between anacor versions 1.0-2 dated 2013-04-05 and 1.0-4 dated 2013-12-03

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