Tue, 15 Sep 2015

Package SimReg updated to version 1.2 with previous version 1.1 dated 2015-08-27

Title: Similarity Regression Functions
Description: Functions for performing Bayesian `similarity regression', adapted to model the association between an HPO-encoded patient phenotype and binary genotype. A `no association' model is compared with one in which the log odds of having a rare genotype is linked to the semantic similarity between patient phenotype and a latent characteristic phenotype. The method estimates the probability of an association together with an HPO-coded phenotype characteristic of the disease.
Author: Daniel Greene
Maintainer: Daniel Greene <dg333@cam.ac.uk>

Diff between SimReg versions 1.1 dated 2015-08-27 and 1.2 dated 2015-09-15

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Package RNiftyReg updated to version 2.0.0 with previous version 1.1.5 dated 2015-09-03

Title: Image Registration Using the NiftyReg Library
Description: Provides an R interface to the NiftyReg image registration tools <http://sourceforge.net/projects/niftyreg/>. Linear and nonlinear registration are supported, in two and three dimensions.
Author: Jon Clayden, based on original code by Marc Modat, Pankaj Daga and others
Maintainer: Jon Clayden <code@clayden.org>

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More information about RNiftyReg at CRAN
Permanent link

Package lgarch updated to version 0.6-2 with previous version 0.5 dated 2014-09-01

Title: Simulation and Estimation of Log-GARCH Models
Description: Simulation and estimation of univariate and multivariate log-GARCH models. The main functions of the package are: lgarchSim(), mlgarchSim(), lgarch() and mlgarch(). The first two functions simulate from a univariate and a multivariate log-GARCH model, respectively, whereas the latter two estimate a univariate and multivariate log-GARCH model, respectively.
Author: Genaro Sucarrat
Maintainer: Genaro Sucarrat <genaro.sucarrat@bi.no>

Diff between lgarch versions 0.5 dated 2014-09-01 and 0.6-2 dated 2015-09-15

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More information about lgarch at CRAN
Permanent link

Package VIM updated to version 4.4.1 with previous version 4.3.0 dated 2015-07-07

Title: Visualization and Imputation of Missing Values
Description: New tools for the visualization of missing and/or imputed values are introduced, which can be used for exploring the data and the structure of the missing and/or imputed values. Depending on this structure of the missing values, the corresponding methods may help to identify the mechanism generating the missing values and allows to explore the data including missing values. In addition, the quality of imputation can be visually explored using various univariate, bivariate, multiple and multivariate plot methods. A graphical user interface available in the separate package VIMGUI allows an easy handling of the implemented plot methods.
Author: Matthias Templ, Andreas Alfons, Alexander Kowarik, Bernd Prantner
Maintainer: Matthias Templ <matthias.templ@gmail.com>

Diff between VIM versions 4.3.0 dated 2015-07-07 and 4.4.1 dated 2015-09-15

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More information about VIM at CRAN
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Package TDA updated to version 1.4 with previous version 1.3 dated 2014-12-22

Title: Statistical Tools for Topological Data Analysis
Description: Tools for the statistical analysis of persistent homology and for density clustering. For that, this package provides an R interface for the efficient algorithms of the C++ libraries GUDHI, Dionysus, and PHAT.
Author: Brittany T. Fasy, Jisu Kim, Fabrizio Lecci, Clement Maria, Vincent Rouvreau. The included GUDHI is authored by Clement Maria, Dionysus by Dmitriy Morozov, and PHAT by Ulrich Bauer, Michael Kerber, and Jan Reininghaus.
Maintainer: Jisu Kim <jisuk1@andrew.cmu.edu>

Diff between TDA versions 1.3 dated 2014-12-22 and 1.4 dated 2015-09-15

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More information about TDA at CRAN
Permanent link

New package Relatedness with initial version 1.0
Package: Relatedness
Type: Package
Title: An Algorithm to Infer Relatedness
Version: 1.0
Date: 2015-09-03
Author: Fabien Laporte
Maintainer: Fabien Laporte <fabien.laporte@moulon.inra.fr>
Description: Inference of relatedness coefficients from a bi-allelic genotype matrix using a Maximum Likelihood estimation.
License: AGPL-3
NeedsCompilation: yes
Packaged: 2015-09-15 11:57:02 UTC; fabien
Repository: CRAN
Date/Publication: 2015-09-15 15:15:16

More information about Relatedness at CRAN
Permanent link

Package QuantumClone updated to version 0.9.15 with previous version 0.6.15 dated 2015-06-12

Title: Clustering Mutations using High Throughput Sequencing (HTS) Data
Description: Using HTS data, clusters mutations in order to recreate putative clones from the data provided. It requires genotype at the location of the variant as well as the depth of coverage and number of reads supporting the mutation. Additional information may be provided, such as the contamination in the tumor sample. This package also provides a function QuantumCat() which simulates data obtained from tumor sequencing. Latest version can be found at github/DeveauP/QuantumClone .
Author: Paul Deveau [aut, cre]
Maintainer: Paul Deveau <paul.deveau@curie.fr>

Diff between QuantumClone versions 0.6.15 dated 2015-06-12 and 0.9.15 dated 2015-09-15

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More information about QuantumClone at CRAN
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Package picasso updated to version 0.4.7 with previous version 0.3.0 dated 2014-10-18

Title: Pathwise Calibrated Sparse Shooting Algorithm
Description: Implement the pathwise calibrated sparse shooting algorithm (PICASSO) for high dimensional regularized sparse linear regression, sparse logistic regression, and sparse undirected graphical model estimation. As a pathwise coordinate optimization algorithm, PICASSO exploits warm start initialization, active set updating, and strong rule for coordinate preselection to boost computation, and attains a linear convergence to a unique sparse local optimum with optimal statistical properties. Moreover, users can choose different regularizers, including L1, MCP, and SCAD regularizers. The computation is memory-optimized using the sparse matrix output.
Author: Xingguo Li, Tuo Zhao, and Han Liu
Maintainer: Xingguo Li <xingguo.leo@gmail.com>

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New package DCchoice with initial version 0.0.13-3
Package: DCchoice
Version: 0.0.13-3
Date: 2015-9-15
Title: Analyzing Dichotomous Choice Contingent Valuation Data
Authors@R: c( person("Tomoaki", "Nakatani", role = c("aut", "cph"), email = "naktom2@gmail.com", comment = "original developer"), person("Hideo", "Aizaki", role = c("aut", "cre"), email = "azk-r@spa.nifty.com", comment = "code patches"), person("Kazuo", "Sato", role = "ctb", email = "satokazu@rakuno.ac.jp", comment = "theoretical part of the manual"))
Depends: R (>= 3.1.0), stats, MASS, Ecdat, interval
License: GPL (>= 2)
Description: Functions for analyzing dichotomous choice contingent valuation (CV) data. It provides functions for estimating parametric and nonparametric models for single- and double-bounded CV data.
URL: http://www.agr.hokudai.ac.jp/spmur/
NeedsCompilation: no
Packaged: 2015-09-15 07:05:53 UTC; nakatani
Author: Tomoaki Nakatani [aut, cph] (original developer), Hideo Aizaki [aut, cre] (code patches), Kazuo Sato [ctb] (theoretical part of the manual)
Maintainer: Hideo Aizaki <azk-r@spa.nifty.com>
Repository: CRAN
Date/Publication: 2015-09-15 15:15:11

More information about DCchoice at CRAN
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Package ClusterStability updated to version 1.0.1 with previous version 1.0.0 dated 2015-09-14

Title: Assessment of Stability of Individual Objects or Clusters in Partitioning Solutions
Description: Allows one to assess the stability of individual objects, clusters and whole clustering solutions based on repeated runs of the K-means and K-medoids partitioning algorithms.
Author: Etienne Lord, Francois-Joseph Lapointe, and Vladimir Makarenkov
Maintainer: Etienne Lord <m.etienne.lord@gmail.com>

Diff between ClusterStability versions 1.0.0 dated 2015-09-14 and 1.0.1 dated 2015-09-15

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Package BBEST updated to version 0.1-5 with previous version 0.1-4 dated 2015-04-06

Title: Bayesian Estimation of Incoherent Neutron Scattering Backgrounds
Description: We implemented a Bayesian-statistics approach for subtraction of incoherent scattering from neutron total-scattering data. In this approach, the estimated background signal associated with incoherent scattering maximizes the posterior probability, which combines the likelihood of this signal in reciprocal and real spaces with the prior that favors smooth lines.
Author: Anton Gagin and Igor Levin with contributions from Charles R. Hogg III
Maintainer: Anton Gagin <av.gagin@gmail.com>

Diff between BBEST versions 0.1-4 dated 2015-04-06 and 0.1-5 dated 2015-09-15

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Package arulesViz updated to version 1.0-4 with previous version 1.0-2 dated 2015-07-01

Title: Visualizing Association Rules and Frequent Itemsets
Description: Extends package arules with various visualization techniques for association rules and itemsets. The package also includes several interactive visualizations for rule exploration.
Author: Michael Hahsler and Sudheer Chelluboina
Maintainer: Michael Hahsler <mhahsler@lyle.smu.edu>

Diff between arulesViz versions 1.0-2 dated 2015-07-01 and 1.0-4 dated 2015-09-15

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Package arules updated to version 1.2-0 with previous version 1.1-9 dated 2015-07-14

Title: Mining Association Rules and Frequent Itemsets
Description: Provides the infrastructure for representing, manipulating and analyzing transaction data and patterns (frequent itemsets and association rules). Also provides interfaces to C implementations of the association mining algorithms Apriori and Eclat by C. Borgelt.
Author: Michael Hahsler [aut, cre, cph], Christian Buchta [aut, cph], Bettina Gruen [aut, cph], Kurt Hornik [aut, cph], Christian Borgelt [ctb, cph]
Maintainer: Michael Hahsler <mhahsler@lyle.smu.edu>

Diff between arules versions 1.1-9 dated 2015-07-14 and 1.2-0 dated 2015-09-15

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Package akima updated to version 0.5-12 with previous version 0.5-11 dated 2013-09-16

Title: Interpolation of Irregularly and Regularly Spaced Data
Description: Several cubic spline interpolation methods of H. Akima for irregular and regular gridded data are available through this package, both for the bivariate case (irregular data: ACM 526 and ACM 761, regular data: ACM 433) and univariate case (ACM 697). Linear interpolation of irregular gridded data is also covered by reusing D. J. Renkas triangulation code which is part of Akimas Fortran code.
Author: Hiroshi Akima [aut, cph] (Fortran code (TOMS 526, 761, 697 and 433)), Albrecht Gebhardt [aut, cre, cph] (R port (interp* functions), bicubic* functions), Thomas Petzold [ctb, cph] (aspline function), Martin Maechler [ctb, cph] (interp2xyz function + enhancements), YYYY Association for Computing Machinery, Inc. [cph] (covers code from TOMS 526, 761, 697 and 433)
Maintainer: Albrecht Gebhardt <albrecht.gebhardt@aau.at>

Diff between akima versions 0.5-11 dated 2013-09-16 and 0.5-12 dated 2015-09-15

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Package sdcTable updated to version 0.19.4 with previous version 0.19.3 dated 2015-08-13

Title: Methods for Statistical Disclosure Control in Tabular Data
Description: Methods for statistical disclosure control in tabular data such as primary and secondary cell suppression are covered in this package.
Author: Bernhard Meindl
Maintainer: Bernhard Meindl <bernhard.meindl@statistik.gv.at>

Diff between sdcTable versions 0.19.3 dated 2015-08-13 and 0.19.4 dated 2015-09-15

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Package rhandsontable updated to version 0.2.1 with previous version 0.2 dated 2015-08-25

Title: Interface to the 'Handsontable.js' Library
Description: An R interface to the 'Handsontable' JavaScript library, which is a minimalist Excel-like data grid editor.
Author: Jonathan Owen [aut, cre, cph], Jeff Allen [ctb], Yihui Xie [ctb], Enzo Martoglio [ctb], Warpechowski Marcin [ctb, cph] (Handsontable.js library), Handsoncode sp. z o.o. [ctb, cph] (Handsontable.js library), Aisch Gregor [ctb, cph] (Chroma.js library), Wood Tim [ctb, cph] (Moment.js library), Chernev Iskren [ctb, cph] (Moment.js library), Moment.js contributors [ctb, cph] (Moment.js library), Bushell David [ctb, cph] (Pikaday.js library), jQuery Foundation [ctb, cph] (jQuery.js library), Splunk Inc [ctb, cph] (Sparkline.js library)
Maintainer: Jonathan Owen <jonathanro@gmail.com>

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Package PPtreeViz updated to version 1.3.0 with previous version 1.1.0 dated 2015-06-25

Title: Projection Pursuit Classification Tree Visualization
Description: Tools for exploring projection pursuit classification tree using various projection pursuit indices.
Author: Eun-Kyung Lee
Maintainer: Eun-Kyung Lee <lee.eunk@gmail.com>

Diff between PPtreeViz versions 1.1.0 dated 2015-06-25 and 1.3.0 dated 2015-09-15

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Package mixsmsn updated to version 1.1-0 with previous version 1.0-9 dated 2013-08-17

Title: Fitting Finite Mixture of Scale Mixture of Skew-Normal Distributions
Description: Functions to fit finite mixture of scale mixture of skew-normal (FM-SMSN) distributions.
Author: Marcos Prates [aut, cre, trl], Victor Lachos [aut], Celso Cabral [aut]
Maintainer: Marcos Prates <marcosop@est.ufmg.br>

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Package letsR updated to version 2.2 with previous version 2.1 dated 2015-04-16

Title: Tools for Data Handling and Analysis in Macroecology
Description: R functions for handling, processing, and analyzing geographic data on species' distributions and environmental variables as well as species' description and conservation information.
Author: Bruno Vilela & Fabricio Villalobos
Maintainer: Bruno Vilela <brunovilelasilva@hotmail.com>

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Package Lahman updated to version 4.0-1 with previous version 3.0-1 dated 2014-09-13

Title: Sean Lahman's Baseball Database
Description: Provides the tables from Sean Lahman's Baseball Database as a set of R data.frames. It uses the data on pitching, hitting and fielding performance and other tables from 1871 through 2014, as recorded in the 2015 version of the database.
Author: Michael Friendly [aut], Dennis Murphy [ctb], Martin Monkman [ctb], Chris Dalzell [cre, ctb]
Maintainer: Chris Dalzell <cdalzell@gmail.com>

Diff between Lahman versions 3.0-1 dated 2014-09-13 and 4.0-1 dated 2015-09-15

 Lahman-3.0-1/Lahman/R/sysdata.rda                  |only
 Lahman-3.0-1/Lahman/data/SchoolsPlayers.RData      |only
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 Lahman-4.0-1/Lahman/DESCRIPTION                    |   29 ++--
 Lahman-4.0-1/Lahman/MD5                            |  128 ++++++++++-----------
 Lahman-4.0-1/Lahman/NEWS                           |   11 -
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 Lahman-4.0-1/Lahman/man/Lahman-package.Rd          |   10 -
 Lahman-4.0-1/Lahman/man/LahmanData.Rd              |    4 
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 Lahman-4.0-1/Lahman/man/Master.Rd                  |    8 -
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 Lahman-4.0-1/Lahman/man/PitchingPost.Rd            |    4 
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 Lahman-4.0-1/Lahman/man/SeriesPost.Rd              |    4 
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 Lahman-4.0-1/Lahman/man/TeamsFranchises.Rd         |    2 
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 70 files changed, 213 insertions(+), 205 deletions(-)

More information about Lahman at CRAN
Permanent link

New package cpgen with initial version 0.1
Package: cpgen
Type: Package
Title: Parallelized Genomic Prediction and GWAS
Version: 0.1
Date: 2015-09-14
Author: Claas Heuer
Maintainer: Claas Heuer <cheuer@tierzucht.uni-kiel.de>
Description: Frequently used methods in genomic applications with emphasis on parallel computing (OpenMP). At its core, the package has a Gibbs Sampler that allows running univariate linear mixed models that have both, sparse and dense design matrices. The parallel sampling method in case of dense design matrices (e.g. Genotypes) allows running Ridge Regression or BayesA for a very large number of individuals. The Gibbs Sampler is capable of running Single Step Genomic Prediction models. In addition, the package offers parallelized functions for common tasks like genome-wide association studies and cross validation in a memory efficient way.
License: GPL (>= 2)
SystemRequirements: C++11
Imports: methods, stats
URL: https://github.com/cheuerde/cpgen
Depends: R(>= 3.1.0), Matrix(>= 1.0-5), pedigreemm(>= 0.3-3)
LinkingTo: Rcpp, RcppEigen, RcppProgress
NeedsCompilation: yes
Packaged: 2015-09-14 21:44:43 UTC; cheuer
Repository: CRAN
Date/Publication: 2015-09-15 08:35:30

More information about cpgen at CRAN
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Package checkpoint updated to version 0.3.15 with previous version 0.3.10 dated 2015-04-27

Title: Install Packages from Snapshots on the Checkpoint Server for Reproducibility
Description: The goal of checkpoint is to solve the problem of package reproducibility in R. Specifically, checkpoint allows you to install packages as they existed on CRAN on a specific snapshot date as if you had a CRAN time machine. To achieve reproducibility, the checkpoint() function installs the packages required or called by your project and scripts to a local library exactly as they existed at the specified point in time. Only those packages are available to your project, thereby avoiding any package updates that came later and may have altered your results. In this way, anyone using checkpoint's checkpoint() can ensure the reproducibility of your scripts or projects at any time. To create the snapshot archives, once a day (at midnight UTC) Revolution Analytics refreshes the Austria CRAN mirror, on the "Managed R Archived Network" server (http://mran.revolutionanalytics.com/). Immediately after completion of the rsync mirror process, the process takes a snapshot, thus creating the archive. Snapshot archives exist starting from 2014-09-17.
Author: Revolution Analytics
Maintainer: Andrie de Vries <adevries@microsoft.com>

Diff between checkpoint versions 0.3.10 dated 2015-04-27 and 0.3.15 dated 2015-09-15

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 checkpoint-0.3.15/checkpoint/DESCRIPTION                            |   12 
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 checkpoint-0.3.15/checkpoint/NAMESPACE                              |   10 
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 checkpoint-0.3.15/checkpoint/R/checkpoint-package.R                 |   10 
 checkpoint-0.3.15/checkpoint/R/checkpoint.R                         |   66 ++---
 checkpoint-0.3.15/checkpoint/R/detach.R                             |    7 
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 checkpoint-0.3.15/checkpoint/R/scanRepoPackages.R                   |   50 ++-
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 checkpoint-0.3.15/checkpoint/inst/examples/example_setSnapshot.R    |    3 
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 checkpoint-0.3.15/checkpoint/tests/testthat/test-0-snapshots.R      |  100 +++++++
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 checkpoint-0.3.15/checkpoint/vignettes/checkpoint.Rmd               |    8 
 23 files changed, 345 insertions(+), 145 deletions(-)

More information about checkpoint at CRAN
Permanent link


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