Thu, 24 Jul 2014

New package ssh.utils with initial version 1.0
Package: ssh.utils
Title: Local and remote system commands with output and error capture.
Version: 1.0
Author: Sergei Izrailev
Maintainer: Sergei Izrailev
Description: This package provides utility functions for system command execution, both locally and remotely using ssh/scp. The command output is captured and provided to the caller. This functionality is intended to streamline calling shell commands from R, retrieving and using their output, while instrumenting the calls with appropriate error handling. NOTE: this first version is limited to unix with local and remote systems running bash as the default shell.
URL: http://github.com/collectivemedia/ssh.utils
Depends: R (>= 3.0.3), stringr
License: Apache License (== 2.0)
Copyright: Copyright (C) Collective, Inc. | file inst/COPYRIGHTS
LazyData: true
OS_type: unix
Packaged: 2014-07-24 02:53:39 UTC; user
NeedsCompilation: no
Repository: CRAN
Date/Publication: 2014-07-24 21:13:49

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Package pocrm updated to version 0.8 with previous version 0.7 dated 2014-03-11

Title: Dose-finding in drug combination Phase I trials using the partial order continual reassessment method (PO-CRM).
Description: This package provides functions to implement and simulate the partial order continual reassessment method (PO-CRM) for use in Phase I trials of combinations of agents. It also provides a function for generating a set of initial guesses (skeleton) for the toxicity probabilities at each combination that correspond to the set of possible orderings of the toxicity probabilities specified by the user.
Author: Nolan A. Wages
Maintainer: "Varhegyi, Nikole (nev4g)"

Diff between pocrm versions 0.7 dated 2014-03-11 and 0.8 dated 2014-07-24

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Package bold updated to version 0.1.2 with previous version 0.1.0 dated 2014-05-28

Title: Interface to Bold Systems API
Description: A programmatic interface to the Web Service methods provided by Bold Systems for genetic barcode data. Functions include methods for searching by sequences by taxonomic names, ids, collectors, and institutions; as well as a function for searching for specimens, and downloading trace files.
Author: Scott Chamberlain [aut, cre]
Maintainer: Scott Chamberlain

Diff between bold versions 0.1.0 dated 2014-05-28 and 0.1.2 dated 2014-07-24

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Package multcomp updated to version 1.3-5 with previous version 1.3-4 dated 2014-07-09

Title: Simultaneous Inference in General Parametric Models
Description: Simultaneous tests and confidence intervals for general linear hypotheses in parametric models, including linear, generalized linear, linear mixed effects, and survival models. The package includes demos reproducing analyzes presented in the book "Multiple Comparisons Using R" (Bretz, Hothorn, Westfall, 2010, CRC Press).
Author: Torsten Hothorn [aut, cre], Frank Bretz [aut], Peter Westfall [aut], Richard M. Heiberger [ctb], Andre Schuetzenmeister [ctb]
Maintainer: Torsten Hothorn

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Package simPH updated to version 1.2.2 with previous version 1.2.1 dated 2014-05-16

Title: Tools for simulating and plotting quantities of interest estimated from Cox Proportional Hazards models
Description: The package simulates and plots quantities of interest (relative hazards, first differences, and hazard ratios) for linear coefficients, multiplicative interactions, polynomials, penalised splines, and non-proportional hazards, as well as stratified survival curves from Cox Proportional Hazard models. It also simulates and plots marginal effects for multiplicative interactions.
Author: Christopher Gandrud
Maintainer: Christopher Gandrud

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Package RItools updated to version 0.1-12 with previous version 0.1-11 dated 2011-03-05

Title: Randomization inference tools
Description: Tools for randomization inference.
Author: Jake Bowers , Mark Fredrickson , and Ben Hansen
Maintainer: Jake Bowers

Diff between RItools versions 0.1-11 dated 2011-03-05 and 0.1-12 dated 2014-07-24

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New package rpg with initial version 1.0
Package: rpg
Type: Package
Title: Easy interface to advanced PostgreSQL features
Version: 1.0
Date: 2014-05-30
Author: Timothy H. Keitt
Maintainer: Timothy H. Keitt
Description: Allows ad hoc queries and reading and writing data frames to and from a database.
License: GPL (>= 2)
URL: http://www.postgresql.org/, http://github.com/thk686/rpg, http://r-forge.r-project.org/projects/rpg/, http://www.keittlab.org/
Imports: Rcpp (>= 0.11.1), uuid (>= 0.1-1), RApiSerialize (>= 0.1.0)
Suggests: foreach (>= 1.4.2), doParallel (>= 1.0.0), hflights (>= 0.1)
LinkingTo: Rcpp, RApiSerialize
SystemRequirements: libpq
Depends: R (>= 3.0.0)
NeedsCompilation: yes
Note: The files configure.in, cleanup, Makevars.in and Makevars.win are based on the same files found in RPostgreSQL. I thank Dirk Eddelbuettel for giving the go ahead to resue thier build setup. Copyright of the unmodified protions remains with the original authors. The files in src/libpq/ are part of PostgreSQL.
Repository: CRAN
Repository/R-Forge/Project: rpg
Repository/R-Forge/Revision: 18
Repository/R-Forge/DateTimeStamp: 2014-07-15 20:57:00
Date/Publication: 2014-07-24 18:53:44
Packaged: 2014-07-15 22:15:29 UTC; rforge

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Package dlnm updated to version 2.1.2 with previous version 2.1.0 dated 2014-05-21

Title: Distributed Lag Non-linear Models
Description: The package dlnm contains functions to specify and run distributed lag linear and non-linear models.
Author: Antonio Gasparrini and Ben Armstrong
Maintainer: Antonio Gasparrini

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Package tables updated to version 0.7.79 with previous version 0.7.64 dated 2013-11-12

Title: Formula-driven table generation
Description: Computes and displays complex tables of summary statistics
Author: Duncan Murdoch
Maintainer: Duncan Murdoch

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Package rebmix updated to version 2.6.1 with previous version 2.6.0 dated 2014-06-25

Title: The Rebmix Package
Description: R functions for random univariate and multivariate finite mixture generation, number of components, component weights and component parameters estimation, printing and plotting of finite mixtures, bootstrapping and class membership prediction. Variables can be either continuous or discrete, may follow normal, lognormal, Weibull, gamma, binomial, Poisson or Dirac parametric families and should be independent within components.
Author: Marko Nagode [aut, cre]
Maintainer: Marko Nagode

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Package randtoolbox updated to version 1.15 with previous version 1.14 dated 2013-06-11

Title: toolbox for pseudo and quasi random number generation and RNG tests.
Description: The package provides (1) pseudo random generators - general linear congruential generators (Park Miller) and multiple recursive generators (Knuth TAOCP), generalized feedback shift register (SF-Mersenne Twister algorithm and WELL generators); (2) quasi random generators - the Torus algorithm, the Sobol sequence, the Halton sequence (thus include Van der Corput sequence) and (3) some additional tests such as the gap test, the serial test, the poker test... The package depends on rngWELL package but it can be provided without this dependency on demand to the maintainer. For true random number generation, use the 'random' package, for Latin Hypercube Sampling (a hybrid QMC method), use the 'lhs' package, a number of RNGs and tests for RNGs are provided by 'RDieHarder', all available on CRAN. There is also a small stand-alone package 'rngwell19937' for the WELL19937a RNG.
Author: R port by Yohan Chalabi, Christophe Dutang, Petr Savicky and Diethelm Wuertz (underlying C codes of (i) the SFMT algorithm from M. Matsumoto and M. Saito, (ii) the Knuth-TAOCP RNG from D. Knuth).
Maintainer: Christophe Dutang

Diff between randtoolbox versions 1.14 dated 2013-06-11 and 1.15 dated 2014-07-24

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Package Power2Stage updated to version 0.1-4 with previous version 0.1-3 dated 2014-07-02

Title: Power and Sample size distribution of 2-stage BE studies via simulations
Description: Contains functions to calculate power and sample size distribution of 2-stage BE studies with a 2x2 crossover design according to Potvin et.al. / Montague et. al. modified to include a futility Nmax and modified to do the sample size estimation step with PE and mse of stage 1 as well as the power calculation steps according to Karalis & Macheras. The third function calculates power and sample size distribution of 2-stage BE studies with a futility criterion for the point estimator of T/R from stage 1. The fourth function calculates power of non-adaptive group sequential (2-stage) BE studies. The fifth function calculates power and sample size distribution of 2-stage BE studies in 2 parallel groups.
Author: Detlew Labes [aut, cre], Helmut Schuetz [ctb]
Maintainer: Detlew Labes

Diff between Power2Stage versions 0.1-3 dated 2014-07-02 and 0.1-4 dated 2014-07-24

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Package mkin updated to version 0.9-32 with previous version 0.9-31 dated 2014-07-14

Title: Routines for fitting kinetic models with one or more state variables to chemical degradation data
Description: Calculation routines based on the FOCUS Kinetics Report (2006). Includes a function for conveniently defining differential equation models, model solution based on eigenvalues if possible or using numerical solvers and a choice of the optimisation methods made available by the FME package (default is a Levenberg-Marquardt variant). Please note that no warranty is implied for correctness of results or fitness for a particular purpose.
Author: Johannes Ranke [aut, cre, cph], Katrin Lindenberger [ctb], René Lehmann [ctb], Eurofins Regulatory AG [cph]
Maintainer: Johannes Ranke

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New package mtk with initial version 1.0
Package: mtk
Type: Package
Title: Mexico ToolKit library (MTK)
Encoding: UTF-8
Version: 1.0
Date: 2014-07-15
Authors@R: c(person("Juhui", "WANG", role = c("aut", "cre"), email = "Juhui.Wang@jouy.inra.fr", comment = "Software and Engineering"), person("Hervé", "MONOD", role = "aut", email = "Herve.Monod@jouy.inra.fr", comment = "Applications and Statistical Methods"), person("Robert", "FAIVRE", role = "ctb", email = "faive@toulouse.inra.fr", comment = "Applications and Statistical Methods"), person("Hervé", "RICHARD", role = "ctb", email = "Herve.Richard@avignon.inra.fr", comment = "Software and Engineering") )
Author: Juhui WANG [aut, cre] (Software and Engineering), Hervé MONOD [aut] (Applications and Statistical Methods), Robert FAIVRE [ctb] (Applications and Statistical Methods), Hervé RICHARD [ctb] (Software and Engineering)
Maintainer: Juhui WANG
Description: MTK (Mexico ToolKit) is a generic platform for the sensitivity and uncertainty analysis of complex models. It provides functions and facilities for experimental design, model simulation, sensitivity and uncertainty analysis, methods integration and data reporting, etc.
License: GPL-3
LazyLoad: yes
Depends: R (>= 2.15.0), base, stringr, graphics, methods, XML, sensitivity, lhs, rgl
Suggests: MASS
Collate: 'mtkAllGenerics.R' 'globalsMtkFuncts.R' 'mtkValue.R' 'mtkFeature.R' 'mtkLevels.R' 'mtkParameter.R' 'mtkDomain.R' 'mtkFactor.R' 'mtkExpFactors.R' 'mtkProcess.R' 'mtkExpWorkflow.R' 'mtkExperiment.R' 'mtkParsor.R' 'mtkResult.R' 'mtkDesignerResult.R' 'mtkDesigner.R' 'mtkMorrisDesigner.R' 'mtkBasicMonteCarloDesigner.R' 'mtkRandLHSDesigner.R' 'mtkNativeDesigner.R' 'mtkSobolDesigner.R' 'mtkFastDesigner.R' 'mtkEvaluatorResult.R' 'mtkEvaluator.R' 'mtkNativeEvaluator.R' 'mtkIshigamiEvaluator.R' 'mtkWWDMEvaluator.R' 'mtkSystemEvaluatorResult.R' 'mtkSystemEvaluator.R' 'mtkAnalyserResult.R' 'mtkAnalyser.R' 'mtkNativeAnalyser.R' 'mtkDefaultAnalyser.R' 'mtkRegressionAnalyser.R' 'mtkMorrisAnalyser.R' 'mtkSobolAnalyser.R' 'mtkPLMMAnalyser.R' 'mtkFastAnalyser.R' 'mtk.addons.R' 'mtkPackage.R'
Packaged: 2014-07-24 08:40:45 UTC; jwang
NeedsCompilation: no
Repository: CRAN
Date/Publication: 2014-07-24 13:12:50

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Package ManyTests updated to version 1.1 with previous version 1.0 dated 2014-03-31

Title: Multiple testing procedures of Cox (2011) and Wang and Cox (2007).
Description: Performs the multiple testing procedures of Cox (2011) and Wang and Cox (2007).
Author: Christiana Kartsonaki
Maintainer: Christiana Kartsonaki

Diff between ManyTests versions 1.0 dated 2014-03-31 and 1.1 dated 2014-07-24

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Package lmerTest updated to version 2.0-11 with previous version 2.0-6 dated 2014-02-24

Title: Tests for random and fixed effects for linear mixed effect models (lmer objects of lme4 package).
Description: The package provides different kinds of tests on lmer objects (of lme4 package). The tests comprise type 3 and type 1 F tests for fixed effects, LRT tests for random effects, calculation of population means for fixed factors with confidence intervals and corresponding plots. Package also provides backward elimination of non-significant effects
Author: Alexandra Kuznetsova [aut, cre], Per Bruun Brockhoff [aut, ths], Rune Haubo Bojesen Christensen [aut]
Maintainer: Alexandra Kuznetsova

Diff between lmerTest versions 2.0-6 dated 2014-02-24 and 2.0-11 dated 2014-07-24

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Package imguR updated to version 1.0.0 with previous version 0.1.5 dated 2012-10-15

Title: Imgur API Client Package for R
Description: A package to share plots using the image hosting service Imgur.com
Author: Thomas J. Leeper [aut, cre], Aaron Statham [ctb], Yihui Xie [ctb]
Maintainer: Thomas J. Leeper

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Package spuRs updated to version 2.0.0 with previous version 1.0.5 dated 2012-08-03

Title: Functions and Datasets for "Introduction to Scientific Programming and Simulation Using R".
Description: This package provides functions and datasets from the book "Introduction to Scientific Programming and Simulation Using R".
Author: Owen Jones, Robert Maillardet, Andrew Robinson, Olga Borovkova, and Steven Carnie
Maintainer: Andrew Robinson

Diff between spuRs versions 1.0.5 dated 2012-08-03 and 2.0.0 dated 2014-07-24

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Package sensitivitymw updated to version 1.1 with previous version 1.0 dated 2014-05-13

Title: Sensitivity analysis using weighted M-statistics
Description: Sensitivity analysis analysis in matched observational studies with multiple controls using weighted M-statistics to increase design sensitivity.
Author: Paul R. Rosenbaum
Maintainer: Paul R. Rosenbaum

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New package rvalues with initial version 0.2
Package: rvalues
Type: Package
Title: Computation of r-values for ranking in high-dimensional settings.
Version: 0.2
Date: 2014-07-23
Author: Nicholas Henderson and Michael Newton
Maintainer: Nicholas Henderson
Description: This package provides several procedures for computing "r-values". Given a large collection of measurement units, the r-value, r, of a particular unit is a reported percentile that may be interpreted as the smallest percentile at which the unit should be placed in the top r-fraction of units.
License: GPL-2
Packaged: 2014-07-23 22:26:43 UTC; nhenders
NeedsCompilation: yes
Repository: CRAN
Date/Publication: 2014-07-24 08:22:43

More information about rvalues at CRAN
Permanent link

Package poppr updated to version 1.1.0 with previous version 1.0.6 dated 2014-03-05

Title: an R package for genetic analysis of populations with mixed reproduction
Description: Population genetic analyses for hierarchical analysis of partially clonal populations built upon the architecture of the adegenet package.
Author: Zhian N. Kamvar , Javier F. Tabima , Niklaus J. Grunwald
Maintainer: Zhian N. Kamvar

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Permanent link

Wed, 23 Jul 2014

New package rowr with initial version 1.0
Package: rowr
Title: Row-based functions for R objects.
Version: 1.0
Author: Craig Varrichio
Maintainer: Craig Varrichio
Description: Rowr allows the manipulation of R objects as if they were organized rows in a way that is familiar to people used to working with databases. It allows more consistent and predictable output to common functions, and generalizes a number of utility functions to to be failsafe with any number and type of input objects.
Depends: R (>= 3.1.0)
License: GPL-3
LazyData: true
Packaged: 2014-07-23 21:03:33 UTC; CVarrichio
NeedsCompilation: no
Repository: CRAN
Date/Publication: 2014-07-23 23:44:16

More information about rowr at CRAN
Permanent link

Package mada updated to version 0.5.6 with previous version 0.5.5 dated 2014-01-01

Title: Meta-Analysis of Diagnostic Accuracy (mada)
Description: This package provides functions for diagnostic meta-analysis. Next to basic analysis and visualization the bivariate Model of Reitsma et al. (2005) that is equivalent to the HSROC of Rutter&Gatsonis (2001) can be fitted. A new approach based to diagnostic meta-analysis of Holling et al. (2012) is also available. Standard methods like summary, plot and so on are provided.
Author: Philipp Doebler
Maintainer: Philipp Doebler

Diff between mada versions 0.5.5 dated 2014-01-01 and 0.5.6 dated 2014-07-23

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Package CAvariants updated to version 2.1 with previous version 2.0 dated 2014-06-26

Title: Correspondence Analysis Variants
Description: Six variants of two-way correspondence analysis can be performed, simple ca singly ordered ca doubly ordered ca non symmetrical ca singly ordered non symmetrical ca doubly ordered non symmetrical ca
Author: Rosaria Lombardo and Eric J Beh
Maintainer: Rosaria Lombardo

Diff between CAvariants versions 2.0 dated 2014-06-26 and 2.1 dated 2014-07-23

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More information about CAvariants at CRAN
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Package pitchRx updated to version 1.5 with previous version 1.4 dated 2014-05-27

Title: Tools for Harnessing MLBAM Gameday data and Visualizing PITCHf/x
Description: With pitchRx, one can easily obtain Major League Baseball Advanced Media's Gameday data (as well as store it in a remote database). The Gameday website hosts a wealth of data in XML format, but perhaps most interesting is PITCHf/x. Among other things, PITCHf/x data can be used to recreate a baseball's flight path from a pitcher's hand to home plate. With pitchRx, one can easily create animations and interactive 3D scatterplots of the baseball's flight path. PITCHf/x data is also commonly used to generate a static plot of baseball locations at the moment they cross home plate. These plots, sometimes called strike-zone plots, can also refer to a plot of event probabilities over the same region. pitchRx provides an easy and robust way to generate strike-zone plots using the ggplot2 package.
Author: Carson Sievert
Maintainer: Carson Sievert

Diff between pitchRx versions 1.4 dated 2014-05-27 and 1.5 dated 2014-07-23

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More information about pitchRx at CRAN
Permanent link

New package ecospat with initial version 1.0
Package: ecospat
Version: 1.0
Date: 2014-07-23
Title: Spatial ecology miscellaneous methods
Author: Olivier Broenniman and Blaise Petitpierre and Christophe Randin and Robin Engler and Frank Breiner and Manuela D`Amen and Loic Pellissier and Julien Pottier and Dorothea Pio and Ruben Garcia Mateo and Valeria Di Cola and Wim Hordijk and Anne Dubuis and Daniel Scherrer and Nicolas Salamin and Antoine Guisan
Maintainer: Valeria Di Cola
Depends: ade4, ape, gam, gbm, sp
Imports: adehabitatHR, adehabitatMA, biomod2, dismo, ecodist, maptools, randomForest, spatstat, raster, rms
Suggests: MigClim, rgdal, rJava, XML
LazyData: true
URL: http://www.unil.ch/ecospat/home/menuinst/tools--data/tools.html
Description: Miscellaneous methods and utilities for spatial ecology analysis, written by current and former members and collaborators of the ecospat group of Prof. Antoine Guisan, Department of Ecology and Evolution (DEE) & Institute of Earth Surface Dynamics (IDYST), University of Lausanne, Switzerland.
License: GPL
Packaged: 2014-07-23 10:30:53 UTC; valeriadicola
NeedsCompilation: no
Repository: CRAN
Date/Publication: 2014-07-23 21:13:51

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Permanent link

Package ecoengine updated to version 1.4 with previous version 1.3 dated 2014-04-14

Title: Programmatic interface to the API serving UC Berkeley's Natural History Data
Description: The ecoengine (http://ecoengine.berkeley.edu/) provides access to more than 2 million georeferenced specimen records from the Berkeley Natural History Museums. http://bnhm.berkeley.edu/
Author: Karthik Ram [aut, cre]
Maintainer: Karthik Ram

Diff between ecoengine versions 1.3 dated 2014-04-14 and 1.4 dated 2014-07-23

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Permanent link

Package survsim updated to version 1.1.2 with previous version 1.1.1 dated 2014-07-21

Title: Simulation of simple and complex survival data
Description: Simulation of simple and complex survival data
Author: David Moriña (Centre for Research in Environmental Epidemiology, CREAL) and Albert Navarro (Universitat Autònoma de Barcelona)
Maintainer: David Moriña Soler

Diff between survsim versions 1.1.1 dated 2014-07-21 and 1.1.2 dated 2014-07-23

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Package rnaseqWrapper updated to version 1.0-1 with previous version 1.0 dated 2014-07-17

Title: Wrapper for several R packages and scripts to automate RNA-seq analysis
Description: This package is designed to streamline several of the common steps for RNA-seq analysis, including differential expression and variant discovery. For the development build, or to contribute changes to this package, please see our repository at https://bitbucket.org/petersmp/rnaseqwrapper/
Author: Mark Peterson
Maintainer: Mark Peterson

Diff between rnaseqWrapper versions 1.0 dated 2014-07-17 and 1.0-1 dated 2014-07-23

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Permanent link

New package ReorderCluster with initial version 1.0
Package: ReorderCluster
Type: Package
Title: Reordering the dendrogram according to the class labels
Version: 1.0
Date: 2014-07-21
Author: Natalia Novoselova,Frank Klawonn, Junxi Wang
Maintainer: Natalia Novoselova
Description: Tools for performing the leaf reordering for the dendrogram that preserves the hierarchical clustering result and at the same time tries to group instances from the same class together.
License: GPL (>= 3)
Depends: R (>= 2.10),gplots,graphics
Imports: Rcpp (>= 0.11.0)
LinkingTo: Rcpp
Packaged: 2014-07-23 12:39:49 UTC; novosel
NeedsCompilation: yes
Repository: CRAN
Date/Publication: 2014-07-23 15:24:32

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New package MPAgenomics with initial version 1.1.0
Package: MPAgenomics
Type: Package
Title: Multi-Patient Analysis of Genomic Markers
Version: 1.1.0
Date: 2014-07-23
Author: Quentin Grimonprez with contributions from Guillemette Marot and Samuel Blanck. Some functions use code created by Sjoerd Vosse, Mark van de Wiel, Pierre Neuvial, Henrik Bengtsson.
Maintainer: Samuel Blanck
Description: MPAgenomics provides functions to preprocess and analyze genomic data. It provides wrappers from commonly used packages to streamline their repeated manipulation, offering an easy-to-use pipeline. The segmentation of successive multiple profiles is performed with an automatic choice of parameters involved in the wrapped packages. Considering multiple profiles in the same time, MPAgenomics wraps efficient penalized regression methods to select relevant markers associated with a given outcome.
License: GPL (>= 2)
Copyright: Inria 2012-2014.
Imports: R.utils,changepoint(>= 1.1),glmnet,cghseg
Suggests: HDPenReg,CGHcall,aroma.affymetrix,aroma.cn,snowfall
Packaged: 2014-07-23 12:43:12 UTC; sblanck
NeedsCompilation: no
Repository: CRAN
Date/Publication: 2014-07-23 15:24:28

More information about MPAgenomics at CRAN
Permanent link

Package miscFuncs updated to version 1.2-6 with previous version 1.2-4 dated 2013-12-14

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

Diff between miscFuncs versions 1.2-4 dated 2013-12-14 and 1.2-6 dated 2014-07-23

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Package hglm updated to version 2.0-8 with previous version 2.0-4 dated 2014-01-21

Title: Hierarchical Generalized Linear Models
Description: The hglm package is used to fit hierarchical generalized linear models. It can be used for linear mixed models and generalized linear mixed models with random effects for a variety of links and a variety of distributions for both the outcomes and the random effects. Fixed effects can also be fitted in the dispersion part of the mean model.
Author: Xia Shen, Moudud Alam, Lars Ronnegard
Maintainer: Xia Shen

Diff between hglm versions 2.0-4 dated 2014-01-21 and 2.0-8 dated 2014-07-23

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Permanent link

New package hglm.data with initial version 1.0-0
Package: hglm.data
Type: Package
Title: Data for The hglm Package
Version: 1.0-0
Date: 2014-07-23
Author: Xia Shen, Moudud Alam, Lars Ronnegard
Maintainer: Xia Shen
Description: This data-only package was created for distributing data used in the examples of the hglm package.
BugReports: https://r-forge.r-project.org/tracker/?group_id=558
License: GPL (>= 2)
LazyLoad: yes
Depends: R (>= 2.10), utils, Matrix, MASS
Packaged: 2014-07-23 11:25:13 UTC; xia
NeedsCompilation: no
Repository: CRAN
Date/Publication: 2014-07-23 15:24:34

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New package acp with initial version 1.0
Package: acp
Title: Autoregressive Conditional Poisson
Version: 1.0
Date: 2014-07-18
Author: Siakoulis Vasileios
Depends: tseries
Maintainer: Siakoulis Vasilios
Description: Package for time series analysis of count data
License: GPL-2
Packaged: 2014-07-22 21:56:52 UTC; siakbill
NeedsCompilation: no
Repository: CRAN
Date/Publication: 2014-07-23 15:30:55

More information about acp at CRAN
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Package nontarget updated to version 1.3 with previous version 1.2 dated 2012-10-18

Title: Detecting, combining and filtering isotope, adduct and homologue series relations in high-resolution mass spectrometry (HRMS) data
Description: Screening a HRMS data set for peaks related by (1) isotope patterns, (2) different adducts of the same molecule and/or (3) homologue series. The resulting isotopic pattern and adduct groups can then be combined to so-called components, with homologue series information attached. Also allows plotting and filtering HRMS data for mass defects, frequent m/z distances and components vs. non-components.
Author: Martin Loos
Maintainer: Martin Loos

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Package frailtypack updated to version 2.6.1 with previous version 2.6 dated 2014-03-24

Title: General Frailty models: shared, joint and nested frailty models with prediction
Description: Frailtypack fits several classes of frailty models using a penalized likelihood estimation on the hazard function but also a parametric estimation. 1) A shared frailty model (with gamma or log-normal frailty distribution) and Cox proportional hazard model. Clustered and recurrent survival times can be studied. 2) Additive frailty models for proportional hazard models with two correlated random effects (intercept random effect with random slope). 3) Nested frailty models for hierarchically clustered data (with 2 levels of clustering) by including two iid gamma random effects. 4) Joint frailty models in the context of joint modelling for recurrent events with terminal event for clustered data or not. Prediction values are available. Left truncated (not for Joint model), right-censored data, interval-censored data (only for Cox proportional hazard and shared frailty model) and strata (max=2) are allowed. In each model, the random effects have a gamma distribution, but you can switch to a log-normal in shared and joint models. Now, you can also consider time-varying covariates effects in Cox, shared and joint models. The package includes concordance measures for Cox proportional hazards models and for shared frailty models.
Author: Virginie Rondeau, Juan R. Gonzalez, Yassin Mazroui, Audrey Mauguen, Agnieszka Krol-Listwon, Amadou Diakite and Alexandre Laurent
Maintainer: Virginie Rondeau

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Package Epi updated to version 1.1.67 with previous version 1.1.65 dated 2014-06-24

Title: A package for statistical analysis in epidemiology.
Description: Functions for demographic and epidemiological analysis in the Lexis diagram, i.e. register and cohort follow-up data, in particular representation and manipulation of multistate data - the Lexis suite of functions. Includes interfaces to mstate, etm and cmprsk packages. Also contains functions for Age-Period-Cohort modeling and a function for interval censored data and some useful functions for tabulation and plotting, as well some epidemiological datasets.
Author: Bendix Carstensen [aut, cre], Martyn Plummer [aut], Esa Laara [ctb], Michael Hills [ctb]
Maintainer: Bendix Carstensen

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Package pdfetch updated to version 0.1.4 with previous version 0.1.3 dated 2014-04-19

Title: Fetch economic and financial time series data from public sources
Description: A package for downloading economic and financial time series from public sources.
Author: Abiel Reinhart
Maintainer: Abiel Reinhart

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Package IBDhaploRtools updated to version 1.7 with previous version 1.5 dated 2013-03-21

Title: Functions for the Analysis of IBD Haplo output
Description: IBDhaploRtools consists of several functions to analyze, plot, and store the output of running IBD_Haplo software package. More information regarding IBD_Haplo can be found at www.stat.washington.edu/thompson/Genepi/pangaea.shtml.
Author: Marshall Brown, Fiona Grimson
Maintainer: Fiona Grimson

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Package hts updated to version 4.4 with previous version 4.3 dated 2014-06-10

Title: Hierarchical and grouped time series
Description: Methods for analysing and forecasting hierarchical and grouped time series.
Author: Rob J Hyndman, Earo Wang and Alan Lee with contributions from Roman A Ahmed and Han Lin Shang to earlier versions of the package
Maintainer: Rob J Hyndman

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Tue, 22 Jul 2014

Package sweSCB updated to version 0.3.5 with previous version 0.3.4 dated 2014-04-15

Title: An R interface to the web API of Statistics Sweden
Description: Interface for the REST API of Statistics Sweden. The package offers methods to fetch information about the data hierarchy stored behind the API; extract metadata; fetch actual data; and clean up the results.
Author: Love Hansson, Thomas Reinholdsson, Mans Magnusson
Maintainer: Mans Magnusson

Diff between sweSCB versions 0.3.4 dated 2014-04-15 and 0.3.5 dated 2014-07-22

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Package spartan updated to version 2.0 with previous version 1.3 dated 2014-03-19

Title: Spartan (Simulation Parameter Analysis R Toolkit ApplicatioN)
Description: Computer simulations are becoming a popular technique to use in attempts to further our understanding of complex systems. SPARTAN, described in our 2013 publication in PLoS Computational Biology, provides code for four techniques described in available literature which aid the analysis of simulation results, at both single and multiple timepoints in the simulation run. The first technique addresses aleatory uncertainty in the system caused through inherent stochasticity, and determines the number of replicate runs necessary to generate a representative result. The second examines how robust a simulation is to parameter perturbation, through the use of a one-at-a-time parameter analysis technique. Thirdly, a latin hypercube based sensitivity analysis technique is included which can elucidate non-linear effects between parameters and indicate implications of epistemic uncertainty with reference to the system being modelled. Finally, a further sensitivity analysis technique, the extended Fourier Amplitude Sampling Test (eFAST) has been included to partition the variance in simulation results between input parameters, to determine the parameters which have a significant effect on simulation behaviour. Version 1.3 adds support for Netlogo simulations, aiding simulation developers who use Netlogo to build their simulations perform the same analyses. We have also added user support through the group spartan-group[AT]york[DOT]ac[DOT]uk.Version 2.0 added the ability to read all simulations in from a single CSV file in addition to the prescribed folder structure in previous versions.
Author: Kieran Alden, Mark Read, Paul Andrews, Jon Timmis, Henrique Veiga-Fernandes, Mark Coles
Maintainer: Kieran Alden

Diff between spartan versions 1.3 dated 2014-03-19 and 2.0 dated 2014-07-22

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Package SIS updated to version 0.7-3 with previous version 0.7-2 dated 2014-05-06

Title: Sure Independence Screening
Description: (Iterative) Sure Independence Screening for Generalized Linear Models and Cox's Proportional Hazards Models
Author: Jianqing Fan, Yang Feng, Diego Franco Saldana, Richard Samworth, Yichao Wu
Maintainer: Diego Franco Saldana

Diff between SIS versions 0.7-2 dated 2014-05-06 and 0.7-3 dated 2014-07-22

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Package deltaPlotR updated to version 1.4 with previous version 1.3 dated 2013-07-22

Title: Identification of dichotomous differential item functioning (DIF) using Angoff's Delta Plot method
Description: The deltaPlotR package proposes an implementation of Angoff's Delta Plot method to detect dichotomous DIF. Several detection thresholds are included, either from multivariate normality assumption or by prior determination. Item purification is supported.
Author: David Magis (U Liege), Bruno Facon (Univ Lille-Nord de France)
Maintainer: David Magis

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New package jSonarR with initial version 1.0
Package: jSonarR
Type: Package
Title: jSonar Analytics Platform API for R
Version: 1.0
Date: 2014-07-02
Author: jSonar Inc.
Maintainer: Dylan McCall
Description: This package enables users to access MongoDB by running queries and returning their results in R data frames. Usually, data in MongoDB is only available in the form of a JSON document. jSonarR uses data processing and conversion capabilities in the jSonar Analytics Platform and the JSON Studio Gateway (http://www.jsonstudio.com), to convert it to a tabular format which is easy to use with existing R packages.
Depends: R (>= 2.12.1), RCurl, methods
SystemRequirements: MongoDB, JSON Studio
Copyright: jSonar Inc.
License: AGPL-3
URL: http://www.jsonstudio.com/
Packaged: 2014-07-22 21:26:38 UTC; dylan
NeedsCompilation: no
Repository: CRAN
Date/Publication: 2014-07-23 00:40:43

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Package SPACECAP updated to version 1.1.0 with previous version 1.0.6 dated 2012-06-14

Title: A Program to Estimate Animal Abundance and Density using Bayesian Spatially-Explicit Capture-Recapture Models
Description: SPACECAP is a user-friendly software package for estimating animal densities using closed model capture-recapture sampling based on photographic captures using Bayesian spatially-explicit capture-recapture models. This approach offers advantage such as: substantially dealing with problems posed by individual heterogeneity in capture probabilities in conventional capture-recapture analyses. It also offers non-asymptotic inferences which are more appropriate for small samples of capture data typical of photo-capture studies.
Author: Arjun M. Gopalaswamy, Andrew J. Royle, Michael E. Meredith, Pallavi Singh, Devcharan Jathanna, N. Samba Kumar and K. Ullas Karanth
Maintainer: Arjun M. Gopalaswamy

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New package RMRAINGEN with initial version 1.0
Package: RMRAINGEN
Maintainer: Emanuele Cordano
License: GPL (>= 2)
Title: RMRAINGEN (R Multi-site RAINfall GENeretor): a package to generate daily time series of rainfall from monthly mean values
Type: Package
Author: Emanuele Cordano
Description: This package contains functions and S3 methods for spatial multi-site stochastic generation of daily precipitation. It generates precipitation occurrence in several sites using Wilks' Approach (1998). Bugs/comments/questions/collaboration of any kind are warmly welcomed.
Version: 1.0
Repository: CRAN
Date: 2014-07-22
Depends: R (>= 3.0), copula, RGENERATE,RMAWGEN,blockmatrix,Matrix
URL: https://github.com/ecor/RMRAINGEN
Packaged: 2014-07-22 14:35:22 UTC; ecor
NeedsCompilation: no
Date/Publication: 2014-07-22 21:18:30

More information about RMRAINGEN at CRAN
Permanent link

Package Rcpp11 updated to version 3.1.1 with previous version 3.1.0.1 dated 2014-04-16

Title: R and C++11
Description: Rcpp11 includes a header only C++11 library that facilitates integration between R and modern C++.
Author: Romain Francois [aut, cre], Kevin Ushey [aut], John Chambers [ctb]
Maintainer: Romain Francois

Diff between Rcpp11 versions 3.1.0.1 dated 2014-04-16 and 3.1.1 dated 2014-07-22

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 Rcpp11-3.1.1/Rcpp11/DESCRIPTION                                                              |   10 
 Rcpp11-3.1.1/Rcpp11/MD5                                                                      |  443 ++++------
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 Rcpp11-3.1.1/Rcpp11/inst/include/Rcpp/Array.h                                                |   43 
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 Rcpp11-3.1.1/Rcpp11/inst/include/Rcpp/grow.h                                                 |   12 
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 Rcpp11-3.1.1/Rcpp11/inst/include/Rcpp/sugar/functions/rep_len.h                              |  147 ++-
 Rcpp11-3.1.1/Rcpp11/inst/include/Rcpp/sugar/functions/replicate.h                            |   76 +
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 Rcpp11-3.1.1/Rcpp11/inst/include/Rcpp/sugar/functions/sapply.h                               |  267 +++---
 Rcpp11-3.1.1/Rcpp11/inst/include/Rcpp/sugar/functions/seq_along.h                            |   64 +
 Rcpp11-3.1.1/Rcpp11/inst/include/Rcpp/sugar/functions/setdiff.h                              |  247 ++---
 Rcpp11-3.1.1/Rcpp11/inst/include/Rcpp/sugar/functions/sign.h                                 |   63 -
 Rcpp11-3.1.1/Rcpp11/inst/include/Rcpp/sugar/functions/sum.h                                  |  152 +--
 Rcpp11-3.1.1/Rcpp11/inst/include/Rcpp/sugar/functions/table.h                                |  102 --
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 Rcpp11-3.1.1/Rcpp11/inst/include/Rcpp/sugar/functions/which_max.h                            |   99 --
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 Rcpp11-3.1.1/Rcpp11/inst/include/Rcpp/sugar/matrix/lower_tri.h                               |   21 
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 Rcpp11-3.1.1/Rcpp11/inst/include/Rcpp/traits/number_to_type.h                                |    2 
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 Rcpp11-3.1.1/Rcpp11/inst/include/Rcpp/traits/r_type_traits.h                                 |   54 -
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 Rcpp11-3.1.1/Rcpp11/inst/include/Rcpp/vector/StrideIterator.h                                |   18 
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 Rcpp11-3.1.1/Rcpp11/inst/include/Rcpp/vector/SugarMatrixExpression.h                         |   16 
 Rcpp11-3.1.1/Rcpp11/inst/include/Rcpp/vector/SugarVectorExpression.h                         |   21 
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 Rcpp11-3.1.1/Rcpp11/inst/include/Rcpp/vector/generic_proxy.h                                 |   69 -
 Rcpp11-3.1.1/Rcpp11/inst/include/Rcpp/vector/impl/CharacterVector.h                          |  118 --
 Rcpp11-3.1.1/Rcpp11/inst/include/Rcpp/vector/impl/ExpressionVector.h                         |  118 --
 Rcpp11-3.1.1/Rcpp11/inst/include/Rcpp/vector/impl/List.h                                     |  113 --
 Rcpp11-3.1.1/Rcpp11/inst/include/Rcpp/vector/impl/LogicalVector.h                            |only
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 Rcpp11-3.1.1/Rcpp11/inst/include/Rcpp/vector/impl/SimpleVector.h                             |  137 +--
 Rcpp11-3.1.1/Rcpp11/inst/include/Rcpp/vector/is_materialized.h                               |    8 
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 Rcpp11-3.1.1/Rcpp11/inst/include/Rcpp/vector/string_proxy.h                                  |  176 +--
 Rcpp11-3.1.1/Rcpp11/inst/include/Rcpp/wrap/ContainerWrapper.h                                |    5 
 Rcpp11-3.1.1/Rcpp11/inst/include/Rcpp/wrap/EnumWrapper.h                                     |    4 
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 Rcpp11-3.1.1/Rcpp11/inst/include/Rcpp/wrap/PrimitiveWrapper.h                                |    5 
 Rcpp11-3.1.1/Rcpp11/inst/include/Rcpp/wrap/SexpConvertibleWrapper.h                          |    2 
 Rcpp11-3.1.1/Rcpp11/inst/include/Rcpp/wrap/Wrapper.h                                         |    3 
 Rcpp11-3.1.1/Rcpp11/inst/include/Rcpp/wrap/forward.h                                         |   11 
 Rcpp11-3.1.1/Rcpp11/inst/include/Rcpp/wrap/make_charsexp.h                                   |   14 
 Rcpp11-3.1.1/Rcpp11/inst/include/Rcpp/wrap/wrap.h                                            |    5 
 Rcpp11-3.1.1/Rcpp11/inst/include/Rcpp/wrap/wrap_impl.h                                       |   13 
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New package nontargetData with initial version 1.1
Package: nontargetData
Type: Package
Title: Quantized simulation data of isotope pattern centroids
Version: 1.1
Date: 2014-07-22
Author: Martin Loos, Francesco Corona
Maintainer: Martin Loos
Description: Data sets for isotope pattern grouping of LC-HRMS peaks with package nontarget. Based on a vast set of unique PubChem molecular formulas, quantized (a) m/z, (b) m/z differences, (c) intensity ratios and (d) marker centroids of simulated centroid pairs are listed for different instrument resolutions.
License: GPL-3
Packaged: 2014-07-22 13:59:18 UTC; uchemadmin
Depends: R (>= 2.10)
NeedsCompilation: no
Repository: CRAN
Date/Publication: 2014-07-22 21:18:38

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Package kinship2 updated to version 1.6.0 with previous version 1.5.7 dated 2014-03-20

Title: Pedigree functions
Description: Routines to handle family data with a pedigree object. The initial purpose was to create correlation structures that describe family relationships such as kinship and identity-by-descent, which can be used to model family data in mixed effects models, such as in the coxme function. Also includes a tool for pedigree drawing which is focused on producing compact layouts without intervention. Recent additions include utilities to trim the pedigree object with various criteria, and kinship for the X chromosome
Author: Terry Therneau, Elizabeth Atkinson, Jason Sinnwell, Daniel Schaid, Shannon McDonnell
Maintainer: Jason Sinnwell

Diff between kinship2 versions 1.5.7 dated 2014-03-20 and 1.6.0 dated 2014-07-22

 DESCRIPTION        |    8 ++++----
 MD5                |   22 ++++++++++++----------
 NAMESPACE          |    3 ++-
 R/align.pedigree.R |    8 ++++++--
 R/ped2df.R         |    3 ---
 R/pedigree.R       |    1 +
 inst/NEWS.Rd       |   13 +++++++++++++
 man/familycheck.Rd |   51 ++++++++++++++++++---------------------------------
 noweb/align.Rnw    |    8 ++++++--
 noweb/all.nw       |   23 +++++++++++++++++------
 noweb/pedigree.Rnw |   15 +++++++++++----
 tests/ped1.pdf     |only
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 13 files changed, 90 insertions(+), 65 deletions(-)

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New package MixGHD with initial version 1.0
Package: MixGHD
Type: Package
Title: Model based clustering and classification using the mixture of generalized hyperbolic distributions.
Version: 1.0
Date: 2014-07-15
Author: Cristina Tortora, Ryan P. Browne, Brian C. Franczak and Paul D. McNicholas.
Maintainer: Cristina Tortora
Description: Carries out model-based clustering using three different models. The models are all based on the generalized hyperbolic distribution.The first model MGHD is the classical mixture of generalized hyperbolic distributions. The MGHFA is the mixture of generalized hyperbolic factor analyzers for high dimensional data sets. The MCGHD, mixture of coalesced generalized hyperbolic distributions is a new more flexible model.
Depends: Bessel, stats, MASS, mvtnorm, ghyp, numDeriv, R (>= 3.1.1)
NeedsCompilation: no
License: GPL (>= 2)
Packaged: 2014-07-22 13:24:40 UTC; cristina
Repository: CRAN
Date/Publication: 2014-07-22 21:18:29

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Package heatmapFit updated to version 2.0 with previous version 1.0 dated 2012-11-20

Title: Fit statistic for binary dependent variable models
Description: Generates a fit plot for diagnosing misspecification in models of binary dependent variables, and calculates the related heatmap fit statistic (Esarey and Pierce, 2012).
Author: Justin Esarey [aut, cre], Andrew Pierce [aut], Jericho Du [aut]
Maintainer: Justin Esarey

Diff between heatmapFit versions 1.0 dated 2012-11-20 and 2.0 dated 2014-07-22

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New package FreeSortR with initial version 1.0
Package: FreeSortR
Type: Package
Title: Free Sorting data analysis.
Version: 1.0
Date: 2014-04-29
Author: Philippe Courcoux
Maintainer: Philippe Courcoux
Description: The package FreeSortR provides tools for describing and analysing free sorting data. Main methods are computation of consensus partition and factorial analysis of the dissimilarity matrix between stimuli (using multidimensional scaling approach).
License: GPL-2
Depends: methods, smacof, vegan, ellipse
Packaged: 2014-07-22 14:33:58 UTC; courcoux
NeedsCompilation: no
Repository: CRAN
Date/Publication: 2014-07-22 21:18:25

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Package clinfun updated to version 1.0.6 with previous version 1.0.5 dated 2013-04-16

Title: Clinical Trial Design and Data Analysis Functions
Description: Utilities to make your clinical collaborations easier if not fun.
Author: Venkatraman E. Seshan
Maintainer: Venkatraman E. Seshan

Diff between clinfun versions 1.0.5 dated 2013-04-16 and 1.0.6 dated 2014-07-22

 CHANGES                  |    6 ++++++
 DESCRIPTION              |    9 ++++-----
 MD5                      |    8 ++++----
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 5 files changed, 25 insertions(+), 17 deletions(-)

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New package rnbn with initial version 1.0.0
Package: rnbn
Type: Package
Title: Access NBN data
Version: 1.0.0
Date: 2014-07-22
Author: Stuart Ball & Tom August
Maintainer: Tom August
Description: Access to data held by the National Biodiversity Network (NBN, www.nbn.org.uk). The NBN acts as a data warehouse for biological records data in the UK and is the UK node of GBIF (Global Biodiversity Information Facility). In this package NBN data is accessed via its web-services.
License: MIT + file LICENSE
Depends: RCurl, RJSONIO, tcltk
BuildVignettes: FALSE
LazyData: TRUE
Packaged: 2014-07-22 12:02:46 UTC; tomaug
NeedsCompilation: no
Repository: CRAN
Date/Publication: 2014-07-22 14:29:38

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Package llama updated to version 0.7 with previous version 0.6 dated 2014-04-29

Title: Leveraging Learning to Automatically Manage Algorithms
Description: Provides functionality to train and evaluate algorithm selection models for portfolios.
Author: Lars Kotthoff [aut,cre], Bernd Bischl [aut], Barry Hurley [ctb], Talal Rahwan [ctb]
Maintainer: Lars Kotthoff

Diff between llama versions 0.6 dated 2014-04-29 and 0.7 dated 2014-07-22

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Package Bergm updated to version 2.9 with previous version 2.8 dated 2014-07-02

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 2.8 dated 2014-07-02 and 2.9 dated 2014-07-22

 DESCRIPTION          |   10 +++++-----
 MD5                  |   23 ++++++++++++++---------
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Package AdaptFitOS updated to version 0.54 with previous version 0.50 dated 2014-03-19

Title: Adaptive Semiparametric Regression with Simultaneous Confidence Bands
Description: Based on the function "asp" of the AdaptFit package fits semiparametric regression models with spatially adaptive penalized splines and computes simultaneous confidence bands.
Author: Manuel Wiesenfarth and Tatyana Krivobokova
Maintainer: Manuel Wiesenfarth

Diff between AdaptFitOS versions 0.50 dated 2014-03-19 and 0.54 dated 2014-07-22

 DESCRIPTION               |   10 
 MD5                       |   62 ++--
 R/almeAux.R               |  126 ++++-----
 R/arg.searchOS.r          |  117 ++++----
 R/asp-internal.r          |    6 
 R/asp2.r                  |    2 
 R/aspHetero.r             |   25 -
 R/aspOS.r                 |    4 
 R/aspmFormReadOS.r        |    5 
 R/firstlib.r              |    2 
 R/fitted.asp.r            |   14 -
 R/plot.scbTest.r          |    4 
 R/plot.scbm.r             |    3 
 R/predict.asp.r           |  591 ++++++++++++++++++++++---------------------
 R/print.asp.r             |   55 +---
 R/residuals.asp.r         |   32 --
 R/scbM.r                  |   15 -
 R/scbTest.r               |   17 -
 R/spmArgReadOS.r          |   47 +--
 R/spmDesignOS.r           |  625 ++++++++++++++++++++++------------------------
 R/spmOS.r                 |    5 
 R/summary.asp.r           |  582 +++++++++++++++++++++---------------------
 man/AdaptFitOS-package.Rd |   32 +-
 man/asp2.Rd               |   39 +-
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 man/fitted.asp.Rd         |   15 -
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 32 files changed, 1216 insertions(+), 1305 deletions(-)

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Package rplos updated to version 0.4.1 with previous version 0.4.0 dated 2014-05-13

Title: Interface to PLoS Journals search API.
Description: A programmatic interface to the Web Service methods provided by the Public Library of Science journals for search.
Author: Scott Chamberlain [aut, cre], Carl Boettiger [aut], Karthik Ram [aut]
Maintainer: Scott Chamberlain

Diff between rplos versions 0.4.0 dated 2014-05-13 and 0.4.1 dated 2014-07-22

 rplos-0.4.0/rplos/tests/test-all.R                   |only
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 rplos-0.4.1/rplos/MD5                                |   66 +++++++++----------
 rplos-0.4.1/rplos/NAMESPACE                          |    2 
 rplos-0.4.1/rplos/NEWS                               |    7 ++
 rplos-0.4.1/rplos/R/fulltext.R                       |    2 
 rplos-0.4.1/rplos/README.md                          |   32 ++++-----
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 rplos-0.4.1/rplos/man/journalnamekey.Rd              |    2 
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 rplos-0.4.1/rplos/man/plosabstract.Rd                |    2 
 rplos-0.4.1/rplos/man/plosauthor.Rd                  |    2 
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 rplos-0.4.1/rplos/man/searchplos.Rd                  |    2 
 rplos-0.4.1/rplos/tests/testthat/test-plosabstract.R |   12 +--
 rplos-0.4.1/rplos/tests/testthat/test-plosauthor.R   |    6 -
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New package nycflights13 with initial version 0.1
Package: nycflights13
Title: Data about flights departing NYC in 2013.
Version: 0.1
Authors@R: 'Hadley Wickham [aut,cre]'
Description: Airline on-time data for all flights departing NYC in 2013. Also includes useful metadata on airlines, airports, weather, and planes.
Depends: R (>= 3.1.0)
License: CC0
LazyData: true
Suggests: dplyr
URL: http://github.com/hadley/nycflights13
Packaged: 2014-07-21 19:26:17 UTC; hadley
Author: 'Hadley Wickham' [aut, cre]
Maintainer: 'Hadley Wickham'
NeedsCompilation: no
Repository: CRAN
Date/Publication: 2014-07-22 11:08:54

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New package nasaweather with initial version 0.1
Package: nasaweather
Title: Collection of datasets from the ASA 2006 data expo
Version: 0.1
Authors@R: 'Hadley Wickham [aut,cre]'
Description: This package contains tidied data from the ASA 2006 data expo, as well as a number of useful other related data sets.
Depends: R (>= 3.1.0)
License: GPL-3
LazyData: true
URL: http://github.com/hadley/nasaweather, http://stat-computing.org/dataexpo/2006/
Packaged: 2014-07-21 19:30:24 UTC; hadley
Author: 'Hadley Wickham' [aut, cre]
Maintainer: 'Hadley Wickham'
NeedsCompilation: no
Repository: CRAN
Date/Publication: 2014-07-22 11:08:36

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Package mewAvg updated to version 0.3.0 with previous version 0.2.0 dated 2014-01-24

Title: A Fixed Memeory Moving Expanding Window Average
Description: Computes the average of a sequence of random vectors in a moving expanding window using a fixed amount of storage
Author: Adam L. Pintar and Zachary H. Levine
Maintainer: Adam L. Pintar

Diff between mewAvg versions 0.2.0 dated 2014-01-24 and 0.3.0 dated 2014-07-22

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Package leapp updated to version 1.2 with previous version 1.1 dated 2014-01-06

Title: latent effect adjustment after primary projection
Description: These functions take a gene expression value matrix, a primary covariate vector, an additional known covariates matrix. A two stage analysis is applied to counter the effects of latent variables on the rankings of hypotheses. The estimation and adjustment of latent effects are proposed by Sun, Zhang and Owen (2011). "leapp" is developed in the context of microarray experiments, but may be used as a general tool for high throughput data sets where dependence may be involved.
Author: Yunting Sun , Nancy R.Zhang , Art B.Owen
Maintainer: Yunting Sun

Diff between leapp versions 1.1 dated 2014-01-06 and 1.2 dated 2014-07-22

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Package jsonlite updated to version 0.9.9 with previous version 0.9.8 dated 2014-06-02

Title: A smarter JSON encoder/decoder for R
Description: This package is a fork of the RJSONIO package by Duncan Temple Lang. It builds on the same libjson c++ parser, but implements a smarter mapping between JSON data and R classes. The vignette describes the behavior in great detail. In addition to drop-in replacements for toJSON and fromJSON, the package contains funtions to validate, prettify and minify JSON, and many unit tests to verify that all edge cases are encoded and decoded consistently for use with dynamic data in systems and applications.
Author: Jeroen Ooms, Duncan Temple Lang, Jonathan Wallace
Maintainer: Jeroen Ooms

Diff between jsonlite versions 0.9.8 dated 2014-06-02 and 0.9.9 dated 2014-07-22

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Package glasso updated to version 1.8 with previous version 1.7 dated 2011-09-14

Title: Graphical lasso- estimation of Gaussian graphical models
Description: Graphical lasso
Author: Jerome Friedman, Trevor Hastie and Rob Tibshirani
Maintainer: Rob Tibshirani

Diff between glasso versions 1.7 dated 2011-09-14 and 1.8 dated 2014-07-22

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New package fueleconomy with initial version 0.1
Package: fueleconomy
Title: EPA fuel economy data
Version: 0.1
Authors@R: 'Hadley Wickham [aut,cre]'
Description: Fuel economy data from the EPA, 1985-2015, conveniently packaged for consumption by R users.
Depends: R (>= 3.1.0)
License: CC0
LazyData: true
Suggests: dplyr
URL: http://github.com/hadley/fueleconomy
Packaged: 2014-07-21 19:31:13 UTC; hadley
Author: 'Hadley Wickham' [aut, cre]
Maintainer: 'Hadley Wickham'
NeedsCompilation: no
Repository: CRAN
Date/Publication: 2014-07-22 11:08:43

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Package COUNT updated to version 1.3.1 with previous version 1.3.0 dated 2014-07-16

Title: Functions, data and code for count data.
Description: Functions, data and code for Hilbe, J.M. 2011. Negative Binomial Regression, 2-nd Edition (Cambridge University Press) and Hilbe, J.M. 2014. Modeling Count Data (Cambridge University Press).
Author: Joseph M Hilbe
Maintainer: Andrew Robinson

Diff between COUNT versions 1.3.0 dated 2014-07-16 and 1.3.1 dated 2014-07-22

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New package babynames with initial version 0.1
Package: babynames
Title: US baby names 1880-2013
Version: 0.1
Authors@R: 'Hadley Wickham [aut,cre]'
Description: US baby names provided by the SSA. This package contains all names used for at least 5 children of either sex.
Depends: R (>= 3.1.0)
License: CC0
LazyData: true
URL: http://github.com/hadley/babynames
Packaged: 2014-07-21 19:46:18 UTC; hadley
Author: 'Hadley Wickham' [aut, cre]
Maintainer: 'Hadley Wickham'
NeedsCompilation: no
Repository: CRAN
Date/Publication: 2014-07-22 11:08:48

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Mon, 21 Jul 2014

New package tidyr with initial version 0.1
Package: tidyr
Title: Easily tidy data with spread and gather functions.
Version: 0.1
Authors@R: 'Hadley Wickham [aut,cre]'
Description: tidyr is an evolution of reshape2. It's design specifically for data tidying (not general reshaping or aggregating) and works well with dplyr data pipelines.
Depends: R (>= 3.1.0)
License: MIT + file LICENSE
LazyData: true
Imports: reshape2, dplyr (>= 0.2)
URL: https://github.com/hadley/tidyr
Suggests: knitr, testthat
VignetteBuilder: knitr
Packaged: 2014-07-21 19:17:00 UTC; hadley
Author: 'Hadley Wickham' [aut, cre]
Maintainer: 'Hadley Wickham'
NeedsCompilation: no
Repository: CRAN
Date/Publication: 2014-07-21 23:16:05

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Package splusTimeDate updated to version 2.5.0-135 with previous version 2.0.0-117 dated 2014-02-02

Title: Times and Dates from S-PLUS
Description: Classes and methods for times and dates (ported from S-PLUS)
Author: TIBCO Software Inc.
Maintainer: Stephen Kaluzny

Diff between splusTimeDate versions 2.0.0-117 dated 2014-02-02 and 2.5.0-135 dated 2014-07-21

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Package rnoaa updated to version 0.2.0 with previous version 0.1.0 dated 2014-03-03

Title: NOAA climate data from R.
Description: This is an R wrapper to many NOAA APIs including the NCDC climate API at http://www.ncdc.noaa.gov/cdo-web/webservices/v2. There are functions for each of the API endpoints: data, data categories, data sets, data types, locations, location categories, and stations. In addition, we have an interface for NOAA sea ice data that is not part of the climate data API, the NOAA severe weather inventory, and ERDDAP data. NOAA buoy data is only on the buoy branch in the Github repository for this package (see url below).
Author: Hart Edmund [aut, cre], Scott Chamberlain [aut], Karthik Ram [aut]
Maintainer: Hart Edmund

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Package MDPtoolbox updated to version 4.0.2 with previous version 4.0.1 dated 2012-12-31

Title: Markov Decision Processes toolbox
Description: The Markov Decision Processes (MDP) toolbox proposes functions related to the resolution of discrete-time Markov Decision Processes: finite horizon, value iteration, policy iteration, linear programming algorithms with some variants and also proposes some functions related to Reinforcement Learning.
Author: Iadine Chades, Guillaume Chapron, Marie-Josee Cros, Frederick Garcia, Regis Sabbadin
Maintainer: Guillaume Chapron

Diff between MDPtoolbox versions 4.0.1 dated 2012-12-31 and 4.0.2 dated 2014-07-21

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Package logitchoice updated to version 0.9.1 with previous version 0.9.0 dated 2014-07-21

Title: Fitting l2-regularized logit choice models via generalized gradient descent
Description: Fits linear discrete logit choice models with l2 regularization. To handle reasonably sized datasets, we employ an accelerated version of generalized gradient descent.
Author: Michael Lim
Maintainer: Michael Lim

Diff between logitchoice versions 0.9.0 dated 2014-07-21 and 0.9.1 dated 2014-07-21

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New package bootSVD with initial version 0.1
Package: bootSVD
Title: Fast, Exact Bootstrap Principal Component Analysis for High Dimensional Data
Description: Implements fast, exact bootstrap Principal Component Analysis and Singular Value Decompositions for high dimensional data, as described in (arxiv.org/abs/1405.0922).
Version: 0.1
Author: Aaron Fisher
Maintainer: Aaron Fisher
Depends: R (>= 3.0.2)
Imports: parallel
License: GPL-2
LazyData: true
Packaged: 2014-07-21 20:05:34 UTC; aaronfisher
NeedsCompilation: no
Repository: CRAN
Date/Publication: 2014-07-21 23:18:12

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Package SuperLearner updated to version 2.0-15 with previous version 2.0-10 dated 2013-09-03

Title: Super Learner Prediction
Description: This package implements the super learner prediction method and contains a library of prediction algorithms to be used in the super learner.
Author: Eric Polley, Mark van der Laan
Maintainer: Eric Polley

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Package texreg updated to version 1.33 with previous version 1.32 dated 2014-05-02

Title: Conversion of R regression output to LaTeX or HTML tables.
Description: texreg converts coefficients, standard errors, significance stars, and goodness-of-fit statistics of statistical models into LaTeX tables or HTML tables/MS Word documents or to nicely formatted screen output for the R console for easy model comparison. A list of several models can be combined in a single table. The output is highly customizable. New model types can be easily implemented.
Author: Philip Leifeld
Maintainer: Philip Leifeld

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New package TableMonster with initial version 1.1
Package: TableMonster
Version: 1.1
Depends: xtable
Date: 2014-07-18
Title: Table Monster
Author: Grant Izmirlian Jr
Maintainer: Grant Izmirlian Jr
Description: Provides a user friendly interface to generation of booktab style tables using xtable.
License: GPL (>= 2)
LazyLoad: yes
Packaged: 2014-07-21 17:14:28 UTC; izmirlig
NeedsCompilation: no
Repository: CRAN
Date/Publication: 2014-07-21 20:07:51

More information about TableMonster at CRAN
Permanent link

Package RANN updated to version 2.4.1 with previous version 2.3.0 dated 2013-07-24

Title: Fast Nearest Neighbour Search (wraps Arya and Mount's ANN library)
Description: Finds the k nearest neighbours for every point in a given dataset in O(N log N) time using Arya and Mount's ANN library (v1.1.3). There is support for approximate as well as exact searches, fixed radius searches and bd as well as kd trees.
Author: Sunil Arya and David Mount (for ANN), Samuel E. Kemp, Gregory Jefferis
Maintainer: Gregory Jefferis

Diff between RANN versions 2.3.0 dated 2013-07-24 and 2.4.1 dated 2014-07-21

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Package mvSLOUCH updated to version 1.1.2 with previous version 1.1.1 dated 2014-05-30

Title: MultiVariate Stochastic Linear Ornstein-Uhlenbeck models for phylogenetic Comparative hypotHeses
Description: Fits multivariate Ornstein-Uhlenbeck types of models to continues trait data from species related by a common evolutionary history.
Author: Krzysztof Bartoszek
Maintainer: Krzysztof Bartoszek

Diff between mvSLOUCH versions 1.1.1 dated 2014-05-30 and 1.1.2 dated 2014-07-21

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Package mlr updated to version 2.1 with previous version 2.0 dated 2014-07-03

Title: mlr: Machine Learning in R.
Description: Interface to a large number of classification and regression techniques, including machine-readable parameter descriptions. There is also an experimental extension for survival analysis, clustering and general, example-specific cost-sensitive learning. Generic resampling, including cross-validation, bootstrapping and subsampling. Hyperparameter tuning with modern optimization techniques, for single- and multi-objective problems. Filter and wrapper methods for feature selection. Extension of basic learners with additional operations common in machine learning, also allowing for easy nested resampling. Most operations can be parallelized.
Author: Bernd Bischl [aut, cre], Michel Lang [aut], Jakob Bossek [aut], Leonard Judt [aut], Jakob Richter [aut], Tobias Kuehn [aut], Erich Studerus [aut]
Maintainer: Bernd Bischl

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Package ineq updated to version 0.2-13 with previous version 0.2-12 dated 2014-05-18

Title: Measuring Inequality, Concentration, and Poverty
Description: Inequality, concentration, and poverty measures. Lorenz curves (empirical and theoretical).
Author: Achim Zeileis [aut, cre], Christian Kleiber [ctb]
Maintainer: Achim Zeileis

Diff between ineq versions 0.2-12 dated 2014-05-18 and 0.2-13 dated 2014-07-21

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Package icd9 updated to version 0.5 with previous version 0.3 dated 2014-07-07

Title: Tools for Working with ICD-9 Codes, and Finding Comorbidities
Description: This package allows accurate manipulation, conversion, validation and comparison of ICD-9-CM (clinical modification) codes. Although ICD-9 codes appear numeric, this is not the case, since trailing zeroes, and a mixture of decimal and non-decimal "short" format codes exist. Tools to map ICD-9 codes to co-morbidities are also provided, with mappings from Quan (Deyo and Elixhauser versions), Elixhauser and AHRQ included.
Author: Jack O. Wasey [aut, cre]
Maintainer: Jack O. Wasey

Diff between icd9 versions 0.3 dated 2014-07-07 and 0.5 dated 2014-07-21

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 icd9-0.5/icd9/tests/testthat/test-validation.R  |  237 ++++++++++-
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More information about icd9 at CRAN
Permanent link

New package HSSVD with initial version 1.1
Package: HSSVD
Type: Package
Title: Biclustering with heterogeneous variance
Version: 1.1
Date: 2014-07-21
Authors@R: c(person("Guanhua", "Chen", role = c("aut","cre"), email = "guanhuac@live.unc.edu"), person("Michael", "Kosorok", role = c("aut"), email = "kosorok@unc.edu"), person("Shannon","Holloway", role="ctb", email="sthollow@ncsu.edu"))
Description: HSSVD is a recently developed data mining tool for discovering subgroups of patients and genes which simultaneously display unusual levels of variability compared to other genes and patients. Previous biclustering methods were restricted to mean level detection, while the new method can detect both mean and variance biclusters.
Depends: R (>= 2.10), bcv
License: GPL-2
Packaged: 2014-07-21 17:38:29 UTC; sthollow
Author: Guanhua Chen [aut, cre], Michael Kosorok [aut], Shannon Holloway [ctb]
Maintainer: Guanhua Chen
NeedsCompilation: no
Repository: CRAN
Date/Publication: 2014-07-21 20:17:46

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Package BTYD updated to version 2.3 with previous version 1.0 dated 2012-08-22

Title: Implementing Buy 'Til You Die Models
Description: This package contains functions for data preparation, parameter estimation, scoring, and plotting for the BG/BB, BG/NBD and Pareto/NBD models.
Author: Lukasz Dziurzynski [aut], Edward Wadsworth [aut], Peter Fader [ctb], Elea McDonnell Feit [ctb], Daniel McCarthy [aut, cre, ctb], Bruce Hardie [ctb], Arun Gopalakrishnan [ctb], Eric Schwartz [ctb], Yao Zhang [ctb]
Maintainer: Daniel McCarthy

Diff between BTYD versions 1.0 dated 2012-08-22 and 2.3 dated 2014-07-21

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 101 files changed, 3353 insertions(+), 2393 deletions(-)

More information about BTYD at CRAN
Permanent link

Package SASxport updated to version 1.5.0 with previous version 1.3.6 dated 2013-10-09

Title: Read and Write SAS XPORT Files
Description: This package provides functions for reading, listing the contents of, and writing SAS xport format files. The functions support reading and writing of either individual data frames or sets of data frames. Further, a mechanism has been provided for customizing how variables of different data types are stored.
Author: Unless otherwise noted, the contents of this package were written by Gregory R. Warnes and are provided under the terms of the GNU General Public License, version 2.0 or later. -- The files 'src/ieee2ibm.c' and 'src/ibm2ieee.c' were extracted from BRL-CAD file /brlcad/src/libbu/htond.c written by Michael John Muuss, Copyright (c) 2004-2007 United States Government as represented by the U.S. Army Research Laboratory, and is utilized and redistributed under the terms of the GNU Lesser General Public License, version 2.1. -- The files 'R/AFirst.lib.s', 'R/all.is.numeric.R', 'R/importConvertDateTime.R', 'R/in.opererator.R', 'R/makeNames.R', 'R/read.xport.R', and 'R/testDateTime.R' are copied or adapted from the 'Hmisc' package created by Frank E. Harrell, Jr. , and are utilized and redistributed under the terms of the GNU General Public License, version 2.0 or later. -- The files 'R/xport.R', 'src/SASxport.c', 'src/SASxport.h', and 'src/foreign.h' are copied or adapted from the R 'foreign' package created by Douglas M. Bates and Saikat DebRoy , and are utilized and redistributed under the terms of the GNU General Public License, version 2.0 or later. -- The creation of this package was partially funded by Metrum Institute .
Maintainer: Gregory R. Warnes

Diff between SASxport versions 1.3.6 dated 2013-10-09 and 1.5.0 dated 2014-07-21

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 54 files changed, 3464 insertions(+), 1865 deletions(-)

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Package PottsUtils updated to version 0.3-1 with previous version 0.3-0 dated 2014-06-16

Title: Utility Functions of the Potts Models
Description: A package including several functions related to the Potts models.
Author: Dai Feng [aut, cre], Luke Tierney [ctb]
Maintainer: Dai Feng

Diff between PottsUtils versions 0.3-0 dated 2014-06-16 and 0.3-1 dated 2014-07-21

 ChangeLog          |    4 ++++
 DESCRIPTION        |    6 +++---
 MD5                |    8 ++++----
 inst/doc/Intro.pdf |binary
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 5 files changed, 31 insertions(+), 19 deletions(-)

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Package BayesLogit updated to version 0.5.1 with previous version 0.4 dated 2014-04-25

Title: Logistic Regression
Description: The BayesLogit package does posterior simulation for binomial and multinomial logistic regression using the Polya-Gamma latent variable technique. This method is fully automatic, exact, and fast. A routine to efficiently sample from the Polya-Gamma class of distributions is included.
Author: Nicholas G. Polson, James G. Scott, and Jesse Windle
Maintainer: Jesse Windle

Diff between BayesLogit versions 0.4 dated 2014-04-25 and 0.5.1 dated 2014-07-21

 DESCRIPTION                                                              |   12 +--
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 5 files changed, 36 insertions(+), 32 deletions(-)

More information about BayesLogit at CRAN
Permanent link

Package BayesBridge updated to version 0.5 with previous version 0.4 dated 2014-04-23

Title: Bridge Regression
Description: This package implements Bayesian bridge regression.
Author: Nicholas G. Polson, James G. Scott, and Jesse Windle
Maintainer: Jesse Windle

Diff between BayesBridge versions 0.4 dated 2014-04-23 and 0.5 dated 2014-07-21

 DESCRIPTION           |    8 ++++----
 MD5                   |   12 ++++++------
 R/BridgeNMix.R        |    2 +-
 R/BridgeWrapper.R     |   23 +++++++++++------------
 src/BridgeWrapper.cpp |    2 +-
 src/Makevars          |    2 +-
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 7 files changed, 25 insertions(+), 26 deletions(-)

More information about BayesBridge at CRAN
Permanent link

New package densityClust with initial version 0.1-1
Package: densityClust
Type: Package
Title: Clustering by fast search and find of density peaks
Version: 0.1-1
Date: 2014-06-30
Author: Thomas Lin Pedersen
Maintainer: Thomas Lin Pedersen
Description: An implementation of the clustering algorithm described by Alex Rodriguez and Alessandro Laio (Science, 2014 vol. 344), along with tools to inspect and visualize the results.
License: GPL (>= 2)
Packaged: 2014-07-21 08:01:51 UTC; Thomas
NeedsCompilation: no
Repository: CRAN
Date/Publication: 2014-07-21 13:29:49

More information about densityClust at CRAN
Permanent link

Package dave updated to version 1.5 with previous version 1.4 dated 2013-05-08

Title: Functions for "Data Analysis in Vegetation Ecology"
Description: A collection of functions accompanying the book "Data Analysis in Vegetation Ecology", Second edition. 2013, Wiley-Blackwell, Chichester
Author: Otto Wildi
Maintainer: Otto Wildi

Diff between dave versions 1.4 dated 2013-05-08 and 1.5 dated 2014-07-21

 DESCRIPTION         |   15 +--
 MD5                 |  105 +++++++++++++------------
 NAMESPACE           |    2 
 R/Mtabs.R           |    2 
 R/Mtabs.default.R   |    2 
 R/davesil.default.R |   24 ++---
 R/dsil.R            |only
 R/fspa2.R           |    2 
 R/mtab.R            |    6 -
 R/orank.R           |    2 
 R/orank.default.R   |    3 
 R/orank1.R          |    7 -
 R/overly2.R         |    2 
 R/pcaser2.R         |    1 
 R/pcoatest.R        |   12 +-
 R/pcocoor.R         |    2 
 R/plot.davesil.R    |   17 ++--
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 R/plot.orank.R      |   21 ++---
 R/plot.pcobiplot.R  |   13 +--
 R/plot.pcovar.R     |   24 ++---
 R/plottab.R         |  218 +++++++++++++++++++++++++++-------------------------
 R/setgroupsize.R    |   48 +++++------
 R/speedprof2.R      |    1 
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 56 files changed, 308 insertions(+), 291 deletions(-)

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Package checkmate updated to version 1.2 with previous version 1.1 dated 2014-06-28

Title: Fast and versatile argument checks
Description: Tests and assertions to perform frequent argument checks. A substantial part of the package was written in C to minimize any worries about execution time overhead.
Author: Michel Lang , Bernd Bischl
Maintainer: Michel Lang

Diff between checkmate versions 1.1 dated 2014-06-28 and 1.2 dated 2014-07-21

 DESCRIPTION                         |    6 +--
 MD5                                 |   71 ++++++++++++++++++------------------
 NAMESPACE                           |    3 +
 NEWS                                |    6 +++
 R/asInteger.r                       |    9 +++-
 R/checkArray.r                      |    4 --
 R/checkAtomic.r                     |    4 --
 R/checkAtomicVector.r               |    4 --
 R/checkCharacter.r                  |   30 +++++++--------
 R/checkComplex.r                    |    4 --
 R/checkCount.r                      |    4 --
 R/checkDataFrame.r                  |    6 +--
 R/checkFactor.r                     |   38 +++++++++----------
 R/checkFlag.r                       |    4 --
 R/checkInt.r                        |    4 --
 R/checkInteger.r                    |    4 --
 R/checkIntegerish.r                 |    4 --
 R/checkList.r                       |   39 +++++++++----------
 R/checkLogical.r                    |    4 --
 R/checkMatrix.r                     |    4 --
 R/checkNamed.r                      |    5 +-
 R/checkNull.r                       |    4 --
 R/checkNumber.r                     |    4 --
 R/checkNumeric.r                    |    4 --
 R/checkScalar.r                     |    4 --
 R/checkScalarNA.r                   |    4 --
 R/checkSetEqual.r                   |only
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 man/checkChoice.Rd                  |    6 ++-
 man/checkNamed.Rd                   |    1 
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 src/checks.c                        |   20 ++++------
 src/checks.h                        |    1 
 tests/testthat/test_asType.r        |   26 ++++++++++++-
 tests/testthat/test_checkList.r     |    1 
 tests/testthat/test_checkMatrix.r   |    3 +
 tests/testthat/test_checkSetEqual.r |only
 38 files changed, 171 insertions(+), 172 deletions(-)

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Package survsim updated to version 1.1.1 with previous version 1.1.0 dated 2014-04-25

Title: Simulation of simple and complex survival data
Description: Simulation of simple and complex survival data
Author: David Moriña (Centre for Research in Environmental Epidemiology, CREAL) and Albert Navarro (Universitat Autònoma de Barcelona)
Maintainer: David Moriña Soler

Diff between survsim versions 1.1.0 dated 2014-04-25 and 1.1.1 dated 2014-07-21

 DESCRIPTION                      |   10 +--
 MD5                              |   21 +++----
 R/print.summary.crisk.data.sim.R |    3 -
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 man/mult.ev.sim.Rd               |    8 ++
 man/rec.ev.sim.Rd                |   11 ++-
 man/simple.surv.sim.Rd           |    6 +-
 man/survsim-package.Rd           |   23 ++++---
 12 files changed, 126 insertions(+), 97 deletions(-)

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Package mgcv updated to version 1.8-2 with previous version 1.8-1 dated 2014-07-05

Title: Mixed GAM Computation Vehicle with GCV/AIC/REML smoothness estimation
Description: Routines for GAMs and other generalized ridge regression with multiple smoothing parameter selection by GCV, REML or UBRE/AIC. Also GAMMs. Includes a gam() function.
Author: Simon Wood
Maintainer: Simon Wood

Diff between mgcv versions 1.8-1 dated 2014-07-05 and 1.8-2 dated 2014-07-21

 ChangeLog                               |   32 +++++++++++++++++
 DESCRIPTION                             |    6 +--
 MD5                                     |   33 +++++++++--------
 NAMESPACE                               |    1 
 R/bam.r                                 |   19 ++++++++--
 R/gam.fit3.r                            |   60 +++++++++++++++++++++++++++-----
 R/gamm.r                                |    4 +-
 R/mgcv.r                                |   47 +++++++++++++++++--------
 R/smooth.r                              |   15 +++++---
 man/bam.Rd                              |    5 ++
 man/gam.Rd                              |    5 ++
 man/gam.control.Rd                      |    5 ++
 man/gam.scale.Rd                        |only
 man/gamm.Rd                             |    6 ++-
 man/predict.gam.Rd                      |    5 +-
 man/smooth.construct.mrf.smooth.spec.Rd |    7 ++-
 man/smooth.construct.re.smooth.spec.Rd  |    4 ++
 po/R-mgcv.pot                           |   16 ++++----
 18 files changed, 201 insertions(+), 69 deletions(-)

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Package gamm4 updated to version 0.2-3 with previous version 0.2-2 dated 2013-09-25

Title: Generalized additive mixed models using mgcv and lme4
Description: Fit generalized additive mixed models via a version of mgcv's gamm function, using lme4 for estimation.
Author: Simon Wood, Fabian Scheipl
Maintainer: Simon Wood

Diff between gamm4 versions 0.2-2 dated 2013-09-25 and 0.2-3 dated 2014-07-21

 ChangeLog    |    7 +++++++
 DESCRIPTION  |    6 +++---
 MD5          |    8 ++++----
 R/gamm4.r    |   30 ++++++++++++++++--------------
 man/gamm4.Rd |    5 +++--
 5 files changed, 33 insertions(+), 23 deletions(-)

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Package msme updated to version 0.5.1 with previous version 0.4.4 dated 2013-07-02

Title: Functions and Datasets for "Methods of Statistical Model Estimation".
Description: This package provides functions and datasets from the book "Methods of Statistical Model Estimation".
Author: Joseph Hilbe and Andrew Robinson
Maintainer: Andrew Robinson

Diff between msme versions 0.4.4 dated 2013-07-02 and 0.5.1 dated 2014-07-21

 ChangeLog      |   13 ++++++++++++-
 DESCRIPTION    |   11 +++++------
 MD5            |    9 +++++----
 NAMESPACE      |    2 +-
 R/nbinomial1.R |    4 ++--
 man/P__disp.Rd |only
 6 files changed, 25 insertions(+), 14 deletions(-)

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Package Sunder updated to version 0.0.2 with previous version 0.0.1 dated 2014-06-30

Title: Quantification of the effect of geographic versus environmental isolation on genetic differentiation
Description: Quantification of the effect of geographic versus environmental isolation on genetic differentiation
Author: Filippo Botta, Casper Eriksen, Gilles Guillot
Maintainer: ORPHANED

Diff between Sunder versions 0.0.1 dated 2014-06-30 and 0.0.2 dated 2014-07-21

 DESCRIPTION  |   11 +++++++----
 MD5          |    4 ++--
 src/tangle.f |    4 ++--
 3 files changed, 11 insertions(+), 8 deletions(-)

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New package logitchoice with initial version 0.9.0
Package: logitchoice
Type: Package
Title: Fitting l2-regularized logit choice models via generalized gradient descent
Version: 0.9.0
Date: 2014-7-20
Author: Michael Lim
Maintainer: Michael Lim
Depends:
Suggests:
Description: Fits linear discrete logic choice models with l2 regularization. To handle reasonably sized datasets, we employ an accelerated version of generalized gradient descent.
License: GPL-2
URL:
Packaged: 2014-07-21 05:13:14 UTC; mlim
NeedsCompilation: yes
Repository: CRAN
Date/Publication: 2014-07-21 07:40:03

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Package gss updated to version 2.1-3 with previous version 2.1-2 dated 2014-06-10

Title: General Smoothing Splines
Description: A comprehensive package for structural multivariate function estimation using smoothing splines.
Author: Chong Gu
Maintainer: Chong Gu

Diff between gss versions 2.1-2 dated 2014-06-10 and 2.1-3 dated 2014-07-21

 ChangeLog       |    8 ++++++++
 DESCRIPTION     |    8 ++++----
 MD5             |   10 +++++-----
 R/family.R      |   23 +++++++++++++----------
 R/family.cv.R   |    9 +++++----
 R/family.proj.R |   25 +++++++++++++++----------
 6 files changed, 50 insertions(+), 33 deletions(-)

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Package GeoGenetix updated to version 0.0.2 with previous version 0.0.1 dated 2014-06-27

Title: Quantification of the effect of geographic versus environmental isolation on genetic differentiation
Description: Quantification of the effect of geographic versus environmental isolation on genetic differentiation
Author: Filippo Botta, Gilles Guillot
Maintainer: ORPHANED

Diff between GeoGenetix versions 0.0.1 dated 2014-06-27 and 0.0.2 dated 2014-07-21

 DESCRIPTION  |   11 +++++++----
 MD5          |    4 ++--
 src/tangle.f |    4 ++--
 3 files changed, 11 insertions(+), 8 deletions(-)

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