Thu, 30 Oct 2014

Package Rcmdr updated to version 2.1-4 with previous version 2.1-3 dated 2014-10-09

Title: R Commander
Description: A platform-independent basic-statistics GUI (graphical user interface) for R, based on the tcltk package.
Author: John Fox [aut, cre], Milan Bouchet-Valat [aut], Liviu Andronic [ctb], Michael Ash [ctb], Theophilius Boye [ctb], Stefano Calza [ctb], Andy Chang [ctb], Philippe Grosjean [ctb], Richard Heiberger [ctb], Kosar Karimi Pour [ctb], G. Jay Kerns [ctb], Renaud Lancelot [ctb], Matthieu Lesnoff [ctb], Uwe Ligges [ctb], Samir Messad [ctb], Martin Maechler [ctb], Robert Muenchen [ctb], Duncan Murdoch [ctb], Erich Neuwirth [ctb], Dan Putler [ctb], Brian Ripley [ctb], Miroslav Ristic [ctb], Peter Wolf [ctb], Kevin Wright [ctb]
Maintainer: John Fox

Diff between Rcmdr versions 2.1-3 dated 2014-10-09 and 2.1-4 dated 2014-10-30

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 20 files changed, 12454 insertions(+), 10427 deletions(-)

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Package hglm updated to version 2.0-11 with previous version 2.0-9 dated 2014-09-27

Title: Hierarchical Generalized Linear Models
Description: This package fits 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 2.0-9 dated 2014-09-27 and 2.0-11 dated 2014-10-30

 hglm-2.0-11/hglm/ChangeLog                                 |   15 +
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 hglm-2.0-11/hglm/MD5                                       |   35 +--
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Package surveillance updated to version 1.8-1 with previous version 1.8-0 dated 2014-06-17

Title: Temporal and Spatio-Temporal Modeling and Monitoring of Epidemic Phenomena
Description: A package implementing statistical methods for the modeling and change-point detection in time series of counts, proportions and categorical data, as well as for the modeling of continuous-time epidemic phenomena, e.g. discrete-space setups such as the spatially enriched Susceptible-Exposed-Infectious-Recovered (SEIR) models for surveillance data, or continuous-space point process data such as the occurrence of disease or earthquakes. Main focus is on outbreak detection in count data time series originating from public health surveillance of infectious diseases, but applications could just as well originate from environmetrics, reliability engineering, econometrics or social sciences. Currently the package contains implementations of typical outbreak detection procedures such as Farrington et al (1996), Noufaily et al (2012) or the negative binomial LR-CUSUM method described in Hoehle and Paul (2008). Furthermore, inference methods for the retrospective infectious disease model in Held et al (2005), Held et al (2006), Paul et al (2008) and Paul and Held (2011) are provided. A novel CUSUM approach combining logistic and multinomial logistic modelling is also included. Continuous self-exciting spatio-temporal point processes are modeled through additive-multiplicative conditional intensities as described in H÷hle (2009) ("twinSIR", discrete space) and Meyer et al (2012) ("twinstim", continuous space). The package contains several real-world data sets, the ability to simulate outbreak data, visualize the results of the monitoring in temporal, spatial or spatio-temporal fashion. Note: The suggested package INLA is unfortunately not available from any mainstream repository - in case one wants to use the 'boda' algorithm one needs to manually install the INLA package as specified at http://www.r-inla.org/download.
Author: Michael H÷hle [aut, cre, ths], Sebastian Meyer [aut], Michaela Paul [aut], Leonhard Held [ctb, ths], Thais Correa [ctb], Mathias Hofmann [ctb], Christian Lang [ctb], Juliane Manitz [ctb], Andrea Riebler [ctb], Daniel SabanÚs BovÚ [ctb], MaŰlle Salmon [ctb], Dirk Schumacher [ctb], Stefan Steiner [ctb], Mikko Virtanen [ctb], Valentin Wimmer [ctb], R Core Team [ctb] (A few code segments are modified versions of code from base R)
Maintainer: Michael H÷hle

Diff between surveillance versions 1.8-0 dated 2014-06-17 and 1.8-1 dated 2014-10-30

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New package fPortfolio with initial version 3011.81
Package: fPortfolio
Title: Rmetrics - Portfolio Selection and Optimization
Date: 2014-10-30
Version: 3011.81
Author: Rmetrics Core Team, Diethelm Wuertz [aut], Tobias Setz [cre], Yohan Chalabi [ctb]
Maintainer: Tobias Setz
Description: Environment for teaching "Financial Engineering and Computational Finance".
Depends: R (>= 2.15.1), methods, timeDate, timeSeries, fBasics, fAssets
Imports: fCopulae, robustbase, MASS, Rglpk, slam, Rsymphony, Rsolnp, kernlab, quadprog, rneos
Suggests: Rsocp, Rnlminb2, Rdonlp2, dplR, bcp, fGarch, mvoutlier
Additional_repositories: http://r-forge.r-project.org/
Note: SEVERAL PARTS ARE STILL PRELIMINARY AND MAY BE CHANGED IN THE FUTURE. THIS TYPICALLY INCLUDES FUNCTION AND ARGUMENT NAMES, AS WELL AS DEFAULTS FOR ARGUMENTS AND RETURN VALUES.
LazyData: yes
License: GPL (>= 2)
URL: https://www.rmetrics.org
Packaged: 2014-10-30 14:13:59 UTC; Tobi
NeedsCompilation: no
Repository: CRAN
Date/Publication: 2014-10-30 15:54:08

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Package RcppArmadillo updated to version 0.4.500.0 with previous version 0.4.450.1.0 dated 2014-09-22

Title: Rcpp Integration for the Armadillo Templated Linear Algebra Library
Description: R and Armadillo integration using Rcpp Armadillo is a templated C++ linear algebra library (by Conrad Sanderson) that aims towards a good balance between speed and ease of use. Integer, floating point and complex numbers are supported, as well as a subset of trigonometric and statistics functions. Various matrix decompositions are provided through optional integration with LAPACK and ATLAS libraries. The RcppArmadillo package includes the header files from the templated Armadillo library. Thus users do not need to install Armadillo itself in order to use RcppArmadillo. Armadillo is licensed under the MPL 2.0, while RcppArmadillo (the Rcpp bindings/bridge to Armadillo) is licensed under the GNU GPL version 2 or later, as is the rest of Rcpp.
Author: Romain Francois, Dirk Eddelbuettel and Doug Bates
Maintainer: Dirk Eddelbuettel

Diff between RcppArmadillo versions 0.4.450.1.0 dated 2014-09-22 and 0.4.500.0 dated 2014-10-30

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Package fAssets updated to version 3011.83 with previous version 3011.82 dated 2014-09-22

Title: Rmetrics - Analysing and Modelling Financial Assets
Description: Environment for teaching "Financial Engineering and Computational Finance".
Author: Rmetrics Core Team, Diethelm Wuertz [aut], Tobias Setz [cre], Yohan Chalabi [ctb]
Maintainer: Tobias Setz

Diff between fAssets versions 3011.82 dated 2014-09-22 and 3011.83 dated 2014-10-30

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Package etasFLP updated to version 1.1.1 with previous version 1.1.0 dated 2014-10-28

Title: Mixed FLP and ML Estimation of ETAS Space-Time Point Processes
Description: Estimation of the components of an ETAS model for earthquake description. Non-parametric background seismicity can be estimated through FLP (Forward Likelihood Predictive), while parametric components are estimated through maximum likelihood. The two estimation steps are alternated until convergence is obtained. For each event the probability of being a background event is estimated and used as a weight for declustering steps. Many options to control the estimation process are present. Some descriptive functions for earthquakes catalogs are present; also plot, print, summary, profile methods are defined for main output (objects of class "etasclass").
Author: Marcello Chiodi [aut, cre], Giada Adelfio [aut]
Maintainer: Marcello Chiodi

Diff between etasFLP versions 1.1.0 dated 2014-10-28 and 1.1.1 dated 2014-10-30

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Package sn updated to version 1.1-1 with previous version 1.1-0 dated 2014-08-04

Title: The skew-normal and skew-t distributions
Description: Define and manipulate probability distributions of the skew-normal family and some related ones (notably the skew-t family) and provide related statistical methods for data fitting and diagnostics, in the univariate and the multivariate case.
Author: Adelchi Azzalini
Maintainer: Adelchi Azzalini

Diff between sn versions 1.1-0 dated 2014-08-04 and 1.1-1 dated 2014-10-30

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New package PrevMap with initial version 1.0
Package: PrevMap
Type: Package
Title: PrevMap - an R package for prevalence mapping
Version: 1.0
Date: 2014-06-25
Author: Emanuele Giorgi, Peter J. Diggle
Maintainer: Emanuele Giorgi
Depends: geoR, maxLik, raster, pdist
Description: The PrevMap package provides functions for both likelihood-based and Bayesian analysis of spatially referenced prevalence data. 'PrevMap' is also an extension of the 'geoR' package which should be installed first together with the 'maxLik', 'raster' and 'pdist' packages.
LazyData: true
License: GPL (>= 2)
Packaged: 2014-10-30 09:40:57 UTC; giorgi
NeedsCompilation: no
Repository: CRAN
Date/Publication: 2014-10-30 11:18:02

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Permanent link

Package MortalitySmooth updated to version 2.3.3 with previous version 2.3.2 dated 2013-12-28

Title: Smoothing and Forecasting Poisson Counts with P-Splines
Description: Smoothing one- and two-dimensional Poisson counts with P-splines specifically tailored to mortality data. Extra-Poisson variation can be accounted as well as forecasting. Collection of mortality data and a specific function for selecting those data by country, sex, age and years.
Author: Carlo G Camarda
Maintainer: Carlo G Camarda

Diff between MortalitySmooth versions 2.3.2 dated 2013-12-28 and 2.3.3 dated 2014-10-30

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New package webutils with initial version 0.2
Package: webutils
Type: Package
Title: Utility Functions for Web Applications
Version: 0.2
Date: 2014-10-29
Author: Jeroen Ooms
Maintainer: Jeroen Ooms
Description: Utility functions for developing web applications. Includes parsers for application/x-www-form-urlencoded as well as multipart/form-data and examples of using the parser with either httpuv or rhttpd.
License: MIT + file LICENSE
URL: https://github.com/jeroenooms/webutils
BugReports: https://github.com/jeroenooms/webutils/issues
Imports: tools, utils, jsonlite
Suggests: httpuv
Packaged: 2014-10-30 00:32:01 UTC; jeroen
NeedsCompilation: no
Repository: CRAN
Date/Publication: 2014-10-30 07:46:54

More information about webutils at CRAN
Permanent link

Package pollstR updated to version 1.1.1 with previous version 1.1.0 dated 2014-08-18

Title: R client for the Huffpost Pollster API
Description: An R interface to the Huffington Post Pollster API, which provides programmatic interface to political polls.
Author: Jeffrey B. Arnold [aut, cre], Thomas J. Leeper [aut]
Maintainer: Jeffrey B. Arnold

Diff between pollstR versions 1.1.0 dated 2014-08-18 and 1.1.1 dated 2014-10-30

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Package multicon updated to version 1.3 with previous version 1.2 dated 2014-04-19

Title: Multivariate Constructs
Description: This packages includes functions designed to examine relationships among multivariate constructs.
Author: Ryne A. Sherman
Maintainer: Ryne A. Sherman

Diff between multicon versions 1.2 dated 2014-04-19 and 1.3 dated 2014-10-30

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Wed, 29 Oct 2014

Package Taxonstand updated to version 1.5 with previous version 1.4 dated 2014-09-17

Title: Taxonomic standardization of plant species names
Description: Automated standardization of taxonomic names and removal of orthographic errors in plant species names using the The Plant List (TPL) website (www.theplantlist.org)
Author: Luis Cayuela and Jari Oksanen
Maintainer: Luis Cayuela

Diff between Taxonstand versions 1.4 dated 2014-09-17 and 1.5 dated 2014-10-29

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New package exCon with initial version 0.1-0
Package: exCon
Type: Package
Title: Interactive Exploration of Contour Data
Version: 0.1-0
Date: 2014-10-29
Authors@R: c(person("Bryan", "Hanson", role = c("aut", "cre"), email = "hanson@depauw.edu"), person("Kristina", "Mulry", role = "ctb"))
Description: exCon is an interactive tool to explore topographic-like data sets. Such data sets take the form of a matrix in which the rows and columns provide location/frequency information, and the matrix elements contain altitude/response information. Such data is found in cartography, 2D spectroscopy and chemometrics. exCon creates an interactive web page showing the contoured data set along with slices from the original matrix parallel to each dimension. The page is written in d3/javascript.
License: GPL-3
Imports: jsonlite
URL: https://github.com/bryanhanson/exCon
ByteCompile: TRUE
BugReports: https://github.com/bryanhanson/exCon/issues
Depends: R (>= 3.0)
Packaged: 2014-10-29 19:41:42 UTC; bryanhanson
Author: Bryan Hanson [aut, cre], Kristina Mulry [ctb]
Maintainer: Bryan Hanson
NeedsCompilation: no
Repository: CRAN
Date/Publication: 2014-10-29 22:05:54

More information about exCon at CRAN
Permanent link

Package alm updated to version 0.3.1 with previous version 0.3.0 dated 2014-10-15

Title: R Client for the Lagotto Altmetrics API Platform.
Description: An R interface to the open source article level metrics API created by the Public Library of Science (PLOS). A number of publishers are using the open source app created by PLOS, so you can drop in a different base URL to the functions in this package to get to not only PLOS data, but data for Crossref, and more as the open source PLOS software is used. rCharts is in Enhances; and can be used for creating interactive charts (e.g., in the function plot_signposts in this package); obtain rCharts at https://github.com/ramnathv/rCharts.
Author: Scott Chamberlain [aut, cre], Carl Boettiger [aut], Karthik Ram [aut], Fenner Martin [aut]
Maintainer: Scott Chamberlain

Diff between alm versions 0.3.0 dated 2014-10-15 and 0.3.1 dated 2014-10-29

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Package R6 updated to version 2.0.1 with previous version 2.0 dated 2014-08-19

Title: Classes with reference semantics
Description: The R6 package allows the creation of classes with reference semantics, similar to R's built-in reference classes. Compared to reference classes, R6 classes are simpler and lighter-weight, and they are not built on S4 classes so they do not require the methods package. These classes allow public and private members, and they support inheritance, even when the classes are defined in different packages.
Author: "Winston Chang" [aut, cre]
Maintainer: "Winston Chang"

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Package qtl updated to version 1.34-16 with previous version 1.33-7 dated 2014-08-12

Title: Tools for analyzing QTL experiments
Description: Analysis of experimental crosses to identify genes (called quantitative trait loci, QTLs) contributing to variation in quantitative traits.
Author: Karl W Broman and Hao Wu, with ideas from Gary Churchill and Saunak Sen and contributions from Danny Arends, Timothee Flutre, Ritsert Jansen, Pjotr Prins, Lars Ronnegard, Rohan Shah, Laura Shannon, Quoc Tran, Aaron Wolen, and Brian Yandell
Maintainer: Karl W Broman

Diff between qtl versions 1.33-7 dated 2014-08-12 and 1.34-16 dated 2014-10-29

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Package isdals updated to version 2.0-4 with previous version 2.0-1 dated 2013-10-01

Title: Provides datasets for Introduction to Statistical Data Analysis for the Life Sciences
Description: Provides datasets for Introduction to Statistical Data Analysis for the Life Sciences
Author: Claus Ekstrom and Helle Sorensen
Maintainer: Claus Ekstrom

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Package fBasics updated to version 3011.87 with previous version 3010.86 dated 2013-05-01

Title: Rmetrics - Markets and Basic Statistics
Description: Environment for teaching "Financial Engineering and Computational Finance".
Author: Rmetrics Core Team, Diethelm Wuertz [aut], Tobias Setz [cre], Yohan Chalabi [ctb]
Maintainer: Tobias Setz

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Package ldr updated to version 1.3.3 with previous version 1.3.2 dated 2014-06-27

Title: Methods for likelihood-based dimension reduction in regression
Description: Functions, methods, and data sets for fitting likelihood-based dimension reduction in regression, using principal fitted components (pfc), likelihood acquired directions (lad), covariance reducing models (core).
Author: Kofi Placid Adragni, Andrew Raim
Maintainer: Kofi Placid Adragni

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Package HTSDiff updated to version 1.0.5 with previous version 1.0.2 dated 2014-07-28

Title: Differential Analysis of RNA-Seq Data with Poisson Mixture Models
Description: This package implements a Poisson mixture model to identify differentially expressed genes from RNA-seq data.
Author: Andrea Rau, Marie-Laure Martin-Magniette, Cathy Maugis-Rabusseau
Maintainer: Andrea Rau

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Package RSQLite.extfuns (with last version 0.0.1) was removed from CRAN

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

2010-05-30 0.0.1

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Package peacots updated to version 1.1 with previous version 1.0 dated 2014-06-05

Title: Periodogram Peaks in Correlated Time Series
Description: Calculates the periodogram of a time series, maximum-likelihood fits an Ornstein-Uhlenbeck state space (OUSS) null model and evaluates the statistical significance of periodogram peaks against the OUSS null hypothesis. The OUSS is a parsimonious model for stochastically fluctuating variables with linear stabilizing forces, subject to uncorrelated measurement errors. Contrary to the classical white noise null model for detecting cyclicity, the OUSS model can account for temporal correlations typically occurring in ecological and geological time series.
Author: Stilianos Louca
Maintainer: Stilianos Louca

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Package pander updated to version 0.5.1 with previous version 0.5.0 dated 2014-10-28

Title: An R Pandoc Writer
Description: Contains some functions catching all messages, stdout and other useful information while evaluating R code and other helpers to return user specified text elements (like: header, paragraph, table, image, lists etc.) in Pandoc's markdown or several type of R objects similarly automatically transformed to markdown format. Also capable of exporting/converting (the resulting) complex Pandoc documents to e.g. HTML, PDF, docx or odt. This latter reporting feature is supported in brew syntax or with a custom reference class with a smarty caching backend.
Author: Gergely Dar├│czi , Roman Tsegelskyi
Maintainer: Gergely Dar├│czi

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Package nullabor updated to version 0.3.0 with previous version 0.2.1 dated 2012-07-23

Title: Tools for Graphical Inference
Description: Tools for visual inference. Generate null data sets and null plots using permutation and simulation. Calculate distance metrics for a lineup, and examine the distributions of metrics.
Author: Hadley Wickham , Niladri Roy Chowdhury , Di Cook
Maintainer: Di Cook

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More information about nullabor at CRAN
Permanent link

New package DAMOCLES with initial version 1.0
Package: DAMOCLES
Type: Package
Title: Dynamic Assembly Model Of Colonization, Local Extinction and Speciation
Version: 1.0
Date: 2014-09-09
Depends: R (>= 2.14.2), geiger, caper, ape, deSolve, matrixStats
Author: Rampal S. Etienne & Alex L. Pigot
Maintainer: Rampal S. Etienne
License: GPL-2
Description: Simulates and computes (maximum) likelihood of a dynamical model of community assembly that takes into account the phylogenetic history
Packaged: 2014-09-09 18:19:08 UTC; p223208
NeedsCompilation: no
Repository: CRAN
Date/Publication: 2014-10-29 09:29:22

More information about DAMOCLES at CRAN
Permanent link

Package RefManageR updated to version 0.8.40 with previous version 0.8.34 dated 2014-08-19

Title: Straightforward BibTeX and BibLaTeX Bibliography Management
Description: RefManageR provides tools for importing and working with bibliographic references. It greatly enhances the bibentry class by providing a class BibEntry which stores BibTeX and BibLaTeX references, supports UTF-8 encoding, and can be easily searched by any field, by date ranges, and by various formats for name lists (author by last names, translator by full names, etc.). Entries can be updated, combined, sorted, printed in a number of styles, and exported. BibTeX and BibLaTeX .bib files can be read into R and converted to BibEntry objects. Interfaces to NCBI's Entrez, CrossRef, and Zotero are provided for importing references and references can be created from locally stored PDFs using Poppler. Includes functions for citing and generating a bibliography with hyperlinks for documents prepared with RMarkdown or RHTML.
Author: Mathew W. McLean [aut, cre]
Maintainer: Mathew W. McLean

Diff between RefManageR versions 0.8.34 dated 2014-08-19 and 0.8.40 dated 2014-10-29

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 MD5                           |  110 ++++++++---------
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 R/05makeBibLatex.R            |    4 
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More information about RefManageR at CRAN
Permanent link

New package rqPen with initial version 1.0
Package: rqPen
Type: Package
Title: R Package for Penalized Quantile Regression
Version: 1.0
Date: 2014-10-25
Author: Ben Sherwood
Depends: R (>= 3.0.0),quantreg
Maintainer: Ben Sherwood
Description: Performs penalized quantile regression for LASSO, SCAD and MCP functions. Provides a function that automatically generates lambdas and evaluates different models with cross validation or BIC, including a large p version of BIC.
ByteCompile: TRUE
License: MIT + file LICENSE
Packaged: 2014-10-29 01:29:00 UTC; bsherwoo
NeedsCompilation: no
Repository: CRAN
Date/Publication: 2014-10-29 07:44:31

More information about rqPen at CRAN
Permanent link

Package mlr updated to version 2.2 with previous version 2.1 dated 2014-07-21

Title: 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 Richter [aut], Jakob Bossek [aut], Leonard Judt [aut], Tobias Kuehn [aut], Erich Studerus [aut], Lars Kotthoff [aut]
Maintainer: Bernd Bischl

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More information about mlr at CRAN
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Package deSolve updated to version 1.11 with previous version 1.10-9 dated 2014-06-25

Title: General Solvers for Initial Value Problems of Ordinary Differential Equations (ODE), Partial Differential Equations (PDE), Differential Algebraic Equations (DAE), and Delay Differential Equations (DDE)
Description: Functions that solve initial value problems of a system of first-order ordinary differential equations (ODE), of partial differential equations (PDE), of differential algebraic equations (DAE), and of delay differential equations. The functions provide an interface to the FORTRAN functions lsoda, lsodar, lsode, lsodes of the ODEPACK collection, to the FORTRAN functions dvode and daspk and a C-implementation of solvers of the Runge-Kutta family with fixed or variable time steps. The package contains routines designed for solving ODEs resulting from 1-D, 2-D and 3-D partial differential equations (PDE) that have been converted to ODEs by numerical differencing.
Author: Karline Soetaert [aut], Thomas Petzoldt [aut, cre], R. Woodrow Setzer [aut], odepack authors [cph]
Maintainer: Thomas Petzoldt

Diff between deSolve versions 1.10-9 dated 2014-06-25 and 1.11 dated 2014-10-29

 DESCRIPTION                    |    8 
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 R/lsode.R                      |   34 +
 R/lsodes.R                     |  805 ++++++++++++++++---------------
 R/radau.R                      |   33 +
 R/rk.R                         |   22 
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New package addreg with initial version 1.2
Package: addreg
Title: Additive Regression for Discrete Data
Description: Methods for fitting identity-link GLMs and GAMs to discrete data. The package uses EM-type algorithms with more stable convergence properties than standard methods.
Version: 1.2
Date: 2014-10-29
Author: Mark Donoghoe
Maintainer: Mark Donoghoe
Depends: R (>= 3.0.1)
Imports: splines, combinat, glm2
License: GPL (>= 2)
LazyData: true
Packaged: 2014-10-28 22:19:48 UTC; 42674999
NeedsCompilation: no
Repository: CRAN
Date/Publication: 2014-10-29 07:36:11

More information about addreg at CRAN
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Tue, 28 Oct 2014

Package TSclust updated to version 1.2.2 with previous version 1.2.1 dated 2014-04-30

Title: Time series clustering utilities
Description: This package contains a set of measures of dissimilarity between time series to perform time series clustering. Metrics based on raw data, on generating models and on the forecast behavior are implemented. Some additional utilities related to time series clustering are also provided, such as clustering algorithms and cluster evaluation metrics.
Author: Pablo Montero Manso, Jos├ę Antonio Vilar
Maintainer: Pablo Montero

Diff between TSclust versions 1.2.1 dated 2014-04-30 and 1.2.2 dated 2014-10-28

 ChangeLog       |    2 ++
 DESCRIPTION     |    6 +++---
 MD5             |   10 +++++-----
 R/diss.R        |    6 +++---
 man/diss.PDC.Rd |    6 +++---
 man/diss.Rd     |    4 ++--
 6 files changed, 18 insertions(+), 16 deletions(-)

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Package robustreg updated to version 0.1-7 with previous version 0.1-5 dated 2014-10-09

Title: Robust Regression Functions
Description: Linear regression functions using Huber and Bisquare psi functions
Author: Ian M. Johnson
Maintainer: Ian M. Johnson

Diff between robustreg versions 0.1-5 dated 2014-10-09 and 0.1-7 dated 2014-10-28

 DESCRIPTION        |   15 ++--
 MD5                |   17 +++-
 NAMESPACE          |    8 +-
 R/RcppExports.R    |only
 R/robustRegBS.R    |  183 ++++++++++++++++++++++++++---------------------------
 R/robustRegH.R     |  180 ++++++++++++++++++++++++++--------------------------
 man/fit.Rd         |only
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 10 files changed, 210 insertions(+), 199 deletions(-)

More information about robustreg at CRAN
Permanent link

New package MfUSampler with initial version 0.9
Package: MfUSampler
Type: Package
Title: Multivariate-from-Univariate (MfU) MCMC Sampler
Version: 0.9
Date: 2014-10-27
Author: Alireza S. Mahani, Mansour T.A. Sharabiani
Maintainer: Alireza S. Mahani
Description: Convenience Functions for Multivariate MCMC Using Univariate Samplers, including Slice Sampler with Stepout and Shrinkage (Neal, 2003), and Adaptive Rejection Sampler (Gilks and Wild, 1992).
License: GPL (>= 2)
Depends: ars
Suggests: sns
Packaged: 2014-10-28 18:54:28 UTC; amahani
NeedsCompilation: no
Repository: CRAN
Date/Publication: 2014-10-28 22:00:52

More information about MfUSampler at CRAN
Permanent link

Package logconPH updated to version 1.3 with previous version 1.2 dated 2014-10-25

Title: CoxPH Model with Log Concave Baseline Distribution
Description: Computes a cox PH model with a log concave baseline distribution. If no covariates are provided, estimates the log concave NPMLE. Built specifically for interval censored data, where data is a n by 2 matrix with [i, 1] as the left side of the interval for subject i and [i,2] as right side. Uncensored data can be entered by setting [i,1] = [i,2]. Alternatively, this can also handle uncensored data. If all the data is uncensored, you may enter data as a length(n) vector.
Author: Clifford Anderson-Bergman
Maintainer: Clifford Anderson-Bergman

Diff between logconPH versions 1.2 dated 2014-10-25 and 1.3 dated 2014-10-28

 DESCRIPTION                  |    8 ++++----
 MD5                          |    6 +++---
 src/Cpp2Source/baseClass.cpp |   20 +++++++-------------
 src/Cpp2Source/baseClass.h   |   15 +--------------
 4 files changed, 15 insertions(+), 34 deletions(-)

More information about logconPH at CRAN
Permanent link

Package FAOSTAT updated to version 1.9 with previous version 1.6 dated 2014-03-14

Title: A complementary package to the FAOSTAT database and the Statistical Yearbook of the Food and Agricultural Organization of the United Nations.
Description: The package hosts a list of functions to automatically download statistics from FAOSTAT (database of the Food and Agricultural Organization of the United Nations) and WDI (database of the World Bank), and to perform some harmonization operations.
Author: Michael C. J. Kao , Markus Gesmann, Filippo Gheri
Maintainer: Filippo Gheri

Diff between FAOSTAT versions 1.6 dated 2014-03-14 and 1.9 dated 2014-10-28

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 FAOSTAT-1.9/FAOSTAT/R/FAOcheck.R                 |   94 ++++++++---
 FAOSTAT-1.9/FAOSTAT/R/FAOsearch.R                |    4 
 FAOSTAT-1.9/FAOSTAT/R/chConstruct.R              |   66 +++----
 FAOSTAT-1.9/FAOSTAT/R/chgr.R                     |   90 +++++-----
 FAOSTAT-1.9/FAOSTAT/R/constructSYB.R             |  192 +++++++++++------------
 FAOSTAT-1.9/FAOSTAT/R/fillCountryCode.R          |   68 ++++----
 FAOSTAT-1.9/FAOSTAT/R/geogr.R                    |   80 ++++-----
 FAOSTAT-1.9/FAOSTAT/R/getFAO.R                   |  106 ++++++++----
 FAOSTAT-1.9/FAOSTAT/R/getFAOtoSYB.R              |   13 +
 FAOSTAT-1.9/FAOSTAT/R/getWDI.R                   |  110 ++++++-------
 FAOSTAT-1.9/FAOSTAT/R/getWDImetaData.R           |  150 ++++++++---------
 FAOSTAT-1.9/FAOSTAT/R/getWDItoSYB.R              |    2 
 FAOSTAT-1.9/FAOSTAT/R/grConstruct.R              |  128 +++++++--------
 FAOSTAT-1.9/FAOSTAT/R/indConstruct.R             |   84 +++++-----
 FAOSTAT-1.9/FAOSTAT/R/lsgr.R                     |  148 ++++++++---------
 FAOSTAT-1.9/FAOSTAT/R/mergeSYB.R                 |   84 +++++-----
 FAOSTAT-1.9/FAOSTAT/R/overlap.R                  |   37 +++-
 FAOSTAT-1.9/FAOSTAT/R/printLab.R                 |   58 +++---
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 FAOSTAT-1.9/FAOSTAT/demo/00Index                 |    2 
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 FAOSTAT-1.9/FAOSTAT/man/FAOcheck.Rd              |   56 ++++--
 FAOSTAT-1.9/FAOSTAT/man/FAOcountryProfile.Rd     |   20 +-
 FAOSTAT-1.9/FAOSTAT/man/FAOmetaTable.Rd          |   22 +-
 FAOSTAT-1.9/FAOSTAT/man/FAOregionProfile.Rd      |   21 +-
 FAOSTAT-1.9/FAOSTAT/man/FAOsearch.Rd             |   25 +-
 FAOSTAT-1.9/FAOSTAT/man/chConstruct.Rd           |   63 +++----
 FAOSTAT-1.9/FAOSTAT/man/chgr.Rd                  |   67 ++++----
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 FAOSTAT-1.9/FAOSTAT/man/ebind.Rd                 |   44 ++---
 FAOSTAT-1.9/FAOSTAT/man/fillCountryCode.Rd       |   40 ++--
 FAOSTAT-1.9/FAOSTAT/man/geogr.Rd                 |   68 ++++----
 FAOSTAT-1.9/FAOSTAT/man/getFAO.Rd                |  112 ++++++-------
 FAOSTAT-1.9/FAOSTAT/man/getFAOtoSYB.Rd           |  116 ++++++-------
 FAOSTAT-1.9/FAOSTAT/man/getWDI.Rd                |   86 +++++-----
 FAOSTAT-1.9/FAOSTAT/man/getWDImetaData.Rd        |   55 +++---
 FAOSTAT-1.9/FAOSTAT/man/getWDItoSYB.Rd           |  106 ++++++------
 FAOSTAT-1.9/FAOSTAT/man/grConstruct.Rd           |   76 ++++-----
 FAOSTAT-1.9/FAOSTAT/man/indConstruct.Rd          |   61 +++----
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 77 files changed, 1964 insertions(+), 1844 deletions(-)

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Permanent link

New package CateSelection with initial version 1.0
Package: CateSelection
Type: Package
Title: Categorical Variable Selection Methods
Version: 1.0
Date: 2014-10-28
Author: Yi Xu and Jixiang Wu
Maintainer: Yi Xu
Description: A multi-factor dimensionality reduction based forward selection method for genetic association mapping.
License: GPL (>= 2)
Depends: R(>= 2.10)
Repository: CRAN
Packaged: 2014-10-28 20:38:02 UTC; Xu
NeedsCompilation: no
Date/Publication: 2014-10-28 21:58:29

More information about CateSelection at CRAN
Permanent link

Package rgl updated to version 0.95.1157 with previous version 0.94.1143 dated 2014-09-30

Title: 3D visualization device system (OpenGL)
Description: Provides medium to high level functions for 3D interactive graphics, including functions modelled on base graphics (plot3d(), etc.) as well as functions for constructing representations of geometric objects (cube3d(), etc.). Output may be on screen using OpenGL, or to various standard 3D file formats including WebGL, PLY, OBJ, STL as well as 2D image formats, including PNG, Postscript, SVG, PGF.
Author: Daniel Adler , Duncan Murdoch , and others (see README)
Maintainer: Duncan Murdoch

Diff between rgl versions 0.94.1143 dated 2014-09-30 and 0.95.1157 dated 2014-10-28

 rgl-0.94.1143/rgl/src/QuadSet.cpp         |only
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 rgl-0.95.1157/rgl/R/obj.R                 |  618 ++++++++++++++--------------
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 rgl-0.95.1157/rgl/R/scene.R               |   17 
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 rgl-0.95.1157/rgl/R/subscenes.R           |    2 
 rgl-0.95.1157/rgl/R/turn3d.R              |  122 ++---
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 rgl-0.95.1157/rgl/man/rgl.pixels.Rd       |   80 +--
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 rgl-0.95.1157/rgl/man/selectpoints3d.Rd   |  186 ++++----
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 rgl-0.95.1157/rgl/src/NULLgui.cpp         |    2 
 rgl-0.95.1157/rgl/src/RenderContext.h     |    2 
 rgl-0.95.1157/rgl/src/Texture.cpp         |  225 +++++-----
 rgl-0.95.1157/rgl/src/Viewpoint.cpp       |   10 
 rgl-0.95.1157/rgl/src/device.cpp          |    3 
 rgl-0.95.1157/rgl/src/rglview.cpp         |   19 
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 rgl-0.95.1157/rgl/src/scene.cpp           |    9 
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 59 files changed, 2883 insertions(+), 2849 deletions(-)

More information about rgl at CRAN
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Package knitcitations updated to version 1.0.4 with previous version 1.0-1 dated 2014-07-12

Title: Citations for knitr markdown files
Description: knitcitations provides the ability to create dynamic citations in which the bibliographic information is pulled from the web rather than having to be entered into a local database such as bibtex ahead of time. Knitcitations is primarily aimed at authoring in the R markdown format, and can provide outputs for web-based authoring such as linked text and tooltips over inline citations. Cite using a DOI, URL, or bibtex file key. See the package URL for details.
Author: Carl Boettiger [aut, cre]
Maintainer: Carl Boettiger

Diff between knitcitations versions 1.0-1 dated 2014-07-12 and 1.0.4 dated 2014-10-28

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 NAMESPACE               |    3 
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More information about knitcitations at CRAN
Permanent link

New package safi with initial version 1.0
Package: safi
Type: Package
Title: Sensitivity Analysis for Functional Input
Version: 1.0
Date: 2014-10-28
Author: Jana Fruth, Malte Jastrow
Maintainer: Jana Fruth
Description: Design and sensitivity analysis for computer experiments with scalar-valued output and functional input, e.g. over time or space. The aim is to explore the behavior of the sensitivity over the functional domain.
License: GPL (>= 2)
Packaged: 2014-10-28 15:53:50 UTC; Jana
NeedsCompilation: no
Repository: CRAN
Date/Publication: 2014-10-28 17:35:33

More information about safi at CRAN
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Package hht updated to version 2.1.1 with previous version 2.1.0 dated 2014-09-23

Title: The Hilbert-Huang Transform: Tools and Methods
Description: This package builds on the EMD package to provide additional tools for empirical mode decomposition (EMD) and Hilbert spectral analysis. It also implements the ensemble empirical decomposition (EEMD) and the complete ensemble empirical mode decomposition (CEEMD) methods to avoid mode mixing and intermittency problems found in EMD analysis. The package comes with several plotting methods that can be used to view intrinsic mode functions, the HHT spectrum, and the Fourier spectrum. To see the version history and download the bleeding-edge version (at your own risk!), see the project website at code.google.com below. See the other links for PDF files describing numerical and exact analytical methods for determining instantaneous frequency, some examples of signals processed with this package, and some examples of the ensemble empirical mode decomposition method.
Author: Daniel C. Bowman [aut, cre], Jonathan M. Lees [ctb]
Maintainer: Daniel C. Bowman

Diff between hht versions 2.1.0 dated 2014-09-23 and 2.1.1 dated 2014-10-28

 DESCRIPTION                      |   10 ++---
 MD5                              |   16 ++++----
 R/empirical_mode_decomposition.R |   16 +++++---
 R/rendering_and_plotting.R       |   71 ++++++++++++++++++++++++++++++---------
 man/CEEMD.Rd                     |    2 -
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 9 files changed, 102 insertions(+), 45 deletions(-)

More information about hht at CRAN
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Package timeSeries updated to version 3011.98 with previous version 3010.97 dated 2013-05-01

Title: Rmetrics - Financial Time Series Objects
Description: Environment for teaching "Financial Engineering and Computational Finance".
Author: Rmetrics Core Team, Diethelm Wuertz [aut], Tobias Setz [cre], Yohan Chalabi [ctb]
Maintainer: Tobias Setz

Diff between timeSeries versions 3010.97 dated 2013-05-01 and 3011.98 dated 2014-10-28

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Package etasFLP updated to version 1.1.0 with previous version 1.0.3 dated 2014-04-14

Title: Mixed FLP and ML Estimation of ETAS Space-Time Point Processes
Description: Estimation of the components of an ETAS model for earthquake description. Non-parametric background seismicity can be estimated through FLP (Forward Likelihood Predictive), while parametric components are estimated through maximum likelihood. The two estimation steps are alternated until convergence is obtained. For each event the probability of being a background event is estimated and used as a weight for declustering steps. Many options to control the estimation process are present. Some descriptive functions for earthquakes catalogs are present; also plot, print, summary, profile methods are defined for main output (objects of class "etasclass").
Author: Marcello Chiodi [aut, cre], Giada Adelfio [aut]
Maintainer: Marcello Chiodi

Diff between etasFLP versions 1.0.3 dated 2014-04-14 and 1.1.0 dated 2014-10-28

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More information about etasFLP at CRAN
Permanent link

Package BSSasymp updated to version 1.1-0 with previous version 1.0-2 dated 2014-08-07

Title: Asymptotic Covariance Matrices of Some BSS Mixing and Unmixing Matrix Estimates.
Description: Functions to compute the asymptotic covariance matrices of mixing and unmixing matrix estimates of the following blind source separation (BSS) methods: symmetric FastICA, regular and adaptive deflation-based FastICA, FOBI, JADE, AMUSE and deflation-based and symmetric SOBI. Also functions to estimate these covariances based on data are available.
Author: Jari Miettinen, Klaus Nordhausen, Hannu Oja, Sara Taskinen
Maintainer: Jari Miettinen

Diff between BSSasymp versions 1.0-2 dated 2014-08-07 and 1.1-0 dated 2014-10-28

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New package settings with initial version 0.1.1
Package: settings
Type: Package
Title: Software Option Settings Manager for R
Version: 0.1.1
Date: 2014-10-22
Author: Mark van der Loo
Maintainer: Mark van der Loo
Description: Provides option settings management that goes beyond R's default 'options' function. With this package, users can define their own option settings manager holding option names and default values. Settings can then be retrieved, altered and reset to defaults with ease. For R programmers and package developers it offers cloning and merging functionality which allows for conveniently defining global and local options, possibly in a multilevel options hierarchy. See the package vignette for some examples concerning functions, S4 classes, and reference classes.
URL: https://github.com/markvanderloo/settings
License: GPL-3
VignetteBuilder: knitr
Suggests: testthat, knitr
Packaged: 2014-10-28 07:43:29 UTC; mark
NeedsCompilation: no
Repository: CRAN
Date/Publication: 2014-10-28 11:18:40

More information about settings at CRAN
Permanent link

Package pander updated to version 0.5.0 with previous version 0.3.8 dated 2013-09-12

Title: An R pandoc writer
Description: Contains some functions catching all messages, stdout and other useful information while evaluating R code and other helpers to return user specified text elements (like: header, paragraph, table, image, lists etc.) in Pandoc's markdown or several type of R objects similarly automatically transformed to markdown format. Also capable of exporting/converting (the resulting) complex Pandoc documents to e.g. HTML, pdf, docx or odt. This latter reporting feature is supported in brew syntax or with a custom reference class with a smarty caching backend.
Author: Gergely Dar├│czi , Roman Tsegelskyi
Maintainer: Gergely Dar├│czi

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Package TR8 updated to version 0.9 with previous version 0.8 dated 2014-08-26

Title: A tool for downloading functional traits data for plant species
Description: Plant ecologists often need to collect "traits" data about plant species which are often scattered among various databases: TR8 contains a set of tools which take care of automatically retrieving some of those functional traits data for plant species from publicly available databases (Biolflor, The Ecological Flora of the British Isles, LEDA traitbase, Ellenberg values for Italian Flora, Mycorrhizal intensity database). The TR8 name, inspired by "car plates" jokes, was chosen since it both reminds of the main object of the package and is extremely short to type.
Author: Gionata Bocci
Maintainer: Gionata Bocci

Diff between TR8 versions 0.8 dated 2014-08-26 and 0.9 dated 2014-10-28

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More information about TR8 at CRAN
Permanent link

Package seqMeta updated to version 1.5 with previous version 1.4 dated 2014-04-10

Title: Meta-Analysis of Region-Based Tests of Rare DNA Variants
Description: Computes necessary information to meta analyze region-based tests for rare genetic variants (e.g. SKAT, T1) in individual studies, and performs meta analysis.
Author: Arie Voorman, Jennifer Brody, Han Chen, Thomas Lumley
Maintainer: Arie Voorman

Diff between seqMeta versions 1.4 dated 2014-04-10 and 1.5 dated 2014-10-28

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More information about seqMeta at CRAN
Permanent link

Package qmethod updated to version 1.2.2 with previous version 1.2 dated 2014-10-24

Title: Analysis of Subjective Perspectives Using Q Methodology
Description: Analysis of Q methodology data to identify the distinct perspectives existing within a group. This methodology is used across social, health and environmental sciences to understand diversity of attitudes, discourses, or decision-making styles (for more information, see http://qmethod.org). The function qmethod() runs the full analysis. Each step can be run separately using the corresponding functions: qflag() for automatic flagging of Q-sorts (manual flagging is optional), qzscores() for scores for statements, qda() for distinguishing and consensus statements, and qfcharact() for general characteristics of the factors. Additional functions import data from PQMethod software, export plain text data for interpretation in two flavours, print and plot Q method results in a synthetic manner. The package uses principal components and it offers the following choices: manual or automatic flagging, a number of mathematical methods for rotation, and a number of correlation coefficients for the initial correlation matrix.
Author: Aiora Zabala [aut, cre]
Maintainer: Aiora Zabala

Diff between qmethod versions 1.2 dated 2014-10-24 and 1.2.2 dated 2014-10-28

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Package lassoscore updated to version 0.6 with previous version 0.5 dated 2014-05-09

Title: High-Dimensional Inference with the Penalized Score Test
Description: Use the lasso regression method to perform approximate inference in high dimensions, by penalizing the effects of nuisance parameters.
Author: Arie Voorman
Maintainer: Arie Voorman

Diff between lassoscore versions 0.5 dated 2014-05-09 and 0.6 dated 2014-10-28

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More information about lassoscore at CRAN
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Package energy updated to version 1.6.2 with previous version 1.6.1 dated 2014-02-23

Title: E-statistics (energy statistics)
Description: E-statistics (energy) tests and statistics for comparing distributions: multivariate normality, multivariate distance components and k-sample test for equal distributions, hierarchical clustering by e-distances, multivariate independence tests, distance correlation, goodness-of-fit tests. Energy- statistics concept based on a generalization of Newton's potential energy is due to Gabor J. Szekely.
Author: Maria L. Rizzo and Gabor J. Szekely
Maintainer: Maria Rizzo

Diff between energy versions 1.6.1 dated 2014-02-23 and 1.6.2 dated 2014-10-28

 DESCRIPTION  |    8 ++++----
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Package Ecfun updated to version 0.1-2 with previous version 0.1-0 dated 2014-04-08

Title: Functions for Ecdat
Description: Functions to update datasets in Ecdat and to create, manipulate, plot and analyze those and similar datasets.
Author: Spencer Graves
Maintainer: Spencer Graves

Diff between Ecfun versions 0.1-0 dated 2014-04-08 and 0.1-2 dated 2014-10-28

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Package HPO.db (with last version 1.2) was removed from CRAN

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

2013-07-04 1.2
2012-10-30 1.0

Permanent link
Package HPOSim (with last version 1.2) was removed from CRAN

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

2014-02-21 1.2
2013-07-05 1.1
2013-03-28 1.0

Permanent link

Mon, 27 Oct 2014

Package timeDate updated to version 3011.99 with previous version 3010.98 dated 2013-05-01

Title: Rmetrics - Chronological and Calendar Objects
Description: Environment for teaching "Financial Engineering and Computational Finance".
Author: Rmetrics Core Team, Diethelm Wuertz [aut], Tobias Setz [cre], Yohan Chalabi [ctb], Martin Maechler [ctb], Joe W. Byers [ctb]
Maintainer: Tobias Setz

Diff between timeDate versions 3010.98 dated 2013-05-01 and 3011.99 dated 2014-10-27

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Package sirt updated to version 1.0-3 with previous version 0.47-36 dated 2014-08-30

Title: Supplementary Item Response Theory Models
Description: Supplementary item response theory models to complement existing functions in R.
Author: Alexander Robitzsch
Maintainer: Alexander Robitzsch

Diff between sirt versions 0.47-36 dated 2014-08-30 and 1.0-3 dated 2014-10-27

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Package RQDA updated to version 0.2-7 with previous version 0.2-6 dated 2014-05-11

Title: R-based Qualitative Data Analysis
Description: R package for Qualitative Data Analysis. Current version only supports plain text, but it can import PDF highlights if the Enhance package of rjpod, which is available on R-Forge, is installed.
Author: HUANG Ronggui
Maintainer: HUANG Ronggui

Diff between RQDA versions 0.2-6 dated 2014-05-11 and 0.2-7 dated 2014-10-27

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More information about RQDA at CRAN
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Package rjags updated to version 3-14 with previous version 3-13 dated 2014-03-06

Title: Bayesian graphical models using MCMC
Description: Interface to the JAGS MCMC library
Author: Martyn Plummer [aut, cre], Alexey Stukalov [ctb]
Maintainer: Martyn Plummer

Diff between rjags versions 3-13 dated 2014-03-06 and 3-14 dated 2014-10-27

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More information about rjags at CRAN
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Package rangeMapper updated to version 0.2-8 with previous version 0.2-6 dated 2014-02-07

Title: A platform for the study of macroecology of life history traits
Description: Tools for easy generation of (life-history) traits maps based on species range (extent-of-occurrence) maps.
Author: Mihai Valcu , James Dale
Maintainer: Mihai Valcu

Diff between rangeMapper versions 0.2-6 dated 2014-02-07 and 0.2-8 dated 2014-10-27

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More information about rangeMapper at CRAN
Permanent link

New package bio3d with initial version 2.1-3
Package: bio3d
Title: Biological Structure Analysis
Version: 2.1-3
Author: Barry Grant, Xin-Qiu Yao, Lars Skjaerven, Julien Ide
VignetteBuilder: knitr
Imports: parallel, grid
Suggests: XML, RCurl, lattice, ncdf, igraph, bigmemory, knitr, testthat (>= 0.9.1)
Depends: R (>= 3.1.0)
LazyData: yes
Description: Utilities to process, organize and explore protein structure, sequence and dynamics data. Features include the ability to read and write structure, sequence and dynamic trajectory data, perform sequence and structure database searches, data summaries, atom selection, alignment, superposition, rigid core identification, clustering, torsion analysis, distance matrix analysis, structure and sequence conservation analysis, normal mode analysis, principal component analysis of heterogeneous structure data, and correlation network analysis from normal mode and molecular dynamics data. In addition, various utility functions are provided to enable the statistical and graphical power of the R environment to work with biological sequence and structural data. Please refer to the URLs below for more information.
Maintainer: Barry Grant
License: GPL (>= 2)
URL: http://thegrantlab.org/bio3d/, http://bitbucket.org/Grantlab/bio3d
Packaged: 2014-10-24 21:47:52 UTC; xinqyao
NeedsCompilation: no
Repository: CRAN
Date/Publication: 2014-10-27 19:03:11

More information about bio3d at CRAN
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New package h2o with initial version 2.8.1.1
Package: h2o
Type: Package
Title: H2O R Interface
Version: 2.8.1.1
Date: 2014-05-15
Author: Anqi Fu, Spencer Aiello, Ariel Rao, Tom Kraljevic and Petr Maj, with contributions from the 0xdata team
Maintainer: Tom Kraljevic
Description: Run H2O via its REST API from within R.
License: Apache License (== 2.0)
Depends: R (>= 2.13.0), RCurl, rjson, statmod, survival, stats, tools, utils, methods
Collate: Wrapper.R Internal.R Classes.R ParseImport.R models.R Algorithms.R zzz.R
NeedsCompilation: no
SystemRequirements: Java (>= 1.6)
Suggests: plyr
URL: http://www.0xdata.com
Packaged: 2014-10-23 02:24:40 UTC; jenkins
Repository: CRAN
Date/Publication: 2014-10-27 18:11:24

More information about h2o at CRAN
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Package DALY updated to version 1.4.0 with previous version 1.3.0 dated 2014-05-10

Title: DALY Calculator - A GUI for stochastic DALY calculation in R
Description: The DALY Calculator is a free, open-source Graphical User Interface (GUI) for stochastic disability-adjusted life year (DALY) calculation.
Author: Brecht Devleesschauwer [aut, cre], Scott McDonald [aut], Juanita Haagsma [aut], Nicolas Praet [aut], Arie Havelaar [aut], Niko Speybroeck [aut]
Maintainer: Brecht Devleesschauwer

Diff between DALY versions 1.3.0 dated 2014-05-10 and 1.4.0 dated 2014-10-27

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Package bdscale updated to version 1.1 with previous version 1.0 dated 2014-10-08

Title: Remove Weekends and Holidays From ggplot2 Axes
Description: Provides a continuous date scale, omitting weekends and holidays.
Author: Dave Mills
Maintainer: Dave Mills

Diff between bdscale versions 1.0 dated 2014-10-08 and 1.1 dated 2014-10-27

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Package RGA updated to version 0.1.3 with previous version 0.1.2 dated 2014-09-01

Title: A Google Analytics API client for R
Description: Provides functions for accessing and retrieving data from the Google Analytics APIs (https://developers.google.com/analytics/). Supports OAuth 2.0 authorization. Package provides access to the Management, Core Reporting, Multi-Channel Funnels Reporting, Real Time Reporting and Metadata APIs. Access to all the Google Analytics accounts which the user has access to. Auto-pagination to return more than 10,000 rows of the results by combining multiple data requests. Also the RGA package provides shiny app to explore the core reporting API dimensions and metrics.
Author: Artem Klevtsov [aut, cre], Philipp Upravitelev [ctb], Olga Shramko [ctb]
Maintainer: Artem Klevtsov

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New package qdm with initial version 0.1-0
Package: qdm
Version: 0.1-0
Date: 2014-10-16
Title: Fitting a Quadrilateral Dissimilarity Model to Same-Different Judgments
Authors@R: c(person("Nora", "Umbach", role = c("aut", "cre"), email = "nora.umbach@web.de"), person("Florian", "Wickelmaier", role = "aut"))
Depends: R (>= 3.1.0), stats, graphics
Description: This package provides different specifications of a Quadrilateral Dissimilarity Model which can be used to fit same-different judgments in order to get a predicted matrix that satisfies regular minimality [Colonius & Dzhafarov, 2006, Measurement and representations of sensations, Erlbaum]. From such a matrix, Fechnerian distances can be computed.
License: GPL (>= 2)
Packaged: 2014-10-27 13:33:02 UTC; noraumbach
Author: Nora Umbach [aut, cre], Florian Wickelmaier [aut]
Maintainer: Nora Umbach
NeedsCompilation: no
Repository: CRAN
Date/Publication: 2014-10-27 15:30:23

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Package fICA updated to version 1.0-2 with previous version 1.0-1 dated 2014-09-05

Title: Classical, Reloaded and Adaptive FastICA Algorithms
Description: Algorithms for classical symmetric and deflation-based FastICA, reloaded deflation-based FastICA algorithm and an algorithm for adaptive deflation-based FastICA using multiple nonlinearities.
Author: Jari Miettinen, Klaus Nordhausen, Hannu Oja, Sara Taskinen
Maintainer: Jari Miettinen

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Package choroplethr updated to version 2.0.0 with previous version 1.7.0 dated 2014-06-14

Title: Simplify the creation of choropleth maps in R.
Description: choroplethr simplifies the creation of choropleth maps in R. Choropleths are thematic maps where geographic regions, such as states, are colored according to some metric, such as the number of people who live in that state. choroplethr simplifies this process by 1. Providing ready-made functions for creating choropleths using four different maps. 2. Providing API connections to interesting data sources for making choropleths. 3. Providing a framework for creating choropleths from arbitrary shapefiles. Please see the vignettes for more details.
Author: Ari Lamstein [cre, aut], Brian P Johnson [ctb, frontend animation code]
Maintainer: Ari Lamstein

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Package astsa updated to version 1.3 with previous version 1.2 dated 2014-03-17

Title: Applied Statistical Time Series Analysis
Description: Data sets and scripts for Time Series Analysis and Its Applications: With R Examples by Shumway and Stoffer, 3rd edition
Author: David Stoffer
Maintainer: David Stoffer

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Package sqldf updated to version 0.4-9 with previous version 0.4-7.1 dated 2014-03-15

Title: Perform SQL Selects on R Data Frames
Description: Description: Manipulate R data frames using SQL.
Author: G. Grothendieck
Maintainer: G. Grothendieck

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Package ropensecretsapi updated to version 1.0.1 with previous version 1.0.0 dated 2014-10-05

Title: R Package for the OpenSecrets.org API
Description: An R package for the OpenSecrets.org web services API.
Author: Thomas P. Fuller
Maintainer: Thomas P. Fuller

Diff between ropensecretsapi versions 1.0.0 dated 2014-10-05 and 1.0.1 dated 2014-10-27

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Package PopGenReport updated to version 2.1 with previous version 2.0 dated 2014-07-04

Title: PopGenReport: A simple way to analyse and visualize population genetic data
Description: This package provides an easy way to analyse population genetic data
Author: Aaron Adamack & Bernd Gruber
Maintainer: Bernd Gruber

Diff between PopGenReport versions 2.0 dated 2014-07-04 and 2.1 dated 2014-10-27

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Package pitchRx updated to version 1.6 with previous version 1.5 dated 2014-07-23

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 1.5 dated 2014-07-23 and 1.6 dated 2014-10-27

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Sun, 26 Oct 2014

Package RSelenium updated to version 1.3.5 with previous version 1.3.1 dated 2014-05-25

Title: R bindings for Selenium WebDriver.
Description: The RSelenium package provides a set of R bindings for the Selenium 2.0 WebDriver using the JsonWireProtocol. Selenium automates web browsers (commonly referred to as browsers). Using RSelenium you can automate browsers locally or remotely.
Author: John Harrison
Maintainer: John Harrison

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Package statar updated to version 0.1.1 with previous version 0.1 dated 2014-10-16

Title: Tools Inspired by Stata to Clean, Explore and Join Datasets
Description: statar makes it easier to work with tabular datasets. statar includes a set of functions to clean and summarize variables, to join datasets with an SQL-syntax, and to manipulate datasets with a panel structure (elapsed dates, lead/lag, fill rows for missing dates, fill in missing values). statar is based on the data.table package and is inspired by Stata.
Author: Matthieu Gomez [aut, cre]
Maintainer: Matthieu Gomez

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Package rdrobust updated to version 0.70 with previous version 0.61 dated 2014-09-04

Title: Robust data-driven statistical inference in Regression-Discontinuity designs
Description: Regression-discontinuity (RD) designs are quasi-experimental research designs popular in social, behavioral and natural sciences. The RD design is usually employed to study the (local) causal effect of a treatment, intervention or policy. This package provides tools for data-driven graphical and analytical statistical inference in RD designs: rdrobust to construct local-polynomial point estimators and robust confidence intervals for average treatment effects at the cutoff in Sharp, Fuzzy and Kink RD settings, rdbwselect to perform bandwidth selection for the different procedures implemented, and rdplot to conduct exploratory data analysis (RD plots).
Author: Sebastian Calonico , Matias D. Cattaneo , Rocio Titiunik
Maintainer: Sebastian Calonico

Diff between rdrobust versions 0.61 dated 2014-09-04 and 0.70 dated 2014-10-26

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Sat, 25 Oct 2014

Package VIM updated to version 4.1.0 with previous version 4.0.0 dated 2013-10-10

Title: Visualization and Imputation of Missing Values
Description: This package introduces new tools for the visualization of missing and/or imputed values, 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

Diff between VIM versions 4.0.0 dated 2013-10-10 and 4.1.0 dated 2014-10-25

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Package simTool updated to version 1.0.3 with previous version 1.0.2 dated 2014-10-14

Title: Conduct Simulation Studies with a Minimal Amount of Source Code.
Description: The simTool package is designed for statistical simulations that have two components. One component generates the data and the other one analyzes the data. The main aims of the simTool package are the reduction of the administrative source code (mainly loops and management code for the results) and a simple applicability of the package that allows the user to quickly learn how to work with the simTool package. Parallel computing is also supported. Finally, convenient functions are provided to summarize the simulation results.
Author: Marsel Scheer
Maintainer: Marsel Scheer

Diff between simTool versions 1.0.2 dated 2014-10-14 and 1.0.3 dated 2014-10-25

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Package rasterVis updated to version 0.32 with previous version 0.31 dated 2014-08-25

Title: Visualization methods for the raster package
Description: The raster package defines classes and methods for spatial raster data access and manipulation. The rasterVis package complements raster providing a set of methods for enhanced visualization and interaction.
Author: Oscar Perpinan Lamigueiro [cre, aut], Robert Hijmans [aut]
Maintainer: Oscar Perpinan Lamigueiro

Diff between rasterVis versions 0.31 dated 2014-08-25 and 0.32 dated 2014-10-25

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Package FSelector updated to version 0.20 with previous version 0.19 dated 2013-02-28

Title: Selecting attributes
Description: This package provides functions for selecting attributes from a given dataset. Attribute subset selection is the process of identifying and removing as much of the irrelevant and redundant information as possible.
Author: Piotr Romanski, Lars Kotthoff
Maintainer: Lars Kotthoff

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Package spBayesSurv updated to version 1.0.1 with previous version 1.0.0 dated 2014-06-12

Title: Bayesian Modeling and Analysis of Spatially Correlated Survival Data
Description: This package provides several Bayesian survival models for spatial/non-spatial survival data: marginal Bayesian Nonparametric models, marginal Bayesian proportional hazards models, and generalized accelerated failure time frailty models.
Author: Haiming Zhou and Tim Hanson
Maintainer: Haiming Zhou

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New package managelocalrepo with initial version 0.1.4
Package: managelocalrepo
Type: Package
Title: Manage a CRAN-style Local Repository
Version: 0.1.4
Date: 2014-10-25
Author: Imanuel Costigan
Maintainer: Imanuel Costigan
Description: This will allow easier management of a CRAN-style repository on local networks (i.e. not on CRAN). This might be necessary where hosted packages contain intellectual property owned by a corporation.
License: GPL-2
Depends: R (>= 3.0)
Imports: stringr (>= 0.6.2), assertthat (>= 0.1), tools (>= 3.0)
Packaged: 2014-10-25 03:44:33 UTC; imanuel
NeedsCompilation: no
Repository: CRAN
Date/Publication: 2014-10-25 08:07:55

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Package logconPH updated to version 1.2 with previous version 1.1 dated 2014-10-20

Title: CoxPH Model with Log Concave Baseline Distribution
Description: Computes a cox PH model with a log concave baseline distribution. If no covariates are provided, estimates the log concave NPMLE. Built specifically for interval censored data, where data is a n by 2 matrix with [i, 1] as the left side of the interval for subject i and [i,2] as right side. Uncensored data can be entered by setting [i,1] = [i,2]. Alternatively, this can also handle uncensored data. If all the data is uncensored, you may enter data as a length(n) vector.
Author: Clifford Anderson-Bergman
Maintainer: Clifford Anderson-Bergman

Diff between logconPH versions 1.1 dated 2014-10-20 and 1.2 dated 2014-10-25

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Package ivpack updated to version 1.2 with previous version 1.1 dated 2014-03-21

Title: Instrumental Variable Estimation.
Description: This package contains functions for carrying out instrumental variable estimation of causal effects and power analyses for instrumental variable studies.
Author: Yang Jiang and Dylan Small
Maintainer: Dylan Small

Diff between ivpack versions 1.1 dated 2014-03-21 and 1.2 dated 2014-10-25

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New package HiDimDA with initial version 0.2-2
Package: HiDimDA
Type: Package
Title: High Dimensional Discriminant Analysis
Version: 0.2-2
Date: 2014-10-24
Author: Antonio Pedro Duarte Silva
Maintainer: Antonio Pedro Duarte Silva
Depends: R (>= 2.10.0)
Imports: splines
Suggests: MASS
LazyLoad: yes
LazyData: yes
Description: Performs linear discriminant analysis in high dimensional problems based on reliable covariance estimators for problems with (many) more variables than observations. Includes routines for classifier training, prediction, cross-validation and variable selection.
License: GPL (>= 3)
URL: http://www.r-project.org
Repository: CRAN
Packaged: 2014-10-24 13:48:10 UTC; apedro
NeedsCompilation: yes
Date/Publication: 2014-10-25 07:51:03

More information about HiDimDA at CRAN
Permanent link

Package DBKGrad updated to version 1.6 with previous version 1.5 dated 2014-04-08

Title: Discrete Beta Kernel Graduation of Mortality Data
Description: This package allows for nonparametric graduation of mortality rates using fixed or adaptive discrete beta kernel estimator.
Author: Angelo Mazza [aut, cre], Antonio Punzo [aut]
Maintainer: Angelo Mazza

Diff between DBKGrad versions 1.5 dated 2014-04-08 and 1.6 dated 2014-10-25

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New package choroplethrMaps with initial version 1.0
Package: choroplethrMaps
Type: Package
Title: Contains maps used by the choroplethr package
Version: 1.0
Date: 2014-10-22
Author: Ari Lamstein
Maintainer: Ari Lamstein
Description: Contains 3 maps. 1) US States 2) US Counties 3) Countries of the world.
License: BSD_3_clause + file LICENSE
URL: https://github.com/trulia/choroplethrMaps/, https://groups.google.com/forum/#!forum/choroplethr
BugReports: https://github.com/trulia/choroplethrMaps/issues
Suggests: ggplot2
Packaged: 2014-10-25 02:51:32 UTC; arilamstein
NeedsCompilation: no
Repository: CRAN
Date/Publication: 2014-10-25 08:07:52

More information about choroplethrMaps at CRAN
Permanent link

Package BiSEp updated to version 2.0 with previous version 1.0 dated 2014-02-25

Title: Toolkit To Identify Candidate Synthetic Lethality
Description: Enables the user to infer potential synthetic lethal relationships by analysing relationships between bimodally distributed gene pairs in big gene expression datasets. Enables the user to visualise these candidate synthetic lethal relationships
Author: Mark Wappett
Maintainer: Mark Wappett

Diff between BiSEp versions 1.0 dated 2014-02-25 and 2.0 dated 2014-10-25

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New package BayesMixSurv with initial version 0.9
Package: BayesMixSurv
Type: Package
Title: Bayesian Mixture Survival Models using Additive Mixture-of-Weibull Hazards, with Lasso Shrinkage and Stratification
Version: 0.9
Date: 2014-10-24
Author: Alireza S. Mahani, Mansour T.A. Sharabiani
Maintainer: Alireza S. Mahani
Description: Bayesian Mixture Survival Models using Additive Mixture-of-Weibull Hazards, with Lasso Shrinkage and Stratification
License: GPL (>= 2)
Depends: survival
Packaged: 2014-10-25 01:34:35 UTC; amahani
NeedsCompilation: no
Repository: CRAN
Date/Publication: 2014-10-25 08:07:48

More information about BayesMixSurv at CRAN
Permanent link

Fri, 24 Oct 2014

Package vecsets updated to version 1.1 with previous version 1.0 dated 2014-02-11

Title: like base::sets tools but keeps duplicate elements.
Description: The base 'sets' tools follow the algebraic definition that each element of a set must be unique. Since it's often helpful to compare all elements of two vectors, this toolset treats every element as unique for counting purposes. For ease of use, all functions in vecsets have an argument 'multiple' which, when set to FALSE, reverts them to the base::set tools functionality.
Author: Carl Witthoft
Maintainer: Carl Witthoft

Diff between vecsets versions 1.0 dated 2014-02-11 and 1.1 dated 2014-10-24

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Package TwoStepCLogit updated to version 1.2.3 with previous version 1.2.2 dated 2013-06-11

Title: Conditional logistic regression: A two-step estimation method
Description: Conditional logistic regression with longitudinal follow up and individual-level random coefficients: A stable and efficient two-step estimation method
Author: Radu V. Craiu, Thierry Duchesne, Daniel Fortin and Sophie Baillargeon
Maintainer: Thierry Duchesne

Diff between TwoStepCLogit versions 1.2.2 dated 2013-06-11 and 1.2.3 dated 2014-10-24

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Package Surrogate updated to version 0.1-3 with previous version 0.1-2 dated 2014-07-30

Title: Evaluation of surrogate endpoints in clinical trials
Description: In a clinical trial, it frequently occurs that the most credible outcome to evaluate the effectiveness of a new therapy (the true endpoint) is difficult to measure. In such a situation, it can be an effective strategy to replace the true endpoint by a biomarker that is easier to measure and that allows for a prediction of the treatment effect on the true endpoint (a surrogate endpoint). The package 'Surrogate' allows for an evaluation of the appropriateness of a candidate surrogate endpoint based on the meta-analytic, information-theoretic, and causal-inference frameworks (for normally distributed endpoints). Part of this software has been developed using funding provided from the European Union's 7th Framework Programme for research, technological development and demonstration under Grant Agreement no 602552.
Author: Wim Van der Elst, Ariel Alonso & Geert Molenberghs
Maintainer: Wim Van der Elst

Diff between Surrogate versions 0.1-2 dated 2014-07-30 and 0.1-3 dated 2014-10-24

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Package sparr updated to version 0.3-6 with previous version 0.3-5 dated 2014-05-30

Title: The sparr package: SPAtial Relative Risk
Description: Provides functions to estimate kernel-smoothed relative risk functions and perform subsequent inference.
Author: T.M. Davies, M.L. Hazelton and J.C. Marshall
Maintainer: Tilman M. Davies

Diff between sparr versions 0.3-5 dated 2014-05-30 and 0.3-6 dated 2014-10-24

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Package RSQLite updated to version 1.0.0 with previous version 0.11.4 dated 2013-05-26

Title: SQLite Interface for R
Description: This package embeds the SQLite database engine in R and provides an interface compliant with the DBI package. The source for the SQLite engine (version 3.8.6) is included.
Author: Hadley Wickham [aut, cre], David A. James [aut], Seth Falcon [aut], SQLite Authors [ctb] (for the included SQLite sources), Liam Healy [ctb] (for the include SQLite extensions), RStudio [cph]
Maintainer: Hadley Wickham

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Package replicationInterval updated to version 0.2 with previous version 0.1 dated 2014-08-27

Title: Replication Interval Functions
Description: A common problem faced by journal reviewers and authors is the question of whether the results of a replication study are consistent with the original published study. One solution to this problem is to examine the effect size from the published study and generate the range of effect sizes that could reasonably be obtained (due to random sampling) in a replication attempt (i.e., calculate a replication interval). If a replication effect size falls outside the replication interval then that value could not have occurred to due the effects of sampling error alone. Alternatively, if a replication effect size falls within the replication interval then the replication results could have reasonably occurred due to the effects of sampling error alone. This package has functions that calculate the replication interval for two different types of effect sizes, namely correlation (i.e., r) and the standardized mean difference (i.e.,d-value).
Author: David Stanley
Maintainer: David Stanley

Diff between replicationInterval versions 0.1 dated 2014-08-27 and 0.2 dated 2014-10-24

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Package qmethod updated to version 1.2 with previous version 1.1 dated 2014-06-23

Title: Analysis of subjective perspectives using Q methodology
Description: Analysis of Q methodology data to identify the distinct perspectives existing within a group. This methodology is used across social, health and environmental sciences to understand diversity of attitudes, discourses, or decision-making styles (for more information, see http://qmethod.org). The function qmethod() runs the full analysis. Each step can be run separately using the corresponding functions: qflag() for automatic flagging of Q-sorts (manual flagging is optional), qzscores() for scores for statements, qda() for distinguishing and consensus statements, and qfcharact() for general characteristics of the factors. Additional functions import data from PQMethod software, export plain text data for interpretation in two flavours, print and plot Q method results in a syntethic manner. The package uses principal components and it offers the following choices: manual or automatic flagging, a number of mathematical methods for rotation, and a number of correlation coefficients for the initial correlation matrix.
Author: Aiora Zabala [aut, cre]
Maintainer: Aiora Zabala

Diff between qmethod versions 1.1 dated 2014-06-23 and 1.2 dated 2014-10-24

 DESCRIPTION               |   10 +-
 MD5                       |   37 ++++-----
 NAMESPACE                 |    1 
 R/plot.QmethodRes.R       |    2 
 R/print.QmethodRes.R      |only
 R/qdc.R                   |    1 
 R/qfcharact.R             |    8 +
 R/qflag.R                 |    8 +
 R/qmethod.R               |   37 +++++++--
 R/qzscores.R              |  186 +++++++++++++++++++++++-----------------------
 R/summary.QmethodRes.R    |only
 man/QmethodRes-class.Rd   |    2 
 man/plot.QmethodRes.Rd    |    3 
 man/print.QmethodRes.Rd   |only
 man/qdc.Rd                |    3 
 man/qfcharact.Rd          |   32 ++++---
 man/qflag.Rd              |    7 -
 man/qmethod-package.Rd    |    9 --
 man/qmethod.Rd            |   24 +----
 man/qzscores.Rd           |   10 --
 man/summary.QmethodRes.Rd |    3 
 21 files changed, 203 insertions(+), 180 deletions(-)

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Package MAINT.Data updated to version 0.3 with previous version 0.2 dated 2011-11-07

Title: Model and Analyse Interval Data
Description: MAINT.Data implements methodologies for modelling interval data, considering appropriate parameterizations of the variance-covariance matrix that take into account the intrinsic nature of interval data, and lead to five different possible configuration structures.
Author: Pedro Duarte Silva Paula Brito
Maintainer: Pedro Duarte Silva

Diff between MAINT.Data versions 0.2 dated 2011-11-07 and 0.3 dated 2014-10-24

 CHANGELOG                  |   11 ++
 DESCRIPTION                |   16 +--
 MD5                        |   44 ++++-----
 NAMESPACE                  |    1 
 R/IData.R                  |    2 
 R/IdtMaxLikNC2.R           |   67 ++++++--------
 R/lqda.R                   |    2 
 R/mle.R                    |  210 ++++++++++++++++++++++++---------------------
 man/ConfTests-class.Rd     |   15 +--
 man/IData-class.Rd         |   16 +--
 man/IdtClMANOVA-class.Rd   |    9 +
 man/IdtE-class.Rd          |   11 +-
 man/IdtHetNMANOVA-class.Rd |    7 -
 man/IdtMANOVA-class.Rd     |   10 +-
 man/IdtMxE-class.Rd        |    7 -
 man/IdtMxNDE-class.Rd      |    9 -
 man/IdtNDE-class.Rd        |   17 +--
 man/IdtSngDE-class.Rd      |   11 +-
 man/IdtSngNDE-class.Rd     |    9 -
 man/Idtlda-class.Rd        |    7 +
 man/Idtqda-class.Rd        |    6 -
 man/MAINT.Data-package.Rd  |   29 +++---
 man/testMod-methods.Rd     |   20 ++--
 23 files changed, 281 insertions(+), 255 deletions(-)

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New package highD2pop with initial version 1.0
Package: highD2pop
Type: Package
Title: Two-Sample Tests for Equality of Means in High Dimension
Version: 1.0
Date: 2012-11-02
Author: Karl Gregory
Maintainer: Karl Gregory
Description: Performs the generalized component test from Gregory et al (2015), as well as the tests from Chen and Qin (2010), Srivastava and Kubokawa (2013), and Cai, Liu, and Xia (2014) for equality of two population mean vectors when the length of the vectors exceeds the sample size.
License: GPL (>= 2)
LazyLoad: true
LazyData: true
ZipData: no
Depends: fastclime
Packaged: 2014-10-24 14:25:33 UTC; karlgregory
NeedsCompilation: yes
Repository: CRAN
Date/Publication: 2014-10-25 01:28:48

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New package ruv with initial version 0.9.4
Package: ruv
Title: Detect and Remove Unwanted Variation using Negative Controls
Description: The algorithms in this package attempt to adjust for systematic errors of unknown origin in high-dimensional data. The algorithms were originally developed for use with genomic data, especially microarray data, but may be useful with other types of high-dimensional data as well. The algorithms included in this package are RUV-2, RUV-4, RUV-inv, and RUV-rinv, along with various supporting algorithms. These algorithms were proposed by Gagnon-Bartsch and Speed (2012), and by Gagnon-Bartsch, Jacob and Speed (2013). The algorithms require the user to specifiy a set of negative control variables, as described in the references.
Version: 0.9.4
Date: 2014-10-24
Author: Johann Gagnon-Bartsch
Maintainer: Johann Gagnon-Bartsch
License: GPL
URL: http://www.stat.berkeley.edu/~johann/ruv
LazyLoad: yes
Packaged: 2014-10-24 09:52:13 UTC; johann
NeedsCompilation: yes
Repository: CRAN
Date/Publication: 2014-10-24 13:55:18

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Package polyCub updated to version 0.5-1 with previous version 0.5-0 dated 2014-05-07

Title: Cubature over Polygonal Domains
Description: A package providing methods for cubature (numerical integration) over polygonal domains. Currently, four cubature methods are implemented: the two-dimensional midpoint rule as a simple wrapper around as.im.function() from package spatstat (Baddeley and Turner, 2005), the product Gauss cubature by Sommariva and Vianello (2007), an adaptive cubature for isotropic functions via line integrate() along the boundary (Meyer and Held, 2014), and quasi-exact methods specific to the integration of the bivariate Gaussian density over polygonal and circular domains (based on formulae from the Abramowitz and Stegun (1972) handbook). For cubature over simple hypercubes, the packages "cubature" and "R2Cuba" are more appropriate.
Author: Sebastian Meyer [aut, cre, trl], Michael Hoehle [ths]
Maintainer: Sebastian Meyer

Diff between polyCub versions 0.5-0 dated 2014-05-07 and 0.5-1 dated 2014-10-24

 DESCRIPTION                |   12 +--
 MD5                        |   70 ++++++++++----------
 NAMESPACE                  |    6 -
 R/coerce-gpc-methods.R     |   83 +++++++++++++++++-------
 R/plotpolyf.R              |   29 +++++---
 R/polyCub.SV.R             |  147 ++++++++++++++++++++++--------------------
 R/polyCub.iso.R            |   35 ++++++----
 R/polyCub.midpoint.R       |    7 --
 R/sysdata.rda              |binary
 R/tools.R                  |   11 +--
 R/xylist.R                 |   33 +++------
 R/zzz.R                    |   11 +--
 inst/CITATION              |   11 +--
 inst/NEWS.Rd               |   18 +++++
 inst/examples/polyCub.R    |   22 +++---
 man/checkintrfr.Rd         |   65 ++++++++----------
 man/circleCub.Gauss.Rd     |   39 +++++------
 man/coerce-gpc-methods.Rd  |   54 +++++++--------
 man/coerce-sp-methods.Rd   |    7 +-
 man/dotprod.Rd             |    3 
 man/gpclibPermit.Rd        |   11 +--
 man/isClosed.Rd            |    9 +-
 man/isScalar.Rd            |    6 -
 man/makegrid.Rd            |   17 ++--
 man/plot_polyregion.Rd     |   23 +++---
 man/plotpolyf.Rd           |   78 ++++++++++------------
 man/polyCub-package.Rd     |  105 +++++++++++++++---------------
 man/polyCub.Rd             |   79 +++++++++++-----------
 man/polyCub.SV.Rd          |  138 +++++++++++++++++++---------------------
 man/polyCub.exact.Gauss.Rd |   93 +++++++++++++--------------
 man/polyCub.iso.Rd         |  155 ++++++++++++++++++++-------------------------
 man/polyCub.midpoint.Rd    |   49 +++++++-------
 man/polygauss.Rd           |   85 +++++++++++-------------
 man/vecnorm.Rd             |    3 
 man/xylist.Rd              |   99 +++++++++++++---------------
 tests/testthat/test-NWGL.R |   12 ++-
 36 files changed, 826 insertions(+), 799 deletions(-)

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