Fri, 29 Aug 2014

Package riverplot updated to version 0.3 with previous version 0.2 dated 2014-02-27

Title: Sankey or ribbon plots
Description: Sankey plots are a type of diagram that is convenient to illustrate how flow of information, resources etc. separates and joins, much like observing how rivers split and merge. For example, they can be used to compare different clusterings.
Author: January Weiner
Maintainer: January Weiner

Diff between riverplot versions 0.2 dated 2014-02-27 and 0.3 dated 2014-08-29

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More information about riverplot at CRAN
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Package BayesFactor updated to version 0.9.8 with previous version 0.9.7 dated 2014-02-22

Title: Computation of Bayes factors for common designs
Description: The BayesFactor package is a suite of functions for computing various Bayes factors for simple designs, including contingency tables, one- and two-sample designs, one-way designs, general ANOVA designs, and linear regression.
Author: Richard D. Morey, Jeffrey N. Rouder, Tahira Jamil
Maintainer: Richard D. Morey

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More information about BayesFactor at CRAN
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Package vows updated to version 0.3 with previous version 0.2-1 dated 2013-03-22

Title: Voxelwise semiparametrics
Description: Parametric and semiparametric inference for massively parallel models, i.e., a large number of models with common design matrix, as often occurs with brain imaging data.
Author: Philip Reiss, Yin-Hsiu Chen, Lei Huang, Lan Huo, and Ruixin Tan
Maintainer: Philip Reiss

Diff between vows versions 0.2-1 dated 2013-03-22 and 0.3 dated 2014-08-29

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Package raincpc updated to version 0.4 with previous version 0.3 dated 2014-08-26

Title: Obtain and Analyze Rainfall Data from the Climate Prediction Center
Description: The Climate Prediction Center's (CPC) rainfall data for the world (1979 to present, 50 km resolution) and the USA (1948 to present, 25 km resolution), is one of the few high quality, long term, observation based, daily rainfall products available for free. Although raw data is available at CPC's ftp site, obtaining, processing and visualizing the data is not straightforward. There are more than 12,000 files for the world and about 24,000 files for the USA. Moreover, file formats and file extensions have not been consistent. This package provides functionality to download, process and visualize over 35 years of global rainfall data and over 65 years of USA rainfall data from CPC.
Author: Gopi Goteti
Maintainer: Gopi Goteti

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Package heatmap3 updated to version 1.0.7 with previous version 1.0.4 dated 2014-06-10

Title: A improved heatmap package
Description: heatmap3 is an improved heatmap package. It is completely compatible with the original R function heatmap, and provides some more powerful and convenient features.
Author: Shilin Zhao, Yan Guo, Quanhu Sheng, Yu Shyr
Maintainer: Shilin Zhao

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Package icamix updated to version 1.0.1 with previous version 1.0 dated 2014-07-02

Title: Estimation of ICA Mixture Models
Description: The icamix package provides R functions as well as a C++ library which facilitate the estimation of ICA mixture models. We have developed and implemented the NSMM-ICA algorithm in the function EMFASTICAALG that currently integrates npEM and Fast-ICA for non-parametric estimation of ICA mixture models.
Author: Xiaotian Zhu, David R. Hunter
Maintainer: Xiaotian Zhu

Diff between icamix versions 1.0 dated 2014-07-02 and 1.0.1 dated 2014-08-29

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Package analogue updated to version 0.14-0 with previous version 0.12-0 dated 2013-12-14

Title: Analogue and weighted averaging methods for palaeoecology
Description: Fits Modern Analogue Technique and Weighted Averaging transfer function models for prediction of environmental data from species data, and related methods used in palaeoecology.
Author: Gavin L. Simpson [aut, cre], Jari Oksanen [aut]
Maintainer: Gavin L. Simpson

Diff between analogue versions 0.12-0 dated 2013-12-14 and 0.14-0 dated 2014-08-29

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More information about analogue at CRAN
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Thu, 28 Aug 2014

Package ttScreening updated to version 1.4 with previous version 1.3 dated 2014-02-28

Title: Genome-wide DNA methylation sites screening by use of training and testing samples.
Description: This package utilizes training and testing samples to filter out uninformative DNA methylation sites. Surrogate variables (SVs) of DNA methylation are included in the filtering process to explain unknown factor effects.
Author: Meredith Ray, Xin Tong, Hongmei Zhang
Maintainer: Meredith Ray

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Package psychotree updated to version 0.14-0 with previous version 0.13-0 dated 2014-02-03

Title: Recursive Partitioning Based on Psychometric Models
Description: Recursive partitioning based on psychometric models, employing the general MOB algorithm (from package partykit) to obtain Bradley-Terry trees, Rasch trees, rating scale and partial credit trees.
Author: Achim Zeileis [aut, cre], Carolin Strobl [aut], Florian Wickelmaier [aut], Basil Abou El-Komboz [aut], Julia Kopf [aut]
Maintainer: Achim Zeileis

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More information about psychotree at CRAN
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Package psychotools updated to version 0.3-0 with previous version 0.2-0 dated 2014-02-03

Title: Infrastructure for Psychometric Modeling
Description: Infrastructure for psychometric modeling such as data classes (for item response data and paired comparisons), basic model fitting functions (for Bradley-Terry, Rasch, partial credit, and rating scale models), extractor functions for different types of parameters (item, person, threshold, discrimination), unified inference and visualizations, and various datasets for illustration. Intended as a common lightweight and efficient toolbox for psychometric modeling and a common building block for fitting psychometric mixture models in package "psychomix" and psychometric tree models in package "psychotree".
Author: Achim Zeileis [aut, cre], Carolin Strobl [aut], Florian Wickelmaier [aut], Basil Abou El-Komboz [aut], Julia Kopf [aut]
Maintainer: Achim Zeileis

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Package MGSDA updated to version 1.1 with previous version 1.0 dated 2014-07-08

Title: Multi-Group Sparse Discriminant Analysis
Description: Implements Multi-Group Sparse Discriminant Analysis proposal of 'I.Gaynanova, J.Booth and M.Wells (2014), Simultaneous sparse estimation of canonical vectors in the p>>N setting'
Author: Irina Gaynanova
Maintainer: Irina Gaynanova

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Package corrgram updated to version 1.6 with previous version 1.5 dated 2013-08-29

Title: Plot a correlogram
Description: Calculates correlation of variables and displays the results graphically.
Author: Kevin Wright
Maintainer: Kevin Wright

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Package SQUAREM updated to version 2014.8-1 with previous version 2012.7-1 dated 2012-07-26

Title: Squared extrapolation methods for accelerating fixed-point iterations
Description: Algorithms for accelerating the convergence of slow, monotone sequences from smooth, contraction mapping such as the EM algorithm. It can be used to accelerate any smooth, linearly convergent acceleration scheme. A tutorial style introduction to this package is available in a vignette on the CRAN download page or, when the package is loaded in an R session, with vignette("SQUAREM").
Author: Ravi Varadhan
Maintainer: Ravi Varadhan

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Package Rcapture updated to version 1.4-2 with previous version 1.3-1 dated 2012-05-31

Title: Loglinear Models for Capture-Recapture Experiments
Description: Estimation of abundance and other of demographic parameters for closed populations, open populations and the robust design in capture-recapture experiments using loglinear models.
Author: Louis-Paul Rivest and Sophie Baillargeon
Maintainer: Louis-Paul Rivest

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Package RcmdrPlugin.DoE updated to version 0.12-3 with previous version 0.12-2 dated 2013-08-29

Title: R Commander Plugin for (industrial) Design of Experiments
Description: The package provides a platform-independent GUI for design of experiments. It is implemented as a plugin to the R-Commander, which is a more general graphical user interface for statistics in R based on tcl/tk. DoE functionality can be accessed through the menu Design that is added to the R-Commander menus.
Author: Ulrike Groemping [aut, cre], Fox John [ctb]
Maintainer: Ulrike Groemping

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Package HiClimR updated to version 1.1.3 with previous version 1.1.2 dated 2014-07-27

Title: Hierarchical Climate Regionalization: An Improved Hierarchical Clustering in R for Climate Regionalization
Description: HiClimR package modifies and improves hierarchical clustering in R ('hclust' function in 'stats' library), for climate regionalization. It adds a new clustering method (called, regional linkage) to the set of available methods together with several features including regridding, coarsening spatial resolution, geographic masking, data thresholds, detrending and standardization preprocessing, faster correlation function, hybrid hierarchical clustering, and cluster validation. Badr et. al (2014) describes the regionalization algorithms and data processing tools included in the package and presents a demonstration application in which the package is used to regionalize Africa on the basis of interannual precipitation variability. It is applicable to any correlation-based clustering.
Author: Hamada S. Badr [aut, cre], Benjamin F. Zaitchik [aut], Amin K. Dezfuli [aut]
Maintainer: Hamada S. Badr

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Package compareGroups updated to version 2.0.5 with previous version 2.0.4 dated 2014-05-02

Title: Descriptive analysis by groups
Description: This package is designed to read, interpret, summarise, display and analyse epidemiological data. Can be used to create data summaries for quality control, extensive reports for exploring data, including publication-ready univariate or bivariate tables in plain text HTML and LaTeX, and a figures to quickly visualise the distribution of your data. Depending on the nature of the variable, various statistics are calculated (mean, median, frequencies, incidences) and appropriate tests are performed (t-test, Analysis of variance, Kruskal-Wallis, Fisher, log-rank, ...). The latest version includes functionality for summarising genetic data, and for performing low-level quality control of your database (see radiograph()) to help identify data-entry errors. This version has also been implemented in a web-interface to make this package accessible to non-R-users (see www.comparegroups.eu).
Author: Isaac Subirana, Joan Vila, Héctor Sanz, Gavin Lucas, Judith Peñafiel and David Giménez
Maintainer: Isaac Subirana

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Package Rlabkey updated to version 2.1.125 with previous version 2.1.123 dated 2013-11-04

Title: Data exchange between R and LabKey Server
Description: This package allows an R user to discover, query and modify data in LabKey Server
Author: Peter Hussey
Maintainer: Cory Nathe

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Package effsize updated to version 0.5.2 with previous version 0.5.1 dated 2014-05-21

Title: Efficient effect size computation
Description: This package contains the functions to compute the standardized effect sizes for experiments (Cohen d, Hedges g, Cliff delta, Vargha and Delaney A). The computation algorithms have been optimized to allow efficient computation even with very large data sets.
Author: Marco Torchiano
Maintainer: Marco Torchiano

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Package BioStatR updated to version 2.0.0 with previous version 1.0.4 dated 2012-03-30

Title: Initiation à la Statistique avec R
Description: This packages provides datasets and functions for the book "Initiation à la Statistique avec R", Dunod, 2ed, 2014.
Author: Frederic Bertrand , Myriam Maumy-Bertrand .
Maintainer: Frederic Bertrand

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Package fscaret updated to version 0.8.5.7 with previous version 0.8.5.6 dated 2014-04-14

Title: Automated caret feature selection
Description: Automated feature selection using variety of models provided by caret package
Author: Jakub Szlek , acknowledgments to Aleksander Mendyk, contributions from stackoverflow and r-help@r-project.org mailing list community. Acknowledgments: This work was funded by Poland-Singapore bilateral cooperation project no 2/3/POL-SIN/2012.
Maintainer: Jakub Szlek

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Package trajectories updated to version 0.1-1 with previous version 0.1-0 dated 2014-08-27

Title: Classes and methods for trajectory data
Description: Classes and methods for trajectory data, with nested classes for individual trips, and collections for different entities. Methods include selection, generalization, aggregation, intersection, and plotting.
Author: Edzer Pebesma [cre, aut], Benedikt Klus [aut]
Maintainer: Edzer Pebesma

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Package QuantifQuantile updated to version 1.0 with previous version 0.2 dated 2014-06-13

Title: Estimation of conditional quantiles using optimal quantization
Description: Estimation of conditional quantiles using optimal quantization. Construction of an optimal grid of N quantizers, estimation of conditional quantiles and data driven selection of the size N of the grid. Graphical illustrations for the selection of N and of resulting estimated curves or surfaces when the dimension of the covariate is one or two.
Author: Isabelle Charlier and Davy Paindaveine and Jerome Saracco
Maintainer: Isabelle Charlier

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Package georob updated to version 0.1-5 with previous version 0.1-4 dated 2014-06-02

Title: Robust Geostatistical Analysis of Spatial Data
Description: The georob package provides functions for fitting linear models with spatially correlated errors by robust and Gaussian Restricted Maximum Likelihood and for computing robust and customary point and block kriging predictions, along with utility functions for cross-validation and for unbiased back-transformation of kriging predictions of log-transformed data.
Author: Andreas Papritz [cre, aut], Cornelia Schwierz [ctb]
Maintainer: Andreas Papritz

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Package cheddar updated to version 0.1-626 with previous version 0.1-625 dated 2014-02-26

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

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Package Bergm updated to version 2.9.1 with previous version 2.9 dated 2014-07-22

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

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Package spatstat updated to version 1.38-1 with previous version 1.38-0 dated 2014-08-15

Title: Spatial Point Pattern analysis, model-fitting, simulation, tests
Description: A package for analysing spatial data, mainly Spatial Point Patterns, including multitype/marked points and spatial covariates, in any two-dimensional spatial region. Also supports three-dimensional point patterns, space-time point patterns in any number of dimensions, and point patterns on a linear network. Contains about 2000 functions for plotting spatial data, exploratory data analysis, model-fitting, simulation, spatial sampling, model diagnostics, and formal inference. Data types include point patterns, line segment patterns, spatial windows, pixel images, tessellations, and linear networks. Exploratory methods include quadrat counts, K-functions and their simulation envelopes, nearest neighbour distance and empty space statistics, Fry plots, pair correlation function, kernel smoothed intensity, relative risk estimation with cross-validated bandwidth selection, mark correlation functions, segregation indices, mark dependence diagnostics, and kernel estimates of covariate effects. Formal hypothesis tests of random pattern (chi-squared, Kolmogorov-Smirnov, Diggle-Cressie-Loosmore-Ford, Dao-Genton) and tests for covariate effects (Cox-Berman-Waller-Lawson, Kolmogorov-Smirnov) are also supported. Parametric models can be fitted to point pattern data using the functions ppm, kppm, slrm similar to glm. Types of models include Poisson, Gibbs, Cox and cluster point processes. Models may involve dependence on covariates, interpoint interaction, cluster formation and dependence on marks. Models are fitted by maximum likelihood, logistic regression, minimum contrast, and composite likelihood methods. Fitted point process models can be simulated, automatically. Formal hypothesis tests of a fitted model are supported (likelihood ratio test, analysis of deviance, Monte Carlo tests) along with basic tools for model selection (stepwise, AIC). Tools for validating the fitted model include simulation envelopes, residuals, residual plots and Q-Q plots, leverage and influence diagnostics, partial residuals, and added variable plots.
Author: Adrian Baddeley , Rolf Turner and Ege Rubak , with substantial contributions of code by Kasper Klitgaard Berthelsen; Abdollah Jalilian; Marie-Colette van Lieshout; Dominic Schuhmacher; and Rasmus Waagepetersen. Additional contributions by Q.W. Ang; S. Azaele; M. Baddeley; C. Beale; M. Bell; R. Bernhardt; T. Bendtsen; A. Bevan; B. Biggerstaff; L. Bischof; R. Bivand; J.M. Blanco Moreno; F. Bonneu; J. Burgos; S. Byers; Y.M. Chang; J.B. Chen; I. Chernayavsky; Y.C. Chin; B. Christensen; J.-F. Coeurjolly; R. Corria Ainslie; M. de la Cruz; P. Dalgaard; S. Das; P.J. Diggle; P. Donnelly; I. Dryden; S. Eglen; O. Flores; E.D. Ford; P. Forbes; J. Franklin; N. Funwi-Gabga; O. Garcia; A. Gault; M. Genton; J. Gilbey; J. Goldstick; P. Grabarnik; C. Graf; U. Hahn; A. Hardegen; M. Hering; M.B. Hansen; M. Hazelton; J. Heikkinen; K. Hornik; P. Hunziker; R. Ihaka; A. Jammalamadaka; R. John-Chandran; D. Johnson; M. Kuhn; J. Laake; F. Lavancier; T. Lawrence; R.A. Lamb; J. Lee; G.P. Leser; H.T. Li; G. Limitsios; B. Madin; J. Marcus; K. Marchikanti; R. Mark; J. Mateu; P. McCullagh; U. Mehlig; S. Meyer; X.C. Mi; L. De Middeleer; R.K. Milne; J. Moller; E. Mudrak; G.M. Nair; L.S. Nielsen; F. Nunes; J. Oehlschlaegel; T. Onkelinx; S. O'Riordan; E. Parilov; J. Picka; N. Picard; M. Porter; S. Protsiv; A. Raftery; S. Rakshit; P. Ramon; X. Raynaud, M. Reiter; T.O. Richardson; B.D. Ripley; E. Rosenbaum; B. Rowlingson; J. Rudokas; J. Rudge; C. Ryan; F. Safavimanesh; A. Sarkka; K. Schladitz; B.T. Scott; G.C. Shen; V. Shcherbakov; I.-M. Sintorn; Y. Song; M. Spiess; M. Stevenson; K. Stucki; M. Sumner; P. Surovy; B. Taylor; T. Thorarinsdottir; B. Turlach; K. Ummer; M. Uppala; A. van Burgel; T. Verbeke; M. Vihtakari; A. Villers; F. Vinatier; H. Wang; H. Wendrock; J. Wild; S. Wong; M.E. Zamboni and A. Zeileis.
Maintainer: Adrian Baddeley

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Package FactoMineR updated to version 1.27 with previous version 1.26 dated 2014-04-09

Title: Multivariate Exploratory Data Analysis and Data Mining with R
Description: an R package for exploratory data analysis
Author: Francois Husson, Julie Josse, Sebastien Le, Jeremy Mazet
Maintainer: Francois Husson

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Package rAvis updated to version 0.1.2 with previous version 0.1.1 dated 2014-03-07

Title: Interface to the bird-watching datasets at proyectoavis.com
Description: Interface to the proyectoavis.com bird observations records database. It provides means to download datasets filtered by species, order, family, and several other criteria. Provides also basic functionality to plot exploratory maps of the datasets.
Author: Javier González Hernández , Sara Varela
Maintainer: Sara Varela

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Package LatticeKrig updated to version 3.4 with previous version 3.3 dated 2014-07-11

Title: Multiresolution Kriging based on Markov random fields
Description: Functions for the interpolation of large spatial datasets. This package follows a "fixed rank Kriging" approach using a large number of basis functions and provides spatial estimates that are comparable to standard families of covariance functions. Using a large number of basis functions allows for estimates that can come close to interpolating the observations (a spatial model with a small nugget variance.) The covariance model for this method can approximate the Matern covariance family but also allows for a multi-resolution model and supports efficient computation of the profile likelihood for estimating covariance parameters. This is accomplished through compactly supported basis functions and a Markov random field model for the basis coefficients. These features lead to sparse matrices for the computations. One benefit of this approach is the facilty to do unconditional and conditional simulation of the field for large numbers of arbitrary points. There is also the flexibility for estimating nonstationary covariances. Included are generic methods for prediction, standard errors for prediction, plotting of the estimated surface and conditional and unconditional simulation.
Author: Douglas Nychka [aut, cre], Dorit Hammerling [aut], Stephan Sain [aut], Nathan Lenssen [aut]
Maintainer: Douglas Nychka

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Package ifultools updated to version 2.0-1 with previous version 2.0-0 dated 2013-12-30

Title: Insightful Research Tools
Description: Insightful Research Tools.
Author: William Constantine and Donald Percival (Applied Physics Laboratory, University of Washington)
Maintainer: Don Percival

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Package fastR updated to version 0.8-1 with previous version 0.4-2 dated 2013-04-11

Title: Data sets and utilities for Foundations and Applications of Statistics by R Pruim
Description: Data sets and utilities for Foundations and Applications of Statistics:an Introduction using R by R Pruim
Author: Randall Pruim
Maintainer: Randall Pruim

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 152 files changed, 1554 insertions(+), 1652 deletions(-)

More information about fastR at CRAN
Permanent link

Package cgAUC updated to version 1.2.1 with previous version 1.1.2 dated 2013-01-16

Title: Calculate AUC-type measure when gold standard is continuous and the corresponding optimal linear combination of variables with respect to it.
Description: The cgAUC can calculate the AUC-type measure of Obuchowski(2006) when gold standard is continuous, and find the optimal linear combination of variables with respect to this measure.
Author: Yuan-chin I. Chang, Yu-chia Chang, and Ling-wan Chen
Maintainer: Yu-chia Chang

Diff between cgAUC versions 1.1.2 dated 2013-01-16 and 1.2.1 dated 2014-08-28

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 cgAUC-1.1.2/cgAUC/man/s.h.Rd              |only
 cgAUC-1.2.1/cgAUC/DESCRIPTION             |   18 +++++++++---------
 cgAUC-1.2.1/cgAUC/MD5                     |   21 ++++++++++++---------
 cgAUC-1.2.1/cgAUC/NAMESPACE               |    2 ++
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 cgAUC-1.2.1/cgAUC/man/cgAUC-package.Rd    |   17 +++++++++++------
 cgAUC-1.2.1/cgAUC/man/cgAUC.Rd            |    1 +
 cgAUC-1.2.1/cgAUC/src                     |only
 17 files changed, 35 insertions(+), 24 deletions(-)

More information about cgAUC at CRAN
Permanent link

Wed, 27 Aug 2014

Package Runuran updated to version 0.21.0 with previous version 0.20.0 dated 2012-09-10

Title: R interface to the UNU.RAN random variate generators
Description: Interface to the UNU.RAN library for Universal Non-Uniform RANdom variate generators. Thus it allows to build non-uniform random number generators from quite arbitrary distributions. In particular, it provides an algorithm for fast numerical inversion for distribution with given density function. In addition, the package contains densities, distribution functions and quantiles from a couple of distributions.
Author: Josef Leydold and Wolfgang H\"ormann
Maintainer: Josef Leydold

Diff between Runuran versions 0.20.0 dated 2012-09-10 and 0.21.0 dated 2014-08-27

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 Runuran-0.21.0/Runuran/DESCRIPTION                                              |   24 
 Runuran-0.21.0/Runuran/MD5                                                      |  739 +++++-----
 Runuran-0.21.0/Runuran/NAMESPACE                                                |    2 
 Runuran-0.21.0/Runuran/NEWS                                                     |   20 
 Runuran-0.21.0/Runuran/R/Runuran.R                                              |   32 
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 Runuran-0.21.0/Runuran/configure                                                |  206 +-
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 Runuran-0.21.0/Runuran/inst/doc/Runuran.pdf                                     |binary
 Runuran-0.21.0/Runuran/inst/include/unuran.h                                    |    2 
 Runuran-0.21.0/Runuran/man/Runuran-package.Rd                                   |    8 
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 Runuran-0.21.0/Runuran/man/pinv.new.Rd                                          |    2 
 Runuran-0.21.0/Runuran/man/unuran.packed-methods.Rd                             |    2 
 Runuran-0.21.0/Runuran/man/up.Rd                                                |    4 
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 Runuran-0.21.0/Runuran/src/Makevars.in                                          |    2 
 Runuran-0.21.0/Runuran/src/Runuran.c                                            |  139 +
 Runuran-0.21.0/Runuran/src/Runuran.h                                            |   15 
 Runuran-0.21.0/Runuran/src/Runuran_distr.c                                      |   10 
 Runuran-0.21.0/Runuran/src/Runuran_pinv.c                                       |   26 
 Runuran-0.21.0/Runuran/src/performance.c                                        |   16 
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 Runuran-0.21.0/Runuran/src/unuran-src/distr/cemp.c                              |    2 
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 Runuran-0.21.0/Runuran/src/unuran-src/distr/condi.h                             |    2 
 Runuran-0.21.0/Runuran/src/unuran-src/distr/cont.c                              |    2 
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 Runuran-0.21.0/Runuran/src/unuran-src/distr/discr.c                             |    2 
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 Runuran-0.21.0/Runuran/src/unuran-src/distr/matr.c                              |    2 
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 Runuran-0.21.0/Runuran/src/unuran-src/distributions/vc_multistudent.c           |    2 
 Runuran-0.21.0/Runuran/src/unuran-src/methods/arou.c                            |    2 
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Package gWidgets updated to version 0.0-54 with previous version 0.0-53 dated 2014-07-20

Title: gWidgets API for building toolkit-independent, interactive GUIs
Description: gWidgets provides a toolkit-independent API for building interactive GUIs. At least one of the 'gWidgetsXXX packages', such as gWidgetstcltk, needs to be installed. Some icons are on loan from the scigraphica project http://scigraphica.sourceforge.net.
Author: John Verzani. Based on the iwidgets code of Simon Urbanek and suggestions by Simon Urbanek, Philippe Grosjean and Michael Lawrence
Maintainer: John Verzani

Diff between gWidgets versions 0.0-53 dated 2014-07-20 and 0.0-54 dated 2014-08-27

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 MD5                        |   12 ++++++------
 NEWS                       |   12 ++++++++++++
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 inst/doc/addingToolkit.pdf |binary
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Package bfast updated to version 1.5.7 with previous version 1.4.4 dated 2013-03-27

Title: Breaks For Additive Season and Trend (BFAST)
Description: BFAST integrates the decomposition of time series into trend, seasonal, and remainder components with methods for detecting and characterizing abrupt changes within the trend and seasonal components. BFAST can be used to analyze different types of satellite image time series and can be applied to other disciplines dealing with seasonal or non-seasonal time series, such as hydrology, climatology, and econometrics. The algorithm can be extended to label detected changes with information on the parameters of the fitted piecewise linear models. BFAST monitoring functionality is added based on a paper that has been submitted to Remote Sensing of Environment. BFAST monitor provides functionality to detect disturbance in near real-time based on BFAST-type models. BFAST approach is flexible approach that handles missing data without interpolation. Furthermore now different models can be used to fit the time series data and detect structural changes (breaks).
Author: Jan Verbesselt [aut, cre], Achim Zeileis [aut], Rob Hyndman [ctb]
Maintainer: Jan Verbesselt

Diff between bfast versions 1.4.4 dated 2013-03-27 and 1.5.7 dated 2014-08-27

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Package gsubfn updated to version 0.6-6 with previous version 0.6-5 dated 2012-10-22

Title: Utilities for strings and function arguments.
Description: gsubfn is like gsub but can take a replacement function or certain other objects instead of the replacement string. Matches and back references are input to the replacement function and replaced by the function output. gsubfn can be used to split strings based on content rather than delimiters and for quasi-perl-style string interpolation. The package also has facilities for translating formulas to functions and allowing such formulas in function calls instead of functions. This can be used with R functions such as apply, sapply, lapply, optim, integrate, xyplot, Filter and any other function that expects another function as an input argument or functions like cat or sql calls that may involve strings where substitution is desirable.
Author: G. Grothendieck
Maintainer: G. Grothendieck

Diff between gsubfn versions 0.6-5 dated 2012-10-22 and 0.6-6 dated 2014-08-27

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Package ptinpoly updated to version 2.4 with previous version 2.1 dated 2014-04-30

Title: Point-In-Polyhedron Test (2D and 3D)
Description: Function 'pip3d' tests whether a point in 3D space is within, exactly on, or outside an enclosed surface defined by a triangular mesh. Function 'pip2d' tests whether a point in 2D space is within, exactly on, or outside a polygon.
Author: Jose M. Maisog, Yuan Wang, George Luta, Jianfei Liu
Maintainer: Jose M. Maisog

Diff between ptinpoly versions 2.1 dated 2014-04-30 and 2.4 dated 2014-08-27

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More information about ptinpoly at CRAN
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Package R.filesets updated to version 2.6.0 with previous version 2.4.0 dated 2014-02-28

Title: Easy handling of and access to files organized in structured directories
Description: A file set refers to a set of files located in one or more directories on the file system. This package provides classes and methods to locate, setup, subset, navigate and iterate such sets. The API is designed such that these classes can be extended via inheritance to provide a richer API for special file formats. Moreover, a specific name format is defined such that filenames and directories can be considered to have full names which consists of a name followed by comma-separated tags. This adds additional flexibility to identify file sets and individual files. NOTE: This package's API should be considered to be in an beta stage. Its main purpose is currently to support the aroma.* packages, where it is one of the main core components; if you decide to build on top of this package, please contact the author first.
Author: Henrik Bengtsson [aut, cre, cph]
Maintainer: Henrik Bengtsson

Diff between R.filesets versions 2.4.0 dated 2014-02-28 and 2.6.0 dated 2014-08-27

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Package pscl updated to version 1.4.6 with previous version 1.04.4 dated 2012-06-13

Title: Political Science Computational Laboratory, Stanford University
Description: Bayesian analysis of item-response theory (IRT) models, roll call analysis; computing highest density regions; maximum likelihood estimation of zero-inflated and hurdle models for count data; goodness-of-fit measures for GLMs; data sets used in writing and teaching at the Political Science Computational Laboratory; seats-votes curves.
Author: Simon Jackman, with contributions from Alex Tahk, Achim Zeileis, Christina Maimone and Jim Fearon
Maintainer: Simon Jackman

Diff between pscl versions 1.04.4 dated 2012-06-13 and 1.4.6 dated 2014-08-27

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Package MultiSV updated to version 0.0-67 with previous version 0.0-62 dated 2014-07-02

Title: MultiSV: an R package for identification of structural variations in multiple populations based on whole genome resequencing
Description: MultiSV is an R package for identification of structural variations in multiple populations based on whole genome resequencing. It fits linear mixed model and identifies structural variations in multiple populations using whole genome sequencing data. It could also be manipulated to use on RNA-seq data for differential gene expression (implementation in future releases). Main steps for analysis include generating read depth in bins using ComputeBinCounts. conversion of bins to MultiSV format using Bin2MultiSV. Finally, identification of structural variations using CallMultiSV.
Author: Khurram Maqbool
Maintainer: Khurram Maqbool

Diff between MultiSV versions 0.0-62 dated 2014-07-02 and 0.0-67 dated 2014-08-27

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More information about MultiSV at CRAN
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Package fwsim updated to version 0.3.2 with previous version 0.3.1 dated 2014-04-25

Title: Fisher-Wright Population Simulation
Description: Simulates a population under the Fisher-Wright model (fixed or stochastic population size) with a one-step neutral mutation process (stepwise mutation model, logistic mutation model and exponential mutation model supported). The stochastic population sizes are random Poisson distributed and different kinds of population growth are supported. For the stepwise mutation model, it is possible to specify locus and direction specific mutation rate (in terms of upwards and downwards mutation rate). Intermediate generations can be saved in order to study e.g. drift.
Author: Mikkel Meyer Andersen and Poul Svante Eriksen
Maintainer: Mikkel Meyer Andersen

Diff between fwsim versions 0.3.1 dated 2014-04-25 and 0.3.2 dated 2014-08-27

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Package WhopGenome updated to version 0.8.9 with previous version 0.8.2 dated 2013-12-03

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

Diff between WhopGenome versions 0.8.2 dated 2013-12-03 and 0.8.9 dated 2014-08-27

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Package mediation updated to version 4.4.2 with previous version 4.4.1 dated 2014-08-13

Title: Causal Mediation Analysis
Description: mediation allows both parametric and nonparametric causal mediation analysis. It implements the methods and suggestions in Imai, Keele and Yamamoto (2010), Imai, Keele and Tingley (2010), Imai, Tingley and Yamamoto (2013), Imai and Yamamoto (2013) and Yamamoto (2013). In addition to the estimation of causal mediation effects, the software also allows researchers to conduct sensitivity analysis for certain parametric models.
Author: Dustin Tingley , Teppei Yamamoto , Kentaro Hirose , Luke Keele , Kosuke Imai
Maintainer: Teppei Yamamoto

Diff between mediation versions 4.4.1 dated 2014-08-13 and 4.4.2 dated 2014-08-27

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More information about mediation at CRAN
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Package SemiParSampleSel updated to version 1.1-1 with previous version 1.1 dated 2014-03-11

Title: Semiparametric Sample Selection Modelling with Continuous Response
Description: Routine for fitting continuous response copula sample selection models with semiparametric predictors, including linear and nonlinear effects.
Author: Giampiero Marra, Rosalba Radice and Malgorzata Wojtys
Maintainer: Giampiero Marra

Diff between SemiParSampleSel versions 1.1 dated 2014-03-11 and 1.1-1 dated 2014-08-27

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Package GMD updated to version 0.3.3 with previous version 0.3.1.1 dated 2012-02-06

Title: Generalized Minimum Distance of distributions
Description: GMD is a package for non-parametric distance measurement between two discrete frequency distributions.
Author: Xiaobei Zhao [aut, cre, cph], Albin Sandelin [aut]
Maintainer: Xiaobei Zhao

Diff between GMD versions 0.3.1.1 dated 2012-02-06 and 0.3.3 dated 2014-08-27

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Package arm updated to version 1.7-07 with previous version 1.7-05 dated 2014-08-01

Title: Data Analysis Using Regression and Multilevel/Hierarchical Models
Description: R functions for processing lm, glm, svy.glm, merMod and polr outputs.
Author: Andrew Gelman [aut], Yu-Sung Su [aut, cre], Masanao Yajima [ctb], Jennifer Hill [ctb], Maria Grazia Pittau [ctb], Jouni Kerman [ctb], Tian Zheng [ctb], Vicent Dorie [ctb]
Maintainer: Yu-Sung Su

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Package RHive updated to version 2.0-0.1 with previous version 2.0-0.0 dated 2014-04-16

Title: R and Hive
Description: RHive is an R extension facilitating distributed computing via HIVE query. It provides an easy to use HQL like SQL and R objects and functions in HQL.
Author: NexR
Maintainer: Johan Ahn

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Package pamr updated to version 1.55 with previous version 1.54.1 dated 2013-07-25

Title: Pam: prediction analysis for microarrays
Description: Some functions for sample classification in microarrays
Author: T. Hastie, R. Tibshirani, Balasubramanian Narasimhan, Gil Chu
Maintainer: Rob Tibshirani

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Package blkergm updated to version 1.1 with previous version 1.0 dated 2013-10-19

Title: Fitting block ERGM given the block structure on social networks
Description: This package is an extension to the "ergm" package which implements the block ergms.
Author: Xiaolin Yang [aut, cre], Stephen E. Fienberg [aut], Alessandro Rinaldo [aut], Han Liu [aut], Michael Rosenblum [aut]
Maintainer: Xiaolin Yang

Diff between blkergm versions 1.0 dated 2013-10-19 and 1.1 dated 2014-08-27

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Tue, 26 Aug 2014

Package GoFKernel updated to version 2.0-4 with previous version 2.0-3 dated 2014-07-15

Title: GoFKernel: Testing Goodness-of-fit with the Kernel Density Estimator
Description: Tests of goodness-of-fit based on kernel smoothing of the data
Author: Jose M. Pavia
Maintainer: Jose M. Pavia

Diff between GoFKernel versions 2.0-3 dated 2014-07-15 and 2.0-4 dated 2014-08-26

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Package bigsplines updated to version 1.0-3 with previous version 1.0-2 dated 2014-07-12

Title: Smoothing splines for large samples
Description: Fits smoothing spline regression models using scalable algorithms designed for large samples. Five marginal spline types are supported: cubic, different cubic, cubic periodic, cubic thin-plate, and nominal. Parametric predictors are also supported. Response can be Gaussian or non-Gaussian: Binomial, Poisson, Gamma, Inverse Gaussian, or Negative Binomial.
Author: Nathaniel E. Helwig
Maintainer: Nathaniel E. Helwig

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Package swirl updated to version 2.2.16 with previous version 2.2.15 dated 2014-08-08

Title: Learn R, in R.
Description: swirl turns the R console into an interactive learning environment. Users receive immediate feedback as they are guided through self-paced lessons in data science and R programming.
Author: Nick Carchedi [aut, cre], Bill Bauer [aut], Gina Grdina [aut], Sean Kross [aut]
Maintainer: Nick Carchedi

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Package phytools updated to version 0.4-31 with previous version 0.4-21 dated 2014-06-28

Title: Phylogenetic Tools for comparative biology (and other things)
Description: phytools provides various functions for phylogenetic analysis, mostly relevant to comparative biology.
Author: Liam J. Revell
Maintainer: Liam J. Revell

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Package HistogramTools updated to version 0.3.1 with previous version 0.3 dated 2013-12-11

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

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Package extRemes updated to version 2.0-3 with previous version 2.0-2 dated 2014-08-18

Title: Extreme Value Analysis
Description: Functions for performing extreme value analysis.
Author: Eric Gilleland
Maintainer: Eric Gilleland

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Package ecoengine updated to version 1.6 with previous version 1.5 dated 2014-08-13

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 1.5 dated 2014-08-13 and 1.6 dated 2014-08-26

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Package visreg updated to version 2.0-6 with previous version 2.0-5 dated 2014-05-29

Title: Visualization of regression models
Description: Provides convenient interface for constructing plots to visualize the fit of regression models arising from a wide variety of models in R (lm, glm, coxph, rlm, gam, locfit, etc.)
Author: Patrick Breheny, Woodrow Burchett
Maintainer: Patrick Breheny

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Package rplexos updated to version 0.9 with previous version 0.8 dated 2014-08-06

Title: Read and analyze PLEXOS solutions from R
Description: Read and analyze PLEXOS solutions from R
Author: Eduardo Ibanez
Maintainer: Eduardo Ibanez

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More information about rplexos at CRAN
Permanent link

Package raincpc updated to version 0.3 with previous version 0.2 dated 2014-06-25

Title: Obtain and Analyze Rainfall Data from the Climate Prediction Center
Description: The Climate Prediction Center's (CPC) rainfall data for the world (1979 to present, 50 km resolution) and the USA (1948 to present, 25 km resolution), is one of the few high quality, long term, observation based, daily rainfall products available for free. Although raw data is available at CPC's ftp site, obtaining, processing and visualizing the data is not straightforward. There are more than 12,000 files for the world and about 24,000 files for the USA. Moreover, file formats and file extensions have not been consistent. This package provides functionality to download, process and visualize over 35 years of global rainfall data and over 65 years of USA rainfall data from CPC.
Author: Gopi Goteti
Maintainer: Gopi Goteti

Diff between raincpc versions 0.2 dated 2014-06-25 and 0.3 dated 2014-08-26

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More information about raincpc at CRAN
Permanent link

Package gmatrix updated to version 0.2 with previous version 0.1 dated 2013-10-31

Title: An R Package for Harnessing GPU Power
Description: This package implements a general framework for utilizing R to harness the power of NVIDIA GPU's. The "gmatrix" and "gvector" classes allow for easy management of the separate device and host memory spaces. Numerous numerical operations are implemented for these objects on the GPU. These operations include matrix multiplication, addition, subtraction, the kronecker product, the outer product, comparison operators, logical operators, trigonometric functions, indexing, sorting, random number generation and many more.
Author: Nathan Morris
Maintainer: Nathan Morris

Diff between gmatrix versions 0.1 dated 2013-10-31 and 0.2 dated 2014-08-26

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More information about gmatrix at CRAN
Permanent link

Package vardpoor updated to version 0.2.0.12 with previous version 0.2.0.9.2 dated 2014-08-01

Title: Variance estimation for sample surveys by the ultimate cluster method
Description: Generation of domain variables, linearisation of several nonlinear population statistics (the ratio of two totals, weighted income percentile, at-risk-of-poverty rate, at-risk-of-poverty threshold, Gini coefficient, gender pay gap, median income below at-risk-of-poverty gap, income quintile share ratio, relative median at-risk-of-poverty gap), computation of regression residuals in case of weight calibration, variance estimation of sample surveys by the ultimate cluster method (Hansen, Hurwitz and Madow, 1953), variance estimation for longitudinal, crossectional measures and measures of change for single and multistage stage cluster sampling designs (Berger, Y.G.). Several other precision measures are derived - standard error, the coefficient of variation, the margin of error, confidence interval, design effect.
Author: Juris Breidaks [aut, cre], Martins Liberts [aut]
Maintainer: Juris Breidaks

Diff between vardpoor versions 0.2.0.9.2 dated 2014-08-01 and 0.2.0.12 dated 2014-08-26

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More information about vardpoor at CRAN
Permanent link

Package tsDyn updated to version 0.9-41 with previous version 0.9-33 dated 2014-03-29

Title: Nonlinear time series models with regime switching
Description: Implements nonlinear autoregressive (AR) time series models. For univariate series, a non-parametric approach is available through additive nonlinear AR. Parametric modeling and testing for regime switching dynamics is available when the transition is either direct (TAR: threshold AR) or smooth (STAR: smooth transition AR, LSTAR). For multivariate series, one can estimate a range of TVAR or threshold cointegration TVECM models with two or three regimes. Tests can be conducted for TVAR as well as for TVECM (Hansen and Seo 2002 and Seo 2006).
Author: Antonio Fabio Di Narzo [aut, cre], Jose Luis Aznarte [ctb], Matthieu Stigler [aut, cre]
Maintainer: Matthieu Stigler

Diff between tsDyn versions 0.9-33 dated 2014-03-29 and 0.9-41 dated 2014-08-26

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More information about tsDyn at CRAN
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Package minerva updated to version 1.4.1 with previous version 1.4 dated 2014-08-15

Title: minerva: Maximal Information-Based Nonparametric Exploration R package for Variable Analysis
Description: R wrapper for cmine implementation of Maximal Information-based Nonparametric Exploration statistics (MIC and MINE family)
Author: Michele Filosi [aut, cre], Roberto Visintainer [aut], Davide Albanese [aut], Samantha Riccadonna [ctb], Giuseppe Jurman [ctb], Cesare Furlanello [ctb]
Maintainer: Michele Filosi

Diff between minerva versions 1.4 dated 2014-08-15 and 1.4.1 dated 2014-08-26

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Package HTSCluster updated to version 2.0.4 with previous version 2.0.3 dated 2014-07-28

Title: Clustering high throughput sequencing (HTS) data
Description: This package implements a Poisson mixture model to cluster observations (e.g., genes) in high throughput sequencing data. Parameter estimation is performed using either the EM or CEM algorithm, and the slope heuristics are used for model selection (i.e., to choose the number of clusters).
Author: Andrea Rau, Gilles Celeux, Marie-Laure Martin-Magniette, Cathy Maugis-Rabusseau
Maintainer: Andrea Rau

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More information about HTSCluster at CRAN
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Package BoolNet updated to version 2.0.1 with previous version 2.0 dated 2014-07-17

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

Diff between BoolNet versions 2.0 dated 2014-07-17 and 2.0.1 dated 2014-08-26

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Package randomForestSRC updated to version 1.5.5 with previous version 1.5.4 dated 2014-07-14

Title: Random Forests for Survival, Regression and Classification (RF-SRC)
Description: A unified treatment of Breiman's random forests for survival, regression and classification problems based on Ishwaran and Kogalur's random survival forests (RSF) package. The package runs in both serial and parallel (OpenMP) modes.
Author: Hemant Ishwaran , Udaya B. Kogalur
Maintainer: Udaya B. Kogalur

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Package LinRegInteractive updated to version 0.2-1 with previous version 0.1-3 dated 2014-08-18

Title: Interactive Interpretation of Linear Regression Models
Description: Interactive visualization of effects and marginal effects for linear regression models and of link functions, response functions and marginal effects for generalized linear regression models with binary dependent variables. A major feature is the handling of the effects of categorical covariates: if two or more factors are used as covariates every combination of the levels of each factor is treated separately. The interactive approach, the automatic calculation of marginal effects and far-reaching possibilities to customize the graphical output are characteristic features as well.
Author: Martin Meermeyer
Maintainer: Martin Meermeyer

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Package ks updated to version 1.9.3 with previous version 1.9.2 dated 2014-04-22

Title: Kernel smoothing
Description: Kernel smoothers for univariate and multivariate data
Author: Tarn Duong
Maintainer: Tarn Duong

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Package chipPCR updated to version 0.0.8-1 with previous version 0.0.7 dated 2014-06-25

Title: Toolkit of helper functions to pre-process amplification data
Description: The chipPCR package is a toolkit of functions to preprocess amplification curve data. Amplification data can be obtained from conventional PCR reactions or isothermal amplification reactions. The package contains functions to normalize and baseline amplification curves, a routine to detect the start of an amplification reaction, several smoothers for amplification data, a function to distinguish positive and negative amplification reactions and a function to determine the amplification efficiency. The smoothers are based on LOWESS, moving average, cubic splines, Savitzky-Golay and others. In addition the first approximate approximate derivative maximum (FDM) and second approximate derivative maximum (SDM) can be calculated by a 5-point-stencil as quantification points from real-time amplification curves. chipPCR contains data sets of experimental nucleic acid amplification systems including the VideoScan HCU and a capillary convective PCR (ccPCR) system. The amplification data were generated by helicase dependent amplification (HDA) or polymerase chain reaction (PCR) under various temperature conditions. As detection system intercalating dyes (EvaGreen, SYBR Green) and hydrolysis probes (TaqMan) were used. The latest source code is available via: https://github.com/michbur/chipPCR
Author: Stefan Roediger, Michal Burdukiewicz
Maintainer: Stefan Roediger

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Package Sunder updated to version 0.0.3 with previous version 0.0.2 dated 2014-07-21

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: Filippo Botta

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Package spcadjust updated to version 0.1-3 with previous version 0.1-2 dated 2013-05-07

Title: Functions for calibrating control charts
Description: This package calibrates thresholds of control charts such as CUSUM charts based on past data, taking estimation error into account.
Author: Axel Gandy and Jan Terje Kvaloy .
Maintainer: Axel Gandy

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Package KANT updated to version 2.0 with previous version 1.0 dated 2014-03-18

Title: Package to identify and sort genes overexpressed
Description: Identify and sort genes overexpressed and associated to transmembrane protein in Affymetrix expression set or any other results of microarray experiment.
Author: Noemie Robil
Maintainer: Noemie Robil

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Package gMCP updated to version 0.8-7 with previous version 0.8-6 dated 2014-02-17

Title: Graph Based Multiple Comparison Procedures
Description: This package provides functions and a graphical user interface for graphical described multiple test procedures.
Author: Kornelius Rohmeyer [aut, cre], Florian Klinglmueller [aut]
Maintainer: Kornelius Rohmeyer

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Package sensitivity updated to version 1.9 with previous version 1.8-2 dated 2014-04-29

Title: Sensitivity Analysis
Description: A collection of functions for factor screening, global sensitivity analysis and reliability sensitivity analysis of model output.
Author: Gilles Pujol, Bertrand Iooss, Alexandre Janon with contributions from Paul Lemaitre, Laurent Gilquin, Loic Le Gratiet, Taieb Touati, Bernardo Ramos, Jana Fruth and Sebastien Da Veiga
Maintainer: Bertrand Iooss

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Package MBmca updated to version 0.0.3-4 with previous version 0.0.3-3 dated 2014-06-25

Title: Nucleic Acid Melting Curve Analysis on Microbead Surfaces with R
Description: The MBmca package provides data sets and lightweight utilities for nucleic acid melting curve analysis and presentation on microbead surfaces.
Author: Stefan Roediger
Maintainer: Stefan Roediger

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Package emplik updated to version 0.9-9-6 with previous version 0.9-9-5 dated 2014-08-13

Title: Empirical likelihood ratio for censored/truncated data
Description: empirical likelihood ratio tests for means/quantiles/hazards from possibly censored and/or truncated data. Now does regression too.
Author: Mai Zhou.(Art Owen for el.test(), Yifan Yang for C part)
Maintainer: Mai Zhou

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Package R.utils updated to version 1.33.0 with previous version 1.32.4 dated 2014-05-15

Title: Various programming utilities
Description: This package provides utility methods useful when programming and developing R packages.
Author: Henrik Bengtsson [aut, cre, cph]
Maintainer: Henrik Bengtsson

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Package pubmed.mineR updated to version 1.0.2 with previous version 1.0.1 dated 2014-03-18

Title: Text mining of PubMed Abstracts.
Description: An R package for text mining of PubMed Abstracts (http://www.ncbi.nlm.nih.gov/pubmed). The algorithms are designed for two formats (text and XML) from PubMed
Author: Jyoti Sharma, S.Ramachandran, Ab Rauf Shah
Maintainer: S. Ramachandran

Diff between pubmed.mineR versions 1.0.1 dated 2014-03-18 and 1.0.2 dated 2014-08-26

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Package logitchoice updated to version 0.9.3 with previous version 0.9.2.1 dated 2014-08-22

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 0.9.2.1 dated 2014-08-22 and 0.9.3 dated 2014-08-26

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Package GGally updated to version 0.4.8 with previous version 0.4.7 dated 2014-07-15

Title: Extension to ggplot2.
Description: GGally is designed to be a helper to ggplot2. It contains templates for different plots to be combined into a plot matrix, a parallel coordinate plot function, as well as a function for making a network plot.
Author: Barret Schloerke , Jason Crowley , Di Cook , Heike Hofmann , Hadley Wickham , and Francois Briatte , Moritz Marbach , and Edwin Thoen
Maintainer: Barret Schloerke

Diff between GGally versions 0.4.7 dated 2014-07-15 and 0.4.8 dated 2014-08-26

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Mon, 25 Aug 2014

Package nanop updated to version 2.0-4 with previous version 2.0-3 dated 2014-05-23

Title: Tools for Nanoparticle Simulation and Calculation of PDF and Total Scattering Structure Function
Description: This software package implements functions to simulate spherical, ellipsoid and cubic polyatomic nanoparticles with arbitrary crystal structures and to calculate the associated pair-distribution function and X-ray/neutron total-scattering signals. It also provides a target function that can be used for simultaneous fitting of small- and wide-angle total scattering data in real and reciprocal spaces. The target function can be generated either as a sum of weighted residuals for individual datasets or as a vector of residuals suitable for optimization using multi-criteria algorithms (e.g. Pareto methods).
Author: Anton Gagin, Katharine Mullen, Igor Levin
Maintainer: Anton Gagin

Diff between nanop versions 2.0-3 dated 2014-05-23 and 2.0-4 dated 2014-08-25

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Package granova updated to version 2.1 with previous version 2.0.1 dated 2014-08-21

Title: Graphical Analysis of Variance
Description: This small collection of functions provides what we call elemental graphics for display of anova results. The term elemental derives from the fact that each function is aimed at construction of graphical displays that afford direct visualizations of data with respect to the fundamental questions that drive the particular anova methods. The two main functions are granova.1w (a graphic for one way anova) and granova.2w (a corresponding graphic for two way anova). These functions were written to display data for any number of groups, regardless of their sizes (however, very large data sets or numbers of groups can be problematic). For these two functions a specialized approach is used to construct data-based contrast vectors for which anova data are displayed. The result is that the graphics use straight lines, and when appropriate flat surfaces, to facilitate clear interpretations while being faithful to the standard effect tests in anova. The graphic results are complementary to standard summary tables for these two basic kinds of analysis of variance; numerical summary results of analyses are also provided as side effects. Two additional functions are granova.ds (for comparing two dependent samples), and granova.contr (which provides graphic displays for a priori contrasts). All functions provide relevant numerical results to supplement the graphic displays of anova data. The graphics based on these functions should be especially helpful for learning how the methods have been applied to answer the question(s) posed. This means they can be particularly helpful for students and non-statistician analysts. But these methods should be quite generally helpful for work-a-day applications of all kinds, as they can help to identify outliers, clusters or patterns, as well as highlight the role of non-linear transformations of data. In the case of granova.1w and granova.ds especially, several arguments are provided to facilitate flexibility in the construction of graphics that accommodate diverse features of data, according to their corresponding display requirements. See the help files for individual functions.
Author: Robert M. Pruzek and James E. Helmreich
Maintainer: James E. Helmreich

Diff between granova versions 2.0.1 dated 2014-08-21 and 2.1 dated 2014-08-25

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Package sde updated to version 2.0.13 with previous version 2.0.10 dated 2009-08-06

Title: Simulation and Inference for Stochastic Differential Equations
Description: Companion package to the book Simulation and Inference for Stochastic Differential Equations With R Examples, ISBN 978-0-387-75838-1, Springer, NY.
Author: Stefano Maria Iacus
Maintainer: Stefano Maria Iacus

Diff between sde versions 2.0.10 dated 2009-08-06 and 2.0.13 dated 2014-08-25

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Package rasterVis updated to version 0.31 with previous version 0.28 dated 2014-03-25

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 0.28 dated 2014-03-25 and 0.31 dated 2014-08-25

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Package ncdf updated to version 1.6.8 with previous version 1.6.7 dated 2014-06-16

Title: Interface to Unidata netCDF data files
Description: This package provides a high-level R interface to Unidata's netCDF data files, which are portable across platforms and include metadata information in addition to the data sets. Using this package netCDF files can be opened and data sets read in easily. It is also easy to create new netCDF dimensions, variables, and files, or manipulate existing netCDF files. This interface provides considerably more functionality than the old "netCDF" package for R, and is not compatible with the old "netCDF" package for R. Release 1.2 (2005-01-24) adds better support for character variables, and miscellaneous bug fixes. Release 1.3 (2005-03-27) is for miscellaneous bug fixes, and improves the documentation. Release 1.4 (2005-06-27) improves the efficiency, and adds small bug fixes. Release 1.5 (2006-02-27) adds support for byte variables, plus small bug fixes. Release 1.6 (2006-06-19) adds various bug fixes, plus support for making dimensions WITHOUT dimvars (coordinate variables), although I think this is a bad idea in general. ALSO, the default behavior for put.var.ncdf with unlimited variables and NO specified start and count parameters has changed! Before, the default was to append to the end of the existing variable. Now, the default is to assume a start of 1 along each dimension, and a count of the current length of each dimension. This really can be ambiguous when using an unlimited dimension. I always specify both start and count when writing to a variable with an unlimited dimension, and suggest you do as well. I may require this in a future release, as it seems to cause people problems.
Author: David Pierce
Maintainer: Brian Ripley

Diff between ncdf versions 1.6.7 dated 2014-06-16 and 1.6.8 dated 2014-08-25

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Package mutossGUI updated to version 0.1-9 with previous version 0.1-8 dated 2013-04-05

Title: A graphical user interface for the MuToss Project
Description: A graphical user interface for the MuToss Project
Author: MuToss Coding Team (Berlin 2010), Gilles Blanchard, Thorsten Dickhaus, Niklas Hack, Frank Konietschke, Kornelius Rohmeyer, Jonathan Rosenblatt, Marsel Scheer, Wiebke Werft
Maintainer: Kornelius Rohmeyer

Diff between mutossGUI versions 0.1-8 dated 2013-04-05 and 0.1-9 dated 2014-08-25

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Package hapassoc updated to version 1.2-7 with previous version 1.2-6 dated 2012-09-22

Title: Inference of trait associations with SNP haplotypes and other attributes using the EM Algorithm
Description: The following R functions are used for inference of trait associations with haplotypes and other covariates in generalized linear models. The functions are developed primarily for data collected in cohort or cross-sectional studies. They can accommodate uncertain haplotype phase and handle missing genotypes at some SNPs.
Author: K. Burkett , B. McNeney , J. Graham , with code for case-control data contributed by Zhijian Chen
Maintainer: K. Burkett

Diff between hapassoc versions 1.2-6 dated 2012-09-22 and 1.2-7 dated 2014-08-25

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Package CommonJavaJars updated to version 1.0-5 with previous version 1.0-4 dated 2014-02-17

Title: Useful libraries for building a Java based GUI under R
Description: Useful libraries for building a Java based GUI under R
Author: Kornelius Rohmeyer (R package), see COPYRIGHTS file for the authors of the java libraries
Maintainer: Kornelius Rohmeyer

Diff between CommonJavaJars versions 1.0-4 dated 2014-02-17 and 1.0-5 dated 2014-08-25

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Package commandr updated to version 1.0.1 with previous version 0.9.5 dated 2012-09-04

Title: Command pattern in R
Description: An S4 representation of the Command design pattern. The Operation class is a simple implementation using closures and supports forward and reverse (undo) evaluation. The more complicated Protocol framework represents each type of command (or analytical protocol) by a formal S4 class. Commands may be grouped and consecutively executed using the Pipeline class. Example use cases include logging, do/undo, analysis pipelines, GUI actions, parallel processing, etc.
Author: Michael Lawrence
Maintainer: Tengfei Yin

Diff between commandr versions 0.9.5 dated 2012-09-04 and 1.0.1 dated 2014-08-25

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Package exact2x2 updated to version 1.4.0 with previous version 1.3.0 dated 2014-04-30

Title: Exact Conditional Tests and Confidence Intervals for 2x2 tables
Description: Calculates Fisher's exact test, Blaker's exact test, or the exact McNemar's test with appropriate matching confidence intervals. Provides power and sample size calculations. Also gives melded confidence intervals for the binomial case.
Author: Michael P. Fay
Maintainer: Michael P. Fay

Diff between exact2x2 versions 1.3.0 dated 2014-04-30 and 1.4.0 dated 2014-08-25

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Package shotGroups updated to version 0.6 with previous version 0.5 dated 2014-07-04

Title: Analyze shot group data
Description: Analyzes shooting data with respect to group shape, precision, and accuracy. This includes graphical methods, descriptive statistics, and inference tests using standard, but also non-parametric and robust statistical methods. Works with files exported by OnTarget PC and OnTarget TDS or with custom data files in text format with a similar structure.
Author: Daniel Wollschlaeger
Maintainer: Daniel Wollschlaeger

Diff between shotGroups versions 0.5 dated 2014-07-04 and 0.6 dated 2014-08-25

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Package nopp updated to version 1.0.4 with previous version 1.0.3 dated 2012-10-22

Title: Nash Optimal Party Positions
Description: Estimation of party/candidate ideological positions that correspond to a Nash equilibrium along a one-dimensional space.
Author: Luigi Curini, Stefano M. Iacus
Maintainer: Stefano M. Iacus

Diff between nopp versions 1.0.3 dated 2012-10-22 and 1.0.4 dated 2014-08-25

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Package phenology updated to version 3.72 with previous version 3.69 dated 2014-06-22

Title: Tools to manage a parametric function that describes phenology
Description: Functions to fit and test the phenology of species based on counts. The package includes also several useful more general functions.
Author: Marc Girondot
Maintainer: Marc Girondot

Diff between phenology versions 3.69 dated 2014-06-22 and 3.72 dated 2014-08-25

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Sun, 24 Aug 2014

Package Rd2roxygen updated to version 1.5 with previous version 1.4 dated 2013-12-06

Title: Convert Rd to roxygen documentation and utilities to improve documentation
Description: Functions to convert Rd to roxygen documentation. It can parse an Rd file to a list, create the roxygen documentation and update the original R script (e.g. the one containing the definition of the function) accordingly. This package also provides utilities which can help developers build packages using roxygen more easily. The formatR package can be used to reformat the R code in the examples sections so that the code will be more readable.
Author: Hadley Wickham [aut], Yihui Xie [aut, cre]
Maintainer: Yihui Xie

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Package formatR updated to version 1.0 with previous version 0.10 dated 2013-10-26

Title: Format R Code Automatically
Description: This package provides a function tidy_source() to format R source code. Spaces and indent will be added to the code automatically, and comments will be preserved under certain conditions, so that R code will be more human-readable and tidy. There is also a Shiny app as a user interface in this package (see tidy_app()).
Author: Yihui Xie
Maintainer: Yihui Xie

Diff between formatR versions 0.10 dated 2013-10-26 and 1.0 dated 2014-08-24

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Package sandwich updated to version 2.3-2 with previous version 2.3-1 dated 2014-07-20

Title: Robust Covariance Matrix Estimators
Description: Model-robust standard error estimators for cross-sectional, time series, and longitudinal data.
Author: Thomas Lumley [aut], Achim Zeileis [aut, cre]
Maintainer: Achim Zeileis

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Package hypervolume updated to version 1.0.2 with previous version 1.0.1 dated 2014-07-08

Title: High-dimensional kernel density estimation and geometry operations.
Description: Estimates the shape and volume of high-dimensional objects and performs set operations: intersection / overlap, union, unique components, inclusion test, and non-convex feature detection. Can measure the n-dimensional ecological hypervolume and perform species distribution modeling.
Author: Benjamin Blonder
Maintainer: Benjamin Blonder

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 DESCRIPTION         |    8 ++++----
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More information about hypervolume at CRAN
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Package caret updated to version 6.0-35 with previous version 6.0-34 dated 2014-08-15

Title: Classification and Regression Training
Description: Misc functions for training and plotting classification and regression models
Author: Max Kuhn. Contributions from Jed Wing, Steve Weston, Andre Williams, Chris Keefer, Allan Engelhardt, Tony Cooper, Zachary Mayer and the R Core Team
Maintainer: Max Kuhn

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Package Rcmdr updated to version 2.1-0 with previous version 2.0-4 dated 2014-03-28

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

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More information about Rcmdr at CRAN
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