Fri, 22 Aug 2014

Package spMC updated to version 0.3.2 with previous version 0.3.1 dated 2013-04-15

Title: Continuous Lag Spatial Markov Chains
Description: The main goal of this package is to provide a set of functions for 1) the stratum lengths analysis along a chosen direction, 2) fast estimation of continuous lag spatial Markov chains model parameters and probability computing (also for large data sets), 3) transition probability maps and transiograms drawing, 4) simulation methods for categorical random fields.
Author: Luca Sartore
Maintainer: Luca Sartore

Diff between spMC versions 0.3.1 dated 2013-04-15 and 0.3.2 dated 2014-08-22

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 53 files changed, 506 insertions(+), 323 deletions(-)

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Package PResiduals updated to version 0.2-0 with previous version 0.1-0 dated 2013-03-14

Title: Probability scale residuals and residual correlations.
Description: Computes probability scale residuals and residual correlations for continuous, ordinal, binary, count, and time-to-event data (currently only implements ordinal data).
Author: Charles Dupont, Jeffrey Horner, Chun Li, Bryan Shepherd
Maintainer: Charles Dupont

Diff between PResiduals versions 0.1-0 dated 2013-03-14 and 0.2-0 dated 2014-08-22

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Package bdsmatrix updated to version 1.3-2 with previous version 1.3-1 dated 2013-03-28

Title: Routines for Block Diagonal Symmetric matrices
Description: This is a special case of sparse matrices, used by coxme
Author: Terry Therneau
Maintainer: Terry Therneau

Diff between bdsmatrix versions 1.3-1 dated 2013-03-28 and 1.3-2 dated 2014-08-22

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 21 files changed, 106 insertions(+), 87 deletions(-)

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Package scholar updated to version 0.1.2 with previous version 0.1.1 dated 2013-10-28

Title: Analyse citation data from Google Scholar
Description: scholar provides functions to extract citation data from Google Scholar. Convenience functions are also provided for comparing multiple scholars and predicting future h-index values.
Author: James Keirstead
Maintainer: James Keirstead

Diff between scholar versions 0.1.1 dated 2013-10-28 and 0.1.2 dated 2014-08-22

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 22 files changed, 676 insertions(+), 634 deletions(-)

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Package pipeR updated to version 0.4-2 with previous version 0.4-1 dated 2014-08-15

Title: Pipe operator and function
Description: Pipe operator and function based on intuitive syntax.
Author: Kun Ren
Maintainer: Kun Ren

Diff between pipeR versions 0.4-1 dated 2014-08-15 and 0.4-2 dated 2014-08-22

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 NAMESPACE                                      |    4 
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 15 files changed, 567 insertions(+), 159 deletions(-)

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Package visova updated to version 1.1 with previous version 1.0 dated 2014-08-09

Title: Visualization of Analysis of Variance(VISOVA)
Description: VISOVA(VISualization Of VAriance) is a novel method for exploratory data analysis. It is basically an extension of the trellis graphics and developing their grid concept with parallel coordinates, permitting visualization of many dimensions at once. This package includes functions allowing users to perform VISOVA analysis and compare different column/variable ordering methods for making the high-dimensional structures easier to perceive even when the data is complicated.
Author: Ali Vala Barbaros
Maintainer: Ali Vala Barbaros

Diff between visova versions 1.0 dated 2014-08-09 and 1.1 dated 2014-08-22

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Package tuple updated to version 0.4-01 with previous version 0.3-06 dated 2014-07-14

Title: Find every match, or orphan, duplicate, triplicate, or other replicated values
Description: Functions to find all matches, or the orphan, duplicate or triplicate or other replicated values in a vector.
Author: Emmanuel Lazaridis [aut, cre]
Maintainer: Emmanuel Lazaridis

Diff between tuple versions 0.3-06 dated 2014-07-14 and 0.4-01 dated 2014-08-22

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Package RMessenger (with last version 0.1.5) was removed from CRAN

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

2014-07-16 0.1.5
2014-03-27 0.1.4
2013-08-02 0.1.3
2013-04-18 0.1.2

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Package easi (with last version 0.2) was removed from CRAN

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

2012-07-04 0.2

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Package xlsxjars updated to version 0.6.1 with previous version 0.6.0 dated 2014-02-26

Title: Package required POI jars for the xlsx package
Description: The xlsxjars package collects all the external jars required for the xlxs package. This release corresponds to POI 3.10.1.
Author: Adrian A. Dragulescu [aut, cre], The Apache Software Foundation Apache Commons Codec [ctb, cph] (Apache POI, Apache XMLBeans), MetaStuff, Ltd. [ctb, cph] (Dom4j)
Maintainer: Adrian A. Dragulescu

Diff between xlsxjars versions 0.6.0 dated 2014-02-26 and 0.6.1 dated 2014-08-22

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Package wppExplorer updated to version 1.4-0 with previous version 1.3-0 dated 2014-08-10

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

Diff between wppExplorer versions 1.3-0 dated 2014-08-10 and 1.4-0 dated 2014-08-22

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Package wpp2012 updated to version 2.2-1 with previous version 2.2-0 dated 2014-08-09

Title: World Population Prospects 2012
Description: Data from the United Nation's World Population Prospects 2012
Author: Hana Sevcikova (hanas@uw.edu), Patrick Gerland (gerland@un.org), Kirill Andreev (andreev@un.org), Nan Li (li32@un.org), Danan Gu (gud@un.org), Thomas Spoorenberg (spoorenberg@un.org)
Maintainer: Hana Sevcikova

Diff between wpp2012 versions 2.2-0 dated 2014-08-09 and 2.2-1 dated 2014-08-22

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Package rlist updated to version 0.3-2 with previous version 0.3-1 dated 2014-08-15

Title: A set of tools for working with list objects
Description: A set of tools for working with lists as dataset, including filtering, mapping, grouping, sorting, updating, searching, and many other functions. It recommends functional programming and collection pipeline in list operations.
Author: Kun Ren
Maintainer: Kun Ren

Diff between rlist versions 0.3-1 dated 2014-08-15 and 0.3-2 dated 2014-08-22

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Package logitchoice updated to version 0.9.2.1 with previous version 0.9.2 dated 2014-08-20

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 dated 2014-08-20 and 0.9.2.1 dated 2014-08-22

 DESCRIPTION |    6 +++---
 MD5         |    4 ++--
 src/mle.c   |    5 +++--
 3 files changed, 8 insertions(+), 7 deletions(-)

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Thu, 21 Aug 2014

New package childsds with initial version 0.5
Package: childsds
Title: Calculation of standard deviation scores adduced from different growth standards
Version: 0.5
Authors@R: c(person("Mandy", "Vogel", role=c("aut","cre"), email="mandy.vogel@medizin.uni-leipzig.de"))
Description: Calculation of standard deviation scores from different growth standards
Depends: R (>= 3.1.1), methods
License: GPL (>= 2)
LazyData: true
Packaged: 2014-08-21 17:06:37 UTC; mvogel
Author: Mandy Vogel [aut, cre]
Maintainer: Mandy Vogel
NeedsCompilation: no
Repository: CRAN
Date/Publication: 2014-08-21 19:22:42

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New package sensory with initial version 1.0
Package: sensory
Type: Package
Title: Simultaneous Model-Based Clustering and Imputation via a Progressive Expectation-Maximization (PEM) algorithm.
Version: 1.0
Date: 2014-08-20
Author: Brian C. Franczak, Ryan P. Browne and Paul D. McNicholas
Maintainer: Brian C. Franczak
Description: Contains the function CUUimpute() which performs model-based clustering and imputation simultaneously.
Depends: Matrix, gtools, MASS, R (>= 3.1.1)
NeedsCompilation: no
License: GPL (>= 2)
Packaged: 2014-08-21 15:59:51 UTC; brianfranczak
Repository: CRAN
Date/Publication: 2014-08-21 18:36:52

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Package nat updated to version 1.5.12 with previous version 1.4.10 dated 2014-04-30

Title: nat: NeuroAnatomy Toolbox for Analysis of 3D Image Data
Description: This package is a reboot of the AnalysisSuite (https://github.com/jefferis/AnalysisSuite) bundle of R code that I have been using for a number of years to analyse and visualise 3D biological image data, especially traced neurons. AnalysisSuite is most easily installed using the nat.as package presently available at https://github.com/jefferis/nat.as. The nat package is considerably cleaner but currently provides only a subset of the full functionality of nat.as / AnalysisSuite. nat can read and write 3D images in NRRD and Amira formats and read surfaces in Amira's hxsurf format. Traced neurons can be imported from and written to SWC and Amira LineSet and SkeletonGraph formats. These data can then be visualised in 3D via rgl, manipulated including applying calculated registrations, e.g. using the CMTK registration suite, and analysed. The package also has a simple representation for neurons that have been subjected to a 3D skeletonisation but not formally traced; this allows morphological comparison between neurons including searches and clustering.
Author: Greg Jefferis and James Manton
Maintainer: Greg Jefferis

Diff between nat versions 1.4.10 dated 2014-04-30 and 1.5.12 dated 2014-08-21

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 tests/testthat/test-.neuronlistfh-remote-nocran.R |   13 
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More information about nat at CRAN
Permanent link

New package RAM with initial version 1.0.0
Package: RAM
Type: Package
Title: R for Amplicon-based Metagenomics
Version: 1.0.0
Date: 2014-08-20
Author: Wen Chen and Joshua Simpson
Copyright: Government of Canada
Maintainer: Wen Chen
Description: This package provides a series of functions to make amplicon-based metagenomic analysis more accessible, and publication-quality plots simple. Amplicon-based (or targeted) metagenomics amplifies and sequences selected DNA regions of environmental samples, but not the entire pool of genetic material, which is referred to as shotgun metagenomics. The amplicon-metagenomics mainly aims at characterizing broad microbiota biodiversity in different environments.
License: MIT + file LICENSE
Depends: vegan, ggplot2, stats
Imports: gridExtra, RColorBrewer, indicspecies, Heatplus, splitstackshape, gplots, plyr, reshape2, scales, labdsv, grid, stringr, ggmap, permute
Suggests: testthat
Packaged: 2014-08-21 14:34:51 UTC; chenw
NeedsCompilation: no
Repository: CRAN
Date/Publication: 2014-08-21 19:00:07

More information about RAM at CRAN
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Package EpiDynamics updated to version 0.2 with previous version 0.1 dated 2014-06-01

Title: Dynamic Models in Epidemiology
Description: Mathematical models of infectious diseases in humans and animals. Both, deterministic and stochastic models can be simulated and plotted.
Author: Oswaldo Santos Baquero [aut, cre], Fernando Silveira Marques [aut]
Maintainer: Oswaldo Santos Baquero

Diff between EpiDynamics versions 0.1 dated 2014-06-01 and 0.2 dated 2014-08-21

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Package PKfit updated to version 1.2.3 with previous version 1.2.2 dated 2014-06-24

Title: A Data Analysis Tool for Pharmacokinetics
Description: PKfit is a nonlinear regression program which is designed to perform model/curve fitting and model simulations for pharmacokinetics.
Author: Chun-ying Lee, Yung-jin Lee
Maintainer: Yung-jin Lee

Diff between PKfit versions 1.2.2 dated 2014-06-24 and 1.2.3 dated 2014-08-21

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 MD5                     |   34 ++++---
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More information about PKfit at CRAN
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Package RcppEigen updated to version 0.3.2.2.0 with previous version 0.3.2.1.2 dated 2014-05-06

Title: Rcpp integration for the Eigen templated linear algebra library.
Description: R and Eigen integration using Rcpp. Eigen is a C++ template library for linear algebra: matrices, vectors, numerical solvers and related algorithms. It supports dense and sparse matrices on integer, floating point and complex numbers, decompositions of such matrices, and solutions of linear systems. Its performance on many algorithms is comparable with some of the best implementations based on Lapack and level-3 BLAS. The RcppEigen package includes the header files from the Eigen C++ template library (currently version 3.2.2). Thus users do not need to install Eigen itself in order to use RcppEigen. Since version 3.1.1, Eigen is licensed under the Mozilla Public License (version 2); earlier version were licensed under the GNU LGPL version 3 or later. RcppEigen (the Rcpp bindings/bridge to Eigen) is licensed under the GNU GPL version 2 or later, as is the rest of Rcpp.
Author: Douglas Bates, Romain Francois and Dirk Eddelbuettel; the authors of Eigen for the included version of Eigen
Maintainer: Dirk Eddelbuettel

Diff between RcppEigen versions 0.3.2.1.2 dated 2014-05-06 and 0.3.2.2.0 dated 2014-08-21

 RcppEigen-0.3.2.1.2/RcppEigen/inst/include/Eigen/src/Sparse                               |only
 RcppEigen-0.3.2.2.0/RcppEigen/ChangeLog                                                   |   24 +
 RcppEigen-0.3.2.2.0/RcppEigen/DESCRIPTION                                                 |   10 
 RcppEigen-0.3.2.2.0/RcppEigen/MD5                                                         |  109 +++-----
 RcppEigen-0.3.2.2.0/RcppEigen/README.md                                                   |    2 
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Package TableToLongForm updated to version 1.3.1 with previous version 1.3.0 dated 2014-01-15

Title: TableToLongForm
Description: TableToLongForm automatically converts hierarchical Tables intended for a human reader into a simple LongForm Dataframe that is machine readable.
Author: Jimmy Oh [aut, cre]
Maintainer: Jimmy Oh

Diff between TableToLongForm versions 1.3.0 dated 2014-01-15 and 1.3.1 dated 2014-08-21

 DESCRIPTION                    |    8 ++++----
 MD5                            |   12 ++++++------
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 man/TCData.Rd                  |    7 +++++++
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 7 files changed, 58 insertions(+), 25 deletions(-)

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Package pegas updated to version 0.6 with previous version 0.5-1 dated 2014-01-10

Title: Population and Evolutionary Genetics Analysis System
Description: pegas provides functions for reading, writing, plotting, analysing, and manipulating allelic and haplotypic data, and for the analysis of population nucleotide sequences and micro-satellites including coalescence analyses.
Author: Emmanuel Paradis [aut, cre, cph], Klaus Schliep [aut, cph], Alastair Potts [aut, cph], David Winter [aut, cph]
Maintainer: Emmanuel Paradis

Diff between pegas versions 0.5-1 dated 2014-01-10 and 0.6 dated 2014-08-21

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Package codetools updated to version 0.2-9 with previous version 0.2-8 dated 2011-02-15

Title: Code Analysis Tools for R
Description: Code analysis tools for R
Author: Luke Tierney
Maintainer: Luke Tierney

Diff between codetools versions 0.2-8 dated 2011-02-15 and 0.2-9 dated 2014-08-21

 DESCRIPTION   |   11 ++++++-----
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Package SocialNetworks updated to version 1.1 with previous version 1.0 dated 2014-03-24

Title: Generates social networks based on distance.
Description: Generates social networks using either of two approaches: using either pairwise distances or territorial area intersections.
Author: Glenna Nightingale, Peter Nightingale
Maintainer: Glenna Nightingale

Diff between SocialNetworks versions 1.0 dated 2014-03-24 and 1.1 dated 2014-08-21

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Package MASS updated to version 7.3-34 with previous version 7.3-33 dated 2014-05-05

Title: Support Functions and Datasets for Venables and Ripley's MASS
Description: Functions and datasets to support Venables and Ripley, 'Modern Applied Statistics with S' (4th edition, 2002).
Author: Brian Ripley [aut, cre, cph], Bill Venables [ctb], Douglas M. Bates [ctb], Kurt Hornik [trl] (partial port ca 1998), Albrecht Gebhardt [trl] (partial port ca 1998), David Firth [ctb]
Maintainer: Brian Ripley

Diff between MASS versions 7.3-33 dated 2014-05-05 and 7.3-34 dated 2014-08-21

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More information about MASS at CRAN
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Package granova updated to version 2.0.1 with previous version 2.0 dated 2010-11-05

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: ORPHANED

Diff between granova versions 2.0 dated 2010-11-05 and 2.0.1 dated 2014-08-21

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Package ssym updated to version 1.5 with previous version 1.3 dated 2014-05-07

Title: Fitting Semiparametric Symmetric Regression Models
Description: This package allows to fit a regression model suitable for data analysis in which the conditional distribution of the response is symmetric and continuous and where its location and dispersion parameters are modelled through semiparametric functions. Supported distributions for the model error include normal, Student-t, power exponential, symmetric hyperbolic, contaminated normal, slash, sinh-normal and sinh-t distributions.
Author: Luis Hernando Vanegas and Gilberto A. Paula
Maintainer: Luis Hernando Vanegas

Diff between ssym versions 1.3 dated 2014-05-07 and 1.5 dated 2014-08-21

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Package metabolomics (with last version 0.1.3) was removed from CRAN

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

2013-09-11 0.1.3
2013-07-25 0.1.2
2013-04-05 0.1.1
2013-03-25 0.1.0

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New package SparseTSCGM with initial version 2.1.1
Package: SparseTSCGM
Type: Package
Title: Sparse time series chain graphical models
Version: 2.1.1
Date: 2014-04-15
Depends: R(>= 3.0.2)
Imports: glasso, longitudinal, flare, MASS, mvtnorm, network, abind
Author: Fentaw Abegaz and Ernst Wit
Maintainer: Fentaw Abegaz
Description: Computes sparse vector autoregressive coefficients and precision matrices for time series chain graphical models.
License: GPL (>= 3)
LazyLoad: yes
Packaged: 2014-08-20 14:47:44 UTC; p261204
NeedsCompilation: yes
Repository: CRAN
Date/Publication: 2014-08-21 06:43:12

More information about SparseTSCGM at CRAN
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Package boilerpipeR updated to version 1.2.2 with previous version 1.2 dated 2014-05-12

Title: Interface to the boilerpipe Java library by Christian Kohlschutter (http://code.google.com/p/boilerpipe/)
Description: Generic Extraction of main text content from HTML files; removal of ads, sidebars and headers using the boilerpipe Java library. The extraction heuristics from boilerpipe show a robust performance for a wide range of web site templates.
Author: See AUTHORS file.
Maintainer: Mario Annau

Diff between boilerpipeR versions 1.2 dated 2014-05-12 and 1.2.2 dated 2014-08-21

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Wed, 20 Aug 2014

Package mvnfast updated to version 0.1.3 with previous version 0.1.2 dated 2014-06-16

Title: Fast multivariate normal methods
Description: The package provides computationally efficient tools related to the multivariate normal distribution. The main functionalities are: simulating multivariate normal random vectors, evaluating multivariate normal densities and Mahalanobis distances. These tools are very efficient thanks to the use of C++ code and of the OpenMP API.
Author: Matteo Fasiolo, using the C++ parallel RNG of Thijs van den Berg and Ziggurat algorithm of Jens Maurer and Steven Watanabe (boost)
Maintainer: Matteo Fasiolo

Diff between mvnfast versions 0.1.2 dated 2014-06-16 and 0.1.3 dated 2014-08-20

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Package RcppMLPACK updated to version 1.0.9-3 with previous version 1.0.9 dated 2014-08-11

Title: Rcpp integration for MLPACK library
Description: MLPACK is an intuitive, fast, scalable C++ machine learning library, meant to be a machine learning analog to LAPACK. It aims to implement a wide array of machine learning methods and function as a Swiss army knife for machine learning researchers: MLPACK is from http://www.mlpack.org/: sources are included in the package.
Author: Qiang Kou
Maintainer: Qiang Kou

Diff between RcppMLPACK versions 1.0.9 dated 2014-08-11 and 1.0.9-3 dated 2014-08-20

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 inst/include/mlpack/core/dists/discrete_distribution.hpp                              |   12 
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 inst/include/mlpack/core/kernels/gaussian_kernel.hpp                                  |    2 
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 inst/include/mlpack/core/metrics/lmetric_impl.hpp                                     |    4 
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 inst/include/mlpack/methods/amf/amf.hpp                                               |    4 
 inst/include/mlpack/methods/amf/amf_impl.hpp                                          |    4 
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 inst/include/mlpack/methods/cf/cf.hpp                                                 |   42 
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 inst/include/mlpack/methods/gmm/gmm.hpp                                               |   26 
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 inst/include/mlpack/methods/gmm/phi.hpp                                               |    4 
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 inst/skeleton/kmeans.cpp                                                              |    4 
 src/Makevars                                                                          |    2 
 src/Makevars.win                                                                      |    2 
 src/kmeans.cpp                                                                        |    2 
 src/mlpack/core/arma_extend/typedef.hpp                                               |    2 
 src/mlpack/core/data/load_impl.hpp                                                    |    2 
 src/mlpack/core/data/normalize_labels.hpp                                             |    4 
 src/mlpack/core/data/normalize_labels_impl.hpp                                        |   12 
 src/mlpack/core/data/save_impl.hpp                                                    |    2 
 src/mlpack/core/dists/discrete_distribution.cpp                                       |   14 
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 src/mlpack/core/dists/gaussian_distribution.cpp                                       |    8 
 src/mlpack/core/dists/gaussian_distribution.hpp                                       |    4 
 src/mlpack/core/dists/laplace_distribution.cpp                                        |    6 
 src/mlpack/core/dists/laplace_distribution.hpp                                        |    6 
 src/mlpack/core/kernels/epanechnikov_kernel.cpp                                       |    2 
 src/mlpack/core/kernels/epanechnikov_kernel.hpp                                       |    2 
 src/mlpack/core/kernels/example_kernel.hpp                                            |    2 
 src/mlpack/core/kernels/gaussian_kernel.hpp                                           |    2 
 src/mlpack/core/kernels/pspectrum_string_kernel.cpp                                   |   10 
 src/mlpack/core/kernels/pspectrum_string_kernel.hpp                                   |   10 
 src/mlpack/core/kernels/spherical_kernel.hpp                                          |    2 
 src/mlpack/core/math/lin_alg.cpp                                                      |   18 
 src/mlpack/core/math/lin_alg.hpp                                                      |    2 
 src/mlpack/core/math/random.hpp                                                       |    4 
 src/mlpack/core/metrics/lmetric_impl.hpp                                              |    4 
 src/mlpack/core/metrics/mahalanobis_distance.hpp                                      |    2 
 src/mlpack/core/optimizers/aug_lagrangian/aug_lagrangian.hpp                          |   10 
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 src/mlpack/core/optimizers/lbfgs/test_functions.cpp                                   |    4 
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 src/mlpack/core/optimizers/lrsdp/lrsdp.cpp                                            |    2 
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 src/mlpack/core/optimizers/sa/sa.hpp                                                  |   38 
 src/mlpack/core/optimizers/sa/sa_impl.hpp                                             |   34 
 src/mlpack/core/optimizers/sgd/sgd.hpp                                                |   14 
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 src/mlpack/core/tree/example_tree.hpp                                                 |   14 
 src/mlpack/core/tree/hrectbound.hpp                                                   |   10 
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 src/mlpack/core/util/string_util.cpp                                                  |    6 
 src/mlpack/core/util/string_util.hpp                                                  |    2 
 src/mlpack/methods/amf/amf.hpp                                                        |    4 
 src/mlpack/methods/amf/amf_impl.hpp                                                   |    4 
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 src/mlpack/methods/cf/cf.hpp                                                          |   42 
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 src/mlpack/methods/emst/dtb.hpp                                                       |    8 
 src/mlpack/methods/emst/dtb_impl.hpp                                                  |   38 
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 src/mlpack/methods/emst/edge_pair.hpp                                                 |   14 
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 src/mlpack/methods/fastmks/fastmks.hpp                                                |   12 
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 src/mlpack/methods/gmm/em_fit.hpp                                                     |   12 
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 src/mlpack/methods/gmm/gmm.hpp                                                        |   26 
 src/mlpack/methods/gmm/gmm_impl.hpp                                                   |   42 
 src/mlpack/methods/gmm/phi.hpp                                                        |    4 
 src/mlpack/methods/hmm/hmm.hpp                                                        |   20 
 src/mlpack/methods/hmm/hmm_impl.hpp                                                   |   70 
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 src/mlpack/methods/kmeans/kmeans.hpp                                                  |   24 
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 src/mlpack/methods/lars/lars.cpp                                                      |   38 
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 src/mlpack/methods/lsh/lsh_search.hpp                                                 |   48 
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 src/mlpack/methods/mvu/mvu.cpp                                                        |   12 
 src/mlpack/methods/mvu/mvu.hpp                                                        |    4 
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 src/mlpack/methods/nca/nca.hpp                                                        |    6 
 src/mlpack/methods/nca/nca_impl.hpp                                                   |    2 
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 src/mlpack/methods/pca/pca.cpp                                                        |    6 
 src/mlpack/methods/pca/pca.hpp                                                        |   10 
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 src/mlpack/methods/rann/ra_search.hpp                                                 |   12 
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Package robumeta updated to version 1.3 with previous version 1.2 dated 2014-08-20

Title: Robust variance meta-regression
Description: Functions for conducting robust variance estimation (RVE) meta-regression using both large and small sample RVE estimators under various weighting schemes. These methods are distribution free and provide valid point estimates, standard errors and hypothesis tests even when the degree and structure of dependence between effect sizes is unknown. Also included in the robumeta package are functions for conducting sensitivity analyses under correlated effects weighting and producing RVE-based forest plots.
Author: Zachary Fisher and Elizabeth Tipton.
Maintainer: Zachary Fisher

Diff between robumeta versions 1.2 dated 2014-08-20 and 1.3 dated 2014-08-20

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Package CCTpack updated to version 1.4 with previous version 1.3 dated 2014-08-16

Title: Cultural Consensus Theory applications to data
Description: A user-friendly GUI for the application of Cultural Consensus Theory (CCT) models and methods to consensus data. The models are applied using hierarchical Bayesian inference. The current package version supports binary, ordinal, and continuous data formats.
Author: Royce Anders
Maintainer: Royce Anders

Diff between CCTpack versions 1.3 dated 2014-08-16 and 1.4 dated 2014-08-20

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New package geoBayes with initial version 0.1.2
Package: geoBayes
Type: Package
Title: Analysis of geostatistical data using Bayes and Empirical Bayes methods
Description: This package provides functions to fit geostatistical data. The data can be continuous, binary or count data and the models implemented are flexible. Conjugate priors are assumed on some parameters while non-conjugate parameters can be estimated either by Monte-Carlo or empirical Bayes methods.
Version: 0.1.2
Date: 2014-08-20
Author: Evangelos Evangelou , Vivekanda Roy
Maintainer: Evangelos Evangelou
Imports: stats, coda, sp
Depends: R (>= 2.0.0)
Suggests: geoR, geoRglm
LazyData: true
License: GPL (>= 2)
Classification/ACM: 86A32, 62M30, 62F15
Packaged: 2014-08-20 18:16:16 UTC; ee224
NeedsCompilation: yes
Repository: CRAN
Date/Publication: 2014-08-20 21:07:01

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Package bold updated to version 0.2.0 with previous version 0.1.2 dated 2014-07-24

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

Diff between bold versions 0.1.2 dated 2014-07-24 and 0.2.0 dated 2014-08-20

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Package TDA updated to version 1.1 with previous version 1.0 dated 2014-08-19

Title: Statistical Tools for Topological Data Analysis
Description: This package provides tools for the statistical analysis of persistent homology and for density clustering.
Author: Brittany T. Fasy, Fabrizio Lecci
Maintainer: Fabrizio Lecci

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Package robumeta updated to version 1.2 with previous version 1.1 dated 2014-03-20

Title: Robust variance meta-regression
Description: The robumeta package provides a host of functions for conducting robust variance estimation (RVE) meta-regression using both large and small sample RVE estimators under various weighting schemes. These methods are distribution free and provide valid point estimates, standard errors and hypothesis tests even when the degree and structure of dependence between effect sizes is unknown. Also included in the robumeta package are functions for conducting sensitivity analyses under correlated effects weighting and producing RVE-based forest plots.
Author: Zachary Fisher and Elizabeth Tipton.
Maintainer: Zachary Fisher

Diff between robumeta versions 1.1 dated 2014-03-20 and 1.2 dated 2014-08-20

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Package mokken updated to version 2.7.7 with previous version 2.7.5 dated 2013-01-27

Title: Mokken Scale Analysis in R
Description: mokken contains functions for performing Mokken scale analysis on test and questionnaire data. It includes an automated item selection algorithm, and various checks of model assumptions.
Author: L. Andries van der Ark
Maintainer: L. Andries van der Ark

Diff between mokken versions 2.7.5 dated 2013-01-27 and 2.7.7 dated 2014-08-20

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Package GLSME updated to version 1.0.2 with previous version 1.0.1 dated 2014-05-25

Title: Generalized Least Squares with Measurement Error
Description: Performs linear regression with correlated predictors, responses and correlated measurement errors in predictors and responses, correcting for biased caused by these.
Author: Krzysztof Bartoszek
Maintainer: Krzysztof Bartoszek

Diff between GLSME versions 1.0.1 dated 2014-05-25 and 1.0.2 dated 2014-08-20

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New package metaplus with initial version 0.6-0
Package: metaplus
Type: Package
Title: Robust meta-analysis and meta-regression.
Version: 0.6-0
Date: 2014-08-20
Author: Ken Beath
Maintainer: Ken Beath
Description: Performs meta-analysis using standard and robust methods with confidence intervals from profile likelihood.
Depends: R(>= 3.1.0), bbmle, metafor
Imports: boot, methods, numDeriv
License: GPL (>= 2)
Packaged: 2014-08-20 09:08:57 UTC; kjbeath
NeedsCompilation: no
Repository: CRAN
Date/Publication: 2014-08-20 14:37:51

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New package DepthProc with initial version 1.0
Package: DepthProc
Version: 1.0
Date: 2014-08-18
Title: DepthProc
Author: Daniel Kosiorowski, Mateusz Bocian, Anna Wegrzynkiewicz and Zygmunt Zawadzki from Cracow University of Economics.
Maintainer: Zygmunt Zawadzki
Description: Package for depths
License: GPL-2
Depends: R (>= 3.0.0), ggplot2, Rcpp (>= 0.11.2), rrcov, np, methods, MASS
Imports: lattice, sm, geometry
Suggests: mvtnorm, rgl, sn, robustbase,
LinkingTo: Rcpp, RcppArmadillo
Repository: CRAN
Repository/R-Forge/Project: depthproc
Repository/R-Forge/Revision: 54
Repository/R-Forge/DateTimeStamp: 2014-08-20 09:54:39
Date/Publication: 2014-08-20 14:33:13
Packaged: 2014-08-20 10:15:11 UTC; rforge
NeedsCompilation: yes

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New package rsunlight with initial version 0.3.0
Package: rsunlight
Description: Interface to four Sunlight Foundation APIs (http://sunlightfoundation.com/api/) for government data, including the Congress API v3, the Capitol Words API, the Influence Explorer API, and the Open States API. Sunlight Foundation is a nonpartison nonprofit that collects and provides data on government activities, and those that influence government. Functions are provided to interact with each of the four APIs. rCharts - https://github.com/ramnathv/rCharts
Title: Interface to Sunlight Foundation APIs.
Version: 0.3.0
Date: 2014-08-19
License: MIT + file LICENSE
URL: https://github.com/ropengov/rsunlight
BugReports: https://github.com/ropengov/rsunlight/issues
Authors@R: c(person("Scott", "Chamberlain", role = c("aut", "cre"), email = "myrmecocystus@gmail.com"), person("Thomas J.", "Leeper", role=c("ctb"), email="thosjleeper@gmail.com"))
VignetteBuilder: knitr
LazyLoad: yes
LazyData: yes
Imports: httr, plyr, jsonlite, stringr, assertthat
Suggests: knitr, testthat, rCharts
Packaged: 2014-08-20 06:53:38 UTC; sacmac
Author: Scott Chamberlain [aut, cre], Thomas J. Leeper [ctb]
Maintainer: Scott Chamberlain
NeedsCompilation: no
Repository: CRAN
Date/Publication: 2014-08-20 10:39:41

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New package RGA with initial version 0.1.1
Package: RGA
Type: Package
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.
URL: https://bitbucket.org/unikum/rga
BugReports: https://bitbucket.org/unikum/rga/issues
Version: 0.1.1
Date: 2014-06-03
Authors@R: c( person(given = "Artem", family = "Klevtsov", email = "a.a.klevtsov@gmail.com", role = c("aut", "cre")), person(given = "Philipp", family = "Upravitelev", email = "upravitelev@gmail.com", role = "ctb"), person(given = "Olga", family = "Shramko", email = "ol1709@yahoo.com", role = "ctb"))
License: GPL (>= 2)
Depends: R (>= 2.15.1)
Imports: RCurl, jsonlite, httr (>= 0.3), httpuv, shiny (>= 0.10.0)
Collate: 'auth.R' 'convert.R' 'data.R' 'utils.R' 'url.R' 'query.R' 'get-data.R' 'mgmt.R' 'onload.R' 'package.R' 'report.R' 'shiny.R'
Packaged: 2014-08-20 07:19:17 UTC; xxx
Author: Artem Klevtsov [aut, cre], Philipp Upravitelev [ctb], Olga Shramko [ctb]
Maintainer: Artem Klevtsov
NeedsCompilation: no
Repository: CRAN
Date/Publication: 2014-08-20 10:39:37

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Package parspatstat (with last version 0.1-4) was removed from CRAN

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

2013-08-23 0.1-4
2013-04-09 0.1-3
2012-09-21 0.1-2

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

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

2012-11-07 1.0

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

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

2012-12-04 1.0

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Package anaglyph (with last version 0.1-1) was removed from CRAN

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

2011-08-14 0.1-1

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Package RcmdrPlugin.doBy (with last version 0.1-3) was removed from CRAN

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

2013-07-12 0.1-3
2013-01-05 0.1-2
2011-12-16 0.1-1
2011-12-13 0.1-0

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

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

2013-04-20 1.0

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New package matpow with initial version 0.1.1
Package: matpow
Type: Package
Title: matrix powers
Version: 0.1.1
Description: A general framework for computing powers of matrices. A key feature is the capability for users to write callback functions, called after each iteration, thus enabling customization for specific applications. Diverse types of matrix classes/matrix multiplication are accommodated. If the multiplication type computes in parallel, then the package computation is also parallel.
License: GPL (>= 2)
Suggests: bigmemory, gputools
NeedsCompilation: no
ByteCompile: yes
Author: Norm Matloff, Jack Norman
Maintainer: Norm Matloff
Repository: CRAN
Packaged: 2014-08-20 05:53:00 UTC; matloff
Date/Publication: 2014-08-20 08:12:37

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Package rcdk (with last version 3.2.9.1) was removed from CRAN

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

2014-08-17 3.2.9.1
2013-10-07 3.2.3.2
2013-03-15 3.2.0.2
2012-11-18 3.1.21
2012-09-01 3.1.20.1
2012-07-06 3.1.9
2012-06-20 3.1.8.1
2012-02-27 3.1.7
2011-11-02 3.1.4
2011-08-11 3.1.3
2011-07-23 3.1.2
2011-06-19 3.1.1
2010-11-08 3.0.5
2010-10-23 3.0.4
2010-10-12 3.0.3
2010-09-29 3.0.1
2010-09-25 3.0
2010-05-22 2.9.23
2010-05-10 2.9.21
2010-05-08 2.9.20
2010-05-06 2.9.19
2009-11-01 2.9.6
2009-08-24 2.9.4
2009-07-18 2.9.3
2009-02-25 2.9.2
2008-04-08 2.8.1
2008-04-04 2.8
2008-02-27 2.7
2006-11-29 2.6.1

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Package SimuChemPC (with last version 1.3) was removed from CRAN

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

2014-02-25 1.3
2014-02-17 1.2
2013-12-02 1.1
2013-09-04 1.0

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Package rcdklibs (with last version 1.5.8.3) was removed from CRAN

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

2014-08-17 1.5.8.3
2013-10-07 1.5.4
2013-03-15 1.5.0.3
2012-06-20 1.5.0
2012-02-27 1.4.7
2011-11-02 1.4.5
2011-07-23 1.4.1
2011-06-19 1.3.11
2010-10-23 1.3.6.3
2010-10-12 1.3.6.2
2010-09-29 1.3.6.1
2010-09-25 1.3.6
2010-05-06 1.3.4.2
2009-11-01 1.2.3
2009-10-29 1.2.2
2009-02-23 1.2.1
2009-01-28 1.2
2009-01-08 1.1

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New package x.ent with initial version 0.0.4
Package: x.ent
Type: Package
Title: eXtraction of ENTity
Description: x.ent is a system for extracting information (entities and relations between them) in text datasets. It also emphasizes results exploration with graphical displays. It is a rule-based system and works with hand-made dictionaries and local grammars defined by users. x.ent has been written in perl and use javascript to define user preferences through a browser. Local grammars are defined and compiled with the tool Unitex, developed by University Paris Est, and supporting multiple languages. See ?xconfig for an introduction.
Version: 0.0.4
Date: 2014-07-14
Author: Nicolas Turenne , Tien Phan
Depends: R (>= 3.0.0),opencpu,rJava
Imports: stringr,xtable,jsonlite,venneuler
Maintainer: Tien Phan
License: GPL-3
SystemRequirements: Perl (>= 5.0), Unitex (>= 3.0 http://www-igm.univ-mlv.fr/~unitex/)
Packaged: 2014-08-19 23:26:06 UTC; phantrongtien
NeedsCompilation: no
Repository: CRAN
Date/Publication: 2014-08-20 06:12:26

More information about x.ent at CRAN
Permanent link

Package reldist updated to version 1.6-3 with previous version 1.6-2 dated 2013-03-03

Title: Relative Distribution Methods
Description: R functions for the comparison of distributions. This includes nonparametric estimation of the relative distribution PDF and CDF and numerical summaries as described in "Relative Distribution Methods in the Social Sciences" by Mark S. Handcock and Martina Morris, Springer-Verlag, 1999, Springer-Verlag, ISBN 0387987789
Author: Mark S. Handcock
Maintainer: Mark S. Handcock

Diff between reldist versions 1.6-2 dated 2013-03-03 and 1.6-3 dated 2014-08-20

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Package PtProcess updated to version 3.3-6 with previous version 3.3-1 dated 2011-12-10

Title: Time Dependent Point Process Modelling
Description: This package fits and analyses time dependent marked point process models with an emphasis on earthquake modelling. For a more detailed introduction to the package, see the topic "PtProcess". A list of recent changes can be found in the topic "Change Log".
Author: David Harte
Maintainer: David Harte

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Package opencpu updated to version 1.4.4 with previous version 1.4.3 dated 2014-06-23

Title: The OpenCPU system for embedded scientific computing and reproducible research.
Description: The OpenCPU system exposes an HTTP API for embedded scientific computing with R. This provides reliable and scalable foundations for integrating R based analysis and visualization modules into pipelines, web applications or big data infrastructures. The OpenCPU server can run either as a single-user development server within the interactive R session, or as a high performance multi-user cloud server that builds on Linux, Nginx and rApache. The current R package forms the core of the system. When loaded in R, it automatically initiates the single-user server and displays the web address in the console. For detailed information and documentation on the API, visit the OpenCPU website.
Author: Jeroen Ooms
Maintainer: Jeroen Ooms

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Package logitchoice updated to version 0.9.2 with previous version 0.9.1 dated 2014-07-21

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

Diff between logitchoice versions 0.9.1 dated 2014-07-21 and 0.9.2 dated 2014-08-20

 DESCRIPTION |    8 ++++----
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Package hydrostats updated to version 0.2.1 with previous version 0.2 dated 2014-08-11

Title: Hydrologic indices for daily time series data.
Description: Calculates a suite of hydrologic indices for daily time series data that are widely used in hydrology and stream ecology.
Author: Nick Bond
Maintainer: Nick Bond

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Tue, 19 Aug 2014

Package arules updated to version 1.1-5 with previous version 1.1-4 dated 2014-07-26

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

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Package teigen updated to version 2.0.7 with previous version 2.0.1 dated 2013-10-03

Title: Model-based clustering and classification with the multivariate t-distribution
Description: Fits mixtures of multivariate t-distributions (with eigen-decomposed covariance structure) via the multi-cycle ECM algorithm under a clustering or classification paradigm.
Author: Jeffrey L. Andrews, Paul D. McNicholas
Maintainer: Jeffrey L. Andrews

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Package party updated to version 1.0-16 with previous version 1.0-15 dated 2014-06-30

Title: A Laboratory for Recursive Partytioning
Description: A computational toolbox for recursive partitioning. The core of the package is ctree(), an implementation of conditional inference trees which embed tree-structured regression models into a well defined theory of conditional inference procedures. This non-parametric class of regression trees is applicable to all kinds of regression problems, including nominal, ordinal, numeric, censored as well as multivariate response variables and arbitrary measurement scales of the covariates. Based on conditional inference trees, cforest() provides an implementation of Breiman's random forests. The function mob() implements an algorithm for recursive partitioning based on parametric models (e.g. linear models, GLMs or survival regression) employing parameter instability tests for split selection. Extensible functionality for visualizing tree-structured regression models is available.
Author: Torsten Hothorn [aut, cre], Kurt Hornik [aut], Carolin Strobl [aut], Achim Zeileis [aut]
Maintainer: Torsten Hothorn

Diff between party versions 1.0-15 dated 2014-06-30 and 1.0-16 dated 2014-08-19

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Package dendextend updated to version 0.17.1 with previous version 0.16.1 dated 2014-07-26

Title: Extending R's dendrogram functionality
Description: The dendextend package offers a set of functions for extending dendrogram objects in R, letting you visualize and compare trees of hierarchical clusterings. You can (1) Adjust a trees graphical parameters - the color, size, type, etc of its branches, nodes and labels. (2) Visually and statistically compare different dendrograms to one another.
Author: Tal Galili [aut, cre, cph] (http://www.r-statistics.com), Gavin Simpson [ctb], Gregory Jefferis [ctb] (imported code from his dendroextras package), Marco Gallotta [ctb] (a.k.a: marcog), Johan Renaudie [ctb] (https://github.com/plannapus), R core team [ctb] (Thanks for the Infastructure, and code in the examples), Kurt Hornik [ctb], Uwe Ligges [ctb], Andrej-Nikolai Spiess [ctb], Steve Horvath [ctb], Peter Langfelder [ctb], skullkey [ctb], Mark Van Der Loo [ctb] (https://github.com/markvanderloo d3dendrogram), Yoav Benjamini [ths]
Maintainer: Tal Galili

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New package DStree with initial version 1.0
Package: DStree
Type: Package
Title: Recursive Partitioning for Discrete-Time Survival Trees
Version: 1.0
Date: 2014-08-19
Author: Peter Mayer, Denis Larocque, Matthias Schmid
Maintainer: Peter Mayer
Description: Building discrete-time survival trees and bagged trees based on the functionalities of the rpart package. Splitting criterion maximizes the likelihood of a covariate-free logistic discrete time hazard model.
License: GPL-2
NeedsCompilation: no
Depends: rpart,pec,Ecdat
Imports: rpart.plot,survival, Rcpp
LazyData: no
LinkingTo: Rcpp
Packaged: 2014-08-19 18:15:30 UTC; Peter
Repository: CRAN
Date/Publication: 2014-08-19 22:25:27

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Package pacose (with last version 1.4) was removed from CRAN

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

2013-02-08 1.4
2012-09-04 1.3

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

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2012-05-14 1.1

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Package mpmi (with last version 0.4) was removed from CRAN

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

2013-10-22 0.4
2013-08-27 0.03

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New package TDA with initial version 1.0
Package: TDA
Type: Package
Title: Statistical Tools for Topological Data Analysis
Version: 1.0
Date: 2014-08-01
Author: Brittany T. Fasy, Fabrizio Lecci
Maintainer: Fabrizio Lecci
Description: This package provides some tools for Topological Data Analysis. In particular it provides functions for the statistical analysis of persistent homology and for density clustering.
Depends: FNN, igraph, parallel, scales
License: GPL (>= 2.0)
Packaged: 2014-08-19 16:16:34 UTC; fabrizio
NeedsCompilation: yes
Repository: CRAN
Date/Publication: 2014-08-19 19:57:29

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Package RcppArmadillo updated to version 0.4.400.0 with previous version 0.4.320.0 dated 2014-07-03

Title: Rcpp integration for 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. A delayed evaluation approach is employed (during compile time) to combine several operations into one, and to reduce (or eliminate) the need for temporaries. This is accomplished through recursive templates and template meta-programming. This library is useful if C++ has been decided as the language of choice (due to speed and/or integration capabilities), rather than another language. 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. This Armadillo integration provides a nice illustration of the capabilities of the Rcpp package for seamless R and C++ integration. 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 0.4.320.0 dated 2014-07-03 and 0.4.400.0 dated 2014-08-19

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Package mRMRe updated to version 2.0.5 with previous version 2.0.4 dated 2013-12-10

Title: R package for parallelized mRMR ensemble feature selection
Description: This package contains a set of function to compute mutual information matrices from continuous, categorical and survival variables. It also contains function to perform feature selection with mRMR and a new ensemble mRMR technique.
Author: Nicolas De Jay, Simon Papillon-Cavanagh, Catharina Olsen, Gianluca Bontempi, Benjamin Haibe-Kains
Maintainer: Benjamin Haibe-Kains

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Package fracprolif (with last version 1.0.5) was removed from CRAN

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

2012-11-08 1.0.5
2012-07-20 1.0.4
2012-07-12 1.0.3
2012-04-27 1.0.2
2012-04-24 1.0.1

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Package gammSlice (with last version 1.2-6) was removed from CRAN

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2012-05-06 1.2-6
2012-04-04 1.2-5

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Package Ace (with last version 0.0.8) was removed from CRAN

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2012-01-27 0.0.8

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

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2012-02-20 1.0

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Package emg (with last version 1.0.5) was removed from CRAN

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2012-01-04 1.0.5
2011-12-14 1.0.4
2011-12-05 1.0.3
2011-10-25 1.0.2
2010-08-31 1.0.1

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Package ARTIVA (with last version 1.2.2) was removed from CRAN

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2013-09-09 1.2.2
2012-12-13 1.2.1
2012-08-30 1.2
2012-07-02 1.1

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Package CompRandFld (with last version 1.0.3) was removed from CRAN

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2013-05-22 1.0.3
2012-04-13 1.0.2
2012-03-30 1.0.1
2011-09-10 1.0.0
2011-08-04 0.9.1
2010-11-30 0.9
2010-11-17 0.8
2010-11-09 0.6
2010-11-07 0.5
2010-10-26 0.4
2010-10-15 0.3
2010-10-01 0.2
2010-06-25 0.1

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

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2012-02-23 1.0

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Package StreamingLm (with last version 0.1) was removed from CRAN

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2011-11-14 0.1

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Package SimHap (with last version 1.2.0) was removed from CRAN

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

2012-06-21 1.2.0

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Package spartan updated to version 2.1 with previous version 2.0 dated 2014-07-22

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

Diff between spartan versions 2.0 dated 2014-07-22 and 2.1 dated 2014-08-19

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Package HSAUR3 updated to version 1.0-2 with previous version 1.0-1 dated 2014-06-26

Title: A Handbook of Statistical Analyses Using R (3rd Edition)
Description: Functions, data sets, analyses and examples from the third edition of the book `A Handbook of Statistical Analyses Using R' (Torsten Hothorn and Brian S. Everitt, Chapman & Hall/CRC, 2014). The first chapter of the book, which is entitled `An Introduction to R', is completely included in this package, for all other chapters, a vignette containing all data analyses is available. In addition, Sweave source code for slides of selected chapters is included in this package (see HSAUR3/inst/slides).
Author: Brian S. Everitt and Torsten Hothorn
Maintainer: Torsten Hothorn

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Package HSAUR2 updated to version 1.1-11 with previous version 1.1-10 dated 2014-06-24

Title: A Handbook of Statistical Analyses Using R (2nd Edition)
Description: Functions, data sets, analyses and examples from the second edition of the book `A Handbook of Statistical Analyses Using R' (Brian S. Everitt and Torsten Hothorn, Chapman & Hall/CRC, 2008). The first chapter of the book, which is entitled `An Introduction to R', is completely included in this package, for all other chapters, a vignette containing all data analyses is available. In addition, the package contains Sweave code for producing slides for selected chapters (see HSAUR2/inst/slides).
Author: Brian S. Everitt and Torsten Hothorn
Maintainer: Torsten Hothorn

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Package HSAUR updated to version 1.3-4 with previous version 1.3-3 dated 2013-09-03

Title: A Handbook of Statistical Analyses Using R
Description: Functions, data sets, analyses and examples from the book `A Handbook of Statistical Analyses Using R' (Brian S. Everitt and Torsten Hothorn, Chapman & Hall/CRC, 2006). The first chapter of the book, which is entitled `An Introduction to R', is completely included in this package, for all other chapters, a vignette containing all data analyses is available.
Author: Brian S. Everitt and Torsten Hothorn
Maintainer: Torsten Hothorn

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Package RefManageR updated to version 0.8.34 with previous version 0.8.32 dated 2014-08-15

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

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New package RcmdrPlugin.EcoVirtual with initial version 0.1
Package: RcmdrPlugin.EcoVirtual
Type: Package
Title: Rcmdr EcoVirtual Plugin
Version: 0.1
Date: 2014-08-15
Author: Alexandre Adalardo de Oliveira and Paulo Inacio Prado
Maintainer: Alexandre Adalardo de Oliveira
Depends: Rcmdr (>= 1.4-0), EcoVirtual
Description: This package provides an Rcmdr "plug-in" for the EcoVirtual package and was designed primarily for teaching ecological models using simulations.
License: GPL (>= 2)
URL: http://ecovirtual.ib.usp.br
LazyLoad: yes
Packaged: 2014-08-19 11:30:31 UTC; ale
NeedsCompilation: no
Repository: CRAN
Date/Publication: 2014-08-19 15:12:37

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Package laeken updated to version 0.4.6 with previous version 0.4.5 dated 2013-08-18

Title: Estimation of indicators on social exclusion and poverty
Description: Estimation of indicators on social exclusion and poverty, as well as Pareto tail modeling for empirical income distributions.
Author: Andreas Alfons [aut, cre], Josef Holzer [aut], Matthias Templ [aut]
Maintainer: Andreas Alfons

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Package FD updated to version 1.0-12 with previous version 1.0-11 dated 2011-03-21

Title: Measuring functional diversity (FD) from multiple traits, and other tools for functional ecology
Description: FD is a package to compute different multidimensional FD indices. It implements a distance-based framework to measure FD that allows any number and type of functional traits, and can also consider species relative abundances. It also contains other useful tools for functional ecology.
Author: Etienne Laliberté, Pierre Legendre, Bill Shipley
Maintainer: Etienne Laliberté

Diff between FD versions 1.0-11 dated 2011-03-21 and 1.0-12 dated 2014-08-19

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New package BAT with initial version 1.0
Package: BAT
Title: Biodiversity Assessment Tools
Version: 1.0
Date: August, 19 2014
Author: Pedro Cardoso, Francois Rigal, Jose Carlos Carvalho
Maintainer: Pedro Cardoso
Description: This package introduces algorithms to assess alpha and beta diversity in all their dimensions (taxon, phylogenetic and functional diversity), whether communities are completely sampled or not. It allows performing a number of analyses based on either species identities or ultrametric trees depicting species relationships.
Depends: R (>= 3.0.0), vegan
License: GPL-3
LazyData: true
Packaged: 2014-08-19 09:16:58 UTC; pcardoso
NeedsCompilation: no
Repository: CRAN
Date/Publication: 2014-08-19 13:42:14

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Package rite updated to version 0.3.4 with previous version 0.3.1 dated 2014-02-24

Title: The Right Editor to Write R
Description: A simple yet powerful script editor built natively in R with tcltk.
Author: Thomas J. Leeper
Maintainer: Thomas J. Leeper

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Package RcmdrPlugin.EZR updated to version 1.25 with previous version 1.24 dated 2014-04-22

Title: R Commander Plug-in for the EZR (Easy R) Package
Description: EZR (Easy R) adds a variety of statistical functions, including survival analyses, ROC analyses, metaanalyses, sample size calculation, and so on, to the R commander. EZR enables point-and-click easy access to statistical functions, especially for medical statistics. EZR is platform-independent and runs on Windows, Mac OS X, and UNIX. Its complete manual is available only in Japanese (Chugai Igakusha, ISBN-10: 4498109007), but an report that introduced the investigation of EZR was published in Bone Marrow Transplantation (Nature Publishing Group) as an Open article. This report can be used as a simple manual. It can be freely downloaded from the journal website as shown below.
Author: Yoshinobu Kanda
Maintainer: Yoshinobu Kanda

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Package Sim.DiffProc updated to version 2.8 with previous version 2.7 dated 2014-07-13

Title: Simulation of Diffusion Processes
Description: The package Sim.DiffProc is an object created in R environment for simulation and modeling of stochastic differential equations (SDE's) the type Ito and Stratonovich. This package contains many objects, the numerical methods to find the solutions to SDE's (1, 2 and 3-dim), with a possibility for simulates a flows trajectories,with good accuracy. Many theoretical problems on the SDE's have become the object of practical research, as statistical analysis and simulation of solution of SDE's, enabled many searchers in different domains to use these equations to modeling and to analyse practical problems, in financial and actuarial modeling and other areas of application, for example modelling and simulate of dispersion in shallow water using the attractive center (Boukhetala K, 1996). We hope that the package presented here and the updated survey on the subject might be of help for practitioners, postgraduate and PhD students, and researchers in the field who might want to implement new methods.
Author: Arsalane Chouaib Guidoum, Kamal Boukhetala
Maintainer: Arsalane Chouaib Guidoum

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Package R6 updated to version 2.0 with previous version 1.0.1 dated 2014-07-17

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 extlasso updated to version 0.2 with previous version 0.1 dated 2014-07-30

Title: Maximum penalized likelihood estimation with extended lasso penalty
Description: The package estimates coefficients of extended LASSO penalized linear regression and generalized linear models. Currently lasso and elastic net penalized linear regression and generalized linear models are considered. The package currently utilizes an accurate approximation of L1 penalty and then a modified Jacobi algorithm to estimate the coefficients. There is provision for plotting of the solutions and predictions of coefficients at given values of lambda. The package also contains functions for cross validation to select a suitable lambda value given the data. The package also provides a function for estimation in fused lasso penalized linear regression.
Author: B N Mandal and Jun Ma
Maintainer: B N Mandal

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Mon, 18 Aug 2014

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

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

2013-06-14 1.1

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Package ivbma (with last version 1.02) was removed from CRAN

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

2012-04-26 1.02
2012-03-19 1.01
2012-02-29 1.00

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

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

2008-04-22 1.0

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

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

2014-01-20 1.0

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