Tue, 16 Dec 2014

New package RSNPset with initial version 0.3
Package: RSNPset
Type: Package
Title: Efficient Score Statistics For Genome-Wide SNP Set Analysis
Version: 0.3
Date: 2014-12-16
Author: Chanhee Yi, Alexander Sibley, and Kouros Owzar
Maintainer: Alexander Sibley
Description: RSNPset is an implementation of the use of efficient score statistics in genome-wide SNP set analysis with complex traits. The package provides three standard score statistics (Cox, Binomial, and Gaussian) but is easily extensible to include others. Code implementing the inferential procedure is primarily written in C++ and utilizes parallelization of the analysis to reduce runtime. A supporting function offers simple computation of observed, permutation, and FWER and FDR adjusted p-values.
License: GPL-3
Imports: fastmatch (>= 1.0-4), foreach (>= 1.4.1), doRNG (>= 1.5.3), qvalue (>= 1.34), Rcpp (>= 0.10.4)
LinkingTo: Rcpp, RcppEigen
Suggests: knitr
VignetteBuilder: knitr
Packaged: 2014-12-16 19:06:52 UTC; abs33
NeedsCompilation: yes
Repository: CRAN
Date/Publication: 2014-12-17 01:59:36

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Package rmatio updated to version 0.11.0 with previous version 0.10.0 dated 2014-05-10

Title: Read and Write Matlab Files
Description: rmatio is a package for reading and writing Matlab MAT files from R. The rmatio package supports reading MAT version 4, MAT version 5 and MAT compressed version 5. The rmatio package can write version 5 MAT files and version 5 files with variable compression.
Author: Stefan Widgren [aut, cre] (Author of the R interface to the C-library matio), Christopher Hulbert [aut] (Author of the C-library matio, http://sourceforge.net/projects/matio/)
Maintainer: Stefan Widgren

Diff between rmatio versions 0.10.0 dated 2014-05-10 and 0.11.0 dated 2014-12-16

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New package refset with initial version 0.1.0
Package: refset
Type: Package
Title: Subsets with Reference Semantics
Version: 0.1.0
Date: 2014-11-20
Author: David Hugh-Jones
Maintainer: David Hugh-Jones
Description: Provides subsets with reference semantics, i.e. subsets which automatically reflect changes in the original object, and which optionally update the original object when they are changed.
License: GPL-2
NeedsCompilation: no
VignetteBuilder: knitr
Suggests: knitr, rmarkdown, testthat
Packaged: 2014-12-16 21:42:46 UTC; david
Repository: CRAN
Date/Publication: 2014-12-17 01:57:34

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Package plsRglm updated to version 1.1.1 with previous version 1.1.0 dated 2014-07-19

Title: Partial Least Squares Regression for Generalized Linear Models
Description: Provides (weighted) Partial least squares Regression for generalized linear models and repeated k-fold cross-validation of such models using various criteria. It allows for missing data in the explanatory variables. Bootstrap confidence intervals constructions are also available.
Author: Frederic Bertrand , Nicolas Meyer , Myriam Maumy-Bertrand .
Maintainer: Frederic Bertrand

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Package lqmm updated to version 1.5.1 with previous version 1.5 dated 2014-05-01

Title: Linear Quantile Mixed Models
Description: Fit quantile regression models for independent and hierarchical data
Author: Marco Geraci
Maintainer: Marco Geraci

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Package lmmot updated to version 0.1.2 with previous version 0.1.1 dated 2014-08-18

Title: Multiple Ordinal Tobit (MOT) model
Description: Fit right censored Multiple Ordinal Tobit (MOT) model.
Author: Marvin N. Wright
Maintainer: Marvin N. Wright

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Package HH updated to version 3.1-8 with previous version 3.1-5 dated 2014-09-13

Title: Statistical Analysis and Data Display: Heiberger and Holland
Description: Support software for Statistical Analysis and Data Display (First Edition, Springer, ISBN 0-387-40270-5, 2004) and (Second Edition, Springer, ISBN 978-1-4939-2121-8, anticipated 2015) by Richard M. Heiberger and Burt Holland. This contemporary presentation of statistical methods features extensive use of graphical displays for exploring data and for displaying the analysis. The second edition includes redesigned graphics and additional chapters. The authors emphasize how to construct and interpret graphs, discuss principles of graphical design, and show how accompanying traditional tabular results are used to confirm the visual impressions derived directly from the graphs. Many of the graphical formats are novel and appear here for the first time in print. All chapters have exercises. All functions introduced in the book are in the package. R code for all examples, both graphs and tables, in the book is included in the scripts directory of the package.
Author: Richard M. Heiberger
Maintainer: Richard M. Heiberger

Diff between HH versions 3.1-5 dated 2014-09-13 and 3.1-8 dated 2014-12-16

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Package gridSVG updated to version 1.4-2 with previous version 1.4-0 dated 2013-09-18

Title: Export grid Graphics as SVG
Description: Functions to export graphics drawn with package grid to SVG format. Additional functions provide access to SVG features that are not available in standard R graphics, such as hyperlinks, animation, filters, masks, clipping paths, and gradient and pattern fills.
Author: Paul Murrell [cre, aut], Simon Potter [aut]
Maintainer: Paul Murrell

Diff between gridSVG versions 1.4-0 dated 2013-09-18 and 1.4-2 dated 2014-12-16

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New package FPDclustering with initial version 1.0
Package: FPDclustering
Type: Package
Title: PD-Clustering and Factor PD-Clustering
Version: 1.0
Date: 2014-12-16
Author: Cristina Tortora and Paul D. McNicholas
Maintainer: Cristina Tortora
Description: Probabilistic distance clustering (PD-clustering) is an iterative, distribution free, probabilistic clustering method. PD-clustering assigns units to a cluster according to their probability of membership, under the constraint that the product of the probability and the distance of each point to any cluster centre is a constant. PD-clustering is a flexible method that can be used with non-spherical clusters, outliers, or noisy data. Facto PD-clustering (FPDC) is a recently proposed factor clustering method that involves a linear transformation of variables and a cluster optimizing the PD-clustering criterion. It allows clustering of high dimensional data sets.
Depends: ThreeWay
License: GPL (>= 2)
Packaged: 2014-12-16 18:46:17 UTC; ctortora
NeedsCompilation: no
Repository: CRAN
Date/Publication: 2014-12-17 01:54:43

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Package EIAdata updated to version 0.0.2 with previous version 0.0.1 dated 2014-08-04

Title: R Wrapper for the Energy Information Administration (EIA) API
Description: An R wrapper to allow the user to query categories and Series IDs, and import data, from the EIA's API.
Author: Matthew Brigida
Maintainer: Matthew Brigida

Diff between EIAdata versions 0.0.1 dated 2014-08-04 and 0.0.2 dated 2014-12-16

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New package rSPACE with initial version 1.0
Package: rSPACE
Type: Package
Title: Spatially-Explicit Power Analysis for Conservation and Ecology
Version: 1.0
Date: 2014-12-15
Author: Martha Ellis, Jake Ivan, Jody Tucker, Mike Schwartz
Maintainer: Martha Ellis
Description: Conducts a spatially-explicit, simulation-based power analysis for detecting trends in population abundance through occupancy-based modeling. Applicable for evaluating monitoring designs in conservation and ecological settings.
License: GPL (>= 2)
Imports: raster, RMark, ggplot2, tcltk2, sp, grid, plyr, tcltk
Packaged: 2014-12-16 18:20:03 UTC; marthamellis
NeedsCompilation: yes
Repository: CRAN
Date/Publication: 2014-12-16 22:38:08

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New package PRROC with initial version 1.0
Package: PRROC
Type: Package
Title: Precision-Recall and ROC Curves for Weighted and Unweighted Data
Version: 1.0
Date: 2014-12-16
Author: Jan Grau and Jens Keilwagen
Maintainer: Jan Grau
Description: Computes the areas under the precision-recall (PR) and ROC curve for weighted (e.g., soft-labeled) and unweighted data. In contrast to other implementations, the interpolation between points of the PR curve is done by a non-linear piecewise function. In addition to the areas under the curves, the curves themselves can also be computed and plotted by a specific S3-method.
License: GPL-3
Packaged: 2014-12-16 21:03:40 UTC; dev
NeedsCompilation: no
Repository: CRAN
Date/Publication: 2014-12-16 22:34:59

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Package flexCWM updated to version 1.3 with previous version 1.1 dated 2013-11-09

Title: Flexible Cluster-Weighted Modeling
Description: This package implements a flexible version of the Cluster Weighted Model (CWM), which is an eminent member of the class of mixtures of regression models with random covariates.
Author: Mazza A., Punzo A., Ingrassia S.
Maintainer: Angelo Mazza

Diff between flexCWM versions 1.1 dated 2013-11-09 and 1.3 dated 2014-12-16

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Package compare updated to version 0.2-5 with previous version 0.2-4 dated 2014-02-24

Title: Comparing Objects for Differences
Description: Functions to compare a model object to a comparison object. If the objects are not identical, the functions can be instructed to explore various modifications of the objects (e.g., sorting rows, dropping names) to see if the modified versions are identical.
Author: Paul Murrell
Maintainer: Paul Murrell

Diff between compare versions 0.2-4 dated 2014-02-24 and 0.2-5 dated 2014-12-16

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Package sdnet updated to version 2.03.3 with previous version 2.01.3 dated 2014-02-27

Title: Soft Discretization-based Bayesian Network Inference
Description: Fitting discrete Bayesian networks using marginal mixture distributions
Author: Nikolay Balov
Maintainer: Nikolay Balov

Diff between sdnet versions 2.01.3 dated 2014-02-27 and 2.03.3 dated 2014-12-16

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Package packrat updated to version 0.4.2-1 with previous version 0.4.2 dated 2014-12-15

Title: A Dependency Management System for Projects and their R Package Dependencies
Description: Packrat is a tool for managing the R packages your project depends on in an isolated, portable, and reproducible way.
Author: Kevin Ushey, Jonathan McPherson, Joe Cheng, JJ Allaire
Maintainer: Kevin Ushey

Diff between packrat versions 0.4.2 dated 2014-12-15 and 0.4.2-1 dated 2014-12-16

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Package PHeval updated to version 0.5.2 with previous version 0.5.1 dated 2014-05-27

Title: Evaluation of the proportional hazards assumption with a standardized score process
Description: This package provides tools for the evaluation of the goodness of fit and the predictive capacity of the proportional hazards model.
Author: Cecile Chauvel
Maintainer: Cecile Chauvel

Diff between PHeval versions 0.5.1 dated 2014-05-27 and 0.5.2 dated 2014-12-16

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New package NeuralNetTools with initial version 1.0.0
Package: NeuralNetTools
Type: Package
Title: Visualization and Analysis Tools for Neural Networks
Version: 1.0.0
Date: 2014-12-10
Author: Marcus W. Beck [aut, cre]
Maintainer: Marcus W. Beck
Description: Visualization and analysis tools to aid in the interpretation of neural network models. Functions are available for plotting, quantifying variable importance, conducting a sensitivity analysis, and obtaining a simple list of model weights.
BugReports: https://github.com/fawda123/NeuralNetTools/issues
License: CC0
LazyData: true
Imports: ggplot2, neuralnet, nnet, reshape2, RSNNS, scales
Depends: R (>= 3.1.1)
Authors@R: person(given = "Marcus W.", family = "Beck", role = c("aut","cre"), email = "mbafs2012@gmail.com")
Packaged: 2014-12-16 16:06:56 UTC; Marcus
NeedsCompilation: no
Repository: CRAN
Date/Publication: 2014-12-16 17:43:30

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Package fda updated to version 2.4.4 with previous version 2.4.3 dated 2014-05-23

Title: Functional Data Analysis
Description: These functions were developed to support functional data analysis as described in Ramsay, J. O. and Silverman, B. W. (2005) Functional Data Analysis. New York: Springer. They were ported from earlier versions in Matlab and S-PLUS. An introduction appears in Ramsay, J. O., Hooker, Giles, and Graves, Spencer (2009) Functional Data Analysis with R and Matlab (Springer). The package includes data sets and script files working many examples including all but one of the 76 figures in this latter book. Matlab versions of the code and sample analyses are no longer distributed through CRAN, as they were when the book was published. For those, ftp from http://www.psych.mcgill.ca/misc/fda/downloads/FDAfuns/ There you find a set of .zip files containing the functions and sample analyses, as well as two .txt files giving instructions for installation and some additional information. The changes from Version 2.4.1 are fixes of bugs in density.fd and removal of functions create.polynomial.basis, polynompen, and polynomial. These were deleted because the monomial basis does the same thing and because there were errors in the code.
Author: J. O. Ramsay , Hadley Wickham , Spencer Graves , Giles Hooker
Maintainer: J. O. Ramsay

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Package epinet updated to version 2.0.9 with previous version 2.0.8 dated 2014-10-14

Title: A Collection of Epidemic/Network-Related Tools
Description: A collection of epidemic/network-related tools. Simulates transmission of diseases through contact networks. Performs Bayesian inference on network and epidemic parameters, given epidemic data.
Author: Chris Groendyke [aut, cre], David Welch [aut], David Hunter [ctb]
Maintainer: Chris Groendyke

Diff between epinet versions 2.0.8 dated 2014-10-14 and 2.0.9 dated 2014-12-16

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Permanent link

Package dti updated to version 1.2-0.1 with previous version 1.2-0 dated 2014-05-12

Title: Analysis of diffusion weighted imaging (DWI) data
Description: Diffusion Weighted Imaging (DWI) is a Magnetic Resonance Imaging modality, that measures diffusion of water in tissues like the human brain. The package contains R-functions to process diffusion-weighted data. The functionality includes diffusion tensor imaging (DTI), diffusion kurtosis imaging (DKI), modeling for high angular resolution diffusion weighted imaging (HARDI) using Q-ball-reconstruction and tensor mixture models, several methods for structural adaptive smoothing including POAS and msPOAS, and a streamline fiber tracking for tensor and tensor mixture models. The package provides functionality to manipulate and visualize results in 2D and 3D.
Author: Karsten Tabelow [aut, cre], Joerg Polzehl [aut], Felix Anker [ctb]
Maintainer: Karsten Tabelow

Diff between dti versions 1.2-0 dated 2014-05-12 and 1.2-0.1 dated 2014-12-16

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Package CARBayes updated to version 4.0 with previous version 3.0 dated 2014-04-04

Title: Spatial Areal Unit Modelling
Description: Implements Bayesian hierarchical spatial areal unit models. In such models the spatial autocorrelation is modelled by a set of random effects, which are assigned a conditional autoregressive (CAR) prior distribution. Examples of the models included are the BYM model as well as a recently developed localised spatial smoothing model.The initial creation of this package was supported by the Economic and Social Research Council (ESRC) grant RES-000-22-4256, and on-going development is supported by the Engineering and Physical Science Research Council (EPSRC) grant EP/J017442/1.
Author: Duncan Lee
Maintainer: Duncan Lee

Diff between CARBayes versions 3.0 dated 2014-04-04 and 4.0 dated 2014-12-16

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Package abctools updated to version 1.0 with previous version 0.3-2 dated 2014-06-25

Title: Tools for ABC analyses
Description: Tools for approximate Bayesian computation including summary statistic selection and assessing coverage
Author: Matt Nunes [aut, cre], Dennis Prangle [aut]
Maintainer: Matt Nunes

Diff between abctools versions 0.3-2 dated 2014-06-25 and 1.0 dated 2014-12-16

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Package SCEPtER updated to version 0.2-0 with previous version 0.1-0 dated 2013-06-04

Title: Stellar CharactEristics Pisa Estimation gRid
Description: SCEPtER pipeline for estimating the stellar age, mass, and radius given observational effective temperature, [Fe/H], and astroseismic parameters. The results are obtained adopting a maximum likelihood technique over a grid of pre-computed stellar models.
Author: Matteo Dell'Omodarme [aut, cre], Giada Valle [aut]
Maintainer: Matteo Dell'Omodarme

Diff between SCEPtER versions 0.1-0 dated 2013-06-04 and 0.2-0 dated 2014-12-16

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Package jomo updated to version 0.1-1 with previous version 0.1-0 dated 2014-12-10

Title: A package for Multilevel Joint Modelling Multiple Imputation
Description: Building on Schafer's pan and on standalone program REALCOM, jomo is a package for multilevel joint modelling multiple imputation. Binary and categorical variables are handled through latent normal variables and algorithms for cluster specific covariance matrices are introduced.
Author: Matteo Quartagno, James Carpenter
Maintainer: Matteo Quartagno

Diff between jomo versions 0.1-0 dated 2014-12-10 and 0.1-1 dated 2014-12-16

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Package Rvcg updated to version 0.10 with previous version 0.9 dated 2014-09-23

Title: Manipulations of triangular meshes (smoothing, quadric edge collapse decimation, im- and export of various mesh file-formats, cleaning, etc.) based on the VCGLIB API.
Description: Operations on triangular meshes based on VCGLIB. This package integrates nicely with the R-package "rgl" to render the meshes processed by Rvcg. The Visualization and Computer Graphics Library (VCG for short) is an open source portable C++ templated library for manipulation, processing and displaying with OpenGL of triangle and tetrahedral meshes. The library, composed by more than 100k lines of code, is released under the GPL license, and it is the base of most of the software tools of the Visual Computing Lab of the Italian National Research Council Institute ISTI (http://vcg.isti.cnr.it), like metro and MeshLab. The vcglib source is pulled from trunk (svn://svn.code.sf.net/p/vcg/code/trunk/vcglib) and patched to work with options determined by the configure script as well as to work with the header files included by RcppEigen.
Author: Stefan Schlager; the authors of VCGLIB for the included version of the code
Maintainer: Stefan Schlager

Diff between Rvcg versions 0.9 dated 2014-09-23 and 0.10 dated 2014-12-16

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Permanent link

New package spca with initial version 0.6.0
Package: spca
Type: Package
Title: Sparse Principal Component Analysis
Version: 0.6.0
Date: 2014-12-14
Author: Giovanni Maria Merola
Maintainer: Giovanni Merola
URL: http://github.com/merolagio/spca
BugReports: http://github.com/merolagio/spca/issues
Description: Computes Least Squares Sparse Principal Components either by a Branch-and-Bound search or with an iterative Backward Elimination algorithm. Sparse solutions can be plotted, printed and compared using the methods included.
Depends: R (>= 3.1)
VignetteBuilder: knitr
Suggests: formatR, knitr (>= 1.8.0), ggplot2, reshape2
Imports: MASS
License: GPL-3
LazyData: true
Packaged: 2014-12-16 11:39:18 UTC; Glovani
NeedsCompilation: no
Repository: CRAN
Date/Publication: 2014-12-16 13:19:52

More information about spca at CRAN
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Package Morpho updated to version 2.2 with previous version 2.1 dated 2014-09-25

Title: Calculations and visualisations related to Geometric Morphometrics
Description: A toolset for Geometric Morphometrics and mesh processing. This includes (among other stuff) mesh deformations based on reference points, permutation tests, detection of outliers, processing of sliding semi-landmarks and semi-automated surface landmark placement.
Author: Stefan Schlager
Maintainer: Stefan Schlager

Diff between Morpho versions 2.1 dated 2014-09-25 and 2.2 dated 2014-12-16

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 Morpho-2.2/Morpho/R/RegScore.r             |   19 ++
 Morpho-2.2/Morpho/R/Semislide.r            |   16 +-
 Morpho-2.2/Morpho/R/applyTransform.r       |    7 
 Morpho-2.2/Morpho/R/calcGamma.r            |   35 ++--
 Morpho-2.2/Morpho/R/calcTang_U_s.r         |  221 +++++++++++++++--------------
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 Morpho-2.2/Morpho/R/relax.lm.r             |  115 ++++++++++-----
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 Morpho-2.2/Morpho/R/retrodeform.r          |   10 -
 Morpho-2.2/Morpho/R/rotmesh.onto.r         |    2 
 Morpho-2.2/Morpho/R/slider3d.r             |   93 ++++++++----
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 Morpho-2.2/Morpho/R/tanplan.r              |   18 +-
 Morpho-2.2/Morpho/R/tps3d.r                |   10 -
 Morpho-2.2/Morpho/R/warp.mesh.r            |    2 
 Morpho-2.2/Morpho/README.md                |   21 --
 Morpho-2.2/Morpho/inst/NEWS.Rd             |   35 ++++
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 Morpho-2.2/Morpho/man/Morpho-deprecated.Rd |    9 +
 Morpho-2.2/Morpho/man/Morpho-package.Rd    |    4 
 Morpho-2.2/Morpho/man/ProcGPA.Rd           |    4 
 Morpho-2.2/Morpho/man/RegScore.Rd          |   19 ++
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 Morpho-2.2/Morpho/man/retroDeformMesh.Rd   |    2 
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 65 files changed, 845 insertions(+), 496 deletions(-)

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Package marmap updated to version 0.9.1 with previous version 0.9 dated 2014-11-06

Title: Import, plot and analyze bathymetric and topographic data
Description: Import, plot and analyze bathymetric and topographic data
Author: Eric Pante, Benoit Simon-Bouhet, and Jean-Olivier Irisson
Maintainer: Eric Pante

Diff between marmap versions 0.9 dated 2014-11-06 and 0.9.1 dated 2014-12-16

 DESCRIPTION                      |   10 +++++-----
 MD5                              |   38 +++++++++++++++++++++++---------------
 NAMESPACE                        |    3 ++-
 R/combine.buffers.R              |only
 R/create.buffer.R                |only
 R/get.area.R                     |    1 +
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 R/outline.buffer.R               |only
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 R/plotProfile.R                  |    4 ++--
 R/read.bathy.R                   |    4 ++--
 R/setSQL.R                       |    4 ++--
 R/subsetBathy.R                  |    2 +-
 R/subsetSQL.R                    |    5 +++--
 inst/doc/marmap-DataAnalysis.pdf |binary
 inst/doc/marmap-ImportExport.pdf |binary
 man/combine.buffers.Rd           |only
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 man/read.bathy.Rd                |    5 ++++-
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 24 files changed, 76 insertions(+), 56 deletions(-)

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Package D2C updated to version 1.1 with previous version 1.0 dated 2014-11-10

Title: Predicting Causal Direction from Dependency Features
Description: The relationship between statistical dependency and causality lies at the heart of all statistical approaches to causal inference. The D2C package implements a supervised machine learning approach to infer the existence of a directed causal link between two variables in multivariate settings with n>2 variables. The approach relies on the asymmetry of some conditional (in)dependence relations between the members of the Markov blankets of two variables causally connected. The D2C algorithm predicts the existence of a direct causal link between two variables in a multivariate setting by (i) creating a set of of features of the relationship based on asymmetric descriptors of the multivariate dependency and (ii) using a classifier to learn a mapping between the features and the presence of a causal link
Author: Gianluca Bontempi, Catharina Olsen, Maxime Flauder
Maintainer: Catharina Olsen

Diff between D2C versions 1.0 dated 2014-11-10 and 1.1 dated 2014-12-16

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 D2C-1.1/D2C/R/D2c.Data.R                             |  312 +++++++++++++------
 D2C-1.1/D2C/R/D2c.network.R                          |  254 ++++++++++-----
 D2C-1.1/D2C/R/d2c.R                                  |   93 ++---
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 44 files changed, 561 insertions(+), 363 deletions(-)

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New package WaveletComp with initial version 1.0
Package: WaveletComp
Type: Package
Title: Computational Wavelet Analysis
Version: 1.0
Date: 2014-12-15
Author: Angi Roesch and Harald Schmidbauer
Maintainer: Angi Roesch
Description: Wavelet analysis and reconstruction of time series, cross-wavelets and phase-difference (with filtering options), significance with simulation algorithms.
Depends: R (>= 2.10)
License: GPL-2
URL: http://www.hs-stat.com/projects/WaveletComp/WaveletComp_guided_tour.pdf
Packaged: 2014-12-16 07:19:23 UTC; angi
NeedsCompilation: no
Repository: CRAN
Date/Publication: 2014-12-16 09:26:23

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Package season updated to version 0.3-5 with previous version 0.3-4 dated 2014-08-23

Title: Seasonal analysis of health data
Description: Routines for the seasonal analysis of health data, including regression models, time-stratified case-crossover, plotting functions and residual checks. Thanks to Yuming Guo for checking the case-crossover code.
Author: Adrian Barnett and Peter Baker
Maintainer: Adrian Barnett

Diff between season versions 0.3-4 dated 2014-08-23 and 0.3-5 dated 2014-12-16

 DESCRIPTION               |    8 ++++----
 MD5                       |   24 +++++++++++++-----------
 R/cosinor.R               |   30 ++++++++++++++++++++----------
 R/invyrfraction.R         |    5 +++++
 R/plot.Cosinor.R          |   11 ++++++++++-
 R/print.summary.Cosinor.R |   10 ++++++++--
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 14 files changed, 80 insertions(+), 38 deletions(-)

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Package rplexos updated to version 0.11 with previous version 0.10.0.1 dated 2014-10-20

Title: Read and Analyze PLEXOS Solutions from R
Description: Efficiently read and analyze PLEXOS solutions by converting them into SQLite databases that can be easily queried. It supports collation of solutions that may have been divided into different time partitions, as well as the comparison across different scenarios.
Author: Eduardo Ibanez [aut, cre], National Renewable Energy Laboratory [cph]
Maintainer: Eduardo Ibanez

Diff between rplexos versions 0.10.0.1 dated 2014-10-20 and 0.11 dated 2014-12-16

 DESCRIPTION            |   17 +-
 MD5                    |   45 +++----
 NAMESPACE              |   12 -
 R/auxiliary.R          |    9 +
 R/globalVariables.R    |    2 
 R/log_parser.R         |   44 +++----
 R/plexos_open.R        |   17 +-
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 vignettes/rplexos.Rmd  |    2 
 24 files changed, 348 insertions(+), 228 deletions(-)

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Package rotations updated to version 1.3 with previous version 1.2 dated 2014-04-07

Title: Tools for Working with Rotation Data
Description: Tools for working with rotational data, including simulation from the most commonly used distributions on SO(3), methods for different Bayes, mean and median type estimators for the central orientation of a sample, confidence/credible regions for the central orientation based on those estimators and a novel visualization technique for rotation data. Most recently, functions to identify potentially discordant (outlying) values have been added.
Author: Bryan Stanfill , Heike Hofmann , Ulrike Genschel
Maintainer: Bryan Stanfill

Diff between rotations versions 1.2 dated 2014-04-07 and 1.3 dated 2014-12-16

 DESCRIPTION                             |   28 
 LICENSE                                 |    2 
 MD5                                     |  161 +--
 NAMESPACE                               |  219 ++--
 NEWS                                    |  229 ++--
 R/RcppExports.R                         |  342 +++---
 R/bayes.R                               |  534 +++++-----
 R/distributions.R                       |  986 +++++++++----------
 R/estimators.R                          |  580 +++++------
 R/grid-search.R                         |  200 +--
 R/help.R                                |   20 
 R/kappa.R                               |  196 +--
 R/parameterizations.R                   | 1004 +++++++++----------
 R/plot.R                                | 1011 +++++++++----------
 R/preliminary.R                         | 1436 ++++++++++++++--------------
 R/primatives.R                          |  644 ++++++------
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 inst/doc/rotations-intro.pdf            |binary
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 man/Angular-distributions.Rd            |   40 
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 man/Cayley.Rd                           |  164 +--
 man/Fisher.Rd                           |  154 +--
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 man/weighted.mean.SO3.Rd                |  168 +--
 man/zhang.Rd                            |  122 +-
 src/CppBayesFunctions.cpp               |    1 
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 src/RcppExports.cpp                     |  146 ++
 src/ZhangMethod.cpp                     |    1 
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 tests/test-all.R                        |    2 
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 tests/testthat/test_metrics.R           |   24 
 vignettes/RJournal_edited.sty           |  670 ++++++-------
 vignettes/rotations-intro.Rnw           |  728 +++++++-------
 vignettes/stanfill-hofmann-genschel.bib |  733 +++++++-------
 84 files changed, 9688 insertions(+), 9350 deletions(-)

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New package networkD3 with initial version 0.1.1
Package: networkD3
Type: Package
Title: Tools for Creating D3 JavaScript Network Graphs from R
Description: Creates D3 JavaScript network, tree, dendrogram, and Sankey graphs from R.
Version: 0.1.1
Date: 2014-12-16
Author: Christopher Gandrud, J.J. Allaire, and B.W. Lewis
Maintainer: Christopher Gandrud
URL: http://github.com/christophergandrud/networkD3/
License: GPL (>= 3)
Depends: R (>= 3.0.0)
Imports: htmlwidgets (>= 0.3.2), plyr, rjson
Suggests: htmltools (>= 0.2.6), RCurl
Enhances: knitr, shiny
Packaged: 2014-12-16 06:52:00 UTC; christophergandrud
NeedsCompilation: no
Repository: CRAN
Date/Publication: 2014-12-16 08:22:39

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Package GrammR updated to version 1.0.1 with previous version 1.0.0 dated 2014-08-11

Title: Graphical Representation and Modeling of Metagenomic Reads
Description: Represents metagenomic samples on the Euclidean space to examine similarity amongst samples by studying clusters in the model. Given the matrix of metagenomic counts for samples, this package (1) quantifies dissimilarity between samples using Kendall's tau-distance, (2) constructs multidimensional models of different dimension, and (3) plots the models for visualization and comparison.
Author: Deepak N. Ayyala, Shili Lin, Department of Statistics, The Ohio State University, Columbus, Ohio, USA.
Maintainer: Deepak Nag Ayyala

Diff between GrammR versions 1.0.0 dated 2014-08-11 and 1.0.1 dated 2014-12-16

 DESCRIPTION          |    8 ++++----
 MD5                  |   24 ++++++++++++------------
 R/GrammRServ.R       |    4 +++-
 R/Make2DPlots.R      |    8 ++------
 R/Make3DPlots.R      |   15 ++-------------
 R/Make4DPlots.R      |   33 +++------------------------------
 R/MakePlots2D.R      |   11 ++---------
 R/MakePlots3D.R      |   17 ++---------------
 R/MakePlots4D.R      |   43 ++-----------------------------------------
 R/OptimClusts.R      |   19 +++++++++++++------
 man/MCError.Rd       |    6 +++++-
 man/MakeGUIPlots.Rd  |   18 +++++++++++++++++-
 man/MakeServPlots.Rd |   19 ++++++++++++++++++-
 13 files changed, 85 insertions(+), 140 deletions(-)

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New package BinNonNor with initial version 1.0
Package: BinNonNor
Type: Package
Title: Data Generation with Binary and Continuous Non-normal Components
Version: 1.0
Date: 2014-12-15
Author: Gul Inan, Hakan Demirtas
Maintainer: Gul Inan
Description: Generation of multiple binary and continuous non-normal variables simultaneously given the marginal characteristics and association structure based on the methodology proposed by Demirtas et al. (2012).
License: GPL (>= 2)
Depends: BB, corpcor, mvtnorm, Matrix
Packaged: 2014-12-15 19:20:02 UTC; arcelik
NeedsCompilation: no
Repository: CRAN
Date/Publication: 2014-12-16 08:17:47

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