Tue, 28 Oct 2014

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

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

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

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

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

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

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

 DESCRIPTION        |   15 ++--
 MD5                |   17 +++-
 NAMESPACE          |    8 +-
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 R/robustRegH.R     |  180 ++++++++++++++++++++++++++--------------------------
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 10 files changed, 210 insertions(+), 199 deletions(-)

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

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

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

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

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

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

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

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

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 FAOSTAT-1.9/FAOSTAT/R/FAOcheck.R                 |   94 ++++++++---
 FAOSTAT-1.9/FAOSTAT/R/FAOsearch.R                |    4 
 FAOSTAT-1.9/FAOSTAT/R/chConstruct.R              |   66 +++----
 FAOSTAT-1.9/FAOSTAT/R/chgr.R                     |   90 +++++-----
 FAOSTAT-1.9/FAOSTAT/R/constructSYB.R             |  192 +++++++++++------------
 FAOSTAT-1.9/FAOSTAT/R/fillCountryCode.R          |   68 ++++----
 FAOSTAT-1.9/FAOSTAT/R/geogr.R                    |   80 ++++-----
 FAOSTAT-1.9/FAOSTAT/R/getFAO.R                   |  106 ++++++++----
 FAOSTAT-1.9/FAOSTAT/R/getFAOtoSYB.R              |   13 +
 FAOSTAT-1.9/FAOSTAT/R/getWDI.R                   |  110 ++++++-------
 FAOSTAT-1.9/FAOSTAT/R/getWDImetaData.R           |  150 ++++++++---------
 FAOSTAT-1.9/FAOSTAT/R/getWDItoSYB.R              |    2 
 FAOSTAT-1.9/FAOSTAT/R/grConstruct.R              |  128 +++++++--------
 FAOSTAT-1.9/FAOSTAT/R/indConstruct.R             |   84 +++++-----
 FAOSTAT-1.9/FAOSTAT/R/lsgr.R                     |  148 ++++++++---------
 FAOSTAT-1.9/FAOSTAT/R/mergeSYB.R                 |   84 +++++-----
 FAOSTAT-1.9/FAOSTAT/R/overlap.R                  |   37 +++-
 FAOSTAT-1.9/FAOSTAT/R/printLab.R                 |   58 +++---
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 FAOSTAT-1.9/FAOSTAT/demo/00Index                 |    2 
 FAOSTAT-1.9/FAOSTAT/demo/FAOSTATdemo.R           |  130 +++++++++++++--
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 FAOSTAT-1.9/FAOSTAT/man/FAOcountryProfile.Rd     |   20 +-
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 FAOSTAT-1.9/FAOSTAT/man/FAOregionProfile.Rd      |   21 +-
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 FAOSTAT-1.9/FAOSTAT/man/ebind.Rd                 |   44 ++---
 FAOSTAT-1.9/FAOSTAT/man/fillCountryCode.Rd       |   40 ++--
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 FAOSTAT-1.9/FAOSTAT/man/getFAO.Rd                |  112 ++++++-------
 FAOSTAT-1.9/FAOSTAT/man/getFAOtoSYB.Rd           |  116 ++++++-------
 FAOSTAT-1.9/FAOSTAT/man/getWDI.Rd                |   86 +++++-----
 FAOSTAT-1.9/FAOSTAT/man/getWDImetaData.Rd        |   55 +++---
 FAOSTAT-1.9/FAOSTAT/man/getWDItoSYB.Rd           |  106 ++++++------
 FAOSTAT-1.9/FAOSTAT/man/grConstruct.Rd           |   76 ++++-----
 FAOSTAT-1.9/FAOSTAT/man/indConstruct.Rd          |   61 +++----
 FAOSTAT-1.9/FAOSTAT/man/lsgr.Rd                  |   86 +++++-----
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 FAOSTAT-1.9/FAOSTAT/man/overlap.Rd               |   49 +++--
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 77 files changed, 1964 insertions(+), 1844 deletions(-)

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

More information about CateSelection at CRAN
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Package rgl updated to version 0.95.1157 with previous version 0.94.1143 dated 2014-09-30

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

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

 rgl-0.94.1143/rgl/src/QuadSet.cpp         |only
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 rgl-0.95.1157/rgl/R/obj.R                 |  618 ++++++++++++++--------------
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 rgl-0.95.1157/rgl/R/subscenes.R           |    2 
 rgl-0.95.1157/rgl/R/turn3d.R              |  122 ++---
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 rgl-0.95.1157/rgl/src/Texture.cpp         |  225 +++++-----
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 59 files changed, 2883 insertions(+), 2849 deletions(-)

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Package knitcitations updated to version 1.0.4 with previous version 1.0-1 dated 2014-07-12

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

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

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

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Package hht updated to version 2.1.1 with previous version 2.1.0 dated 2014-09-23

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

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

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

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Package timeSeries updated to version 3011.98 with previous version 3010.97 dated 2013-05-01

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

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

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

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

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

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More information about etasFLP at CRAN
Permanent link

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

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

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

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

More information about settings at CRAN
Permanent link

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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Package energy updated to version 1.6.2 with previous version 1.6.1 dated 2014-02-23

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

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Package Ecfun updated to version 0.1-2 with previous version 0.1-0 dated 2014-04-08

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

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

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

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

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

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

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

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