Thu, 30 Oct 2014

Package surveillance updated to version 1.8-1 with previous version 1.8-0 dated 2014-06-17

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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Wed, 29 Oct 2014

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

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

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

 DESCRIPTION |    8 ++++----
 MD5         |    4 ++--
 R/TPL.R     |    1 +
 3 files changed, 7 insertions(+), 6 deletions(-)

More information about Taxonstand at CRAN
Permanent link

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

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

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

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More information about alm at CRAN
Permanent link

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

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

Diff between R6 versions 2.0 dated 2014-08-19 and 2.0.1 dated 2014-10-29

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More information about R6 at CRAN
Permanent link

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

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

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

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More information about qtl at CRAN
Permanent link

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

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

Diff between isdals versions 2.0-1 dated 2013-10-01 and 2.0-4 dated 2014-10-29

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

Title: Machine Learning in R.
Description: Interface to a large number of classification and regression techniques, including machine-readable parameter descriptions. There is also an experimental extension for survival analysis, clustering and general, example-specific cost-sensitive learning. Generic resampling, including cross-validation, bootstrapping and subsampling. Hyperparameter tuning with modern optimization techniques, for single- and multi-objective problems. Filter and wrapper methods for feature selection. Extension of basic learners with additional operations common in machine learning, also allowing for easy nested resampling. Most operations can be parallelized.
Author: Bernd Bischl [aut, cre], Michel Lang [aut], Jakob Richter [aut], Jakob Bossek [aut], Leonard Judt [aut], Tobias Kuehn [aut], Erich Studerus [aut], Lars Kotthoff [aut]
Maintainer: Bernd Bischl

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Package deSolve updated to version 1.11 with previous version 1.10-9 dated 2014-06-25

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

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

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Tue, 28 Oct 2014

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

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

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More information about TSclust at CRAN
Permanent link

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

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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

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Permanent link

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

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

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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

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More information about rgl at CRAN
Permanent link

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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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

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Permanent link

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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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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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

Diff between pander versions 0.3.8 dated 2013-09-12 and 0.5.0 dated 2014-10-28

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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

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

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Permanent link

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

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

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

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Mon, 27 Oct 2014

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

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

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

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

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

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

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

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Package rjags updated to version 3-14 with previous version 3-13 dated 2014-03-06

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

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Package rangeMapper updated to version 0.2-8 with previous version 0.2-6 dated 2014-02-07

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

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Package DALY updated to version 1.4.0 with previous version 1.3.0 dated 2014-05-10

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

Title: Tools for Harnessing MLBAM Gameday data and Visualizing PITCHf/x
Description: With pitchRx, one can easily obtain Major League Baseball Advanced Media's Gameday data (as well as store it in a remote database). The Gameday website hosts a wealth of data in XML format, but perhaps most interesting is PITCHf/x. Among other things, PITCHf/x data can be used to recreate a baseball's flight path from a pitcher's hand to home plate. With pitchRx, one can easily create animations and interactive 3D scatterplots of the baseball's flight path. PITCHf/x data is also commonly used to generate a static plot of baseball locations at the moment they cross home plate. These plots, sometimes called strike-zone plots, can also refer to a plot of event probabilities over the same region. pitchRx provides an easy and robust way to generate strike-zone plots using the ggplot2 package.
Author: Carson Sievert
Maintainer: Carson Sievert

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Sun, 26 Oct 2014

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

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

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

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

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

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

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Sat, 25 Oct 2014

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

Title: Visualization and Imputation of Missing Values
Description: This package introduces new tools for the visualization of missing and/or imputed values, which can be used for exploring the data and the structure of the missing and/or imputed values. Depending on this structure of the missing values, the corresponding methods may help to identify the mechanism generating the missing values and allows to explore the data including missing values. In addition, the quality of imputation can be visually explored using various univariate, bivariate, multiple and multivariate plot methods. A graphical user interface available in the separate package VIMGUI allows an easy handling of the implemented plot methods.
Author: Matthias Templ, Andreas Alfons, Alexander Kowarik, Bernd Prantner
Maintainer: Matthias Templ

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

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

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

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

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

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

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

Diff between FSelector versions 0.19 dated 2013-02-28 and 0.20 dated 2014-10-25

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

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

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

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

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

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

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

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

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

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

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

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Fri, 24 Oct 2014

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

 DESCRIPTION                        |   13 +++++++------
 MD5                                |   12 ++++++------
 NAMESPACE                          |    2 +-
 R/replicationInterval.R            |   35 +++++++++++++++++++++++------------
 man/replicationInterval-package.Rd |   16 ++++++++--------
 man/ri.d.Rd                        |    8 ++++++--
 man/ri.r.Rd                        |    2 +-
 7 files changed, 52 insertions(+), 36 deletions(-)

More information about replicationInterval at CRAN
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Package qmethod updated to version 1.2 with previous version 1.1 dated 2014-06-23

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

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

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

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

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

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More information about MAINT.Data at CRAN
Permanent link

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

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

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

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More information about polyCub at CRAN
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Package spatstat updated to version 1.39-1 with previous version 1.39-0 dated 2014-10-23

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

Diff between spatstat versions 1.39-0 dated 2014-10-23 and 1.39-1 dated 2014-10-24

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More information about spatstat at CRAN
Permanent link

Package matrixpls updated to version 0.4.0 with previous version 0.3.0 dated 2014-04-30

Title: Matrix-based Partial Least Squares estimation
Description: matrixpls is implements Partial Least Squares Path Modeling algorithm and related algorithms. The algorithm implementations aim for computational efficiency using matrix algebra and covariance data. The package is designed toward Monte Carlo simulations and includes functions to perform simple Monte Carlo simulations.
Author: Mikko Rönkkö [aut, cre]
Maintainer: Mikko Rönkkö

Diff between matrixpls versions 0.3.0 dated 2014-04-30 and 0.4.0 dated 2014-10-24

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Package WRS2 updated to version 0.2-0 with previous version 0.1-0 dated 2014-10-03

Title: Wilcox Robust Estimation and Testing.
Description: A user-friendly version of Wilcox' robust statistics functions (WRS package on GitHub). It implements robust tests for ANOVA and ANCOVA as described in R. Wilcox (2012) 'Introduction to Robust Estimation and Hypothesis Testing'.
Author: Patrick Mair [cre, aut], Felix Schoenbrodt [aut], Rand Wilcox [aut]
Maintainer: Patrick Mair

Diff between WRS2 versions 0.1-0 dated 2014-10-03 and 0.2-0 dated 2014-10-24

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Permanent link

Package spocc updated to version 0.2.2 with previous version 0.2.0 dated 2014-08-06

Title: R Interface to Many Species Occurrence Data Sources.
Description: A programmatic interface to many species occurrence data sources, including GBIF, USGS's BISON, iNaturalist, Berkeley Ecoinformatics Engine eBird, AntWeb, and more as they sources become easily available.
Author: Scott Chamberlain [aut, cre], Karthik Ram [aut], Ted Hart [aut]
Maintainer: Scott Chamberlain

Diff between spocc versions 0.2.0 dated 2014-08-06 and 0.2.2 dated 2014-10-24

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More information about spocc at CRAN
Permanent link

Thu, 23 Oct 2014

Package splitstackshape updated to version 1.4.2 with previous version 1.4.0 dated 2014-10-13

Title: Stack and Reshape Datasets After Splitting Concatenated Values
Description: Online data collection tools like Google Forms often export multiple-response questions with data concatenated in cells. The concat.split (cSplit) family of functions splits such data into separate cells. The package also includes functions to stack groups of columns and to reshape wide data, even when the data are "unbalanced"---something which reshape (from base R) does not handle, and which melt and dcast from reshape2 do not easily handle.
Author: Ananda Mahto
Maintainer: Ananda Mahto

Diff between splitstackshape versions 1.4.0 dated 2014-10-13 and 1.4.2 dated 2014-10-23

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More information about splitstackshape at CRAN
Permanent link

Package rtkpp updated to version 0.8.3 with previous version 0.8.2 dated 2014-10-21

Title: STK++ Integration To R Using Rcpp
Description: STK++ (http://www.stkpp.org) is a collection of C++ classes for statistics, clustering, linear algebra, arrays (with an Eigen-like API), regression, dimension reduction, etc. The integration of the library to R is using Rcpp. Some functionalities of the Clustering project provided by the library are available in the R environment as R functions. The rtkpp package includes the header files from the STK++ library (currently version 0.8.2). Thus users do not need to install STK++ itself in order to use it. STK++ is licensed under the GNU LGPL version 2 or later. rtkpp (the stkpp integration into R) is licensed under the GNU GPL version 2 or later.
Author: Serge Iovleff [aut, cre], Vincent Kubicki [ctb], Quentin Grimonprez [ctb], Parmeet Bhatia [ctb]
Maintainer: Serge Iovleff

Diff between rtkpp versions 0.8.2 dated 2014-10-21 and 0.8.3 dated 2014-10-23

 src/makefile                                                                                                          |    4 
 tmp/cranberry21822d5a0c3b/rtkpp-0.8.3/rtkpp/DESCRIPTION                                                               |   11 
 tmp/cranberry21822d5a0c3b/rtkpp-0.8.3/rtkpp/MD5                                                                       |   82 ++--
 tmp/cranberry21822d5a0c3b/rtkpp-0.8.3/rtkpp/R/ClusterCategorical.R                                                    |   10 
 tmp/cranberry21822d5a0c3b/rtkpp-0.8.3/rtkpp/R/ClusterDiagGaussian.R                                                   |   61 ++-
 tmp/cranberry21822d5a0c3b/rtkpp-0.8.3/rtkpp/R/ClusterGamma.R                                                          |    7 
 tmp/cranberry21822d5a0c3b/rtkpp-0.8.3/rtkpp/R/ClusterModelNames.R                                                     |   12 
 tmp/cranberry21822d5a0c3b/rtkpp-0.8.3/rtkpp/R/IClusterModel.R                                                         |    4 
 tmp/cranberry21822d5a0c3b/rtkpp-0.8.3/rtkpp/cleanup                                                                   |    2 
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 tmp/cranberry21822d5a0c3b/rtkpp-0.8.3/rtkpp/inst/makefile                                                             |   14 
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 tmp/cranberry21822d5a0c3b/rtkpp-0.8.3/rtkpp/inst/projects/Sdk/src/makefile                                            |    4 
 tmp/cranberry21822d5a0c3b/rtkpp-0.8.3/rtkpp/man/clusterCategorical.Rd                                                 |   12 
 tmp/cranberry21822d5a0c3b/rtkpp-0.8.3/rtkpp/man/clusterDiagGaussian.Rd                                                |    9 
 tmp/cranberry21822d5a0c3b/rtkpp-0.8.3/rtkpp/man/clusterGamma.Rd                                                       |    7 
 tmp/cranberry21822d5a0c3b/rtkpp-0.8.3/rtkpp/man/diagGaussianNames.Rd                                                  |   38 --
 tmp/cranberry21822d5a0c3b/rtkpp-0.8.3/rtkpp/man/gammaNames.Rd                                                         |   36 --
 tmp/cranberry21822d5a0c3b/rtkpp-0.8.3/rtkpp/src/Makevars                                                              |   22 -
 tmp/cranberry21822d5a0c3b/rtkpp-0.8.3/rtkpp/src/STK_ClusterFacade.cpp                                                 |    2 
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 tmp/cranberry21822d5a0c3b/rtkpp-0.8.3/rtkpp/src/STK_RDataHandler.cpp                                                  |    2 
 tmp/cranberry21822d5a0c3b/rtkpp-0.8.3/rtkpp/src/clusterMixture.cpp                                                    |    2 
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More information about rtkpp at CRAN
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Package leafletR updated to version 0.3-1 with previous version 0.3-0 dated 2014-09-12

Title: Interactive Web-Maps Based on the Leaflet JavaScript Library
Description: Display your spatial data on interactive web-maps using the open-source JavaScript library Leaflet. The package provides basic web-mapping functionality to combine vector data and online map tiles from different sources.
Author: Christian Graul, with contributions from Francois Guillem
Maintainer: Christian Graul

Diff between leafletR versions 0.3-0 dated 2014-09-12 and 0.3-1 dated 2014-10-23

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Package sgof updated to version 2.1.1 with previous version 2.1 dated 2014-07-11

Title: Multiple hypothesis testing
Description: This package implements six different methods for multiple testing problems. The SGoF-type methods and the BH and BY false discovery rate controlling procedures.
Author: Irene Castro Conde and Jacobo de Una Alvarez.
Maintainer: Irene Castro Conde

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Package sld updated to version 0.3 with previous version 0.2.1 dated 2014-08-15

Title: Estimation and Use of the Quantile-Based Skew Logistic Distribution
Description: The skew logistic distribution is a quantile-defined generalisation of the logistic distribution (van Staden and King 2015). Provides random numbers, quantiles, probabilities, densities and density quantiles for the distribution. It provides Quantile-Quantile plots and method of L-Moments estimation (including asymptotic standard errors) for the distribution.
Author: Robert King , Paul van Staden
Maintainer: Robert King

Diff between sld versions 0.2.1 dated 2014-08-15 and 0.3 dated 2014-10-23

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Package CAMAN updated to version 0.72 with previous version 0.71 dated 2014-08-09

Title: Finite Mixture Models and meta-analysis tools - based on C.A.MAN
Description: Tools for the analysis of finite semiparametric mixtures. These are useful when data is heterogeneous, e.g. in pharmacokinetics or meta-analysis. The NPMLE and VEM algorithms (flexible support size) and EM algorithms (fixed support size) are provided for univariate and bivariate data
Author: Peter Schlattmann , Johannes Hoehne, Maryna Verba
Maintainer: Philipp Doebler

Diff between CAMAN versions 0.71 dated 2014-08-09 and 0.72 dated 2014-10-23

 DESCRIPTION |   14 +++++++-------
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Permanent link

Package IsingFit updated to version 0.3.0 with previous version 0.2.0 dated 2014-04-23

Title: Fitting Ising models using the eLasso method
Description: This network estimation procedure eLasso, which is based on the Ising model, combines l1-regularized logistic regression with model selection based on the Extended Bayesian Information Criterion (EBIC). EBIC is a fit measure that identifies relevant relationships between variables. The resulting network consists of variables as nodes and relevant relationships as edges. Can deal with binary data.
Author: Claudia van Borkulo, Sacha Epskamp, with contributions from Alexander Robitzsch
Maintainer: Claudia van Borkulo

Diff between IsingFit versions 0.2.0 dated 2014-04-23 and 0.3.0 dated 2014-10-23

 DESCRIPTION             |    8 -
 MD5                     |    8 -
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 man/isingfit-package.rd |    6 -
 man/isingfit.rd         |   10 +-
 5 files changed, 131 insertions(+), 107 deletions(-)

More information about IsingFit at CRAN
Permanent link

Package spatstat updated to version 1.39-0 with previous version 1.38-1 dated 2014-08-28

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

Diff between spatstat versions 1.38-1 dated 2014-08-28 and 1.39-0 dated 2014-10-23

 spatstat-1.38-1/spatstat/R/morishita.R              |only
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More information about spatstat at CRAN
Permanent link

Package MRH updated to version 1.1 with previous version 1.0 dated 2014-10-17

Title: Multi-Resolution Estimation of the Hazard Rate
Description: Used on survival data to jointly estimate the hazard rate and the effects of covariates on failure times.
Author: Yolanda Hagar, Yuanting Chen, Vanja Dukic
Maintainer: Yolanda Hagar

Diff between MRH versions 1.0 dated 2014-10-17 and 1.1 dated 2014-10-23

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More information about MRH at CRAN
Permanent link

Package JADE updated to version 1.9-92 with previous version 1.9-91 dated 2013-11-11

Title: JADE and other BSS methods as well as some BSS performance criteria
Description: The package ports JF Cardoso's JADE algorithm as well as his function for joint diagonalization. The package also includes several other blind source separation (BSS) methods, like AMUSE and SOBI, as well as some criteria for performance evaluation of BSS algorithms.
Author: Klaus Nordhausen, Jean-Francois Cardoso, Jari Miettinen, Hannu Oja, Esa Ollila, Sara Taskinen
Maintainer: Klaus Nordhausen

Diff between JADE versions 1.9-91 dated 2013-11-11 and 1.9-92 dated 2014-10-23

 DESCRIPTION         |   10 +++++-----
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 5 files changed, 19 insertions(+), 12 deletions(-)

More information about JADE at CRAN
Permanent link

Package httpuv updated to version 1.3.2 with previous version 1.3.0 dated 2014-04-04

Title: HTTP and WebSocket server library
Description: httpuv provides low-level socket and protocol support for handling HTTP and WebSocket requests directly from within R. It is primarily intended as a building block for other packages, rather than making it particularly easy to create complete web applications using httpuv alone. httpuv is built on top of the libuv and http-parser C libraries, both of which were developed by Joyent, Inc. (See LICENSE file for libuv and http-parser license information.)
Author: RStudio, Inc.
Maintainer: Joe Cheng

Diff between httpuv versions 1.3.0 dated 2014-04-04 and 1.3.2 dated 2014-10-23

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Package highr updated to version 0.4 with previous version 0.3 dated 2013-10-26

Title: Syntax highlighting for R
Description: This package provides syntax highlighting for R source code. Currently it supports LaTeX and HTML output. Source code of other languages can be supported via Andre Simon's Highlight package.
Author: Christopher Gandrud [ctb], Qiang Li [ctb], Yixuan Qiu [aut], Yihui Xie [aut, cre]
Maintainer: Yihui Xie

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Wed, 22 Oct 2014

Package RAM updated to version 1.1.0 with previous version 1.0.0 dated 2014-08-21

Title: R for Amplicon-based Metagenomics
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.
Author: Wen Chen and Joshua Simpson
Maintainer: Wen Chen

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Package MixGHD updated to version 1.1 with previous version 1.0 dated 2014-07-22

Title: Model based clustering, classification and discriminant analysis using the mixture of generalized hyperbolic distributions.
Description: Carries out model-based clustering, classification and discriminant analysis using four different models. The models are all based on the generalized hyperbolic distribution.The first model MGHD is the classical mixture of generalized hyperbolic distributions. The MGHFA is the mixture of generalized hyperbolic factor analyzers for high dimensional data sets. The MSGHD, mixture of multiple scaled generalized hyperbolic distributions. The MCGHD, mixture of coalesced generalized hyperbolic distributions is a new more flexible model.
Author: Cristina Tortora, Ryan P. Browne, Brian C. Franczak and Paul D. McNicholas.
Maintainer: Cristina Tortora

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Package JMdesign updated to version 1.1 with previous version 1.0 dated 2014-10-20

Title: Joint Modeling of Longitudinal and Survival Data - Power Calculation
Description: Performs power calculations for joint modeling of longitudinal and survival data with k-th order trajectories when the variance-covariance matrix, Sigma_theta, is unknown.
Author: Emil A. Cornea, Liddy M. Chen, Bahjat F. Qaqish, Haitao Chu, and Joseph G. Ibrahim
Maintainer: Shannon T. Holloway

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Package FLSSS updated to version 3.0 with previous version 2.0.1 dated 2014-10-01

Title: Fixed Size Subset Sum Solution
Description: Solve an approximate Subset Sum Problem by introducing a recursive compression algorithm
Author: Charlie Wusuo Liu
Maintainer: Charlie Wusuo Liu

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Package confidence updated to version 1.1-0 with previous version 1.0-0 dated 2014-09-19

Title: Confidence Estimation of Environmental State Classifications
Description: Functions for estimating and reporting multiyear averages and corresponding confidence intervals and distributions. A potential use case is reporting the chemical and ecological status of surface waters according to the European Water Framework Directive.
Author: Willem M. G. M. van Loon [aut, cph], Dennis J. J. Walvoort [aut, cre]
Maintainer: Dennis J. J. Walvoort

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Package timeordered updated to version 0.9.7 with previous version 0.9.6 dated 2014-03-10

Title: Time-ordered and time-aggregated network analyses
Description: Methods for incorporating time into network analysis. Construction of time-ordered networks (temporal graphs). Shortest-time and shortest-path-length analyses. Resource spread calculations. Data resampling and rarefaction for null model construction. Reduction to time-aggregated networks with variable window sizes; application of common descriptive statistics to these networks. Vector clock latencies. Plotting functionalities.
Author: Benjamin Blonder
Maintainer: Benjamin Blonder

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Package synbreed updated to version 0.10-3 with previous version 0.10-2 dated 2014-09-10

Title: Framework for the analysis of genomic prediction data using R
Description: The package was developed within the Synbreed project for synergistic plant and animal breeding (www.synbreed.tum.de). It contains a collection of functions required for genomic prediction in both plant and animal breeding. This covers data processing, data visualization and analysis. All functions are embedded within the framework of a single, unified data object. The implementation is flexible with respect to a wide range of data formats. This research was funded by the German Federal Ministry of Education and Research (BMBF) within the AgroClustEr Synbreed - Synergistic plant and animal breeding (FKZ 0315528A).
Author: Valentin Wimmer, Hans-Juergen Auinger, Theresa Albrecht, Chris-Carolin Schoen with contributions by Larry Schaeffer, Malena Erbe, Ulrike Ober, Christian Reimer, Yvonne Badke and Peter VandeHaar
Maintainer: Valentin Wimmer

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Package speedglm updated to version 0.2-1.0 with previous version 0.2 dated 2013-07-24

Title: Fitting Linear and Generalized Linear Models to large data sets.
Description: Fitting LMs and GLMs to large data sets by updating algorithms.
Author: Marco ENEA
Maintainer: Marco ENEA

Diff between speedglm versions 0.2 dated 2013-07-24 and 0.2-1.0 dated 2014-10-22

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Package rpf updated to version 0.40 with previous version 0.39 dated 2014-09-22

Title: Response Probability Functions
Description: The purpose of this package is to factor out logic and math common to Item Factor Analysis fitting, diagnostics, and analysis. It is envisioned as core support code suitable for more specialized IRT packages to build upon. Complete access to optimized C functions are made available with R_RegisterCCallable.
Author: Joshua Pritikin [cre, aut], Jonathan Weeks [ctb], Li Cai [ctb], Carrie Houts [ctb], Phil Chalmers [ctb]
Maintainer: Joshua Pritikin

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