Tue, 25 Nov 2014

New package lucid with initial version 1.0
Package: lucid
Version: 1.0
Date: 2014-11-24
Title: Lucid Printing of Floating Point Numbers
Author: Kevin Wright
Maintainer: Kevin Wright
Description: Print vectors (and data frames) of floating point numbers using a non-scientific format optimized for human readers. Vectors of numbers are rounded using significant digits, aligned at the decimal point, and all zeros trailing the decimal point are dropped.
LazyData: yes
License: GPL-2
URL: https://github.com/kwstat/lucid
BugReports: https://github.com/kwstat/lucid/issues
VignetteBuilder: knitr
Imports: nlme
Suggests: knitr, lattice, lme4
Packaged: 2014-11-25 22:00:33 UTC; wrightkevi
NeedsCompilation: no
Repository: CRAN
Date/Publication: 2014-11-26 00:52:34

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New package GMDH with initial version 1.0
Package: GMDH
Type: Package
Title: Predicting and Forecasting Time Series via GMDH-Type Neural Network Algorithms
Version: 1.0
Date: 2014-11-25
Depends: MASS, stats
Author: Osman Dag, Ceylan Yozgatligil
Maintainer: Osman Dag
Description: Group method of data handling (GMDH) - type neural network algorithm is the heuristic self-organization method for modelling the complex systems. In this package, GMDH-type neural network algorithms are applied to predict and forecast a univariate time series.
License: GPL (>= 2)
Packaged: 2014-11-25 19:14:40 UTC; osmndg
NeedsCompilation: no
Repository: CRAN
Date/Publication: 2014-11-26 00:48:49

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New package EnsembleCV with initial version 0.7
Package: EnsembleCV
Type: Package
Title: Extensible Package for Cross-Validation-Based Integration of Base Learners
Version: 0.7
Date: 2014-11-17
Author: Mansour T.A. Sharabiani, Alireza S. Mahani
Maintainer: Alireza S. Mahani
Description: This package extends the base classes and methods of EnsembleBase package for cross-validation-based integration of base learners. Default implementation calculates average of repeated CV errors, and selects the base learner / configuration with minimum average error. The package takes advantage of the file method provided in EnsembleBase package for writing estimation objects to disk in order to circumvent RAM bottleneck. Special save and load methods are provided to allow estimation objects to be saved to permanent files on disk, and to be loaded again into temporary files in a later R session. The package can be extended, e.g. by adding variants of the current implementation.
License: GPL (>= 2)
Depends: EnsembleBase
Imports: parallel,methods
Packaged: 2014-11-25 21:39:34 UTC; amahani
NeedsCompilation: no
Repository: CRAN
Date/Publication: 2014-11-26 00:59:47

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Package SMR updated to version 2.0.1 with previous version 2.0 dated 2014-10-16

Title: Externally Studentized Midrange Distribution
Description: Computes the studentized midrange distribution (pdf, cdf and quantile) and generates random numbers
Author: Ben Deivide de Oliveira Batista, Daniel Furtado Ferreira
Maintainer: Daniel Furtado Ferreira

Diff between SMR versions 2.0 dated 2014-10-16 and 2.0.1 dated 2014-11-25

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New package gridGraphics with initial version 0.1-1
Package: gridGraphics
Title: Redraw Base Graphics Using grid Graphics
Version: 0.1-1
Authors@R: person("Paul", "Murrell", role = c("cre", "aut"), email = "paul@stat.auckland.ac.nz")
Description: Functions to convert a page of plots drawn with the graphics package into identical output drawn with the grid package. The result looks like the original graphics-based plot, but consists of grid grobs and viewports that can then be manipulated with grid functions (e.g., edit grobs and revisit viewports).
Depends: grid, graphics
Suggests: KernSmooth
SystemRequirements: ImageMagick (for testing)
License: GPL (>= 2)
URL: https://github.com/pmur002/gridgraphics
Packaged: 2014-11-25 20:01:49 UTC; EC\pmur002
Author: Paul Murrell [cre, aut]
Maintainer: Paul Murrell
NeedsCompilation: no
Repository: CRAN
Date/Publication: 2014-11-25 22:24:13

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New package KODAMA with initial version 0.0.1
Package: KODAMA
Version: 0.0.1
Date: 2013-11-20
Author: Stefano Cacciatore, Claudio Luchinat, Leonardo Tenori
Maintainer: Stefano Cacciatore
Title: Knowledge discovery by accuracy maximization
Description: KODAMA (KnOwledge Discovery by Accuracy MAximization) is an unsupervised and semisupervised learning algorithm that performs feature extraction from noisy and high-dimensional data.
Depends: R (>= 2.10.0),e1071,plsgenomics,class
Suggests: rgl,
SuggestsNote: No suggestions
License: GPL (>= 2)
Packaged: 2014-11-25 15:41:39 UTC; Stefano
NeedsCompilation: no
Repository: CRAN
Date/Publication: 2014-11-25 18:05:43

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New package empiricalFDR.DESeq2 with initial version 1.0
Package: empiricalFDR.DESeq2
Type: Package
Title: Simulation-based False Discovery Rate in RNA-seq
Version: 1.0
Date: 2014-11-25
Author: Mikhail V. Matz
Maintainer: Mikhail V. Matz
Description: Auxiliary functions for the DESeq2 package to simulate read counts according to the null hypothesis (i.e., with empirical sample size factors, per-gene total counts and dispersions, but without effects of predictor variables) and to compute the empirical false discovery rate.
License: GPL-3
Depends: DESeq2,GenomicRanges
Packaged: 2014-11-25 15:48:11 UTC; c-monster
NeedsCompilation: no
Repository: CRAN
Date/Publication: 2014-11-25 18:03:34

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Package synbreed updated to version 0.10-5 with previous version 0.10-4 dated 2014-11-11

Title: Framework for the analysis of genomic prediction data using R
Description: The package 'synbreed' 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

Diff between synbreed versions 0.10-4 dated 2014-11-11 and 0.10-5 dated 2014-11-25

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Package redcapAPI updated to version 1.1 with previous version 1.0.1 dated 2014-10-20

Title: R interface to REDCap
Description: Access data stored in REDCap databases using the Application Programming Interface (API). REDCap (Research Electronic Data CAPture) is a web application for building and managing online surveys and databases developed at Vanderbilt University. The API allows users to access data and project meta data (such as the data dictionary) from the web programmatically. The redcapAPI package facilitates the process of accessing data with options to prepare an analysis-ready data set consistent with the definitions in a database's data dictionary.
Author: Benjamin Nutter. Initiated by Jeffrey Horner and Will Gray with contributions from Jeremy Stephens, and Will Beasley
Maintainer: Benjamin Nutter

Diff between redcapAPI versions 1.0.1 dated 2014-10-20 and 1.1 dated 2014-11-25

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Package mistral updated to version 1.1-1 with previous version 1.1-0 dated 2014-02-15

Title: Methods in Structural Reliability
Description: Various reliability analysis methods for: 1) computing failure probability (probability that the output of a numerical model exceeds a threshold); 2) computing the size of a sample to estimate a quantile with a confidence level.
Author: Nicolas BOUSQUET, Gilles DEFAUX, Bertrand IOOSS, Vincent MOUTOUSSAMY, Clement WALTER
Maintainer: Bertrand Iooss

Diff between mistral versions 1.1-0 dated 2014-02-15 and 1.1-1 dated 2014-11-25

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New package maboost with initial version 1.0-0
Package: maboost
Version: 1.0-0
Date: 2014-11-01
Title: Binary and Multiclass Boosting Algorithms
Author: Tofigh Naghibi
Depends: R(>= 2.10),rpart,C50
Description: Performs binary and multiclass boosting in maximum-margin, sparse, smooth and normal settings as described in "A Boosting Framework on Grounds of Online Learning" by T. Naghibi and B. Pfister, (2014). For further information regarding the algorithms, please refer to http://arxiv.org/abs/1409.7202
Maintainer: Tofigh Naghibi
License: GPL (>= 2)
Packaged: 2014-11-25 15:05:38 UTC; tofighn
Repository: CRAN
Date/Publication: 2014-11-25 17:03:41
Collate: 'maboost-package.r' 'maboost.R' 'maboost.default.R' 'maboost.formula.R' 'maboost.machine.bin.R' 'maboost.machine.multi.R' 'predict.maboost.R' 'print.maboost.R' 'projsplx.R' 'projsplx_k.R' 'summary.maboost.R' 'update.maboost.R' 'varplot.maboost.R'
NeedsCompilation: no

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Package effects updated to version 3.0-2 with previous version 3.0-1 dated 2014-08-14

Title: Effect Displays for Linear, Generalized Linear, Multinomial-Logit, Proportional-Odds Logit Models and Mixed-Effects Models
Description: Graphical and tabular effect displays, e.g., of interactions, for various statistical models with linear predictors.
Author: John Fox [aut, cre], Sanford Weisberg [aut], Michael Friendly [aut], Jangman Hong [aut], Robert Andersen [ctb], David Firth [ctb], Steve Taylor [ctb]
Maintainer: John Fox

Diff between effects versions 3.0-1 dated 2014-08-14 and 3.0-2 dated 2014-11-25

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Package dslice updated to version 1.1.4 with previous version 1.1.3 dated 2014-11-24

Title: Dynamic slicing
Description: Dynamic slicing is a method designed for dependency detection between a categorical variable and a continuous variable. It could be applied for non-parametric hypothesis testing and gene set enrichment analysis.
Author: Chao Ye and Bo Jiang
Maintainer: Chao Ye

Diff between dslice versions 1.1.3 dated 2014-11-24 and 1.1.4 dated 2014-11-25

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Package diptest updated to version 0.75-6 with previous version 0.75-5 dated 2013-07-23

Title: Hartigan's dip test statistic for unimodality - corrected code
Description: Compute Hartigan's dip test statistic for unimodality / multimodality and provide a test with simulation based p-values.
Author: Martin Maechler (originally from Fortran and S-plus by Dario Ringach, NYU.edu)
Maintainer: Martin Maechler

Diff between diptest versions 0.75-5 dated 2013-07-23 and 0.75-6 dated 2014-11-25

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Package metrumrg (with last version 5.55) was removed from CRAN

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

2014-02-18 5.55
2013-11-26 5.54
2013-06-06 5.50
2013-05-23 5.49
2013-05-01 5.45
2013-04-24 5.44
2013-03-28 5.36
2013-03-21 5.34
2012-11-27 5.27
2012-11-24 5.26
2012-11-05 5.25
2012-10-25 5.24
2012-10-01 5.23
2012-05-05 5.17
2012-02-09 5.13
2011-11-11 5.5
2011-10-24 5.3
2011-09-20 5.2
2011-09-08 5.1

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Package StressStrength updated to version 1.0.1 with previous version 1.0 dated 2012-01-16

Title: Computation and estimation of reliability of stress-strength models
Description: The package provide functions for computing the reliability of stress-strength models and for building two-sided or one-sided confidence intervals according to different approximate procedures
Author: Alessandro Barbiero , Riccardo Inchingolo
Maintainer: Alessandro Barbiero

Diff between StressStrength versions 1.0 dated 2012-01-16 and 1.0.1 dated 2014-11-25

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Package audited (with last version 1.9) was removed from CRAN

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

2014-09-20 1.9

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Package R0 updated to version 1.2-5 with previous version 1.2-4 dated 2013-12-13

Title: Estimation of R0 and real-time reproduction number from epidemics
Description: This package is designed to estimate reproduction numbers for disease outbreak, based on incidence data. It implements several documented methods. It is therefore possible to compare estimations according to the methods used. Depending on the methods requested by user, basic reproduction number (commonly denoted as R0) or real-time reproduction number (referred to as R(t)) is computed, along with a 95% Confidence Interval. Plotting outputs will give different graphs depending on the methods requested : basic reproductive number estimations will only show the epidemic curve (collected data) and an adjusted model, whereas real-time methods will also show the R(t) variations throughout the outbreak time period. Sensitivity analysis tools are also provided, and allow for investigating effects of varying Generation Time distribution or time window on estimates.
Author: Pierre-Yves Boelle, Thomas Obadia
Maintainer: Thomas Obadia

Diff between R0 versions 1.2-4 dated 2013-12-13 and 1.2-5 dated 2014-11-25

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Package questionr updated to version 0.4.2 with previous version 0.4.1 dated 2014-07-16

Title: Functions to make surveys processing easier.
Description: This package provides some convenience functions to make the processing and analysis of surveys easier.
Author: Julien Barnier [aut, cre], François Briatte [aut], Joseph Larmarange [aut]
Maintainer: Julien Barnier

Diff between questionr versions 0.4.1 dated 2014-07-16 and 0.4.2 dated 2014-11-25

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Package PrevMap updated to version 1.1 with previous version 1.0 dated 2014-10-30

Title: Geostatistical Modelling of Spatially Referenced Prevalence Data
Description: The PrevMap package provides functions for both likelihood-based and Bayesian analysis of spatially referenced prevalence data. 'PrevMap' is also an extension of the 'geoR' package which should be installed first together with the 'maxLik', 'raster' and 'pdist' packages.
Author: Emanuele Giorgi, Peter J. Diggle
Maintainer: Emanuele Giorgi

Diff between PrevMap versions 1.0 dated 2014-10-30 and 1.1 dated 2014-11-25

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Package kinfit updated to version 1.1.13 with previous version 1.1.12 dated 2013-11-27

Title: Routines for fitting kinetic models to chemical degradation data
Description: Simple calculation routines based on the FOCUS Kinetics Report (2006). Only kinetic models for parent only datasets are included (no metabolite formation/decline or multicompartment kinetics). Please note that no warranty is implied for correctness of results or fitness for a particular purpose. This package is not actively developed at the moment. Please check the mkin package for an actively maintained package for kinetic evaluations of degradation data
Author: Johannes Ranke, with contributions from Katrin Lindenberger
Maintainer: Johannes Ranke

Diff between kinfit versions 1.1.12 dated 2013-11-27 and 1.1.13 dated 2014-11-25

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Package Julia updated to version 1.1 with previous version 1.0 dated 2011-02-12

Title: Fractal Image Data Generator
Description: Generates image data for fractals (Julia and Mandelbrot sets) on the complex plane in the given region and resolution.
Author: Mehmet Suzen [aut, main]
Maintainer: Mehmet Suzen

Diff between Julia versions 1.0 dated 2011-02-12 and 1.1 dated 2014-11-25

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New package IRTShiny with initial version 1.0
Package: IRTShiny
Type: Package
Title: Item Response Theory via Shiny
Version: 1.0
Date: 2014-11-24
Author: William Kyle Hamilton , Atsushi Mizumoto
Maintainer: William Kyle Hamilton
Description: Interactive shiny application for running Item Response Theory analysis.
License: GPL-3
Imports: shiny, shinyAce, beeswarm, CTT, ltm, parallel,
Suggests: psych
LazyData: true
Packaged: 2014-11-25 08:29:49 UTC; Kyle
NeedsCompilation: no
Repository: CRAN
Date/Publication: 2014-11-25 11:33:45

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Package distrMod updated to version 2.5.3 with previous version 2.5.2 dated 2013-09-12

Title: Object Oriented Implementation of Probability Models
Description: Object oriented implementation of probability models based on packages 'distr' and 'distrEx'
Author: Matthias Kohl, Peter Ruckdeschel
Maintainer: Peter Ruckdeschel

Diff between distrMod versions 2.5.2 dated 2013-09-12 and 2.5.3 dated 2014-11-25

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Package DiscreteInverseWeibull updated to version 1.0.1 with previous version 1.0 dated 2012-10-19

Title: Discrete inverse Weibull distribution
Description: Probability mass function, distribution function, quantile function, random generation and parameter estimation for the discrete inverse Weibull distribution
Author: Alessandro Barbiero, Riccardo Inchingolo, Mario Samigli
Maintainer: Alessandro Barbiero

Diff between DiscreteInverseWeibull versions 1.0 dated 2012-10-19 and 1.0.1 dated 2014-11-25

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

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

2014-11-25 1.1

Permanent link
Package vcrpart updated to version 0.2-3 with previous version 0.2-2 dated 2014-11-07

Title: Tree-Based Varying Coefficient Regression for Generalized Linear and Ordinal Mixed Models
Description: Recursive partitioning for varying coefficient generalized linear models and ordinal linear mixed models. Special features are coefficient-wise partitioning, non-varying coefficients and partitioning of time-varying variables in longitudinal regression.
Author: Reto Buergin [aut, cre, cph], Gilbert Ritschard [ctb, ths]
Maintainer: Reto Buergin

Diff between vcrpart versions 0.2-2 dated 2014-11-07 and 0.2-3 dated 2014-11-25

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New package USAboundaries with initial version 0.1
Package: USAboundaries
Type: Package
Title: Historical boundaries of the United States of America, 1629-2000
Date: 2014
Version: 0.1
Authors@R: c(person("Lincoln", "Mullen", email = "lincoln@lincolnmullen.com", role = c("aut", "cre")), person("Dr. William M. Scholl Center for American History and Culture, The Newberry Library", role = c("cph")))
Description: This package provides spatial objects with the boundaries of states or counties in the United States of America from 1629 to 2000. It provides data from the Atlas of Historical County Boundaries.
License: CC BY-NC-SA 4.0
LazyData: true
LazyDataCompression: xz
URL: https://github.com/ropensci/USAboundaries
BugReports: https://github.com/ropensci/USAboundaries/issues
Depends: R (>= 3.1.1),
Imports: assertthat (>= 0.1), dplyr (>= 0.3.0.1), ggplot2 (>= 1.0.0), lubridate (>= 1.3.3), maptools (>= 0.8-30), rgeos (>= 0.3-8), sp (>= 1.0.15)
Suggests: knitr, mapproj, testthat (>= 0.9.1)
VignetteBuilder: knitr
Packaged: 2014-11-24 18:25:13 UTC; lmullen
Author: Lincoln Mullen [aut, cre], Dr. William M. Scholl Center for American History and Culture, The Newberry Library [cph]
Maintainer: Lincoln Mullen
NeedsCompilation: no
Repository: CRAN
Date/Publication: 2014-11-25 09:42:09

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Package soma updated to version 1.1.1 with previous version 1.1.0 dated 2011-07-28

Title: General-Purpose Optimisation With the Self-Organising Migrating Algorithm
Description: This package provides an R implementation of the Self-Organising Migrating Algorithm, a general-purpose, stochastic optimisation algorithm. The approach is similar to that of genetic algorithms, although it is based on the idea of a series of ``migrations'' by a fixed set of individuals, rather than the development of successive generations. It can be applied to any cost-minimisation problem with a bounded parameter space, and is robust to local minima.
Author: Jon Clayden; based on the work of Ivan Zelinka
Maintainer: Jon Clayden

Diff between soma versions 1.1.0 dated 2011-07-28 and 1.1.1 dated 2014-11-25

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Package ore updated to version 1.0.4 with previous version 1.0.1 dated 2014-10-21

Title: An R Interface to the Oniguruma Regular Expression Library
Description: Provides an alternative to R's built-in functionality for handling regular expressions, based on the Oniguruma library. It offers first-class compiled regex objects, partial matching and function-based substitutions, amongst other features.
Author: Jon Clayden, based on Onigmo by K. Kosako and K. Takata
Maintainer: Jon Clayden

Diff between ore versions 1.0.1 dated 2014-10-21 and 1.0.4 dated 2014-11-25

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New package musicNMR with initial version 0.0.2
Package: musicNMR
Version: 0.0.2
Date: 2013-11-21
Author: Stefano Cacciatore, Edoardo Saccenti, Mario Piccioli
Maintainer: Stefano Cacciatore
Title: Conversion of Nuclear Magnetic Resonance spectrum in audio file
Description: This package is a collection of function for converting and modifying mono dimensional nuclear magnetic resonance spectra.
Depends: R (>= 2.10.0), seewave
Suggests: plsgenomics
SuggestsNote: No suggestions
License: GPL (>= 2)
Packaged: 2014-11-25 06:58:47 UTC; Stefano
NeedsCompilation: no
Repository: CRAN
Date/Publication: 2014-11-25 09:50:06

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Package dataframes2xls updated to version 0.4.6 with previous version 0.4.5 dated 2011-05-03

Title: dataframes2xls writes data frames to xls files
Description: dataframes2xls writes data frames to xls files. It supports multiple sheets and basic formatting.
Author: Guido van Steen
Maintainer: Guido van Steen

Diff between dataframes2xls versions 0.4.5 dated 2011-05-03 and 0.4.6 dated 2014-11-25

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New package cjoint with initial version 1.0.2
Package: cjoint
Version: 1.0.2
Date: 2014-10-18
Title: AMCE Estimator for Conjoint Experiments
Author: Anton Strezhnev, Jens Hainmueller, Daniel Hopkins, Teppei Yamamoto
Maintainer: Anton Strezhnev
Depends: R (>= 2.0.0), sandwich, lmtest, ggplot2
Description: An R implementation of the Average Marginal Component-specific Effects (AMCE) estimator presented in Hainmueller, J., Hopkins, D., and Yamamoto T. (2014) Causal Inference in Conjoint Analysis: Understanding Multi-Dimensional Choices via Stated Preference Experiments. Political Analysis 22(1):1-30.
License: GPL (>= 2)
Packaged: 2014-11-25 07:53:08 UTC; anton
NeedsCompilation: no
Repository: CRAN
Date/Publication: 2014-11-25 09:24:01

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Package bipartite updated to version 2.05 with previous version 2.04 dated 2014-03-25

Title: Visualising bipartite networks and calculating some (ecological) indices.
Description: Bipartite provides functions to visualise webs and calculate a series of indices commonly used to describe pattern in ecological webs. It focuses on webs consisting of only two trophic levels, e.g. pollination webs or predator-prey-webs. Visualisation is important to get an idea of what we are actually looking at, while the indices summarise different aspects of the webs topology.
Author: Carsten F. Dormann, Jochen Fruend and Bernd Gruber, with additional code from Mariano Devoto, Jose Iriondo, Rouven Strauss and Diego Vazquez, also based on C-code developed by Nils Bluethgen, Aaron Clauset/Rouven Strauss and Miguel Rodriguez-Girones.
Maintainer: Carsten F. Dormann

Diff between bipartite versions 2.04 dated 2014-03-25 and 2.05 dated 2014-11-25

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Package SweaveListingUtils updated to version 0.6.2 with previous version 0.6.1 dated 2013-02-09

Title: Utilities for Sweave together with TeX listings package
Description: provides utilities for defining R / Rd as Tex-package-listings "language" and including R / Rd source file (sniplets) copied from R-forge in its most recent version (or another url) thereby avoiding inconsistencies between vignette and documented source code
Author: Peter Ruckdeschel
Maintainer: Peter Ruckdeschel

Diff between SweaveListingUtils versions 0.6.1 dated 2013-02-09 and 0.6.2 dated 2014-11-25

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Package summarytools updated to version 0.2 with previous version 0.1 dated 2014-08-10

Title: Dataframe Summaries, Frequency Tables and Numerical Summaries with Customizable Output
Description: Includes 3 summarizing functions; one for categorical data (freq), one for numerical (uni or multidimensional) data (desc), and one exclusively for dataframes. 'freq' generates frequency tables with valid and total proportions. 'desc' generates common central tendency statistics and measures of dispersion for numerical data. 'dfSummary' will generate a table containing as many rows as there are columns, each row giving variable information (class and type), labels if any, common statistics for numerical data and frequency tables for any type of data, along with number and proportion of valid (non-missing) values.
Author: Dominic Comtois
Maintainer: Dominic Comtois

Diff between summarytools versions 0.1 dated 2014-08-10 and 0.2 dated 2014-11-25

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Package setRNG updated to version 2013.9-1 with previous version 2011.11-2 dated 2012-03-27

Title: Set (Normal) Random Number Generator and Seed
Description: SetRNG provides utilities to help set and record the setting of the seed and the uniform and normal generators used when a random experiment is run. The utilities can be used in other functions that do random experiments to simplify recording and/or setting all the necessary information for reproducibility. See the vignette and reference manual for examples.
Author: Paul Gilbert
Maintainer: Paul Gilbert

Diff between setRNG versions 2011.11-2 dated 2012-03-27 and 2013.9-1 dated 2014-11-25

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Package rstiefel updated to version 0.10 with previous version 0.9 dated 2012-01-12

Title: Random orthonormal matrix generation on the Stiefel manifold
Description: This package simulates random orthonormal matrices from linear and quadratic exponential family distributions on the Stiefel manifold. The most general type of distribution covered is the matrix-variate Bingham-von Mises-Fisher distribution. Most of the simulation methods are presented in Hoff(2009) "Simulation of the Matrix Bingham-von Mises-Fisher Distribution, With Applications to Multivariate and Relational Data."
Author: Peter Hoff
Maintainer: Peter Hoff

Diff between rstiefel versions 0.9 dated 2012-01-12 and 0.10 dated 2014-11-25

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Package multilevelPSA updated to version 1.2.2 with previous version 1.2 dated 2013-05-10

Title: Multilevel Propensity Score Analysis
Description: Functions to estimate and visualize propensity score analysis for multilevel, or clustered, data.
Author: Jason Bryer
Maintainer: Jason Bryer

Diff between multilevelPSA versions 1.2 dated 2013-05-10 and 1.2.2 dated 2014-11-25

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 man/mlpsa.distribution.plot.Rd         |   37 ++----
 man/mlpsa.logistic.Rd                  |   27 ++---
 man/multilevelPSA-package.Rd           |   63 +++++------
 man/pisa.colnames.Rd                   |   11 --
 man/pisa.countries.Rd                  |    7 -
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 man/pisana.Rd                          |   27 ++---
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 67 files changed, 891 insertions(+), 706 deletions(-)

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Permanent link

New package mads with initial version 0.1.0
Package: mads
Depends: mrds
Suggests: testthat
Type: Package
Title: Multi-Analysis Distance Sampling.
Version: 0.1.0
Date: 2014-11-27
Author: Laura Marshall
Maintainer: Laura Marshall
Description: Performs distance sampling analyses on a number of species accounting for unidentified sightings, model uncertainty and covariate uncertainty.
License: GPL (>= 2)
Packaged: 2014-11-25 02:50:52 UTC; laura
NeedsCompilation: no
Repository: CRAN
Date/Publication: 2014-11-25 09:01:38

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Package GPArotation updated to version 2014.11-1 with previous version 2012.3-1 dated 2012-03-27

Title: GPA Factor Rotation
Description: Gradient Projection Algorithm Rotation for Factor Analysis. See ?GPArotation.Intro for more details.
Author: Coen Bernaards and Robert Jennrich
Maintainer: Paul Gilbert

Diff between GPArotation versions 2012.3-1 dated 2012-03-27 and 2014.11-1 dated 2014-11-25

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 GPArotation-2014.11-1/GPArotation/inst/doc/Guide.Stex     |    7 ----
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 GPArotation-2014.11-1/GPArotation/vignettes/Guide.Stex    |    7 ----
 12 files changed, 32 insertions(+), 35 deletions(-)

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New package iccbeta with initial version 1.0
Package: iccbeta
Type: Package
Title: Multilevel model intraclass correlation for slope heterogeneity
Version: 1.0
Date: 2014-11-21
Authors@R: c(person("Steven Andrew", "Culpepper", role = c("aut", "cph","cre"), email = "sculpepp@illinois.edu"),person("Herman", "Aguinis", role = c("aut", "cph"), email = "haguinis@indiana.edu"))
Maintainer: Steven Andrew Culpepper
Description: A function and vignettes for computing an intraclass correlation described in Aguinis & Culpepper (in press). iccbeta quantifies the share of variance in a dependent variable that is attributed to group heterogeneity in slopes.
License: GPL (>= 2)
Imports: Rcpp (>= 0.11.1)
LinkingTo: Rcpp (>= 0.11.1), RcppArmadillo
Depends: R (>= 3.0.2), lme4
Packaged: 2014-11-25 02:21:38 UTC; sculpepp
Author: Steven Andrew Culpepper [aut, cph, cre], Herman Aguinis [aut, cph]
NeedsCompilation: yes
Repository: CRAN
Date/Publication: 2014-11-25 08:52:58

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New package GCPM with initial version 1.1
Package: GCPM
Type: Package
Title: Generalized Credit Portfolio Model
Version: 1.1
Date: 2014-11-24
Author: Kevin Jakob
Maintainer: Kevin Jakob
Description: The package helps to analyze the default risk of credit portfolios. Commonly known models, like CreditRisk+ or the CreditMetrics model are implemented in their very basic settings. The portfolio loss distribution can be achieved either by simulation or analytically in case of the classic CreditRisk+ model. Models are only implemented to respect losses caused by defaults, i.e. migration risk is not included. The package structure is kept flexible especially with respect to distributional assumptions in order to quantify the sensitivity of risk figures with respect to several assumptions. Therefore the package can be used to determine the credit risk of a given portfolio as well as to quantify model sensitivities.
License: GPL-2
Imports: Rcpp (>= 0.11.2), methods, RcppProgress(>= 0.1)
LinkingTo: Rcpp, RcppProgress
Packaged: 2014-11-24 18:46:01 UTC; Kevin_Jakob
NeedsCompilation: yes
Repository: CRAN
Date/Publication: 2014-11-25 08:40:13

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Package emdbook updated to version 1.3.6 with previous version 1.3.4 dated 2013-03-07

Title: Ecological models and data (book support)
Description: Auxiliary functions and data sets for _Ecological Models and Data_, a book presenting maximum likelihood estimation and related topics for ecologists (ISBN 978-0-691-12522-0)
Author: Ben Bolker
Maintainer: Ben Bolker

Diff between emdbook versions 1.3.4 dated 2013-03-07 and 1.3.6 dated 2014-11-25

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 emdbook-1.3.6/emdbook/man/curve3d.Rd      |    2 +-
 emdbook-1.3.6/emdbook/man/gridsearch2d.Rd |    4 +++-
 13 files changed, 42 insertions(+), 42 deletions(-)

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Package dse updated to version 2014.11-1 with previous version 2013.3-2 dated 2013-03-07

Title: Dynamic Systems Estimation (time series package)
Description: Package dse provides tools for multivariate, linear, time-invariant, time series models. It includes ARMA and state-space representations, and methods for converting between them. It also includes simulation methods and several estimation functions. The package has functions for looking at model roots, stability, and forecasts at different horizons. The ARMA model representation is general, so that VAR, VARX, ARIMA, ARMAX, ARIMAX can all be considered to be special cases. Kalman filter and smoother estimates can be obtained from the state space model, and state-space model reduction techniques are implemented. An introduction and User's Guide is available in a vignette.
Author: Paul Gilbert
Maintainer: Paul Gilbert

Diff between dse versions 2013.3-2 dated 2013-03-07 and 2014.11-1 dated 2014-11-25

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 dse-2014.11-1/dse/DESCRIPTION                 |   40 +++++++++++-------------
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 dse-2014.11-1/dse/tests/dse2tst2.R            |    8 +++-
 dse-2014.11-1/dse/tests/dse2tstgd1.R          |    6 +++
 dse-2014.11-1/dse/vignettes/Guide.Stex        |    3 -
 23 files changed, 127 insertions(+), 94 deletions(-)

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Package BayesLCA updated to version 1.6 with previous version 1.5 dated 2014-04-29

Title: Bayesian Latent Class Analysis
Description: Bayesian Latent Class Analysis using several different methods.
Author: Arthur White and Brendan Murphy
Maintainer: Arthur White

Diff between BayesLCA versions 1.5 dated 2014-04-29 and 1.6 dated 2014-11-25

 DESCRIPTION             |   11 ++++++-----
 MD5                     |    9 +++++----
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 man/BayesLCA-package.Rd |    5 +++++
 man/blca.Rd             |    5 +++++
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 6 files changed, 26 insertions(+), 9 deletions(-)

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Package acss updated to version 0.2-5 with previous version 0.2-4 dated 2014-06-01

Title: Algorithmic Complexity for Short Strings
Description: Main functionality is to provide the algorithmic complexity for short strings, an approximation of the Kolmogorov Complexity of a short string using the coding theorem method (see ?acss). The database containing the complexity is provided in the data only package acss.data, this package provides functions accessing the data such as prob_random returning the posterior probability that a given string was produced by a random process. In addition, two traditional (but problematic) measures of complexity are also provided: entropy and change complexity.
Author: Nicolas Gauvrit [aut], Henrik Singmann [aut, cre], Fernando Soler Toscano [ctb], Hector Zenil [ctb]
Maintainer: Henrik Singmann

Diff between acss versions 0.2-4 dated 2014-06-01 and 0.2-5 dated 2014-11-25

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 acss-0.2-5/acss/MD5                                  |   30 +--
 acss-0.2-5/acss/NAMESPACE                            |    2 
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 acss-0.2-5/acss/R/exp2-data.R                        |   32 +--
 acss-0.2-5/acss/R/matthews2013-data.R                |   30 +--
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 acss-0.2-5/acss/tests/testthat/test-acss.R           |  158 +++++++++----------
 acss-0.2-5/acss/tests/testthat/test-manuscript2014.R |only
 18 files changed, 223 insertions(+), 290 deletions(-)

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Mon, 24 Nov 2014

Package dse2 (with last version 2011.11-2) was removed from CRAN

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

2011-11-28 2011.11-2
2011-11-03 2011.11-1
2009-10-13 2009.10-1

Permanent link
Package dse1 (with last version 2011.11-2) was removed from CRAN

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

2011-11-28 2011.11-2
2011-11-03 2011.11-1
2009-10-13 2009.10-1

Permanent link
Package RNCEP updated to version 1.0.7 with previous version 1.0.6 dated 2013-03-21

Title: Obtain, Organize, and Visualize NCEP Weather Data
Description: This package contains functions to retrieve, organize, and visualize weather data from the NCEP/NCAR Reanalysis (http://www.esrl.noaa.gov/psd/data/gridded/data.ncep.reanalysis.html) and NCEP/DOE Reanalysis II (http://www.esrl.noaa.gov/psd/data/gridded/data.ncep.reanalysis2.html) datasets. Data are queried via the Internet and may be obtained for a specified spatial and temporal extent or interpolated to a point in space and time. We also provide functions to visualize these weather data on a map. There are also functions to simulate flight trajectories according to specified behavior using either NCEP wind data or data specified by the user.
Author: Michael U. Kemp with contributions from E. Emiel van Loon, Judy Shamoun-Baranes, and Willem Bouten
Maintainer: Michael U. Kemp

Diff between RNCEP versions 1.0.6 dated 2013-03-21 and 1.0.7 dated 2014-11-24

 DESCRIPTION                     |   28 ++++++++-------------------
 MD5                             |   34 ++++++++++++++++-----------------
 NAMESPACE                       |   26 +++++++++++++------------
 R/NCEP.bind.R                   |    3 --
 R/NCEP.gather.R                 |    4 ++-
 R/NCEP.gather.gaussian.R        |   11 ++++++----
 R/NCEP.gather.pressure.R        |   13 +++++++-----
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 R/NCEP.interp.surface.R         |   41 +++++++++++++++++++++++++++++-----------
 R/NCEP.track2kml.R              |    4 +--
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 R/robust.NCEP.interp.gaussian.R |   37 ++++++++++++++++++++++++++----------
 R/robust.NCEP.interp.pressure.R |   35 +++++++++++++++++++++++++---------
 R/robust.NCEP.interp.surface.R  |   35 +++++++++++++++++++++++++---------
 man/RNCEP-package.Rd            |    4 +--
 18 files changed, 247 insertions(+), 131 deletions(-)

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Package rdatamarket updated to version 0.6.5 with previous version 0.6.4 dated 2012-02-06

Title: Data access API for DataMarket.com
Description: Fetches data from DataMarket.com, either as timeseries in zoo form (dmseries) or as long-form data frames (dmlist). Metadata including dimension structure is fetched with dminfo, or just the dimensions with dmdims.
Author: Gunnlaugur Thor Briem
Maintainer: Gunnlaugur Thor Briem

Diff between rdatamarket versions 0.6.4 dated 2012-02-06 and 0.6.5 dated 2014-11-24

 DESCRIPTION                |   19 +++++-----
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 NAMESPACE                  |   20 ++++++-----
 NEWS                       |    9 +++++
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 man/rdatamarket-package.Rd |   79 ++++++++++++++++++++++-----------------------
 13 files changed, 177 insertions(+), 180 deletions(-)

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Package RCMIP5 updated to version 1.1 with previous version 1.0 dated 2014-10-16

Title: Tools for Manipulating and Summarizing CMIP5 Data
Description: Working with CMIP5 data can be tricky, forcing scientists to write custom scripts and programs. The `RCMIP5` package aims to ease this process, providing a standard, robust, and high-performance set of scripts to (i) explore what data have been downloaded, (ii) identify missing data, (iii) average (or apply other mathematical operations) across experimental ensembles, (iv) produce both temporal and spatial statistical summaries, and (v) produce easy-to-work-with graphical and data summaries.
Author: Ben Bond-Lamberty [aut], Kathe Todd-Brown [aut, cre]
Maintainer: Kathe Todd-Brown

Diff between RCMIP5 versions 1.0 dated 2014-10-16 and 1.1 dated 2014-11-24

 DESCRIPTION                             |   18 ++--
 MD5                                     |  105 +++++++++++++--------------
 NAMESPACE                               |    4 -
 NEWS                                    |   14 +++
 R/RCMIP5.R                              |  124 ++++++++++++++++++++------------
 R/addProvenance.R                       |    9 ++
 R/calcGridArea.R                        |    2 
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 R/filterDimensions.R                    |   35 ++++-----
 R/getFileInfo.R                         |    9 --
 R/loadCMIP5.R                           |   93 ++++++++++++++----------
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 R/makeAnnualStat.R                      |  113 +++++++++++------------------
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 R/makeZStat.R                           |  111 ++++++----------------------
 R/mergeExperiments.R                    |    2 
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 R/worldPlot.R                           |   74 +++++++++----------
 README.md                               |    8 +-
 build/vignette.rds                      |binary
 demo/RCMIP5.R                           |    8 --
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 tests/testthat/test_checkTimePeriod.R   |    8 +-
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 tests/testthat/test_filterDimensions.R  |   19 +---
 tests/testthat/test_getFileInfo.R       |   26 ++----
 tests/testthat/test_loadCMIP5.R         |   86 ++++++++++++----------
 tests/testthat/test_loadEnsemble.R      |   54 +++++++------
 tests/testthat/test_makeAnnualStat.R    |  121 +++++++++++++++----------------
 tests/testthat/test_makeGlobalStat.R    |   99 +++++++++++++++++--------
 tests/testthat/test_makeMonthlyStat.R   |   84 +++++++++++----------
 tests/testthat/test_makeZStat.R         |   58 ++++++--------
 tests/testthat/test_mergeExperiments.R  |    6 -
 tests/testthat/test_saveNetCDF.R        |   19 +++-
 vignettes/atmospheric_co2.Rmd           |   13 +--
 54 files changed, 1050 insertions(+), 1159 deletions(-)

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Package genridge updated to version 0.6-5 with previous version 0.6-3 dated 2012-02-08

Title: Generalized Ridge Trace Plots for Ridge Regression
Description: The genridge package introduces generalizations of the standard univariate ridge trace plot used in ridge regression and related methods. These graphical methods show both bias (actually, shrinkage) and precision, by plotting the covariance ellipsoids of the estimated coefficients, rather than just the estimates themselves. 2D and 3D plotting methods are provided, both in the space of the predictor variables and in the transformed space of the PCA/SVD of the predictors.
Author: Michael Friendly [aut, cre]
Maintainer: Michael Friendly

Diff between genridge versions 0.6-3 dated 2012-02-08 and 0.6-5 dated 2014-11-24

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 genridge-0.6-5/genridge/man/plot3d.ridge.Rd     |    6 ++-
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 genridge-0.6-5/genridge/man/vif.ridge.Rd        |    3 +
 18 files changed, 80 insertions(+), 60 deletions(-)

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New package EGRET with initial version 2.0.1
Package: EGRET
Type: Package
Title: Exploration and Graphics for RivEr Trends (EGRET)
Version: 2.0.1
Date: 2014-11-24
Authors@R: c( person("Robert", "Hirsch", role = c("aut"), email = "rhirsch@usgs.gov"), person("Laura", "DeCicco", role = c("aut","cre"), email = "ldecicco@usgs.gov"))
Description: EGRET includes statistics and graphics for streamflow history, water quality trends, and the statistical modeling algorithm Weighted Regressions on Time, Discharge, and Season (WRTDS).
License: CC0
Depends: R (>= 3.0)
Imports: dataRetrieval, survival, fields, stats, lubridate, methods
Suggests: xtable, knitr, extrafont
LazyLoad: yes
LazyData: yes
VignetteBuilder: knitr
BuildVignettes: true
URL: http://pubs.usgs.gov/tm/04/a10/, https://github.com/USGS-R/EGRET/wiki
Copyright: This software is in the public domain because it contains materials that originally came from the United States Geological Survey, an agency of the United States Department of Interior. For more information, see the official USGS copyright policy at http://www.usgs.gov/visual-id/credit_usgs.html#copyright
Packaged: 2014-11-24 15:17:25 UTC; ldecicco
Author: Robert Hirsch [aut], Laura DeCicco [aut, cre]
Maintainer: Laura DeCicco
NeedsCompilation: no
Repository: CRAN
Date/Publication: 2014-11-24 18:31:16

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New package choiceDes with initial version 0.9-1
Package: choiceDes
Type: Package
Title: Design Functions for Choice Studies
Version: 0.9-1
Date: 2014-11-24
Authors@R: person("Jack", "Horne", role=c("aut", "cre"), email="jack@jackhorne.net")
Maintainer: Jack Horne
Description: This package consists of functions to design DCMs and other types of choice studies (including MaxDiff and other tradeoffs)
License: GPL (>= 2)
Depends: R (>= 2.15.2), AlgDesign
Packaged: 2014-11-24 16:12:17 UTC; Jack
Author: Jack Horne [aut, cre]
NeedsCompilation: no
Repository: CRAN
Date/Publication: 2014-11-24 18:38:56

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Package someKfwer updated to version 1.2 with previous version 1.1 dated 2010-07-01

Title: Controlling the Generalized Familywise Error Rate
Description: This package collects some procedures controlling the Generalized Familywise Error Rate.
Author: L. Finos and A. Farcomeni
Maintainer: L. Finos

Diff between someKfwer versions 1.1 dated 2010-07-01 and 1.2 dated 2014-11-24

 DESCRIPTION         |    9 +++++----
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 man/kfwe.Rd         |   16 ++++++----------
 4 files changed, 13 insertions(+), 16 deletions(-)

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Package Rsolnp updated to version 1.15 with previous version 1.14 dated 2012-12-14

Title: General Non-linear Optimization
Description: General Non-linear Optimization Using Augmented Lagrange Multiplier Method
Author: Alexios Ghalanos and Stefan Theussl
Maintainer: Alexios Ghalanos

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Package paleobioDB updated to version 0.3 with previous version 0.2 dated 2014-09-09

Title: Download and Process Data from the Paleobiology Database
Description: 19 functions to wrap each endpoint of the PaleobioDB API, plus 8 functions to visualize and process the fossil data. The API documentation for the Paleobiology Database can be found in
Author: Sara Varela [aut, cre], Javier González Hernández [aut], Luciano Fabris Sgarbi [aut]
Maintainer: Sara Varela

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Package metafor updated to version 1.9-5 with previous version 1.9-4 dated 2014-07-30

Title: Meta-Analysis Package for R
Description: The metafor package provides a comprehensive collection of functions for conducting meta-analyses in R. The package includes functions to calculate various effect sizes or outcome measures, fit fixed-, random-, and mixed-effects models to such data, carry out moderator and meta-regression analyses, and create various types of meta-analytical plots (e.g., forest, funnel, radial, L'Abbe, Baujat plots). For meta-analyses of binomial and person-time data, the package also provides functions that implement specialized methods, including the Mantel-Haenszel method, Peto's method, and a variety of suitable generalized linear (mixed-effects) models (i.e., mixed-effects (conditional) logistic and Poisson regression models). Finally, the package provides functionality for fitting meta-analytic multivariate/multilevel models that account for non-independent sampling errors and/or true effects (e.g., due to the inclusion of multiple treatment studies, multiple endpoints, or other forms of clustering). Network meta-analyses and meta-analyses accounting for known correlation structures (e.g., due to phylogenetic relatedness) can also be conducted.
Author: Wolfgang Viechtbauer [aut, cre]
Maintainer: Wolfgang Viechtbauer

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Package indicspecies updated to version 1.7.4 with previous version 1.7.3 dated 2014-09-25

Title: Relationship between Species and Groups of Sites
Description: Functions to assess the strength and statistical significance of the relationship between species occurrence/abundance and groups of sites. Also includes functions to measure species niche breadth using resource categories.
Author: Miquel De Caceres, Florian Jansen
Maintainer: Miquel De Caceres

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Package dslice updated to version 1.1.3 with previous version 1.1.0 dated 2014-11-12

Title: Dynamic slicing
Description: Dynamic slicing is a method designed for dependency detection between a categorical variable and a continuous variable. It could be applied for non-parametric hypothesis testing and gene set enrichment analysis.
Author: Chao Ye and Bo Jiang
Maintainer: Chao Ye

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Package choplump updated to version 1.0-0.4 with previous version 1.0-0.3 dated 2014-01-23

Title: Choplump tests
Description: Choplump Tests are Permutation Tests for Comparing Two Groups with Some Positive but Many Zero Responses
Author: Michael P. Fay
Maintainer: Michael P. Fay

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

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

2011-08-06 1.0

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Package visualizationTools (with last version 0.2.05) was removed from CRAN

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

2012-08-01 0.2.05
2011-10-19 0.2.04
2011-08-23 0.2.03
2011-07-23 0.2.02
2011-05-23 0.2.01
2011-04-24 0.2
2011-02-28 0.1

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Package SesIndexCreatoR (with last version 1.0-2) was removed from CRAN

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2013-05-27 1.0-2

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

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

2009-11-17 1.1
2009-08-05 1.0

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Package MMST (with last version 0.6-1.1) was removed from CRAN

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

2011-02-11 0.6-1.1
2010-07-05 0.6-1

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Package mrdrc (with last version 1.0-6) was removed from CRAN

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

2011-04-13 1.0-6
2010-06-10 1.0-5
2010-05-30 1.0-4
2010-05-04 1.0-3
2009-02-17 1.0-2
2008-05-06 1.0-0

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Package xpose4 updated to version 4.5.3 with previous version 4.5.0 dated 2014-05-20

Title: Tools for Nonlinear Mixed-Effect Model Building and Diagnostics
Description: Xpose is collection of functions to be used as a model building aid for non-linear mixed effects (population) analysis using NONMEM. It facilitates data set checkout, exploration and visualization, model diagnostics, candidate covariate identification and model comparison.
Author: Andrew C. Hooker [aut, cre, cph], Mats O. Karlsson [aut, cph], Justin J. Wilkins [aut], E. Niclas Jonsson [aut, trl, cph], Ron Keizer [ctb] (functionality for bootstrap of GAM and SCM)
Maintainer: Andrew C. Hooker

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Package TH.data updated to version 1.0-5 with previous version 1.0-4 dated 2014-11-10

Title: TH's Data Archive
Description: Contains data sets used in other packages Torsten Hothorn maintains.
Author: Torsten Hothorn [aut, cre]
Maintainer: Torsten Hothorn

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Package sgr updated to version 1.3 with previous version 1.2 dated 2014-09-02

Title: Sample Generation by Replacement
Description: The package for Sample Generation by Replacement simulations (SGR; Lombardi & Pastore, 2014; Pastore & Lombardi, 2014). The package can be used to perform fake data analysis according to the sample generation by replacement approach. It includes functions for making simple inferences about discrete/ordinal fake data. The package allows to study the implications of fake data for empirical results.
Author: Massimiliano Pastore & Luigi Lombardi
Maintainer: Massimiliano Pastore

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Package fdatest updated to version 2.0 with previous version 1.0 dated 2013-07-23

Title: Interval Testing Procedure for functional data
Description: The package implements the Interval Testing Procedure for functional data in different frameworks (i.e., one or two-population frameworks, functional linear models) by means of different basis expansions (i.e., B-spline, Fourier, and phase-amplitude Fourier). The current version of the package requires functional data evaluated on a uniform grid; it automatically projects each function on a chosen functional basis; it performs the entire family of multivariate tests; and, finally, it provides the matrix of the p-values of the previous tests and the vector of the corrected p-values. The functional basis, the coupled or uncoupled scenario, and the kind of test can be chosen by the user. The package provides also a plotting function creating a graphical output of the procedure: the p-value heat-map, the plot of the corrected p-values, and the plot of the functional data.
Author: Alessia Pini, Simone Vantini
Maintainer: Alessia Pini

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Package Bergm updated to version 3.0.1 with previous version 3.0 dated 2014-10-12

Title: Bayesian analysis for exponential random graph models
Description: Set of tools to analyse Bayesian exponential random graph models
Author: Alberto Caimo [aut, cre], Nial Friel [ctb]
Maintainer: Alberto Caimo

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Package SimRAD updated to version 0.95 with previous version 0.94 dated 2014-05-15

Title: Simulations to predict the number of loci expected in RAD and GBS approaches.
Description: This package provides a number of functions to simulate restriction enzyme digestion, library construction and fragments size selection to predict the number of loci expected from most of the Restriction site Associated DNA (RAD) and Genotyping By Sequencing (GBS) approaches. SimRAD aims is to provide an estimation of the number of loci expected from a particular genome depending on the protocol type and parameters allowing to assess feasibility, multiplexing capacity and the amount of sequencing required.
Author: Olivier Lepais [aut, cre], Jason Weir [aut]
Maintainer: Olivier Lepais

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New package wux with initial version 1.2-2
Package: wux
Type: Package
Title: Wegener Center Climate Uncertainty Explorer
Version: 1.2-2
Date: 2014-10-20
Author: Thomas Mendlik, Georg Heinrich, Andreas Gobiet and Armin Leuprecht
Maintainer: Thomas Mendlik
Depends: sp, ncdf, reshape, abind, fields
Imports: rgdal, rgeos, class, stringr, Hmisc, gdata, corpcor
Suggests: lattice
Description: Analysis of climate model output uncertainties for specified geographical regions.
License: GPL (>= 2)
LazyLoad: yes
LazyData: yes
Packaged: 2014-11-24 08:28:33 UTC; tommaschku
NeedsCompilation: no
Repository: CRAN
Date/Publication: 2014-11-24 10:36:38

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Package missMDA updated to version 1.7.3 with previous version 1.7.2 dated 2013-12-15

Title: Handling missing values with/in multivariate data analysis (principal component methods)
Description: Imputation of incomplete continuous or categorical datasets; Missing values are imputed with a principal component analysis (PCA), a multiple correspondence analysis (MCA) model or a multiple factor analysis (MFA) model; Perform multiple imputation with and in PCA
Author: Francois Husson, Julie Josse
Maintainer: Francois Husson

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Package pvclass updated to version 1.2 with previous version 1.1 dated 2014-06-11

Title: P-values for Classification
Description: Computes nonparametric p-values for the potential class memberships of new observations as well as cross-validated p-values for the training data. The p-values are based on permutation tests applied to an estimated Bayesian likelihood ratio, using a plug-in statistic for the Gaussian model, 'k nearest neighbors', 'weighted nearest neighbors' or 'penalized logistic regression'. Additionally, it provides graphical displays and quantitative analyses of the p-values.
Author: Niki Zumbrunnen , Lutz Duembgen .
Maintainer: Niki Zumbrunnen

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Package ClickClust updated to version 1.1.3 with previous version 1.1.2 dated 2014-09-23

Title: Model-Based Clustering of Categorical Sequences
Description: ClickClust allows clustering categorical sequences by means of finite mixtures with Markov model components. ClickClust also allows detecting blocks of equivalent states by forward and backward state selection procedures.
Author: Volodymyr Melnykov [aut, cre]
Maintainer: Volodymyr Melnykov

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Package accelerometry updated to version 2.2.3 with previous version 2.2.2 dated 2014-08-11

Title: Functions for Processing Minute-to-Minute Accelerometer Data
Description: This package contains a collection of functions that perform operations on time-series accelerometer data, such as identify non-wear time, flag minutes that are part of an activity bout, and find the maximum 10-minute average count value. The functions are generally very flexible, allowing for a variety of algorithms to be implemented. Most of the functions are written in C++ for efficiency.
Author: Dane R. Van Domelen
Maintainer: Dane R. Van Domelen

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 src/bouts.cpp                |    2 -
 src/intensities.cpp          |    4 +-
 src/movingaves.cpp           |    4 +-
 src/movingaves_max.cpp       |    6 ++--
 src/rle2_num.cpp             |    8 ++---
 src/sedbreaks.cpp            |    2 -
 src/sedbreaks_flags.cpp      |    2 -
 src/weartime.cpp             |    2 -
 32 files changed, 100 insertions(+), 98 deletions(-)

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Sun, 23 Nov 2014

Package sirt updated to version 1.1 with previous version 1.0-3 dated 2014-10-27

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

Diff between sirt versions 1.0-3 dated 2014-10-27 and 1.1 dated 2014-11-23

 sirt-1.0-3/sirt/man/lavaanify.sirt.Rd     |only
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 sirt-1.1/sirt/R/personfit.R               |   48 ++++----
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 sirt-1.1/sirt/R/tam2mirt.R                |    1 
 sirt-1.1/sirt/R/tam2mirt.aux.R            |    9 +
 sirt-1.1/sirt/data/data.big5.qgraph.rda   |binary
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New package RCryptsy with initial version 0.2
Package: RCryptsy
Type: Package
Title: Access to Cryptsy Crypto-Currency Exchange Public Information API via R
Version: 0.2
Date: 2014-11-19
Author: William Kyle Hamilton
Maintainer: William Kyle Hamilton
Description: Basic Public API for the Crypto-Currency exchange Cryptsy
Depends: R (>= 3.0.3), RJSONIO, RCurl
License: GPL-3
URL: https://github.com/kylehamilton/RCryptsy
BugReports: https://github.com/kylehamilton/RCryptsy/issues
Packaged: 2014-11-22 13:33:36 UTC; Kyle
NeedsCompilation: no
Repository: CRAN
Date/Publication: 2014-11-23 23:41:18

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New package NHMSAR with initial version 1.0
Package: NHMSAR
Type: Package
Title: Non-Homogeneous Markov Switching Autoregressive Models: Fitting, Simulating, Validating.
Version: 1.0
Date: 2014-08-11
Author: Valerie Monbet
Maintainer: Valerie Monbet
Description: Calibration, simulation, validation of (non-)homogeneous Markov switching autoregressive models with Gaussian or von Mises innovations.
License: GPL
Depends: R (>= 2.10), ucminf
Packaged: 2014-11-23 12:24:14 UTC; monbet
NeedsCompilation: no
Repository: CRAN
Date/Publication: 2014-11-23 23:32:31

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Package EloRating updated to version 0.43 with previous version 0.41 dated 2014-03-20

Title: Animal Dominance Hierarchies by Elo Rating
Description: Calculate Elo ratings as means to describe animal dominance hierarchies
Author: Christof Neumann & Lars Kulik
Maintainer: Christof Neumann

Diff between EloRating versions 0.41 dated 2014-03-20 and 0.43 dated 2014-11-23

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Package care updated to version 1.1.7 with previous version 1.1.6 dated 2014-11-16

Title: High-Dimensional Regression and CAR Score Variable Selection
Description: The "care" package implements the regression approach of Zuber and Strimmer (2011) "High-dimensional regression and variable selection using CAR scores" SAGMB 10: 34. CAR scores measure the correlation between the response and the Mahalanobis-decorrelated predictors. The squared CAR score is a natural measure of variable importance and provides a canonical ordering of variables. This package provides functions for estimating CAR scores, for variable selection using CAR scores, and for estimating corresponding regression coefficients. Both shrinkage as well as empirical estimators are available.
Author: Verena Zuber and Korbinian Strimmer.
Maintainer: Korbinian Strimmer

Diff between care versions 1.1.6 dated 2014-11-16 and 1.1.7 dated 2014-11-23

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 care-1.1.7/care/NEWS                |   12 +++-
 care-1.1.7/care/R/predict.slm.R     |   33 +++++++----
 care-1.1.7/care/R/slm.R             |  100 ++++++++++++++++++++++++++++++++----
 care-1.1.7/care/inst/doc/brain.R    |   25 ++++-----
 care-1.1.7/care/inst/doc/diabetes.R |   11 ++-
 care-1.1.7/care/man/care.package.Rd |    2 
 care-1.1.7/care/man/carscore.Rd     |    2 
 care-1.1.7/care/man/slm.Rd          |   74 ++++++++++++++++++++++++--
 13 files changed, 224 insertions(+), 68 deletions(-)

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Package ppiPre (with last version 1.5) was removed from CRAN

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

2013-07-28 1.5
2013-07-04 1.4
2012-03-21 1.3
2011-10-19 1.2

Permanent link
New package jiebaR with initial version 0.2
Package: jiebaR
Type: Package
Title: Chinese Text Segmentation
Description: Chinese text segmentation, keyword extraction and speech tagging For R.
Version: 0.2
Date: 2014-11-23
Author: Qin Wenfeng, and the authors of CppJieba for the included version of CppJieba
Maintainer: Qin Wenfeng
License: MIT + file LICENSE
Depends: R (>= 3.1)
Imports: Rcpp,methods
LinkingTo: Rcpp
Suggests: testthat, knitr
URL: https://github.com/qinwf/jiebaR/
BugReports: https://github.com/qinwf/jiebaR/issues
VignetteBuilder: knitr
NeedsCompilation: yes
Packaged: 2014-11-23 10:36:47 UTC; outwen
Repository: CRAN
Date/Publication: 2014-11-23 12:47:46

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Package mediation updated to version 4.4.3 with previous version 4.4.2 dated 2014-08-27

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

Diff between mediation versions 4.4.2 dated 2014-08-27 and 4.4.3 dated 2014-11-23

 ChangeLog                  |    1 
 DESCRIPTION                |   11 +-
 MD5                        |   22 ++--
 NAMESPACE                  |    1 
 R/multimed.R               |  222 +++++++++++++++++++++++++++------------------
 build/vignette.rds         |binary
 inst/doc/mediation-old.pdf |binary
 inst/doc/mediation.Rnw     |    4 
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 vignettes/mediation.Rnw    |    4 
 vignettes/v59i05.bib       |    2 
 12 files changed, 161 insertions(+), 109 deletions(-)

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New package matchingMarkets with initial version 0.1-2
Package: matchingMarkets
Version: 0.1-2
Depends: R (>= 2.15.2)
Imports: Rcpp (>= 0.11.2), lpSolve (>= 5.6.6), partitions
LinkingTo: Rcpp, RcppArmadillo
Date: 2014-08-14
Title: An R package for the analysis of stable matchings
Author: Thilo Klein
Maintainer: Thilo Klein
Description: This package implements a structural estimator to correct for the sample selection bias from observed outcomes in matching markets. It also contains R code for matching algorithms such as the deferred-acceptance algorithm for college admissions, the top-trading-cycles algorithm for house allocation and a partitioning linear program for the roommates problem.
URL: https://github.com/thiloklein/matchingMarkets
License: GPL (>= 2) | file LICENSE
Repository: CRAN
Repository/R-Forge/Project: matchingmarkets
Repository/R-Forge/Revision: 16
Repository/R-Forge/DateTimeStamp: 2014-11-22 23:10:11
Date/Publication: 2014-11-23 09:35:22
Packaged: 2014-11-22 23:25:30 UTC; rforge
NeedsCompilation: yes

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New package broom with initial version 0.3.4
Package: broom
Type: Package
Title: Convert Statistical Analysis Objects Into Tidy Data Frames
Version: 0.3.4
Date: 2014-09-11
Authors@R: as.person(c( "David Robinson [aut, cre]", "Matthieu Gomez [ctb]", "Boris Demeshev [ctb]", "Hadley Wickham [ctb]" ))
Maintainer: David Robinson
Description: Convert statistical analysis objects from R into tidy data frames, so that they can more easily be combined, reshaped and otherwise processed with tools like dplyr, tidyr and ggplot2. The package provides three S3 generics: tidy, which summarizes a model's statistical findings such as coefficients of a regression; augment, which adds columns to the original data such as predictions, residuals and cluster assignments; and glance, which provides a one-row summary of model-level statistics.
Imports: plyr, dplyr, tidyr, psych
Suggests: knitr, survival, glmnet, lfe, Lahman, MASS, sp, maps, maptools, multcomp, testthat, lme4, zoo, ggplot2
URL: http://github.com/dgrtwo/broom
BugReports: http://github.com/dgrtwo/broom/issues
VignetteBuilder: knitr
License: MIT + file LICENSE
Packaged: 2014-11-23 06:37:25 UTC; dgrtwo
Author: David Robinson [aut, cre], Matthieu Gomez [ctb], Boris Demeshev [ctb], Hadley Wickham [ctb]
NeedsCompilation: no
Repository: CRAN
Date/Publication: 2014-11-23 09:23:10

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Package BiodiversityR updated to version 2.5-1 with previous version 2.4-4 dated 2014-05-15

Title: GUI for biodiversity, suitability and community ecology analysis
Description: This package provides a GUI (Graphical User Interface, via the R-Commander) and some utility functions (often based on the vegan package) for statistical analysis of biodiversity and ecological communities, including species accumulation curves, diversity indices, Renyi profiles, GLMs for analysis of species abundance and presence-absence, distance matrices, Mantel tests, and cluster, constrained and unconstrained ordination analysis. A book on biodiversity and community ecology analysis is available for free download from the website. In 2012, methods for (ensemble) suitability modelling and mapping were expanded in the package.
Author: Roeland Kindt
Maintainer: Roeland Kindt

Diff between BiodiversityR versions 2.4-4 dated 2014-05-15 and 2.5-1 dated 2014-11-23

 DESCRIPTION                          |   22 -
 MD5                                  |  121 ++++--
 NAMESPACE                            |    8 
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 R/ensemble.simplified.categories.R   |   12 
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 77 files changed, 1452 insertions(+), 1047 deletions(-)

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Sat, 22 Nov 2014

Package TAM updated to version 1.2 with previous version 1.1 dated 2014-10-19

Title: Test Analysis Modules
Description: The package includes marginal and joint maximum likelihood estimation of uni- and multidimensional item response models (Rasch, 2PL, 3PL, Generalized Partial Credit, Multi Facets, Nominal Item Response, Structured Latent Class Analysis, Mixture Distribution IRT Models, Located Latent Class Models, Cognitive Diagnostic Models), fit statistics and person parameter estimation.
Author: Thomas Kiefer [aut], Alexander Robitzsch [aut, cre], Margaret Wu [aut]
Maintainer: Alexander Robitzsch

Diff between TAM versions 1.1 dated 2014-10-19 and 1.2 dated 2014-11-22

 DESCRIPTION                   |   23 ++--
 MD5                           |   92 ++++++++++--------
 NAMESPACE                     |   45 +++++++--
 R/IRT.factor.scores.tam.R     |only
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 R/TAM-internal_intermediate.R |  186 ++-----------------------------------
 R/TAM-internal_mstep.R        |    1 
 R/TAM-internal_postproc.R     |    7 +
 R/anova.tam.R                 |   12 +-
 R/designMatrices.mfr2.R       |   58 ++++++++++-
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 R/summary.tam.mml.3pl.R       |   49 ++++++++-
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 54 files changed, 1109 insertions(+), 670 deletions(-)

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Package robustbase updated to version 0.92-2 with previous version 0.92-1 dated 2014-11-18

Title: Basic Robust Statistics
Description: "Essential" Robust Statistics. Tools allowing to analyze data with robust methods. This includes regression methodology including model selections and multivariate statistics where we strive to cover the book "Robust Statistics, Theory and Methods" by Maronna, Martin and Yohai; Wiley 2006.
Author: Original code by many authors, notably Peter Rousseeuw and Christophe Croux, see file 'Copyrights'; Valentin Todorov , Andreas Ruckstuhl , Matias Salibian-Barrera , Tobias Verbeke , Manuel Koller , Martin Maechler
Maintainer: Martin Maechler

Diff between robustbase versions 0.92-1 dated 2014-11-18 and 0.92-2 dated 2014-11-22

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 robustbase-0.92-2/robustbase/TODO                           |    1 
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New package MAVIS with initial version 0.2
Package: MAVIS
Type: Package
Title: Meta Analysis via Shiny
Version: 0.2
Date: 2014-11-21
Author: William Kyle Hamilton , Atsushi Mizumoto
Maintainer: William Kyle Hamilton
Description: Interactive shiny application for running a meta-analysis, provides support for both random effects and fixed effects models.
License: GPL-3
Imports: shiny, shinyAce, metafor, MAd, MAc, quantreg, ggplot2
LazyData: true
Packaged: 2014-11-22 13:29:53 UTC; Kyle
NeedsCompilation: no
Repository: CRAN
Date/Publication: 2014-11-22 19:06:45

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Package magrittr updated to version 1.5 with previous version 1.0.1 dated 2014-05-15

Title: A Forward-Pipe Operator for R
Description: Provides a mechanism for chaining commands with a new forward-pipe operator, %>%. This operator will forward a value, or the result of an expression, into the next function call/expression. There is flexible support for the type of right-hand side expressions. For more information, see package vignette. To quote Rene Magritte, "Ceci n'est pas un pipe."
Author: Stefan Milton Bache and Hadley Wickham
Maintainer: Stefan Milton Bache

Diff between magrittr versions 1.0.1 dated 2014-05-15 and 1.5 dated 2014-11-22

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Package classyfire updated to version 0.1-1 with previous version 0.1-0 dated 2014-09-04

Title: Robust multivariate classification using highly optimised SVM ensembles
Description: A collection of functions for the creation and application of highly optimised, robustly evaluated ensembles of support vector machines (SVMs). The package takes care of training individual SVM classifiers using a fast parallel heuristic algorithm, and combines individual classifiers into ensembles. Robust metrics of classification performance are offered by bootstrap resampling and permutation testing.
Author: Eleni Chatzimichali and Conrad Bessant
Maintainer: Eleni Chatzimichali

Diff between classyfire versions 0.1-0 dated 2014-09-04 and 0.1-1 dated 2014-11-22

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Package BIFIEsurvey updated to version 1.1 with previous version 1.0 dated 2014-10-12

Title: Some Tools for Survey Statistics in Educational Assessment, Developed by BIFIE
Description: Some Tools for Survey Statistics in Educational Assessment, Developed by BIFIE. Bundesinstitut fuer Bildungsforschung, Entwicklung und Innovation im oesterreichischen Schulwesen; Federal Institute for Educational Research, Innovation and Development of the Austrian School System; Salzburg, Austria.
Author: BIFIE [aut], Alexander Robitzsch [ctb,cre], Konrad Oberwimmer [ctb]
Maintainer: Alexander Robitzsch

Diff between BIFIEsurvey versions 1.0 dated 2014-10-12 and 1.1 dated 2014-11-22

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Package EGRET (with last version 2.0.0) was removed from CRAN

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

2014-11-20 2.0.0

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New package MATA with initial version 0.1
Package: MATA
Title: Model-Averaged Tail Area Wald (MATA-Wald) Confidence Interval
Version: 0.1
Authors@R: person('Daniel', 'Turek', email='dturek@maths.otago.ac.nz', role=c('aut','cre'))
Description: Provides a function for calculating the Model-Averaged Tail Area Wald (MATA-Wald) confidence interval, which is generated from single-model estimators and AIC model weights
Depends: R (>= 3.1.1)
License: GPL-2
LazyData: true
Packaged: 2014-11-22 01:27:25 UTC; dturek
Author: Daniel Turek [aut, cre]
Maintainer: Daniel Turek
NeedsCompilation: no
Repository: CRAN
Date/Publication: 2014-11-22 08:23:28

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New package EnsembleBase with initial version 0.7
Package: EnsembleBase
Type: Package
Title: Extensible Package for Parallel, Batch Training of Base Learners for Ensemble Modeling
Version: 0.7
Date: 2014-11-17
Author: Alireza S. Mahani, Mansour T.A. Sharabiani
Maintainer: Alireza S. Mahani
Description: Extensible S4 classes and methods for batch training of regression and classification algorithms such as Random Forest, Gradient Boosting Machine, Neural Network, Support Vector Machines, and K-Nearest Neighbors. These algorithms constitute a set of 'base learners', which can subsequently be combined together to form ensemble predictions. This package provides cross-validation wrappers to allow for downstream application of ensemble integration techniques, including best-error selection. All base learner estimation objects are retained, allowing for repeated prediction calls without the need for re-training. For large problems, an option is provided to save estimation objects to disk, along with prediction methods that utilize these objects. This allows users to train and predict with large ensembles of base learners without being constrained by system RAM.
License: GPL (>= 2)
Depends: kknn,methods
Imports: gbm,nnet,e1071,randomForest,doParallel,foreach
Packaged: 2014-11-22 01:26:03 UTC; amahani
NeedsCompilation: no
Repository: CRAN
Date/Publication: 2014-11-22 08:23:23

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Fri, 21 Nov 2014

Package yhatr updated to version 0.13.1 with previous version 0.12.1 dated 2014-07-19

Title: R binder for the Yhat API
Description: yhatr lets you deploy, maintain, and invoke models via the Yhat REST API.
Author: Greg Lamp , Eric Chiang
Maintainer: Greg Lamp

Diff between yhatr versions 0.12.1 dated 2014-07-19 and 0.13.1 dated 2014-11-21

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