Thu, 05 Nov 2015

Package markophylo updated to version 1.0.3 with previous version 1.0.2 dated 2015-08-31

Title: Markov Chain Models for Phylogenetic Trees
Description: Allows for fitting of maximum likelihood models using Markov chains on phylogenetic trees for analysis of discrete character data. Examples of such discrete character data include restriction sites, gene family presence/absence, intron presence/absence, and gene family size data. Hypothesis-driven user- specified substitution rate matrices can be estimated. Allows for biologically realistic models combining constrained substitution rate matrices, site rate variation, site partitioning, branch-specific rates, allowing for non-stationary prior root probabilities, correcting for sampling bias, etc.
Author: Utkarsh J. Dang and G. Brian Golding
Maintainer: Utkarsh J. Dang <udang@mcmaster.ca>

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Package vtreat updated to version 0.5.20 with previous version 0.5.18 dated 2015-10-07

Title: Simple Variable Treatment
Description: Prepares variables so that data has fewer exceptional cases, making it easier to safely use models in production. Common problems 'vtreat' defends against: Inf, NA, too many categorical values, rare categorical values, new categorical values (levels seen during application, but not during training). 'vtreat::prepare' should be used as you would use 'model.matrix'.
Author: John Mount, Nina Zumel
Maintainer: John Mount <jmount@win-vector.com>

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Package survJamda updated to version 1.1.4 with previous version 1.1.3 dated 2015-05-02

Title: Survival Prediction by Joint Analysis of Microarray Gene Expression Data
Description: Microarray gene expression data can be analyzed individually or jointly using merging methods or meta-analysis to predict patients' survival and risk assessment.
Author: Haleh Yasrebi
Maintainer: Haleh Yasrebi<hyasrebi@yahoo.com>

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Package party updated to version 1.0-25 with previous version 1.0-23 dated 2015-08-16

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

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Package MCDA updated to version 0.0.12 with previous version 0.0.11 dated 2015-08-26

Title: Functions to Support the Multicriteria Decision Aiding Process
Description: Functions which can be useful to support the analyst in the Multicriteria Decision Aiding (MCDA) process involving multiple, conflicting criteria.
Author: Patrick Meyer, Sébastien Bigaret, Richard Hodgett, Alexandru-Liviu Olteanu
Maintainer: Patrick Meyer <patrick.meyer@telecom-bretagne.eu>

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Package imputeTS updated to version 0.3 with previous version 0.1 dated 2015-07-22

Title: Time Series Missing Value Imputation
Description: Imputation (replacement) of missing values in univariate time series.
Author: Steffen Moritz
Maintainer: Steffen Moritz <steffen.moritz10@gmail.com>

Diff between imputeTS versions 0.1 dated 2015-07-22 and 0.3 dated 2015-11-05

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New package dad with initial version 1.0.2
Package: dad
Type: Package
Title: Three-Way Data Analysis Through Densities
Version: 1.0.2
Date: 2015-11-05
Author: Rachid Boumaza, Pierre Santagostini, Smail Yousfi, Sabine Demotes-Mainard
Maintainer: Rachid Boumaza <rachid.boumaza@agrocampus-ouest.fr>
Description: The three-way data consists of a set of variables measured on several groups of individuals. To each group is associated an estimated probability density function. The package provides functional methods (principal component analysis, multidimensional scaling, discriminant analysis...) for such probability densities.
Depends: R (>= 3.0.0), methods, stats, graphics, grDevices, utils, lattice, e1071
Suggests: MASS
Encoding: latin1
License: GPL (>= 2)
NeedsCompilation: no
Packaged: 2015-11-05 15:34:04 UTC; psantago
Repository: CRAN
Date/Publication: 2015-11-05 20:03:59

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New package rchess with initial version 0.1
Package: rchess
Version: 0.1
Title: Chess Move, Generation/Validation, Piece Placement/ Movement, and Check/Checkmate/Stalemate Detection
Description: R package for chess validations, pieces movements and check detection. Also integrates functions to plot chess boards given a Forsyth Edwards and Portable Game notations.
Author: Joshua Kunst <jbkunst@gmail.com>
Maintainer: Joshua Kunst <jbkunst@gmail.com>
License: MIT + file LICENSE
URL: https://github.com/jbkunst/rchess
BugReports: https://github.com/jbkunst/rchess/issues
Imports: htmlwidgets, V8, R6, ggplot2, plyr, dplyr, assertthat
RoxygenNote: 5.0.0
NeedsCompilation: no
Packaged: 2015-11-05 15:44:44 UTC; jkunst
Repository: CRAN
Date/Publication: 2015-11-05 17:18:05

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Package pcnetmeta updated to version 2.3 with previous version 2.2.2 dated 2015-10-21

Title: Patient-Centered Network Meta-Analysis
Description: Provides functions to perform arm-based network meta-analysis for datasets with binary, continuous, and count outcomes.
Author: Lifeng Lin, Jing Zhang, and Haitao Chu
Maintainer: Lifeng Lin <linl@umn.edu>

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Package rucm (with last version 0.5) was removed from CRAN

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

2015-11-02 0.5
2014-09-07 0.4
2014-08-26 0.3

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New package tolBasis with initial version 1.0
Package: tolBasis
Type: Package
Title: Fundamental Definitions and Utilities of the Time Oriented Language (TOL)
Version: 1.0
Date: 2015-11-02
Author: Pedro Gea
Maintainer: Pedro Gea <pgea@bayesforecast.com>
Description: Imports the fundamental definitions and utilities of the Time Oriented Language (TOL), focused on time series analysis and stochastic processes, and provides the basis for the integration of TOL in R. See <https://www.tol-project.org> for more information about the TOL project.
URL: https://www.tol-project.org/browser/tolp/Rprojects/tolBasis
License: GPL-3
Depends: lubridate
Imports: polynom
Suggests: xts, zoo
NeedsCompilation: no
Packaged: 2015-11-05 12:02:28 UTC; pgea
Repository: CRAN
Date/Publication: 2015-11-05 13:38:39

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Package RSAGA updated to version 0.94-4 with previous version 0.94-3 dated 2015-08-26

Title: SAGA Geoprocessing and Terrain Analysis in R
Description: Provides access to geocomputing and terrain analysis functions of the geographical information system (GIS) 'SAGA' (System for Automated Geoscientific Analyses) from within R by running the command line version of SAGA. This package furthermore provides several R functions for handling ASCII grids, including a flexible framework for applying local functions (including predict methods of fitted models) and focal functions to multiple grids. SAGA GIS is available under GPLv2 / LGPLv2 licence from http://sourceforge.net/projects/saga-gis/.
Author: Alexander Brenning and Donovan Bangs
Maintainer: Alexander Brenning <alexander.brenning@uni-jena.de>

Diff between RSAGA versions 0.94-3 dated 2015-08-26 and 0.94-4 dated 2015-11-05

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New package midrangeMCP with initial version 1.0
Package: midrangeMCP
Type: Package
Title: Multiples Comparisons Procedures Based on Studentized Midrange and Range Distributions
Version: 1.0
Date: 2015-11-05
Authors@R: c( person("Ben", "Deivide", email = "ben.deivide@gmail.com", role = "cre"), person("Daniel", "Furtado", email = "danielff@dex.ufla.br", role = "aut"))
Description: Apply tests of multiple comparisons based on studentized midrange and range distributions. The tests are: Tukey Midrange test, Student-Newman-Keuls Midrange test, Skott-Knott Midrange test and Skott-Knott Range test.
Imports: stats, utils, graphics, grDevices, SMR, WriteXLS, xtable
License: GPL (>= 2)
LazyData: TRUE
NeedsCompilation: no
Packaged: 2015-11-05 12:41:27 UTC; BenDeivide
Author: Ben Deivide [cre], Daniel Furtado [aut]
Maintainer: Ben Deivide <ben.deivide@gmail.com>
Repository: CRAN
Date/Publication: 2015-11-05 14:05:55

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Package lessR updated to version 3.3.6 with previous version 3.3.4 dated 2015-08-22

Title: Less Code, More Results
Description: Each function accomplishes the work of several or more standard R functions. For example, two function calls, Read() and CountAll(), read the data and generate summary statistics for all variables in the data frame, plus histograms and bar charts as appropriate. Other functions provide for descriptive statistics, a comprehensive regression analysis, analysis of variance and t-test, plotting, bar chart, histogram, box plot, density curves, calibrated power curve, reading multiple data formats with the same function, variable labels, color themes, and a built-in help system. A confirmatory factor analysis of multiple indicator measurement models is also available as are pedagogical routines for data simulation such as for the Central Limit Theorem. Compatible with 'RStudio' and 'knitr' including generation of 'knitr' instructions for interpretative output.
Author: David W. Gerbing, School of Business Administration, Portland State University
Maintainer: David W. Gerbing <gerbing@pdx.edu>

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Package statnetWeb updated to version 0.4.0 with previous version 0.3.6 dated 2015-08-21

Title: A Graphical User Interface for Network Modeling with 'Statnet'
Description: A graphical user interface for network modeling with the 'statnet' software.
Author: Emily Beylerian [cre, aut], Kirk Li [ctb], Samuel Jenness [ctb], Martina Morris [ctb]
Maintainer: Emily Beylerian <ebey@uw.edu>

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Package SSDforR updated to version 1.4.12 with previous version 1.4.11 dated 2015-08-18

Title: Functions to Analyze Single System Data
Description: Functions to visually and statistically analyze single system data.
Author: Charles Auerbach [aut, cre], Wendy Zeitlin [aut]
Maintainer: Charles Auerbach <auerbach@yu.edu>

Diff between SSDforR versions 1.4.11 dated 2015-08-18 and 1.4.12 dated 2015-11-05

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Package rcbalance updated to version 1.7.3 with previous version 1.7.2 dated 2015-10-27

Title: Large, Sparse Optimal Matching with Refined Covariate Balance
Description: Tools for large, sparse optimal matching of treated units and control units in observational studies. Provisions are made for refined covariate balance constraints, which include fine and near-fine balance as special cases. Matches are optimal in the sense that they are computed as solutions to network optimization problems rather than greedy algorithms.
Author: Samuel D. Pimentel
Maintainer: Samuel D. Pimentel <spi@wharton.upenn.edu>

Diff between rcbalance versions 1.7.2 dated 2015-10-27 and 1.7.3 dated 2015-11-05

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Package rattle updated to version 4.0.0 with previous version 3.5.0 dated 2015-07-14

Title: Graphical User Interface for Data Mining in R
Description: The R Analytic Tool To Learn Easily (Rattle) provides a Gnome (RGtk2) based interface to R functionality for data mining. The aim is to provide a simple and intuitive interface that allows a user to quickly load data from a CSV file (or via ODBC), transform and explore the data, build and evaluate models, and export models as PMML (predictive modelling markup language) or as scores. All of this with knowing little about R. All R commands are logged and commented through the log tab. Thus they are available to the user as a script file or as an aide for the user to learn R or to copy-and-paste directly into R itself. Rattle also exports a number of utility functions and the graphical user interface, invoked as rattle(), does not need to be run to deploy these.
Author: Graham Williams [aut, cph, cre], Mark Vere Culp [cph], Ed Cox [ctb], Anthony Nolan [ctb], Denis White [cph], Daniele Medri [ctb], Akbar Waljee [ctb] (OOB AUC for Random Forest), Brian Ripley [cph] (Author of original print.summary.nnet), Jose Magana [ctb] (Contributed the ggpairs plots.)
Maintainer: Graham Williams <Graham.Williams@togaware.com>

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Package RandomFieldsUtils updated to version 0.0.12 with previous version 0.0.10 dated 2015-07-10

Title: Utilities for the Simulation and Analysis of Random Fields
Description: Various utilities are provided that might be used in spatial statistics and elsewhere. It delivers a method for solving linear equations that checks the sparsity of the matrix before any algorithm is used. Furthermore, it includes the Struve functions.
Author: Martin Schlather [aut, cre], Reinhard Furrer [ctb], Martin Kroll [ctb]
Maintainer: Martin Schlather <schlather@math.uni-mannheim.de>

Diff between RandomFieldsUtils versions 0.0.10 dated 2015-07-10 and 0.0.12 dated 2015-11-05

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Package RandomFields updated to version 3.1.3 with previous version 3.1.1 dated 2015-07-25

Title: Simulation and Analysis of Random Fields
Description: Methods for the inference on and the simulation of Gaussian fields are provided, as well as methods for the simulation of extreme value random fields.
Author: Martin Schlather [aut, cre], Alexander Malinowski [aut], Marco Oesting [aut], Daphne Boecker [aut], Kirstin Strokorb [aut], Sebastian Engelke [aut], Johannes Martini [aut], Felix Ballani [aut], Olga Moreva [aut], Christoph Berreth [ctr], Peter Menck [ctr], Sebastian Gross [ctr], Ulrike Ober [ctb], Katharina Burmeister [ctb], Juliane Manitz [ctb], Paulo Ribeiro [ctb], Richard Singleton [ctb], Ben Pfaff [ctb], R Core Team [ctb]
Maintainer: Martin Schlather <schlather@math.uni-mannheim.de>

Diff between RandomFields versions 3.1.1 dated 2015-07-25 and 3.1.3 dated 2015-11-05

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Package pRF updated to version 1.1 with previous version 1.0 dated 2015-03-03

Title: Permutation Significance for Random Forests
Description: Estimate False Discovery Rates (FDRs) for importance metrics from random forest runs.
Author: Ankur Chakravarthy
Maintainer: Ankur Chakravarthy <ankur.chakravarthy.10@ucl.ac.uk>

Diff between pRF versions 1.0 dated 2015-03-03 and 1.1 dated 2015-11-05

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Package packrat updated to version 0.4.6-1 with previous version 0.4.6 dated 2015-11-03

Title: A Dependency Management System for Projects and their R Package Dependencies
Description: Manage the R packages your project depends on in an isolated, portable, and reproducible way.
Author: Kevin Ushey, Jonathan McPherson, Joe Cheng, Aron Atkins, JJ Allaire
Maintainer: Kevin Ushey <kevin@rstudio.com>

Diff between packrat versions 0.4.6 dated 2015-11-03 and 0.4.6-1 dated 2015-11-05

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Package multilevelPSA updated to version 1.2.3 with previous version 1.2.2 dated 2014-11-25

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

Diff between multilevelPSA versions 1.2.2 dated 2014-11-25 and 1.2.3 dated 2015-11-05

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New package matlib with initial version 0.4.1
Package: matlib
Type: Package
Title: Matrix Functions for Teaching and Learning Linear Algebra and Multivariate Statistics
Version: 0.4.1
Date: 2015-11-03
Authors@R: c(person(given = "Michael", family = "Friendly", role=c("aut", "cre"), email="friendly@yorku.ca"), person(given = "John", family = "Fox", role="ctb"), person(given = "Georges", family = "Monette", role="ctb"))
Author: Michael Friendly [aut, cre], John Fox [ctb], Georges Monette [ctb]
Maintainer: Michael Friendly <friendly@yorku.ca>
Description: A collection of matrix functions for teaching and learning matrix linear algebra as used in multivariate statistical methods. These functions are mainly for tutorial purposes in learning matrix algebra ideas using R. In some cases, functions are provided for concepts available elsewhere in R, but where the function call or name is not obvious. In other cases, functions are provided to show or demonstrate an algorithm.
License: GPL (>= 2)
URL: https://github.com/friendly/matlib
LazyData: TRUE
Suggests: MASS, knitr, rmarkdown
VignetteBuilder: knitr
RoxygenNote: 5.0.0
NeedsCompilation: no
Packaged: 2015-11-04 22:51:46 UTC; Friendly
Repository: CRAN
Date/Publication: 2015-11-05 08:31:49

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Package LPM updated to version 2.6 with previous version 2.5 dated 2015-07-08

Title: Linear Parametric Models Applied to Hydrological Series
Description: Apply Univariate Long Memory Models, Multivariate Short Memory Models To Hydrological Dataset.
Author: Corrado Tallerini [aut, cre], Salvatore Grimaldi [aut]
Maintainer: Corrado Tallerini <corrado.tallerini@vodafone.it>

Diff between LPM versions 2.5 dated 2015-07-08 and 2.6 dated 2015-11-05

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Package LatticeKrig updated to version 5.4-1 with previous version 5.4 dated 2015-10-22

Title: Multiresolution Kriging Based on Markov Random Fields
Description: Functions for the interpolation of large spatial datasets. This package follows a "fixed rank Kriging" approach using a large number of basis functions and provides spatial estimates that are comparable to standard families of covariance functions. Using a large number of basis functions allows for estimates that can come close to interpolating the observations (a spatial model with a small nugget variance.) Moreover, the covariance model for this method can approximate the Matern covariance family but also allows for a multi-resolution model and supports efficient computation of the profile likelihood for estimating covariance parameters. This is accomplished through compactly supported basis functions and a Markov random field model for the basis coefficients. These features lead to sparse matrices for the computations. An extension of this version over previous ones ( < 5.4 ) is the support for different geometries besides a rectangular domain. One benefit of the LatticeKrig model/approach is the facility to do unconditional and conditional simulation of the field for large numbers of arbitrary points. There is also the flexibility for estimating non-stationary covariances. Included are generic methods for prediction, standard errors for prediction, plotting of the estimated surface and conditional and unconditional simulation.
Author: Douglas Nychka [aut, cre], Dorit Hammerling [aut], Stephan Sain [aut], Nathan Lenssen [aut]
Maintainer: Douglas Nychka <nychka@ucar.edu>

Diff between LatticeKrig versions 5.4 dated 2015-10-22 and 5.4-1 dated 2015-11-05

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New package kmeans.ddR with initial version 0.1.0
Package: kmeans.ddR
Type: Package
Title: Distributed k-Means for Big Data using 'ddR' API
Version: 0.1.0
Date: 2015-10-28
Author: Vishrut Gupta, Arash Fard
Maintainer: Vishrut Gupta <vishrut.gupta@hpe.com>
Depends: R (>= 3.0.0)
Imports: ddR, Rcpp (>= 0.11.0)
Suggests: testthat
LinkingTo: Rcpp
Description: Distributed k-means clustering algorithm written using 'ddR' (Distributed Data Structures) API in the 'ddR' package.
License: GPL (>= 2) | file LICENSE
NeedsCompilation: yes
Packaged: 2015-11-05 01:49:17 UTC; guptavis
Repository: CRAN
Date/Publication: 2015-11-05 08:31:48

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Package EEM updated to version 1.0.4 with previous version 1.0.1 dated 2015-08-05

Title: Read and Preprocess Fluorescence Excitation-Emission Matrix (EEM) Data
Description: Read raw EEM data and prepares them for further analysis.
Author: Vipavee Trivittayasil
Maintainer: Vipavee Trivittayasil <vipavee.tri@gmail.com>

Diff between EEM versions 1.0.1 dated 2015-08-05 and 1.0.4 dated 2015-11-05

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Package dglm updated to version 1.8.2 with previous version 1.8.1 dated 2014-11-07

Title: Double Generalized Linear Models
Description: Model fitting and evaluation tools for double generalized linear models (DGLMs). This class of models uses one generalized linear model (GLM) to fit the specified response and a second GLM to fit the deviance of the first model.
Author: Peter K Dunn <pdunn2@usc.edu.au> and Gordon K Smyth
Maintainer: Robert Corty <robert_corty@med.unc.edu>

Diff between dglm versions 1.8.1 dated 2014-11-07 and 1.8.2 dated 2015-11-05

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Package APSIM updated to version 0.8.3 with previous version 0.8.2 dated 2015-09-28

Title: General Utility Functions for the 'Agricultural Production Systems Simulator'
Description: Contains functions designed to facilitate the loading and transformation of 'Agricultural Production Systems Simulator' output files <https://www.apsim.info>. Input meteorological data (also known as "weather" or "met") files can also be generated from user supplied data.
Author: Justin Fainges
Maintainer: Justin Fainges <Justin.Fainges@csiro.au>

Diff between APSIM versions 0.8.2 dated 2015-09-28 and 0.8.3 dated 2015-11-05

 DESCRIPTION       |    8 ++++----
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