Tue, 02 Dec 2014

New package retistruct with initial version 0.5.9
Package: retistruct
License: CC BY-NC-SA 4.0
Title: Retistruct - Retinal Reconstruction Program
Authors@R: c(person("David C.", "Sterratt", role=c("aut", "cre", "cph"), email="david.c.sterratt@ed.ac.uk"), person("Daniel", "Lyngholm", role=c("aut", "cph")))
Description: Program to reconstruct retinae from flattened retinae in which there are incisions and tears
Version: 0.5.9
URL: http://retistruct.r-forge.r-project.org/
BugReports: https://github.com/davidcsterratt/retistruct/issues
Date: 2014-12-02
Depends: R (>= 3.1.0)
Imports: foreign, RImageJROI, png, ttutils, sp, geometry (>= 0.2-1), RTriangle (>= 1.6-0.4), rgl, R.matlab
Suggests: testthat, gWidgetsRGtk2, gWidgets, cairoDevice
Packaged: 2014-12-02 16:59:26 UTC; sterratt
Author: David C. Sterratt [aut, cre, cph], Daniel Lyngholm [aut, cph]
Maintainer: David C. Sterratt
NeedsCompilation: yes
Repository: CRAN
Date/Publication: 2014-12-02 20:19:11

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Package MPSEM updated to version 0.2-6 with previous version 0.2-5 dated 2014-06-20

Title: Modeling Phylogenetic Signals using Eigenvector Maps
Description: Computational tools to represent phylogenetic signals using adapted eigenvector maps.
Author: Guillaume Guenard, with contribution from Pierre Legendre
Maintainer: Guillaume Guenard

Diff between MPSEM versions 0.2-5 dated 2014-06-20 and 0.2-6 dated 2014-12-02

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Package intsvy updated to version 1.5 with previous version 1.4 dated 2014-09-11

Title: International Assessment Data Manager
Description: Provides tools for importing, merging, and analysing data from international assessment studies (TIMSS, PIRLS, PISA and PIAAC)
Author: Daniel Caro , Przemyslaw Biecek
Maintainer: Daniel Caro

Diff between intsvy versions 1.4 dated 2014-09-11 and 1.5 dated 2014-12-02

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New package hnp with initial version 1.0
Package: hnp
Type: Package
Title: Half-Normal Plots with Simulation Envelopes
Version: 1.0
Date: 2014-11-27
Authors@R: c(person("Rafael", "de Andrade Moral", role = c("aut", "cre"), email = "rafael_moral@yahoo.com.br"), person("John", "Hinde", role = "aut"), person("Clarice", "Garcia Borges Demetrio", role = "aut"))
Author: Rafael de Andrade Moral [aut, cre], John Hinde [aut], Clarice Garcia Borges Demetrio [aut]
Maintainer: Rafael de Andrade Moral
Depends: R (>= 3.0.0), MASS (>= 7.3-35)
Suggests: lme4, gamlss, gamlss.dist, pscl, nnet, aods3, VGAM, glmmADMB, latticeExtra
Additional_repositories: http://www.hafro.is/~arnima/repos
Description: Generates (half-)normal plots with simulation envelopes using different diagnostics from a range of different fitted models. A few example datasets are included.
License: GPL (>= 2)
Packaged: 2014-12-02 18:49:32 UTC; Rafael
NeedsCompilation: no
Repository: CRAN
Date/Publication: 2014-12-02 20:22:29

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New package rncl with initial version 0.2.0
Package: rncl
Title: An interface to the Nexus Class Library
Version: 0.2.0
Date: 2014-12-01
Authors@R: c(person("Francois", "Michonneau", role=c("aut", "cre"), email="francois.michonneau@gmail.com"), person("Ben", "Bolker", role=c("aut")), person("Mark", "Holder", role=c("aut", "cre")), person("Paul", "Lewis", role=c("aut", "cre")), person("Brian", "O'Meara", role=c("aut", "cre")))
Maintainer: Francois Michonneau
Description: An interface to the Nexus Class Library which allows parsing of NEXUS, Newick and other phylogenetic tree file formats. It provides elements of the file that can be used to build phylogenetic objects such as ape's phylo or phylobase's phylo4(d).
Imports: Rcpp (>= 0.11.0), ape
Suggests: testthat
LinkingTo: Rcpp
Depends: R (>= 3.1.1)
License: BSD_2_clause + file LICENSE
URL: https://github.com/fmichonneau/rncl
BugReports: https://github.com/fmichonneau/rncl/issues
LazyData: true
Packaged: 2014-12-02 16:52:49 UTC; francois
Author: Francois Michonneau [aut, cre], Ben Bolker [aut], Mark Holder [aut, cre], Paul Lewis [aut, cre], Brian O'Meara [aut, cre]
NeedsCompilation: yes
Repository: CRAN
Date/Publication: 2014-12-02 18:23:19

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Package gplots updated to version 2.15.0 with previous version 2.14.2 dated 2014-09-18

Title: Various R programming tools for plotting data
Description: Various R programming tools for plotting data
Author: Gregory R. Warnes, Ben Bolker, Lodewijk Bonebakker, Robert Gentleman, Wolfgang Huber Andy Liaw, Thomas Lumley, Martin Maechler, Arni Magnusson, Steffen Moeller, Marc Schwartz, Bill Venables
Maintainer: Gregory R. Warnes

Diff between gplots versions 2.14.2 dated 2014-09-18 and 2.15.0 dated 2014-12-02

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Package TIMP updated to version 1.12.0 with previous version 1.11.0 dated 2014-01-25

Title: Fitting Seperable Nonlinear Models in Spectroscopy and Microscopy
Description: TIMP is a problem-solving environment (PSE) for fitting separable nonlinear models to measurements arising in physics and chemistry experiments, and has been extensively applied to time-resolved spectroscopy and FLIM-FRET data.
Author: Katharine M. Mullen, Joris J. Snellenburg, Sergey P. Laptenok, David Nicolaides, Ivo H.M. van Stokkum
Maintainer: Joris J. Snellenburg

Diff between TIMP versions 1.11.0 dated 2014-01-25 and 1.12.0 dated 2014-12-02

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Package rrcovNA updated to version 0.4-7 with previous version 0.4-4 dated 2013-08-28

Title: Scalable Robust Estimators with High Breakdown Point for Incomplete Data
Description: Robust Location and Scatter Estimation and Robust Multivariate Analysis with High Breakdown Point for Incomplete Data
Author: Valentin Todorov
Maintainer: Valentin Todorov

Diff between rrcovNA versions 0.4-4 dated 2013-08-28 and 0.4-7 dated 2014-12-02

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Package rrcovHD updated to version 0.2-3 with previous version 0.2-2 dated 2013-08-28

Title: Robust multivariate Methods for High Dimensional Data
Description: Robust multivariate methods for high dimensional data: outlier detection, PCA, PLS, classification
Author: Valentin Todorov
Maintainer: Valentin Todorov

Diff between rrcovHD versions 0.2-2 dated 2013-08-28 and 0.2-3 dated 2014-12-02

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New package radar with initial version 1.0.0
Package: radar
Type: Package
Title: Fundamental Formulas for Radar
Version: 1.0.0
Encoding: UTF-8
Authors@R: c(person(given = "Jose'", family = "Gama", role = c("aut","cre"),email = "rxprtgama@gmail.com"), person(given = "Nick", family = "Guy", role = c("aut")))
Description: Fundamental formulas for Radar, for attenuation, range, velocity, effectiveness, power, scatter, doppler, geometry, radar equations, etc. Based on Nick Guy's Python package PyRadarMet
License: GPL (>= 3)
Depends: R (>= 2.7.0)
Packaged: 2014-12-02 15:31:46.027 UTC; poky
Author: Jose' Gama [aut, cre], Nick Guy [aut]
Maintainer: Jose' Gama
NeedsCompilation: no
Repository: CRAN
Date/Publication: 2014-12-02 17:04:26

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Package gamboostMSM updated to version 1.1.87 with previous version 1.1.5 dated 2014-02-11

Title: Estimating multistate models using gamboost()
Description: Provides features to use function gamboost() from package mboost for estimation of multistate models
Author: Holger Reulen
Maintainer: Holger Reulen

Diff between gamboostMSM versions 1.1.5 dated 2014-02-11 and 1.1.87 dated 2014-12-02

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Package rrcov updated to version 1.3-8 with previous version 1.3-4 dated 2013-08-26

Title: Scalable Robust Estimators with High Breakdown Point
Description: Robust Location and Scatter Estimation and Robust Multivariate Analysis with High Breakdown Point.
Author: Valentin Todorov
Maintainer: Valentin Todorov

Diff between rrcov versions 1.3-4 dated 2013-08-26 and 1.3-8 dated 2014-12-02

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New package RPANDA with initial version 1.0
Package: RPANDA
Version: 1.0
Date: 2014-02-04
Type: Package
Title: Phylogenetic ANalyses of DiversificAtion
Depends: R (>= 2.14.2), ape, picante, pspline, deSolve
Suggests: testthat
Encoding: UTF-8
Author: Hélène Morlon [aut, cre, cph]
Authors@R: c(person("Hélène", "Morlon", role = c("aut", "cre", "cph"), email = "morlon@biologie.ens.fr"))
Maintainer: Hélène Morlon
Description: Implements fits of diversification models to phylogenetic data. See Morlon et al. PLoSB (2010), Morlon et al. PNAS (2011), Condamine et al. Eco Lett (2013), Morlon et al. Eco Lett (2014) and Manceau et al. (in prep).
License: GPL-2
URL: https://github.com/hmorlon/PANDA
Packaged: 2014-12-02 11:24:04 UTC; helenemorlon
NeedsCompilation: no
Repository: CRAN
Date/Publication: 2014-12-02 14:36:08

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Package FLIM updated to version 1.2 with previous version 1.1 dated 2014-05-19

Title: Farewell’s Linear Increments Model
Description: FLIM fits linear models for the observed increments in a longitudinal dataset, and imputes missing values according to the models.
Author: Rune Hoff with contributions from Jon Michael Gran and Daniel Farewell
Maintainer: Rune Hoff

Diff between FLIM versions 1.1 dated 2014-05-19 and 1.2 dated 2014-12-02

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New package choroplethrAdmin1 with initial version 1.0.0
Package: choroplethrAdmin1
Type: Package
Title: Contains an Administrative-Level-1 Map of the World
Version: 1.0.0
Date: 2014-12-02
Author: Ari Lamstein
Maintainer: Ari Lamstein
Description: Contains an administrative-level-1 map of the world. Administrative-level-1 is the generic term for the largest sub-national subdivision of a country. This package was created for use with the choroplethr package.
License: BSD_3_clause + file LICENSE
URL: https://groups.google.com/forum/#!forum/choroplethr
Imports: ggplot2
Packaged: 2014-12-02 11:47:09 UTC; arilamstein
NeedsCompilation: no
Repository: CRAN
Date/Publication: 2014-12-02 14:30:53

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Package BcDiag updated to version 1.0.6 with previous version 1.0.5 dated 2014-10-17

Title: Diagnostics plots for Bicluster Data
Description: This package provides Diagnostic tools based on two way anova and median polish residual plots for Bicluster output obtained from packages; "biclust" by Kaiser et al.(2008),"isa2" by Csardi et al. (2010) and "fabia" by Hochreiter et al. (2010). Moreover, It provides visualization tools for bicluster output and corresponding non bicluster rows or columns outcomes. It has also extended the idea of Kaiser et al.(2008) which is, extracting bicluster output in a text format, by adding by adding two bicluster methods from fabia and isa2 r packages.
Author: Aregay Mengsteab, Martin Otava, Tatsiana Khamiakova, Ewoud De Troyer
Maintainer: Ewoud De Troyer

Diff between BcDiag versions 1.0.5 dated 2014-10-17 and 1.0.6 dated 2014-12-02

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New package ASPBay with initial version 1.0
Package: ASPBay
Type: Package
Title: Bayesian Inference on Causal Genetic Variants using Affected Sib-Pairs Data
Depends: hexbin, Rcpp
LinkingTo: Rcpp, RcppArmadillo
Version: 1.0
Date: 2014-11-18
Author: Claire Dandine-Roulland
Maintainer: Claire Dandine-Roulland
Description: This package allows to make inference on the properties of causal genetic variants in linkage disequilibrium with genotyped markers. In a first step, we select a subset of variants using a score statistic for affected sib-pairs. In a second step, on the selected subset, we make inference on causal genetic variants in the considered region.
License: GPL-2
Packaged: 2014-12-02 11:25:15 UTC; dandine
NeedsCompilation: yes
Repository: CRAN
Date/Publication: 2014-12-02 14:28:23

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Package nacopula (with last version 0.8-1) was removed from CRAN

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

2012-03-30 0.8-1
2012-02-06 0.8-0
2011-09-24 0.7-9-1
2011-09-21 0.7-9
2011-03-04 0.4-4
2010-08-18 0.4-3
2010-07-02 0.4-2

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Package RQuantLib updated to version 0.4.0 with previous version 0.3.12 dated 2014-03-09

Title: R Interface to the QuantLib Library
Description: The RQuantLib package makes parts of QuantLib accessible from R The QuantLib project aims to provide a comprehensive software framework for quantitative finance. The goal is to provide a standard open source library for quantitative analysis, modeling, trading, and risk management of financial assets.
Author: Dirk Eddelbuettel, Khanh Nguyen (during 2009-2010)
Maintainer: Dirk Eddelbuettel

Diff between RQuantLib versions 0.3.12 dated 2014-03-09 and 0.4.0 dated 2014-12-02

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Package qgraph updated to version 1.3 with previous version 1.2.5 dated 2014-05-22

Title: Network-based data visualization
Description: The qgraph package can be used to visualize data as networks as well as provides an interface for visualizing weighted graphical models.
Author: Sacha Epskamp, Giulio Costantini, Angelique O. J. Cramer, Lourens J. Waldorp, Verena D. Schmittmann and Denny Borsboom
Maintainer: Sacha Epskamp

Diff between qgraph versions 1.2.5 dated 2014-05-22 and 1.3 dated 2014-12-02

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Package PrevMap updated to version 1.1.1 with previous version 1.1 dated 2014-11-25

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 1.1 dated 2014-11-25 and 1.1.1 dated 2014-12-02

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New package ARTool with initial version 0.9.3
Package: ARTool
Title: Aligned Rank Transform
Version: 0.9.3
Date: 2014-11-20
Authors@R: c(person("Matthew", "Kay", role = c("aut", "cre"), email = "mjskay@uw.edu"), person("Jacob O.", "Wobbrock", role = "aut", email = "wobbrock@uw.edu"))
Maintainer: Matthew Kay
Description: Aligned Rank Transform for nonparametric factorial ANOVAs
Depends: lme4, car
Imports: plyr, pbkrtest
Suggests: testthat, lsmeans
License: GPL (>= 2)
BugReports: https://github.com/mjskay/ARTool/issues/new
URL: https://github.com/mjskay/ARTool
Packaged: 2014-12-02 09:30:57 UTC; Matthew
Author: Matthew Kay [aut, cre], Jacob O. Wobbrock [aut]
NeedsCompilation: no
Repository: CRAN
Date/Publication: 2014-12-02 12:24:50

More information about ARTool at CRAN
Permanent link

Package seqinr updated to version 3.1-2 with previous version 3.0-9 dated 2014-10-31

Title: Biological Sequences Retrieval and Analysis
Description: Exploratory data analysis and data visualization for biological sequence (DNA and protein) data. Includes also utilities for sequence data management under the ACNUC system.
Author: Delphine Charif and Jean R. Lobry and Anamaria Necsulea and Leonor Palmeira and Simon Penel and Guy Perriere
Maintainer: Simon Penel

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 seqinr-3.1-2/seqinr/src/alignment.c                     |   36 ++-
 seqinr-3.1-2/seqinr/src/getzlibsock.c                   |    6 
 seqinr-3.1-2/seqinr/src/kaks.c                          |    4 
 107 files changed, 240 insertions(+), 224 deletions(-)

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New package secrlinear with initial version 1.0.3
Package: secrlinear
Type: Package
Title: Spatially Explicit Capture-Recapture for Linear Habitats
Version: 1.0.3
Depends: R (>= 3.0.0), secr(>= 2.9.1), sp, igraph
Imports: parallel, maptools, rgeos, MASS
Suggests: knitr, secrdesign
VignetteBuilder: knitr
Date: 2014-12-02
Author: Murray Efford
Maintainer: Murray Efford
Description: Tools for spatially explicit capture-recapture analysis of animal populations in linear habitats, extending package 'secr'
License: GPL (>= 2)
LazyData: yes
URL: http://www.otago.ac.nz/density
Packaged: 2014-12-02 07:18:35 UTC; Murray
NeedsCompilation: no
Repository: CRAN
Date/Publication: 2014-12-02 09:45:03

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Package VAR.etp updated to version 0.7 with previous version 0.6 dated 2014-11-09

Title: VAR modelling: estimation, testing, and prediction
Description: Estimation, Hypothesis Testing, Prediction for Stationary Vector Autoregressive Models
Author: Jae. H. Kim
Maintainer: Jae H. Kim

Diff between VAR.etp versions 0.6 dated 2014-11-09 and 0.7 dated 2014-12-02

 DESCRIPTION            |    8 ++++----
 MD5                    |   18 +++++++++---------
 R/ARM2.Fore.R          |    2 +-
 R/ARM3.Fore.R          |    2 +-
 R/VAR.Fore.R           |    2 +-
 R/VAR.ForeB.R          |    2 +-
 R/VAR.Rmat.R           |    2 +-
 man/VAR.etp-package.Rd |   10 ++++++----
 man/VAR.irf.Rd         |    4 ++--
 man/data1.Rd           |    2 +-
 10 files changed, 27 insertions(+), 25 deletions(-)

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Package turfR updated to version 0.8-7 with previous version 0.8-4 dated 2014-05-12

Title: TURF Analysis for R
Description: Package for analyzing TURF (Total Unduplicated Reach and Frequency) data in R. No looping in TURF algorithm results in fast processing times. Allows for individual-level weights, depth specification, and user-truncated combination set(s). Allows user to substitute Monte Carlo simulated combination set(s) after set(s) exceed a user-specified limit.
Author: Jack Horne [aut, cre]
Maintainer: Jack Horne

Diff between turfR versions 0.8-4 dated 2014-05-12 and 0.8-7 dated 2014-12-02

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 4 files changed, 7 insertions(+), 7 deletions(-)

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New package netgsa with initial version 1.0
Package: netgsa
Type: Package
Title: Network-based Gene Set Analysis
Version: 1.0
Date: 2014-12-01
Author: Ali Shojaie and Jing Ma
Maintainer: Jing Ma
Description: Functions for carrying out Network-based Gene Set Analysis by incorporating external information about interactions among genes, as well as novel interactions learned from data
Depends: cvTools, corpcor, glasso, glmnet, igraph
Suggests: MASS
License: GPL (>= 2)
LazyLoad: yes
URL: http://arxiv.org/abs/1411.7919
Packaged: 2014-12-02 02:14:06 UTC; jingma
NeedsCompilation: no
Repository: CRAN
Date/Publication: 2014-12-02 07:29:28

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New package MOrder with initial version 0.1
Package: MOrder
Title: Check Time Homogeneity and Markov Chain Order
Description: MOrder provide functions to check time homogeneity and order of markov chain by using chi-squared test, AIC value and BIC value.
Version: 0.1
Date: 2014-03-04
Author: Akshay Chougule , Dr Robert Canales
Maintainer: Dr Robert Canales
License: GPL-2
LazyData: true
Packaged: 2014-12-01 22:49:02 UTC; akshaychougule
NeedsCompilation: no
Repository: CRAN
Date/Publication: 2014-12-02 07:23:02

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Package krm updated to version 2014.12-1 with previous version 13.11-03 dated 2013-11-04

Title: Kernel-based Regression Models
Description: Testing methods for kernel-based regression models.
Author: Youyi Fong , Saheli Datta, Krisztian Sebestyen
Maintainer: Youyi Fong

Diff between krm versions 13.11-03 dated 2013-11-04 and 2014.12-1 dated 2014-12-02

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 krm-2014.12-1/krm/MD5                                   |   39 ++---
 krm-2014.12-1/krm/NAMESPACE                             |    3 
 krm-2014.12-1/krm/R/getSeqKernel.r                      |   37 +++-
 krm-2014.12-1/krm/R/krm.most.R                          |  122 +++++++---------
 krm-2014.12-1/krm/R/sim.liu.R                           |    4 
 krm-2014.12-1/krm/inst/unitTests/runit.getSeqKernel.R   |   32 ++--
 krm-2014.12-1/krm/inst/unitTests/runit.krm.most.R       |   24 +--
 krm-2014.12-1/krm/inst/unitTests/runit.krm.score.test.R |   11 -
 krm-2014.12-1/krm/man/getSeqKernel.Rd                   |   10 +
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 krm-2014.12-1/krm/man/krm.score.test.Rd                 |    4 
 krm-2014.12-1/krm/src/MI_kernel.cpp                     |   21 ++
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 krm-2014.12-1/krm/src/ProteinSequence.cpp               |   43 +++--
 krm-2014.12-1/krm/src/ProteinSequence.h                 |    2 
 krm-2014.12-1/krm/src/RandomPlus.h                      |    2 
 krm-2014.12-1/krm/src/U.h                               |    5 
 22 files changed, 261 insertions(+), 181 deletions(-)

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Package bartMachine updated to version 1.1.1 with previous version 1.0.4 dated 2014-09-05

Title: Bayesian Additive Regression Trees
Description: An advanced implementation of Bayesian Additive Regression Trees with expanded features for data analysis and visualization.
Author: Adam Kapelner and Justin Bleich (R package), see COPYRIGHTS file for the authors of the java libraries
Maintainer: Adam Kapelner

Diff between bartMachine versions 1.0.4 dated 2014-09-05 and 1.1.1 dated 2014-12-02

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 bartMachine-1.1.1/bartMachine/MD5                                                       |  133 +++++-----
 bartMachine-1.1.1/bartMachine/NAMESPACE                                                 |    8 
 bartMachine-1.1.1/bartMachine/R/bartMachine.R                                           |   61 ++--
 bartMachine-1.1.1/bartMachine/R/bart_package_builders.R                                 |   68 +++--
 bartMachine-1.1.1/bartMachine/R/bart_package_cross_validation.R                         |   66 +++-
 bartMachine-1.1.1/bartMachine/R/bart_package_f_tests.R                                  |    4 
 bartMachine-1.1.1/bartMachine/R/bart_package_inits.R                                    |   45 ---
 bartMachine-1.1.1/bartMachine/R/bart_package_plots.R                                    |   77 +----
 bartMachine-1.1.1/bartMachine/R/bart_package_predicts.R                                 |   41 +--
 bartMachine-1.1.1/bartMachine/R/bart_package_summaries.R                                |    5 
 bartMachine-1.1.1/bartMachine/R/bart_package_variable_selection.R                       |   36 +-
 bartMachine-1.1.1/bartMachine/R/zzz.R                                                   |    4 
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 bartMachine-1.1.1/bartMachine/java/README                                               |    2 
 bartMachine-1.1.1/bartMachine/java/bartMachine/Classifier.java                          |    3 
 bartMachine-1.1.1/bartMachine/java/bartMachine/TreeArrayIllustration.java               |    4 
 bartMachine-1.1.1/bartMachine/java/bartMachine/TreeIllustration.java                    |    4 
 bartMachine-1.1.1/bartMachine/java/bartMachine/bartMachineClassification.java           |    4 
 bartMachine-1.1.1/bartMachine/java/bartMachine/bartMachineClassificationMultThread.java |    4 
 bartMachine-1.1.1/bartMachine/java/bartMachine/bartMachineRegression.java               |    4 
 bartMachine-1.1.1/bartMachine/java/bartMachine/bartMachineRegressionMultThread.java     |   29 --
 bartMachine-1.1.1/bartMachine/java/bartMachine/bartMachineTreeNode.java                 |    9 
 bartMachine-1.1.1/bartMachine/java/bartMachine/bartMachine_a_base.java                  |    4 
 bartMachine-1.1.1/bartMachine/java/bartMachine/bartMachine_b_hyperparams.java           |    8 
 bartMachine-1.1.1/bartMachine/java/bartMachine/bartMachine_c_debug.java                 |    4 
 bartMachine-1.1.1/bartMachine/java/bartMachine/bartMachine_d_init.java                  |    8 
 bartMachine-1.1.1/bartMachine/java/bartMachine/bartMachine_e_gibbs_base.java            |    4 
 bartMachine-1.1.1/bartMachine/java/bartMachine/bartMachine_f_gibbs_internal.java        |    4 
 bartMachine-1.1.1/bartMachine/java/bartMachine/bartMachine_g_mh.java                    |    3 
 bartMachine-1.1.1/bartMachine/java/bartMachine/bartMachine_h_eval.java                  |    3 
 bartMachine-1.1.1/bartMachine/java/bartMachine/bartMachine_i_prior_cov_spec.java        |    4 
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 bartMachine-1.1.1/bartMachine/man/bartMachineCV.Rd                                      |    5 
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 bartMachine-1.1.1/bartMachine/man/bart_predict_for_test_data.Rd                         |    9 
 bartMachine-1.1.1/bartMachine/man/calc_credible_intervals.Rd                            |    3 
 bartMachine-1.1.1/bartMachine/man/calc_prediction_intervals.Rd                          |    3 
 bartMachine-1.1.1/bartMachine/man/check_bart_error_assumptions.Rd                       |    3 
 bartMachine-1.1.1/bartMachine/man/cov_importance_test.Rd                                |    3 
 bartMachine-1.1.1/bartMachine/man/destroy_bart_machine.Rd                               |   30 --
 bartMachine-1.1.1/bartMachine/man/get_sigsqs.Rd                                         |    3 
 bartMachine-1.1.1/bartMachine/man/get_var_counts_over_chain.Rd                          |    3 
 bartMachine-1.1.1/bartMachine/man/get_var_props_over_chain.Rd                           |    3 
 bartMachine-1.1.1/bartMachine/man/interaction_investigator.Rd                           |    3 
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 bartMachine-1.1.1/bartMachine/man/k_fold_cv.Rd                                          |   14 -
 bartMachine-1.1.1/bartMachine/man/pd_plot.Rd                                            |    6 
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 bartMachine-1.1.1/bartMachine/man/predict.Rd                                            |    6 
 bartMachine-1.1.1/bartMachine/man/print.Rd                                              |    3 
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 75 files changed, 427 insertions(+), 455 deletions(-)

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