Sun, 17 May 2015

New package rotationForest with initial version 0.1
Package: rotationForest
Type: Package
Title: Fit and Deploy Rotation Forest Models
Version: 0.1
Date: 2015-05-15
Imports: rpart
Author: Michel Ballings and Dirk Van den Poel
Maintainer: Michel Ballings <michel.ballings@gmail.com>
Description: Fit and deploy rotation forest models ("Rodriguez, J.J., Kuncheva, L.I., 2006. Rotation forest: A new classifier ensemble method. IEEE Trans. Pattern Anal. Mach. Intell. 28, 1619-1630") for binary classification. Rotation forest is an ensemble method where each base classifier (tree) is fit on the principal components of the variables of random partitions of the feature set.
License: GPL (>= 2)
NeedsCompilation: no
Packaged: 2015-05-17 15:11:09 UTC; michelballings
Repository: CRAN
Date/Publication: 2015-05-18 01:14:15

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Package rankdist updated to version 0.4.1 with previous version 0.3.1 dated 2015-05-05

Title: Distance Based Ranking Models
Description: Implements distance based probability models for ranking data. The supported models include Mallow's Phi-model (Kendall distance), Weighted Kendall distance model and Phi-Component model. Mixture models are also supported.
Author: Zhaozhi Qian
Maintainer: Zhaozhi Qian <qianzhaozhi@connect.hku.hk>

Diff between rankdist versions 0.3.1 dated 2015-05-05 and 0.4.1 dated 2015-05-17

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Package random updated to version 0.2.4 with previous version 0.2.3 dated 2015-01-08

Title: True Random Numbers using RANDOM.ORG
Description: The true random number service provided by the RANDOM.ORG website created by Mads Haahr samples atmospheric noise via radio tuned to an unused broadcasting frequency together with a skew correction algorithm due to John von Neumann. More background is available in the included vignette based on an essay by Mads Haahr. In its current form, the package offers functions to retrieve random integers, randomized sequences and random strings.
Author: Dirk Eddelbuettel <edd@debian.org>
Maintainer: Dirk Eddelbuettel <edd@debian.org>

Diff between random versions 0.2.3 dated 2015-01-08 and 0.2.4 dated 2015-05-17

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Package ocedata updated to version 0.1.3 with previous version 0.1.2 dated 2014-05-07

Title: Oceanographic Datasets for Oce
Description: Several important and Oceanographic datasets are provided. These are particularly useful to the Oce package, but can be helpful in a general context, as well.
Author: Dan Kelley <Dan.Kelley@Dal.Ca>
Maintainer: Dan Kelley <Dan.Kelley@Dal.Ca>

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Package crayon updated to version 1.2.1 with previous version 1.2.0 dated 2015-04-08

Title: Colored Terminal Output
Description: Colored terminal output on terminals that support ANSI color and highlight codes. ANSI color support is automatically detected. Colors and highlighting can be combined and nested. New styles can also be created easily. This package was inspired by the chalk JavaScript project.
Author: Gabor Csardi [aut, cre]
Maintainer: Gabor Csardi <csardi.gabor@gmail.com>

Diff between crayon versions 1.2.0 dated 2015-04-08 and 1.2.1 dated 2015-05-17

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Package clickstream updated to version 1.1.4 with previous version 1.1.3 dated 2015-01-09

Title: Analyzes Clickstreams Based on Markov Chains
Description: A set of tools to read, analyze and write lists of click sequences on websites (i.e. clickstream). A click can be represented by a number, character or string. Clickstreams can be modeled as zero- (only computes occurrence probabilities), first- or higher-order Markov chains.
Author: Michael Scholz
Maintainer: Michael Scholz <michael.scholz@uni-passau.de>

Diff between clickstream versions 1.1.3 dated 2015-01-09 and 1.1.4 dated 2015-05-17

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Package WikipediR updated to version 1.2.0 with previous version 1.1.0 dated 2014-12-06

Title: A MediaWiki API Wrapper
Description: A wrapper for the MediaWiki API, aimed particularly at the Wikimedia 'production' wikis, such as Wikipedia. It can be used to retrieve page text, information about users or the history of pages, and elements of the category tree.
Author: Oliver Keyes
Maintainer: Oliver Keyes <ironholds@gmail.com>

Diff between WikipediR versions 1.1.0 dated 2014-12-06 and 1.2.0 dated 2015-05-17

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New package ssfa with initial version 1.0
Package: ssfa
Type: Package
Title: Spatial Stochastic Frontier Analysis
Version: 1.0
Date: 2015-05-15
Author: Elisa Fusco, Francesco Vidoli
Maintainer: Elisa Fusco <fusco_elisa@libero.it>
Description: Spatial Stochastic Frontier Analysis (SSFA) is an original method for controlling the spatial heterogeneity in Stochastic Frontier Analysis (SFA) models by splitting the inefficiency term into three terms: the first one related to spatial peculiarities of the territory in which each single unit operates, the second one related to the specific production features and the third one representing the error term.
Depends: Matrix, maxLik, spdep, sp
License: GPL-3
NeedsCompilation: no
Packaged: 2015-05-17 20:00:39 UTC; Elisa
Repository: CRAN
Date/Publication: 2015-05-18 00:52:19

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Package sjmisc updated to version 1.0.2 with previous version 1.0.1 dated 2015-04-18

Title: Miscellaneous Data Management Tools
Description: Collection of several utility functions for reading or writing data, recoding and labelling variables and some frequently used statistical tests.
Author: Daniel Lüdecke <d.luedecke@uke.de>
Maintainer: Daniel Lüdecke <d.luedecke@uke.de>

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New package MInt with initial version 1.0.1
Package: MInt
Type: Package
Title: Learn Direct Interaction Networks
Version: 1.0.1
Date: 2015-05-17
Author: Surojit Biswas, Meredith McDonald, Derek S. Lundberg, Jeffery L. Dangl, Vladimir Jojic
Maintainer: Surojit Biswas <surojitbiswas@g.harvard.edu>
Description: Learns direct microbe-microbe interaction networks using a Poisson multivariate-normal hierarchical model with an L1 penalized precision matrix. Optimization is carried out using an iterative conditional modes algorithm.
License: GPL-2
Depends: R (>= 3.1.2), glasso (>= 1.8), trust (>= 0.1-6), MASS (>= 7.3-35), testthat (>= 0.9.1)
Suggests: knitr
VignetteBuilder: knitr
Packaged: 2015-05-17 15:32:02 UTC; sbiswas
NeedsCompilation: no
Repository: CRAN
Date/Publication: 2015-05-18 00:57:24

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Package HelpersMG updated to version 1.1 with previous version 1.0 dated 2015-04-07

Title: Tools for Earth Meteorological Analysis
Description: Contains many functions useful for managing 'NetCDF' files (see http://en.wikipedia.org/wiki/NetCDF), get tide levels on any point of the globe, get moon phase and time for sun rise and fall, analyse and reconstruct daily time series of temperature with irregular sinusoidal pattern, show scales and wind rose in plot with change of color of text, Metropolis-Hastings algorithm for Bayesian MCMC analysis, plot graphs or boxplot with error bars, search files in disk by there names or their content, read the contents of all files from a folder at one time.
Author: Marc Girondot
Maintainer: Marc Girondot <marc.girondot@u-psud.fr>

Diff between HelpersMG versions 1.0 dated 2015-04-07 and 1.1 dated 2015-05-17

 DESCRIPTION                  |    8 +--
 MD5                          |   78 ++++++++++++++++++------------------
 NAMESPACE                    |    2 
 NEWS                         |   11 ++++-
 R/HelpersMG-package.R        |   11 +++--
 R/MHalgoGen.R                |   92 +++++++++++++++++++++----------------------
 R/ScalePreviousPlot.R        |    1 
 R/barplot_errbar.R           |    5 +-
 R/plot_add.R                 |    1 
 R/plot_errbar.R              |    1 
 man/ChangeCoordinate.Rd      |    2 
 man/HelpersMG-package.Rd     |   13 +++---
 man/MHalgoGen.Rd             |   30 +++++++-------
 man/ScalePreviousPlot.Rd     |    6 ++
 man/as.mcmc.mcmcComposite.Rd |    2 
 man/as.parameters.Rd         |    2 
 man/asc.Rd                   |    2 
 man/barplot_errbar.Rd        |    8 ++-
 man/chr.Rd                   |    2 
 man/clean.knitr.Rd           |    2 
 man/compare_AIC.Rd           |    2 
 man/compassRose2.Rd          |    2 
 man/convert.tz.Rd            |    2 
 man/getTide.Rd               |    2 
 man/growlnotify.Rd           |    2 
 man/ind_long_lat.Rd          |    2 
 man/inside.search.Rd         |    2 
 man/local.search.Rd          |    2 
 man/map.scale2.Rd            |    2 
 man/merge.mcmcComposite.Rd   |    2 
 man/minmax.periodic.Rd       |    2 
 man/moon_phase.Rd            |    2 
 man/plot.mcmcComposite.Rd    |    2 
 man/plot_add.Rd              |    6 ++
 man/plot_errbar.Rd           |    5 +-
 man/read_folder.Rd           |    2 
 man/similar.Rd               |    2 
 man/summary.mcmcComposite.Rd |    2 
 man/sun.info.Rd              |    2 
 man/temperature.periodic.Rd  |    2 
 40 files changed, 182 insertions(+), 144 deletions(-)

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New package Dark with initial version 0.9.4
Package: Dark
Type: Package
Title: The Analysis of Dark Adaptation Data
Version: 0.9.4
Date: 2015-05-17
Author: Dr Jeremiah MF Kelly
Maintainer: Dr Jeremiah MF Kelly <emkayoh@mac.com>
Description: The recovery of visual sensitivity in a dark environment is known as dark adaptation. In a clinical or research setting the recovery is typically measured after a dazzling flash of light and can be described by the Mahroo, Lamb and Pugh (MLP) model of dark adaptation. The functions in this package take dark adaptation data and use nonlinear regression to find the parameters of the model that 'best' describe the data. They do this by firstly, generating rapid initial objective estimates of data adaptation parameters, then a multi-start algorithm is used to reduce the possibility of a local minimum. There is also a bootstrap method to calculate parameter confidence intervals. The functions rely upon a 'dark' list or object. This object is created as the first step in the workflow and parts of the object are updated as it is processed.
License: GPL-3
LazyData: yes
URL: https://github.com/emkayoh/Dark, http://www.nihr.ac.uk
BugReports: https://github.com/emkayoh/Dark/issues
Suggests: knitr, rmarkdown,testthat
VignetteBuilder: knitr
Packaged: 2015-05-17 13:51:18 UTC; mqbxgjk2
NeedsCompilation: no
Repository: CRAN
Date/Publication: 2015-05-18 00:56:57

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New package rchallenge with initial version 1.1
Package: rchallenge
Title: A Simple Datascience Challenge System
Version: 1.1
Authors@R: c(person("Adrien", "Todeschini", email = "adrien.todeschini@gmail.com",role=c("aut", "cre")), person("Robin", "Genuer", email = "robin.genuer@isped.u-bordeaux2.fr",role=c("ctb")))
Description: A simple datascience challenge system using R Markdown and Dropbox. It requires no network configuration, does not depend on external platforms like e.g. Kaggle and can be easily installed on a personal computer.
URL: http://adrtod.github.io/rchallenge
BugReports: https://github.com/adrtod/rchallenge/issues
Depends: R (>= 3.2.0)
Imports: rmarkdown (>= 0.5.1), knitr (>= 1.6)
SystemRequirements: pandoc (>= 1.12.3) - http://johnmacfarlane.net/pandoc
License: GPL-2
LazyData: true
NeedsCompilation: no
Packaged: 2015-05-16 11:45:43 UTC; adrien-alea
Author: Adrien Todeschini [aut, cre], Robin Genuer [ctb]
Maintainer: Adrien Todeschini <adrien.todeschini@gmail.com>
Repository: CRAN
Date/Publication: 2015-05-17 16:38:17

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Package odeintr updated to version 1.3 with previous version 1.0 dated 2015-05-12

Title: C++ ODE Solvers Compiled on-Demand
Description: Wraps the Boost 'odeint' library for integration of differential equations.
Author: Timothy H. Keitt
Maintainer: Timothy H. Keitt <tkeitt@gmail.com>

Diff between odeintr versions 1.0 dated 2015-05-12 and 1.3 dated 2015-05-17

 DESCRIPTION                                   |   16 ++++++++-----
 MD5                                           |   30 +++++++++++++-------------
 NAMESPACE                                     |    2 -
 R/RcppExports.R                               |    8 +++---
 R/odeintr.R                                   |    9 +++++--
 inst/include/odeintr.h                        |    3 +-
 inst/templates/compile_implicit_template.cpp  |   15 ++++++++-----
 inst/templates/compile_sys_r_obs_template.cpp |   12 ++++++----
 inst/templates/compile_sys_template.cpp       |    9 +++++--
 man/compile_sys.Rd                            |    2 -
 man/implicit.Rd                               |    2 -
 man/integrate_sys.Rd                          |    9 ++++++-
 man/odeintr_package.Rd                        |    2 -
 man/set-opt.Rd                                |    2 -
 src/RcppExports.cpp                           |   16 ++++++++-----
 src/odeintr.cpp                               |   14 ++++++------
 16 files changed, 91 insertions(+), 60 deletions(-)

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Package bnlearn updated to version 3.8.1 with previous version 3.8 dated 2015-05-03

Title: Bayesian Network Structure Learning, Parameter Learning and Inference
Description: Bayesian network structure learning, parameter learning and inference. This package implements constraint-based (GS, IAMB, Inter-IAMB, Fast-IAMB, MMPC, Hiton-PC), pairwise (ARACNE and Chow-Liu), score-based (Hill-Climbing and Tabu Search) and hybrid (MMHC and RSMAX2) structure learning algorithms for discrete, Gaussian and conditional Gaussian networks, along with many score functions and conditional independence tests. The Naive Bayes and the Tree-Augmented Naive Bayes (TAN) classifiers are also implemented. Some utility functions (model comparison and manipulation, random data generation, arc orientation testing, simple and advanced plots) are included, as well as support for parameter estimation (maximum likelihood and Bayesian) and inference, conditional probability queries and cross-validation. Development snapshots with the latest bugfixes are available from www.bnlearn.com.
Author: Marco Scutari
Maintainer: Marco Scutari <marco.scutari@gmail.com>

Diff between bnlearn versions 3.8 dated 2015-05-03 and 3.8.1 dated 2015-05-17

 Changelog                 |    6 ++
 DESCRIPTION               |    8 +--
 MD5                       |   16 +++----
 R/custom.fit.R            |    4 -
 R/fitted.assignment.R     |    2 
 man/bnlearn-package.Rd    |    4 -
 src/allocations.c         |   96 ++++++++--------------------------------------
 src/data.frame.c          |   17 ++++++--
 src/include/allocations.h |   13 +++---
 9 files changed, 61 insertions(+), 105 deletions(-)

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New package PoisBinOrdNonNor with initial version 1.0
Package: PoisBinOrdNonNor
Type: Package
Title: Generation of up to Four Different Types of Variables
Version: 1.0
Date: 2015-04-12
Author: Rachel Nordgren, Hakan Demirtas
Maintainer: Rachel Nordgren <rnordg2@uic.edu>
Description: Generation of a chosen number of count, binary, ordinal, and continuous (via Fleishman polynomials) random variables, with specified correlations and marginal properties.
License: GPL (>= 2)
Depends: Matrix, corpcor, MASS, GenOrd, BB
Suggests: moments
Packaged: 2015-05-17 02:00:48 UTC; Rachel
NeedsCompilation: no
Repository: CRAN
Date/Publication: 2015-05-17 09:53:54

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New package infuser with initial version 0.1
Package: infuser
Type: Package
Title: A Very Basic Templating Engine
Version: 0.1
Date: 2015-05-15
Author: Bart Smeets
Maintainer: Bart Smeets <bartsmeets86@gmail.com>
Description: Replace parameters in strings and/or text files with specified values.
License: MIT + file LICENSE
LazyData: TRUE
Suggests: testthat
URL: https://github.com/bart6114/infuser/
BugReports: https://github.com/bart6114/infuser/issues
Packaged: 2015-05-16 18:50:04 UTC; bart
NeedsCompilation: no
Repository: CRAN
Date/Publication: 2015-05-17 10:04:52

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Package hergm updated to version 2.2-2 with previous version 2.2-1 dated 2015-03-08

Title: Hierarchical Exponential-Family Random Graph Models
Description: Estimate and simulate hierarchical exponential-family random graph models with local dependence.
Author: Michael Schweinberger <michael.schweinberger@rice.edu> [aut, cre], Mark S. Handcock <handcock@ucla.edu> [ctb], Pamela Luna <pamela.luna@rice.edu> [ctb]
Maintainer: Michael Schweinberger <michael.schweinberger@rice.edu>

Diff between hergm versions 2.2-1 dated 2015-03-08 and 2.2-2 dated 2015-05-17

 DESCRIPTION          |    8 ++++----
 MD5                  |    4 ++--
 R/hergm.preprocess.R |   13 +++++++------
 3 files changed, 13 insertions(+), 12 deletions(-)

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Package FWDselect updated to version 2.0 with previous version 1.1 dated 2013-04-16

Title: Selecting Variables in Regression Models
Description: A simple method to select the best model or best subset of variables using different types of data (binary, Gaussian or Poisson) and applying it in different contexts (parametric or non-parametric).
Author: Marta Sestelo [aut, cre], Nora M. Villanueva [aut], Javier Roca-Pardinas [aut]
Maintainer: Marta Sestelo <sestelo@uvigo.es>

Diff between FWDselect versions 1.1 dated 2013-04-16 and 2.0 dated 2015-05-17

 FWDselect-1.1/FWDselect/R/qselection2.R          |only
 FWDselect-1.1/FWDselect/inst                     |only
 FWDselect-1.1/FWDselect/man/FWDselect-package.Rd |only
 FWDselect-2.0/FWDselect/DESCRIPTION              |   36 -
 FWDselect-2.0/FWDselect/LICENSE                  |only
 FWDselect-2.0/FWDselect/MD5                      |   45 -
 FWDselect-2.0/FWDselect/NAMESPACE                |   22 
 FWDselect-2.0/FWDselect/NEWS                     |only
 FWDselect-2.0/FWDselect/R/FWDselect.R            |only
 FWDselect-2.0/FWDselect/R/diabetes.R             |only
 FWDselect-2.0/FWDselect/R/episode.R              |only
 FWDselect-2.0/FWDselect/R/plot.qselection.R      |   48 +
 FWDselect-2.0/FWDselect/R/pollution.R            |only
 FWDselect-2.0/FWDselect/R/print.qselection.R     |   41 -
 FWDselect-2.0/FWDselect/R/print.selection.R      |  131 ++-
 FWDselect-2.0/FWDselect/R/qselection.R           |   99 ++
 FWDselect-2.0/FWDselect/R/selection.R            |  804 ++++++++++++++---------
 FWDselect-2.0/FWDselect/R/test.R                 |  335 +++++++--
 FWDselect-2.0/FWDselect/data/diabetes.RData      |only
 FWDselect-2.0/FWDselect/man/FWDselect.Rd         |only
 FWDselect-2.0/FWDselect/man/diabetes.Rd          |only
 FWDselect-2.0/FWDselect/man/episode.Rd           |   38 -
 FWDselect-2.0/FWDselect/man/plot.qselection.Rd   |   60 -
 FWDselect-2.0/FWDselect/man/pollution.Rd         |   44 -
 FWDselect-2.0/FWDselect/man/print.qselection.Rd  |   61 -
 FWDselect-2.0/FWDselect/man/print.selection.Rd   |   67 -
 FWDselect-2.0/FWDselect/man/qselection.Rd        |   98 +-
 FWDselect-2.0/FWDselect/man/selection.Rd         |  125 +--
 FWDselect-2.0/FWDselect/man/test.Rd              |  135 +--
 29 files changed, 1373 insertions(+), 816 deletions(-)

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