Mon, 22 Dec 2014

Package rmarkdown updated to version 0.4.2 with previous version 0.3.3 dated 2014-09-17

Title: Dynamic Documents for R
Description: Convert R Markdown documents into a variety of formats including HTML, MS Word, PDF, and Beamer.
Author: JJ Allaire, Jonathan McPherson, Yihui Xie, Hadley Wickham, Joe Cheng, Jeff Allen
Maintainer: JJ Allaire

Diff between rmarkdown versions 0.3.3 dated 2014-09-17 and 0.4.2 dated 2014-12-22

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 tmp/cranberry1a3865c87e5a/rmarkdown-0.4.2/rmarkdown/NAMESPACE                                                          |    1 
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Package MPDiR updated to version 0.1-16 with previous version 0.1-15 dated 2014-03-26

Title: Data sets and scripts for Modeling Psychophysical Data in R.
Description: Data sets and scripts for Modeling Psychophysical Data in R (Springer).
Author: Kenneth Knoblauch and Laurence T. Maloney
Maintainer: Ken Knoblauch

Diff between MPDiR versions 0.1-15 dated 2014-03-26 and 0.1-16 dated 2014-12-22

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Package MixGHD updated to version 1.3 with previous version 1.2 dated 2014-12-10

Title: Model Based Clustering, Classification and Discriminant Analysis Using the Mixture of Generalized Hyperbolic Distributions
Description: Carries out model-based clustering, classification and discriminant analysis using five different models. The models are all based on the generalized hyperbolic distribution.The first model MGHD is the classical mixture of generalized hyperbolic distributions. The MGHFA is the mixture of generalized hyperbolic factor analyzers for high dimensional data sets. The MSGHD, mixture of multiple scaled generalized hyperbolic distributions. The cMSGHD is a MSGHD with convex contour plots. The MCGHD, mixture of coalesced generalized hyperbolic distributions is a new more flexible model.
Author: Cristina Tortora, Ryan P. Browne, Brian C. Franczak and Paul D. McNicholas.
Maintainer: Cristina Tortora

Diff between MixGHD versions 1.2 dated 2014-12-10 and 1.3 dated 2014-12-22

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Package diveRsity updated to version 1.9.73 with previous version 1.9.5 dated 2014-04-29

Title: A Comprehensive, General Purpose Population Genetics Analysis Package
Description: Allows the calculation of both genetic diversity partition statistics,genetic differentiation statistics and locus informativeness for ancestry assignment. It also provides users with various option to calculate bootstrapped 95% confidence intervals both across loci, for pairwise population comparisons and to plot these results interactively. V1.2 and up provides parallel computing capabilities and pairwise results without bootstrapping. Weir and Cockerham's 1984 F-statistics are now also calculated. Various plotting features are also provided. Chi-square tests of genetic heterogeneity are also provided. Functionality for the calculation of various diversity parameters is also possible for RAD-seq derived SNP data sets containing thousands of marker loci. A shiny application for the development of microsatellite multiplexes is also available
Author: Kevin Keenan
Maintainer: Kevin Keenan

Diff between diveRsity versions 1.9.5 dated 2014-04-29 and 1.9.73 dated 2014-12-22

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Package vardpoor updated to version 0.2.2 with previous version 0.2.1 dated 2014-12-19

Title: Variance Estimation for Sample Surveys by the Ultimate Cluster Method
Description: Generation of domain variables, linearisation of several nonlinear population statistics (the ratio of two totals, weighted income percentile, at-risk-of-poverty rate, at-risk-of-poverty threshold, Gini coefficient, gender pay gap, median income below at-risk-of-poverty gap, income quintile share ratio, relative median at-risk-of-poverty gap), computation of regression residuals in case of weight calibration, variance estimation of sample surveys by the ultimate cluster method (Hansen, Hurwitz and Madow, 1953), variance estimation for longitudinal, crossectional measures and measures of change for single and multistage stage cluster sampling designs (Berger, Y.G.). Several other precision measures are derived - standard error, the coefficient of variation, the margin of error, confidence interval, design effect.
Author: Juris Breidaks [aut, cre], Martins Liberts [aut], Santa Ivanova [aut]
Maintainer: Juris Breidaks

Diff between vardpoor versions 0.2.1 dated 2014-12-19 and 0.2.2 dated 2014-12-22

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Package timma updated to version 1.0.0 with previous version 0.99.0 dated 2014-12-09

Title: Target Inhibition Interaction using Maximization and Minimization Averaging
Description: Target Inhibition Interaction using Maximization/Minimization Averaging
Author: Liye
Maintainer: Liye He

Diff between timma versions 0.99.0 dated 2014-12-09 and 1.0.0 dated 2014-12-22

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Package gets updated to version 0.2 with previous version 0.1 dated 2014-10-15

Title: General-to-Specific (GETS) Modelling and Indicator Saturation Methods
Description: Automated multi-path General-to-Specific (GETS) modelling of the mean and variance of a regression, and indicator saturation methods for detecting structural breaks in the mean. The mean can be specified as an autoregressive model with covariates (an 'AR-X' model), and the variance can be specified as a log-variance model with covariates (a 'log-ARCH-X' model). The four main functions of the package are arx, getsm, getsv and isat. The first function, arx, estimates an AR-X model with log-ARCH-X errors. The second function, getsm, undertakes GETS model selection of the mean specification of an arx object. The third function, getsv, undertakes GETS model selection of the log-variance specification of an arx object. The fourth function, isat, undertakes GETS model selection of an indicator saturated mean specification.
Author: Felix Pretis, James Reade, Genaro Sucarrat
Maintainer: Genaro Sucarrat

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More information about gets at CRAN
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Package AutoSEARCH updated to version 1.4 with previous version 1.3 dated 2014-10-22

Title: General-to-Specific (GETS) Model Selection
Description: Automated multi-path General-to-Specific (GETS) model selection of either an AR-X model with log-ARCH-X errors, or of a log-ARCH-X model of the error. NOTE: The package has been succeeded by the package gets, also available on the CRAN, which is intended to be more user-friendly, faster and easier to extend. AutoSEARCH will continue to be maintained, but the development focus will switch to gets. Users are therefore encouraged to consider gets instead.
Author: Genaro Sucarrat
Maintainer: Genaro Sucarrat

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Package Rvcg updated to version 0.10.1 with previous version 0.10 dated 2014-12-16

Title: Manipulations of Triangular Meshes Based on the VCGLIB API
Description: Operations on triangular meshes based on VCGLIB. This package integrates nicely with the R-package "rgl" to render the meshes processed by Rvcg. The Visualization and Computer Graphics Library (VCG for short) is an open source portable C++ templated library for manipulation, processing and displaying with OpenGL of triangle and tetrahedral meshes. The library, composed by more than 100k lines of code, is released under the GPL license, and it is the base of most of the software tools of the Visual Computing Lab of the Italian National Research Council Institute ISTI (http://vcg.isti.cnr.it), like metro and MeshLab. The vcglib source is pulled from trunk (svn://svn.code.sf.net/p/vcg/code/trunk/vcglib) and patched to work with options determined by the configure script as well as to work with the header files included by RcppEigen.
Author: Stefan Schlager; the authors of VCGLIB for the included version of the code
Maintainer: Stefan Schlager

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Package mhsmm updated to version 0.4.14 with previous version 0.4.12 dated 2014-01-09

Title: Inference for Hidden Markov and Semi-Markov Models
Description: Parameter estimation and prediction for hidden Markov and semi-Markov models for data with multiple observation sequences. Suitable for equidistant time series data, with multivariate and/or missing data. Allows user defined emission distributions.
Author: Jared O'Connell , S°ren H°jsgaard
Maintainer: Jared O'Connell

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Package helsinki updated to version 0.9.24 with previous version 0.9.22 dated 2014-12-19

Title: Helsinki Open Data R Tools
Description: Tools for accessing various open data sources in the Helsinki region in Finland. Current data sources include the Real Estate Department (district maps), the Environmental Services Authority, Service Map API, Linked Events API and Helsinki Region Infoshare statistics API.
Author: Juuso Parkkinen, Leo Lahti, Joona Lehtomaki
Maintainer: Juuso Parkkinen

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Package RSNNS updated to version 0.4-6 with previous version 0.4-5 dated 2014-05-23

Title: Neural Networks in R using the Stuttgart Neural Network Simulator (SNNS)
Description: The Stuttgart Neural Network Simulator (SNNS) is a library containing many standard implementations of neural networks. This package wraps the SNNS functionality to make it available from within R. Using the RSNNS low-level interface, all of the algorithmic functionality and flexibility of SNNS can be accessed. Furthermore, the package contains a convenient high-level interface, so that the most common neural network topologies and learning algorithms integrate seamlessly into R.
Author: Christoph Bergmeir and Jos├ę M. Ben├ştez
Maintainer: Christoph Bergmeir

Diff between RSNNS versions 0.4-5 dated 2014-05-23 and 0.4-6 dated 2014-12-22

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Package pvclust updated to version 1.3-2 with previous version 1.3-1 dated 2014-12-05

Title: Hierarchical Clustering with P-Values via Multiscale Bootstrap Resampling
Description: An implementation of multiscale bootstrap resampling for assessing the uncertainty in hierarchical cluster analysis. It provides AU (approximately unbiased) p-value as well as BP (bootstrap probability) value for each cluster in a dendrogram.
Author: Ryota Suzuki , Hidetoshi Shimodaira
Maintainer: Ryota Suzuki

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Sun, 21 Dec 2014

Package V8 updated to version 0.3 with previous version 0.2 dated 2014-12-15

Title: Embedded JavaScript Engine
Description: V8 is Google's open source, high performance JavaScript engine. It is written in C++ and implements ECMAScript as specified in ECMA-262, 5th edition.
Author: Jeroen Ooms
Maintainer: Jeroen Ooms

Diff between V8 versions 0.2 dated 2014-12-15 and 0.3 dated 2014-12-21

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Package qdapTools updated to version 1.1.0 with previous version 1.0.3 dated 2014-10-04

Title: Tools for the qdap Package
Description: A collection of tools associated with the qdap package that may be useful outside of the context of text analysis.
Author: Bryan Goodrich [ctb], Dason Kurkiewicz [ctb], Kirill Muller [ctb], Tyler Rinker [aut, cre]
Maintainer: Tyler Rinker

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Package qdapRegex updated to version 0.2.0 with previous version 0.1.2 dated 2014-09-23

Title: Regular Expression Removal, Extraction, and Replacement Tools
Description: A collection of regular expression tools associated with the qdap package that may be useful outside of the context of discourse analysis. Tools include removal/extraction/replacement of abbreviations, dates, dollar amounts, email addresses, hash tags, numbers, percentages, person tags, phone numbers, times, and zip codes.
Author: Jason Gray [ctb], Tyler Rinker [aut, cre]
Maintainer: Tyler Rinker

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Package hydrostats updated to version 0.2.3 with previous version 0.2.1 dated 2014-08-20

Title: Hydrologic indices for daily time series data
Description: Calculates a suite of hydrologic indices for daily time series data that are widely used in hydrology and stream ecology.
Author: Nick Bond
Maintainer: Nick Bond

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Package MAd updated to version 0.8-2 with previous version 0.8-1 dated 2014-02-02

Title: Meta-Analysis with Mean Differences
Description: A collection of functions for conducting a meta-analysis with mean differences data. It uses recommended procedures as described in The Handbook of Research Synthesis and Meta-Analysis (Cooper, Hedges, & Valentine, 2009).
Author: AC Del Re & William T. Hoyt
Maintainer: AC Del Re

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Package AGD updated to version 0.31 with previous version 0.30 dated 2013-07-15

Title: Analysis of Growth Data
Description: Tools for NIHES course EP18 'Analysis of Growth Data', May 22-23 2012, Rotterdam.
Author: Stef van Buuren
Maintainer: Stef van Buuren

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Package sysfonts updated to version 0.3 with previous version 0.2 dated 2014-02-23

Title: Loading System Fonts into R
Description: This package uses FreeType to load system fonts and Google Fonts (https://www.google.com/fonts) into R. It is supposed to support other packages like R2SWF and showtext.
Author: Yixuan Qiu and authors/contributors of the included fonts. See file AUTHORS for details.
Maintainer: Yixuan Qiu

Diff between sysfonts versions 0.2 dated 2014-02-23 and 0.3 dated 2014-12-21

 DESCRIPTION                 |   16 +++----
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More information about sysfonts at CRAN
Permanent link

Package graphicsQC updated to version 1.0-6 with previous version 1.0-5 dated 2014-02-24

Title: Quality Control for Graphics in R
Description: The package provides functions to generate graphics files, compare them with ``model'' files, and report the results.
Author: Stephen Gardiner and Paul Murrell
Maintainer: Paul Murrell

Diff between graphicsQC versions 1.0-5 dated 2014-02-24 and 1.0-6 dated 2014-12-21

 ChangeLog               |   73 +++++++++++++++++++++++++-----------------------
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More information about graphicsQC at CRAN
Permanent link

Package depmix updated to version 0.9.13 with previous version 0.9.12 dated 2014-04-02

Title: Dependent Mixture Models
Description: Fit (multigroup) mixtures of latent Markov models on mixed categorical and continuous (timeseries) data. The Rdonlp2 package can optionally be used for optimization of the log-likelihood and is available from R-forge: https://r-forge.r-project.org/R/?group_id=156
Author: Ingmar Visser
Maintainer: Ingmar Visser

Diff between depmix versions 0.9.12 dated 2014-04-02 and 0.9.13 dated 2014-12-21

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Package adabag updated to version 4.0 with previous version 3.2 dated 2013-08-16

Title: Applies Multiclass AdaBoost.M1, SAMME and Bagging
Description: It implements Freund and Schapire's Adaboost.M1 algorithm and Breiman's Bagging algorithm using classification trees as individual classifiers. Once these classifiers have been trained, they can be used to predict on new data. Also, cross validation estimation of the error can be done. Since version 2.0 the function "margins" is available to calculate the margins for these classifiers. Also a higher flexibility is achieved giving access to the "rpart.control" argument of "rpart". Four important new features were introduced on version 3.0, AdaBoost-SAMME (Zhu et al., 2009) is implemented and a new function "errorevol" shows the error of the ensembles as a function of the number of iterations. In addition, the ensembles can be pruned using the option "newmfinal" in the predict.bagging and predict.boosting functions and the posterior probability of each class for observations can be obtained. Version 3.1 modifies the relative importance measure to take into account the gain of the Gini index given by a variable in each tree and the weights of these trees. Version 4.0 includes the margin-based ordered aggregation for Bagging pruning (Guo and Boukir, 2013) and a function to auto prune the rpart tree. Moreover, three new plots are also available importanceplot, plot.errorevol and plot.margins.
Author: Alfaro, Esteban; Gamez, Matias and Garcia, Noelia; with contributions from Li Guo
Maintainer: Esteban Alfaro

Diff between adabag versions 3.2 dated 2013-08-16 and 4.0 dated 2014-12-21

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Package BH updated to version 1.55.0-1 with previous version 1.54.0-5 dated 2014-11-10

Title: Boost C++ Header Files
Description: Boost provides free peer-reviewed portable C++ source libraries. A large part of Boost is provided as C++ template code which is resolved entirely at compile-time without linking. This package aims to provide the most useful subset of Boost libraries for template use among CRAN package. By placing these libraries in this package, we offer a more efficient distribution system for CRAN as replication of this code in the sources of other packages is avoided.
Author: Dirk Eddelbuettel, John W. Emerson and Michael J. Kane
Maintainer: Dirk Eddelbuettel

Diff between BH versions 1.54.0-5 dated 2014-11-10 and 1.55.0-1 dated 2014-12-21

 BH-1.55.0-1/BH/ChangeLog                                                                                   |   15 
 BH-1.55.0-1/BH/DESCRIPTION                                                                                 |   24 
 BH-1.55.0-1/BH/MD5                                                                                         | 1788 ++++--
 BH-1.55.0-1/BH/inst/include/boost/accumulators/numeric/functional.hpp                                      |   24 
 BH-1.55.0-1/BH/inst/include/boost/accumulators/numeric/functional/valarray.hpp                             |    4 
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 BH-1.55.0-1/BH/inst/include/boost/accumulators/numeric/functional_fwd.hpp                                  |    8 
 BH-1.55.0-1/BH/inst/include/boost/accumulators/statistics/covariance.hpp                                   |    8 
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 BH-1.55.0-1/BH/inst/include/boost/accumulators/statistics/error_of_mean.hpp                                |    4 
 BH-1.55.0-1/BH/inst/include/boost/accumulators/statistics/extended_p_square.hpp                            |    2 
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 BH-1.55.0-1/BH/inst/include/boost/accumulators/statistics/kurtosis.hpp                                     |    4 
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 BH-1.55.0-1/BH/inst/include/boost/accumulators/statistics/pot_quantile.hpp                                 |    2 
 BH-1.55.0-1/BH/inst/include/boost/accumulators/statistics/pot_tail_mean.hpp                                |    2 
 BH-1.55.0-1/BH/inst/include/boost/accumulators/statistics/skewness.hpp                                     |    4 
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 BH-1.55.0-1/BH/inst/include/boost/accumulators/statistics/tail_variate_means.hpp                           |    2 
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 BH-1.55.0-1/BH/inst/include/boost/accumulators/statistics/weighted_covariance.hpp                          |    8 
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 BH-1.55.0-1/BH/inst/include/boost/accumulators/statistics/weighted_median.hpp                              |   12 
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 BH-1.55.0-1/BH/inst/include/boost/accumulators/statistics/weighted_variance.hpp                            |   10 
 BH-1.55.0-1/BH/inst/include/boost/algorithm/cxx14/equal.hpp                                                |   82 
 BH-1.55.0-1/BH/inst/include/boost/algorithm/cxx14/mismatch.hpp                                             |   19 
 BH-1.55.0-1/BH/inst/include/boost/algorithm/string/concept.hpp                                             |    2 
 BH-1.55.0-1/BH/inst/include/boost/algorithm/string/detail/find_format.hpp                                  |    2 
 BH-1.55.0-1/BH/inst/include/boost/algorithm/string/detail/find_format_all.hpp                              |    2 
 BH-1.55.0-1/BH/inst/include/boost/algorithm/string/detail/find_format_store.hpp                            |    2 
 BH-1.55.0-1/BH/inst/include/boost/algorithm/string/detail/find_iterator.hpp                                |    2 
 BH-1.55.0-1/BH/inst/include/boost/algorithm/string/detail/finder.hpp                                       |    7 
 BH-1.55.0-1/BH/inst/include/boost/algorithm/string/detail/finder_regex.hpp                                 |    2 
 BH-1.55.0-1/BH/inst/include/boost/algorithm/string/detail/formatter.hpp                                    |    2 
 BH-1.55.0-1/BH/inst/include/boost/algorithm/string/detail/util.hpp                                         |    2 
 BH-1.55.0-1/BH/inst/include/boost/algorithm/string/erase.hpp                                               |    2 
 BH-1.55.0-1/BH/inst/include/boost/algorithm/string/find.hpp                                                |    2 
 BH-1.55.0-1/BH/inst/include/boost/algorithm/string/find_format.hpp                                         |    2 
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 BH-1.55.0-1/BH/inst/include/boost/algorithm/string/iter_find.hpp                                           |    2 
 BH-1.55.0-1/BH/inst/include/boost/algorithm/string/predicate.hpp                                           |    2 
 BH-1.55.0-1/BH/inst/include/boost/algorithm/string/regex.hpp                                               |    2 
 BH-1.55.0-1/BH/inst/include/boost/algorithm/string/replace.hpp                                             |    2 
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 BH-1.55.0-1/BH/inst/include/boost/any.hpp                                                                  |   65 
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 BH-1.55.0-1/BH/inst/include/boost/config.hpp                                                               |   17 
 BH-1.55.0-1/BH/inst/include/boost/config/auto_link.hpp                                                     |    8 
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 BH-1.55.0-1/BH/inst/include/boost/config/compiler/cray.hpp                                                 |    5 
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 BH-1.55.0-1/BH/inst/include/boost/config/compiler/gcc_xml.hpp                                              |   13 
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 BH-1.55.0-1/BH/inst/include/boost/config/compiler/nvcc.hpp                                                 |   12 
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 BH-1.55.0-1/BH/inst/include/boost/config/compiler/pgi.hpp                                                  |    6 
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 BH-1.55.0-1/BH/inst/include/boost/container/detail/utilities.hpp                                           |   43 
 BH-1.55.0-1/BH/inst/include/boost/container/detail/value_init.hpp                                          |    2 
 BH-1.55.0-1/BH/inst/include/boost/container/detail/variadic_templates_tools.hpp                            |    2 
 BH-1.55.0-1/BH/inst/include/boost/container/detail/workaround.hpp                                          |    6 
 BH-1.55.0-1/BH/inst/include/boost/container/flat_map.hpp                                                   |   41 
 BH-1.55.0-1/BH/inst/include/boost/container/flat_set.hpp                                                   |   46 
 BH-1.55.0-1/BH/inst/include/boost/container/list.hpp                                                       |  125 
 BH-1.55.0-1/BH/inst/include/boost/container/map.hpp                                                        |   32 
 BH-1.55.0-1/BH/inst/include/boost/container/scoped_allocator.hpp                                           |  107 
 BH-1.55.0-1/BH/inst/include/boost/container/scoped_allocator_fwd.hpp                                       |    2 
 BH-1.55.0-1/BH/inst/include/boost/container/set.hpp                                                        |   26 
 BH-1.55.0-1/BH/inst/include/boost/container/slist.hpp                                                      |  113 
 BH-1.55.0-1/BH/inst/include/boost/container/stable_vector.hpp                                              |  228 
 BH-1.55.0-1/BH/inst/include/boost/container/static_vector.hpp                                              |   48 
 BH-1.55.0-1/BH/inst/include/boost/container/string.hpp                                                     |   24 
 BH-1.55.0-1/BH/inst/include/boost/container/throw_exception.hpp                                            |    2 
 BH-1.55.0-1/BH/inst/include/boost/container/vector.hpp                                                     |  255 
 BH-1.55.0-1/BH/inst/include/boost/cstdint.hpp                                                              |  219 
 BH-1.55.0-1/BH/inst/include/boost/date_time/format_date_parser.hpp                                         |   14 
 BH-1.55.0-1/BH/inst/include/boost/date_time/local_time/custom_time_zone.hpp                                |    4 
 BH-1.55.0-1/BH/inst/include/boost/date_time/strings_from_facet.hpp                                         |    2 
 BH-1.55.0-1/BH/inst/include/boost/date_time/time_facet.hpp                                                 |    6 
 BH-1.55.0-1/BH/inst/include/boost/date_time/tz_db_base.hpp                                                 |    2 
 BH-1.55.0-1/BH/inst/include/boost/detail/endian.hpp                                                        |  121 
 BH-1.55.0-1/BH/inst/include/boost/detail/interlocked.hpp                                                   |   72 
 BH-1.55.0-1/BH/inst/include/boost/detail/winapi                                                            |only
 BH-1.55.0-1/BH/inst/include/boost/exception/detail/clone_current_exception.hpp                             |   11 
 BH-1.55.0-1/BH/inst/include/boost/exception/detail/exception_ptr.hpp                                       |    7 
 BH-1.55.0-1/BH/inst/include/boost/exception/detail/type_info.hpp                                           |   10 
 BH-1.55.0-1/BH/inst/include/boost/exception/diagnostic_information.hpp                                     |    8 
 BH-1.55.0-1/BH/inst/include/boost/function_types/function_arity.hpp                                        |only
 BH-1.55.0-1/BH/inst/include/boost/functional/hash/detail/hash_float.hpp                                    |   42 
 BH-1.55.0-1/BH/inst/include/boost/functional/hash/hash.hpp                                                 |   11 
 BH-1.55.0-1/BH/inst/include/boost/fusion/adapted/struct/detail/define_struct_inline.hpp                    |  133 
 BH-1.55.0-1/BH/inst/include/boost/fusion/algorithm/auxiliary/copy.hpp                                      |    2 
 BH-1.55.0-1/BH/inst/include/boost/fusion/container/deque.hpp                                               |    1 
 BH-1.55.0-1/BH/inst/include/boost/fusion/container/deque/back_extended_deque.hpp                           |    2 
 BH-1.55.0-1/BH/inst/include/boost/fusion/container/deque/convert.hpp                                       |   38 
 BH-1.55.0-1/BH/inst/include/boost/fusion/container/deque/deque.hpp                                         |   23 
 BH-1.55.0-1/BH/inst/include/boost/fusion/container/deque/deque_fwd.hpp                                     |    8 
 BH-1.55.0-1/BH/inst/include/boost/fusion/container/deque/detail/build_deque.hpp                            |only
 BH-1.55.0-1/BH/inst/include/boost/fusion/container/deque/detail/convert_impl.hpp                           |   17 
 BH-1.55.0-1/BH/inst/include/boost/fusion/container/deque/detail/cpp03                                      |only
 BH-1.55.0-1/BH/inst/include/boost/fusion/container/deque/detail/deque_keyed_values.hpp                     |only
 BH-1.55.0-1/BH/inst/include/boost/fusion/container/deque/detail/keyed_element.hpp                          |   10 
 BH-1.55.0-1/BH/inst/include/boost/fusion/container/deque/front_extended_deque.hpp                          |    2 
 BH-1.55.0-1/BH/inst/include/boost/fusion/container/generation/cons_tie.hpp                                 |    4 
 BH-1.55.0-1/BH/inst/include/boost/fusion/container/generation/deque_tie.hpp                                |  100 
 BH-1.55.0-1/BH/inst/include/boost/fusion/container/generation/detail/pp_deque_tie.hpp                      |only
 BH-1.55.0-1/BH/inst/include/boost/fusion/container/generation/detail/pp_make_deque.hpp                     |only
 BH-1.55.0-1/BH/inst/include/boost/fusion/container/generation/detail/pp_make_map.hpp                       |only
 BH-1.55.0-1/BH/inst/include/boost/fusion/container/generation/detail/pp_map_tie.hpp                        |only
 BH-1.55.0-1/BH/inst/include/boost/fusion/container/generation/make_cons.hpp                                |    4 
 BH-1.55.0-1/BH/inst/include/boost/fusion/container/generation/make_deque.hpp                               |  113 
 BH-1.55.0-1/BH/inst/include/boost/fusion/container/generation/make_map.hpp                                 |  142 
 BH-1.55.0-1/BH/inst/include/boost/fusion/container/generation/map_tie.hpp                                  |  136 
 BH-1.55.0-1/BH/inst/include/boost/fusion/container/list/cons.hpp                                           |    8 
 BH-1.55.0-1/BH/inst/include/boost/fusion/container/list/cons_fwd.hpp                                       |    7 
 BH-1.55.0-1/BH/inst/include/boost/fusion/container/list/cons_iterator.hpp                                  |   22 
 BH-1.55.0-1/BH/inst/include/boost/fusion/container/list/detail/begin_impl.hpp                              |    2 
 BH-1.55.0-1/BH/inst/include/boost/fusion/container/list/detail/build_cons.hpp                              |    6 
 BH-1.55.0-1/BH/inst/include/boost/fusion/container/list/detail/empty_impl.hpp                              |    4 
 BH-1.55.0-1/BH/inst/include/boost/fusion/container/list/detail/end_impl.hpp                                |    4 
 BH-1.55.0-1/BH/inst/include/boost/fusion/container/list/detail/list_to_cons.hpp                            |    4 
 BH-1.55.0-1/BH/inst/include/boost/fusion/container/list/detail/preprocessed/list10.hpp                     |    2 
 BH-1.55.0-1/BH/inst/include/boost/fusion/container/list/detail/preprocessed/list20.hpp                     |    2 
 BH-1.55.0-1/BH/inst/include/boost/fusion/container/list/detail/preprocessed/list30.hpp                     |    2 
 BH-1.55.0-1/BH/inst/include/boost/fusion/container/list/detail/preprocessed/list40.hpp                     |    2 
 BH-1.55.0-1/BH/inst/include/boost/fusion/container/list/detail/preprocessed/list50.hpp                     |    2 
 BH-1.55.0-1/BH/inst/include/boost/fusion/container/list/detail/preprocessed/list_to_cons10.hpp             |    2 
 BH-1.55.0-1/BH/inst/include/boost/fusion/container/list/detail/preprocessed/list_to_cons20.hpp             |    2 
 BH-1.55.0-1/BH/inst/include/boost/fusion/container/list/detail/preprocessed/list_to_cons30.hpp             |    2 
 BH-1.55.0-1/BH/inst/include/boost/fusion/container/list/detail/preprocessed/list_to_cons40.hpp             |    2 
 BH-1.55.0-1/BH/inst/include/boost/fusion/container/list/detail/preprocessed/list_to_cons50.hpp             |    2 
 BH-1.55.0-1/BH/inst/include/boost/fusion/container/list/detail/reverse_cons.hpp                            |    6 
 BH-1.55.0-1/BH/inst/include/boost/fusion/container/list/list.hpp                                           |    2 
 BH-1.55.0-1/BH/inst/include/boost/fusion/container/map.hpp                                                 |    1 
 BH-1.55.0-1/BH/inst/include/boost/fusion/container/map/convert.hpp                                         |   64 
 BH-1.55.0-1/BH/inst/include/boost/fusion/container/map/detail/at_impl.hpp                                  |   40 
 BH-1.55.0-1/BH/inst/include/boost/fusion/container/map/detail/at_key_impl.hpp                              |only
 BH-1.55.0-1/BH/inst/include/boost/fusion/container/map/detail/begin_impl.hpp                               |   51 
 BH-1.55.0-1/BH/inst/include/boost/fusion/container/map/detail/build_map.hpp                                |only
 BH-1.55.0-1/BH/inst/include/boost/fusion/container/map/detail/cpp03                                        |only
 BH-1.55.0-1/BH/inst/include/boost/fusion/container/map/detail/end_impl.hpp                                 |   51 
 BH-1.55.0-1/BH/inst/include/boost/fusion/container/map/detail/map_impl.hpp                                 |only
 BH-1.55.0-1/BH/inst/include/boost/fusion/container/map/detail/value_at_impl.hpp                            |   19 
 BH-1.55.0-1/BH/inst/include/boost/fusion/container/map/detail/value_at_key_impl.hpp                        |only
 BH-1.55.0-1/BH/inst/include/boost/fusion/container/map/map.hpp                                             |  143 
 BH-1.55.0-1/BH/inst/include/boost/fusion/container/map/map_fwd.hpp                                         |   50 
 BH-1.55.0-1/BH/inst/include/boost/fusion/container/map/map_iterator.hpp                                    |only
 BH-1.55.0-1/BH/inst/include/boost/fusion/container/vector/detail/vector_forward_ctor.hpp                   |   11 
 BH-1.55.0-1/BH/inst/include/boost/fusion/container/vector/detail/vector_n.hpp                              |   87 
 BH-1.55.0-1/BH/inst/include/boost/fusion/container/vector/vector.hpp                                       |   11 
 BH-1.55.0-1/BH/inst/include/boost/fusion/include/adapt_struct_named.hpp                                    |only
 BH-1.55.0-1/BH/inst/include/boost/fusion/include/tag_of.hpp                                                |only
 BH-1.55.0-1/BH/inst/include/boost/fusion/iterator/detail/segmented_equal_to.hpp                            |    4 
 BH-1.55.0-1/BH/inst/include/boost/fusion/iterator/detail/segmented_iterator.hpp                            |    2 
 BH-1.55.0-1/BH/inst/include/boost/fusion/iterator/detail/segmented_next_impl.hpp                           |    2 
 BH-1.55.0-1/BH/inst/include/boost/fusion/sequence/intrinsic/detail/segmented_begin.hpp                     |    8 
 BH-1.55.0-1/BH/inst/include/boost/fusion/sequence/intrinsic/detail/segmented_end.hpp                       |    6 
 BH-1.55.0-1/BH/inst/include/boost/fusion/support/deduce_sequence.hpp                                       |    2 
 BH-1.55.0-1/BH/inst/include/boost/fusion/support/pair.hpp                                                  |   40 
 BH-1.55.0-1/BH/inst/include/boost/fusion/support/segmented_fold_until.hpp                                  |    8 
 BH-1.55.0-1/BH/inst/include/boost/fusion/view/detail/strictest_traversal.hpp                               |    2 
 BH-1.55.0-1/BH/inst/include/boost/fusion/view/iterator_range/detail/segmented_iterator_range.hpp           |    8 
 BH-1.55.0-1/BH/inst/include/boost/fusion/view/nview/nview.hpp                                              |    2 
 BH-1.55.0-1/BH/inst/include/boost/fusion/view/zip_view/detail/value_at_impl.hpp                            |    2 
 BH-1.55.0-1/BH/inst/include/boost/fusion/view/zip_view/detail/value_of_impl.hpp                            |    2 
 BH-1.55.0-1/BH/inst/include/boost/fusion/view/zip_view/zip_view.hpp                                        |    4 
 BH-1.55.0-1/BH/inst/include/boost/geometry                                                                 |only
 BH-1.55.0-1/BH/inst/include/boost/geometry.hpp                                                             |only
 BH-1.55.0-1/BH/inst/include/boost/graph/accounting.hpp                                                     |only
 BH-1.55.0-1/BH/inst/include/boost/graph/breadth_first_search.hpp                                           |   19 
 BH-1.55.0-1/BH/inst/include/boost/graph/detail/adjacency_list.hpp                                          |    1 
 BH-1.55.0-1/BH/inst/include/boost/graph/dijkstra_shortest_paths.hpp                                        |only
 BH-1.55.0-1/BH/inst/include/boost/graph/distributed/breadth_first_search.hpp                               |    3 
 BH-1.55.0-1/BH/inst/include/boost/graph/distributed/concepts.hpp                                           |    4 
 BH-1.55.0-1/BH/inst/include/boost/graph/distributed/crauser_et_al_shortest_paths.hpp                       |only
 BH-1.55.0-1/BH/inst/include/boost/graph/distributed/detail/dijkstra_shortest_paths.hpp                     |only
 BH-1.55.0-1/BH/inst/include/boost/graph/distributed/detail/remote_update_set.hpp                           |only
 BH-1.55.0-1/BH/inst/include/boost/graph/distributed/dijkstra_shortest_paths.hpp                            |only
 BH-1.55.0-1/BH/inst/include/boost/graph/distributed/eager_dijkstra_shortest_paths.hpp                      |only
 BH-1.55.0-1/BH/inst/include/boost/graph/exception.hpp                                                      |only
 BH-1.55.0-1/BH/inst/include/boost/graph/graph_traits.hpp                                                   |    8 
 BH-1.55.0-1/BH/inst/include/boost/graph/named_function_params.hpp                                          |    1 
 BH-1.55.0-1/BH/inst/include/boost/graph/relax.hpp                                                          |only
 BH-1.55.0-1/BH/inst/include/boost/graph/visitors.hpp                                                       |    3 
 BH-1.55.0-1/BH/inst/include/boost/heap/d_ary_heap.hpp                                                      |    2 
 BH-1.55.0-1/BH/inst/include/boost/heap/detail/heap_node.hpp                                                |    1 
 BH-1.55.0-1/BH/inst/include/boost/heap/detail/mutable_heap.hpp                                             |   14 
 BH-1.55.0-1/BH/inst/include/boost/integer_traits.hpp                                                       |    2 
 BH-1.55.0-1/BH/inst/include/boost/interprocess/detail/atomic.hpp                                           |    2 
 BH-1.55.0-1/BH/inst/include/boost/interprocess/detail/intermodule_singleton_common.hpp                     |    9 
 BH-1.55.0-1/BH/inst/include/boost/interprocess/detail/managed_open_or_create_impl.hpp                      |   10 
 BH-1.55.0-1/BH/inst/include/boost/interprocess/detail/os_thread_functions.hpp                              |  377 +
 BH-1.55.0-1/BH/inst/include/boost/interprocess/detail/robust_emulation.hpp                                 |   16 
 BH-1.55.0-1/BH/inst/include/boost/interprocess/detail/tmp_dir_helpers.hpp                                  |    2 
 BH-1.55.0-1/BH/inst/include/boost/interprocess/detail/win32_api.hpp                                        |  119 
 BH-1.55.0-1/BH/inst/include/boost/interprocess/detail/windows_intermodule_singleton.hpp                    |    5 
 BH-1.55.0-1/BH/inst/include/boost/interprocess/detail/workaround.hpp                                       |   21 
 BH-1.55.0-1/BH/inst/include/boost/interprocess/errors.hpp                                                  |    2 
 BH-1.55.0-1/BH/inst/include/boost/interprocess/segment_manager.hpp                                         |    2 
 BH-1.55.0-1/BH/inst/include/boost/interprocess/smart_ptr/detail/sp_counted_impl.hpp                        |    9 
 BH-1.55.0-1/BH/inst/include/boost/interprocess/streams/bufferstream.hpp                                    |  137 
 BH-1.55.0-1/BH/inst/include/boost/interprocess/streams/vectorstream.hpp                                    |  113 
 BH-1.55.0-1/BH/inst/include/boost/interprocess/sync/file_lock.hpp                                          |    8 
 BH-1.55.0-1/BH/inst/include/boost/interprocess/sync/named_mutex.hpp                                        |   10 
 BH-1.55.0-1/BH/inst/include/boost/interprocess/sync/posix/mutex.hpp                                        |    4 
 BH-1.55.0-1/BH/inst/include/boost/interprocess/sync/posix/recursive_mutex.hpp                              |    5 
 BH-1.55.0-1/BH/inst/include/boost/interprocess/sync/posix/semaphore_wrapper.hpp                            |    4 
 BH-1.55.0-1/BH/inst/include/boost/interprocess/sync/spin/condition.hpp                                     |   13 
 BH-1.55.0-1/BH/inst/include/boost/interprocess/sync/spin/mutex.hpp                                         |    7 
 BH-1.55.0-1/BH/inst/include/boost/interprocess/sync/spin/semaphore.hpp                                     |    9 
 BH-1.55.0-1/BH/inst/include/boost/interprocess/sync/spin/wait.hpp                                          |only
 BH-1.55.0-1/BH/inst/include/boost/intrusive/any_hook.hpp                                                   |   27 
 BH-1.55.0-1/BH/inst/include/boost/intrusive/avl_set.hpp                                                    | 2682 +--------
 BH-1.55.0-1/BH/inst/include/boost/intrusive/avl_set_hook.hpp                                               |   14 
 BH-1.55.0-1/BH/inst/include/boost/intrusive/avltree.hpp                                                    | 1860 +-----
 BH-1.55.0-1/BH/inst/include/boost/intrusive/avltree_algorithms.hpp                                         |  665 --
 BH-1.55.0-1/BH/inst/include/boost/intrusive/bs_set.hpp                                                     |only
 BH-1.55.0-1/BH/inst/include/boost/intrusive/bs_set_hook.hpp                                                |   24 
 BH-1.55.0-1/BH/inst/include/boost/intrusive/bstree.hpp                                                     |only
 BH-1.55.0-1/BH/inst/include/boost/intrusive/bstree_algorithms.hpp                                          |only
 BH-1.55.0-1/BH/inst/include/boost/intrusive/circular_list_algorithms.hpp                                   |   13 
 BH-1.55.0-1/BH/inst/include/boost/intrusive/circular_slist_algorithms.hpp                                  |   13 
 BH-1.55.0-1/BH/inst/include/boost/intrusive/derivation_value_traits.hpp                                    |    2 
 BH-1.55.0-1/BH/inst/include/boost/intrusive/detail/any_node_and_algorithms.hpp                             |    2 
 BH-1.55.0-1/BH/inst/include/boost/intrusive/detail/assert.hpp                                              |    2 
 BH-1.55.0-1/BH/inst/include/boost/intrusive/detail/avltree_node.hpp                                        |    2 
 BH-1.55.0-1/BH/inst/include/boost/intrusive/detail/clear_on_destructor_base.hpp                            |    8 
 BH-1.55.0-1/BH/inst/include/boost/intrusive/detail/common_slist_algorithms.hpp                             |    2 
 BH-1.55.0-1/BH/inst/include/boost/intrusive/detail/config_begin.hpp                                        |    2 
 BH-1.55.0-1/BH/inst/include/boost/intrusive/detail/config_end.hpp                                          |    2 
 BH-1.55.0-1/BH/inst/include/boost/intrusive/detail/ebo_functor_holder.hpp                                  |    2 
 BH-1.55.0-1/BH/inst/include/boost/intrusive/detail/function_detector.hpp                                   |    2 
 BH-1.55.0-1/BH/inst/include/boost/intrusive/detail/generic_hook.hpp                                        |  167 
 BH-1.55.0-1/BH/inst/include/boost/intrusive/detail/has_member_function_callable_with.hpp                   |    2 
 BH-1.55.0-1/BH/inst/include/boost/intrusive/detail/hashtable_node.hpp                                      |  160 
 BH-1.55.0-1/BH/inst/include/boost/intrusive/detail/is_stateful_value_traits.hpp                            |    2 
 BH-1.55.0-1/BH/inst/include/boost/intrusive/detail/list_node.hpp                                           |   92 
 BH-1.55.0-1/BH/inst/include/boost/intrusive/detail/memory_util.hpp                                         |    6 
 BH-1.55.0-1/BH/inst/include/boost/intrusive/detail/mpl.hpp                                                 |   21 
 BH-1.55.0-1/BH/inst/include/boost/intrusive/detail/parent_from_member.hpp                                  |   28 
 BH-1.55.0-1/BH/inst/include/boost/intrusive/detail/preprocessor.hpp                                        |    2 
 BH-1.55.0-1/BH/inst/include/boost/intrusive/detail/rbtree_node.hpp                                         |    4 
 BH-1.55.0-1/BH/inst/include/boost/intrusive/detail/slist_node.hpp                                          |   88 
 BH-1.55.0-1/BH/inst/include/boost/intrusive/detail/transform_iterator.hpp                                  |    2 
 BH-1.55.0-1/BH/inst/include/boost/intrusive/detail/tree_node.hpp                                           |   83 
 BH-1.55.0-1/BH/inst/include/boost/intrusive/detail/utilities.hpp                                           |  696 +-
 BH-1.55.0-1/BH/inst/include/boost/intrusive/detail/workaround.hpp                                          |    6 
 BH-1.55.0-1/BH/inst/include/boost/intrusive/hashtable.hpp                                                  | 1839 +++---
 BH-1.55.0-1/BH/inst/include/boost/intrusive/intrusive_fwd.hpp                                              |  360 -
 BH-1.55.0-1/BH/inst/include/boost/intrusive/linear_slist_algorithms.hpp                                    |   13 
 BH-1.55.0-1/BH/inst/include/boost/intrusive/link_mode.hpp                                                  |    2 
 BH-1.55.0-1/BH/inst/include/boost/intrusive/list.hpp                                                       |  134 
 BH-1.55.0-1/BH/inst/include/boost/intrusive/list_hook.hpp                                                  |   14 
 BH-1.55.0-1/BH/inst/include/boost/intrusive/member_value_traits.hpp                                        |    2 
 BH-1.55.0-1/BH/inst/include/boost/intrusive/options.hpp                                                    |  144 
 BH-1.55.0-1/BH/inst/include/boost/intrusive/parent_from_member.hpp                                         |    2 
 BH-1.55.0-1/BH/inst/include/boost/intrusive/pointer_plus_bits.hpp                                          |    2 
 BH-1.55.0-1/BH/inst/include/boost/intrusive/pointer_traits.hpp                                             |    6 
 BH-1.55.0-1/BH/inst/include/boost/intrusive/priority_compare.hpp                                           |   17 
 BH-1.55.0-1/BH/inst/include/boost/intrusive/rbtree.hpp                                                     | 1825 +-----
 BH-1.55.0-1/BH/inst/include/boost/intrusive/rbtree_algorithms.hpp                                          |  721 --
 BH-1.55.0-1/BH/inst/include/boost/intrusive/set.hpp                                                        | 2621 +--------
 BH-1.55.0-1/BH/inst/include/boost/intrusive/set_hook.hpp                                                   |   14 
 BH-1.55.0-1/BH/inst/include/boost/intrusive/sg_set.hpp                                                     | 2735 +--------
 BH-1.55.0-1/BH/inst/include/boost/intrusive/sgtree.hpp                                                     | 1783 +-----
 BH-1.55.0-1/BH/inst/include/boost/intrusive/sgtree_algorithms.hpp                                          |  735 --
 BH-1.55.0-1/BH/inst/include/boost/intrusive/slist.hpp                                                      |  188 
 BH-1.55.0-1/BH/inst/include/boost/intrusive/slist_hook.hpp                                                 |   14 
 BH-1.55.0-1/BH/inst/include/boost/intrusive/splay_set.hpp                                                  | 2861 ++--------
 BH-1.55.0-1/BH/inst/include/boost/intrusive/splay_set_hook.hpp                                             |   68 
 BH-1.55.0-1/BH/inst/include/boost/intrusive/splaytree.hpp                                                  | 1867 +-----
 BH-1.55.0-1/BH/inst/include/boost/intrusive/splaytree_algorithms.hpp                                       |  849 --
 BH-1.55.0-1/BH/inst/include/boost/intrusive/treap.hpp                                                      | 1335 +---
 BH-1.55.0-1/BH/inst/include/boost/intrusive/treap_algorithms.hpp                                           |  479 -
 BH-1.55.0-1/BH/inst/include/boost/intrusive/treap_set.hpp                                                  | 2626 +--------
 BH-1.55.0-1/BH/inst/include/boost/intrusive/trivial_value_traits.hpp                                       |    2 
 BH-1.55.0-1/BH/inst/include/boost/intrusive/unordered_set.hpp                                              |  383 -
 BH-1.55.0-1/BH/inst/include/boost/intrusive/unordered_set_hook.hpp                                         |   20 
 BH-1.55.0-1/BH/inst/include/boost/lexical_cast.hpp                                                         |   49 
 BH-1.55.0-1/BH/inst/include/boost/math/bindings/mpfr.hpp                                                   |   24 
 BH-1.55.0-1/BH/inst/include/boost/math/constants/constants.hpp                                             |   16 
 BH-1.55.0-1/BH/inst/include/boost/math/distributions/beta.hpp                                              |    2 
 BH-1.55.0-1/BH/inst/include/boost/math/distributions/binomial.hpp                                          |   10 
 BH-1.55.0-1/BH/inst/include/boost/math/distributions/cauchy.hpp                                            |    8 
 BH-1.55.0-1/BH/inst/include/boost/math/distributions/detail/common_error_handling.hpp                      |    7 
 BH-1.55.0-1/BH/inst/include/boost/math/distributions/detail/inv_discrete_quantile.hpp                      |  158 
 BH-1.55.0-1/BH/inst/include/boost/math/distributions/exponential.hpp                                       |    6 
 BH-1.55.0-1/BH/inst/include/boost/math/distributions/gamma.hpp                                             |    6 
 BH-1.55.0-1/BH/inst/include/boost/math/distributions/hypergeometric.hpp                                    |    6 
 BH-1.55.0-1/BH/inst/include/boost/math/distributions/inverse_chi_squared.hpp                               |    2 
 BH-1.55.0-1/BH/inst/include/boost/math/distributions/inverse_gamma.hpp                                     |    6 
 BH-1.55.0-1/BH/inst/include/boost/math/distributions/inverse_gaussian.hpp                                  |   10 
 BH-1.55.0-1/BH/inst/include/boost/math/distributions/laplace.hpp                                           |    4 
 BH-1.55.0-1/BH/inst/include/boost/math/distributions/logistic.hpp                                          |   42 
 BH-1.55.0-1/BH/inst/include/boost/math/distributions/lognormal.hpp                                         |    8 
 BH-1.55.0-1/BH/inst/include/boost/math/distributions/negative_binomial.hpp                                 |    4 
 BH-1.55.0-1/BH/inst/include/boost/math/distributions/non_central_chi_squared.hpp                           |   45 
 BH-1.55.0-1/BH/inst/include/boost/math/distributions/non_central_t.hpp                                     |   22 
 BH-1.55.0-1/BH/inst/include/boost/math/distributions/normal.hpp                                            |   34 
 BH-1.55.0-1/BH/inst/include/boost/math/distributions/pareto.hpp                                            |    6 
 BH-1.55.0-1/BH/inst/include/boost/math/distributions/poisson.hpp                                           |   68 
 BH-1.55.0-1/BH/inst/include/boost/math/distributions/rayleigh.hpp                                          |    6 
 BH-1.55.0-1/BH/inst/include/boost/math/distributions/skew_normal.hpp                                       |   10 
 BH-1.55.0-1/BH/inst/include/boost/math/distributions/students_t.hpp                                        |   12 
 BH-1.55.0-1/BH/inst/include/boost/math/distributions/triangular.hpp                                        |    6 
 BH-1.55.0-1/BH/inst/include/boost/math/distributions/uniform.hpp                                           |    6 
 BH-1.55.0-1/BH/inst/include/boost/math/distributions/weibull.hpp                                           |    6 
 BH-1.55.0-1/BH/inst/include/boost/math/policies/error_handling.hpp                                         |   31 
 BH-1.55.0-1/BH/inst/include/boost/math/special_functions/airy.hpp                                          |    8 
 BH-1.55.0-1/BH/inst/include/boost/math/special_functions/bessel.hpp                                        |   14 
 BH-1.55.0-1/BH/inst/include/boost/math/special_functions/beta.hpp                                          |   45 
 BH-1.55.0-1/BH/inst/include/boost/math/special_functions/detail/bessel_ik.hpp                              |   17 
 BH-1.55.0-1/BH/inst/include/boost/math/special_functions/detail/bessel_jy_series.hpp                       |    6 
 BH-1.55.0-1/BH/inst/include/boost/math/special_functions/detail/ibeta_inverse.hpp                          |   73 
 BH-1.55.0-1/BH/inst/include/boost/math/special_functions/detail/t_distribution_inv.hpp                     |   19 
 BH-1.55.0-1/BH/inst/include/boost/math/special_functions/ellint_1.hpp                                      |    7 
 BH-1.55.0-1/BH/inst/include/boost/math/special_functions/ellint_2.hpp                                      |    7 
 BH-1.55.0-1/BH/inst/include/boost/math/special_functions/ellint_3.hpp                                      |    7 
 BH-1.55.0-1/BH/inst/include/boost/math/special_functions/ellint_rj.hpp                                     |    2 
 BH-1.55.0-1/BH/inst/include/boost/math/special_functions/fpclassify.hpp                                    |    8 
 BH-1.55.0-1/BH/inst/include/boost/math/special_functions/gamma.hpp                                         |    2 
 BH-1.55.0-1/BH/inst/include/boost/math/special_functions/math_fwd.hpp                                      |    4 
 BH-1.55.0-1/BH/inst/include/boost/math/special_functions/sign.hpp                                          |   10 
 BH-1.55.0-1/BH/inst/include/boost/math/tools/big_constant.hpp                                              |    4 
 BH-1.55.0-1/BH/inst/include/boost/math/tools/fraction.hpp                                                  |    2 
 BH-1.55.0-1/BH/inst/include/boost/math/tools/promotion.hpp                                                 |   27 
 BH-1.55.0-1/BH/inst/include/boost/math/tools/tuple.hpp                                                     |    2 
 BH-1.55.0-1/BH/inst/include/boost/move/algorithm.hpp                                                       |    1 
 BH-1.55.0-1/BH/inst/include/boost/move/core.hpp                                                            |    7 
 BH-1.55.0-1/BH/inst/include/boost/move/detail/move_helpers.hpp                                             |   26 
 BH-1.55.0-1/BH/inst/include/boost/move/traits.hpp                                                          |   12 
 BH-1.55.0-1/BH/inst/include/boost/move/utility.hpp                                                         |   22 
 BH-1.55.0-1/BH/inst/include/boost/mpi/collectives.hpp                                                      |   30 
 BH-1.55.0-1/BH/inst/include/boost/mpi/collectives/all_reduce.hpp                                           |   31 
 BH-1.55.0-1/BH/inst/include/boost/mpi/collectives/gather.hpp                                               |    7 
 BH-1.55.0-1/BH/inst/include/boost/mpi/collectives/reduce.hpp                                               |   19 
 BH-1.55.0-1/BH/inst/include/boost/mpi/communicator.hpp                                                     |    3 
 BH-1.55.0-1/BH/inst/include/boost/mpi/config.hpp                                                           |    7 
 BH-1.55.0-1/BH/inst/include/boost/mpi/detail/binary_buffer_iprimitive.hpp                                  |    4 
 BH-1.55.0-1/BH/inst/include/boost/mpi/detail/forward_skeleton_iarchive.hpp                                 |    1 
 BH-1.55.0-1/BH/inst/include/boost/mpi/detail/ignore_iprimitive.hpp                                         |    2 
 BH-1.55.0-1/BH/inst/include/boost/mpi/detail/ignore_oprimitive.hpp                                         |    2 
 BH-1.55.0-1/BH/inst/include/boost/mpi/detail/mpi_datatype_primitive.hpp                                    |   27 
 BH-1.55.0-1/BH/inst/include/boost/mpi/detail/packed_iprimitive.hpp                                         |    4 
 BH-1.55.0-1/BH/inst/include/boost/mpi/detail/packed_oprimitive.hpp                                         |    3 
 BH-1.55.0-1/BH/inst/include/boost/mpi/environment.hpp                                                      |   84 
 BH-1.55.0-1/BH/inst/include/boost/mpi/inplace.hpp                                                          |only
 BH-1.55.0-1/BH/inst/include/boost/mpi/packed_iarchive.hpp                                                  |   44 
 BH-1.55.0-1/BH/inst/include/boost/mpi/packed_oarchive.hpp                                                  |   39 
 BH-1.55.0-1/BH/inst/include/boost/mpl/assert.hpp                                                           |    8 
 BH-1.55.0-1/BH/inst/include/boost/multi_index/detail/do_not_copy_elements_tag.hpp                          |only
 BH-1.55.0-1/BH/inst/include/boost/multi_index/detail/index_base.hpp                                        |  100 
 BH-1.55.0-1/BH/inst/include/boost/multi_index/detail/scope_guard.hpp                                       |    3 
 BH-1.55.0-1/BH/inst/include/boost/multi_index/detail/vartempl_support.hpp                                  |only
 BH-1.55.0-1/BH/inst/include/boost/multi_index/hashed_index.hpp                                             |  158 
 BH-1.55.0-1/BH/inst/include/boost/multi_index/ordered_index.hpp                                            |  153 
 BH-1.55.0-1/BH/inst/include/boost/multi_index/sequenced_index.hpp                                          |  199 
 BH-1.55.0-1/BH/inst/include/boost/multi_index_container.hpp                                                |  330 +
 BH-1.55.0-1/BH/inst/include/boost/multiprecision/cpp_dec_float.hpp                                         |   90 
 BH-1.55.0-1/BH/inst/include/boost/multiprecision/detail/default_ops.hpp                                    |  172 
 BH-1.55.0-1/BH/inst/include/boost/multiprecision/detail/digits.hpp                                         |only
 BH-1.55.0-1/BH/inst/include/boost/multiprecision/detail/et_ops.hpp                                         |   13 
 BH-1.55.0-1/BH/inst/include/boost/multiprecision/detail/functions/constants.hpp                            |    1 
 BH-1.55.0-1/BH/inst/include/boost/multiprecision/detail/functions/pow.hpp                                  |   61 
 BH-1.55.0-1/BH/inst/include/boost/multiprecision/detail/functions/trig.hpp                                 |  101 
 BH-1.55.0-1/BH/inst/include/boost/multiprecision/detail/generic_interconvert.hpp                           |    1 
 BH-1.55.0-1/BH/inst/include/boost/multiprecision/detail/integer_ops.hpp                                    |only
 BH-1.55.0-1/BH/inst/include/boost/multiprecision/gmp.hpp                                                   |only
 BH-1.55.0-1/BH/inst/include/boost/multiprecision/mpfr.hpp                                                  |only
 BH-1.55.0-1/BH/inst/include/boost/multiprecision/number.hpp                                                |   89 
 BH-1.55.0-1/BH/inst/include/boost/phoenix/function/function.hpp                                            |    7 
 BH-1.55.0-1/BH/inst/include/boost/polygon                                                                  |only
 BH-1.55.0-1/BH/inst/include/boost/predef                                                                   |only
 BH-1.55.0-1/BH/inst/include/boost/preprocessor/tuple/rem.hpp                                               |    1 
 BH-1.55.0-1/BH/inst/include/boost/program_options                                                          |only
 BH-1.55.0-1/BH/inst/include/boost/program_options.hpp                                                      |only
 BH-1.55.0-1/BH/inst/include/boost/progress.hpp                                                             |    4 
 BH-1.55.0-1/BH/inst/include/boost/property_map/parallel/caching_property_map.hpp                           |only
 BH-1.55.0-1/BH/inst/include/boost/property_map/property_map.hpp                                            |    3 
 BH-1.55.0-1/BH/inst/include/boost/property_map/property_map_iterator.hpp                                   |only
 BH-1.55.0-1/BH/inst/include/boost/random/detail/integer_log2.hpp                                           |    2 
 BH-1.55.0-1/BH/inst/include/boost/random/discrete_distribution.hpp                                         |    2 
 BH-1.55.0-1/BH/inst/include/boost/random/piecewise_constant_distribution.hpp                               |    2 
 BH-1.55.0-1/BH/inst/include/boost/random/piecewise_linear_distribution.hpp                                 |    2 
 BH-1.55.0-1/BH/inst/include/boost/random/seed_seq.hpp                                                      |    2 
 BH-1.55.0-1/BH/inst/include/boost/random/subtract_with_carry.hpp                                           |    2 
 BH-1.55.0-1/BH/inst/include/boost/ratio/detail/ratio_io.hpp                                                |only
 BH-1.55.0-1/BH/inst/include/boost/ratio/ratio_io.hpp                                                       |only
 BH-1.55.0-1/BH/inst/include/boost/ratio/ratio_static_string.hpp                                            |only
 BH-1.55.0-1/BH/inst/include/boost/rational.hpp                                                             |   12 
 BH-1.55.0-1/BH/inst/include/boost/regex/v4/perl_matcher_non_recursive.hpp                                  |   24 
 BH-1.55.0-1/BH/inst/include/boost/regex/v4/perl_matcher_recursive.hpp                                      |   16 
 BH-1.55.0-1/BH/inst/include/boost/smart_ptr/detail/yield_k.hpp                                             |    1 
 BH-1.55.0-1/BH/inst/include/boost/smart_ptr/intrusive_ref_counter.hpp                                      |only
 BH-1.55.0-1/BH/inst/include/boost/spirit/home/karma/directive/omit.hpp                                     |    2 
 BH-1.55.0-1/BH/inst/include/boost/spirit/home/karma/nonterminal/rule.hpp                                   |    2 
 BH-1.55.0-1/BH/inst/include/boost/spirit/home/karma/numeric/detail/numeric_utils.hpp                       |   16 
 BH-1.55.0-1/BH/inst/include/boost/spirit/home/karma/numeric/detail/real_utils.hpp                          |    4 
 BH-1.55.0-1/BH/inst/include/boost/spirit/home/karma/numeric/real_policies.hpp                              |   13 
 BH-1.55.0-1/BH/inst/include/boost/spirit/home/karma/operator/alternative.hpp                               |    2 
 BH-1.55.0-1/BH/inst/include/boost/spirit/home/karma/operator/sequence.hpp                                  |    2 
 BH-1.55.0-1/BH/inst/include/boost/spirit/home/karma/string/symbols.hpp                                     |    2 
 BH-1.55.0-1/BH/inst/include/boost/spirit/home/lex/lexer/lexer.hpp                                          |    2 
 BH-1.55.0-1/BH/inst/include/boost/spirit/home/phoenix/core/value.hpp                                       |    4 
 BH-1.55.0-1/BH/inst/include/boost/spirit/home/phoenix/function/function.hpp                                |    2 
 BH-1.55.0-1/BH/inst/include/boost/spirit/home/phoenix/object/construct.hpp                                 |    2 
 BH-1.55.0-1/BH/inst/include/boost/spirit/home/qi/action/action.hpp                                         |    4 
 BH-1.55.0-1/BH/inst/include/boost/spirit/home/qi/auxiliary/attr.hpp                                        |    4 
 BH-1.55.0-1/BH/inst/include/boost/spirit/home/qi/auxiliary/attr_cast.hpp                                   |   12 
 BH-1.55.0-1/BH/inst/include/boost/spirit/home/qi/auxiliary/eps.hpp                                         |    4 
 BH-1.55.0-1/BH/inst/include/boost/spirit/home/qi/auxiliary/lazy.hpp                                        |   14 
 BH-1.55.0-1/BH/inst/include/boost/spirit/home/qi/binary/binary.hpp                                         |   12 
 BH-1.55.0-1/BH/inst/include/boost/spirit/home/qi/char/char.hpp                                             |    8 
 BH-1.55.0-1/BH/inst/include/boost/spirit/home/qi/char/char_parser.hpp                                      |    8 
 BH-1.55.0-1/BH/inst/include/boost/spirit/home/qi/detail/alternative_function.hpp                           |   14 
 BH-1.55.0-1/BH/inst/include/boost/spirit/home/qi/detail/expect_function.hpp                                |   12 
 BH-1.55.0-1/BH/inst/include/boost/spirit/home/qi/detail/fail_function.hpp                                  |   12 
 BH-1.55.0-1/BH/inst/include/boost/spirit/home/qi/detail/pass_container.hpp                                 |    4 
 BH-1.55.0-1/BH/inst/include/boost/spirit/home/qi/detail/pass_function.hpp                                  |   12 
 BH-1.55.0-1/BH/inst/include/boost/spirit/home/qi/detail/permute_function.hpp                               |   12 
 BH-1.55.0-1/BH/inst/include/boost/spirit/home/qi/detail/unused_skipper.hpp                                 |    4 
 BH-1.55.0-1/BH/inst/include/boost/spirit/home/qi/directive/as.hpp                                          |   12 
 BH-1.55.0-1/BH/inst/include/boost/spirit/home/qi/directive/hold.hpp                                        |   10 
 BH-1.55.0-1/BH/inst/include/boost/spirit/home/qi/directive/lexeme.hpp                                      |    8 
 BH-1.55.0-1/BH/inst/include/boost/spirit/home/qi/directive/matches.hpp                                     |    8 
 BH-1.55.0-1/BH/inst/include/boost/spirit/home/qi/directive/no_skip.hpp                                     |    8 
 BH-1.55.0-1/BH/inst/include/boost/spirit/home/qi/directive/omit.hpp                                        |    8 
 BH-1.55.0-1/BH/inst/include/boost/spirit/home/qi/directive/raw.hpp                                         |    8 
 BH-1.55.0-1/BH/inst/include/boost/spirit/home/qi/directive/repeat.hpp                                      |   28 
 BH-1.55.0-1/BH/inst/include/boost/spirit/home/qi/directive/skip.hpp                                        |   16 
 BH-1.55.0-1/BH/inst/include/boost/spirit/home/qi/nonterminal/debug_handler.hpp                             |   12 
 BH-1.55.0-1/BH/inst/include/boost/spirit/home/qi/nonterminal/detail/parameterized.hpp                      |    8 
 BH-1.55.0-1/BH/inst/include/boost/spirit/home/qi/nonterminal/detail/parser_binder.hpp                      |    8 
 BH-1.55.0-1/BH/inst/include/boost/spirit/home/qi/nonterminal/error_handler.hpp                             |    6 
 BH-1.55.0-1/BH/inst/include/boost/spirit/home/qi/nonterminal/grammar.hpp                                   |    8 
 BH-1.55.0-1/BH/inst/include/boost/spirit/home/qi/nonterminal/rule.hpp                                      |   28 
 BH-1.55.0-1/BH/inst/include/boost/spirit/home/qi/nonterminal/success_handler.hpp                           |    6 
 BH-1.55.0-1/BH/inst/include/boost/spirit/home/qi/numeric/bool.hpp                                          |    8 
 BH-1.55.0-1/BH/inst/include/boost/spirit/home/qi/numeric/bool_policies.hpp                                 |   16 
 BH-1.55.0-1/BH/inst/include/boost/spirit/home/qi/numeric/int.hpp                                           |    8 
 BH-1.55.0-1/BH/inst/include/boost/spirit/home/qi/numeric/numeric_utils.hpp                                 |   22 
 BH-1.55.0-1/BH/inst/include/boost/spirit/home/qi/numeric/real.hpp                                          |   12 
 BH-1.55.0-1/BH/inst/include/boost/spirit/home/qi/numeric/real_policies.hpp                                 |   20 
 BH-1.55.0-1/BH/inst/include/boost/spirit/home/qi/numeric/uint.hpp                                          |    8 
 BH-1.55.0-1/BH/inst/include/boost/spirit/home/qi/operator/alternative.hpp                                  |    8 
 BH-1.55.0-1/BH/inst/include/boost/spirit/home/qi/operator/and_predicate.hpp                                |    4 
 BH-1.55.0-1/BH/inst/include/boost/spirit/home/qi/operator/difference.hpp                                   |    8 
 BH-1.55.0-1/BH/inst/include/boost/spirit/home/qi/operator/expect.hpp                                       |    4 
 BH-1.55.0-1/BH/inst/include/boost/spirit/home/qi/operator/kleene.hpp                                       |   10 
 BH-1.55.0-1/BH/inst/include/boost/spirit/home/qi/operator/list.hpp                                         |   10 
 BH-1.55.0-1/BH/inst/include/boost/spirit/home/qi/operator/not_predicate.hpp                                |    4 
 BH-1.55.0-1/BH/inst/include/boost/spirit/home/qi/operator/optional.hpp                                     |   16 
 BH-1.55.0-1/BH/inst/include/boost/spirit/home/qi/operator/permutation.hpp                                  |    8 
 BH-1.55.0-1/BH/inst/include/boost/spirit/home/qi/operator/plus.hpp                                         |   10 
 BH-1.55.0-1/BH/inst/include/boost/spirit/home/qi/operator/sequence_base.hpp                                |   12 
 BH-1.55.0-1/BH/inst/include/boost/spirit/home/qi/operator/sequential_or.hpp                                |    8 
 BH-1.55.0-1/BH/inst/include/boost/spirit/home/qi/parse_attr.hpp                                            |    8 
 BH-1.55.0-1/BH/inst/include/boost/spirit/home/qi/reference.hpp                                             |    4 
 BH-1.55.0-1/BH/inst/include/boost/spirit/home/qi/stream/detail/iterator_source.hpp                         |    2 
 BH-1.55.0-1/BH/inst/include/boost/spirit/home/qi/string/detail/tst.hpp                                     |    4 
 BH-1.55.0-1/BH/inst/include/boost/spirit/home/qi/string/lit.hpp                                            |   12 
 BH-1.55.0-1/BH/inst/include/boost/spirit/home/qi/string/symbols.hpp                                        |   14 
 BH-1.55.0-1/BH/inst/include/boost/spirit/home/support/action_dispatch.hpp                                  |    8 
 BH-1.55.0-1/BH/inst/include/boost/spirit/home/support/attributes.hpp                                       |    8 
 BH-1.55.0-1/BH/inst/include/boost/spirit/home/support/char_encoding/unicode/query.hpp                      |    2 
 BH-1.55.0-1/BH/inst/include/boost/spirit/home/support/char_set/range.hpp                                   |    2 
 BH-1.55.0-1/BH/inst/include/boost/spirit/home/support/context.hpp                                          |    4 
 BH-1.55.0-1/BH/inst/include/boost/spirit/home/support/detail/scoped_enum_emulation.hpp                     |    4 
 BH-1.55.0-1/BH/inst/include/boost/spirit/home/support/detail/what_function.hpp                             |    4 
 BH-1.55.0-1/BH/inst/include/boost/spirit/home/support/extended_variant.hpp                                 |    4 
 BH-1.55.0-1/BH/inst/include/boost/spirit/home/support/info.hpp                                             |   36 
 BH-1.55.0-1/BH/inst/include/boost/spirit/home/support/iterators/detail/buffering_input_iterator_policy.hpp |    4 
 BH-1.55.0-1/BH/inst/include/boost/spirit/home/support/nonterminal/expand_arg.hpp                           |    4 
 BH-1.55.0-1/BH/inst/include/boost/spirit/home/support/numeric_traits.hpp                                   |   13 
 BH-1.55.0-1/BH/inst/include/boost/spirit/home/support/terminal.hpp                                         |   58 
 BH-1.55.0-1/BH/inst/include/boost/spirit/repository/home/qi/operator/detail/keywords.hpp                   |   11 
 BH-1.55.0-1/BH/inst/include/boost/thread/barrier.hpp                                                       |  216 
 BH-1.55.0-1/BH/inst/include/boost/thread/detail/config.hpp                                                 |    5 
 BH-1.55.0-1/BH/inst/include/boost/thread/detail/is_convertible.hpp                                         |    7 
 BH-1.55.0-1/BH/inst/include/boost/thread/detail/memory.hpp                                                 |    7 
 BH-1.55.0-1/BH/inst/include/boost/thread/detail/thread.hpp                                                 |   13 
 BH-1.55.0-1/BH/inst/include/boost/thread/future.hpp                                                        | 1727 +++---
 BH-1.55.0-1/BH/inst/include/boost/thread/lock_types.hpp                                                    |    6 
 BH-1.55.0-1/BH/inst/include/boost/thread/pthread/condition_variable.hpp                                    |   16 
 BH-1.55.0-1/BH/inst/include/boost/thread/pthread/condition_variable_fwd.hpp                                |   18 
 BH-1.55.0-1/BH/inst/include/boost/thread/pthread/thread_data.hpp                                           |    6 
 BH-1.55.0-1/BH/inst/include/boost/thread/win32/condition_variable.hpp                                      |   30 
 BH-1.55.0-1/BH/inst/include/boost/thread/win32/once.hpp                                                    |    2 
 BH-1.55.0-1/BH/inst/include/boost/thread/win32/thread_data.hpp                                             |    8 
 BH-1.55.0-1/BH/inst/include/boost/thread/win32/thread_primitives.hpp                                       |    3 
 BH-1.55.0-1/BH/inst/include/boost/throw_exception.hpp                                                      |    7 
 BH-1.55.0-1/BH/inst/include/boost/type_erasure                                                             |only
 BH-1.55.0-1/BH/inst/include/boost/type_traits.hpp                                                          |    1 
 BH-1.55.0-1/BH/inst/include/boost/type_traits/is_copy_constructible.hpp                                    |only
 BH-1.55.0-1/BH/inst/include/boost/type_traits/is_integral.hpp                                              |    6 
 BH-1.55.0-1/BH/inst/include/boost/unordered/detail/allocate.hpp                                            |   54 
 BH-1.55.0-1/BH/inst/include/boost/unordered/detail/buckets.hpp                                             |   80 
 BH-1.55.0-1/BH/inst/include/boost/unordered/detail/extract_key.hpp                                         |   32 
 BH-1.55.0-1/BH/inst/include/boost/unordered/detail/table.hpp                                               |    4 
 BH-1.55.0-1/BH/inst/include/boost/unordered/detail/unique.hpp                                              |    2 
 BH-1.55.0-1/BH/inst/include/boost/unordered/detail/util.hpp                                                |    5 
 BH-1.55.0-1/BH/inst/include/boost/unordered/unordered_map.hpp                                              |   12 
 BH-1.55.0-1/BH/inst/include/boost/unordered/unordered_set.hpp                                              |   12 
 BH-1.55.0-1/BH/inst/include/boost/utility/base_from_member.hpp                                             |   73 
 BH-1.55.0-1/BH/inst/include/boost/utility/declval.hpp                                                      |   41 
 BH-1.55.0-1/BH/inst/include/boost/utility/detail/result_of_iterate.hpp                                     |   23 
 BH-1.55.0-1/BH/inst/include/boost/utility/empty_deleter.hpp                                                |only
 BH-1.55.0-1/BH/inst/include/boost/utility/explicit_operator_bool.hpp                                       |only
 BH-1.55.0-1/BH/inst/include/boost/utility/result_of.hpp                                                    |   29 
 BH-1.55.0-1/BH/inst/include/boost/variant/detail/move.hpp                                                  |   92 
 BH-1.55.0-1/BH/inst/include/boost/variant/get.hpp                                                          |    7 
 BH-1.55.0-1/BH/inst/include/boost/variant/variant.hpp                                                      |   81 
 BH-1.55.0-1/BH/inst/include/boost/variant/visitor_ptr.hpp                                                  |    3 
 BH-1.55.0-1/BH/inst/include/boost/version.hpp                                                              |    4 
 BH-1.55.0-1/BH/man/BH-package.Rd                                                                           |    4 
 614 files changed, 19549 insertions(+), 29752 deletions(-)

More information about BH at CRAN
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Package spfrontier updated to version 0.1.12 with previous version 0.1.10 dated 2014-07-03

Title: Spatial Stochastic Frontier models estimation
Description: A set of tools for estimation of various spatial specifications of stochastic frontier models
Author: Dmitry Pavlyuk
Maintainer: Dmitry Pavlyuk

Diff between spfrontier versions 0.1.10 dated 2014-07-03 and 0.1.12 dated 2014-12-21

 DESCRIPTION                 |   16 ++---
 MD5                         |   40 ++++++------
 NAMESPACE                   |    5 -
 NEWS                        |    6 +
 R/spfrontier.R              |  136 +++++++++++++++++++++++++++++++++-----------
 R/spfrontier_mle.R          |   80 ++++++++++++-------------
 R/test_ezsim.R              |   21 ++++--
 R/util_mle.R                |   47 +++++++++++----
 data/airports.greece.rda    |binary
 data/airports.rda           |binary
 demo/airports.R             |   95 ++++++------------------------
 demo/frontier_comparison.R  |   10 ++-
 demo/simulation.R           |   68 +++++++++++++---------
 man/ModelEstimates-class.Rd |   20 ++----
 man/data-airports-greece.Rd |   15 ++--
 man/data-airports.Rd        |   25 +++-----
 man/logLikelihood.Rd        |   46 ++++++--------
 man/simulation.Rd           |   63 +++++++-------------
 man/spfrontier-package.Rd   |    5 -
 man/spfrontier.Rd           |   88 +++++++++++-----------------
 man/util-misc.Rd            |   57 ++++++------------
 21 files changed, 428 insertions(+), 415 deletions(-)

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Package rgl updated to version 0.95.1201 with previous version 0.95.1158 dated 2014-11-12

Title: 3D visualization device system (OpenGL)
Description: Provides medium to high level functions for 3D interactive graphics, including functions modelled on base graphics (plot3d(), etc.) as well as functions for constructing representations of geometric objects (cube3d(), etc.). Output may be on screen using OpenGL, or to various standard 3D file formats including WebGL, PLY, OBJ, STL as well as 2D image formats, including PNG, Postscript, SVG, PGF.
Author: Daniel Adler , Duncan Murdoch , and others (see README)
Maintainer: Duncan Murdoch

Diff between rgl versions 0.95.1158 dated 2014-11-12 and 0.95.1201 dated 2014-12-21

 rgl-0.95.1158/rgl/inst/WebGL/CanvasMatrix.js |only
 rgl-0.95.1201/rgl/DESCRIPTION                |   14 --
 rgl-0.95.1201/rgl/MD5                        |  171 ++++++++++++------------
 rgl-0.95.1201/rgl/NAMESPACE                  |    4 
 rgl-0.95.1201/rgl/R/bgplot3d.R               |   17 +-
 rgl-0.95.1201/rgl/R/getscene.R               |   27 +++
 rgl-0.95.1201/rgl/R/obj.R                    |   52 +++++++
 rgl-0.95.1201/rgl/R/par3d.R                  |    2 
 rgl-0.95.1201/rgl/R/persp3d.R                |  185 ++++++++++++++++-----------
 rgl-0.95.1201/rgl/R/plot3d.R                 |   70 +++++-----
 rgl-0.95.1201/rgl/R/subscenes.R              |   10 +
 rgl-0.95.1201/rgl/R/triangulate.R            |   19 ++
 rgl-0.95.1201/rgl/R/webGL.R                  |  154 +++++++++++++++-------
 rgl-0.95.1201/rgl/build                      |only
 rgl-0.95.1201/rgl/configure.win              |   17 +-
 rgl-0.95.1201/rgl/inst/NEWS                  |   25 +++
 rgl-0.95.1201/rgl/inst/doc                   |only
 rgl-0.95.1201/rgl/man/3dobjects.Rd           |   28 ++--
 rgl-0.95.1201/rgl/man/GramSchmidt.Rd         |only
 rgl-0.95.1201/rgl/man/abclines.Rd            |   10 -
 rgl-0.95.1201/rgl/man/addNormals.Rd          |    4 
 rgl-0.95.1201/rgl/man/aspect3d.Rd            |    3 
 rgl-0.95.1201/rgl/man/attributes.Rd          |    6 
 rgl-0.95.1201/rgl/man/axes3d.Rd              |   22 +--
 rgl-0.95.1201/rgl/man/bbox.Rd                |   34 ++--
 rgl-0.95.1201/rgl/man/bg.Rd                  |   12 -
 rgl-0.95.1201/rgl/man/bgplot3d.Rd            |   14 --
 rgl-0.95.1201/rgl/man/callbacks.Rd           |    8 -
 rgl-0.95.1201/rgl/man/cylinder3d.Rd          |   16 +-
 rgl-0.95.1201/rgl/man/ellipse3d.Rd           |   10 -
 rgl-0.95.1201/rgl/man/extrude3d.Rd           |    4 
 rgl-0.95.1201/rgl/man/grid3d.Rd              |    4 
 rgl-0.95.1201/rgl/man/identify3d.Rd          |    4 
 rgl-0.95.1201/rgl/man/light.Rd               |   23 +--
 rgl-0.95.1201/rgl/man/material.Rd            |   12 -
 rgl-0.95.1201/rgl/man/matrices.Rd            |   10 -
 rgl-0.95.1201/rgl/man/mesh3d.Rd              |   18 +-
 rgl-0.95.1201/rgl/man/mfrow3d.Rd             |   27 ++-
 rgl-0.95.1201/rgl/man/observer3d.Rd          |    4 
 rgl-0.95.1201/rgl/man/par3d.Rd               |   37 +++--
 rgl-0.95.1201/rgl/man/par3dinterp.Rd         |    2 
 rgl-0.95.1201/rgl/man/persp3d.Rd             |   70 +++++-----
 rgl-0.95.1201/rgl/man/persp3d.function.Rd    |   45 +++---
 rgl-0.95.1201/rgl/man/planes.Rd              |   13 +
 rgl-0.95.1201/rgl/man/play3d.Rd              |   15 +-
 rgl-0.95.1201/rgl/man/plot3d.Rd              |   44 ++++--
 rgl-0.95.1201/rgl/man/polygon3d.Rd           |    9 -
 rgl-0.95.1201/rgl/man/postscript.Rd          |   36 ++---
 rgl-0.95.1201/rgl/man/primitive.Rd           |   14 +-
 rgl-0.95.1201/rgl/man/r3d.Rd                 |   20 +-
 rgl-0.95.1201/rgl/man/readSTL.Rd             |   10 -
 rgl-0.95.1201/rgl/man/rgl-internal.Rd        |    2 
 rgl-0.95.1201/rgl/man/rgl-package.Rd         |    2 
 rgl-0.95.1201/rgl/man/rgl.Sweave.Rd          |    6 
 rgl-0.95.1201/rgl/man/rgl.bringtotop.Rd      |    2 
 rgl-0.95.1201/rgl/man/rgl.open.Rd            |    4 
 rgl-0.95.1201/rgl/man/rgl.pixels.Rd          |    5 
 rgl-0.95.1201/rgl/man/rgl.user2window.Rd     |    3 
 rgl-0.95.1201/rgl/man/scene.Rd               |    6 
 rgl-0.95.1201/rgl/man/scene3d.Rd             |    4 
 rgl-0.95.1201/rgl/man/select3d.Rd            |   12 -
 rgl-0.95.1201/rgl/man/selectpoints3d.Rd      |   32 ++--
 rgl-0.95.1201/rgl/man/shapelist3d.Rd         |    2 
 rgl-0.95.1201/rgl/man/snapshot.Rd            |   12 -
 rgl-0.95.1201/rgl/man/spheres.Rd             |    2 
 rgl-0.95.1201/rgl/man/spin3d.Rd              |   24 +--
 rgl-0.95.1201/rgl/man/sprites.Rd             |   18 +-
 rgl-0.95.1201/rgl/man/subdivision3d.Rd       |   10 -
 rgl-0.95.1201/rgl/man/subscene3d.Rd          |   32 ++--
 rgl-0.95.1201/rgl/man/surface.Rd             |   14 +-
 rgl-0.95.1201/rgl/man/surface3d.Rd           |    8 -
 rgl-0.95.1201/rgl/man/texts.Rd               |   24 +--
 rgl-0.95.1201/rgl/man/triangulate.Rd         |   19 +-
 rgl-0.95.1201/rgl/man/viewpoint.Rd           |   13 +
 rgl-0.95.1201/rgl/man/writeOBJ.Rd            |   38 ++++-
 rgl-0.95.1201/rgl/man/writePLY.Rd            |    4 
 rgl-0.95.1201/rgl/man/writeWebGL.Rd          |   33 +++-
 rgl-0.95.1201/rgl/src/ClipPlane.cpp          |   46 ++++++
 rgl-0.95.1201/rgl/src/ClipPlane.h            |    2 
 rgl-0.95.1201/rgl/src/par3d.cpp              |    8 +
 rgl-0.95.1201/rgl/src/pngpixmap.h            |    5 
 rgl-0.95.1201/rgl/src/rglview.cpp            |  103 +++++++++------
 rgl-0.95.1201/rgl/src/subscene.cpp           |   66 ++++++---
 rgl-0.95.1201/rgl/src/subscene.h             |   17 ++
 rgl-0.95.1201/rgl/src/x11gui.cpp             |    8 -
 rgl-0.95.1201/rgl/tests/demos.R              |    3 
 rgl-0.95.1201/rgl/vignettes                  |only
 87 files changed, 1203 insertions(+), 741 deletions(-)

More information about rgl at CRAN
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Package PredictABEL updated to version 1.2-2 with previous version 1.2-1 dated 2012-07-27

Title: Assessment of Risk Prediction Models
Description: PredictABEL includes functions to assess the performance of risk models. The package contains functions for the various measures that are used in empirical studies, including univariate and multivariate odds ratios (OR) of the predictors, the c-statistic (or area under the receiver operating characteristic (ROC) curve (AUC)), Hosmer-Lemeshow goodness of fit test, reclassification table, net reclassification improvement (NRI) and integrated discrimination improvement (IDI). Also included are functions to create plots, such as risk distributions, ROC curves, calibration plot, discrimination box plot and predictiveness curves. In addition to functions to assess the performance of risk models, the package includes functions to obtain weighted and unweighted risk scores as well as predicted risks using logistic regression analysis. These logistic regression functions are specifically written for models that include genetic variables, but they can also be applied to models that are based on non-genetic risk factors only. Finally, the package includes function to construct a simulated dataset with genotypes, genetic risks, and disease status for a hypothetical population, which is used for the evaluation of genetic risk models.
Author: Suman Kundu, Yurii S. Aulchenko, A. Cecile J.W. Janssens
Maintainer: Suman Kundu

Diff between PredictABEL versions 1.2-1 dated 2012-07-27 and 1.2-2 dated 2014-12-21

 DESCRIPTION     |   52 ++++++++++++++++++++++++----------------------------
 MD5             |    4 ++--
 R/PredictABEL.R |    2 +-
 3 files changed, 27 insertions(+), 31 deletions(-)

More information about PredictABEL at CRAN
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Package OPI updated to version 2.1 with previous version 1.6 dated 2013-11-15

Title: Open Perimetry Interface
Description: Implementation of the Open Perimetry Interface (OPI) for simulating and controlling visual field machines using R. The OPI is a standard for interfacing with visual field testing machines (perimeters). It specifies basic functions that allow many visual field tests to be constructed. As of December 2014 it is fully implemented on the Octopus 600 and Octopus 900 and partially on the Heidelberg Edge Perimeter and the Kowa AP 7000. It also has a cousin: the R package visualFields, which has tools for analysing and manipulating visual field data.
Author: Andrew Turpin, David Lawson
Maintainer: Andrew Turpin

Diff between OPI versions 1.6 dated 2013-11-15 and 2.1 dated 2014-12-21

 OPI-1.6/OPI/R/octopus900.r            |only
 OPI-2.1/OPI/ChangeLog                 |   16 +++++
 OPI-2.1/OPI/DESCRIPTION               |   15 ++---
 OPI-2.1/OPI/MD5                       |   46 +++++++++--------
 OPI-2.1/OPI/NAMESPACE                 |   92 +++++++++++++++++++---------------
 OPI-2.1/OPI/R/dbTocd.r                |   20 +++----
 OPI-2.1/OPI/R/fourTwo.r               |only
 OPI-2.1/OPI/R/kowaAP7000Client.r      |only
 OPI-2.1/OPI/R/octopus600.r            |only
 OPI-2.1/OPI/R/octopus900Client.r      |only
 OPI-2.1/OPI/R/opi.r                   |   32 +++++++++--
 OPI-2.1/OPI/R/simG.r                  |   10 ++-
 OPI-2.1/OPI/R/simH.r                  |   26 +++++++--
 OPI-2.1/OPI/R/simH_RT.r               |   29 ++++++++--
 OPI-2.1/OPI/R/zest.r                  |    7 +-
 OPI-2.1/OPI/man/FT.Rd                 |    3 -
 OPI-2.1/OPI/man/OPI-package.Rd        |    2 
 OPI-2.1/OPI/man/cdTodb.Rd             |   10 ++-
 OPI-2.1/OPI/man/chooseOpi.Rd          |    1 
 OPI-2.1/OPI/man/dbTocd.Rd             |   14 +++--
 OPI-2.1/OPI/man/fourTwo.Rd            |only
 OPI-2.1/OPI/man/opiInitialize.Rd      |   85 +++++++++++++++++++++++++------
 OPI-2.1/OPI/man/opiKineticStimulus.Rd |   13 ++++
 OPI-2.1/OPI/man/opiPresent.Rd         |   42 ++++++++++++++-
 OPI-2.1/OPI/man/opiQueryDevice.Rd     |   24 +++++++-
 OPI-2.1/OPI/man/opiSetBackground.Rd   |   17 ++++++
 OPI-2.1/OPI/man/opiStaticStimulus.Rd  |   11 ++++
 27 files changed, 380 insertions(+), 135 deletions(-)

More information about OPI at CRAN
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Package reports updated to version 0.1.4 with previous version 0.1.2 dated 2013-03-12

Title: Assist the Workflow of Writing Academic Articles and Other Reports
Description: Assists in writing reports and presentations by providing a frame work that brings together existing R, LaTeX/.docx and Pandoc tools. The package is designed to be used with RStudio, MiKTex/Tex Live/LibreOffice, knitr, knitcitations, Pandoc and pander. The user will want to download these free programs/packages to maximize the effectiveness of the reports package. Functions with two letter names are general text formatting functions for copying text from articles for inclusion as a citation.
Author: Tyler Rinker
Maintainer: Tyler Rinker

Diff between reports versions 0.1.2 dated 2013-03-12 and 0.1.4 dated 2014-12-21

 DESCRIPTION      |   15 +++++++--------
 MD5              |   10 +++++-----
 R/presentation.R |    7 +++++++
 README.md        |    6 +++---
 data/themes.rda  |binary
 inst/CITATION    |    4 ++--
 6 files changed, 24 insertions(+), 18 deletions(-)

More information about reports at CRAN
Permanent link

Package RcppMLPACK updated to version 1.0.10 with previous version 1.0.9-3 dated 2014-08-20

Title: Rcpp Integration for MLPACK Library
Description: MLPACK is an intuitive, fast, scalable C++ machine learning library, meant to be a machine learning analog to LAPACK. It aims to implement a wide array of machine learning methods and function as a Swiss army knife for machine learning researchers: MLPACK is from http://www.mlpack.org/: sources are included in the package.
Author: Qiang Kou, Ryan Curtin
Maintainer: Qiang Kou

Diff between RcppMLPACK versions 1.0.9-3 dated 2014-08-20 and 1.0.10 dated 2014-12-21

 RcppMLPACK-1.0.10/RcppMLPACK/DESCRIPTION                                                                               |   14 
 RcppMLPACK-1.0.10/RcppMLPACK/MD5                                                                                       |  959 ++---
 RcppMLPACK-1.0.10/RcppMLPACK/R/RcppMLPACK.package.skeleton.R                                                           |    4 
 RcppMLPACK-1.0.10/RcppMLPACK/build/vignette.rds                                                                        |binary
 RcppMLPACK-1.0.10/RcppMLPACK/inst/doc/RcppMLPACK-intro.pdf                                                             |binary
 RcppMLPACK-1.0.10/RcppMLPACK/inst/include/mlpack/core.hpp                                                              |    8 
 RcppMLPACK-1.0.10/RcppMLPACK/inst/include/mlpack/core/arma_extend/arma_extend.hpp                                      |    1 
 RcppMLPACK-1.0.10/RcppMLPACK/inst/include/mlpack/core/arma_extend/typedef.hpp                                          |    2 
 RcppMLPACK-1.0.10/RcppMLPACK/inst/include/mlpack/core/data/load.hpp                                                    |    9 
 RcppMLPACK-1.0.10/RcppMLPACK/inst/include/mlpack/core/data/load_impl.hpp                                               |  347 +-
 RcppMLPACK-1.0.10/RcppMLPACK/inst/include/mlpack/core/data/normalize_labels.hpp                                        |   12 
 RcppMLPACK-1.0.10/RcppMLPACK/inst/include/mlpack/core/data/normalize_labels_impl.hpp                                   |   76 
 RcppMLPACK-1.0.10/RcppMLPACK/inst/include/mlpack/core/data/save.hpp                                                    |    9 
 RcppMLPACK-1.0.10/RcppMLPACK/inst/include/mlpack/core/data/save_impl.hpp                                               |  242 -
 RcppMLPACK-1.0.10/RcppMLPACK/inst/include/mlpack/core/dists/discrete_distribution.hpp                                  |   14 
 RcppMLPACK-1.0.10/RcppMLPACK/inst/include/mlpack/core/dists/gaussian_distribution.hpp                                  |    6 
 RcppMLPACK-1.0.10/RcppMLPACK/inst/include/mlpack/core/dists/laplace_distribution.hpp                                   |    8 
 RcppMLPACK-1.0.10/RcppMLPACK/inst/include/mlpack/core/kernels/cosine_distance.hpp                                      |    2 
 RcppMLPACK-1.0.10/RcppMLPACK/inst/include/mlpack/core/kernels/cosine_distance_impl.hpp                                 |    2 
 RcppMLPACK-1.0.10/RcppMLPACK/inst/include/mlpack/core/kernels/epanechnikov_kernel.hpp                                  |    4 
 RcppMLPACK-1.0.10/RcppMLPACK/inst/include/mlpack/core/kernels/epanechnikov_kernel_impl.hpp                             |    2 
 RcppMLPACK-1.0.10/RcppMLPACK/inst/include/mlpack/core/kernels/example_kernel.hpp                                       |    4 
 RcppMLPACK-1.0.10/RcppMLPACK/inst/include/mlpack/core/kernels/gaussian_kernel.hpp                                      |    4 
 RcppMLPACK-1.0.10/RcppMLPACK/inst/include/mlpack/core/kernels/hyperbolic_tangent_kernel.hpp                            |    2 
 RcppMLPACK-1.0.10/RcppMLPACK/inst/include/mlpack/core/kernels/kernel_traits.hpp                                        |    2 
 RcppMLPACK-1.0.10/RcppMLPACK/inst/include/mlpack/core/kernels/laplacian_kernel.hpp                                     |    2 
 RcppMLPACK-1.0.10/RcppMLPACK/inst/include/mlpack/core/kernels/linear_kernel.hpp                                        |    2 
 RcppMLPACK-1.0.10/RcppMLPACK/inst/include/mlpack/core/kernels/polynomial_kernel.hpp                                    |    2 
 RcppMLPACK-1.0.10/RcppMLPACK/inst/include/mlpack/core/kernels/pspectrum_string_kernel.hpp                              |   12 
 RcppMLPACK-1.0.10/RcppMLPACK/inst/include/mlpack/core/kernels/pspectrum_string_kernel_impl.hpp                         |    2 
 RcppMLPACK-1.0.10/RcppMLPACK/inst/include/mlpack/core/kernels/spherical_kernel.hpp                                     |    4 
 RcppMLPACK-1.0.10/RcppMLPACK/inst/include/mlpack/core/kernels/triangular_kernel.hpp                                    |    2 
 RcppMLPACK-1.0.10/RcppMLPACK/inst/include/mlpack/core/math/clamp.hpp                                                   |    2 
 RcppMLPACK-1.0.10/RcppMLPACK/inst/include/mlpack/core/math/lin_alg.hpp                                                 |    4 
 RcppMLPACK-1.0.10/RcppMLPACK/inst/include/mlpack/core/math/random.hpp                                                  |    6 
 RcppMLPACK-1.0.10/RcppMLPACK/inst/include/mlpack/core/math/range.hpp                                                   |    2 
 RcppMLPACK-1.0.10/RcppMLPACK/inst/include/mlpack/core/math/range_impl.hpp                                              |    2 
 RcppMLPACK-1.0.10/RcppMLPACK/inst/include/mlpack/core/math/round.hpp                                                   |    2 
 RcppMLPACK-1.0.10/RcppMLPACK/inst/include/mlpack/core/metrics/ip_metric.hpp                                            |    2 
 RcppMLPACK-1.0.10/RcppMLPACK/inst/include/mlpack/core/metrics/ip_metric_impl.hpp                                       |    2 
 RcppMLPACK-1.0.10/RcppMLPACK/inst/include/mlpack/core/metrics/lmetric.hpp                                              |    2 
 RcppMLPACK-1.0.10/RcppMLPACK/inst/include/mlpack/core/metrics/lmetric_impl.hpp                                         |    6 
 RcppMLPACK-1.0.10/RcppMLPACK/inst/include/mlpack/core/metrics/mahalanobis_distance.hpp                                 |    4 
 RcppMLPACK-1.0.10/RcppMLPACK/inst/include/mlpack/core/metrics/mahalanobis_distance_impl.hpp                            |    2 
 RcppMLPACK-1.0.10/RcppMLPACK/inst/include/mlpack/core/optimizers/aug_lagrangian/aug_lagrangian.hpp                     |   12 
 RcppMLPACK-1.0.10/RcppMLPACK/inst/include/mlpack/core/optimizers/aug_lagrangian/aug_lagrangian_function.hpp            |    2 
 RcppMLPACK-1.0.10/RcppMLPACK/inst/include/mlpack/core/optimizers/aug_lagrangian/aug_lagrangian_function_impl.hpp       |    6 
 RcppMLPACK-1.0.10/RcppMLPACK/inst/include/mlpack/core/optimizers/aug_lagrangian/aug_lagrangian_impl.hpp                |   16 
 RcppMLPACK-1.0.10/RcppMLPACK/inst/include/mlpack/core/optimizers/aug_lagrangian/aug_lagrangian_test_functions.hpp      |   22 
 RcppMLPACK-1.0.10/RcppMLPACK/inst/include/mlpack/core/optimizers/lbfgs/lbfgs.hpp                                       |   34 
 RcppMLPACK-1.0.10/RcppMLPACK/inst/include/mlpack/core/optimizers/lbfgs/lbfgs_impl.hpp                                  |   36 
 RcppMLPACK-1.0.10/RcppMLPACK/inst/include/mlpack/core/optimizers/lbfgs/test_functions.hpp                              |    8 
 RcppMLPACK-1.0.10/RcppMLPACK/inst/include/mlpack/core/optimizers/lrsdp/lrsdp.hpp                                       |    6 
 RcppMLPACK-1.0.10/RcppMLPACK/inst/include/mlpack/core/optimizers/lrsdp/lrsdp_function.hpp                              |   10 
 RcppMLPACK-1.0.10/RcppMLPACK/inst/include/mlpack/core/optimizers/sa/exponential_schedule.hpp                           |    2 
 RcppMLPACK-1.0.10/RcppMLPACK/inst/include/mlpack/core/optimizers/sa/sa.hpp                                             |   40 
 RcppMLPACK-1.0.10/RcppMLPACK/inst/include/mlpack/core/optimizers/sa/sa_impl.hpp                                        |   36 
 RcppMLPACK-1.0.10/RcppMLPACK/inst/include/mlpack/core/optimizers/sgd/sgd.hpp                                           |   16 
 RcppMLPACK-1.0.10/RcppMLPACK/inst/include/mlpack/core/optimizers/sgd/sgd_impl.hpp                                      |   12 
 RcppMLPACK-1.0.10/RcppMLPACK/inst/include/mlpack/core/optimizers/sgd/test_function.hpp                                 |    8 
 RcppMLPACK-1.0.10/RcppMLPACK/inst/include/mlpack/core/tree/ballbound.hpp                                               |    6 
 RcppMLPACK-1.0.10/RcppMLPACK/inst/include/mlpack/core/tree/ballbound_impl.hpp                                          |    8 
 RcppMLPACK-1.0.10/RcppMLPACK/inst/include/mlpack/core/tree/binary_space_tree.hpp                                       |    2 
 RcppMLPACK-1.0.10/RcppMLPACK/inst/include/mlpack/core/tree/binary_space_tree/binary_space_tree.hpp                     |   96 
 RcppMLPACK-1.0.10/RcppMLPACK/inst/include/mlpack/core/tree/binary_space_tree/binary_space_tree_impl.hpp                |   99 
 RcppMLPACK-1.0.10/RcppMLPACK/inst/include/mlpack/core/tree/binary_space_tree/dual_tree_traverser.hpp                   |   26 
 RcppMLPACK-1.0.10/RcppMLPACK/inst/include/mlpack/core/tree/binary_space_tree/dual_tree_traverser_impl.hpp              |    6 
 RcppMLPACK-1.0.10/RcppMLPACK/inst/include/mlpack/core/tree/binary_space_tree/mean_split.hpp                            |   38 
 RcppMLPACK-1.0.10/RcppMLPACK/inst/include/mlpack/core/tree/binary_space_tree/mean_split_impl.hpp                       |   53 
 RcppMLPACK-1.0.10/RcppMLPACK/inst/include/mlpack/core/tree/binary_space_tree/single_tree_traverser.hpp                 |   10 
 RcppMLPACK-1.0.10/RcppMLPACK/inst/include/mlpack/core/tree/binary_space_tree/single_tree_traverser_impl.hpp            |    8 
 RcppMLPACK-1.0.10/RcppMLPACK/inst/include/mlpack/core/tree/binary_space_tree/traits.hpp                                |    2 
 RcppMLPACK-1.0.10/RcppMLPACK/inst/include/mlpack/core/tree/bounds.hpp                                                  |    2 
 RcppMLPACK-1.0.10/RcppMLPACK/inst/include/mlpack/core/tree/cosine_tree/cosine_tree.hpp                                 |   26 
 RcppMLPACK-1.0.10/RcppMLPACK/inst/include/mlpack/core/tree/cover_tree.hpp                                              |    2 
 RcppMLPACK-1.0.10/RcppMLPACK/inst/include/mlpack/core/tree/cover_tree/cover_tree.hpp                                   |   88 
 RcppMLPACK-1.0.10/RcppMLPACK/inst/include/mlpack/core/tree/cover_tree/cover_tree_impl.hpp                              |  175 -
 RcppMLPACK-1.0.10/RcppMLPACK/inst/include/mlpack/core/tree/cover_tree/dual_tree_traverser.hpp                          |   14 
 RcppMLPACK-1.0.10/RcppMLPACK/inst/include/mlpack/core/tree/cover_tree/dual_tree_traverser_impl.hpp                     |   17 
 RcppMLPACK-1.0.10/RcppMLPACK/inst/include/mlpack/core/tree/cover_tree/first_point_is_root.hpp                          |    4 
 RcppMLPACK-1.0.10/RcppMLPACK/inst/include/mlpack/core/tree/cover_tree/single_tree_traverser.hpp                        |   10 
 RcppMLPACK-1.0.10/RcppMLPACK/inst/include/mlpack/core/tree/cover_tree/single_tree_traverser_impl.hpp                   |   20 
 RcppMLPACK-1.0.10/RcppMLPACK/inst/include/mlpack/core/tree/cover_tree/traits.hpp                                       |    2 
 RcppMLPACK-1.0.10/RcppMLPACK/inst/include/mlpack/core/tree/example_tree.hpp                                            |   16 
 RcppMLPACK-1.0.10/RcppMLPACK/inst/include/mlpack/core/tree/hrectbound.hpp                                              |   12 
 RcppMLPACK-1.0.10/RcppMLPACK/inst/include/mlpack/core/tree/hrectbound_impl.hpp                                         |   50 
 RcppMLPACK-1.0.10/RcppMLPACK/inst/include/mlpack/core/tree/mrkd_statistic.hpp                                          |   26 
 RcppMLPACK-1.0.10/RcppMLPACK/inst/include/mlpack/core/tree/mrkd_statistic_impl.hpp                                     |   10 
 RcppMLPACK-1.0.10/RcppMLPACK/inst/include/mlpack/core/tree/rectangle_tree.hpp                                          |    2 
 RcppMLPACK-1.0.10/RcppMLPACK/inst/include/mlpack/core/tree/statistic.hpp                                               |    2 
 RcppMLPACK-1.0.10/RcppMLPACK/inst/include/mlpack/core/tree/traversal_info.hpp                                          |    2 
 RcppMLPACK-1.0.10/RcppMLPACK/inst/include/mlpack/core/tree/tree_traits.hpp                                             |    2 
 RcppMLPACK-1.0.10/RcppMLPACK/inst/include/mlpack/core/util/arma_traits.hpp                                             |    2 
 RcppMLPACK-1.0.10/RcppMLPACK/inst/include/mlpack/core/util/nulloutstream.hpp                                           |    2 
 RcppMLPACK-1.0.10/RcppMLPACK/inst/include/mlpack/core/util/option.hpp                                                  |    2 
 RcppMLPACK-1.0.10/RcppMLPACK/inst/include/mlpack/core/util/option_impl.hpp                                             |    2 
 RcppMLPACK-1.0.10/RcppMLPACK/inst/include/mlpack/core/util/prefixedoutstream.hpp                                       |    2 
 RcppMLPACK-1.0.10/RcppMLPACK/inst/include/mlpack/core/util/prefixedoutstream_impl.hpp                                  |    6 
 RcppMLPACK-1.0.10/RcppMLPACK/inst/include/mlpack/core/util/sfinae_utility.hpp                                          |    2 
 RcppMLPACK-1.0.10/RcppMLPACK/inst/include/mlpack/core/util/string_util.hpp                                             |    4 
 RcppMLPACK-1.0.10/RcppMLPACK/inst/include/mlpack/core/util/timers.hpp                                                  |only
 RcppMLPACK-1.0.10/RcppMLPACK/inst/include/mlpack/core/util/version.hpp                                                 |    2 
 RcppMLPACK-1.0.10/RcppMLPACK/inst/include/mlpack/methods/amf/amf.hpp                                                   |    6 
 RcppMLPACK-1.0.10/RcppMLPACK/inst/include/mlpack/methods/amf/amf_impl.hpp                                              |    6 
 RcppMLPACK-1.0.10/RcppMLPACK/inst/include/mlpack/methods/amf/init_rules/random_acol_init.hpp                           |   14 
 RcppMLPACK-1.0.10/RcppMLPACK/inst/include/mlpack/methods/amf/init_rules/random_init.hpp                                |    8 
 RcppMLPACK-1.0.10/RcppMLPACK/inst/include/mlpack/methods/amf/termination_policies/complete_incremental.hpp             |    8 
 RcppMLPACK-1.0.10/RcppMLPACK/inst/include/mlpack/methods/amf/termination_policies/complete_incremental_termination.hpp |only
 RcppMLPACK-1.0.10/RcppMLPACK/inst/include/mlpack/methods/amf/termination_policies/incomplete_incremental.hpp           |    8 
 RcppMLPACK-1.0.10/RcppMLPACK/inst/include/mlpack/methods/amf/termination_policies/simple_residue_termination.hpp       |   18 
 RcppMLPACK-1.0.10/RcppMLPACK/inst/include/mlpack/methods/amf/termination_policies/simple_tolerance_termination.hpp     |   28 
 RcppMLPACK-1.0.10/RcppMLPACK/inst/include/mlpack/methods/amf/termination_policies/validation_RMSE_termination.hpp      |   38 
 RcppMLPACK-1.0.10/RcppMLPACK/inst/include/mlpack/methods/amf/update_rules/nmf_als.hpp                                  |    8 
 RcppMLPACK-1.0.10/RcppMLPACK/inst/include/mlpack/methods/amf/update_rules/nmf_mult_dist.hpp                            |    4 
 RcppMLPACK-1.0.10/RcppMLPACK/inst/include/mlpack/methods/amf/update_rules/nmf_mult_div.hpp                             |   16 
 RcppMLPACK-1.0.10/RcppMLPACK/inst/include/mlpack/methods/amf/update_rules/svd_batch_learning.hpp                       |   48 
 RcppMLPACK-1.0.10/RcppMLPACK/inst/include/mlpack/methods/amf/update_rules/svd_complete_incremental_learning.hpp        |   26 
 RcppMLPACK-1.0.10/RcppMLPACK/inst/include/mlpack/methods/amf/update_rules/svd_incomplete_incremental_learning.hpp      |   18 
 RcppMLPACK-1.0.10/RcppMLPACK/inst/include/mlpack/methods/cf/cf.hpp                                                     |   44 
 RcppMLPACK-1.0.10/RcppMLPACK/inst/include/mlpack/methods/cf/cf_impl.hpp                                                |   50 
 RcppMLPACK-1.0.10/RcppMLPACK/inst/include/mlpack/methods/decision_stump/decision_stump.hpp                             |   24 
 RcppMLPACK-1.0.10/RcppMLPACK/inst/include/mlpack/methods/decision_stump/decision_stump_impl.hpp                        |   63 
 RcppMLPACK-1.0.10/RcppMLPACK/inst/include/mlpack/methods/det/dt_utils.hpp                                              |   12 
 RcppMLPACK-1.0.10/RcppMLPACK/inst/include/mlpack/methods/det/dtree.hpp                                                 |   52 
 RcppMLPACK-1.0.10/RcppMLPACK/inst/include/mlpack/methods/emst/dtb.hpp                                                  |   10 
 RcppMLPACK-1.0.10/RcppMLPACK/inst/include/mlpack/methods/emst/dtb_impl.hpp                                             |   53 
 RcppMLPACK-1.0.10/RcppMLPACK/inst/include/mlpack/methods/emst/dtb_rules.hpp                                            |   30 
 RcppMLPACK-1.0.10/RcppMLPACK/inst/include/mlpack/methods/emst/dtb_rules_impl.hpp                                       |   36 
 RcppMLPACK-1.0.10/RcppMLPACK/inst/include/mlpack/methods/emst/dtb_stat.hpp                                             |    2 
 RcppMLPACK-1.0.10/RcppMLPACK/inst/include/mlpack/methods/emst/edge_pair.hpp                                            |   19 
 RcppMLPACK-1.0.10/RcppMLPACK/inst/include/mlpack/methods/emst/union_find.hpp                                           |   16 
 RcppMLPACK-1.0.10/RcppMLPACK/inst/include/mlpack/methods/fastmks/fastmks.hpp                                           |  344 +-
 RcppMLPACK-1.0.10/RcppMLPACK/inst/include/mlpack/methods/fastmks/fastmks_impl.hpp                                      |  306 -
 RcppMLPACK-1.0.10/RcppMLPACK/inst/include/mlpack/methods/fastmks/fastmks_rules.hpp                                     |  256 -
 RcppMLPACK-1.0.10/RcppMLPACK/inst/include/mlpack/methods/fastmks/fastmks_rules_impl.hpp                                |  804 ++--
 RcppMLPACK-1.0.10/RcppMLPACK/inst/include/mlpack/methods/fastmks/fastmks_stat.hpp                                      |  206 -
 RcppMLPACK-1.0.10/RcppMLPACK/inst/include/mlpack/methods/gmm/diagonal_constraint.hpp                                   |    2 
 RcppMLPACK-1.0.10/RcppMLPACK/inst/include/mlpack/methods/gmm/eigenvalue_ratio_constraint.hpp                           |    4 
 RcppMLPACK-1.0.10/RcppMLPACK/inst/include/mlpack/methods/gmm/em_fit.hpp                                                |   14 
 RcppMLPACK-1.0.10/RcppMLPACK/inst/include/mlpack/methods/gmm/em_fit_impl.hpp                                           |   40 
 RcppMLPACK-1.0.10/RcppMLPACK/inst/include/mlpack/methods/gmm/gmm.hpp                                                   |   32 
 RcppMLPACK-1.0.10/RcppMLPACK/inst/include/mlpack/methods/gmm/gmm_impl.hpp                                              |   52 
 RcppMLPACK-1.0.10/RcppMLPACK/inst/include/mlpack/methods/gmm/no_constraint.hpp                                         |    2 
 RcppMLPACK-1.0.10/RcppMLPACK/inst/include/mlpack/methods/gmm/phi.hpp                                                   |    6 
 RcppMLPACK-1.0.10/RcppMLPACK/inst/include/mlpack/methods/gmm/positive_definite_constraint.hpp                          |    2 
 RcppMLPACK-1.0.10/RcppMLPACK/inst/include/mlpack/methods/hmm/hmm.hpp                                                   |   22 
 RcppMLPACK-1.0.10/RcppMLPACK/inst/include/mlpack/methods/hmm/hmm_impl.hpp                                              |   72 
 RcppMLPACK-1.0.10/RcppMLPACK/inst/include/mlpack/methods/hmm/hmm_util.hpp                                              |only
 RcppMLPACK-1.0.10/RcppMLPACK/inst/include/mlpack/methods/hmm/hmm_util_impl.hpp                                         |only
 RcppMLPACK-1.0.10/RcppMLPACK/inst/include/mlpack/methods/kernel_pca/kernel_pca.hpp                                     |    6 
 RcppMLPACK-1.0.10/RcppMLPACK/inst/include/mlpack/methods/kernel_pca/kernel_pca_impl.hpp                                |    6 
 RcppMLPACK-1.0.10/RcppMLPACK/inst/include/mlpack/methods/kernel_pca/kernel_rules/naive_method.hpp                      |   14 
 RcppMLPACK-1.0.10/RcppMLPACK/inst/include/mlpack/methods/kernel_pca/kernel_rules/nystroem_method.hpp                   |    4 
 RcppMLPACK-1.0.10/RcppMLPACK/inst/include/mlpack/methods/kmeans/allow_empty_clusters.hpp                               |   10 
 RcppMLPACK-1.0.10/RcppMLPACK/inst/include/mlpack/methods/kmeans/kmeans.hpp                                             |   26 
 RcppMLPACK-1.0.10/RcppMLPACK/inst/include/mlpack/methods/kmeans/kmeans_impl.hpp                                        |   94 
 RcppMLPACK-1.0.10/RcppMLPACK/inst/include/mlpack/methods/kmeans/max_variance_new_cluster.hpp                           |   10 
 RcppMLPACK-1.0.10/RcppMLPACK/inst/include/mlpack/methods/kmeans/max_variance_new_cluster_impl.hpp                      |   18 
 RcppMLPACK-1.0.10/RcppMLPACK/inst/include/mlpack/methods/kmeans/random_partition.hpp                                   |    8 
 RcppMLPACK-1.0.10/RcppMLPACK/inst/include/mlpack/methods/kmeans/refined_start.hpp                                      |   14 
 RcppMLPACK-1.0.10/RcppMLPACK/inst/include/mlpack/methods/kmeans/refined_start_impl.hpp                                 |   22 
 RcppMLPACK-1.0.10/RcppMLPACK/inst/include/mlpack/methods/lars/lars.hpp                                                 |   16 
 RcppMLPACK-1.0.10/RcppMLPACK/inst/include/mlpack/methods/linear_regression/linear_regression.hpp                       |    4 
 RcppMLPACK-1.0.10/RcppMLPACK/inst/include/mlpack/methods/local_coordinate_coding/lcc.hpp                               |    8 
 RcppMLPACK-1.0.10/RcppMLPACK/inst/include/mlpack/methods/local_coordinate_coding/lcc_impl.hpp                          |   58 
 RcppMLPACK-1.0.10/RcppMLPACK/inst/include/mlpack/methods/logistic_regression/logistic_regression.hpp                   |    2 
 RcppMLPACK-1.0.10/RcppMLPACK/inst/include/mlpack/methods/logistic_regression/logistic_regression_function.hpp          |    8 
 RcppMLPACK-1.0.10/RcppMLPACK/inst/include/mlpack/methods/logistic_regression/logistic_regression_impl.hpp              |   18 
 RcppMLPACK-1.0.10/RcppMLPACK/inst/include/mlpack/methods/lsh/lsh_search.hpp                                            |   50 
 RcppMLPACK-1.0.10/RcppMLPACK/inst/include/mlpack/methods/lsh/lsh_search_impl.hpp                                       |  107 
 RcppMLPACK-1.0.10/RcppMLPACK/inst/include/mlpack/methods/mvu/mvu.hpp                                                   |    8 
 RcppMLPACK-1.0.10/RcppMLPACK/inst/include/mlpack/methods/naive_bayes/naive_bayes_classifier.hpp                        |   12 
 RcppMLPACK-1.0.10/RcppMLPACK/inst/include/mlpack/methods/naive_bayes/naive_bayes_classifier_impl.hpp                   |   41 
 RcppMLPACK-1.0.10/RcppMLPACK/inst/include/mlpack/methods/nca/nca.hpp                                                   |    8 
 RcppMLPACK-1.0.10/RcppMLPACK/inst/include/mlpack/methods/nca/nca_impl.hpp                                              |    7 
 RcppMLPACK-1.0.10/RcppMLPACK/inst/include/mlpack/methods/nca/nca_softmax_error_function.hpp                            |   12 
 RcppMLPACK-1.0.10/RcppMLPACK/inst/include/mlpack/methods/nca/nca_softmax_error_function_impl.hpp                       |   22 
 RcppMLPACK-1.0.10/RcppMLPACK/inst/include/mlpack/methods/neighbor_search/neighbor_search.hpp                           |   10 
 RcppMLPACK-1.0.10/RcppMLPACK/inst/include/mlpack/methods/neighbor_search/neighbor_search_impl.hpp                      |   59 
 RcppMLPACK-1.0.10/RcppMLPACK/inst/include/mlpack/methods/neighbor_search/neighbor_search_rules.hpp                     |   34 
 RcppMLPACK-1.0.10/RcppMLPACK/inst/include/mlpack/methods/neighbor_search/neighbor_search_rules_impl.hpp                |  239 -
 RcppMLPACK-1.0.10/RcppMLPACK/inst/include/mlpack/methods/neighbor_search/neighbor_search_stat.hpp                      |    2 
 RcppMLPACK-1.0.10/RcppMLPACK/inst/include/mlpack/methods/neighbor_search/ns_traversal_info.hpp                         |    2 
 RcppMLPACK-1.0.10/RcppMLPACK/inst/include/mlpack/methods/neighbor_search/sort_policies/furthest_neighbor_sort.hpp      |   10 
 RcppMLPACK-1.0.10/RcppMLPACK/inst/include/mlpack/methods/neighbor_search/sort_policies/furthest_neighbor_sort_impl.hpp |    2 
 RcppMLPACK-1.0.10/RcppMLPACK/inst/include/mlpack/methods/neighbor_search/sort_policies/nearest_neighbor_sort.hpp       |   10 
 RcppMLPACK-1.0.10/RcppMLPACK/inst/include/mlpack/methods/neighbor_search/sort_policies/nearest_neighbor_sort_impl.hpp  |    2 
 RcppMLPACK-1.0.10/RcppMLPACK/inst/include/mlpack/methods/neighbor_search/typedef.hpp                                   |    2 
 RcppMLPACK-1.0.10/RcppMLPACK/inst/include/mlpack/methods/neighbor_search/unmap.hpp                                     |   16 
 RcppMLPACK-1.0.10/RcppMLPACK/inst/include/mlpack/methods/nystroem_method/kmeans_selection.hpp                          |   12 
 RcppMLPACK-1.0.10/RcppMLPACK/inst/include/mlpack/methods/nystroem_method/nystroem_method.hpp                           |   12 
 RcppMLPACK-1.0.10/RcppMLPACK/inst/include/mlpack/methods/nystroem_method/nystroem_method_impl.hpp                      |   26 
 RcppMLPACK-1.0.10/RcppMLPACK/inst/include/mlpack/methods/nystroem_method/ordered_selection.hpp                         |   12 
 RcppMLPACK-1.0.10/RcppMLPACK/inst/include/mlpack/methods/nystroem_method/random_selection.hpp                          |   12 
 RcppMLPACK-1.0.10/RcppMLPACK/inst/include/mlpack/methods/pca/pca.hpp                                                   |   12 
 RcppMLPACK-1.0.10/RcppMLPACK/inst/include/mlpack/methods/perceptron/initialization_methods/random_init.hpp             |   10 
 RcppMLPACK-1.0.10/RcppMLPACK/inst/include/mlpack/methods/perceptron/initialization_methods/zero_init.hpp               |   10 
 RcppMLPACK-1.0.10/RcppMLPACK/inst/include/mlpack/methods/perceptron/learning_policies/simple_weight_update.hpp         |   12 
 RcppMLPACK-1.0.10/RcppMLPACK/inst/include/mlpack/methods/perceptron/perceptron.hpp                                     |   12 
 RcppMLPACK-1.0.10/RcppMLPACK/inst/include/mlpack/methods/perceptron/perceptron_impl.hpp                                |   18 
 RcppMLPACK-1.0.10/RcppMLPACK/inst/include/mlpack/methods/quic_svd/quic_svd.hpp                                         |    2 
 RcppMLPACK-1.0.10/RcppMLPACK/inst/include/mlpack/methods/quic_svd/quic_svd_impl.hpp                                    |    2 
 RcppMLPACK-1.0.10/RcppMLPACK/inst/include/mlpack/methods/radical/radical.hpp                                           |   34 
 RcppMLPACK-1.0.10/RcppMLPACK/inst/include/mlpack/methods/range_search/range_search.hpp                                 |   14 
 RcppMLPACK-1.0.10/RcppMLPACK/inst/include/mlpack/methods/range_search/range_search_impl.hpp                            |   45 
 RcppMLPACK-1.0.10/RcppMLPACK/inst/include/mlpack/methods/range_search/range_search_rules.hpp                           |   22 
 RcppMLPACK-1.0.10/RcppMLPACK/inst/include/mlpack/methods/range_search/range_search_rules_impl.hpp                      |   26 
 RcppMLPACK-1.0.10/RcppMLPACK/inst/include/mlpack/methods/range_search/range_search_stat.hpp                            |    6 
 RcppMLPACK-1.0.10/RcppMLPACK/inst/include/mlpack/methods/rann/ra_query_stat.hpp                                        |   82 
 RcppMLPACK-1.0.10/RcppMLPACK/inst/include/mlpack/methods/rann/ra_search.hpp                                            |  466 +-
 RcppMLPACK-1.0.10/RcppMLPACK/inst/include/mlpack/methods/rann/ra_search_impl.hpp                                       |  521 +--
 RcppMLPACK-1.0.10/RcppMLPACK/inst/include/mlpack/methods/rann/ra_search_rules.hpp                                      |  587 +--
 RcppMLPACK-1.0.10/RcppMLPACK/inst/include/mlpack/methods/rann/ra_search_rules_impl.hpp                                 | 1622 ++++------
 RcppMLPACK-1.0.10/RcppMLPACK/inst/include/mlpack/methods/rann/ra_typedef.hpp                                           |   12 
 RcppMLPACK-1.0.10/RcppMLPACK/inst/include/mlpack/methods/regularized_svd/regularized_svd.hpp                           |   10 
 RcppMLPACK-1.0.10/RcppMLPACK/inst/include/mlpack/methods/regularized_svd/regularized_svd_function.hpp                  |   20 
 RcppMLPACK-1.0.10/RcppMLPACK/inst/include/mlpack/methods/regularized_svd/regularized_svd_impl.hpp                      |   14 
 RcppMLPACK-1.0.10/RcppMLPACK/inst/include/mlpack/methods/sparse_autoencoder/sparse_autoencoder.hpp                     |   26 
 RcppMLPACK-1.0.10/RcppMLPACK/inst/include/mlpack/methods/sparse_autoencoder/sparse_autoencoder_function.hpp            |   18 
 RcppMLPACK-1.0.10/RcppMLPACK/inst/include/mlpack/methods/sparse_autoencoder/sparse_autoencoder_impl.hpp                |   22 
 RcppMLPACK-1.0.10/RcppMLPACK/inst/include/mlpack/methods/sparse_coding/data_dependent_random_initializer.hpp           |   10 
 RcppMLPACK-1.0.10/RcppMLPACK/inst/include/mlpack/methods/sparse_coding/nothing_initializer.hpp                         |    8 
 RcppMLPACK-1.0.10/RcppMLPACK/inst/include/mlpack/methods/sparse_coding/random_initializer.hpp                          |   10 
 RcppMLPACK-1.0.10/RcppMLPACK/inst/include/mlpack/methods/sparse_coding/sparse_coding.hpp                               |   12 
 RcppMLPACK-1.0.10/RcppMLPACK/inst/include/mlpack/methods/sparse_coding/sparse_coding_impl.hpp                          |   44 
 RcppMLPACK-1.0.10/RcppMLPACK/inst/include/mlpack/prereqs.hpp                                                           |    2 
 RcppMLPACK-1.0.10/RcppMLPACK/inst/skeleton/kmeans.cpp                                                                  |    4 
 RcppMLPACK-1.0.10/RcppMLPACK/man/RcppMLPACK-package.Rd                                                                 |    2 
 RcppMLPACK-1.0.10/RcppMLPACK/src/Makevars                                                                              |    2 
 RcppMLPACK-1.0.10/RcppMLPACK/src/Makevars.win                                                                          |    2 
 RcppMLPACK-1.0.10/RcppMLPACK/src/RcppMLPACK.h                                                                          |    1 
 RcppMLPACK-1.0.10/RcppMLPACK/src/kmeans.cpp                                                                            |    2 
 RcppMLPACK-1.0.10/RcppMLPACK/src/mlpack/core.hpp                                                                       |    8 
 RcppMLPACK-1.0.10/RcppMLPACK/src/mlpack/core/arma_extend/arma_extend.hpp                                               |    1 
 RcppMLPACK-1.0.10/RcppMLPACK/src/mlpack/core/arma_extend/typedef.hpp                                                   |    2 
 RcppMLPACK-1.0.10/RcppMLPACK/src/mlpack/core/data/load.hpp                                                             |    9 
 RcppMLPACK-1.0.10/RcppMLPACK/src/mlpack/core/data/load_impl.hpp                                                        |  347 +-
 RcppMLPACK-1.0.10/RcppMLPACK/src/mlpack/core/data/normalize_labels.hpp                                                 |   12 
 RcppMLPACK-1.0.10/RcppMLPACK/src/mlpack/core/data/normalize_labels_impl.hpp                                            |   76 
 RcppMLPACK-1.0.10/RcppMLPACK/src/mlpack/core/data/save.hpp                                                             |    9 
 RcppMLPACK-1.0.10/RcppMLPACK/src/mlpack/core/data/save_impl.hpp                                                        |  242 -
 RcppMLPACK-1.0.10/RcppMLPACK/src/mlpack/core/dists/discrete_distribution.cpp                                           |   16 
 RcppMLPACK-1.0.10/RcppMLPACK/src/mlpack/core/dists/discrete_distribution.hpp                                           |   14 
 RcppMLPACK-1.0.10/RcppMLPACK/src/mlpack/core/dists/gaussian_distribution.cpp                                           |   10 
 RcppMLPACK-1.0.10/RcppMLPACK/src/mlpack/core/dists/gaussian_distribution.hpp                                           |    6 
 RcppMLPACK-1.0.10/RcppMLPACK/src/mlpack/core/dists/laplace_distribution.cpp                                            |    8 
 RcppMLPACK-1.0.10/RcppMLPACK/src/mlpack/core/dists/laplace_distribution.hpp                                            |    8 
 RcppMLPACK-1.0.10/RcppMLPACK/src/mlpack/core/kernels/cosine_distance.hpp                                               |    2 
 RcppMLPACK-1.0.10/RcppMLPACK/src/mlpack/core/kernels/cosine_distance_impl.hpp                                          |    2 
 RcppMLPACK-1.0.10/RcppMLPACK/src/mlpack/core/kernels/epanechnikov_kernel.cpp                                           |    4 
 RcppMLPACK-1.0.10/RcppMLPACK/src/mlpack/core/kernels/epanechnikov_kernel.hpp                                           |    4 
 RcppMLPACK-1.0.10/RcppMLPACK/src/mlpack/core/kernels/epanechnikov_kernel_impl.hpp                                      |    2 
 RcppMLPACK-1.0.10/RcppMLPACK/src/mlpack/core/kernels/example_kernel.hpp                                                |    4 
 RcppMLPACK-1.0.10/RcppMLPACK/src/mlpack/core/kernels/gaussian_kernel.hpp                                               |    4 
 RcppMLPACK-1.0.10/RcppMLPACK/src/mlpack/core/kernels/hyperbolic_tangent_kernel.hpp                                     |    2 
 RcppMLPACK-1.0.10/RcppMLPACK/src/mlpack/core/kernels/kernel_traits.hpp                                                 |    2 
 RcppMLPACK-1.0.10/RcppMLPACK/src/mlpack/core/kernels/laplacian_kernel.hpp                                              |    2 
 RcppMLPACK-1.0.10/RcppMLPACK/src/mlpack/core/kernels/linear_kernel.hpp                                                 |    2 
 RcppMLPACK-1.0.10/RcppMLPACK/src/mlpack/core/kernels/polynomial_kernel.hpp                                             |    2 
 RcppMLPACK-1.0.10/RcppMLPACK/src/mlpack/core/kernels/pspectrum_string_kernel.cpp                                       |   12 
 RcppMLPACK-1.0.10/RcppMLPACK/src/mlpack/core/kernels/pspectrum_string_kernel.hpp                                       |   12 
 RcppMLPACK-1.0.10/RcppMLPACK/src/mlpack/core/kernels/pspectrum_string_kernel_impl.hpp                                  |    2 
 RcppMLPACK-1.0.10/RcppMLPACK/src/mlpack/core/kernels/spherical_kernel.hpp                                              |    4 
 RcppMLPACK-1.0.10/RcppMLPACK/src/mlpack/core/kernels/triangular_kernel.hpp                                             |    2 
 RcppMLPACK-1.0.10/RcppMLPACK/src/mlpack/core/math/clamp.hpp                                                            |    2 
 RcppMLPACK-1.0.10/RcppMLPACK/src/mlpack/core/math/lin_alg.cpp                                                          |   20 
 RcppMLPACK-1.0.10/RcppMLPACK/src/mlpack/core/math/lin_alg.hpp                                                          |    4 
 RcppMLPACK-1.0.10/RcppMLPACK/src/mlpack/core/math/random.cpp                                                           |    2 
 RcppMLPACK-1.0.10/RcppMLPACK/src/mlpack/core/math/random.hpp                                                           |    6 
 RcppMLPACK-1.0.10/RcppMLPACK/src/mlpack/core/math/range.hpp                                                            |    2 
 RcppMLPACK-1.0.10/RcppMLPACK/src/mlpack/core/math/range_impl.hpp                                                       |    2 
 RcppMLPACK-1.0.10/RcppMLPACK/src/mlpack/core/math/round.hpp                                                            |    2 
 RcppMLPACK-1.0.10/RcppMLPACK/src/mlpack/core/metrics/ip_metric.hpp                                                     |    2 
 RcppMLPACK-1.0.10/RcppMLPACK/src/mlpack/core/metrics/ip_metric_impl.hpp                                                |    2 
 RcppMLPACK-1.0.10/RcppMLPACK/src/mlpack/core/metrics/lmetric.hpp                                                       |    2 
 RcppMLPACK-1.0.10/RcppMLPACK/src/mlpack/core/metrics/lmetric_impl.hpp                                                  |    6 
 RcppMLPACK-1.0.10/RcppMLPACK/src/mlpack/core/metrics/mahalanobis_distance.hpp                                          |    4 
 RcppMLPACK-1.0.10/RcppMLPACK/src/mlpack/core/metrics/mahalanobis_distance_impl.hpp                                     |    2 
 RcppMLPACK-1.0.10/RcppMLPACK/src/mlpack/core/optimizers/aug_lagrangian/aug_lagrangian.hpp                              |   12 
 RcppMLPACK-1.0.10/RcppMLPACK/src/mlpack/core/optimizers/aug_lagrangian/aug_lagrangian_function.hpp                     |    2 
 RcppMLPACK-1.0.10/RcppMLPACK/src/mlpack/core/optimizers/aug_lagrangian/aug_lagrangian_function_impl.hpp                |    6 
 RcppMLPACK-1.0.10/RcppMLPACK/src/mlpack/core/optimizers/aug_lagrangian/aug_lagrangian_impl.hpp                         |   16 
 RcppMLPACK-1.0.10/RcppMLPACK/src/mlpack/core/optimizers/aug_lagrangian/aug_lagrangian_test_functions.cpp               |   42 
 RcppMLPACK-1.0.10/RcppMLPACK/src/mlpack/core/optimizers/aug_lagrangian/aug_lagrangian_test_functions.hpp               |   22 
 RcppMLPACK-1.0.10/RcppMLPACK/src/mlpack/core/optimizers/lbfgs/lbfgs.hpp                                                |   34 
 RcppMLPACK-1.0.10/RcppMLPACK/src/mlpack/core/optimizers/lbfgs/lbfgs_impl.hpp                                           |   36 
 RcppMLPACK-1.0.10/RcppMLPACK/src/mlpack/core/optimizers/lbfgs/test_functions.cpp                                       |    6 
 RcppMLPACK-1.0.10/RcppMLPACK/src/mlpack/core/optimizers/lbfgs/test_functions.hpp                                       |    8 
 RcppMLPACK-1.0.10/RcppMLPACK/src/mlpack/core/optimizers/lrsdp/lrsdp.cpp                                                |    4 
 RcppMLPACK-1.0.10/RcppMLPACK/src/mlpack/core/optimizers/lrsdp/lrsdp.hpp                                                |    6 
 RcppMLPACK-1.0.10/RcppMLPACK/src/mlpack/core/optimizers/lrsdp/lrsdp_function.cpp                                       |   20 
 RcppMLPACK-1.0.10/RcppMLPACK/src/mlpack/core/optimizers/lrsdp/lrsdp_function.hpp                                       |   10 
 RcppMLPACK-1.0.10/RcppMLPACK/src/mlpack/core/optimizers/sa/exponential_schedule.hpp                                    |    2 
 RcppMLPACK-1.0.10/RcppMLPACK/src/mlpack/core/optimizers/sa/sa.hpp                                                      |   40 
 RcppMLPACK-1.0.10/RcppMLPACK/src/mlpack/core/optimizers/sa/sa_impl.hpp                                                 |   36 
 RcppMLPACK-1.0.10/RcppMLPACK/src/mlpack/core/optimizers/sgd/sgd.hpp                                                    |   16 
 RcppMLPACK-1.0.10/RcppMLPACK/src/mlpack/core/optimizers/sgd/sgd_impl.hpp                                               |   12 
 RcppMLPACK-1.0.10/RcppMLPACK/src/mlpack/core/optimizers/sgd/test_function.cpp                                          |    6 
 RcppMLPACK-1.0.10/RcppMLPACK/src/mlpack/core/optimizers/sgd/test_function.hpp                                          |    8 
 RcppMLPACK-1.0.10/RcppMLPACK/src/mlpack/core/tree/ballbound.hpp                                                        |    6 
 RcppMLPACK-1.0.10/RcppMLPACK/src/mlpack/core/tree/ballbound_impl.hpp                                                   |    8 
 RcppMLPACK-1.0.10/RcppMLPACK/src/mlpack/core/tree/binary_space_tree.hpp                                                |    2 
 RcppMLPACK-1.0.10/RcppMLPACK/src/mlpack/core/tree/binary_space_tree/binary_space_tree.hpp                              |   96 
 RcppMLPACK-1.0.10/RcppMLPACK/src/mlpack/core/tree/binary_space_tree/binary_space_tree_impl.hpp                         |   99 
 RcppMLPACK-1.0.10/RcppMLPACK/src/mlpack/core/tree/binary_space_tree/dual_tree_traverser.hpp                            |   26 
 RcppMLPACK-1.0.10/RcppMLPACK/src/mlpack/core/tree/binary_space_tree/dual_tree_traverser_impl.hpp                       |    6 
 RcppMLPACK-1.0.10/RcppMLPACK/src/mlpack/core/tree/binary_space_tree/mean_split.hpp                                     |   38 
 RcppMLPACK-1.0.10/RcppMLPACK/src/mlpack/core/tree/binary_space_tree/mean_split_impl.hpp                                |   53 
 RcppMLPACK-1.0.10/RcppMLPACK/src/mlpack/core/tree/binary_space_tree/single_tree_traverser.hpp                          |   10 
 RcppMLPACK-1.0.10/RcppMLPACK/src/mlpack/core/tree/binary_space_tree/single_tree_traverser_impl.hpp                     |    8 
 RcppMLPACK-1.0.10/RcppMLPACK/src/mlpack/core/tree/binary_space_tree/traits.hpp                                         |    2 
 RcppMLPACK-1.0.10/RcppMLPACK/src/mlpack/core/tree/bounds.hpp                                                           |    2 
 RcppMLPACK-1.0.10/RcppMLPACK/src/mlpack/core/tree/cosine_tree/cosine_tree.cpp                                          |   52 
 RcppMLPACK-1.0.10/RcppMLPACK/src/mlpack/core/tree/cosine_tree/cosine_tree.hpp                                          |   26 
 RcppMLPACK-1.0.10/RcppMLPACK/src/mlpack/core/tree/cover_tree.hpp                                                       |    2 
 RcppMLPACK-1.0.10/RcppMLPACK/src/mlpack/core/tree/cover_tree/cover_tree.hpp                                            |   88 
 RcppMLPACK-1.0.10/RcppMLPACK/src/mlpack/core/tree/cover_tree/cover_tree_impl.hpp                                       |  175 -
 RcppMLPACK-1.0.10/RcppMLPACK/src/mlpack/core/tree/cover_tree/dual_tree_traverser.hpp                                   |   14 
 RcppMLPACK-1.0.10/RcppMLPACK/src/mlpack/core/tree/cover_tree/dual_tree_traverser_impl.hpp                              |   17 
 RcppMLPACK-1.0.10/RcppMLPACK/src/mlpack/core/tree/cover_tree/first_point_is_root.hpp                                   |    4 
 RcppMLPACK-1.0.10/RcppMLPACK/src/mlpack/core/tree/cover_tree/single_tree_traverser.hpp                                 |   10 
 RcppMLPACK-1.0.10/RcppMLPACK/src/mlpack/core/tree/cover_tree/single_tree_traverser_impl.hpp                            |   20 
 RcppMLPACK-1.0.10/RcppMLPACK/src/mlpack/core/tree/cover_tree/traits.hpp                                                |    2 
 RcppMLPACK-1.0.10/RcppMLPACK/src/mlpack/core/tree/example_tree.hpp                                                     |   16 
 RcppMLPACK-1.0.10/RcppMLPACK/src/mlpack/core/tree/hrectbound.hpp                                                       |   12 
 RcppMLPACK-1.0.10/RcppMLPACK/src/mlpack/core/tree/hrectbound_impl.hpp                                                  |   50 
 RcppMLPACK-1.0.10/RcppMLPACK/src/mlpack/core/tree/mrkd_statistic.cpp                                                   |    2 
 RcppMLPACK-1.0.10/RcppMLPACK/src/mlpack/core/tree/mrkd_statistic.hpp                                                   |   26 
 RcppMLPACK-1.0.10/RcppMLPACK/src/mlpack/core/tree/mrkd_statistic_impl.hpp                                              |   10 
 RcppMLPACK-1.0.10/RcppMLPACK/src/mlpack/core/tree/rectangle_tree.hpp                                                   |    2 
 RcppMLPACK-1.0.10/RcppMLPACK/src/mlpack/core/tree/statistic.hpp                                                        |    2 
 RcppMLPACK-1.0.10/RcppMLPACK/src/mlpack/core/tree/traversal_info.hpp                                                   |    2 
 RcppMLPACK-1.0.10/RcppMLPACK/src/mlpack/core/tree/tree_traits.hpp                                                      |    2 
 RcppMLPACK-1.0.10/RcppMLPACK/src/mlpack/core/util/arma_traits.hpp                                                      |    2 
 RcppMLPACK-1.0.10/RcppMLPACK/src/mlpack/core/util/nulloutstream.hpp                                                    |    2 
 RcppMLPACK-1.0.10/RcppMLPACK/src/mlpack/core/util/option.cpp                                                           |    2 
 RcppMLPACK-1.0.10/RcppMLPACK/src/mlpack/core/util/option.hpp                                                           |    2 
 RcppMLPACK-1.0.10/RcppMLPACK/src/mlpack/core/util/option_impl.hpp                                                      |    2 
 RcppMLPACK-1.0.10/RcppMLPACK/src/mlpack/core/util/prefixedoutstream.cpp                                                |    2 
 RcppMLPACK-1.0.10/RcppMLPACK/src/mlpack/core/util/prefixedoutstream.hpp                                                |    2 
 RcppMLPACK-1.0.10/RcppMLPACK/src/mlpack/core/util/prefixedoutstream_impl.hpp                                           |    6 
 RcppMLPACK-1.0.10/RcppMLPACK/src/mlpack/core/util/sfinae_utility.hpp                                                   |    2 
 RcppMLPACK-1.0.10/RcppMLPACK/src/mlpack/core/util/string_util.cpp                                                      |    8 
 RcppMLPACK-1.0.10/RcppMLPACK/src/mlpack/core/util/string_util.hpp                                                      |    4 
 RcppMLPACK-1.0.10/RcppMLPACK/src/mlpack/core/util/timers.cpp                                                           |only
 RcppMLPACK-1.0.10/RcppMLPACK/src/mlpack/core/util/timers.hpp                                                           |only
 RcppMLPACK-1.0.10/RcppMLPACK/src/mlpack/core/util/version.cpp                                                          |    2 
 RcppMLPACK-1.0.10/RcppMLPACK/src/mlpack/core/util/version.hpp                                                          |    2 
 RcppMLPACK-1.0.10/RcppMLPACK/src/mlpack/methods/amf/amf.hpp                                                            |    6 
 RcppMLPACK-1.0.10/RcppMLPACK/src/mlpack/methods/amf/amf_impl.hpp                                                       |    6 
 RcppMLPACK-1.0.10/RcppMLPACK/src/mlpack/methods/amf/init_rules/random_acol_init.hpp                                    |   14 
 RcppMLPACK-1.0.10/RcppMLPACK/src/mlpack/methods/amf/init_rules/random_init.hpp                                         |    8 
 RcppMLPACK-1.0.10/RcppMLPACK/src/mlpack/methods/amf/termination_policies/complete_incremental_termination.hpp          |only
 RcppMLPACK-1.0.10/RcppMLPACK/src/mlpack/methods/amf/termination_policies/incomplete_incremental_termination.hpp        |only
 RcppMLPACK-1.0.10/RcppMLPACK/src/mlpack/methods/amf/termination_policies/simple_residue_termination.hpp                |   18 
 RcppMLPACK-1.0.10/RcppMLPACK/src/mlpack/methods/amf/termination_policies/simple_tolerance_termination.hpp              |   28 
 RcppMLPACK-1.0.10/RcppMLPACK/src/mlpack/methods/amf/termination_policies/validation_RMSE_termination.hpp               |   38 
 RcppMLPACK-1.0.10/RcppMLPACK/src/mlpack/methods/amf/update_rules/nmf_als.hpp                                           |    8 
 RcppMLPACK-1.0.10/RcppMLPACK/src/mlpack/methods/amf/update_rules/nmf_mult_dist.hpp                                     |    4 
 RcppMLPACK-1.0.10/RcppMLPACK/src/mlpack/methods/amf/update_rules/nmf_mult_div.hpp                                      |   16 
 RcppMLPACK-1.0.10/RcppMLPACK/src/mlpack/methods/amf/update_rules/svd_batch_learning.hpp                                |   48 
 RcppMLPACK-1.0.10/RcppMLPACK/src/mlpack/methods/amf/update_rules/svd_complete_incremental_learning.hpp                 |   26 
 RcppMLPACK-1.0.10/RcppMLPACK/src/mlpack/methods/amf/update_rules/svd_incomplete_incremental_learning.hpp               |   18 
 RcppMLPACK-1.0.10/RcppMLPACK/src/mlpack/methods/cf/cf.hpp                                                              |   44 
 RcppMLPACK-1.0.10/RcppMLPACK/src/mlpack/methods/cf/cf_impl.hpp                                                         |   50 
 RcppMLPACK-1.0.10/RcppMLPACK/src/mlpack/methods/decision_stump/decision_stump.hpp                                      |   24 
 RcppMLPACK-1.0.10/RcppMLPACK/src/mlpack/methods/decision_stump/decision_stump_impl.hpp                                 |   63 
 RcppMLPACK-1.0.10/RcppMLPACK/src/mlpack/methods/det/dt_utils.cpp                                                       |   57 
 RcppMLPACK-1.0.10/RcppMLPACK/src/mlpack/methods/det/dt_utils.hpp                                                       |   12 
 RcppMLPACK-1.0.10/RcppMLPACK/src/mlpack/methods/det/dtree.cpp                                                          |   99 
 RcppMLPACK-1.0.10/RcppMLPACK/src/mlpack/methods/det/dtree.hpp                                                          |   52 
 RcppMLPACK-1.0.10/RcppMLPACK/src/mlpack/methods/emst/dtb.hpp                                                           |   10 
 RcppMLPACK-1.0.10/RcppMLPACK/src/mlpack/methods/emst/dtb_impl.hpp                                                      |   53 
 RcppMLPACK-1.0.10/RcppMLPACK/src/mlpack/methods/emst/dtb_rules.hpp                                                     |   30 
 RcppMLPACK-1.0.10/RcppMLPACK/src/mlpack/methods/emst/dtb_rules_impl.hpp                                                |   36 
 RcppMLPACK-1.0.10/RcppMLPACK/src/mlpack/methods/emst/dtb_stat.hpp                                                      |    2 
 RcppMLPACK-1.0.10/RcppMLPACK/src/mlpack/methods/emst/edge_pair.hpp                                                     |   19 
 RcppMLPACK-1.0.10/RcppMLPACK/src/mlpack/methods/emst/union_find.hpp                                                    |   16 
 RcppMLPACK-1.0.10/RcppMLPACK/src/mlpack/methods/fastmks/fastmks.hpp                                                    |  344 +-
 RcppMLPACK-1.0.10/RcppMLPACK/src/mlpack/methods/fastmks/fastmks_impl.hpp                                               |  306 -
 RcppMLPACK-1.0.10/RcppMLPACK/src/mlpack/methods/fastmks/fastmks_rules.hpp                                              |  256 -
 RcppMLPACK-1.0.10/RcppMLPACK/src/mlpack/methods/fastmks/fastmks_rules_impl.hpp                                         |  804 ++--
 RcppMLPACK-1.0.10/RcppMLPACK/src/mlpack/methods/fastmks/fastmks_stat.hpp                                               |  206 -
 RcppMLPACK-1.0.10/RcppMLPACK/src/mlpack/methods/gmm/diagonal_constraint.hpp                                            |    2 
 RcppMLPACK-1.0.10/RcppMLPACK/src/mlpack/methods/gmm/eigenvalue_ratio_constraint.hpp                                    |    4 
 RcppMLPACK-1.0.10/RcppMLPACK/src/mlpack/methods/gmm/em_fit.hpp                                                         |   14 
 RcppMLPACK-1.0.10/RcppMLPACK/src/mlpack/methods/gmm/em_fit_impl.hpp                                                    |   40 
 RcppMLPACK-1.0.10/RcppMLPACK/src/mlpack/methods/gmm/gmm.hpp                                                            |   32 
 RcppMLPACK-1.0.10/RcppMLPACK/src/mlpack/methods/gmm/gmm_impl.hpp                                                       |   52 
 RcppMLPACK-1.0.10/RcppMLPACK/src/mlpack/methods/gmm/no_constraint.hpp                                                  |    2 
 RcppMLPACK-1.0.10/RcppMLPACK/src/mlpack/methods/gmm/phi.hpp                                                            |    6 
 RcppMLPACK-1.0.10/RcppMLPACK/src/mlpack/methods/gmm/positive_definite_constraint.hpp                                   |    2 
 RcppMLPACK-1.0.10/RcppMLPACK/src/mlpack/methods/hmm/hmm.hpp                                                            |   22 
 RcppMLPACK-1.0.10/RcppMLPACK/src/mlpack/methods/hmm/hmm_impl.hpp                                                       |   72 
 RcppMLPACK-1.0.10/RcppMLPACK/src/mlpack/methods/hmm/hmm_util.hpp                                                       |only
 RcppMLPACK-1.0.10/RcppMLPACK/src/mlpack/methods/hmm/hmm_util_impl.hpp                                                  |only
 RcppMLPACK-1.0.10/RcppMLPACK/src/mlpack/methods/kernel_pca/kernel_pca.hpp                                              |    6 
 RcppMLPACK-1.0.10/RcppMLPACK/src/mlpack/methods/kernel_pca/kernel_pca_impl.hpp                                         |    6 
 RcppMLPACK-1.0.10/RcppMLPACK/src/mlpack/methods/kernel_pca/kernel_rules/naive_method.hpp                               |   14 
 RcppMLPACK-1.0.10/RcppMLPACK/src/mlpack/methods/kernel_pca/kernel_rules/nystroem_method.hpp                            |    4 
 RcppMLPACK-1.0.10/RcppMLPACK/src/mlpack/methods/kmeans/allow_empty_clusters.hpp                                        |   10 
 RcppMLPACK-1.0.10/RcppMLPACK/src/mlpack/methods/kmeans/kmeans.hpp                                                      |   26 
 RcppMLPACK-1.0.10/RcppMLPACK/src/mlpack/methods/kmeans/kmeans_impl.hpp                                                 |   94 
 RcppMLPACK-1.0.10/RcppMLPACK/src/mlpack/methods/kmeans/max_variance_new_cluster.hpp                                    |   10 
 RcppMLPACK-1.0.10/RcppMLPACK/src/mlpack/methods/kmeans/max_variance_new_cluster_impl.hpp                               |   18 
 RcppMLPACK-1.0.10/RcppMLPACK/src/mlpack/methods/kmeans/random_partition.hpp                                            |    8 
 RcppMLPACK-1.0.10/RcppMLPACK/src/mlpack/methods/kmeans/refined_start.hpp                                               |   14 
 RcppMLPACK-1.0.10/RcppMLPACK/src/mlpack/methods/kmeans/refined_start_impl.hpp                                          |   22 
 RcppMLPACK-1.0.10/RcppMLPACK/src/mlpack/methods/lars/lars.cpp                                                          |   46 
 RcppMLPACK-1.0.10/RcppMLPACK/src/mlpack/methods/lars/lars.hpp                                                          |   16 
 RcppMLPACK-1.0.10/RcppMLPACK/src/mlpack/methods/linear_regression/linear_regression.cpp                                |   14 
 RcppMLPACK-1.0.10/RcppMLPACK/src/mlpack/methods/linear_regression/linear_regression.hpp                                |    4 
 RcppMLPACK-1.0.10/RcppMLPACK/src/mlpack/methods/local_coordinate_coding/lcc.hpp                                        |    8 
 RcppMLPACK-1.0.10/RcppMLPACK/src/mlpack/methods/local_coordinate_coding/lcc_impl.hpp                                   |   58 
 RcppMLPACK-1.0.10/RcppMLPACK/src/mlpack/methods/logistic_regression/logistic_regression.hpp                            |    2 
 RcppMLPACK-1.0.10/RcppMLPACK/src/mlpack/methods/logistic_regression/logistic_regression_function.cpp                   |    8 
 RcppMLPACK-1.0.10/RcppMLPACK/src/mlpack/methods/logistic_regression/logistic_regression_function.hpp                   |    8 
 RcppMLPACK-1.0.10/RcppMLPACK/src/mlpack/methods/logistic_regression/logistic_regression_impl.hpp                       |   18 
 RcppMLPACK-1.0.10/RcppMLPACK/src/mlpack/methods/lsh/lsh_search.hpp                                                     |   50 
 RcppMLPACK-1.0.10/RcppMLPACK/src/mlpack/methods/lsh/lsh_search_impl.hpp                                                |  107 
 RcppMLPACK-1.0.10/RcppMLPACK/src/mlpack/methods/mvu/mvu.cpp                                                            |   14 
 RcppMLPACK-1.0.10/RcppMLPACK/src/mlpack/methods/mvu/mvu.hpp                                                            |    8 
 RcppMLPACK-1.0.10/RcppMLPACK/src/mlpack/methods/naive_bayes/naive_bayes_classifier.hpp                                 |   12 
 RcppMLPACK-1.0.10/RcppMLPACK/src/mlpack/methods/naive_bayes/naive_bayes_classifier_impl.hpp                            |   41 
 RcppMLPACK-1.0.10/RcppMLPACK/src/mlpack/methods/nca/nca.hpp                                                            |    8 
 RcppMLPACK-1.0.10/RcppMLPACK/src/mlpack/methods/nca/nca_impl.hpp                                                       |    7 
 RcppMLPACK-1.0.10/RcppMLPACK/src/mlpack/methods/nca/nca_softmax_error_function.hpp                                     |   12 
 RcppMLPACK-1.0.10/RcppMLPACK/src/mlpack/methods/nca/nca_softmax_error_function_impl.hpp                                |   22 
 RcppMLPACK-1.0.10/RcppMLPACK/src/mlpack/methods/neighbor_search/neighbor_search.hpp                                    |   10 
 RcppMLPACK-1.0.10/RcppMLPACK/src/mlpack/methods/neighbor_search/neighbor_search_impl.hpp                               |   59 
 RcppMLPACK-1.0.10/RcppMLPACK/src/mlpack/methods/neighbor_search/neighbor_search_rules.hpp                              |   34 
 RcppMLPACK-1.0.10/RcppMLPACK/src/mlpack/methods/neighbor_search/neighbor_search_rules_impl.hpp                         |  239 -
 RcppMLPACK-1.0.10/RcppMLPACK/src/mlpack/methods/neighbor_search/neighbor_search_stat.hpp                               |    2 
 RcppMLPACK-1.0.10/RcppMLPACK/src/mlpack/methods/neighbor_search/ns_traversal_info.hpp                                  |    2 
 RcppMLPACK-1.0.10/RcppMLPACK/src/mlpack/methods/neighbor_search/sort_policies/furthest_neighbor_sort.cpp               |   14 
 RcppMLPACK-1.0.10/RcppMLPACK/src/mlpack/methods/neighbor_search/sort_policies/furthest_neighbor_sort.hpp               |   10 
 RcppMLPACK-1.0.10/RcppMLPACK/src/mlpack/methods/neighbor_search/sort_policies/furthest_neighbor_sort_impl.hpp          |    2 
 RcppMLPACK-1.0.10/RcppMLPACK/src/mlpack/methods/neighbor_search/sort_policies/nearest_neighbor_sort.cpp                |   14 
 RcppMLPACK-1.0.10/RcppMLPACK/src/mlpack/methods/neighbor_search/sort_policies/nearest_neighbor_sort.hpp                |   10 
 RcppMLPACK-1.0.10/RcppMLPACK/src/mlpack/methods/neighbor_search/sort_policies/nearest_neighbor_sort_impl.hpp           |    2 
 RcppMLPACK-1.0.10/RcppMLPACK/src/mlpack/methods/neighbor_search/typedef.hpp                                            |    2 
 RcppMLPACK-1.0.10/RcppMLPACK/src/mlpack/methods/neighbor_search/unmap.cpp                                              |   22 
 RcppMLPACK-1.0.10/RcppMLPACK/src/mlpack/methods/neighbor_search/unmap.hpp                                              |   16 
 RcppMLPACK-1.0.10/RcppMLPACK/src/mlpack/methods/nystroem_method/kmeans_selection.hpp                                   |   12 
 RcppMLPACK-1.0.10/RcppMLPACK/src/mlpack/methods/nystroem_method/nystroem_method.hpp                                    |   12 
 RcppMLPACK-1.0.10/RcppMLPACK/src/mlpack/methods/nystroem_method/nystroem_method_impl.hpp                               |   26 
 RcppMLPACK-1.0.10/RcppMLPACK/src/mlpack/methods/nystroem_method/ordered_selection.hpp                                  |   12 
 RcppMLPACK-1.0.10/RcppMLPACK/src/mlpack/methods/nystroem_method/random_selection.hpp                                   |   12 
 RcppMLPACK-1.0.10/RcppMLPACK/src/mlpack/methods/pca/pca.cpp                                                            |   12 
 RcppMLPACK-1.0.10/RcppMLPACK/src/mlpack/methods/pca/pca.hpp                                                            |   12 
 RcppMLPACK-1.0.10/RcppMLPACK/src/mlpack/methods/perceptron/initialization_methods/random_init.hpp                      |   10 
 RcppMLPACK-1.0.10/RcppMLPACK/src/mlpack/methods/perceptron/initialization_methods/zero_init.hpp                        |   10 
 RcppMLPACK-1.0.10/RcppMLPACK/src/mlpack/methods/perceptron/learning_policies/simple_weight_update.hpp                  |   12 
 RcppMLPACK-1.0.10/RcppMLPACK/src/mlpack/methods/perceptron/perceptron.hpp                                              |   12 
 RcppMLPACK-1.0.10/RcppMLPACK/src/mlpack/methods/perceptron/perceptron_impl.hpp                                         |   18 
 RcppMLPACK-1.0.10/RcppMLPACK/src/mlpack/methods/quic_svd/quic_svd.hpp                                                  |    2 
 RcppMLPACK-1.0.10/RcppMLPACK/src/mlpack/methods/quic_svd/quic_svd_impl.hpp                                             |    2 
 RcppMLPACK-1.0.10/RcppMLPACK/src/mlpack/methods/radical/radical.cpp                                                    |   42 
 RcppMLPACK-1.0.10/RcppMLPACK/src/mlpack/methods/radical/radical.hpp                                                    |   34 
 RcppMLPACK-1.0.10/RcppMLPACK/src/mlpack/methods/range_search/range_search.hpp                                          |   14 
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Package qmrparser updated to version 0.1.5 with previous version 0.1.4 dated 2013-12-12

Title: Parser combinator in R
Description: Basic functions for building parsers, with an application to PC-AXIS format files.
Author: Juan Gea Rosat, Ramon Mart├şnez Coscoll├á .
Maintainer: Juan Gea

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Package powerGWASinteraction updated to version 1.1.1 with previous version 1.1.0 dated 2014-09-05

Title: Power Calculations for GxE and GxG Interactions for GWAS
Description: Analytical power calculations for GxE and GxG interactions for case-control studies of candidate genes and genome-wide association studies (GWAS). This includes power calculation for four two-step screening and testing procedures. It can also calculate power for GxE and GxG without any screening.
Author: Charles Kooperberg and Li Hsu
Maintainer: Charles Kooperberg

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Package hypred updated to version 0.5 with previous version 0.4 dated 2013-11-20

Title: Simulation of Genomic Data in Applied Genetics
Description: The package is intended for simulating high density genomic data. The meiosis is simulated under a count-location model, the genetic structure can include additive and dominance effects. The low level nature of the package provides great flexibility in creating all kinds of populations.
Author: Frank Technow
Maintainer: Frank Technow

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Package breakpoint updated to version 1.1 with previous version 1.0 dated 2014-01-17

Title: Multiple Break-Point Detection via the Cross-Entropy Method
Description: Implements the cross-entropy (CE) method, which is a model based stochastic optimization technique to estimate both the number and their corresponding locations of break-points in biological sequences of continuous and discrete measurements as described in Priyadarshana and Sofronov (2014, 2012a, 2012b).
Author: Priyadarshana W.J.R.M. and Georgy Sofronov
Maintainer: Priyadarshana W.J.R.M.

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Package berryFunctions updated to version 1.7.1 with previous version 1.6 dated 2014-10-14

Title: Function Collection related to Plotting and Hydrology
Description: miscellaneous functions to: draw horizontal histograms, color scatterpoints by 3rd dimension, enhance log-axis plots, zoom in X11 graphics, use the unit hydrograph in a linear storage cascade, convert lists to data.frames, fit multiple functions by regression (power, reciprocal, exponential, logarithmic, polynomial, rational). Development version: https://github.com/BerryBoessenkool
Author: Berry Boessenkool
Maintainer: Berry Boessenkool

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Sat, 20 Dec 2014

Package RPublica updated to version 0.1.2 with previous version 0.1.1 dated 2014-05-09

Title: ProPublica API Client
Description: Client for accessing ProPublica's data journalism APIs
Author: Thomas J. Leeper [aut, cre], Jeroen Ooms [ctb]
Maintainer: Thomas J. Leeper

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Package rnoaa updated to version 0.3.3 with previous version 0.2.0 dated 2014-07-21

Title: NOAA Climate Data from R
Description: An R client for many NOAA data sources including the NCDC climate API at http://www.ncdc.noaa.gov/cdo-web/webservices/v2, with functions for each of the API endpoints: data, data categories, data sets, data types, locations, location categories, and stations. In addition, we have an interface for NOAA sea ice data, the NOAA severe weather inventory, ERDDAP data, NOAA Historical Observing Metadata Repository (HOMR) data, NOAA storm data via IBTrACS, and tornado data via the NOAA storm prediction center. NOAA buoy data is only on the buoy branch in the Github repository for this package (see url below).
Author: Hart Edmund [aut], Scott Chamberlain [aut, cre], Karthik Ram [aut]
Maintainer: Scott Chamberlain

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Package RcmdrPlugin.ROC updated to version 1.0-17 with previous version 1.0-16 dated 2014-07-08

Title: Rcmdr Receiver Operator Characteristic Plug-In package
Description: Rcmdr GUI extension plug-in for Receiver Operator Characteristic tools from pROC and ROCR packages. Also it ads a Rcmdr GUI extension for Hosmer and Lemeshow GOF test from the package ResourceSelection.
Author: Daniel-Corneliu Leucuta [aut, cre], Mihaela Hedesiu [ctb], Andrei Achimas [ctb], Oana Almasan [ctb]
Maintainer: Daniel-Corneliu Leucuta

Diff between RcmdrPlugin.ROC versions 1.0-16 dated 2014-07-08 and 1.0-17 dated 2014-12-20

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Permanent link

Package pse updated to version 0.4.0 with previous version 0.3.4 dated 2014-06-17

Title: Parameter space exploration with Latin Hypercubes
Description: Functions for creating Latin Hypercubes with prescribed correlations and performing parameter space exploration. Also implements the PLUE method. Based on the package sensitivity, by Gilles Pujol, Bertrand Iooss & Alexandre Janon.
Author: Andre Chalom, Paulo Inacio Knegt Lopez de Prado
Maintainer: Andre Chalom

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Package digest updated to version 0.6.7 with previous version 0.6.6 dated 2014-12-10

Title: Create Cryptographic Hash Digests of R Objects
Description: Implementation of a function 'digest()' for the creation of hash digests of arbitrary R objects (using the md5, sha-1, sha-256, crc32, xxhash and murmurhash algorithms) permitting easy comparison of R language objects, as well as a function 'hmac()' to create hash-based message authentication code. The md5 algorithm by Ron Rivest is specified in RFC 1321, the sha-1 and sha-256 algorithms are specified in FIPS-180-1 and FIPS-180-2, and the crc32 algorithm is described in ftp://ftp.rocksoft.com/cliens/rocksoft/papers/crc_v3.txt. For md5, sha-1, sha-256 and aes, this package uses a small standalone implementations that were provided by Christophe Devine. For crc32, code from the zlib library is used. For sha-512, an implementation by Aaron D. Gifford is used. For xxHash, the implementation by Yann Collet is used. For murmurhash, an implementation by Shane Day is used. Please note that this package is not meant to be deployed for cryptographic purposes for which more comprehensive (and widely tested) libraries such as OpenSSL should be used.
Author: Dirk Eddelbuettel with contributions by Antoine Lucas, Jarek Tuszynski, Henrik Bengtsson, Simon Urbanek, Mario Frasca, Bryan Lewis, Murray Stokely, Hannes Muehleisen, Duncan Murdoch and Jim Hester.
Maintainer: Dirk Eddelbuettel

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More information about digest at CRAN
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Package colourlovers updated to version 0.1.4 with previous version 0.1.3 dated 2014-08-06

Title: R client for the COLOURlovers API
Description: Provides access to the COLOURlovers API, which provides color inspiration and color palettes.
Author: Thomas J. Leeper
Maintainer: Thomas J. Leeper

Diff between colourlovers versions 0.1.3 dated 2014-08-06 and 0.1.4 dated 2014-12-20

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Permanent link

Package surveillance updated to version 1.8-2 with previous version 1.8-1 dated 2014-10-30

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

Diff between surveillance versions 1.8-1 dated 2014-10-30 and 1.8-2 dated 2014-12-20

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More information about surveillance at CRAN
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Package splm updated to version 1.3-7 with previous version 1.1-0 dated 2013-07-02

Title: Econometric Models for Spatial Panel Data
Description: ML and GM estimation and diagnostic testing of econometric models for spatial panel data.
Author: Giovanni Millo [aut, cre], Gianfranco Piras [aut]
Maintainer: Giovanni Millo

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Package npcp updated to version 0.1-1 with previous version 0.1-0 dated 2014-07-08

Title: Some nonparametric tests for change-point detection in (multivariate) observations
Description: Provides nonparametric tests for assessing whether possibly serially dependent (multivariate) observations have the same c.d.f. or not. In addition to tests focusing directly on the (multivariate) c.d.f., the package contains tests designed to be particularly sensitive to changes in the underlying copula, Spearman's rho or certain quantities that can be estimated using one-sample U-statistics of order two such as the variance, Gini's mean difference or Kendall's tau.
Author: Ivan Kojadinovic
Maintainer: Ivan Kojadinovic

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Package googleVis updated to version 0.5.7 with previous version 0.5.6 dated 2014-10-12

Title: R Interface to Google Charts
Description: R interface to Google Charts API, allowing users to create interactive charts based on data frames. Charts are displayed locally via the R HTTP help server. A modern browser with Internet connection is required and for some charts Flash. The data remains local and is not uploaded to Google.
Author: Markus Gesmann [aut, cre], Diego de Castillo [aut], Joe Cheng [ctb]
Maintainer: Markus Gesmann

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Package ChainLadder updated to version 0.1.9 with previous version 0.1.8 dated 2014-08-23

Title: Statistical Methods and Models for Claims Reserving in General Insurance
Description: Various statistical methods and models which are typically used for the estimation of outstanding claims reserves in general insurance. The package has implementations of the Mack, Munich, Bootstrap, multivariate, and chain-ladder factor models (CLFM), as well as the loss development factor curve fitting methods of Dave Clark and generalised linear model based reserving models.
Author: Markus Gesmann [aut, cre], Daniel Murphy [aut], Wayne Zhang [aut]
Maintainer: Markus Gesmann

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Package RMAWGEN updated to version 1.3.0 with previous version 1.2.6.1 dated 2014-04-29

Title: Multi-site Auto-regressive Weather GENerator
Description: S3 and S4 functions are implemented for spatial multi-site stochastic generation of daily time series of temperature and precipitation. These tools make use of Vector AutoRegressive models (VARs). The weather generator model is then saved as an object and is calibrated by daily instrumental "Gaussianized" time series through the 'vars' package tools. Once obtained this model, it can it can be used for weather generations and be adapted to work with several climatic monthly time series.
Author: Emanuele Cordano, Emanuele Eccel
Maintainer: Emanuele Cordano

Diff between RMAWGEN versions 1.2.6.1 dated 2014-04-29 and 1.3.0 dated 2014-12-20

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Package pubmed.mineR updated to version 1.0.2.1 with previous version 1.0.2 dated 2014-08-26

Title: Text mining of PubMed Abstracts
Description: Text mining of PubMed Abstracts (http://www.ncbi.nlm.nih.gov/pubmed). The algorithms are designed for two formats (text and XML) from PubMed
Author: Jyoti Sharma, S.Ramachandran, Ab Rauf Shah
Maintainer: S. Ramachandran

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Package tcltk2 updated to version 1.2-11 with previous version 1.2-10 dated 2014-03-02

Title: Tcl/Tk Additions
Description: A series of additional Tcl commands and Tk widgets with style and various functions (under Windows: DDE exchange, access to the registry and icon manipulation) to supplement the tcltk package
Author: Philippe Grosjean [aut, cre]
Maintainer: Philippe Grosjean

Diff between tcltk2 versions 1.2-10 dated 2014-03-02 and 1.2-11 dated 2014-12-20

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Package svDialogs updated to version 0.9-57 with previous version 0.9-55 dated 2014-03-02

Title: SciViews GUI API - Dialog boxes
Description: Rapidly construct dialog boxes for your GUI, including an automatic function assistant
Author: Philippe Grosjean [aut, cre]
Maintainer: Philippe Grosjean

Diff between svDialogs versions 0.9-55 dated 2014-03-02 and 0.9-57 dated 2014-12-20

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Package ddalpha updated to version 1.1.0 with previous version 1.0.6 dated 2014-03-28

Title: Depth-based Classification and Calculation of Data Depth
Description: Contains procedures for depth-based supervised learning, which are entirely nonparametric, in particular the DDalpha-procedure. The training data sample is transformed by a statistical depth function to a compact low-dimensional space, where the final classification is done. It also offers an extension to functional data and routines for calculating certain notions of statistical depth functions. 50 multivariate and 5 functional classification problems are included.
Author: Oleksii Pokotylo [aut, cre], Pavlo Mozharovskyi [aut]
Maintainer: Oleksii Pokotylo

Diff between ddalpha versions 1.0.6 dated 2014-03-28 and 1.1.0 dated 2014-12-20

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

Title: A Simple Package for Testing R Packages
Description: Provides two convenience functions assert() and test_pkg() to facilitate testing R packages.
Author: Yihui Xie
Maintainer: Yihui Xie

Diff between testit versions 0.3 dated 2013-10-26 and 0.4 dated 2014-12-20

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Package knockoff updated to version 0.1.1 with previous version 0.1 dated 2014-12-06

Title: Knockoff Filter
Description: The knockoff filter for controlling the false discovery rate
Author: Rina Foygel Barber, Emmanuel Candes, Evan Patterson
Maintainer: Evan Patterson

Diff between knockoff versions 0.1 dated 2014-12-06 and 0.1.1 dated 2014-12-20

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Package doMPI updated to version 0.2.1 with previous version 0.2 dated 2013-06-14

Title: Foreach parallel adaptor for the Rmpi package
Description: Provides a parallel backend for the %dopar% function using the Rmpi package.
Author: Steve Weston
Maintainer: Steve Weston

Diff between doMPI versions 0.2 dated 2013-06-14 and 0.2.1 dated 2014-12-20

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Fri, 19 Dec 2014

Package GPLTR updated to version 1.1 with previous version 0.95 dated 2014-05-27

Title: Generalized Partially Linear Tree-based Regression Model
Description: Combining a generalized linear model with an additional tree part on the same scale. A four-step procedure is proposed to fit the model and test the joint effect of the selected tree part while adjusting on confounding factors. We also proposed an ensemble procedure based on the bagging to improve prediction accuracy and computed several scores of importance for variable selection.
Author: Cyprien Mbogning and Wilson Toussile
Maintainer: Cyprien Mbogning

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Package sBF updated to version 1.1.1 with previous version 1.1 dated 2012-08-01

Title: Smooth Backfitting
Description: Smooth Backfitting for additive models using Nadaraya-Watson estimator
Author: A. Arcagni, L. Bagnato
Maintainer: Alberto Arcagni

Diff between sBF versions 1.1 dated 2012-08-01 and 1.1.1 dated 2014-12-19

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Package RGA updated to version 0.1.4 with previous version 0.1.3 dated 2014-10-27

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

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Package penalized updated to version 0.9-45 with previous version 0.9-42 dated 2012-11-06

Title: L1 (lasso and fused lasso) and L2 (ridge) penalized estimation in GLMs and in the Cox model
Description: A package for fitting possibly high dimensional penalized regression models. The penalty structure can be any combination of an L1 penalty (lasso and fused lasso), an L2 penalty (ridge) and a positivity constraint on the regression coefficients. The supported regression models are linear, logistic and Poisson regression and the Cox Proportional Hazards model. Cross-validation routines allow optimization of the tuning parameters.
Author: Jelle Goeman, Rosa Meijer, Nimisha Chaturvedi
Maintainer: Jelle Goeman

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Package geonames updated to version 0.998 with previous version 0.997 dated 2014-10-19

Title: Interface to www.geonames.org web service
Description: Code for querying the web service at www.geonames.org
Author: Barry Rowlingson
Maintainer: Barry Rowlingson

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Package vardpoor updated to version 0.2.1 with previous version 0.2.0.14 dated 2014-11-04

Title: Variance Estimation for Sample Surveys by the Ultimate Cluster Method
Description: Generation of domain variables, linearisation of several nonlinear population statistics (the ratio of two totals, weighted income percentile, at-risk-of-poverty rate, at-risk-of-poverty threshold, Gini coefficient, gender pay gap, median income below at-risk-of-poverty gap, income quintile share ratio, relative median at-risk-of-poverty gap), computation of regression residuals in case of weight calibration, variance estimation of sample surveys by the ultimate cluster method (Hansen, Hurwitz and Madow, 1953), variance estimation for longitudinal, crossectional measures and measures of change for single and multistage stage cluster sampling designs (Berger, Y.G.). Several other precision measures are derived - standard error, the coefficient of variation, the margin of error, confidence interval, design effect.
Author: Juris Breidaks [aut, cre], Martins Liberts [aut], Santa Ivanova [aut]
Maintainer: Juris Breidaks

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Package cgdsr updated to version 1.1.32 with previous version 1.1.31 dated 2014-12-12

Title: R-Based API for accessing the MSKCC Cancer Genomics Data Server (CGDS).
Description: The package provides a basic set of R functions for querying the Cancer Genomics Data Server (CGDS), hosted by the Computational Biology Center at Memorial-Sloan-Kettering Cancer Center (MSKCC).
Author: Anders Jacobsen Skanderup
Maintainer: Anders Jacobsen Skanderup

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Package bgmm updated to version 1.7 with previous version 1.6 dated 2013-11-19

Title: Gaussian Mixture Modeling Algorithms And The Belief-based Mixture Modeling
Description: Two partially supervised mixture modeling methods: soft-label and belief-based modeling are implemented. For completeness, we equipped the package also with the functionality of unsupervised, semi- and fully supervised mixture modeling. The package can be applied also to selection of the best-fitting from a set of models with different component numbers or constraints on their structures. For detailed introduction see: Przemyslaw Biecek, Ewa Szczurek, Martin Vingron, Jerzy Tiuryn (2012), The R Package bgmm: Mixture Modeling with Uncertain Knowledge, Journal of Statistical Software.
Author: Przemyslaw Biecek \& Ewa Szczurek
Maintainer: Przemyslaw Biecek

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Package rcicr updated to version 0.2.6 with previous version 0.2.5 dated 2014-11-17

Title: Reverse correlation image classification toolbox
Description: Functions to generate stimuli and analyze data of reverse correlation image classification experiments.
Author: Ron Dotsch
Maintainer: Ron Dotsch

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Package aoos updated to version 0.1.0 with previous version 0.0.3 dated 2014-11-14

Title: Another Object Orientation System
Description: Another implementation of object-orientation in R. Has reference semantics and is build around S4.
Author: Sebastian Warnholz
Maintainer: Sebastian Warnholz

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Package PowerTOST updated to version 1.2-04 with previous version 1.2-03 dated 2014-11-13

Title: Power and Sample Size Based on Two One-sided t-Tests (TOST) for (Bio)Equivalence Studies
Description: Contains functions to calculate power and sample size for various study designs used for bioequivalence studies. See function known.designs() for study designs covered. Moreover the package contains functions for power and sample size based on 'expected' power in case of uncertain (estimated) variability. ----- Added are functions for the power and sample size for the ratio of two means with normally distributed data on the original scale (based on Fieller's confidence ('fiducial') interval). ----- Contains further functions for power and sample size calculations based on non-inferiority t-test. This is not a TOST procedure but eventually useful if the question of 'non-superiority' must be evaluated. The power and sample size calculations based on non-inferiority test may also performed via 'expected' power in case of uncertain (estimated) variability. ----- Contains functions power.scABEL() and sampleN.scABEL() to calculate power and sample size for the BE decision via scaled (widened) BE acceptance limits based on simulations. Contains further functions power.RSABE() and sampleN.RSABE() to calculate power and sample size for the BE decision via reference scaled ABE criterion according to the FDA procedure based on simulations. Contains further functions power.NTIDFDA() and sampleN.NTIDFDA() to calculate power and sample size for the BE decision via the FDA procedure for NTID's based on simulations. ----- Contains functions for power analysis of a sample size plan for ABE (pa.ABE()), scaled ABE (pa.scABE()) and scaled ABE for NTID's (pa.NTIDFDA()) analysing power if deviating from assumptions of the plan. ----- Contains further functions for power calculations / samplesize estimation for dose proportionality studies using the Power model.
Author: Detlew Labes [aut, cre], Helmut Schuetz [aut]
Maintainer: Detlew Labes

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Package helsinki updated to version 0.9.22 with previous version 0.9.20 dated 2014-06-09

Title: Helsinki open data R tools
Description: Tools for accessing various open data sources in the Helsinki region in Finland. Current data sources include the Real Estate Department (district maps), the Environmental Services Authority, Service Map API, Linked Events API and Helsinki Region Infoshare statistics API.
Author: Juuso Parkkinen, Leo Lahti, Joona Lehtomaki
Maintainer: Juuso Parkkinen

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Package ztable updated to version 0.1.1 with previous version 0.1.0 dated 2014-12-15

Title: Zebra-Striped Tables in LaTeX and HTML Formats
Description: Makes zebra-striped tables (tables with alternating row colors) in LaTeX and HTML formats easily from a data.frame, matrix, lm, aov, anova, glm or coxph objects.
Author: "Keon-Woong Moon" [aut, cre]
Maintainer: "Keon-Woong Moon"

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Package taxize updated to version 0.5.2 with previous version 0.4.0 dated 2014-09-09

Title: Taxonomic Information from Around the Web
Description: Taxonomic information from around the web. This package interacts with a suite of web APIs for taxonomic tasks, such as verifying species names, getting taxonomic hierarchies, and verifying name spelling.
Author: Scott Chamberlain [aut, cre], Eduard Szoecs [aut], Zachary Foster [aut], Carl Boettiger [aut], Karthik Ram [aut], Ignasi Bartomeus [aut], John Baumgartner [aut]
Maintainer: Scott Chamberlain

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 taxize-0.5.2/taxize/tests/testthat/test-eol_invasive.R                             |    4 
 taxize-0.5.2/taxize/tests/testthat/test-eol_ping.R                                 |    8 
 taxize-0.5.2/taxize/tests/testthat/test-eol_search.R                               |    6 
 taxize-0.5.2/taxize/tests/testthat/test-get_boldid.R                               |    8 
 taxize-0.5.2/taxize/tests/testthat/test-get_ids.R                                  |   12 
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 taxize-0.5.2/taxize/tests/testthat/test-gisd_isinvasive.R                          |    2 
 taxize-0.5.2/taxize/tests/testthat/test-itis.R                                     |    4 
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 taxize-0.5.2/taxize/tests/testthat/test-itis_lsid.R                                |    4 
 taxize-0.5.2/taxize/tests/testthat/test-itis_native.R                              |    5 
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 taxize-0.5.2/taxize/tests/testthat/test-itis_ping.R                                |    9 
 taxize-0.5.2/taxize/tests/testthat/test-itis_refs.R                                |    4 
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 taxize-0.5.2/taxize/tests/testthat/test-ncbi_search.R                              |    4 
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 taxize-0.5.2/taxize/tests/testthat/test-tax_name.R                                 |   40 
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 taxize-0.5.2/taxize/tests/testthat/test-vascan_search.r                            |   12 
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More information about taxize at CRAN
Permanent link

Package streamMOA updated to version 1.0-0 with previous version 0.1-1 dated 2014-06-17

Title: stream - Interface to MOA Algorithms
Description: This package provides an interface to algorithms implemented in the MOA (Massive Online Analysis) framework for data stream mining.
Author: Michael Hahsler [aut, cre, cph], Matthew Bolanos [aut, cph], John Forrest [aut, cph]
Maintainer: Michael Hahsler

Diff between streamMOA versions 0.1-1 dated 2014-06-17 and 1.0-0 dated 2014-12-19

 DESCRIPTION                         |   10 -
 MD5                                 |   35 +++--
 NAMESPACE                           |    2 
 R/DSC_CluStream.R                   |   37 ++----
 R/DSC_ClusTree.R                    |   31 ++---
 R/DSC_DenStream.R                   |   29 ++--
 R/DSC_MOA.R                         |   50 ++++----
 R/DSD_MOA.R                         |   23 +--
 build/vignette.rds                  |binary
 inst/NEWS                           |    3 
 inst/doc/streamMOA.R                |  145 +++++++++---------------
 inst/doc/streamMOA.Rnw              |  216 +++++++-----------------------------
 inst/doc/streamMOA.pdf              |binary
 java                                |only
 man/DSC_CluStream.Rd                |   26 ++--
 man/DSC_ClusTree.Rd                 |   26 ++--
 man/DSC_DenStream.Rd                |   18 +--
 man/DSD_RandomRBFGeneratorEvents.Rd |    5 
 vignettes/streamMOA.Rnw             |  216 +++++++-----------------------------
 19 files changed, 301 insertions(+), 571 deletions(-)

More information about streamMOA at CRAN
Permanent link

Package spBayesSurv updated to version 1.0.2 with previous version 1.0.1 dated 2014-10-25

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

Diff between spBayesSurv versions 1.0.1 dated 2014-10-25 and 1.0.2 dated 2014-12-19

 DESCRIPTION                    |    6 
 MD5                            |   36 +-
 R/anovaDDP.R                   |  281 +++++++++--------
 R/spCopulaDDP.R                |  490 +++++++++++++++---------------
 man/anovaDDP.Rd                |   35 +-
 man/spBayesSurv-package.Rd     |    2 
 man/spCopulaDDP.Rd             |  664 ++++++++++++++++++++---------------------
 src/spSurv_Coxph_tools.cpp     |    9 
 src/spSurv_DDP_tools.cpp       |  173 +++++++++-
 src/spSurv_DDP_tools.h         |   14 
 src/spSurv_anovaDDP.cpp        |   50 ++-
 src/spSurv_common.cpp          |  174 +++++++---
 src/spSurv_common.h            |    7 
 src/spSurv_frailtyLDTFP.cpp    |    3 
 src/spSurv_indeptCoxph.cpp     |   10 
 src/spSurv_nonfrailtyLDTFP.cpp |    3 
 src/spSurv_spCopulaCoxph.cpp   |    6 
 src/spSurv_spCopulaDDP.cpp     |  124 +++++--
 src/spSurv_spCopulaDDP.h       |    4 
 19 files changed, 1211 insertions(+), 880 deletions(-)

More information about spBayesSurv at CRAN
Permanent link

Package RJDBC updated to version 0.2-5 with previous version 0.2-4 dated 2014-06-26

Title: Provides access to databases through the JDBC interface
Description: RJDBC is an implementation of R's DBI interface using JDBC as a back-end. This allows R to connect to any DBMS that has a JDBC driver.
Author: Simon Urbanek
Maintainer: Simon Urbanek

Diff between RJDBC versions 0.2-4 dated 2014-06-26 and 0.2-5 dated 2014-12-19

 DESCRIPTION                  |    6 +++---
 MD5                          |   12 ++++++------
 NEWS                         |   15 ++++++++++++++-
 R/class.R                    |   12 +++++++-----
 inst/java/RJDBC.jar          |binary
 java-src/JDBCResultPull.java |   11 +++++++++--
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 7 files changed, 48 insertions(+), 17 deletions(-)

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Package R2SWF updated to version 0.8-2 with previous version 0.8-1 dated 2014-12-10

Title: Convert R Graphics to Flash Animations
Description: This package uses the Ming library (http://www.libming.org/) to create Flash animations. Users can either use the SWF device swf() to generate SWF file directly through plotting functions like plot() and lines(), or convert images of other formats (SVG, PNG, JPEG) into SWF.
Author: Yixuan Qiu, Yihui Xie, Cameron Bracken and authors of included software. See file AUTHORS for details.
Maintainer: Yixuan Qiu

Diff between R2SWF versions 0.8-1 dated 2014-12-10 and 0.8-2 dated 2014-12-19

 DESCRIPTION              |    8 ++++----
 MD5                      |    6 +++---
 NEWS                     |   12 +++++++++++-
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 4 files changed, 19 insertions(+), 9 deletions(-)

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Package lpme updated to version 1.0.1 with previous version 1.0.0 dated 2014-11-05

Title: Local Polynomial Estimator in Measurement Error Models
Description: Two local polynomial estimators for solving the errors-in-variables problem: one is in Delaigle, Fan, and Carroll (2009), and one is in Huang and Zhou (2014+). The SIMEX bandwidth selection method is also provided for both estimators.
Author: Haiming Zhou and Xianzheng Huang
Maintainer: Haiming Zhou

Diff between lpme versions 1.0.0 dated 2014-11-05 and 1.0.1 dated 2014-12-19

 DESCRIPTION         |    6 +++---
 MD5                 |    4 ++--
 src/lpme_common.cpp |    4 ++--
 3 files changed, 7 insertions(+), 7 deletions(-)

More information about lpme at CRAN
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Package io updated to version 0.2.1 with previous version 0.2 dated 2014-12-11

Title: A Unified Framework for Input-Output Operations in R
Description: One function to read files. One function to write files. One function to direct plots to screen or file. Automatic file format inference and directory structure creation.
Author: David J. H. Shih
Maintainer: David J. H. Shih

Diff between io versions 0.2 dated 2014-12-11 and 0.2.1 dated 2014-12-19

 DESCRIPTION             |    8 ++++----
 MD5                     |   14 +++++++-------
 R/hdf5.R                |    6 ++++--
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 8 files changed, 41 insertions(+), 20 deletions(-)

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Package interpretR updated to version 0.2.0 with previous version 0.1.0 dated 2014-11-21

Title: Binary Classifier Interpretation Functions
Description: Compute permutation- based performance measures and create partial dependence plots for binary (cross-validated) classification models. Currently only binary classification models estimated with the packages randomForest and ada are supported.
Author: Michel Ballings and Dirk Van den Poel
Maintainer: Michel Ballings

Diff between interpretR versions 0.1.0 dated 2014-11-21 and 0.2.0 dated 2014-12-19

 DESCRIPTION               |   19 +++---
 MD5                       |   14 ++--
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More information about interpretR at CRAN
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Package hypervolume updated to version 1.1.1 with previous version 1.1 dated 2014-12-04

Title: High-dimensional Kernel Density Estimation and Geometry Operations
Description: Estimates the shape and volume of high-dimensional datasets and performs set operations: intersection / overlap, union, unique components, inclusion test, and negative feature detection. Uses stochastic geometry approach to high-dimensional kernel density estimation. Builds n-dimensional convex hulls (polytopes). Can measure the n-dimensional ecological hypervolume and perform species distribution modeling.
Author: Benjamin Blonder
Maintainer: Benjamin Blonder

Diff between hypervolume versions 1.1 dated 2014-12-04 and 1.1.1 dated 2014-12-19

 DESCRIPTION    |   14 +++++++-------
 MD5            |    6 +++---
 demo/finch.R   |    4 ++--
 demo/quercus.R |   15 ++++++---------
 4 files changed, 18 insertions(+), 21 deletions(-)

More information about hypervolume at CRAN
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Package BDgraph updated to version 2.14 with previous version 2.13 dated 2014-11-17

Title: Graph Estimation Based on Birth-Death MCMC Approach
Description: This package provides a Bayesian methodology for structure learning in undirected graphical models. Our Bayesian methodology is based on birth-death Markov chain Monte Carlo (BDMCMC) algorithm which is the main function with the name 'bdgraph'. The main target of this package is high-dimensional data analysis wherein usually p >> n. The computation is memory-optimized using the sparse matrix output.
Author: Abdolreza Mohammadi and Ernst Wit
Maintainer: Abdolreza Mohammadi

Diff between BDgraph versions 2.13 dated 2014-11-17 and 2.14 dated 2014-12-19

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More information about BDgraph at CRAN
Permanent link

Thu, 18 Dec 2014

Package stream updated to version 1.1-0 with previous version 1.0-3 dated 2014-07-14

Title: Infrastructure for Data Stream Mining
Description: A framework for data stream modeling and associated data mining tasks such as clustering and classification. The development of this package was supported in part by NSF IIS-0948893 and NIH R21HG005912.
Author: Michael Hahsler [aut, cre, cph], Matthew Bolanos [aut, cph], John Forrest [aut, cph]
Maintainer: Michael Hahsler

Diff between stream versions 1.0-3 dated 2014-07-14 and 1.1-0 dated 2014-12-18

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More information about stream at CRAN
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Package SemiParBIVProbit updated to version 3.2-13 with previous version 3.2-12.1 dated 2014-11-12

Title: Semiparametric Bivariate Probit Modelling
Description: Routine for fitting bivariate models for binary responses with semiparametric predictors (including linear and nonlinear effects) in the presence of correlated error equations, endogeneity, non-random sample selection or partial observability.
Author: Giampiero Marra and Rosalba Radice
Maintainer: Giampiero Marra

Diff between SemiParBIVProbit versions 3.2-12.1 dated 2014-11-12 and 3.2-13 dated 2014-12-18

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More information about SemiParBIVProbit at CRAN
Permanent link

Package hermite updated to version 1.0.1 with previous version 1.0 dated 2014-10-31

Title: Generalized Hermite Distribution
Description: Probability functions and utilities for the generalized Hermite distribution
Author: David Mori├▒a (Centre for Research in Environmental Epidemiology, CREAL), Manuel Higueras (Universitat Aut├▓noma de Barcelona and Public Health England) and Pedro Puig (Universitat Aut├▓noma de Barcelona)
Maintainer: David Mori├▒a Soler

Diff between hermite versions 1.0 dated 2014-10-31 and 1.0.1 dated 2014-12-18

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More information about hermite at CRAN
Permanent link

Package Luminescence updated to version 0.4.0 with previous version 0.3.4 dated 2014-06-08

Title: Package for Luminescence Dating data analysis
Description: Package provides a collection of various R functions for Luminescence Dating data analysis.
Author: Sebastian Kreutzer [aut, trl, cre], Michael Dietze [aut], Christoph Burow [aut], Margret C. Fuchs [aut], Christoph Schmidt [aut], Manfred Fischer [aut, trl], Markus Fuchs [ths]
Maintainer: Sebastian Kreutzer

Diff between Luminescence versions 0.3.4 dated 2014-06-08 and 0.4.0 dated 2014-12-18

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Package crs updated to version 0.15-24 with previous version 0.15-23 dated 2014-08-11

Title: Categorical Regression Splines
Description: Regression splines that handle a mix of continuous and categorical (discrete) data often encountered in applied settings. I would like to gratefully acknowledge support from the Natural Sciences and Engineering Research Council of Canada (NSERC:www.nserc.ca), the Social Sciences and Humanities Research Council of Canada (SSHRC:www.sshrc.ca), and the Shared Hierarchical Academic Research Computing Network (SHARCNET:www.sharcnet.ca).
Author: Jeffrey S. Racine [aut, cre], Zhenghua Nie [aut], Brian D. Ripley [ctb] (stepCV.R)
Maintainer: Jeffrey S. Racine

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Package sprinter updated to version 1.1.0 with previous version 1.0.0 dated 2014-11-20

Title: Framework for Screening Prognostic Interactions
Description: The main function of this package builds prognostic models that consider interactions by combining available statistical components. Furthermore, it provides a function for evaluating the relevance of the selected interactions by resampling techniques.
Author: Isabell Hoffmann
Maintainer: Isabell Hoffmann

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Package RnavGraph updated to version 0.1.8 with previous version 0.1.7 dated 2014-10-21

Title: Using Graphs as a Navigational Infrastructure
Description: GUI to explore high dimensional data (including image data) using graphs as navigational infrastructure.
Author: Adrian R. Waddell and R. Wayne Oldford
Maintainer: Adrian Waddell

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Package party updated to version 1.0-19 with previous version 1.0-18 dated 2014-11-10

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

Diff between party versions 1.0-18 dated 2014-11-10 and 1.0-19 dated 2014-12-18

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Package mvtnorm updated to version 1.0-2 with previous version 1.0-1 dated 2014-11-13

Title: Multivariate Normal and t Distributions
Description: Computes multivariate normal and t probabilities, quantiles, random deviates and densities.
Author: Alan Genz [aut], Frank Bretz [aut], Tetsuhisa Miwa [aut], Xuefei Mi [aut], Friedrich Leisch [ctb], Fabian Scheipl [ctb], Bjoern Bornkamp [ctb], Martin Maechler [ctb], Torsten Hothorn [aut, cre]
Maintainer: Torsten Hothorn

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Package IsoGene updated to version 1.0-23 with previous version 1.0-22 dated 2013-11-05

Title: Order-Restricted Inference for Microarray Experiments
Description: The package offers framework for testing for monotonic relationship between gene expression and doses in a microarray experiment. Several testing procedures including the global likelihood-ratio test (Bartholomew, 1961), Williams (1971, 1972), Marcus (1976), M (Hu et al. 2005) and the modified M (Lin et al. 2007) are used to test for the monotonic trend in gene expression with respect to doses. BH (Benjamini and Hochberg 1995) and BY (Benjamini and Yekutieli 2004) FDR controlling procedures are applied to adjust the raw p-values obtained from the permutations.
Author: Dan Lin, Setia Pramana, Tobias Verbeke and Ziv Shkedy
Maintainer: Martin Otava

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Package REDCapR updated to version 0.7-1 with previous version 0.4-28 dated 2014-09-20

Title: Interaction between R and REDCap
Description: Encapsulates functions to streamline calls from R to the REDCap API. REDCap (Research Electronic Data CAPture) is a web application for building and managing online surveys and databases developed at Vanderbilt University. The Application Programming Interface (API) offers an avenue to access and modify data programmatically, improving the capacity for literate and reproducible programming.
Author: Will Beasley [aut, cre], David Bard [ctb], Thomas Wilson [ctb], John J Aponte [ctb], Rollie Parrish [ctb], Benjamin Nutter [ctb], Andrew Peters [ctb]
Maintainer: Will Beasley

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Package ggthemes updated to version 2.1.0 with previous version 1.7.0 dated 2014-04-22

Title: Extra themes, scales and geoms for ggplot
Description: Some extra themes, geoms, and scales for ggplot2.
Author: Jeffrey B. Arnold [aut, cre], Gergely Daroczi [ctb], Bo Werth [ctb], Brian Weitzner [ctb], Joshua Kunst [ctb]
Maintainer: Jeffrey B. Arnold

Diff between ggthemes versions 1.7.0 dated 2014-04-22 and 2.1.0 dated 2014-12-18

 DESCRIPTION                           |   33 +++--
 MD5                                   |  173 +++++++++++++++------------
 NAMESPACE                             |   18 ++
 NEWS                                  |   27 ++++
 R/economist.R                         |    4 
 R/excel.R                             |    2 
 R/fivethirtyeight.R                   |only
 R/geom-tufteboxplot.R                 |   58 +++++++--
 R/ggthemes-data.R                     |   16 ++
 R/ggthemes-package.R                  |    2 
 R/hc.R                                |only
 R/pander.R                            |only
 R/stata.R                             |   21 +--
 R/tableau.R                           |   16 +-
 R/theme-foundation.R                  |    3 
 R/theme-solid.R                       |    7 -
 R/tufte.R                             |    2 
 R/wsj.R                               |    6 
 build/partial.rdb                     |binary
 build/vignette.rds                    |only
 inst                                  |only
 man/bank_slopes.Rd                    |  214 ++++++++++++++++++----------------
 man/calc_pal.Rd                       |    5 
 man/calc_shape_pal.Rd                 |    1 
 man/circlefill_shape_pal.Rd           |   24 +--
 man/cleveland_shape_pal.Rd            |   47 +++----
 man/colorblind.Rd                     |   16 +-
 man/economist_pal.Rd                  |   19 +--
 man/excel_pal.Rd                      |   22 +--
 man/few_pal.Rd                        |   15 +-
 man/fivethirtyeight_pal.Rd            |only
 man/gdocs_pal.Rd                      |    5 
 man/geom_rangeframe.Rd                |   65 ++++------
 man/geom_tufteboxplot.Rd              |   70 +++++------
 man/ggthemes.Rd                       |    6 
 man/ggthemes_data.Rd                  |   36 +++--
 man/hc_pal.Rd                         |only
 man/palette_pander.Rd                 |only
 man/range_breaks.Rd                   |   46 ++-----
 man/scale_calc.Rd                     |    6 
 man/scale_color_tableau.Rd            |   33 ++---
 man/scale_colour_gradient2_tableau.Rd |   41 +++---
 man/scale_colour_gradient_tableau.Rd  |   42 +++---
 man/scale_economist.Rd                |    9 -
 man/scale_excel.Rd                    |    9 -
 man/scale_few.Rd                      |    8 -
 man/scale_fivethirtyeight.Rd          |only
 man/scale_gdocs.Rd                    |    6 
 man/scale_hc.Rd                       |only
 man/scale_linetype_stata.Rd           |    8 -
 man/scale_pander.Rd                   |only
 man/scale_shape_calc.Rd               |    8 -
 man/scale_shape_circlefill.Rd         |   19 +--
 man/scale_shape_cleveland.Rd          |   27 +---
 man/scale_shape_stata.Rd              |    8 -
 man/scale_shape_tableau.Rd            |   11 -
 man/scale_shape_tremmel.Rd            |   29 ++--
 man/scale_solarized.Rd                |   10 -
 man/scale_stata.Rd                    |   10 -
 man/scale_tufte.Rd                    |   12 -
 man/scale_wsj.Rd                      |   18 +-
 man/show_linetypes.Rd                 |   11 -
 man/show_shapes.Rd                    |   11 -
 man/smart_digits.Rd                   |   12 -
 man/solarized_pal.Rd                  |   24 +--
 man/solarized_rebase.Rd               |    9 -
 man/stat_fivenumber.Rd                |   64 +++++-----
 man/stata_linetype_pal.Rd             |    1 
 man/stata_pal.Rd                      |   10 -
 man/stata_shape_pal.Rd                |    5 
 man/tableau_color_pal.Rd              |   43 +++---
 man/tableau_div_gradient_pal.Rd       |   33 ++---
 man/tableau_seq_gradient_pal.Rd       |   33 ++---
 man/tableau_shape_pal.Rd              |    4 
 man/theme_calc.Rd                     |    8 -
 man/theme_economist.Rd                |   53 +++-----
 man/theme_excel.Rd                    |    9 -
 man/theme_few.Rd                      |    5 
 man/theme_fivethirtyeight.Rd          |only
 man/theme_foundation.Rd               |   26 +---
 man/theme_gdocs.Rd                    |    5 
 man/theme_hc.Rd                       |only
 man/theme_igray.Rd                    |   24 ++-
 man/theme_pander.Rd                   |only
 man/theme_solarized.Rd                |   16 +-
 man/theme_solid.Rd                    |   18 +-
 man/theme_stata.Rd                    |   33 ++---
 man/theme_tufte.Rd                    |   35 ++---
 man/theme_wsj.Rd                      |   13 +-
 man/tremmel_shape_pal.Rd              |   44 +++---
 man/wsj_pal.Rd                        |   45 +++----
 vignettes                             |only
 92 files changed, 1008 insertions(+), 879 deletions(-)

More information about ggthemes at CRAN
Permanent link

Package EGRET updated to version 2.1.0 with previous version 2.0.2 dated 2014-12-03

Title: Exploration and Graphics for RivEr Trends (EGRET)
Description: Statistics and graphics for streamflow history, water quality trends, and the statistical modeling algorithm: Weighted Regressions on Time, Discharge, and Season (WRTDS).
Author: Robert Hirsch [aut], Laura DeCicco [aut, cre]
Maintainer: Laura DeCicco

Diff between EGRET versions 2.0.2 dated 2014-12-03 and 2.1.0 dated 2014-12-18

 EGRET-2.0.2/EGRET/data/fluxConst.RData                         |only
 EGRET-2.0.2/EGRET/data/monthInfo.RData                         |only
 EGRET-2.0.2/EGRET/data/parameterCdFile.RData                   |only
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 EGRET-2.1.0/EGRET/DESCRIPTION                                  |    8 
 EGRET-2.1.0/EGRET/MD5                                          |  345 ++++------
 EGRET-2.1.0/EGRET/NAMESPACE                                    |    2 
 EGRET-2.1.0/EGRET/NEWS                                         |    5 
 EGRET-2.1.0/EGRET/R/EGRET.R                                    |   56 -
 EGRET-2.1.0/EGRET/R/boxQTwice.R                                |    2 
 EGRET-2.1.0/EGRET/R/flowDuration.R                             |    2 
 EGRET-2.1.0/EGRET/R/fluxBiasEight.R                            |    4 
 EGRET-2.1.0/EGRET/R/multiPlotDataOverview.R                    |    2 
 EGRET-2.1.0/EGRET/R/plotConcQ.R                                |    2 
 EGRET-2.1.0/EGRET/R/plotConcQSmooth.R                          |    2 
 EGRET-2.1.0/EGRET/R/plotConcTime.R                             |    2 
 EGRET-2.1.0/EGRET/R/plotConcTimeSmooth.R                       |    2 
 EGRET-2.1.0/EGRET/R/plotContours.R                             |    2 
 EGRET-2.1.0/EGRET/R/plotDiffContours.R                         |    2 
 EGRET-2.1.0/EGRET/R/plotFlowSingle.R                           |    2 
 EGRET-2.1.0/EGRET/R/plotFluxHist.R                             |    2 
 EGRET-2.1.0/EGRET/R/plotFluxPred.R                             |    2 
 EGRET-2.1.0/EGRET/R/plotFluxQ.R                                |    4 
 EGRET-2.1.0/EGRET/R/plotFluxTimeDaily.R                        |    2 
 EGRET-2.1.0/EGRET/R/plotFour.R                                 |    2 
 EGRET-2.1.0/EGRET/R/plotFourStats.R                            |    2 
 EGRET-2.1.0/EGRET/R/plotQTimeDaily.R                           |    2 
 EGRET-2.1.0/EGRET/R/plotResidQ.R                               |    2 
 EGRET-2.1.0/EGRET/R/populateParameterINFO.r                    |   18 
 EGRET-2.1.0/EGRET/R/populateSiteINFO.r                         |   56 -
 EGRET-2.1.0/EGRET/R/printSeries.R                              |    2 
 EGRET-2.1.0/EGRET/R/processQWData.r                            |   21 
 EGRET-2.1.0/EGRET/R/readMetaData.r                             |  139 ++--
 EGRET-2.1.0/EGRET/R/readNWISDaily.r                            |    8 
 EGRET-2.1.0/EGRET/R/readNWISSample.r                           |    5 
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 EGRET-2.1.0/EGRET/R/tableChange.R                              |    2 
 EGRET-2.1.0/EGRET/R/tableChangeSingle.R                        |    2 
 EGRET-2.1.0/EGRET/R/tableFlowChange.R                          |    2 
 EGRET-2.1.0/EGRET/R/tableResults.R                             |    4 
 EGRET-2.1.0/EGRET/man/Choptank_eList.Rd                        |    3 
 EGRET-2.1.0/EGRET/man/EGRET-package.Rd                         |    3 
 EGRET-2.1.0/EGRET/man/as.egret.Rd                              |    3 
 EGRET-2.1.0/EGRET/man/blankTime.Rd                             |    3 
 EGRET-2.1.0/EGRET/man/boxConcMonth.Rd                          |    3 
 EGRET-2.1.0/EGRET/man/boxConcThree.Rd                          |    3 
 EGRET-2.1.0/EGRET/man/boxQTwice.Rd                             |    5 
 EGRET-2.1.0/EGRET/man/boxResidMonth.Rd                         |    3 
 EGRET-2.1.0/EGRET/man/calculateMonthlyResults.Rd               |    3 
 EGRET-2.1.0/EGRET/man/censoredSegments.Rd                      |    3 
 EGRET-2.1.0/EGRET/man/checkStartEndDate.Rd                     |    3 
 EGRET-2.1.0/EGRET/man/compressData.Rd                          |    3 
 EGRET-2.1.0/EGRET/man/dataOverview.Rd                          |    3 
 EGRET-2.1.0/EGRET/man/dateFormatCheck.Rd                       |    3 
 EGRET-2.1.0/EGRET/man/estCrossVal.Rd                           |    3 
 EGRET-2.1.0/EGRET/man/estDailyFromSurfaces.Rd                  |    3 
 EGRET-2.1.0/EGRET/man/estSurfaces.Rd                           |    3 
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 EGRET-2.1.0/EGRET/man/flowDuration.Rd                          |    5 
 EGRET-2.1.0/EGRET/man/fluxBiasMulti.Rd                         |    7 
 EGRET-2.1.0/EGRET/man/fluxBiasStat.Rd                          |    3 
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 EGRET-2.1.0/EGRET/man/formatCheckDate.Rd                       |    3 
 EGRET-2.1.0/EGRET/man/formatCheckParameterCd.Rd                |    3 
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 EGRET-2.1.0/EGRET/man/getDaily.Rd                              |    3 
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 EGRET-2.1.0/EGRET/man/getSurfaces.Rd                           |    3 
 EGRET-2.1.0/EGRET/man/is.egret.Rd                              |    3 
 EGRET-2.1.0/EGRET/man/logPretty1.Rd                            |    3 
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 EGRET-2.1.0/EGRET/man/plotFlowSingle.Rd                        |    5 
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 EGRET-2.1.0/EGRET/man/plotFourStats.Rd                         |    5 
 EGRET-2.1.0/EGRET/man/plotQTimeDaily.Rd                        |    5 
 EGRET-2.1.0/EGRET/man/plotResidPred.Rd                         |    3 
 EGRET-2.1.0/EGRET/man/plotResidQ.Rd                            |    5 
 EGRET-2.1.0/EGRET/man/plotResidTime.Rd                         |    3 
 EGRET-2.1.0/EGRET/man/plotSDLogQ.Rd                            |    3 
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 EGRET-2.1.0/EGRET/man/readDataFromFile.Rd                      |    3 
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 EGRET-2.1.0/EGRET/man/readNWISInfo.Rd                          |    3 
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 EGRET-2.1.0/EGRET/man/runSurvReg.Rd                            |    3 
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 EGRET-2.1.0/EGRET/man/setSeasonLabelByUser.Rd                  |    3 
 EGRET-2.1.0/EGRET/man/setupYears.Rd                            |    3 
 EGRET-2.1.0/EGRET/man/surfaceIndex.Rd                          |    3 
 EGRET-2.1.0/EGRET/man/tableChange.Rd                           |    5 
 EGRET-2.1.0/EGRET/man/tableChangeSingle.Rd                     |    5 
 EGRET-2.1.0/EGRET/man/tableFlowChange.Rd                       |    5 
 EGRET-2.1.0/EGRET/man/tableResults.Rd                          |    7 
 EGRET-2.1.0/EGRET/man/triCube.Rd                               |    3 
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 178 files changed, 595 insertions(+), 479 deletions(-)

More information about EGRET at CRAN
Permanent link

Package DDD updated to version 2.6 with previous version 2.5 dated 2014-05-26

Title: Diversity-Dependent Diversification
Description: implements maximum likelihood methods based on the diversity-dependent birth-death process to test whether speciation or extinction are diversity-dependent. See Etienne et al. 2012, Proc. Roy. Soc. B 279: 1300-1309, doi: 10.1098/rspb.2011.1439. DDD also implements a maximum likelihood method to detect key innovations defined as decoupling of diversity-dependence. See Etienne & Haegeman 2012, Am. Nat. 180: E75-E89, doi: 10.1086/667574. Finally, DDD contains a function to simulate the diversity-dependent process.
Author: Rampal S. Etienne & Bart Haegeman
Maintainer: Rampal S. Etienne

Diff between DDD versions 2.5 dated 2014-05-26 and 2.6 dated 2014-12-18

 DESCRIPTION          |   12 +++---
 MD5                  |   40 ++++++++++----------
 R/dd_KI_ML.R         |   10 ++---
 R/dd_KI_loglik.R     |   99 ++++++++++++++++++++++++++++++++++++++++-----------
 R/dd_ML.R            |    4 +-
 R/dd_SR_ML.R         |    6 +--
 R/dd_SR_loglik.R     |   44 +++++++++++++++-------
 R/dd_loglik.R        |   22 ++++++++---
 R/dd_loglik_bw_rhs.R |   13 ++++++
 R/dd_loglik_rhs.R    |   13 ++++++
 R/dd_sim.R           |   17 ++++++++
 R/flavec.R           |    4 ++
 man/DDD-package.Rd   |   27 ++-----------
 man/bd_ML.Rd         |    2 -
 man/dd_KI_ML.Rd      |   29 ++++++++------
 man/dd_KI_loglik.Rd  |   11 +++--
 man/dd_ML.Rd         |   39 +++++++-------------
 man/dd_SR_ML.Rd      |    7 ++-
 man/dd_SR_loglik.Rd  |    8 ++--
 man/dd_loglik.Rd     |    8 ++--
 man/dd_sim.Rd        |   12 ++++--
 21 files changed, 272 insertions(+), 155 deletions(-)

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Permanent link

Package DCGL updated to version 2.1.2 with previous version 2.1.1 dated 2013-12-31

Title: Differential Co-expression Analysis and Differential Regulation Analysis of Gene Expression Microarray Data
Description: Functions for 1) gene filtration; 2) link filtration; 3) differential co-expression analysis: DCG (Differential Coexpressed Gene) identification and DCL (Differentially Coexpressed Link) identification; and 4) differential regulation analysis: DRG (Differential Regulated Gene) identification, DRL (Differential Regulated Link) identification, DRL visualization and regulator ranking.
Author: Jing Yang, Hui Yu, Bao-Hong Liu, Zhongming Zhao, Lei Liu, Liang-Xiao Ma, Yi-Xue Li, Yuan-Yuan Li
Maintainer: Bao-Hong Liu

Diff between DCGL versions 2.1.1 dated 2013-12-31 and 2.1.2 dated 2014-12-18

 DESCRIPTION         |    8 ++++----
 MD5                 |    8 ++++----
 man/DCGL-package.Rd |   32 ++++++++++++++++----------------
 man/DRrank.Rd       |   12 ++++++------
 man/DRsort.Rd       |    9 +++++----
 5 files changed, 35 insertions(+), 34 deletions(-)

More information about DCGL at CRAN
Permanent link

Wed, 17 Dec 2014

Package Rlabkey updated to version 2.1.126 with previous version 2.1.125 dated 2014-08-28

Title: Data Exchange between R and LabKey Server
Description: Allow a user to discover, query and modify data from a LabKey Server.
Author: Peter Hussey
Maintainer: Cory Nathe

Diff between Rlabkey versions 2.1.125 dated 2014-08-28 and 2.1.126 dated 2014-12-17

 DESCRIPTION                         |   12 ++++++------
 MD5                                 |   18 +++++++++---------
 NEWS                                |    4 ++++
 R/labkey.executeSql.R               |    4 +++-
 R/labkey.getQueryLists.R            |    2 +-
 R/labkey.setCurlOptions.R           |    4 ++--
 build/vignette.rds                  |binary
 man/Rlabkey-package.Rd              |    4 ++--
 man/labkey.acceptSelfSignedCerts.Rd |    2 +-
 man/labkey.executeSql.Rd            |   12 +++++++++++-
 10 files changed, 39 insertions(+), 23 deletions(-)

More information about Rlabkey at CRAN
Permanent link

Package RcppDL updated to version 0.0.5 with previous version 0.0.3 dated 2014-12-15

Title: Deep Learning Methods via Rcpp
Description: This package is based on the C++ code from Yusuke Sugomori, which implements basic machine learning methods with many layers (deep learning), including dA (Denoising Autoencoder), SdA (Stacked Denoising Autoencoder), RBM (Restricted Boltzmann machine) and DBN (Deep Belief Nets).
Author: Qiang Kou, Yusuke Sugomori
Maintainer: Qiang Kou

Diff between RcppDL versions 0.0.3 dated 2014-12-15 and 0.0.5 dated 2014-12-17

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Package Rchoice updated to version 0.2 with previous version 0.1 dated 2014-04-02

Title: Discrete Choice (Binary, Poisson and Ordered) Models with Random Parameters
Description: Estimate Binary (Probit and Logit), Ordered (Probit and Logit) and Poisson models with random parameters using Simulated Maximum Likelihood. Rchoice handles cross-sectional and panel databases.
Author: Mauricio Sarrias
Maintainer: Mauricio Sarrias

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Package plotpc updated to version 1.0.3 with previous version 1.0-2 dated 2009-03-23

Title: Plot principal component histograms around a scatter plot.
Description: Plot principal component histograms around a bivariate scatter plot.
Author: Stephen Milborrow
Maintainer: Stephen Milborrow

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Package extRemes updated to version 2.0-4 with previous version 2.0-3 dated 2014-08-26

Title: Extreme Value Analysis
Description: Functions for performing extreme value analysis.
Author: Eric Gilleland
Maintainer: Eric Gilleland

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Package eha updated to version 2.4-2 with previous version 2.4-1 dated 2014-02-17

Title: Event History Analysis
Description: Sampling of risk sets in Cox regression, selections in the Lexis diagram, bootstrapping. Parametric proportional hazards fitting with left truncation and right censoring for common families of distributions, piecewise constant hazards, and discrete models. AFT regression for left truncated and right censored data. Binary and Poisson regression for clustered data, fixed and random effects with bootstrapping.
Author: G├Âran Brostr├Âm [aut, cre]
Maintainer: G├Âran Brostr├Âm

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Package earth updated to version 4.1.0 with previous version 4.0.0 dated 2014-12-12

Title: Multivariate Adaptive Regression Splines
Description: Build regression models using the techniques in Friedman's papers "Fast MARS" and "Multivariate Adaptive Regression Splines". (The term "MARS" is trademarked and thus not used in the name of the package.)
Author: Stephen Milborrow. Derived from mda:mars by Trevor Hastie and Rob Tibshirani. Uses Alan Miller's Fortran utilities with Thomas Lumley's leaps wrapper.
Maintainer: Stephen Milborrow

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Package dataRetrieval updated to version 2.1.0 with previous version 2.0.1 dated 2014-12-03

Title: Retrieval Functions for USGS and EPA Hydrologic and Water Quality Data
Description: Collection of functions to help retrieve U.S. Geological Survey (USGS) and U.S. Environmental Protection Agency (EPA) water quality and hydrology data from web services. USGS web services are discovered from the National Water Information Services (NWIS) tools found here: http://waterservices.usgs.gov/ Both EPA and USGS water quality data are obtained from the Water Quality Portal found here: http://www.waterqualitydata.us/portal.jsp
Author: Robert Hirsch [aut], Laura DeCicco [aut, cre], David Lorenz [aut]
Maintainer: Laura DeCicco

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