Sat, 04 Mar 2017

New package shinyjqui with initial version 0.1.0
Package: shinyjqui
Type: Package
Title: 'jQuery UI' Interactions and Effects for Shiny
Version: 0.1.0
Authors@R: person("Yang", "Tang", email = "tang_yang@outlook.com", role = c("aut", "cre"))
Maintainer: Yang Tang <tang_yang@outlook.com>
Description: An extension to shiny that brings interactions and animation effects from 'jQuery UI' library.
License: MIT + file LICENSE
Encoding: UTF-8
LazyData: true
Depends: R (>= 3.2.0)
Imports: shiny, htmlwidgets, jsonlite
Suggests: ggplot2, highcharter, knitr, rmarkdown
URL: https://github.com/yang-tang/shinyjqui
BugReports: https://github.com/yang-tang/shinyjqui/issues
RoxygenNote: 5.0.1
VignetteBuilder: knitr
NeedsCompilation: no
Packaged: 2017-03-04 11:28:52 UTC; c164560
Author: Yang Tang [aut, cre]
Repository: CRAN
Date/Publication: 2017-03-04 17:12:34

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Package RcppGSL updated to version 0.3.2 with previous version 0.3.1 dated 2016-10-03

Title: 'Rcpp' Integration for 'GNU GSL' Vectors and Matrices
Description: 'Rcpp' integration for 'GNU GSL' vectors and matrices The 'GNU Scientific Library' (or 'GSL') is a collection of numerical routines for scientific computing. It is particularly useful for C and C++ programs as it provides a standard C interface to a wide range of mathematical routines. There are over 1000 functions in total with an extensive test suite. The 'RcppGSL' package provides an easy-to-use interface between 'GSL' data structures and R using concepts from 'Rcpp' which is itself a package that eases the interfaces between R and C++. This package also serves as a prime example of how to build a package that uses 'Rcpp' to connect to another third-party library. The 'autoconf' script, 'inline' plugin and example package can all be used as a stanza to write a similar package against another library.
Author: Dirk Eddelbuettel and Romain Francois
Maintainer: Dirk Eddelbuettel <edd@debian.org>

Diff between RcppGSL versions 0.3.1 dated 2016-10-03 and 0.3.2 dated 2017-03-04

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Package PWEALL updated to version 1.1.0 with previous version 1.0.0 dated 2016-12-22

Title: Design and Monitoring of Survival Trials Accounting for Complex Situations
Description: Calculates various functions needed for design and monitoring survival trials accounting for complex situations such as delayed treatment effect, treatment crossover, non-uniform accrual, and different censoring distributions between groups. The event time distribution is assumed to be piecewise exponential (PWE) distribution and the entry time is assumed to be piecewise uniform distribution.
Author: Xiaodong Luo [aut, cre], Xuezhou Mao [ctb], Xun Chen [ctb], Hui Quan [ctb], Sanofi [cph]
Maintainer: Xiaodong Luo <Xiaodong.Luo@sanofi.com>

Diff between PWEALL versions 1.0.0 dated 2016-12-22 and 1.1.0 dated 2017-03-04

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Package nproc updated to version 2.0.6 with previous version 2.0.4 dated 2017-01-13

Title: Neyman-Pearson Receiver Operating Characteristics
Description: Given a sample of class 0 and class 1 and a classification method, the package generates the corresponding Neyman-Pearson classifier with a pre-specified type-I error control and Neyman-Pearson Receiver Operating Characteristics.
Author: Yang Feng, Jessica Li and Xin Tong
Maintainer: Yang Feng <yang.feng@columbia.edu>

Diff between nproc versions 2.0.4 dated 2017-01-13 and 2.0.6 dated 2017-03-04

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Package nleqslv updated to version 3.2 with previous version 3.1 dated 2017-02-16

Title: Solve Systems of Nonlinear Equations
Description: Solve a system of nonlinear equations using a Broyden or a Newton method with a choice of global strategies such as line search and trust region. There are options for using a numerical or user supplied Jacobian, for specifying a banded numerical Jacobian and for allowing a singular or ill-conditioned Jacobian.
Author: Berend Hasselman
Maintainer: Berend Hasselman <bhh@xs4all.nl>

Diff between nleqslv versions 3.1 dated 2017-02-16 and 3.2 dated 2017-03-04

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Package maGUI updated to version 2.2 with previous version 2.1 dated 2017-02-16

Title: A Graphical User Interface for Microarray Data Analysis and Annotation
Description: Provides a Graphical User Interface for Analysing DNA Microarray Data. It performs functional enrichment on genes of interest, identifies gene symbols and also builds co-expression network.
Author: Dhammapal Bharne, Vaibhav Vindal
Maintainer: Dhammapal Bharne <dhammapalb@uohyd.ac.in>

Diff between maGUI versions 2.1 dated 2017-02-16 and 2.2 dated 2017-03-04

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Package icarus updated to version 0.3.0 with previous version 0.2.2 dated 2016-10-27

Title: Calibrates and Reweights Units in Samples
Description: Provides user-friendly tools for calibration in survey sampling. The package is production-oriented, and its interface is inspired by the famous popular macro 'Calmar' for SAS, so that 'Calmar' users can quickly get used to 'icarus'. In addition to calibration (with linear, raking and logit methods), 'icarus' features functions for calibration on tight bounds and penalized calibration.
Author: Antoine Rebecq [aut, cre]
Maintainer: Antoine Rebecq <antoine.rebecq@m4x.org>

Diff between icarus versions 0.2.2 dated 2016-10-27 and 0.3.0 dated 2017-03-04

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New package CNLTreg with initial version 0.1
Package: CNLTreg
Type: Package
Title: Complex-Valued Wavelet Lifting for Signal Denoising
Version: 0.1
Date: 2017-03-4
Author: Matt Nunes [aut, cre], Marina Knight [aut], Jean Hamilton [ctb], Piotr Fryzlewicz [ctb]
Authors@R: c(person("Matt","Nunes", role=c("aut","cre"),email="m.nunes@lancaster.ac.uk"),person("Marina", "Knight", role="aut"), person("Jean", "Hamilton", role="ctb"), person("Piotr", "Fryzlewicz", role="ctb"))
Maintainer: Matt Nunes <m.nunes@lancaster.ac.uk>
Description: Implementations of recent complex-valued wavelet shrinkage procedures for smoothing irregularly sampled signals.
License: GPL-2
Depends: adlift, miscTools, nlt
Suggests: MASS
NeedsCompilation: no
Packaged: 2017-03-04 13:34:38 UTC; nunes
Repository: CRAN
Date/Publication: 2017-03-04 17:12:16

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New package VertexSort with initial version 0.1-0
Package: VertexSort
Type: Package
Title: Network Decomposition and Randomization
Version: 0.1-0
Date: 2017-03-03
Author: Diala Abd-Rabbo
Maintainer: Diala Abd-Rabbo <diala.abd.rabbo@gmail.com>
Description: Permits to apply the 'Vertex Sort' algorithm (Jothi et al. (2009) <10.1038/msb.2009.52>) to a graph in order to elucidate its hierarchical structure. It also allows graphic visualization of the sorted graph by exporting the results to a cytoscape friendly format. Moreover, it offers five different algorithms of graph randomization: 1) Randomize a graph with preserving node degrees, 2) with preserving similar node degrees, 3) without preserving node degrees, 4) with preserving node in-degrees and 5) with preserving node out-degrees.
Depends: R (>= 3.3.2), igraph, snowfall
License: GPL (>= 2)
NeedsCompilation: no
Packaged: 2017-03-03 23:39:31 UTC; Diala_Abd_Rabbo
Repository: CRAN
Date/Publication: 2017-03-04 08:21:44

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Package SubgrpID updated to version 0.11 with previous version 0.10 dated 2017-02-28

Title: Patient Subgroup Identification for Clinical Drug Development
Description: Function Wrapper contains four algorithms for developing threshold-based multivariate (prognostic/predictive) biomarker signatures via bootstrapping and aggregating of thresholds from trees, Monte-Carlo variations of the Adaptive Indexing method and Patient Rule Induction Method. Variable selection is automatically built-in to these algorithms. Final signatures are returned with interaction plots for predictive signatures. Cross-validation performance evaluation and testing dataset results are also output.
Author: Xin Huang, Yan Sun, Saptarshi Chatterjee and Paul Trow
Maintainer: Xin Huang <xhuang.stats@gmail.com>

Diff between SubgrpID versions 0.10 dated 2017-02-28 and 0.11 dated 2017-03-04

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Package sitree updated to version 0.1-1 with previous version 0.1-0 dated 2017-01-10

Title: Single Tree Simulator
Description: Forecasts plots at tree level.
Author: Clara Anton Fernandez [aut, cre], Nikolas von Lupke [ctb]
Maintainer: Clara Anton Fernandez <caf@nibio.no>

Diff between sitree versions 0.1-0 dated 2017-01-10 and 0.1-1 dated 2017-03-04

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Package Sequential updated to version 2.3.1 with previous version 2.3 dated 2017-01-01

Title: Exact Sequential Analysis for Poisson and Binomial Data
Description: Functions to calculate exact critical values, statistical power, expected time to signal and required sample sizes for performing exact sequential analysis. All these calculations can be done for either Poisson or binomial data, for continuous or group sequential analyses, and for different types of rejection boundaries. In case of group sequential analyses, the group sizes do not have to be specified in advance and the alpha spending can be arbitrarily settled.
Author: Ivair Ramos Silva and Martin Kulldorff
Maintainer: Ivair Ramos Silva <jamesivair@yahoo.com.br>

Diff between Sequential versions 2.3 dated 2017-01-01 and 2.3.1 dated 2017-03-04

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Package grattan updated to version 1.4.1.2 with previous version 1.3.0.3 dated 2017-01-18

Title: Perform Common Quantitative Tasks for Australian Analysts and to Support Grattan Institute Analysis
Description: A series of functions focused on costing and evaluating Australian tax policy in support of the Grattan Institute's Australian Perspectives program. For access to the taxstats package, please run install.packages("taxstats", repos = "https://hughparsonage.github.io/drat/", type = "source"). N.B. The taxstats package is approximately 50 MB.
Author: Hugh Parsonage [aut, cre], Tim Cameron [aut], Brendan Coates [aut], William Young [aut], Ittima Cherastidtham [dtc]
Maintainer: Hugh Parsonage <hugh.parsonage@gmail.com>

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New package CPsurv with initial version 1.0.0
Package: CPsurv
Type: Package
Title: Nonparametric Change Point Estimation for Survival Data
Version: 1.0.0
Date: 2017-03-03
Author: Stefanie Krügel [aut, cre], Alessandra R. Brazzale, [aut], Helmut Kuechenhoff [aut]
Maintainer: Stefanie Krügel <stefanie.kruegel@gmail.com>
Description: Nonparametric change point estimation for survival data based on p-values of exact binomial tests.
License: GPL-2
LazyData: TRUE
Encoding: UTF-8
Depends: R (>= 3.1.0)
Imports: survival (>= 2.40-1), muhaz (>= 1.2.6), parallel (>= 3.2.3)
Suggests: testthat (>= 0.11.0)
RoxygenNote: 6.0.1
Collate: 'CPsurv-package.R' 'bootbiascorrect.R' 'cpest.R' 'cpsurv-data.R' 'cpsurv.R' 'km.sim.survtimes.R' 'methods.R' 'neg.loglik.WeibExp.R' 'sim.survdata.R'
NeedsCompilation: no
Packaged: 2017-03-03 21:55:38 UTC; Steffi
Repository: CRAN
Date/Publication: 2017-03-04 08:21:36

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Package ziphsmm updated to version 1.0.4 with previous version 1.0.3 dated 2017-02-09

Title: Zero-Inflated Poisson Hidden (Semi-)Markov Models
Description: Fit zero-inflated Poisson hidden (semi-)Markov models with or without covariates by directly maximizing the log likelihood function. Multiple starting values should be used to avoid local minima.
Author: Zekun (Jack) Xu, Ye Liu
Maintainer: Zekun (Jack) Xu <zekunxu@gmail.com>

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Package RSiteCatalyst updated to version 1.4.11 with previous version 1.4.10 dated 2016-12-08

Title: R Client for Adobe Analytics API V1.4
Description: Functions for interacting with the Adobe Analytics API V1.4 (https://api.omniture.com/admin/1.4/rest/).
Author: Willem Paling, Randy Zwitch & Jowanza Joseph
Maintainer: Randy Zwitch <rzwitch+rsitecatalyst@gmail.com>

Diff between RSiteCatalyst versions 1.4.10 dated 2016-12-08 and 1.4.11 dated 2017-03-04

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More information about RSiteCatalyst at CRAN
Permanent link

Package rotl updated to version 3.0.3 with previous version 3.0.1 dated 2016-09-19

Title: Interface to the 'Open Tree of Life' API
Description: An interface to the 'Open Tree of Life' API to retrieve phylogenetic trees, information about studies used to assemble the synthetic tree, and utilities to match taxonomic names to 'Open Tree identifiers'. The 'Open Tree of Life' aims at assembling a comprehensive phylogenetic tree for all named species.
Author: Francois Michonneau [aut, cre], Joseph Brown [aut], David Winter [aut]
Maintainer: Francois Michonneau <francois.michonneau@gmail.com>

Diff between rotl versions 3.0.1 dated 2016-09-19 and 3.0.3 dated 2017-03-04

 DESCRIPTION                       |    8 +-
 LICENSE                           |    2 
 MD5                               |  106 ++++++++++++++-------------
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More information about rotl at CRAN
Permanent link

Package RcppShark updated to version 3.1.1 with previous version 3.1.0 dated 2016-07-03

Title: R Interface to the Shark Machine Learning Library
Description: An R interface to the C++/Boost Shark machine learning library.
Author: Aydin Demircioglu
Maintainer: Aydin Demircioglu <aydin.demircioglu@ini.rub.de>

Diff between RcppShark versions 3.1.0 dated 2016-07-03 and 3.1.1 dated 2017-03-04

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 RcppShark-3.1.0/RcppShark/src/shark/LinAlg/BLAS/blas.h                                                               |only
 RcppShark-3.1.0/RcppShark/src/shark/LinAlg/BLAS/fwd.hpp                                                              |only
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 RcppShark-3.1.1/RcppShark/ChangeLog                                                                                  |    6 
 RcppShark-3.1.1/RcppShark/DESCRIPTION                                                                                |   12 
 RcppShark-3.1.1/RcppShark/MD5                                                                                        | 2050 +++++-----
 RcppShark-3.1.1/RcppShark/NAMESPACE                                                                                  |    4 
 RcppShark-3.1.1/RcppShark/R/RcppExports.R                                                                            |    2 
 RcppShark-3.1.1/RcppShark/R/RcppShark.package.skeleton.R                                                             |  145 
 RcppShark-3.1.1/RcppShark/R/zzz.R                                                                                    |    4 
 RcppShark-3.1.1/RcppShark/build/vignette.rds                                                                         |binary
 RcppShark-3.1.1/RcppShark/cleanup                                                                                    |    3 
 RcppShark-3.1.1/RcppShark/inst/doc/RcppShark.Rmd                                                                     |    2 
 RcppShark-3.1.1/RcppShark/inst/doc/RcppShark.html                                                                    |   96 
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 RcppShark-3.1.1/RcppShark/inst/include/shark/Algorithms/GradientDescent/Rprop.h                                      |    4 
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 RcppShark-3.1.1/RcppShark/inst/include/shark/Algorithms/JaakkolaHeuristic.h                                          |    5 
 RcppShark-3.1.1/RcppShark/inst/include/shark/Algorithms/KMeans.h                                                     |   79 
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 RcppShark-3.1.1/RcppShark/inst/include/shark/Algorithms/Pegasos.h                                                    |    4 
 RcppShark-3.1.1/RcppShark/inst/include/shark/Algorithms/QP/BoxConstrainedProblems.h                                  |  134 
 RcppShark-3.1.1/RcppShark/inst/include/shark/Algorithms/QP/Impl/AnalyticProblems.h                                   |    5 
 RcppShark-3.1.1/RcppShark/inst/include/shark/Algorithms/QP/QpBoxLinear.h                                             |  729 +--
 RcppShark-3.1.1/RcppShark/inst/include/shark/Algorithms/QP/QpMcBoxDecomp.h                                           |   48 
 RcppShark-3.1.1/RcppShark/inst/include/shark/Algorithms/QP/QpMcLinear.h                                              |  361 -
 RcppShark-3.1.1/RcppShark/inst/include/shark/Algorithms/QP/QpMcSimplexDecomp.h                                       |   35 
 RcppShark-3.1.1/RcppShark/inst/include/shark/Algorithms/QP/QpSolver.h                                                |   30 
 RcppShark-3.1.1/RcppShark/inst/include/shark/Algorithms/QP/QpSparseArray.h                                           |   15 
 RcppShark-3.1.1/RcppShark/inst/include/shark/Algorithms/QP/QuadraticProgram.h                                        |    4 
 RcppShark-3.1.1/RcppShark/inst/include/shark/Algorithms/QP/SvmProblems.h                                             |  133 
 RcppShark-3.1.1/RcppShark/inst/include/shark/Algorithms/StoppingCriteria/AbstractStoppingCriterion.h                 |    4 
 RcppShark-3.1.1/RcppShark/inst/include/shark/Algorithms/StoppingCriteria/GeneralizationLoss.h                        |    6 
 RcppShark-3.1.1/RcppShark/inst/include/shark/Algorithms/StoppingCriteria/GeneralizationQuotient.h                    |    6 
 RcppShark-3.1.1/RcppShark/inst/include/shark/Algorithms/StoppingCriteria/MaxIterations.h                             |    6 
 RcppShark-3.1.1/RcppShark/inst/include/shark/Algorithms/StoppingCriteria/TrainingError.h                             |    5 
 RcppShark-3.1.1/RcppShark/inst/include/shark/Algorithms/StoppingCriteria/TrainingProgress.h                          |    5 
 RcppShark-3.1.1/RcppShark/inst/include/shark/Algorithms/StoppingCriteria/ValidatedStoppingCriterion.h                |    6 
 RcppShark-3.1.1/RcppShark/inst/include/shark/Algorithms/Trainers/AbstractSvmTrainer.h                                |   28 
 RcppShark-3.1.1/RcppShark/inst/include/shark/Algorithms/Trainers/AbstractTrainer.h                                   |    4 
 RcppShark-3.1.1/RcppShark/inst/include/shark/Algorithms/Trainers/AbstractWeightedTrainer.h                           |    4 
 RcppShark-3.1.1/RcppShark/inst/include/shark/Algorithms/Trainers/Budgeted/AbstractBudgetMaintenanceStrategy.h        |    4 
 RcppShark-3.1.1/RcppShark/inst/include/shark/Algorithms/Trainers/Budgeted/KernelBudgetedSGDTrainer.h                 |    4 
 RcppShark-3.1.1/RcppShark/inst/include/shark/Algorithms/Trainers/Budgeted/MergeBudgetMaintenanceStrategy.h           |    4 
 RcppShark-3.1.1/RcppShark/inst/include/shark/Algorithms/Trainers/Budgeted/ProjectBudgetMaintenanceStrategy.h         |    4 
 RcppShark-3.1.1/RcppShark/inst/include/shark/Algorithms/Trainers/Budgeted/RemoveBudgetMaintenanceStrategy.h          |    4 
 RcppShark-3.1.1/RcppShark/inst/include/shark/Algorithms/Trainers/CARTTrainer.h                                       |   42 
 RcppShark-3.1.1/RcppShark/inst/include/shark/Algorithms/Trainers/CARTcommon.h                                        |only
 RcppShark-3.1.1/RcppShark/inst/include/shark/Algorithms/Trainers/CSvmTrainer.h                                       |  705 +++
 RcppShark-3.1.1/RcppShark/inst/include/shark/Algorithms/Trainers/Distribution/DistTrainerContainer.h                 |    4 
 RcppShark-3.1.1/RcppShark/inst/include/shark/Algorithms/Trainers/Distribution/GenericDistTrainer.h                   |    4 
 RcppShark-3.1.1/RcppShark/inst/include/shark/Algorithms/Trainers/Distribution/NormalTrainer.h                        |    5 
 RcppShark-3.1.1/RcppShark/inst/include/shark/Algorithms/Trainers/EpsilonSvmTrainer.h                                 |    4 
 RcppShark-3.1.1/RcppShark/inst/include/shark/Algorithms/Trainers/FisherLDA.h                                         |    4 
 RcppShark-3.1.1/RcppShark/inst/include/shark/Algorithms/Trainers/KernelMeanClassifier.h                              |    4 
 RcppShark-3.1.1/RcppShark/inst/include/shark/Algorithms/Trainers/KernelSGDTrainer.h                                  |    4 
 RcppShark-3.1.1/RcppShark/inst/include/shark/Algorithms/Trainers/LDA.h                                               |    4 
 RcppShark-3.1.1/RcppShark/inst/include/shark/Algorithms/Trainers/LassoRegression.h                                   |    6 
 RcppShark-3.1.1/RcppShark/inst/include/shark/Algorithms/Trainers/LinearRegression.h                                  |    4 
 RcppShark-3.1.1/RcppShark/inst/include/shark/Algorithms/Trainers/LinearSAGTrainer.h                                  |  119 
 RcppShark-3.1.1/RcppShark/inst/include/shark/Algorithms/Trainers/MissingFeatureSvmTrainer.h                          |    4 
 RcppShark-3.1.1/RcppShark/inst/include/shark/Algorithms/Trainers/NBClassifierTrainer.h                               |    5 
 RcppShark-3.1.1/RcppShark/inst/include/shark/Algorithms/Trainers/NormalizeComponentsUnitInterval.h                   |    4 
 RcppShark-3.1.1/RcppShark/inst/include/shark/Algorithms/Trainers/NormalizeComponentsUnitVariance.h                   |    4 
 RcppShark-3.1.1/RcppShark/inst/include/shark/Algorithms/Trainers/NormalizeComponentsWhitening.h                      |    7 
 RcppShark-3.1.1/RcppShark/inst/include/shark/Algorithms/Trainers/NormalizeComponentsZCA.h                            |    6 
 RcppShark-3.1.1/RcppShark/inst/include/shark/Algorithms/Trainers/NormalizeKernelUnitVariance.h                       |    4 
 RcppShark-3.1.1/RcppShark/inst/include/shark/Algorithms/Trainers/OneClassSvmTrainer.h                                |    8 
 RcppShark-3.1.1/RcppShark/inst/include/shark/Algorithms/Trainers/OptimizationTrainer.h                               |    4 
 RcppShark-3.1.1/RcppShark/inst/include/shark/Algorithms/Trainers/PCA.h                                               |    4 
 RcppShark-3.1.1/RcppShark/inst/include/shark/Algorithms/Trainers/Perceptron.h                                        |    4 
 RcppShark-3.1.1/RcppShark/inst/include/shark/Algorithms/Trainers/RFTrainer.h                                         |  114 
 RcppShark-3.1.1/RcppShark/inst/include/shark/Algorithms/Trainers/RankingSvmTrainer.h                                 |only
 RcppShark-3.1.1/RcppShark/inst/include/shark/Algorithms/Trainers/RegularizationNetworkTrainer.h                      |   10 
 RcppShark-3.1.1/RcppShark/inst/include/shark/Algorithms/Trainers/SigmoidFit.h                                        |    4 
 RcppShark-3.1.1/RcppShark/inst/include/shark/Core/DLLSupport.h                                                       |    5 
 RcppShark-3.1.1/RcppShark/inst/include/shark/Core/Exception.h                                                        |    4 
 RcppShark-3.1.1/RcppShark/inst/include/shark/Core/Flags.h                                                            |    5 
 RcppShark-3.1.1/RcppShark/inst/include/shark/Core/INameable.h                                                        |    4 
 RcppShark-3.1.1/RcppShark/inst/include/shark/Core/IParameterizable.h                                                 |    4 
 RcppShark-3.1.1/RcppShark/inst/include/shark/Core/Math.h                                                             |    5 
 RcppShark-3.1.1/RcppShark/inst/include/shark/Core/OpenMP.h                                                           |    5 
 RcppShark-3.1.1/RcppShark/inst/include/shark/Core/ResultSets.h                                                       |    4 
 RcppShark-3.1.1/RcppShark/inst/include/shark/Core/Shark.h                                                            |   25 
 RcppShark-3.1.1/RcppShark/inst/include/shark/Core/State.h                                                            |    5 
 RcppShark-3.1.1/RcppShark/inst/include/shark/Core/Timer.h                                                            |    4 
 RcppShark-3.1.1/RcppShark/inst/include/shark/Core/Traits/ProxyReferenceTraits.h                                      |    6 
 RcppShark-3.1.1/RcppShark/inst/include/shark/Core/utility/CanBeCalled.h                                              |    6 
 RcppShark-3.1.1/RcppShark/inst/include/shark/Core/utility/Impl/boost_iterator_facade_fixed.hpp                       |    1 
 RcppShark-3.1.1/RcppShark/inst/include/shark/Core/utility/Iterators.h                                                |    5 
 RcppShark-3.1.1/RcppShark/inst/include/shark/Core/utility/KeyValuePair.h                                             |    5 
 RcppShark-3.1.1/RcppShark/inst/include/shark/Core/utility/Range.h                                                    |    5 
 RcppShark-3.1.1/RcppShark/inst/include/shark/Core/utility/ScopedHandle.h                                             |    5 
 RcppShark-3.1.1/RcppShark/inst/include/shark/Core/utility/ZipPair.h                                                  |    7 
 RcppShark-3.1.1/RcppShark/inst/include/shark/Core/utility/functional.h                                               |    5 
 RcppShark-3.1.1/RcppShark/inst/include/shark/Data/BatchInterface.h                                                   |   57 
 RcppShark-3.1.1/RcppShark/inst/include/shark/Data/BatchInterfaceAdaptStruct.h                                        |    5 
 RcppShark-3.1.1/RcppShark/inst/include/shark/Data/CVDatasetTools.h                                                   |    4 
 RcppShark-3.1.1/RcppShark/inst/include/shark/Data/Csv.h                                                              |    5 
 RcppShark-3.1.1/RcppShark/inst/include/shark/Data/DataDistribution.h                                                 |    6 
 RcppShark-3.1.1/RcppShark/inst/include/shark/Data/DataView.h                                                         |   18 
 RcppShark-3.1.1/RcppShark/inst/include/shark/Data/Dataset.h                                                          |   17 
 RcppShark-3.1.1/RcppShark/inst/include/shark/Data/Download.h                                                         |only
 RcppShark-3.1.1/RcppShark/inst/include/shark/Data/ExportKernelMatrix.h                                               |    4 
 RcppShark-3.1.1/RcppShark/inst/include/shark/Data/HDF5.h                                                             |    5 
 RcppShark-3.1.1/RcppShark/inst/include/shark/Data/Impl/BoostFusion151DefineStructInl.hpp                             |    5 
 RcppShark-3.1.1/RcppShark/inst/include/shark/Data/Impl/BoostFusionCopy.hpp                                           |    5 
 RcppShark-3.1.1/RcppShark/inst/include/shark/Data/Impl/CVDatasetTools.inl                                            |    4 
 RcppShark-3.1.1/RcppShark/inst/include/shark/Data/Impl/Dataset.inl                                                   |   11 
 RcppShark-3.1.1/RcppShark/inst/include/shark/Data/Impl/Downloader.hpp                                                |only
 RcppShark-3.1.1/RcppShark/inst/include/shark/Data/Impl/Statistics.inl                                                |   16 
 RcppShark-3.1.1/RcppShark/inst/include/shark/Data/LabelOrder.h                                                       |    4 
 RcppShark-3.1.1/RcppShark/inst/include/shark/Data/Libsvm.h                                                           |    4 
 RcppShark-3.1.1/RcppShark/inst/include/shark/Data/Pgm.h                                                              |  116 
 RcppShark-3.1.1/RcppShark/inst/include/shark/Data/SparseData.h                                                       |    5 
 RcppShark-3.1.1/RcppShark/inst/include/shark/Data/Statistics.h                                                       |   16 
 RcppShark-3.1.1/RcppShark/inst/include/shark/Data/WeightedDataset.h                                                  |    5 
 RcppShark-3.1.1/RcppShark/inst/include/shark/LinAlg/BLAS/assignment.hpp                                              |  428 +-
 RcppShark-3.1.1/RcppShark/inst/include/shark/LinAlg/BLAS/decompositions.hpp                                          |only
 RcppShark-3.1.1/RcppShark/inst/include/shark/LinAlg/BLAS/detail/check.hpp                                            |only
 RcppShark-3.1.1/RcppShark/inst/include/shark/LinAlg/BLAS/detail/evaluation_tags.hpp                                  |only
 RcppShark-3.1.1/RcppShark/inst/include/shark/LinAlg/BLAS/detail/expression_optimizers.hpp                            |only
 RcppShark-3.1.1/RcppShark/inst/include/shark/LinAlg/BLAS/detail/functional.hpp                                       |  803 ---
 RcppShark-3.1.1/RcppShark/inst/include/shark/LinAlg/BLAS/detail/iterator.hpp                                         |   87 
 RcppShark-3.1.1/RcppShark/inst/include/shark/LinAlg/BLAS/detail/matrix_expression_classes.hpp                        | 1222 +++--
 RcppShark-3.1.1/RcppShark/inst/include/shark/LinAlg/BLAS/detail/matrix_proxy_classes.hpp                             |only
 RcppShark-3.1.1/RcppShark/inst/include/shark/LinAlg/BLAS/detail/storage.hpp                                          |only
 RcppShark-3.1.1/RcppShark/inst/include/shark/LinAlg/BLAS/detail/structure.hpp                                        |only
 RcppShark-3.1.1/RcppShark/inst/include/shark/LinAlg/BLAS/detail/traits.hpp                                           |  454 --
 RcppShark-3.1.1/RcppShark/inst/include/shark/LinAlg/BLAS/detail/vector_expression_classes.hpp                        |only
 RcppShark-3.1.1/RcppShark/inst/include/shark/LinAlg/BLAS/detail/vector_proxy_classes.hpp                             |only
 RcppShark-3.1.1/RcppShark/inst/include/shark/LinAlg/BLAS/expression_types.hpp                                        |  105 
 RcppShark-3.1.1/RcppShark/inst/include/shark/LinAlg/BLAS/gpu                                                         |only
 RcppShark-3.1.1/RcppShark/inst/include/shark/LinAlg/BLAS/io.hpp                                                      |   41 
 RcppShark-3.1.1/RcppShark/inst/include/shark/LinAlg/BLAS/kernels/atlas/potrf.hpp                                     |   19 
 RcppShark-3.1.1/RcppShark/inst/include/shark/LinAlg/BLAS/kernels/cblas/cblas_inc.hpp                                 |   26 
 RcppShark-3.1.1/RcppShark/inst/include/shark/LinAlg/BLAS/kernels/cblas/dense_gemm.hpp                                |only
 RcppShark-3.1.1/RcppShark/inst/include/shark/LinAlg/BLAS/kernels/cblas/gemv.hpp                                      |   40 
 RcppShark-3.1.1/RcppShark/inst/include/shark/LinAlg/BLAS/kernels/cblas/syrk.hpp                                      |only
 RcppShark-3.1.1/RcppShark/inst/include/shark/LinAlg/BLAS/kernels/cblas/tpmv.hpp                                      |   35 
 RcppShark-3.1.1/RcppShark/inst/include/shark/LinAlg/BLAS/kernels/cblas/trmm.hpp                                      |   29 
 RcppShark-3.1.1/RcppShark/inst/include/shark/LinAlg/BLAS/kernels/cblas/trmv.hpp                                      |   33 
 RcppShark-3.1.1/RcppShark/inst/include/shark/LinAlg/BLAS/kernels/cblas/trsm.hpp                                      |   66 
 RcppShark-3.1.1/RcppShark/inst/include/shark/LinAlg/BLAS/kernels/cblas/trsv.hpp                                      |   63 
 RcppShark-3.1.1/RcppShark/inst/include/shark/LinAlg/BLAS/kernels/conv2d.hpp                                          |only
 RcppShark-3.1.1/RcppShark/inst/include/shark/LinAlg/BLAS/kernels/default/boost_align                                 |only
 RcppShark-3.1.1/RcppShark/inst/include/shark/LinAlg/BLAS/kernels/default/conv2d.hpp                                  |only
 RcppShark-3.1.1/RcppShark/inst/include/shark/LinAlg/BLAS/kernels/default/dense_gemm.hpp                              |only
 RcppShark-3.1.1/RcppShark/inst/include/shark/LinAlg/BLAS/kernels/default/dot.hpp                                     |   69 
 RcppShark-3.1.1/RcppShark/inst/include/shark/LinAlg/BLAS/kernels/default/gemm.hpp                                    |  348 -
 RcppShark-3.1.1/RcppShark/inst/include/shark/LinAlg/BLAS/kernels/default/gemv.hpp                                    |   70 
 RcppShark-3.1.1/RcppShark/inst/include/shark/LinAlg/BLAS/kernels/default/getrf.hpp                                   |only
 RcppShark-3.1.1/RcppShark/inst/include/shark/LinAlg/BLAS/kernels/default/matrix_assign.hpp                           |only
 RcppShark-3.1.1/RcppShark/inst/include/shark/LinAlg/BLAS/kernels/default/matrix_fold.hpp                             |only
 RcppShark-3.1.1/RcppShark/inst/include/shark/LinAlg/BLAS/kernels/default/mgemm.hpp                                   |only
 RcppShark-3.1.1/RcppShark/inst/include/shark/LinAlg/BLAS/kernels/default/potrf.hpp                                   |  101 
 RcppShark-3.1.1/RcppShark/inst/include/shark/LinAlg/BLAS/kernels/default/pstrf.hpp                                   |only
 RcppShark-3.1.1/RcppShark/inst/include/shark/LinAlg/BLAS/kernels/default/simd.hpp                                    |only
 RcppShark-3.1.1/RcppShark/inst/include/shark/LinAlg/BLAS/kernels/default/simple_proxies.hpp                          |only
 RcppShark-3.1.1/RcppShark/inst/include/shark/LinAlg/BLAS/kernels/default/sum_rows.hpp                                |only
 RcppShark-3.1.1/RcppShark/inst/include/shark/LinAlg/BLAS/kernels/default/syev.hpp                                    |   26 
 RcppShark-3.1.1/RcppShark/inst/include/shark/LinAlg/BLAS/kernels/default/syrk.hpp                                    |only
 RcppShark-3.1.1/RcppShark/inst/include/shark/LinAlg/BLAS/kernels/default/tpmv.hpp                                    |   62 
 RcppShark-3.1.1/RcppShark/inst/include/shark/LinAlg/BLAS/kernels/default/trmm.hpp                                    |  177 
 RcppShark-3.1.1/RcppShark/inst/include/shark/LinAlg/BLAS/kernels/default/trmv.hpp                                    |  133 
 RcppShark-3.1.1/RcppShark/inst/include/shark/LinAlg/BLAS/kernels/default/trsm.hpp                                    |  341 +
 RcppShark-3.1.1/RcppShark/inst/include/shark/LinAlg/BLAS/kernels/default/trsv.hpp                                    |  174 
 RcppShark-3.1.1/RcppShark/inst/include/shark/LinAlg/BLAS/kernels/default/vector_assign.hpp                           |only
 RcppShark-3.1.1/RcppShark/inst/include/shark/LinAlg/BLAS/kernels/default/vector_fold.hpp                             |only
 RcppShark-3.1.1/RcppShark/inst/include/shark/LinAlg/BLAS/kernels/default/vector_max.hpp                              |only
 RcppShark-3.1.1/RcppShark/inst/include/shark/LinAlg/BLAS/kernels/dot.hpp                                             |   35 
 RcppShark-3.1.1/RcppShark/inst/include/shark/LinAlg/BLAS/kernels/gemm.hpp                                            |   98 
 RcppShark-3.1.1/RcppShark/inst/include/shark/LinAlg/BLAS/kernels/gemv.hpp                                            |   34 
 RcppShark-3.1.1/RcppShark/inst/include/shark/LinAlg/BLAS/kernels/getrf.hpp                                           |only
 RcppShark-3.1.1/RcppShark/inst/include/shark/LinAlg/BLAS/kernels/gpu                                                 |only
 RcppShark-3.1.1/RcppShark/inst/include/shark/LinAlg/BLAS/kernels/lapack/fortran.hpp                                  |    5 
 RcppShark-3.1.1/RcppShark/inst/include/shark/LinAlg/BLAS/kernels/lapack/syev.hpp                                     |   45 
 RcppShark-3.1.1/RcppShark/inst/include/shark/LinAlg/BLAS/kernels/matrix_assign.hpp                                   |  731 ---
 RcppShark-3.1.1/RcppShark/inst/include/shark/LinAlg/BLAS/kernels/matrix_fold.hpp                                     |only
 RcppShark-3.1.1/RcppShark/inst/include/shark/LinAlg/BLAS/kernels/potrf.hpp                                           |   26 
 RcppShark-3.1.1/RcppShark/inst/include/shark/LinAlg/BLAS/kernels/pstrf.hpp                                           |only
 RcppShark-3.1.1/RcppShark/inst/include/shark/LinAlg/BLAS/kernels/sum_rows.hpp                                        |only
 RcppShark-3.1.1/RcppShark/inst/include/shark/LinAlg/BLAS/kernels/syev.hpp                                            |   16 
 RcppShark-3.1.1/RcppShark/inst/include/shark/LinAlg/BLAS/kernels/syrk.hpp                                            |only
 RcppShark-3.1.1/RcppShark/inst/include/shark/LinAlg/BLAS/kernels/tpmv.hpp                                            |   23 
 RcppShark-3.1.1/RcppShark/inst/include/shark/LinAlg/BLAS/kernels/trmm.hpp                                            |   27 
 RcppShark-3.1.1/RcppShark/inst/include/shark/LinAlg/BLAS/kernels/trmv.hpp                                            |   27 
 RcppShark-3.1.1/RcppShark/inst/include/shark/LinAlg/BLAS/kernels/trsm.hpp                                            |   31 
 RcppShark-3.1.1/RcppShark/inst/include/shark/LinAlg/BLAS/kernels/trsv.hpp                                            |   27 
 RcppShark-3.1.1/RcppShark/inst/include/shark/LinAlg/BLAS/kernels/vector_assign.hpp                                   |  394 -
 RcppShark-3.1.1/RcppShark/inst/include/shark/LinAlg/BLAS/kernels/vector_fold.hpp                                     |only
 RcppShark-3.1.1/RcppShark/inst/include/shark/LinAlg/BLAS/kernels/vector_max.hpp                                      |only
 RcppShark-3.1.1/RcppShark/inst/include/shark/LinAlg/BLAS/matrix.hpp                                                  |  147 
 RcppShark-3.1.1/RcppShark/inst/include/shark/LinAlg/BLAS/matrix_expression.hpp                                       |  912 +---
 RcppShark-3.1.1/RcppShark/inst/include/shark/LinAlg/BLAS/matrix_proxy.hpp                                            | 1622 -------
 RcppShark-3.1.1/RcppShark/inst/include/shark/LinAlg/BLAS/matrix_sparse.hpp                                           |  205 -
 RcppShark-3.1.1/RcppShark/inst/include/shark/LinAlg/BLAS/permutation.hpp                                             |   86 
 RcppShark-3.1.1/RcppShark/inst/include/shark/LinAlg/BLAS/remora.hpp                                                  |only
 RcppShark-3.1.1/RcppShark/inst/include/shark/LinAlg/BLAS/solve.hpp                                                   |only
 RcppShark-3.1.1/RcppShark/inst/include/shark/LinAlg/BLAS/triangular_matrix.hpp                                       |  231 -
 RcppShark-3.1.1/RcppShark/inst/include/shark/LinAlg/BLAS/vector.hpp                                                  |  386 -
 RcppShark-3.1.1/RcppShark/inst/include/shark/LinAlg/BLAS/vector_expression.hpp                                       |  891 +---
 RcppShark-3.1.1/RcppShark/inst/include/shark/LinAlg/BLAS/vector_proxy.hpp                                            |  673 ---
 RcppShark-3.1.1/RcppShark/inst/include/shark/LinAlg/BLAS/vector_sparse.hpp                                           |  124 
 RcppShark-3.1.1/RcppShark/inst/include/shark/LinAlg/Base.h                                                           |   34 
 RcppShark-3.1.1/RcppShark/inst/include/shark/LinAlg/BlockMatrix2x2.h                                                 |    8 
 RcppShark-3.1.1/RcppShark/inst/include/shark/LinAlg/CachedMatrix.h                                                   |    4 
 RcppShark-3.1.1/RcppShark/inst/include/shark/LinAlg/DifferenceKernelMatrix.h                                         |only
 RcppShark-3.1.1/RcppShark/inst/include/shark/LinAlg/ExampleModifiedKernelMatrix.h                                    |    6 
 RcppShark-3.1.1/RcppShark/inst/include/shark/LinAlg/GaussianKernelMatrix.h                                           |    6 
 RcppShark-3.1.1/RcppShark/inst/include/shark/LinAlg/Impl/Initialize.h                                                |   67 
 RcppShark-3.1.1/RcppShark/inst/include/shark/LinAlg/Initialize.h                                                     |   23 
 RcppShark-3.1.1/RcppShark/inst/include/shark/LinAlg/KernelMatrix.h                                                   |  126 
 RcppShark-3.1.1/RcppShark/inst/include/shark/LinAlg/LRUCache.h                                                       |    6 
 RcppShark-3.1.1/RcppShark/inst/include/shark/LinAlg/Metrics.h                                                        |  118 
 RcppShark-3.1.1/RcppShark/inst/include/shark/LinAlg/ModifiedKernelMatrix.h                                           |    6 
 RcppShark-3.1.1/RcppShark/inst/include/shark/LinAlg/PartlyPrecomputedMatrix.h                                        |    4 
 RcppShark-3.1.1/RcppShark/inst/include/shark/LinAlg/PrecomputedMatrix.h                                              |    8 
 RcppShark-3.1.1/RcppShark/inst/include/shark/LinAlg/RegularizedKernelMatrix.h                                        |    6 
 RcppShark-3.1.1/RcppShark/inst/include/shark/LinAlg/Tools.h                                                          |   95 
 RcppShark-3.1.1/RcppShark/inst/include/shark/LinAlg/eigenvalues.h                                                    |   10 
 RcppShark-3.1.1/RcppShark/inst/include/shark/LinAlg/rotations.h                                                      |   30 
 RcppShark-3.1.1/RcppShark/inst/include/shark/Models/AbstractModel.h                                                  |    5 
 RcppShark-3.1.1/RcppShark/inst/include/shark/Models/Autoencoder.h                                                    |    5 
 RcppShark-3.1.1/RcppShark/inst/include/shark/Models/CMAC.h                                                           |    7 
 RcppShark-3.1.1/RcppShark/inst/include/shark/Models/Clustering/AbstractClustering.h                                  |    7 
 RcppShark-3.1.1/RcppShark/inst/include/shark/Models/Clustering/Centroids.h                                           |    4 
 RcppShark-3.1.1/RcppShark/inst/include/shark/Models/Clustering/ClusteringModel.h                                     |    4 
 RcppShark-3.1.1/RcppShark/inst/include/shark/Models/Clustering/HardClusteringModel.h                                 |    4 
 RcppShark-3.1.1/RcppShark/inst/include/shark/Models/Clustering/HierarchicalClustering.h                              |    5 
 RcppShark-3.1.1/RcppShark/inst/include/shark/Models/Clustering/SoftClusteringModel.h                                 |    4 
 RcppShark-3.1.1/RcppShark/inst/include/shark/Models/ConcatenatedModel.h                                              |    5 
 RcppShark-3.1.1/RcppShark/inst/include/shark/Models/Converter.h                                                      |    5 
 RcppShark-3.1.1/RcppShark/inst/include/shark/Models/ConvexCombination.h                                              |    7 
 RcppShark-3.1.1/RcppShark/inst/include/shark/Models/FFNet.h                                                          |   19 
 RcppShark-3.1.1/RcppShark/inst/include/shark/Models/GaussianNoiseModel.h                                             |    5 
 RcppShark-3.1.1/RcppShark/inst/include/shark/Models/ImpulseNoiseModel.h                                              |    5 
 RcppShark-3.1.1/RcppShark/inst/include/shark/Models/Kernels/AbstractKernelFunction.h                                 |    9 
 RcppShark-3.1.1/RcppShark/inst/include/shark/Models/Kernels/AbstractMetric.h                                         |    5 
 RcppShark-3.1.1/RcppShark/inst/include/shark/Models/Kernels/ArdKernel.h                                              |    6 
 RcppShark-3.1.1/RcppShark/inst/include/shark/Models/Kernels/CSvmDerivative.h                                         |   32 
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 RcppShark-3.1.1/RcppShark/inst/include/shark/Models/Kernels/GaussianRbfKernel.h                                      |    5 
 RcppShark-3.1.1/RcppShark/inst/include/shark/Models/Kernels/Impl/MklKernelBase.h                                     |    6 
 RcppShark-3.1.1/RcppShark/inst/include/shark/Models/Kernels/KernelExpansion.h                                        |   10 
 RcppShark-3.1.1/RcppShark/inst/include/shark/Models/Kernels/KernelHelpers.h                                          |   14 
 RcppShark-3.1.1/RcppShark/inst/include/shark/Models/Kernels/LinearKernel.h                                           |    5 
 RcppShark-3.1.1/RcppShark/inst/include/shark/Models/Kernels/MissingFeaturesKernelExpansion.h                         |    5 
 RcppShark-3.1.1/RcppShark/inst/include/shark/Models/Kernels/MklKernel.h                                              |    5 
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 RcppShark-3.1.1/RcppShark/inst/include/shark/Models/Kernels/PolynomialKernel.h                                       |    5 
 RcppShark-3.1.1/RcppShark/inst/include/shark/Models/Kernels/ProductKernel.h                                          |    4 
 RcppShark-3.1.1/RcppShark/inst/include/shark/Models/Kernels/ScaledKernel.h                                           |    7 
 RcppShark-3.1.1/RcppShark/inst/include/shark/Models/Kernels/SubrangeKernel.h                                         |    5 
 RcppShark-3.1.1/RcppShark/inst/include/shark/Models/Kernels/WeightedSumKernel.h                                      |    5 
 RcppShark-3.1.1/RcppShark/inst/include/shark/Models/LinearClassifier.h                                               |    4 
 RcppShark-3.1.1/RcppShark/inst/include/shark/Models/LinearModel.h                                                    |   13 
 RcppShark-3.1.1/RcppShark/inst/include/shark/Models/LinearNorm.h                                                     |    5 
 RcppShark-3.1.1/RcppShark/inst/include/shark/Models/MeanModel.h                                                      |    4 
 RcppShark-3.1.1/RcppShark/inst/include/shark/Models/NBClassifier.h                                                   |    5 
 RcppShark-3.1.1/RcppShark/inst/include/shark/Models/NearestNeighborClassifier.h                                      |    5 
 RcppShark-3.1.1/RcppShark/inst/include/shark/Models/NearestNeighborRegression.h                                      |    5 
 RcppShark-3.1.1/RcppShark/inst/include/shark/Models/Neurons.h                                                        |   28 
 RcppShark-3.1.1/RcppShark/inst/include/shark/Models/Normalizer.h                                                     |    5 
 RcppShark-3.1.1/RcppShark/inst/include/shark/Models/OneVersusOneClassifier.h                                         |   11 
 RcppShark-3.1.1/RcppShark/inst/include/shark/Models/OnlineRNNet.h                                                    |  108 
 RcppShark-3.1.1/RcppShark/inst/include/shark/Models/RBFLayer.h                                                       |    5 
 RcppShark-3.1.1/RcppShark/inst/include/shark/Models/RNNet.h                                                          |    5 
 RcppShark-3.1.1/RcppShark/inst/include/shark/Models/RecurrentStructure.h                                             |    4 
 RcppShark-3.1.1/RcppShark/inst/include/shark/Models/SigmoidModel.h                                                   |    5 
 RcppShark-3.1.1/RcppShark/inst/include/shark/Models/SoftNearestNeighborClassifier.h                                  |    5 
 RcppShark-3.1.1/RcppShark/inst/include/shark/Models/Softmax.h                                                        |    5 
 RcppShark-3.1.1/RcppShark/inst/include/shark/Models/TiedAutoencoder.h                                                |    5 
 RcppShark-3.1.1/RcppShark/inst/include/shark/Models/Trees/BinaryTree.h                                               |    5 
 RcppShark-3.1.1/RcppShark/inst/include/shark/Models/Trees/CARTClassifier.h                                           |   83 
 RcppShark-3.1.1/RcppShark/inst/include/shark/Models/Trees/General.h                                                  |only
 RcppShark-3.1.1/RcppShark/inst/include/shark/Models/Trees/KDTree.h                                                   |    5 
 RcppShark-3.1.1/RcppShark/inst/include/shark/Models/Trees/KHCTree.h                                                  |    5 
 RcppShark-3.1.1/RcppShark/inst/include/shark/Models/Trees/LCTree.h                                                   |    5 
 RcppShark-3.1.1/RcppShark/inst/include/shark/Models/Trees/RFClassifier.h                                             |   36 
 RcppShark-3.1.1/RcppShark/inst/include/shark/ObjectiveFunctions/AbstractConstraintHandler.h                          |    5 
 RcppShark-3.1.1/RcppShark/inst/include/shark/ObjectiveFunctions/AbstractCost.h                                       |    4 
 RcppShark-3.1.1/RcppShark/inst/include/shark/ObjectiveFunctions/AbstractObjectiveFunction.h                          |   13 
 RcppShark-3.1.1/RcppShark/inst/include/shark/ObjectiveFunctions/Benchmarks/Ackley.h                                  |    4 
 RcppShark-3.1.1/RcppShark/inst/include/shark/ObjectiveFunctions/Benchmarks/Benchmarks.h                              |    4 
 RcppShark-3.1.1/RcppShark/inst/include/shark/ObjectiveFunctions/Benchmarks/CIGTAB1.h                                 |    4 
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 RcppShark-3.1.1/RcppShark/inst/include/shark/ObjectiveFunctions/Benchmarks/CigarDiscus.h                             |    4 
 RcppShark-3.1.1/RcppShark/inst/include/shark/ObjectiveFunctions/Benchmarks/ConstrainedSphere.h                       |    4 
 RcppShark-3.1.1/RcppShark/inst/include/shark/ObjectiveFunctions/Benchmarks/DTLZ1.h                                   |    4 
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 RcppShark-3.1.1/RcppShark/inst/include/shark/ObjectiveFunctions/Benchmarks/DiffPowers.h                              |    4 
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 RcppShark-3.1.1/RcppShark/inst/include/shark/ObjectiveFunctions/Benchmarks/ELLI1.h                                   |    4 
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 RcppShark-3.1.1/RcppShark/inst/include/shark/ObjectiveFunctions/Benchmarks/GruauPole.h                               |    5 
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 RcppShark-3.1.1/RcppShark/inst/include/shark/ObjectiveFunctions/Benchmarks/LZ1.h                                     |    4 
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 RcppShark-3.1.1/RcppShark/inst/include/shark/ObjectiveFunctions/BoxConstraintHandler.h                               |    5 
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 RcppShark-3.1.1/RcppShark/inst/include/shark/ObjectiveFunctions/CrossValidationError.h                               |    4 
 RcppShark-3.1.1/RcppShark/inst/include/shark/ObjectiveFunctions/ErrorFunction.h                                      |    5 
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 RcppShark-3.1.1/RcppShark/inst/include/shark/ObjectiveFunctions/KernelBasisDistance.h                                |    4 
 RcppShark-3.1.1/RcppShark/inst/include/shark/ObjectiveFunctions/KernelTargetAlignment.h                              |    5 
 RcppShark-3.1.1/RcppShark/inst/include/shark/ObjectiveFunctions/LooError.h                                           |    5 
 RcppShark-3.1.1/RcppShark/inst/include/shark/ObjectiveFunctions/LooErrorCSvm.h                                       |    4 
 RcppShark-3.1.1/RcppShark/inst/include/shark/ObjectiveFunctions/Loss/AbsoluteLoss.h                                  |    4 
 RcppShark-3.1.1/RcppShark/inst/include/shark/ObjectiveFunctions/Loss/AbstractLoss.h                                  |    4 
 RcppShark-3.1.1/RcppShark/inst/include/shark/ObjectiveFunctions/Loss/CrossEntropy.h                                  |   18 
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 RcppShark-3.1.1/RcppShark/inst/include/shark/ObjectiveFunctions/NegativeAUC.h                                        |    4 
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 RcppShark-3.1.1/RcppShark/inst/include/shark/ObjectiveFunctions/NoisyErrorFunction.h                                 |    5 
 RcppShark-3.1.1/RcppShark/inst/include/shark/ObjectiveFunctions/ROC.h                                                |    4 
 RcppShark-3.1.1/RcppShark/inst/include/shark/ObjectiveFunctions/RadiusMarginQuotient.h                               |    6 
 RcppShark-3.1.1/RcppShark/inst/include/shark/ObjectiveFunctions/Regularizer.h                                        |    7 
 RcppShark-3.1.1/RcppShark/inst/include/shark/ObjectiveFunctions/SparseAutoencoderError.h                             |    5 
 RcppShark-3.1.1/RcppShark/inst/include/shark/ObjectiveFunctions/SvmLogisticInterpretation.h                          |    6 
 RcppShark-3.1.1/RcppShark/inst/include/shark/Rng/AbstractDistribution.h                                              |    4 
 RcppShark-3.1.1/RcppShark/inst/include/shark/Rng/Bernoulli.h                                                         |    5 
 RcppShark-3.1.1/RcppShark/inst/include/shark/Rng/Binomial.h                                                          |    7 
 RcppShark-3.1.1/RcppShark/inst/include/shark/Rng/Cauchy.h                                                            |    5 
 RcppShark-3.1.1/RcppShark/inst/include/shark/Rng/DiffGeometric.h                                                     |    5 
 RcppShark-3.1.1/RcppShark/inst/include/shark/Rng/Dirichlet.h                                                         |    5 
 RcppShark-3.1.1/RcppShark/inst/include/shark/Rng/DiscreteUniform.h                                                   |    5 
 RcppShark-3.1.1/RcppShark/inst/include/shark/Rng/Entropy.h                                                           |    5 
 RcppShark-3.1.1/RcppShark/inst/include/shark/Rng/Erlang.h                                                            |    5 
 RcppShark-3.1.1/RcppShark/inst/include/shark/Rng/Gamma.h                                                             |    5 
 RcppShark-3.1.1/RcppShark/inst/include/shark/Rng/Geometric.h                                                         |    5 
 RcppShark-3.1.1/RcppShark/inst/include/shark/Rng/GlobalRng.h                                                         |    5 
 RcppShark-3.1.1/RcppShark/inst/include/shark/Rng/HyperGeometric.h                                                    |    5 
 RcppShark-3.1.1/RcppShark/inst/include/shark/Rng/KullbackLeiberDivergence.h                                          |    5 
 RcppShark-3.1.1/RcppShark/inst/include/shark/Rng/LogNormal.h                                                         |    5 
 RcppShark-3.1.1/RcppShark/inst/include/shark/Rng/NegExponential.h                                                    |    5 
 RcppShark-3.1.1/RcppShark/inst/include/shark/Rng/Normal.h                                                            |    5 
 RcppShark-3.1.1/RcppShark/inst/include/shark/Rng/Poisson.h                                                           |    5 
 RcppShark-3.1.1/RcppShark/inst/include/shark/Rng/Rng.h                                                               |    6 
 RcppShark-3.1.1/RcppShark/inst/include/shark/Rng/TruncatedExponential.h                                              |    5 
 RcppShark-3.1.1/RcppShark/inst/include/shark/Rng/Uniform.h                                                           |    5 
 RcppShark-3.1.1/RcppShark/inst/include/shark/Rng/Weibull.h                                                           |    5 
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 RcppShark-3.1.1/RcppShark/inst/include/shark/Statistics/Statistics.h                                                 |    5 
 RcppShark-3.1.1/RcppShark/inst/include/shark/Unsupervised/RBM/BinaryRBM.h                                            |    4 
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 RcppShark-3.1.1/RcppShark/inst/include/shark/Unsupervised/RBM/Problems/Shifter.h                                     |    4 
 RcppShark-3.1.1/RcppShark/inst/include/shark/Unsupervised/RBM/RBM.h                                                  |    5 
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 RcppShark-3.1.1/RcppShark/inst/include/shark/Unsupervised/RBM/Sampling/MarkovChain.h                                 |    4 
 RcppShark-3.1.1/RcppShark/inst/include/shark/Unsupervised/RBM/Sampling/TemperedMarkovChain.h                         |    4 
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 RcppShark-3.1.1/RcppShark/inst/include/shark/Unsupervised/RBM/Tags.h                                                 |    5 
 RcppShark-3.1.1/RcppShark/inst/include/shark/Unsupervised/RBM/TruncExpBinaryRBM.h                                    |    4 
 RcppShark-3.1.1/RcppShark/inst/include/shark/Unsupervised/RBM/analytics.h                                            |    4 
 RcppShark-3.1.1/RcppShark/inst/skeleton/Makevars                                                                     |    3 
 RcppShark-3.1.1/RcppShark/inst/skeleton/Makevars.win                                                                 |    5 
 RcppShark-3.1.1/RcppShark/man/DeepNetworkPredict.Rd                                                                  |    1 
 RcppShark-3.1.1/RcppShark/man/DeepNetworkTrain.Rd                                                                    |    1 
 RcppShark-3.1.1/RcppShark/man/RcppShark.package.skeleton.Rd                                                          |   13 
 RcppShark-3.1.1/RcppShark/man/SharkBSGDPredict.Rd                                                                    |    1 
 RcppShark-3.1.1/RcppShark/man/SharkBSGDTrain.Rd                                                                      |    1 
 RcppShark-3.1.1/RcppShark/src/Makevars                                                                               |  175 
 RcppShark-3.1.1/RcppShark/src/RcppExports.cpp                                                                        |   34 
 RcppShark-3.1.1/RcppShark/src/init.c                                                                                 |only
 RcppShark-3.1.1/RcppShark/src/shark/Algorithms/AbstractMultiObjectiveOptimizer.h                                     |    5 
 RcppShark-3.1.1/RcppShark/src/shark/Algorithms/AbstractOptimizer.h                                                   |    4 
 RcppShark-3.1.1/RcppShark/src/shark/Algorithms/AbstractSingleObjectiveOptimizer.h                                    |    4 
 RcppShark-3.1.1/RcppShark/src/shark/Algorithms/DirectSearch/CMA.h                                                    |  115 
 RcppShark-3.1.1/RcppShark/src/shark/Algorithms/DirectSearch/CMA/CMAIndividual.h                                      |    4 
 RcppShark-3.1.1/RcppShark/src/shark/Algorithms/DirectSearch/CMA/Chromosome.h                                         |    5 
 RcppShark-3.1.1/RcppShark/src/shark/Algorithms/DirectSearch/CMSA.h                                                   |   17 
 RcppShark-3.1.1/RcppShark/src/shark/Algorithms/DirectSearch/CrossEntropyMethod.h                                     |    5 
 RcppShark-3.1.1/RcppShark/src/shark/Algorithms/DirectSearch/ElitistCMA.h                                             |    4 
 RcppShark-3.1.1/RcppShark/src/shark/Algorithms/DirectSearch/Grid.h                                                   |    4 
 RcppShark-3.1.1/RcppShark/src/shark/Algorithms/DirectSearch/GridSearch.h                                             |    4 
 RcppShark-3.1.1/RcppShark/src/shark/Algorithms/DirectSearch/Individual.h                                             |    5 
 RcppShark-3.1.1/RcppShark/src/shark/Algorithms/DirectSearch/LMCMA.h                                                  |    4 
 RcppShark-3.1.1/RcppShark/src/shark/Algorithms/DirectSearch/MOCMA.h                                                  |    4 
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 RcppShark-3.1.1/RcppShark/src/shark/Algorithms/DirectSearch/SimplexDownhill.h                                        |    4 
 RcppShark-3.1.1/RcppShark/src/shark/Algorithms/DirectSearch/SteadyStateMOCMA.h                                       |    4 
 RcppShark-3.1.1/RcppShark/src/shark/Algorithms/DirectSearch/VDCMA.h                                                  |    4 
 RcppShark-3.1.1/RcppShark/src/shark/Algorithms/GradientDescent/AbstractLineSearchOptimizer.h                         |    4 
 RcppShark-3.1.1/RcppShark/src/shark/Algorithms/GradientDescent/BFGS.h                                                |    4 
 RcppShark-3.1.1/RcppShark/src/shark/Algorithms/GradientDescent/CG.h                                                  |    4 
 RcppShark-3.1.1/RcppShark/src/shark/Algorithms/GradientDescent/Impl/dlinmin.inl                                      |    4 
 RcppShark-3.1.1/RcppShark/src/shark/Algorithms/GradientDescent/Impl/wolfecubic.inl                                   |    4 
 RcppShark-3.1.1/RcppShark/src/shark/Algorithms/GradientDescent/LBFGS.h                                               |    4 
 RcppShark-3.1.1/RcppShark/src/shark/Algorithms/GradientDescent/LineSearch.h                                          |    4 
 RcppShark-3.1.1/RcppShark/src/shark/Algorithms/GradientDescent/Rprop.h                                               |    4 
 RcppShark-3.1.1/RcppShark/src/shark/Algorithms/GradientDescent/SteepestDescent.h                                     |    4 
 RcppShark-3.1.1/RcppShark/src/shark/Algorithms/GradientDescent/TrustRegionNewton.h                                   |    4 
 RcppShark-3.1.1/RcppShark/src/shark/Algorithms/JaakkolaHeuristic.h                                                   |    5 
 RcppShark-3.1.1/RcppShark/src/shark/Algorithms/KMeans.h                                                              |   79 
 RcppShark-3.1.1/RcppShark/src/shark/Algorithms/NearestNeighbors/AbstractNearestNeighbors.h                           |    4 
 RcppShark-3.1.1/RcppShark/src/shark/Algorithms/NearestNeighbors/SimpleNearestNeighbors.h                             |    4 
 RcppShark-3.1.1/RcppShark/src/shark/Algorithms/NearestNeighbors/TreeNearestNeighbors.h                               |    5 
 RcppShark-3.1.1/RcppShark/src/shark/Algorithms/Pegasos.h                                                             |    4 
 RcppShark-3.1.1/RcppShark/src/shark/Algorithms/QP/BoxConstrainedProblems.h                                           |  134 
 RcppShark-3.1.1/RcppShark/src/shark/Algorithms/QP/Impl/AnalyticProblems.h                                            |    5 
 RcppShark-3.1.1/RcppShark/src/shark/Algorithms/QP/QpBoxLinear.h                                                      |  729 +--
 RcppShark-3.1.1/RcppShark/src/shark/Algorithms/QP/QpMcBoxDecomp.h                                                    |   48 
 RcppShark-3.1.1/RcppShark/src/shark/Algorithms/QP/QpMcLinear.h                                                       |  361 -
 RcppShark-3.1.1/RcppShark/src/shark/Algorithms/QP/QpMcSimplexDecomp.h                                                |   35 
 RcppShark-3.1.1/RcppShark/src/shark/Algorithms/QP/QpSolver.h                                                         |   30 
 RcppShark-3.1.1/RcppShark/src/shark/Algorithms/QP/QpSparseArray.h                                                    |   15 
 RcppShark-3.1.1/RcppShark/src/shark/Algorithms/QP/QuadraticProgram.h                                                 |    4 
 RcppShark-3.1.1/RcppShark/src/shark/Algorithms/QP/SvmProblems.h                                                      |  133 
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 RcppShark-3.1.1/RcppShark/src/shark/Algorithms/StoppingCriteria/MaxIterations.h                                      |    6 
 RcppShark-3.1.1/RcppShark/src/shark/Algorithms/StoppingCriteria/TrainingError.h                                      |    5 
 RcppShark-3.1.1/RcppShark/src/shark/Algorithms/StoppingCriteria/TrainingProgress.h                                   |    5 
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 RcppShark-3.1.1/RcppShark/src/shark/Algorithms/Trainers/AbstractSvmTrainer.h                                         |   28 
 RcppShark-3.1.1/RcppShark/src/shark/Algorithms/Trainers/AbstractTrainer.h                                            |    4 
 RcppShark-3.1.1/RcppShark/src/shark/Algorithms/Trainers/AbstractWeightedTrainer.h                                    |    4 
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 RcppShark-3.1.1/RcppShark/src/shark/Algorithms/Trainers/Budgeted/KernelBudgetedSGDTrainer.h                          |    4 
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 RcppShark-3.1.1/RcppShark/src/shark/Algorithms/Trainers/CARTTrainer.h                                                |   42 
 RcppShark-3.1.1/RcppShark/src/shark/Algorithms/Trainers/CARTcommon.h                                                 |only
 RcppShark-3.1.1/RcppShark/src/shark/Algorithms/Trainers/CSvmTrainer.h                                                |  705 +++
 RcppShark-3.1.1/RcppShark/src/shark/Algorithms/Trainers/Distribution/DistTrainerContainer.h                          |    4 
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 RcppShark-3.1.1/RcppShark/src/shark/Algorithms/Trainers/EpsilonSvmTrainer.h                                          |    4 
 RcppShark-3.1.1/RcppShark/src/shark/Algorithms/Trainers/FisherLDA.h                                                  |    4 
 RcppShark-3.1.1/RcppShark/src/shark/Algorithms/Trainers/KernelMeanClassifier.h                                       |    4 
 RcppShark-3.1.1/RcppShark/src/shark/Algorithms/Trainers/KernelSGDTrainer.h                                           |    4 
 RcppShark-3.1.1/RcppShark/src/shark/Algorithms/Trainers/LDA.h                                                        |    4 
 RcppShark-3.1.1/RcppShark/src/shark/Algorithms/Trainers/LassoRegression.h                                            |    6 
 RcppShark-3.1.1/RcppShark/src/shark/Algorithms/Trainers/LinearRegression.h                                           |    4 
 RcppShark-3.1.1/RcppShark/src/shark/Algorithms/Trainers/LinearSAGTrainer.h                                           |  119 
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 RcppShark-3.1.1/RcppShark/src/shark/Algorithms/Trainers/NBClassifierTrainer.h                                        |    5 
 RcppShark-3.1.1/RcppShark/src/shark/Algorithms/Trainers/NormalizeComponentsUnitInterval.h                            |    4 
 RcppShark-3.1.1/RcppShark/src/shark/Algorithms/Trainers/NormalizeComponentsUnitVariance.h                            |    4 
 RcppShark-3.1.1/RcppShark/src/shark/Algorithms/Trainers/NormalizeComponentsWhitening.h                               |    7 
 RcppShark-3.1.1/RcppShark/src/shark/Algorithms/Trainers/NormalizeComponentsZCA.h                                     |    6 
 RcppShark-3.1.1/RcppShark/src/shark/Algorithms/Trainers/NormalizeKernelUnitVariance.h                                |    4 
 RcppShark-3.1.1/RcppShark/src/shark/Algorithms/Trainers/OneClassSvmTrainer.h                                         |    8 
 RcppShark-3.1.1/RcppShark/src/shark/Algorithms/Trainers/OptimizationTrainer.h                                        |    4 
 RcppShark-3.1.1/RcppShark/src/shark/Algorithms/Trainers/PCA.h                                                        |    4 
 RcppShark-3.1.1/RcppShark/src/shark/Algorithms/Trainers/Perceptron.h                                                 |    4 
 RcppShark-3.1.1/RcppShark/src/shark/Algorithms/Trainers/RFTrainer.h                                                  |  114 
 RcppShark-3.1.1/RcppShark/src/shark/Algorithms/Trainers/RankingSvmTrainer.h                                          |only
 RcppShark-3.1.1/RcppShark/src/shark/Algorithms/Trainers/RegularizationNetworkTrainer.h                               |   10 
 RcppShark-3.1.1/RcppShark/src/shark/Algorithms/Trainers/SigmoidFit.h                                                 |    4 
 RcppShark-3.1.1/RcppShark/src/shark/Core/DLLSupport.h                                                                |    5 
 RcppShark-3.1.1/RcppShark/src/shark/Core/Exception.h                                                                 |    4 
 RcppShark-3.1.1/RcppShark/src/shark/Core/Flags.h                                                                     |    5 
 RcppShark-3.1.1/RcppShark/src/shark/Core/INameable.h                                                                 |    4 
 RcppShark-3.1.1/RcppShark/src/shark/Core/IParameterizable.h                                                          |    4 
 RcppShark-3.1.1/RcppShark/src/shark/Core/Math.h                                                                      |    5 
 RcppShark-3.1.1/RcppShark/src/shark/Core/OpenMP.h                                                                    |    5 
 RcppShark-3.1.1/RcppShark/src/shark/Core/ResultSets.h                                                                |    4 
 RcppShark-3.1.1/RcppShark/src/shark/Core/Shark.h                                                                     |   25 
 RcppShark-3.1.1/RcppShark/src/shark/Core/State.h                                                                     |    5 
 RcppShark-3.1.1/RcppShark/src/shark/Core/Timer.h                                                                     |    4 
 RcppShark-3.1.1/RcppShark/src/shark/Core/Traits/ProxyReferenceTraits.h                                               |    6 
 RcppShark-3.1.1/RcppShark/src/shark/Core/utility/CanBeCalled.h                                                       |    6 
 RcppShark-3.1.1/RcppShark/src/shark/Core/utility/Impl/boost_iterator_facade_fixed.hpp                                |    1 
 RcppShark-3.1.1/RcppShark/src/shark/Core/utility/Iterators.h                                                         |    5 
 RcppShark-3.1.1/RcppShark/src/shark/Core/utility/KeyValuePair.h                                                      |    5 
 RcppShark-3.1.1/RcppShark/src/shark/Core/utility/Range.h                                                             |    5 
 RcppShark-3.1.1/RcppShark/src/shark/Core/utility/ScopedHandle.h                                                      |    5 
 RcppShark-3.1.1/RcppShark/src/shark/Core/utility/ZipPair.h                                                           |    7 
 RcppShark-3.1.1/RcppShark/src/shark/Core/utility/functional.h                                                        |    5 
 RcppShark-3.1.1/RcppShark/src/shark/Data/BatchInterface.h                                                            |   57 
 RcppShark-3.1.1/RcppShark/src/shark/Data/BatchInterfaceAdaptStruct.h                                                 |    5 
 RcppShark-3.1.1/RcppShark/src/shark/Data/CVDatasetTools.h                                                            |    4 
 RcppShark-3.1.1/RcppShark/src/shark/Data/Csv.h                                                                       |    5 
 RcppShark-3.1.1/RcppShark/src/shark/Data/DataDistribution.h                                                          |    6 
 RcppShark-3.1.1/RcppShark/src/shark/Data/DataView.h                                                                  |   18 
 RcppShark-3.1.1/RcppShark/src/shark/Data/Dataset.h                                                                   |   17 
 RcppShark-3.1.1/RcppShark/src/shark/Data/Download.h                                                                  |only
 RcppShark-3.1.1/RcppShark/src/shark/Data/ExportKernelMatrix.h                                                        |    4 
 RcppShark-3.1.1/RcppShark/src/shark/Data/HDF5.h                                                                      |    5 
 RcppShark-3.1.1/RcppShark/src/shark/Data/Impl/BoostFusion151DefineStructInl.hpp                                      |    5 
 RcppShark-3.1.1/RcppShark/src/shark/Data/Impl/BoostFusionCopy.hpp                                                    |    5 
 RcppShark-3.1.1/RcppShark/src/shark/Data/Impl/CVDatasetTools.inl                                                     |    4 
 RcppShark-3.1.1/RcppShark/src/shark/Data/Impl/Dataset.inl                                                            |   11 
 RcppShark-3.1.1/RcppShark/src/shark/Data/Impl/Downloader.hpp                                                         |only
 RcppShark-3.1.1/RcppShark/src/shark/Data/Impl/Statistics.inl                                                         |   16 
 RcppShark-3.1.1/RcppShark/src/shark/Data/LabelOrder.h                                                                |    4 
 RcppShark-3.1.1/RcppShark/src/shark/Data/Libsvm.h                                                                    |    4 
 RcppShark-3.1.1/RcppShark/src/shark/Data/Pgm.h                                                                       |  116 
 RcppShark-3.1.1/RcppShark/src/shark/Data/SparseData.h                                                                |    5 
 RcppShark-3.1.1/RcppShark/src/shark/Data/Statistics.h                                                                |   16 
 RcppShark-3.1.1/RcppShark/src/shark/Data/WeightedDataset.h                                                           |    5 
 RcppShark-3.1.1/RcppShark/src/shark/LinAlg/BLAS/assignment.hpp                                                       |  428 +-
 RcppShark-3.1.1/RcppShark/src/shark/LinAlg/BLAS/decompositions.hpp                                                   |only
 RcppShark-3.1.1/RcppShark/src/shark/LinAlg/BLAS/detail/check.hpp                                                     |only
 RcppShark-3.1.1/RcppShark/src/shark/LinAlg/BLAS/detail/evaluation_tags.hpp                                           |only
 RcppShark-3.1.1/RcppShark/src/shark/LinAlg/BLAS/detail/expression_optimizers.hpp                                     |only
 RcppShark-3.1.1/RcppShark/src/shark/LinAlg/BLAS/detail/functional.hpp                                                |  803 ---
 RcppShark-3.1.1/RcppShark/src/shark/LinAlg/BLAS/detail/iterator.hpp                                                  |   87 
 RcppShark-3.1.1/RcppShark/src/shark/LinAlg/BLAS/detail/matrix_expression_classes.hpp                                 | 1222 +++--
 RcppShark-3.1.1/RcppShark/src/shark/LinAlg/BLAS/detail/matrix_proxy_classes.hpp                                      |only
 RcppShark-3.1.1/RcppShark/src/shark/LinAlg/BLAS/detail/storage.hpp                                                   |only
 RcppShark-3.1.1/RcppShark/src/shark/LinAlg/BLAS/detail/structure.hpp                                                 |only
 RcppShark-3.1.1/RcppShark/src/shark/LinAlg/BLAS/detail/traits.hpp                                                    |  454 --
 RcppShark-3.1.1/RcppShark/src/shark/LinAlg/BLAS/detail/vector_expression_classes.hpp                                 |only
 RcppShark-3.1.1/RcppShark/src/shark/LinAlg/BLAS/detail/vector_proxy_classes.hpp                                      |only
 RcppShark-3.1.1/RcppShark/src/shark/LinAlg/BLAS/expression_types.hpp                                                 |  105 
 RcppShark-3.1.1/RcppShark/src/shark/LinAlg/BLAS/gpu                                                                  |only
 RcppShark-3.1.1/RcppShark/src/shark/LinAlg/BLAS/io.hpp                                                               |   41 
 RcppShark-3.1.1/RcppShark/src/shark/LinAlg/BLAS/kernels/atlas/potrf.hpp                                              |   19 
 RcppShark-3.1.1/RcppShark/src/shark/LinAlg/BLAS/kernels/cblas/cblas_inc.hpp                                          |   26 
 RcppShark-3.1.1/RcppShark/src/shark/LinAlg/BLAS/kernels/cblas/dense_gemm.hpp                                         |only
 RcppShark-3.1.1/RcppShark/src/shark/LinAlg/BLAS/kernels/cblas/gemv.hpp                                               |   40 
 RcppShark-3.1.1/RcppShark/src/shark/LinAlg/BLAS/kernels/cblas/syrk.hpp                                               |only
 RcppShark-3.1.1/RcppShark/src/shark/LinAlg/BLAS/kernels/cblas/tpmv.hpp                                               |   35 
 RcppShark-3.1.1/RcppShark/src/shark/LinAlg/BLAS/kernels/cblas/trmm.hpp                                               |   29 
 RcppShark-3.1.1/RcppShark/src/shark/LinAlg/BLAS/kernels/cblas/trmv.hpp                                               |   33 
 RcppShark-3.1.1/RcppShark/src/shark/LinAlg/BLAS/kernels/cblas/trsm.hpp                                               |   66 
 RcppShark-3.1.1/RcppShark/src/shark/LinAlg/BLAS/kernels/cblas/trsv.hpp                                               |   63 
 RcppShark-3.1.1/RcppShark/src/shark/LinAlg/BLAS/kernels/conv2d.hpp                                                   |only
 RcppShark-3.1.1/RcppShark/src/shark/LinAlg/BLAS/kernels/default/boost_align                                          |only
 RcppShark-3.1.1/RcppShark/src/shark/LinAlg/BLAS/kernels/default/conv2d.hpp                                           |only
 RcppShark-3.1.1/RcppShark/src/shark/LinAlg/BLAS/kernels/default/dense_gemm.hpp                                       |only
 RcppShark-3.1.1/RcppShark/src/shark/LinAlg/BLAS/kernels/default/dot.hpp                                              |   69 
 RcppShark-3.1.1/RcppShark/src/shark/LinAlg/BLAS/kernels/default/gemm.hpp                                             |  348 -
 RcppShark-3.1.1/RcppShark/src/shark/LinAlg/BLAS/kernels/default/gemv.hpp                                             |   70 
 RcppShark-3.1.1/RcppShark/src/shark/LinAlg/BLAS/kernels/default/getrf.hpp                                            |only
 RcppShark-3.1.1/RcppShark/src/shark/LinAlg/BLAS/kernels/default/matrix_assign.hpp                                    |only
 RcppShark-3.1.1/RcppShark/src/shark/LinAlg/BLAS/kernels/default/matrix_fold.hpp                                      |only
 RcppShark-3.1.1/RcppShark/src/shark/LinAlg/BLAS/kernels/default/mgemm.hpp                                            |only
 RcppShark-3.1.1/RcppShark/src/shark/LinAlg/BLAS/kernels/default/potrf.hpp                                            |  101 
 RcppShark-3.1.1/RcppShark/src/shark/LinAlg/BLAS/kernels/default/pstrf.hpp                                            |only
 RcppShark-3.1.1/RcppShark/src/shark/LinAlg/BLAS/kernels/default/simd.hpp                                             |only
 RcppShark-3.1.1/RcppShark/src/shark/LinAlg/BLAS/kernels/default/simple_proxies.hpp                                   |only
 RcppShark-3.1.1/RcppShark/src/shark/LinAlg/BLAS/kernels/default/sum_rows.hpp                                         |only
 RcppShark-3.1.1/RcppShark/src/shark/LinAlg/BLAS/kernels/default/syev.hpp                                             |   26 
 RcppShark-3.1.1/RcppShark/src/shark/LinAlg/BLAS/kernels/default/syrk.hpp                                             |only
 RcppShark-3.1.1/RcppShark/src/shark/LinAlg/BLAS/kernels/default/tpmv.hpp                                             |   62 
 RcppShark-3.1.1/RcppShark/src/shark/LinAlg/BLAS/kernels/default/trmm.hpp                                             |  177 
 RcppShark-3.1.1/RcppShark/src/shark/LinAlg/BLAS/kernels/default/trmv.hpp                                             |  133 
 RcppShark-3.1.1/RcppShark/src/shark/LinAlg/BLAS/kernels/default/trsm.hpp                                             |  341 +
 RcppShark-3.1.1/RcppShark/src/shark/LinAlg/BLAS/kernels/default/trsv.hpp                                             |  174 
 RcppShark-3.1.1/RcppShark/src/shark/LinAlg/BLAS/kernels/default/vector_assign.hpp                                    |only
 RcppShark-3.1.1/RcppShark/src/shark/LinAlg/BLAS/kernels/default/vector_fold.hpp                                      |only
 RcppShark-3.1.1/RcppShark/src/shark/LinAlg/BLAS/kernels/default/vector_max.hpp                                       |only
 RcppShark-3.1.1/RcppShark/src/shark/LinAlg/BLAS/kernels/dot.hpp                                                      |   35 
 RcppShark-3.1.1/RcppShark/src/shark/LinAlg/BLAS/kernels/gemm.hpp                                                     |   98 
 RcppShark-3.1.1/RcppShark/src/shark/LinAlg/BLAS/kernels/gemv.hpp                                                     |   34 
 RcppShark-3.1.1/RcppShark/src/shark/LinAlg/BLAS/kernels/getrf.hpp                                                    |only
 RcppShark-3.1.1/RcppShark/src/shark/LinAlg/BLAS/kernels/gpu                                                          |only
 RcppShark-3.1.1/RcppShark/src/shark/LinAlg/BLAS/kernels/lapack/fortran.hpp                                           |    5 
 RcppShark-3.1.1/RcppShark/src/shark/LinAlg/BLAS/kernels/lapack/syev.hpp                                              |   45 
 RcppShark-3.1.1/RcppShark/src/shark/LinAlg/BLAS/kernels/matrix_assign.hpp                                            |  731 ---
 RcppShark-3.1.1/RcppShark/src/shark/LinAlg/BLAS/kernels/matrix_fold.hpp                                              |only
 RcppShark-3.1.1/RcppShark/src/shark/LinAlg/BLAS/kernels/potrf.hpp                                                    |   26 
 RcppShark-3.1.1/RcppShark/src/shark/LinAlg/BLAS/kernels/pstrf.hpp                                                    |only
 RcppShark-3.1.1/RcppShark/src/shark/LinAlg/BLAS/kernels/sum_rows.hpp                                                 |only
 RcppShark-3.1.1/RcppShark/src/shark/LinAlg/BLAS/kernels/syev.hpp                                                     |   16 
 RcppShark-3.1.1/RcppShark/src/shark/LinAlg/BLAS/kernels/syrk.hpp                                                     |only
 RcppShark-3.1.1/RcppShark/src/shark/LinAlg/BLAS/kernels/tpmv.hpp                                                     |   23 
 RcppShark-3.1.1/RcppShark/src/shark/LinAlg/BLAS/kernels/trmm.hpp                                                     |   27 
 RcppShark-3.1.1/RcppShark/src/shark/LinAlg/BLAS/kernels/trmv.hpp                                                     |   27 
 RcppShark-3.1.1/RcppShark/src/shark/LinAlg/BLAS/kernels/trsm.hpp                                                     |   31 
 RcppShark-3.1.1/RcppShark/src/shark/LinAlg/BLAS/kernels/trsv.hpp                                                     |   27 
 RcppShark-3.1.1/RcppShark/src/shark/LinAlg/BLAS/kernels/vector_assign.hpp                                            |  394 -
 RcppShark-3.1.1/RcppShark/src/shark/LinAlg/BLAS/kernels/vector_fold.hpp                                              |only
 RcppShark-3.1.1/RcppShark/src/shark/LinAlg/BLAS/kernels/vector_max.hpp                                               |only
 RcppShark-3.1.1/RcppShark/src/shark/LinAlg/BLAS/matrix.hpp                                                           |  147 
 RcppShark-3.1.1/RcppShark/src/shark/LinAlg/BLAS/matrix_expression.hpp                                                |  912 +---
 RcppShark-3.1.1/RcppShark/src/shark/LinAlg/BLAS/matrix_proxy.hpp                                                     | 1622 -------
 RcppShark-3.1.1/RcppShark/src/shark/LinAlg/BLAS/matrix_sparse.hpp                                                    |  205 -
 RcppShark-3.1.1/RcppShark/src/shark/LinAlg/BLAS/permutation.hpp                                                      |   86 
 RcppShark-3.1.1/RcppShark/src/shark/LinAlg/BLAS/remora.hpp                                                           |only
 RcppShark-3.1.1/RcppShark/src/shark/LinAlg/BLAS/solve.hpp                                                            |only
 RcppShark-3.1.1/RcppShark/src/shark/LinAlg/BLAS/triangular_matrix.hpp                                                |  231 -
 RcppShark-3.1.1/RcppShark/src/shark/LinAlg/BLAS/vector.hpp                                                           |  386 -
 RcppShark-3.1.1/RcppShark/src/shark/LinAlg/BLAS/vector_expression.hpp                                                |  891 +---
 RcppShark-3.1.1/RcppShark/src/shark/LinAlg/BLAS/vector_proxy.hpp                                                     |  673 ---
 RcppShark-3.1.1/RcppShark/src/shark/LinAlg/BLAS/vector_sparse.hpp                                                    |  124 
 RcppShark-3.1.1/RcppShark/src/shark/LinAlg/Base.h                                                                    |   34 
 RcppShark-3.1.1/RcppShark/src/shark/LinAlg/BlockMatrix2x2.h                                                          |    8 
 RcppShark-3.1.1/RcppShark/src/shark/LinAlg/CachedMatrix.h                                                            |    4 
 RcppShark-3.1.1/RcppShark/src/shark/LinAlg/DifferenceKernelMatrix.h                                                  |only
 RcppShark-3.1.1/RcppShark/src/shark/LinAlg/ExampleModifiedKernelMatrix.h                                             |    6 
 RcppShark-3.1.1/RcppShark/src/shark/LinAlg/GaussianKernelMatrix.h                                                    |    6 
 RcppShark-3.1.1/RcppShark/src/shark/LinAlg/Impl/Initialize.h                                                         |   67 
 RcppShark-3.1.1/RcppShark/src/shark/LinAlg/Initialize.h                                                              |   23 
 RcppShark-3.1.1/RcppShark/src/shark/LinAlg/KernelMatrix.h                                                            |  126 
 RcppShark-3.1.1/RcppShark/src/shark/LinAlg/LRUCache.h                                                                |    6 
 RcppShark-3.1.1/RcppShark/src/shark/LinAlg/Metrics.h                                                                 |  118 
 RcppShark-3.1.1/RcppShark/src/shark/LinAlg/ModifiedKernelMatrix.h                                                    |    6 
 RcppShark-3.1.1/RcppShark/src/shark/LinAlg/PartlyPrecomputedMatrix.h                                                 |    4 
 RcppShark-3.1.1/RcppShark/src/shark/LinAlg/PrecomputedMatrix.h                                                       |    8 
 RcppShark-3.1.1/RcppShark/src/shark/LinAlg/RegularizedKernelMatrix.h                                                 |    6 
 RcppShark-3.1.1/RcppShark/src/shark/LinAlg/Tools.h                                                                   |   95 
 RcppShark-3.1.1/RcppShark/src/shark/LinAlg/eigenvalues.h                                                             |   10 
 RcppShark-3.1.1/RcppShark/src/shark/LinAlg/rotations.h                                                               |   30 
 RcppShark-3.1.1/RcppShark/src/shark/Models/AbstractModel.h                                                           |    5 
 RcppShark-3.1.1/RcppShark/src/shark/Models/Autoencoder.h                                                             |    5 
 RcppShark-3.1.1/RcppShark/src/shark/Models/CMAC.h                                                                    |    7 
 RcppShark-3.1.1/RcppShark/src/shark/Models/Clustering/AbstractClustering.h                                           |    7 
 RcppShark-3.1.1/RcppShark/src/shark/Models/Clustering/Centroids.h                                                    |    4 
 RcppShark-3.1.1/RcppShark/src/shark/Models/Clustering/ClusteringModel.h                                              |    4 
 RcppShark-3.1.1/RcppShark/src/shark/Models/Clustering/HardClusteringModel.h                                          |    4 
 RcppShark-3.1.1/RcppShark/src/shark/Models/Clustering/HierarchicalClustering.h                                       |    5 
 RcppShark-3.1.1/RcppShark/src/shark/Models/Clustering/SoftClusteringModel.h                                          |    4 
 RcppShark-3.1.1/RcppShark/src/shark/Models/ConcatenatedModel.h                                                       |    5 
 RcppShark-3.1.1/RcppShark/src/shark/Models/Converter.h                                                               |    5 
 RcppShark-3.1.1/RcppShark/src/shark/Models/ConvexCombination.h                                                       |    7 
 RcppShark-3.1.1/RcppShark/src/shark/Models/FFNet.h                                                                   |   19 
 RcppShark-3.1.1/RcppShark/src/shark/Models/GaussianNoiseModel.h                                                      |    5 
 RcppShark-3.1.1/RcppShark/src/shark/Models/ImpulseNoiseModel.h                                                       |    5 
 RcppShark-3.1.1/RcppShark/src/shark/Models/Kernels/AbstractKernelFunction.h                                          |    9 
 RcppShark-3.1.1/RcppShark/src/shark/Models/Kernels/AbstractMetric.h                                                  |    5 
 RcppShark-3.1.1/RcppShark/src/shark/Models/Kernels/ArdKernel.h                                                       |    6 
 RcppShark-3.1.1/RcppShark/src/shark/Models/Kernels/CSvmDerivative.h                                                  |   32 
 RcppShark-3.1.1/RcppShark/src/shark/Models/Kernels/DiscreteKernel.h                                                  |    5 
 RcppShark-3.1.1/RcppShark/src/shark/Models/Kernels/EvalSkipMissingFeatures.h                                         |    5 
 RcppShark-3.1.1/RcppShark/src/shark/Models/Kernels/GaussianRbfKernel.h                                               |    5 
 RcppShark-3.1.1/RcppShark/src/shark/Models/Kernels/Impl/MklKernelBase.h                                              |    6 
 RcppShark-3.1.1/RcppShark/src/shark/Models/Kernels/KernelExpansion.h                                                 |   10 
 RcppShark-3.1.1/RcppShark/src/shark/Models/Kernels/KernelHelpers.h                                                   |   14 
 RcppShark-3.1.1/RcppShark/src/shark/Models/Kernels/LinearKernel.h                                                    |    5 
 RcppShark-3.1.1/RcppShark/src/shark/Models/Kernels/MissingFeaturesKernelExpansion.h                                  |    5 
 RcppShark-3.1.1/RcppShark/src/shark/Models/Kernels/MklKernel.h                                                       |    5 
 RcppShark-3.1.1/RcppShark/src/shark/Models/Kernels/ModelKernel.h                                                     |    5 
 RcppShark-3.1.1/RcppShark/src/shark/Models/Kernels/MonomialKernel.h                                                  |    5 
 RcppShark-3.1.1/RcppShark/src/shark/Models/Kernels/MultiTaskKernel.h                                                 |    5 
 RcppShark-3.1.1/RcppShark/src/shark/Models/Kernels/NormalizedKernel.h                                                |    5 
 RcppShark-3.1.1/RcppShark/src/shark/Models/Kernels/PolynomialKernel.h                                                |    5 
 RcppShark-3.1.1/RcppShark/src/shark/Models/Kernels/ProductKernel.h                                                   |    4 
 RcppShark-3.1.1/RcppShark/src/shark/Models/Kernels/ScaledKernel.h                                                    |    7 
 RcppShark-3.1.1/RcppShark/src/shark/Models/Kernels/SubrangeKernel.h                                                  |    5 
 RcppShark-3.1.1/RcppShark/src/shark/Models/Kernels/WeightedSumKernel.h                                               |    5 
 RcppShark-3.1.1/RcppShark/src/shark/Models/LinearClassifier.h                                                        |    4 
 RcppShark-3.1.1/RcppShark/src/shark/Models/LinearModel.h                                                             |   13 
 RcppShark-3.1.1/RcppShark/src/shark/Models/LinearNorm.h                                                              |    5 
 RcppShark-3.1.1/RcppShark/src/shark/Models/MeanModel.h                                                               |    4 
 RcppShark-3.1.1/RcppShark/src/shark/Models/NBClassifier.h                                                            |    5 
 RcppShark-3.1.1/RcppShark/src/shark/Models/NearestNeighborClassifier.h                                               |    5 
 RcppShark-3.1.1/RcppShark/src/shark/Models/NearestNeighborRegression.h                                               |    5 
 RcppShark-3.1.1/RcppShark/src/shark/Models/Neurons.h                                                                 |   28 
 RcppShark-3.1.1/RcppShark/src/shark/Models/Normalizer.h                                                              |    5 
 RcppShark-3.1.1/RcppShark/src/shark/Models/OneVersusOneClassifier.h                                                  |   11 
 RcppShark-3.1.1/RcppShark/src/shark/Models/OnlineRNNet.h                                                             |  108 
 RcppShark-3.1.1/RcppShark/src/shark/Models/RBFLayer.h                                                                |    5 
 RcppShark-3.1.1/RcppShark/src/shark/Models/RNNet.h                                                                   |    5 
 RcppShark-3.1.1/RcppShark/src/shark/Models/RecurrentStructure.h                                                      |    4 
 RcppShark-3.1.1/RcppShark/src/shark/Models/SigmoidModel.h                                                            |    5 
 RcppShark-3.1.1/RcppShark/src/shark/Models/SoftNearestNeighborClassifier.h                                           |    5 
 RcppShark-3.1.1/RcppShark/src/shark/Models/Softmax.h                                                                 |    5 
 RcppShark-3.1.1/RcppShark/src/shark/Models/TiedAutoencoder.h                                                         |    5 
 RcppShark-3.1.1/RcppShark/src/shark/Models/Trees/BinaryTree.h                                                        |    5 
 RcppShark-3.1.1/RcppShark/src/shark/Models/Trees/CARTClassifier.h                                                    |   83 
 RcppShark-3.1.1/RcppShark/src/shark/Models/Trees/General.h                                                           |only
 RcppShark-3.1.1/RcppShark/src/shark/Models/Trees/KDTree.h                                                            |    5 
 RcppShark-3.1.1/RcppShark/src/shark/Models/Trees/KHCTree.h                                                           |    5 
 RcppShark-3.1.1/RcppShark/src/shark/Models/Trees/LCTree.h                                                            |    5 
 RcppShark-3.1.1/RcppShark/src/shark/Models/Trees/RFClassifier.h                                                      |   36 
 RcppShark-3.1.1/RcppShark/src/shark/ObjectiveFunctions/AbstractConstraintHandler.h                                   |    5 
 RcppShark-3.1.1/RcppShark/src/shark/ObjectiveFunctions/AbstractCost.h                                                |    4 
 RcppShark-3.1.1/RcppShark/src/shark/ObjectiveFunctions/AbstractObjectiveFunction.h                                   |   13 
 RcppShark-3.1.1/RcppShark/src/shark/ObjectiveFunctions/Benchmarks/Ackley.h                                           |    4 
 RcppShark-3.1.1/RcppShark/src/shark/ObjectiveFunctions/Benchmarks/Benchmarks.h                                       |    4 
 RcppShark-3.1.1/RcppShark/src/shark/ObjectiveFunctions/Benchmarks/CIGTAB1.h                                          |    4 
 RcppShark-3.1.1/RcppShark/src/shark/ObjectiveFunctions/Benchmarks/CIGTAB2.h                                          |    4 
 RcppShark-3.1.1/RcppShark/src/shark/ObjectiveFunctions/Benchmarks/Cigar.h                                            |    4 
 RcppShark-3.1.1/RcppShark/src/shark/ObjectiveFunctions/Benchmarks/CigarDiscus.h                                      |    4 
 RcppShark-3.1.1/RcppShark/src/shark/ObjectiveFunctions/Benchmarks/ConstrainedSphere.h                                |    4 
 RcppShark-3.1.1/RcppShark/src/shark/ObjectiveFunctions/Benchmarks/DTLZ1.h                                            |    4 
 RcppShark-3.1.1/RcppShark/src/shark/ObjectiveFunctions/Benchmarks/DTLZ2.h                                            |    4 
 RcppShark-3.1.1/RcppShark/src/shark/ObjectiveFunctions/Benchmarks/DTLZ3.h                                            |    4 
 RcppShark-3.1.1/RcppShark/src/shark/ObjectiveFunctions/Benchmarks/DTLZ4.h                                            |    4 
 RcppShark-3.1.1/RcppShark/src/shark/ObjectiveFunctions/Benchmarks/DTLZ5.h                                            |    4 
 RcppShark-3.1.1/RcppShark/src/shark/ObjectiveFunctions/Benchmarks/DTLZ6.h                                            |    4 
 RcppShark-3.1.1/RcppShark/src/shark/ObjectiveFunctions/Benchmarks/DTLZ7.h                                            |    4 
 RcppShark-3.1.1/RcppShark/src/shark/ObjectiveFunctions/Benchmarks/DiffPowers.h                                       |    4 
 RcppShark-3.1.1/RcppShark/src/shark/ObjectiveFunctions/Benchmarks/Discus.h                                           |    4 
 RcppShark-3.1.1/RcppShark/src/shark/ObjectiveFunctions/Benchmarks/ELLI1.h                                            |    4 
 RcppShark-3.1.1/RcppShark/src/shark/ObjectiveFunctions/Benchmarks/ELLI2.h                                            |    4 
 RcppShark-3.1.1/RcppShark/src/shark/ObjectiveFunctions/Benchmarks/Ellipsoid.h                                        |    4 
 RcppShark-3.1.1/RcppShark/src/shark/ObjectiveFunctions/Benchmarks/Fonseca.h                                          |    4 
 RcppShark-3.1.1/RcppShark/src/shark/ObjectiveFunctions/Benchmarks/GSP.h                                              |    4 
 RcppShark-3.1.1/RcppShark/src/shark/ObjectiveFunctions/Benchmarks/GruauPole.h                                        |    5 
 RcppShark-3.1.1/RcppShark/src/shark/ObjectiveFunctions/Benchmarks/Himmelblau.h                                       |    4 
 RcppShark-3.1.1/RcppShark/src/shark/ObjectiveFunctions/Benchmarks/IHR1.h                                             |    4 
 RcppShark-3.1.1/RcppShark/src/shark/ObjectiveFunctions/Benchmarks/IHR2.h                                             |    4 
 RcppShark-3.1.1/RcppShark/src/shark/ObjectiveFunctions/Benchmarks/IHR3.h                                             |    4 
 RcppShark-3.1.1/RcppShark/src/shark/ObjectiveFunctions/Benchmarks/IHR4.h                                             |    4 
 RcppShark-3.1.1/RcppShark/src/shark/ObjectiveFunctions/Benchmarks/IHR6.h                                             |    4 
 RcppShark-3.1.1/RcppShark/src/shark/ObjectiveFunctions/Benchmarks/LZ1.h                                              |    4 
 RcppShark-3.1.1/RcppShark/src/shark/ObjectiveFunctions/Benchmarks/LZ2.h                                              |    4 
 RcppShark-3.1.1/RcppShark/src/shark/ObjectiveFunctions/Benchmarks/LZ3.h                                              |    4 
 RcppShark-3.1.1/RcppShark/src/shark/ObjectiveFunctions/Benchmarks/LZ4.h                                              |    4 
 RcppShark-3.1.1/RcppShark/src/shark/ObjectiveFunctions/Benchmarks/LZ5.h                                              |    4 
 RcppShark-3.1.1/RcppShark/src/shark/ObjectiveFunctions/Benchmarks/LZ6.h                                              |    4 
 RcppShark-3.1.1/RcppShark/src/shark/ObjectiveFunctions/Benchmarks/LZ7.h                                              |    4 
 RcppShark-3.1.1/RcppShark/src/shark/ObjectiveFunctions/Benchmarks/LZ8.h                                              |    4 
 RcppShark-3.1.1/RcppShark/src/shark/ObjectiveFunctions/Benchmarks/LZ9.h                                              |    4 
 RcppShark-3.1.1/RcppShark/src/shark/ObjectiveFunctions/Benchmarks/MarkovPole.h                                       |    4 
 RcppShark-3.1.1/RcppShark/src/shark/ObjectiveFunctions/Benchmarks/MultiObjectiveBenchmark.h                          |    4 
 RcppShark-3.1.1/RcppShark/src/shark/ObjectiveFunctions/Benchmarks/NonMarkovPole.h                                    |    5 
 RcppShark-3.1.1/RcppShark/src/shark/ObjectiveFunctions/Benchmarks/PoleSimulators/DoublePole.h                        |    4 
 RcppShark-3.1.1/RcppShark/src/shark/ObjectiveFunctions/Benchmarks/PoleSimulators/SinglePole.h                        |    4 
 RcppShark-3.1.1/RcppShark/src/shark/ObjectiveFunctions/Benchmarks/Rosenbrock.h                                       |    4 
 RcppShark-3.1.1/RcppShark/src/shark/ObjectiveFunctions/Benchmarks/RotatedErrorFunction.h                             |    4 
 RcppShark-3.1.1/RcppShark/src/shark/ObjectiveFunctions/Benchmarks/Schwefel.h                                         |    4 
 RcppShark-3.1.1/RcppShark/src/shark/ObjectiveFunctions/Benchmarks/Sphere.h                                           |    4 
 RcppShark-3.1.1/RcppShark/src/shark/ObjectiveFunctions/Benchmarks/ZDT1.h                                             |    4 
 RcppShark-3.1.1/RcppShark/src/shark/ObjectiveFunctions/Benchmarks/ZDT2.h                                             |    4 
 RcppShark-3.1.1/RcppShark/src/shark/ObjectiveFunctions/Benchmarks/ZDT3.h                                             |    4 
 RcppShark-3.1.1/RcppShark/src/shark/ObjectiveFunctions/Benchmarks/ZDT4.h                                             |    4 
 RcppShark-3.1.1/RcppShark/src/shark/ObjectiveFunctions/Benchmarks/ZDT6.h                                             |    4 
 RcppShark-3.1.1/RcppShark/src/shark/ObjectiveFunctions/BoxConstraintHandler.h                                        |    5 
 RcppShark-3.1.1/RcppShark/src/shark/ObjectiveFunctions/CombinedObjectiveFunction.h                                   |    4 
 RcppShark-3.1.1/RcppShark/src/shark/ObjectiveFunctions/CrossValidationError.h                                        |    4 
 RcppShark-3.1.1/RcppShark/src/shark/ObjectiveFunctions/ErrorFunction.h                                               |    5 
 RcppShark-3.1.1/RcppShark/src/shark/ObjectiveFunctions/EvaluationArchive.h                                           |    4 
 RcppShark-3.1.1/RcppShark/src/shark/ObjectiveFunctions/Impl/ErrorFunction.inl                                        |    5 
 RcppShark-3.1.1/RcppShark/src/shark/ObjectiveFunctions/Impl/FunctionWrapperBase.h                                    |    4 
 RcppShark-3.1.1/RcppShark/src/shark/ObjectiveFunctions/Impl/NoisyErrorFunction.inl                                   |    5 
 RcppShark-3.1.1/RcppShark/src/shark/ObjectiveFunctions/Impl/SparseAutoencoderError.inl                               |    5 
 RcppShark-3.1.1/RcppShark/src/shark/ObjectiveFunctions/KernelBasisDistance.h                                         |    4 
 RcppShark-3.1.1/RcppShark/src/shark/ObjectiveFunctions/KernelTargetAlignment.h                                       |    5 
 RcppShark-3.1.1/RcppShark/src/shark/ObjectiveFunctions/LooError.h                                                    |    5 
 RcppShark-3.1.1/RcppShark/src/shark/ObjectiveFunctions/LooErrorCSvm.h                                                |    4 
 RcppShark-3.1.1/RcppShark/src/shark/ObjectiveFunctions/Loss/AbsoluteLoss.h                                           |    4 
 RcppShark-3.1.1/RcppShark/src/shark/ObjectiveFunctions/Loss/AbstractLoss.h                                           |    4 
 RcppShark-3.1.1/RcppShark/src/shark/ObjectiveFunctions/Loss/CrossEntropy.h                                           |   18 
 RcppShark-3.1.1/RcppShark/src/shark/ObjectiveFunctions/Loss/DiscreteLoss.h                                           |    4 
 RcppShark-3.1.1/RcppShark/src/shark/ObjectiveFunctions/Loss/EpsilonHingeLoss.h                                       |    4 
 RcppShark-3.1.1/RcppShark/src/shark/ObjectiveFunctions/Loss/HingeLoss.h                                              |    4 
 RcppShark-3.1.1/RcppShark/src/shark/ObjectiveFunctions/Loss/HuberLoss.h                                              |    4 
 RcppShark-3.1.1/RcppShark/src/shark/ObjectiveFunctions/Loss/SquaredEpsilonHingeLoss.h                                |    4 
 RcppShark-3.1.1/RcppShark/src/shark/ObjectiveFunctions/Loss/SquaredHingeLoss.h                                       |    4 
 RcppShark-3.1.1/RcppShark/src/shark/ObjectiveFunctions/Loss/SquaredLoss.h                                            |    4 
 RcppShark-3.1.1/RcppShark/src/shark/ObjectiveFunctions/Loss/TukeyBiweightLoss.h                                      |    4 
 RcppShark-3.1.1/RcppShark/src/shark/ObjectiveFunctions/Loss/ZeroOneLoss.h                                            |    4 
 RcppShark-3.1.1/RcppShark/src/shark/ObjectiveFunctions/NegativeAUC.h                                                 |    4 
 RcppShark-3.1.1/RcppShark/src/shark/ObjectiveFunctions/NegativeGaussianProcessEvidence.h                             |   38 
 RcppShark-3.1.1/RcppShark/src/shark/ObjectiveFunctions/NegativeLogLikelihood.h                                       |    5 
 RcppShark-3.1.1/RcppShark/src/shark/ObjectiveFunctions/NoisyErrorFunction.h                                          |    5 
 RcppShark-3.1.1/RcppShark/src/shark/ObjectiveFunctions/ROC.h                                                         |    4 
 RcppShark-3.1.1/RcppShark/src/shark/ObjectiveFunctions/RadiusMarginQuotient.h                                        |    6 
 RcppShark-3.1.1/RcppShark/src/shark/ObjectiveFunctions/Regularizer.h                                                 |    7 
 RcppShark-3.1.1/RcppShark/src/shark/ObjectiveFunctions/SparseAutoencoderError.h                                      |    5 
 RcppShark-3.1.1/RcppShark/src/shark/ObjectiveFunctions/SvmLogisticInterpretation.h                                   |    6 
 RcppShark-3.1.1/RcppShark/src/shark/Rng/AbstractDistribution.h                                                       |    4 
 RcppShark-3.1.1/RcppShark/src/shark/Rng/Bernoulli.h                                                                  |    5 
 RcppShark-3.1.1/RcppShark/src/shark/Rng/Binomial.h                                                                   |    7 
 RcppShark-3.1.1/RcppShark/src/shark/Rng/Cauchy.h                                                                     |    5 
 RcppShark-3.1.1/RcppShark/src/shark/Rng/DiffGeometric.h                                                              |    5 
 RcppShark-3.1.1/RcppShark/src/shark/Rng/Dirichlet.h                                                                  |    5 
 RcppShark-3.1.1/RcppShark/src/shark/Rng/DiscreteUniform.h                                                            |    5 
 RcppShark-3.1.1/RcppShark/src/shark/Rng/Entropy.h                                                                    |    5 
 RcppShark-3.1.1/RcppShark/src/shark/Rng/Erlang.h                                                                     |    5 
 RcppShark-3.1.1/RcppShark/src/shark/Rng/Gamma.h                                                                      |    5 
 RcppShark-3.1.1/RcppShark/src/shark/Rng/Geometric.h                                                                  |    5 
 RcppShark-3.1.1/RcppShark/src/shark/Rng/GlobalRng.h                                                                  |    5 
 RcppShark-3.1.1/RcppShark/src/shark/Rng/HyperGeometric.h                                                             |    5 
 RcppShark-3.1.1/RcppShark/src/shark/Rng/KullbackLeiberDivergence.h                                                   |    5 
 RcppShark-3.1.1/RcppShark/src/shark/Rng/LogNormal.h                                                                  |    5 
 RcppShark-3.1.1/RcppShark/src/shark/Rng/NegExponential.h                                                             |    5 
 RcppShark-3.1.1/RcppShark/src/shark/Rng/Normal.h                                                                     |    5 
 RcppShark-3.1.1/RcppShark/src/shark/Rng/Poisson.h                                                                    |    5 
 RcppShark-3.1.1/RcppShark/src/shark/Rng/Rng.h                                                                        |    6 
 RcppShark-3.1.1/RcppShark/src/shark/Rng/TruncatedExponential.h                                                       |    5 
 RcppShark-3.1.1/RcppShark/src/shark/Rng/Uniform.h                                                                    |    5 
 RcppShark-3.1.1/RcppShark/src/shark/Rng/Weibull.h                                                                    |    5 
 RcppShark-3.1.1/RcppShark/src/shark/Statistics/Distributions/MultiNomialDistribution.h                               |    4 
 RcppShark-3.1.1/RcppShark/src/shark/Statistics/Distributions/MultiVariateNormalDistribution.h                        |   44 
 RcppShark-3.1.1/RcppShark/src/shark/Statistics/Statistics.h                                                          |    5 
 RcppShark-3.1.1/RcppShark/src/shark/Unsupervised/RBM/BinaryRBM.h                                                     |    4 
 RcppShark-3.1.1/RcppShark/src/shark/Unsupervised/RBM/BipolarRBM.h                                                    |    4 
 RcppShark-3.1.1/RcppShark/src/shark/Unsupervised/RBM/ConvolutionalBinaryRBM.h                                        |    4 
 RcppShark-3.1.1/RcppShark/src/shark/Unsupervised/RBM/ConvolutionalRBM.h                                              |    5 
 RcppShark-3.1.1/RcppShark/src/shark/Unsupervised/RBM/Energy.h                                                        |    4 
 RcppShark-3.1.1/RcppShark/src/shark/Unsupervised/RBM/GaussianBinaryRBM.h                                             |    4 
 RcppShark-3.1.1/RcppShark/src/shark/Unsupervised/RBM/GradientApproximations/ContrastiveDivergence.h                  |    4 
 RcppShark-3.1.1/RcppShark/src/shark/Unsupervised/RBM/GradientApproximations/ExactGradient.h                          |    4 
 RcppShark-3.1.1/RcppShark/src/shark/Unsupervised/RBM/GradientApproximations/Impl/DataEvaluator.h                     |    4 
 RcppShark-3.1.1/RcppShark/src/shark/Unsupervised/RBM/GradientApproximations/MultiChainApproximator.h                 |    4 
 RcppShark-3.1.1/RcppShark/src/shark/Unsupervised/RBM/GradientApproximations/SingleChainApproximator.h                |    4 
 RcppShark-3.1.1/RcppShark/src/shark/Unsupervised/RBM/Impl/AverageEnergyGradient.h                                    |    5 
 RcppShark-3.1.1/RcppShark/src/shark/Unsupervised/RBM/Impl/ConvolutionalEnergyGradient.h                              |    5 
 RcppShark-3.1.1/RcppShark/src/shark/Unsupervised/RBM/Impl/analytics.h                                                |    5 
 RcppShark-3.1.1/RcppShark/src/shark/Unsupervised/RBM/Neuronlayers/BinaryLayer.h                                      |    4 
 RcppShark-3.1.1/RcppShark/src/shark/Unsupervised/RBM/Neuronlayers/BipolarLayer.h                                     |    4 
 RcppShark-3.1.1/RcppShark/src/shark/Unsupervised/RBM/Neuronlayers/GaussianLayer.h                                    |    4 
 RcppShark-3.1.1/RcppShark/src/shark/Unsupervised/RBM/Neuronlayers/TruncatedExponentialLayer.h                        |    4 
 RcppShark-3.1.1/RcppShark/src/shark/Unsupervised/RBM/Problems/BarsAndStripes.h                                       |    4 
 RcppShark-3.1.1/RcppShark/src/shark/Unsupervised/RBM/Problems/DistantModes.h                                         |    4 
 RcppShark-3.1.1/RcppShark/src/shark/Unsupervised/RBM/Problems/MNIST.h                                                |    4 
 RcppShark-3.1.1/RcppShark/src/shark/Unsupervised/RBM/Problems/Shifter.h                                              |    4 
 RcppShark-3.1.1/RcppShark/src/shark/Unsupervised/RBM/RBM.h                                                           |    5 
 RcppShark-3.1.1/RcppShark/src/shark/Unsupervised/RBM/Sampling/EnergyStoringTemperedMarkovChain.h                     |    4 
 RcppShark-3.1.1/RcppShark/src/shark/Unsupervised/RBM/Sampling/GibbsOperator.h                                        |    4 
 RcppShark-3.1.1/RcppShark/src/shark/Unsupervised/RBM/Sampling/Impl/SampleTypes.h                                     |    5 
 RcppShark-3.1.1/RcppShark/src/shark/Unsupervised/RBM/Sampling/MarkovChain.h                                          |    4 
 RcppShark-3.1.1/RcppShark/src/shark/Unsupervised/RBM/Sampling/TemperedMarkovChain.h                                  |    4 
 RcppShark-3.1.1/RcppShark/src/shark/Unsupervised/RBM/StateSpaces/RealSpace.h                                         |    5 
 RcppShark-3.1.1/RcppShark/src/shark/Unsupervised/RBM/StateSpaces/TwoStateSpace.h                                     |    4 
 RcppShark-3.1.1/RcppShark/src/shark/Unsupervised/RBM/Tags.h                                                          |    5 
 RcppShark-3.1.1/RcppShark/src/shark/Unsupervised/RBM/TruncExpBinaryRBM.h                                             |    4 
 RcppShark-3.1.1/RcppShark/src/shark/Unsupervised/RBM/analytics.h                                                     |    4 
 RcppShark-3.1.1/RcppShark/src/src/Algorithms/CARTTrainer.cpp                                                         |  457 --
 RcppShark-3.1.1/RcppShark/src/src/Algorithms/CARTcommon.cpp                                                          |only
 RcppShark-3.1.1/RcppShark/src/src/Algorithms/DirectSearch/CMA.cpp                                                    |  112 
 RcppShark-3.1.1/RcppShark/src/src/Algorithms/DirectSearch/CMSA.cpp                                                   |   23 
 RcppShark-3.1.1/RcppShark/src/src/Algorithms/DirectSearch/CrossEntropyMethod.cpp                                     |    5 
 RcppShark-3.1.1/RcppShark/src/src/Algorithms/DirectSearch/ElitistCMA.cpp                                             |    4 
 RcppShark-3.1.1/RcppShark/src/src/Algorithms/FisherLDA.cpp                                                           |    9 
 RcppShark-3.1.1/RcppShark/src/src/Algorithms/GradientDescent/AbstractLineSearchOptimizer.cpp                         |    4 
 RcppShark-3.1.1/RcppShark/src/src/Algorithms/GradientDescent/BFGS.cpp                                                |    4 
 RcppShark-3.1.1/RcppShark/src/src/Algorithms/GradientDescent/CG.cpp                                                  |    4 
 RcppShark-3.1.1/RcppShark/src/src/Algorithms/GradientDescent/LBFGS.cpp                                               |    5 
 RcppShark-3.1.1/RcppShark/src/src/Algorithms/GradientDescent/Rprop.cpp                                               |    5 
 RcppShark-3.1.1/RcppShark/src/src/Algorithms/GradientDescent/TrustRegionNewton.cpp                                   |    5 
 RcppShark-3.1.1/RcppShark/src/src/Algorithms/KMeans.cpp                                                              |    5 
 RcppShark-3.1.1/RcppShark/src/src/Algorithms/LDA.cpp                                                                 |   14 
 RcppShark-3.1.1/RcppShark/src/src/Algorithms/LinearRegression.cpp                                                    |   14 
 RcppShark-3.1.1/RcppShark/src/src/Algorithms/NormalizeComponentsWhitening.cpp                                        |   58 
 RcppShark-3.1.1/RcppShark/src/src/Algorithms/PCA.cpp                                                                 |   14 
 RcppShark-3.1.1/RcppShark/src/src/Algorithms/RFTrainer.cpp                                                           |  655 +--
 RcppShark-3.1.1/RcppShark/src/src/Algorithms/SigmoidFit.cpp                                                          |    5 
 RcppShark-3.1.1/RcppShark/src/src/Data/Csv.cpp                                                                       |   19 
 RcppShark-3.1.1/RcppShark/src/src/Data/SparseData.cpp                                                                |   74 
 RcppShark-3.1.1/RcppShark/src/src/Models/CMAC.cpp                                                                    |    6 
 RcppShark-3.1.1/RcppShark/src/src/Models/Centroids.cpp                                                               |    6 
 RcppShark-3.1.1/RcppShark/src/src/Models/Converter.cpp                                                               |    4 
 RcppShark-3.1.1/RcppShark/src/src/Models/LinearNorm.cpp                                                              |    4 
 RcppShark-3.1.1/RcppShark/src/src/Models/OnlineRNNet.cpp                                                             |  107 
 RcppShark-3.1.1/RcppShark/src/src/Models/RBFLayer.cpp                                                                |    7 
 RcppShark-3.1.1/RcppShark/src/src/Models/RNNet.cpp                                                                   |    4 
 RcppShark-3.1.1/RcppShark/src/src/Models/RecurrentStructure.cpp                                                      |    7 
 RcppShark-3.1.1/RcppShark/src/src/Models/SigmoidModel.cpp                                                            |    5 
 RcppShark-3.1.1/RcppShark/src/src/Models/Softmax.cpp                                                                 |    4 
 RcppShark-3.1.1/RcppShark/src/src/ObjectiveFunctions/DiscreteLoss.cpp                                                |    5 
 RcppShark-3.1.1/RcppShark/src/src/ObjectiveFunctions/KernelBasisDistance.cpp                                         |   12 
 RcppShark-3.1.1/RcppShark/src/src/ObjectiveFunctions/ROC.cpp                                                         |    4 
 RcppShark-3.1.1/RcppShark/src/src/Version.cpp                                                                        |    5 
 RcppShark-3.1.1/RcppShark/tools/Makevars_template                                                                    |    6 
 RcppShark-3.1.1/RcppShark/tools/prepareShark.py                                                                      |   87 
 1067 files changed, 16656 insertions(+), 22812 deletions(-)

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