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
ChangeLog | 25 +++++++++++++++++++++++++ DESCRIPTION | 33 ++++++++++++--------------------- MD5 | 30 ++++++++++++++++-------------- NAMESPACE | 6 +++--- R/fastLm.R | 4 ++-- R/inline.R | 18 +++++++++--------- README.md | 2 +- build/vignette.rds |binary inst/NEWS.Rd | 10 ++++++++++ inst/doc/RcppGSL-intro.pdf |binary inst/doc/RcppGSL-unitTests.pdf |binary inst/skeleton/Makevars.in | 3 +-- inst/skeleton/Makevars.win | 2 +- inst/skeleton/configure | 3 --- inst/skeleton/configure.win | 2 -- src/init.c |only vignettes/buildVig.R |only 17 files changed, 80 insertions(+), 58 deletions(-)
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
DESCRIPTION | 10 - MD5 | 47 +++++-- NAMESPACE | 16 ++ R/cp.R |only R/cpboundary.R |only R/cpstop.R |only R/fourhr.R |only R/innercov.R | 220 ++++++++++++++++++----------------- R/innervar.R | 233 +++++++++++++++++++------------------ R/instudyfindt.R |only R/ovbeta.R | 18 ++ R/overallcovp1.R | 267 ++++++++++++++++++++++--------------------- R/overallcovp2.R | 315 ++++++++++++++++++++++++++------------------------- R/overallvar.R | 261 +++++++++++++++++++++--------------------- R/pwecx.R | 99 +++++++--------- R/pwecxcens.R |only R/pwecxpwufindt.R | 3 R/pwepower.R | 160 ++++++++++++------------- R/pwepowereq.R |only R/pwepowerni.R |only build/partial.rdb |binary man/cp.Rd |only man/cpboundary.Rd |only man/cpstop.Rd |only man/fourhr.Rd |only man/instudyfindt.Rd |only man/pwecxcens.Rd |only man/pwecxpwufindt.Rd | 7 - man/pwepower.Rd | 7 - man/pwepowereq.Rd |only man/pwepowerni.Rd |only src/PWEALL_REAL8.f90 | 245 ++++++++++++++++++++------------------- src/init.c |only 33 files changed, 1000 insertions(+), 908 deletions(-)
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
ChangeLog | 4 DESCRIPTION | 10 - MD5 | 28 ++-- NAMESPACE | 5 R/lines.nproc.R | 10 - R/npc.R | 20 +- R/npfuns.R | 333 ++++++++++++++++++++++++------------------------ R/nproc.R | 10 - R/plot.nproc.R | 12 - R/rocCV.R |only inst/doc/nproc-demo.pdf |binary man/lines.nproc.Rd | 4 man/npc.Rd | 10 - man/nproc.Rd | 10 - man/plot.nproc.Rd | 4 man/rocCV.Rd |only 16 files changed, 239 insertions(+), 221 deletions(-)
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
DESCRIPTION | 8 ++++---- MD5 | 6 +++--- NEWS | 4 ++++ src/nleqslv.c | 3 +-- 4 files changed, 12 insertions(+), 9 deletions(-)
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
DESCRIPTION | 8 ++--- MD5 | 30 ++++++++++----------- R/class.R | 4 +- R/dge.R | 7 ++--- R/dmo.R | 3 +- R/dmsm.R | 5 ++- R/graph_gsea_goBP.R | 70 +++++++++++++++++++++++++++++++++++---------------- R/graph_gsea_goCC.R | 70 +++++++++++++++++++++++++++++++++++---------------- R/graph_gsea_goMF.R | 70 +++++++++++++++++++++++++++++++++++---------------- R/graph_gsta_goBP.R | 70 +++++++++++++++++++++++++++++++++++---------------- R/graph_gsta_goCC.R | 70 +++++++++++++++++++++++++++++++++++---------------- R/graph_gsta_goMF.R | 70 +++++++++++++++++++++++++++++++++++---------------- R/maGUI.R | 45 ++------------------------------ man/filter_sp2.Rd | 2 - man/filter_unsp.Rd | 2 - man/maGUI-package.Rd | 4 +- 16 files changed, 332 insertions(+), 198 deletions(-)
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
DESCRIPTION | 6 - MD5 | 28 ++--- R/calib.R | 12 -- R/calibration.R | 69 ++++++++++---- R/calmarFunctions.R | 118 +++++------------------- R/datasets.R | 5 - README.md | 2 data/ex2.RData |binary data/population_test.RData |binary man/calibration.Rd | 8 + man/dataPop.Rd | 1 man/poptest_calmar.Rd | 2 man/poptest_calmar_nr.Rd | 2 tests/testthat/test_calibration.R | 74 ++++++++++++++- tests/testthat/test_calibration_small_dataset.R | 32 +++--- 15 files changed, 206 insertions(+), 153 deletions(-)
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
DESCRIPTION | 10 +++++----- MD5 | 8 +++++--- inst |only man/SubgrpID-package.Rd | 3 ++- man/SubgrpID.Rd | 2 +- 5 files changed, 13 insertions(+), 10 deletions(-)
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
sitree-0.1-0/sitree/inst/doc/TestEquations.pdf |only sitree-0.1-0/sitree/vignettes/TestEquations.html |only sitree-0.1-1/sitree/DESCRIPTION | 12 - sitree-0.1-1/sitree/MD5 | 44 +++--- sitree-0.1-1/sitree/NAMESPACE | 2 sitree-0.1-1/sitree/R/ManagementProb.R | 4 sitree-0.1-1/sitree/R/PrepCommonVars.R | 33 ++-- sitree-0.1-1/sitree/R/grow.dbhinc.hgtinc.R | 1 sitree-0.1-1/sitree/R/height.korf.R | 28 +++- sitree-0.1-1/sitree/R/recr.BBG2008.R | 88 ++++++++---- sitree-0.1-1/sitree/R/sitree.R | 161 ++++++++++++----------- sitree-0.1-1/sitree/R/sitreesummary.R |only sitree-0.1-1/sitree/build/vignette.rds |binary sitree-0.1-1/sitree/data/StandWestSt.RData |only sitree-0.1-1/sitree/data/StandWestTr.RData |only sitree-0.1-1/sitree/data/fl.RData |binary sitree-0.1-1/sitree/inst/CITATION |only sitree-0.1-1/sitree/inst/doc/TestEquations.R | 23 ++- sitree-0.1-1/sitree/inst/doc/TestEquations.Rmd | 28 ++-- sitree-0.1-1/sitree/inst/doc/TestEquations.html |only sitree-0.1-1/sitree/man/height.korf.Rd | 10 + sitree-0.1-1/sitree/man/management.prob.Rd | 4 sitree-0.1-1/sitree/man/mng.tree.removal.Rd | 4 sitree-0.1-1/sitree/man/sitree.Rd | 29 ++++ sitree-0.1-1/sitree/man/sitreesummary.Rd |only sitree-0.1-1/sitree/man/stand.west.st.Rd |only sitree-0.1-1/sitree/man/stand.west.tr.Rd |only sitree-0.1-1/sitree/vignettes/TestEquations.Rmd | 28 ++-- 28 files changed, 312 insertions(+), 187 deletions(-)
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
DESCRIPTION | 8 MD5 | 20 NAMESPACE | 1 R/Analyze.Binomial.R | 2317 +++++++++++++++++++++++++++++++--------------- R/Analyze.CondPoisson.R | 4 R/Analyze.Poisson.R | 16 R/AnalyzeSetUp.Binomial.R | 56 - R/AnalyzeSetUp.Poisson.R | 16 R/CV.Poisson.R | 12 man/Analyze.Binomial.Rd | 8 man/Sequential-package.Rd | 15 11 files changed, 1705 insertions(+), 768 deletions(-)
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>
Diff between grattan versions 1.3.0.3 dated 2017-01-18 and 1.4.1.2 dated 2017-03-04
DESCRIPTION | 10 +- MD5 | 120 +++++++++++++------------ NAMESPACE | 4 R/income_tax.R | 60 ++++++------ R/income_tax_sapto.R |only R/medicare_levy.R | 31 +++--- R/new_medicare_levy.R | 25 +++-- R/new_sapto.R |only R/sapto.R | 56 ++++++++++- R/sysdata.rda |binary R/wage_inflator.R | 2 R/zzz.R | 4 README.md | 18 ++- build/vignette.rds |binary inst/doc/Modelling-superannuation-changes.html | 32 +++--- inst/doc/Performance-of-project.html | 6 - inst/doc/companion-to-sample-file-1314.html | 4 inst/doc/differential-uprating.html | 4 man/CG_population_inflator.Rd | 3 man/age_grouper.Rd | 1 man/apply_super_caps_and_div293.Rd | 1 man/aus_pop_qtr.Rd | 1 man/aus_pop_qtr_age.Rd | 1 man/cpi_inflator.Rd | 1 man/cpi_inflator_general_date.Rd | 1 man/cpi_inflator_quarters.Rd | 1 man/differentially_uprate_wage.Rd | 1 man/gdp.Rd | 3 man/generic_inflator.Rd | 1 man/gni.Rd | 3 man/income_tax.Rd | 1 man/income_tax_sapto.Rd |only man/inflator.Rd | 1 man/inverse_average_rate.Rd | 1 man/inverse_income.Rd | 1 man/is.fy.Rd | 9 - man/lf_inflator.Rd | 2 man/lito.Rd | 2 man/max_super_contr_base.Rd | 1 man/medicare_levy.Rd | 1 man/model_new_caps_and_div293.Rd | 1 man/new_income_tax.Rd | 1 man/new_medicare_levy.Rd | 1 man/new_sapto.Rd |only man/npv.Rd | 11 +- man/pmax3.Rd | 1 man/pmaxC.Rd | 1 man/pmaxV.Rd | 1 man/pminC.Rd | 1 man/pminV.Rd | 1 man/prohibit_length0_vectors.Rd | 1 man/prohibit_unequal_length_vectors.Rd | 1 man/prohibit_vector_recycling.Rd | 1 man/project.Rd | 1 man/project_to.Rd | 1 man/rebate_income.Rd | 1 man/sapto.Rd | 5 - man/student_repayment.Rd | 1 man/wage_inflator.Rd | 1 man/weighted_ntile.Rd | 1 src/init.c |only tests/testthat/test_lf_inflator.R | 9 + tests/testthat/test_medicare_levy.R | 59 +++++++++++- tests/testthat/test_sapto.R |only 64 files changed, 305 insertions(+), 209 deletions(-)
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>
Diff between ziphsmm versions 1.0.3 dated 2017-02-09 and 1.0.4 dated 2017-03-04
DESCRIPTION | 10 - MD5 | 37 ++-- NAMESPACE | 1 R/package.R | 6 man/CAT.Rd | 1 man/dzip.Rd | 1 man/hmmfit.Rd | 1 man/hmmsim.Rd | 1 man/hmmsim2.Rd | 1 man/hmmviterbi.Rd | 1 man/hmmviterbi2.Rd | 1 man/hsmmfit.Rd | 1 man/hsmmsim.Rd | 1 man/hsmmsim2.Rd | 1 man/hsmmviterbi.Rd | 1 man/hsmmviterbi2.Rd | 1 man/package-ziphsmm.Rd | 7 man/rzip.Rd | 1 src/init.c |only src/rcpparma_hello_world.cpp | 356 +++++++++++++++++++++++++------------------ 20 files changed, 246 insertions(+), 184 deletions(-)
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
DESCRIPTION | 10 - MD5 | 212 +++++++++++++-------------- NAMESPACE | 2 NEWS | 11 + R/ApiRequest.R | 19 +- R/BuildInnerBreakdownsRecursively.R | 3 R/GetClickMapReporting.R | 41 +++-- R/GetFeeds.R | 8 - R/GetPreviousServerCalls.R |only R/GetReport.R | 27 ++- R/ParseDW.R | 49 +++--- R/QueueDataWarehouse.R | 46 +++++ R/RSiteCatalyst.R | 4 R/SubmitJsonQueueReport.R | 7 man/ApiRequest.Rd | 4 man/BuildClassificationValueSegment.Rd | 1 man/BuildHeader.Rd | 1 man/BuildInnerBreakdownsRecursively.Rd | 1 man/BuildLineItemSegment.Rd | 1 man/BuildRealTimeReportStructure.Rd | 1 man/CancelReport.Rd | 1 man/GetActivation.Rd | 1 man/GetAxleStartDate.Rd | 1 man/GetBaseCurrency.Rd | 1 man/GetBaseURL.Rd | 1 man/GetBookmarks.Rd | 1 man/GetCalculatedMetrics.Rd | 1 man/GetClassifications.Rd | 1 man/GetClickMapReporting.Rd | 1 man/GetCustomCalendar.Rd | 1 man/GetDashboards.Rd | 1 man/GetDataWarehouseDisplay.Rd | 1 man/GetDefaultPage.Rd | 1 man/GetDiscoverEnabled.Rd | 1 man/GetEcommerce.Rd | 1 man/GetElements.Rd | 1 man/GetEndpoint.Rd | 1 man/GetEvars.Rd | 1 man/GetFeed.Rd | 1 man/GetFeeds.Rd | 1 man/GetFunctions.Rd | 1 man/GetGeoSegmentation.Rd | 1 man/GetGroups.Rd | 1 man/GetIPAddressExclusions.Rd | 1 man/GetIPObfuscation.Rd | 1 man/GetInternalURLFilters.Rd | 1 man/GetKeyVisitors.Rd | 1 man/GetListVariables.Rd | 1 man/GetLocalization.Rd | 1 man/GetLogin.Rd | 1 man/GetLogins.Rd | 1 man/GetMarketingChannelExpiration.Rd | 1 man/GetMarketingChannelRules.Rd | 1 man/GetMarketingChannels.Rd | 1 man/GetMetrics.Rd | 1 man/GetMobileAppReporting.Rd | 1 man/GetPaidSearchDetection.Rd | 1 man/GetPermanentTraffic.Rd | 1 man/GetPreviousServerCalls.Rd |only man/GetPrivacySettings.Rd | 1 man/GetProps.Rd | 1 man/GetQueue.Rd | 1 man/GetRealTimeReport.Rd | 1 man/GetRealTimeSettings.Rd | 1 man/GetReport.Rd | 7 man/GetReportDescription.Rd | 1 man/GetReportSuiteGroups.Rd | 1 man/GetReportSuites.Rd | 1 man/GetReportsByIds.Rd | 1 man/GetScheduledSpike.Rd | 1 man/GetSegments.Rd | 1 man/GetSiteTitle.Rd | 1 man/GetSuccessEvents.Rd | 1 man/GetTemplate.Rd | 1 man/GetTimeStampEnabled.Rd | 1 man/GetTimeZone.Rd | 1 man/GetTrackingServer.Rd | 1 man/GetTransactionEnabled.Rd | 1 man/GetUniqueVisitorVariable.Rd | 1 man/GetUsageLog.Rd | 1 man/GetVersionAccess.Rd | 1 man/GetVideoSettings.Rd | 1 man/GetVirtualReportSuiteSettings.Rd | 1 man/JsonQueueRealTimeReport.Rd | 1 man/ParseDW.Rd | 5 man/ParseFallout.Rd | 1 man/ParseOvertime.Rd | 1 man/ParsePathing.Rd | 1 man/ParseRanked.Rd | 1 man/ParseSummary.Rd | 1 man/ParseTrended.Rd | 1 man/QueueDataWarehouse.Rd | 7 man/QueueFallout.Rd | 1 man/QueueOvertime.Rd | 1 man/QueuePathing.Rd | 1 man/QueueRanked.Rd | 1 man/QueueSummary.Rd | 1 man/QueueTrended.Rd | 1 man/RSiteCatalyst.Rd | 11 - man/SCAuth.Rd | 1 man/SaveRealTimeSettings.Rd | 1 man/SubmitJsonQueueReport.Rd | 6 man/ValidateReport.Rd | 1 man/ViewProcessingRules.Rd | 1 tests/testthat/test-getclickmapreporting.R |only tests/testthat/test-getpreviousservercalls.R |only tests/testthat/test-getreportdescription.R | 2 tests/testthat/test-queuedatawarehouse.R | 27 ++- tests/testthat/test-queuetrended.R | 24 +++ 109 files changed, 345 insertions(+), 270 deletions(-)
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 ++++++++++++++------------- NAMESPACE | 3 NEWS.md | 23 +++++ R/api-studies.R | 9 +- R/deduplicate_labels.R | 3 R/is_in_tree.R |only R/studies.R | 56 +++++++++----- R/tax_utils.R | 7 + README.md | 146 ++++++++++++++------------------------ build/vignette.rds |binary inst/CITATION | 75 ++++++++++++++----- inst/doc/data_mashups.html | 22 ++--- inst/doc/how-to-use-rotl.R | 15 ++- inst/doc/how-to-use-rotl.Rmd | 48 ++++++++---- inst/doc/how-to-use-rotl.html | 92 ++++++++++++++--------- inst/doc/meta-analysis.R | 3 inst/doc/meta-analysis.Rmd | 5 - inst/doc/meta-analysis.html | 20 ++--- man/get_study.Rd | 1 man/get_study_meta.Rd | 13 +-- man/get_study_subtree.Rd | 29 +++++-- man/get_study_tree.Rd | 9 +- man/is_in_tree.Rd |only man/list_trees.Rd | 1 man/match_names-methods.Rd | 5 - man/match_names.Rd | 3 man/source_list.Rd | 1 man/strip_ott_ids.Rd | 1 man/studies_find_studies.Rd | 1 man/studies_find_trees.Rd | 1 man/studies_properties.Rd | 1 man/study_external_IDs.Rd | 1 man/synonyms.match_names.Rd | 1 man/tax_lineage.Rd | 1 man/taxon_external_IDs.Rd | 1 man/taxonomy-methods.Rd | 7 - man/taxonomy_about.Rd | 1 man/taxonomy_mrca.Rd | 13 +-- man/taxonomy_subtree.Rd | 1 man/taxonomy_taxon_info.Rd | 15 +-- man/tnrs_contexts.Rd | 1 man/tnrs_infer_context.Rd | 1 man/tnrs_match_names.Rd | 1 man/tol_about.Rd | 7 - man/tol_induced_subtree.Rd | 1 man/tol_mrca.Rd | 11 +- man/tol_node_info.Rd | 13 +-- man/tol_subtree.Rd | 1 tests/testthat/test-match_names.R | 14 +-- tests/testthat/test-studies.R | 57 +++++++++----- tests/testthat/test-taxonomy.R | 38 +++++++++ vignettes/how-to-use-rotl.Rmd | 48 ++++++++---- vignettes/meta-analysis.Rmd | 5 - 55 files changed, 547 insertions(+), 401 deletions(-)
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
RcppShark-3.1.0/RcppShark/inst/include/shark/Algorithms/DirectSearch/Operators/Hypervolume/HypervolumeCalculatorMD.h |only RcppShark-3.1.0/RcppShark/inst/include/shark/Algorithms/QP/QpMcDecomp.h |only RcppShark-3.1.0/RcppShark/inst/include/shark/Algorithms/Trainers/McReinforcedSvmTrainer.h |only RcppShark-3.1.0/RcppShark/inst/include/shark/Algorithms/Trainers/McSvmADMTrainer.h |only RcppShark-3.1.0/RcppShark/inst/include/shark/Algorithms/Trainers/McSvmATMTrainer.h |only RcppShark-3.1.0/RcppShark/inst/include/shark/Algorithms/Trainers/McSvmATSTrainer.h |only RcppShark-3.1.0/RcppShark/inst/include/shark/Algorithms/Trainers/McSvmCSTrainer.h |only RcppShark-3.1.0/RcppShark/inst/include/shark/Algorithms/Trainers/McSvmLLWTrainer.h |only RcppShark-3.1.0/RcppShark/inst/include/shark/Algorithms/Trainers/McSvmMMRTrainer.h |only RcppShark-3.1.0/RcppShark/inst/include/shark/Algorithms/Trainers/McSvmOVATrainer.h |only RcppShark-3.1.0/RcppShark/inst/include/shark/Algorithms/Trainers/McSvmWWTrainer.h |only RcppShark-3.1.0/RcppShark/inst/include/shark/LinAlg/BLAS/blas.h |only RcppShark-3.1.0/RcppShark/inst/include/shark/LinAlg/BLAS/fwd.hpp |only RcppShark-3.1.0/RcppShark/inst/include/shark/LinAlg/BLAS/kernels/cblas/dot.hpp |only RcppShark-3.1.0/RcppShark/inst/include/shark/LinAlg/BLAS/kernels/cblas/gemm.hpp |only RcppShark-3.1.0/RcppShark/inst/include/shark/LinAlg/BLAS/kernels/traits.hpp |only RcppShark-3.1.0/RcppShark/inst/include/shark/LinAlg/Cholesky.h |only RcppShark-3.1.0/RcppShark/inst/include/shark/LinAlg/Impl/Cholesky.inl |only RcppShark-3.1.0/RcppShark/inst/include/shark/LinAlg/Impl/eigensymm.inl |only RcppShark-3.1.0/RcppShark/inst/include/shark/LinAlg/Impl/pivotingRQ.inl |only RcppShark-3.1.0/RcppShark/inst/include/shark/LinAlg/Impl/solveSystem.inl |only RcppShark-3.1.0/RcppShark/inst/include/shark/LinAlg/Impl/solveTriangular.inl |only RcppShark-3.1.0/RcppShark/inst/include/shark/LinAlg/Impl/svd.inl |only RcppShark-3.1.0/RcppShark/inst/include/shark/LinAlg/RQ.h |only RcppShark-3.1.0/RcppShark/inst/include/shark/LinAlg/solveSystem.h |only RcppShark-3.1.0/RcppShark/inst/include/shark/LinAlg/solveTriangular.h |only RcppShark-3.1.0/RcppShark/inst/include/shark/LinAlg/svd.h |only RcppShark-3.1.0/RcppShark/src/shark/Algorithms/DirectSearch/Operators/Hypervolume/HypervolumeCalculatorMD.h |only RcppShark-3.1.0/RcppShark/src/shark/Algorithms/QP/QpMcDecomp.h |only RcppShark-3.1.0/RcppShark/src/shark/Algorithms/Trainers/McReinforcedSvmTrainer.h |only RcppShark-3.1.0/RcppShark/src/shark/Algorithms/Trainers/McSvmADMTrainer.h |only RcppShark-3.1.0/RcppShark/src/shark/Algorithms/Trainers/McSvmATMTrainer.h |only RcppShark-3.1.0/RcppShark/src/shark/Algorithms/Trainers/McSvmATSTrainer.h |only RcppShark-3.1.0/RcppShark/src/shark/Algorithms/Trainers/McSvmCSTrainer.h |only RcppShark-3.1.0/RcppShark/src/shark/Algorithms/Trainers/McSvmLLWTrainer.h |only RcppShark-3.1.0/RcppShark/src/shark/Algorithms/Trainers/McSvmMMRTrainer.h |only RcppShark-3.1.0/RcppShark/src/shark/Algorithms/Trainers/McSvmOVATrainer.h |only RcppShark-3.1.0/RcppShark/src/shark/Algorithms/Trainers/McSvmWWTrainer.h |only RcppShark-3.1.0/RcppShark/src/shark/LinAlg/BLAS/blas.h |only RcppShark-3.1.0/RcppShark/src/shark/LinAlg/BLAS/fwd.hpp |only RcppShark-3.1.0/RcppShark/src/shark/LinAlg/BLAS/kernels/cblas/dot.hpp |only RcppShark-3.1.0/RcppShark/src/shark/LinAlg/BLAS/kernels/cblas/gemm.hpp |only RcppShark-3.1.0/RcppShark/src/shark/LinAlg/BLAS/kernels/traits.hpp |only RcppShark-3.1.0/RcppShark/src/shark/LinAlg/Cholesky.h |only RcppShark-3.1.0/RcppShark/src/shark/LinAlg/Impl/Cholesky.inl |only RcppShark-3.1.0/RcppShark/src/shark/LinAlg/Impl/eigensymm.inl |only RcppShark-3.1.0/RcppShark/src/shark/LinAlg/Impl/pivotingRQ.inl |only RcppShark-3.1.0/RcppShark/src/shark/LinAlg/Impl/solveSystem.inl |only RcppShark-3.1.0/RcppShark/src/shark/LinAlg/Impl/solveTriangular.inl |only RcppShark-3.1.0/RcppShark/src/shark/LinAlg/Impl/svd.inl |only RcppShark-3.1.0/RcppShark/src/shark/LinAlg/RQ.h |only RcppShark-3.1.0/RcppShark/src/shark/LinAlg/solveSystem.h |only RcppShark-3.1.0/RcppShark/src/shark/LinAlg/solveTriangular.h |only RcppShark-3.1.0/RcppShark/src/shark/LinAlg/svd.h |only 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 RcppShark-3.1.1/RcppShark/inst/include/shark/Algorithms/AbstractMultiObjectiveOptimizer.h | 5 RcppShark-3.1.1/RcppShark/inst/include/shark/Algorithms/AbstractOptimizer.h | 4 RcppShark-3.1.1/RcppShark/inst/include/shark/Algorithms/AbstractSingleObjectiveOptimizer.h | 4 RcppShark-3.1.1/RcppShark/inst/include/shark/Algorithms/DirectSearch/CMA.h | 115 RcppShark-3.1.1/RcppShark/inst/include/shark/Algorithms/DirectSearch/CMA/CMAIndividual.h | 4 RcppShark-3.1.1/RcppShark/inst/include/shark/Algorithms/DirectSearch/CMA/Chromosome.h | 5 RcppShark-3.1.1/RcppShark/inst/include/shark/Algorithms/DirectSearch/CMSA.h | 17 RcppShark-3.1.1/RcppShark/inst/include/shark/Algorithms/DirectSearch/CrossEntropyMethod.h | 5 RcppShark-3.1.1/RcppShark/inst/include/shark/Algorithms/DirectSearch/ElitistCMA.h | 4 RcppShark-3.1.1/RcppShark/inst/include/shark/Algorithms/DirectSearch/Grid.h | 4 RcppShark-3.1.1/RcppShark/inst/include/shark/Algorithms/DirectSearch/GridSearch.h | 4 RcppShark-3.1.1/RcppShark/inst/include/shark/Algorithms/DirectSearch/Individual.h | 5 RcppShark-3.1.1/RcppShark/inst/include/shark/Algorithms/DirectSearch/LMCMA.h | 4 RcppShark-3.1.1/RcppShark/inst/include/shark/Algorithms/DirectSearch/MOCMA.h | 4 RcppShark-3.1.1/RcppShark/inst/include/shark/Algorithms/DirectSearch/Operators/Domination/DCNonDominatedSort.h | 6 RcppShark-3.1.1/RcppShark/inst/include/shark/Algorithms/DirectSearch/Operators/Domination/FastNonDominatedSort.h | 4 RcppShark-3.1.1/RcppShark/inst/include/shark/Algorithms/DirectSearch/Operators/Domination/NonDominatedSort.h | 4 RcppShark-3.1.1/RcppShark/inst/include/shark/Algorithms/DirectSearch/Operators/Domination/ParetoDominance.h | 4 RcppShark-3.1.1/RcppShark/inst/include/shark/Algorithms/DirectSearch/Operators/Evaluation/PenalizingEvaluator.h | 29 RcppShark-3.1.1/RcppShark/inst/include/shark/Algorithms/DirectSearch/Operators/Hypervolume/HVCalculatorMDHOY.h |only RcppShark-3.1.1/RcppShark/inst/include/shark/Algorithms/DirectSearch/Operators/Hypervolume/HVCalculatorMDWFG.h |only RcppShark-3.1.1/RcppShark/inst/include/shark/Algorithms/DirectSearch/Operators/Hypervolume/HVContrApproximator.h | 110 RcppShark-3.1.1/RcppShark/inst/include/shark/Algorithms/DirectSearch/Operators/Hypervolume/HVContribution2D.h | 11 RcppShark-3.1.1/RcppShark/inst/include/shark/Algorithms/DirectSearch/Operators/Hypervolume/HVContribution3D.h | 5 RcppShark-3.1.1/RcppShark/inst/include/shark/Algorithms/DirectSearch/Operators/Hypervolume/HVContributionMD.h | 90 RcppShark-3.1.1/RcppShark/inst/include/shark/Algorithms/DirectSearch/Operators/Hypervolume/HVSubsetSelection2D.h | 5 RcppShark-3.1.1/RcppShark/inst/include/shark/Algorithms/DirectSearch/Operators/Hypervolume/HypervolumeApproximator.h | 5 RcppShark-3.1.1/RcppShark/inst/include/shark/Algorithms/DirectSearch/Operators/Hypervolume/HypervolumeCalculator.h | 18 RcppShark-3.1.1/RcppShark/inst/include/shark/Algorithms/DirectSearch/Operators/Hypervolume/HypervolumeCalculator2D.h | 5 RcppShark-3.1.1/RcppShark/inst/include/shark/Algorithms/DirectSearch/Operators/Hypervolume/HypervolumeCalculator3D.h | 97 RcppShark-3.1.1/RcppShark/inst/include/shark/Algorithms/DirectSearch/Operators/Hypervolume/HypervolumeContribution.h | 5 RcppShark-3.1.1/RcppShark/inst/include/shark/Algorithms/DirectSearch/Operators/Indicators/AdditiveEpsilonIndicator.h | 4 RcppShark-3.1.1/RcppShark/inst/include/shark/Algorithms/DirectSearch/Operators/Indicators/HypervolumeIndicator.h | 4 RcppShark-3.1.1/RcppShark/inst/include/shark/Algorithms/DirectSearch/Operators/Mutation/BitflipMutator.h | 4 RcppShark-3.1.1/RcppShark/inst/include/shark/Algorithms/DirectSearch/Operators/Mutation/PolynomialMutation.h | 4 RcppShark-3.1.1/RcppShark/inst/include/shark/Algorithms/DirectSearch/Operators/PopulationBasedStepSizeAdaptation.h | 5 RcppShark-3.1.1/RcppShark/inst/include/shark/Algorithms/DirectSearch/Operators/Recombination/BinaryCrossover.h | 4 RcppShark-3.1.1/RcppShark/inst/include/shark/Algorithms/DirectSearch/Operators/Recombination/OnePointCrossover.h | 4 RcppShark-3.1.1/RcppShark/inst/include/shark/Algorithms/DirectSearch/Operators/Recombination/UniformCrossover.h | 4 RcppShark-3.1.1/RcppShark/inst/include/shark/Algorithms/DirectSearch/Operators/Selection/EPTournamentSelection.h | 4 RcppShark-3.1.1/RcppShark/inst/include/shark/Algorithms/DirectSearch/Operators/Selection/ElitistSelection.h | 4 RcppShark-3.1.1/RcppShark/inst/include/shark/Algorithms/DirectSearch/Operators/Selection/IndicatorBasedSelection.h | 4 RcppShark-3.1.1/RcppShark/inst/include/shark/Algorithms/DirectSearch/Operators/Selection/LinearRanking.h | 4 RcppShark-3.1.1/RcppShark/inst/include/shark/Algorithms/DirectSearch/Operators/Selection/RouletteWheelSelection.h | 5 RcppShark-3.1.1/RcppShark/inst/include/shark/Algorithms/DirectSearch/Operators/Selection/TournamentSelection.h | 5 RcppShark-3.1.1/RcppShark/inst/include/shark/Algorithms/DirectSearch/Operators/Selection/UniformRanking.h | 4 RcppShark-3.1.1/RcppShark/inst/include/shark/Algorithms/DirectSearch/Operators/TwoPointStepSizeAdaptation.h | 5 RcppShark-3.1.1/RcppShark/inst/include/shark/Algorithms/DirectSearch/RealCodedNSGAII.h | 4 RcppShark-3.1.1/RcppShark/inst/include/shark/Algorithms/DirectSearch/SMS-EMOA.h | 4 RcppShark-3.1.1/RcppShark/inst/include/shark/Algorithms/DirectSearch/SimplexDownhill.h | 4 RcppShark-3.1.1/RcppShark/inst/include/shark/Algorithms/DirectSearch/SteadyStateMOCMA.h | 4 RcppShark-3.1.1/RcppShark/inst/include/shark/Algorithms/DirectSearch/VDCMA.h | 4 RcppShark-3.1.1/RcppShark/inst/include/shark/Algorithms/GradientDescent/AbstractLineSearchOptimizer.h | 4 RcppShark-3.1.1/RcppShark/inst/include/shark/Algorithms/GradientDescent/BFGS.h | 4 RcppShark-3.1.1/RcppShark/inst/include/shark/Algorithms/GradientDescent/CG.h | 4 RcppShark-3.1.1/RcppShark/inst/include/shark/Algorithms/GradientDescent/Impl/dlinmin.inl | 4 RcppShark-3.1.1/RcppShark/inst/include/shark/Algorithms/GradientDescent/Impl/wolfecubic.inl | 4 RcppShark-3.1.1/RcppShark/inst/include/shark/Algorithms/GradientDescent/LBFGS.h | 4 RcppShark-3.1.1/RcppShark/inst/include/shark/Algorithms/GradientDescent/LineSearch.h | 4 RcppShark-3.1.1/RcppShark/inst/include/shark/Algorithms/GradientDescent/Rprop.h | 4 RcppShark-3.1.1/RcppShark/inst/include/shark/Algorithms/GradientDescent/SteepestDescent.h | 4 RcppShark-3.1.1/RcppShark/inst/include/shark/Algorithms/GradientDescent/TrustRegionNewton.h | 4 RcppShark-3.1.1/RcppShark/inst/include/shark/Algorithms/JaakkolaHeuristic.h | 5 RcppShark-3.1.1/RcppShark/inst/include/shark/Algorithms/KMeans.h | 79 RcppShark-3.1.1/RcppShark/inst/include/shark/Algorithms/NearestNeighbors/AbstractNearestNeighbors.h | 4 RcppShark-3.1.1/RcppShark/inst/include/shark/Algorithms/NearestNeighbors/SimpleNearestNeighbors.h | 4 RcppShark-3.1.1/RcppShark/inst/include/shark/Algorithms/NearestNeighbors/TreeNearestNeighbors.h | 5 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 RcppShark-3.1.1/RcppShark/inst/include/shark/Models/Kernels/DiscreteKernel.h | 5 RcppShark-3.1.1/RcppShark/inst/include/shark/Models/Kernels/EvalSkipMissingFeatures.h | 5 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 RcppShark-3.1.1/RcppShark/inst/include/shark/Models/Kernels/ModelKernel.h | 5 RcppShark-3.1.1/RcppShark/inst/include/shark/Models/Kernels/MonomialKernel.h | 5 RcppShark-3.1.1/RcppShark/inst/include/shark/Models/Kernels/MultiTaskKernel.h | 5 RcppShark-3.1.1/RcppShark/inst/include/shark/Models/Kernels/NormalizedKernel.h | 5 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 RcppShark-3.1.1/RcppShark/inst/include/shark/ObjectiveFunctions/Benchmarks/CIGTAB2.h | 4 RcppShark-3.1.1/RcppShark/inst/include/shark/ObjectiveFunctions/Benchmarks/Cigar.h | 4 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 RcppShark-3.1.1/RcppShark/inst/include/shark/ObjectiveFunctions/Benchmarks/DTLZ2.h | 4 RcppShark-3.1.1/RcppShark/inst/include/shark/ObjectiveFunctions/Benchmarks/DTLZ3.h | 4 RcppShark-3.1.1/RcppShark/inst/include/shark/ObjectiveFunctions/Benchmarks/DTLZ4.h | 4 RcppShark-3.1.1/RcppShark/inst/include/shark/ObjectiveFunctions/Benchmarks/DTLZ5.h | 4 RcppShark-3.1.1/RcppShark/inst/include/shark/ObjectiveFunctions/Benchmarks/DTLZ6.h | 4 RcppShark-3.1.1/RcppShark/inst/include/shark/ObjectiveFunctions/Benchmarks/DTLZ7.h | 4 RcppShark-3.1.1/RcppShark/inst/include/shark/ObjectiveFunctions/Benchmarks/DiffPowers.h | 4 RcppShark-3.1.1/RcppShark/inst/include/shark/ObjectiveFunctions/Benchmarks/Discus.h | 4 RcppShark-3.1.1/RcppShark/inst/include/shark/ObjectiveFunctions/Benchmarks/ELLI1.h | 4 RcppShark-3.1.1/RcppShark/inst/include/shark/ObjectiveFunctions/Benchmarks/ELLI2.h | 4 RcppShark-3.1.1/RcppShark/inst/include/shark/ObjectiveFunctions/Benchmarks/Ellipsoid.h | 4 RcppShark-3.1.1/RcppShark/inst/include/shark/ObjectiveFunctions/Benchmarks/Fonseca.h | 4 RcppShark-3.1.1/RcppShark/inst/include/shark/ObjectiveFunctions/Benchmarks/GSP.h | 4 RcppShark-3.1.1/RcppShark/inst/include/shark/ObjectiveFunctions/Benchmarks/GruauPole.h | 5 RcppShark-3.1.1/RcppShark/inst/include/shark/ObjectiveFunctions/Benchmarks/Himmelblau.h | 4 RcppShark-3.1.1/RcppShark/inst/include/shark/ObjectiveFunctions/Benchmarks/IHR1.h | 4 RcppShark-3.1.1/RcppShark/inst/include/shark/ObjectiveFunctions/Benchmarks/IHR2.h | 4 RcppShark-3.1.1/RcppShark/inst/include/shark/ObjectiveFunctions/Benchmarks/IHR3.h | 4 RcppShark-3.1.1/RcppShark/inst/include/shark/ObjectiveFunctions/Benchmarks/IHR4.h | 4 RcppShark-3.1.1/RcppShark/inst/include/shark/ObjectiveFunctions/Benchmarks/IHR6.h | 4 RcppShark-3.1.1/RcppShark/inst/include/shark/ObjectiveFunctions/Benchmarks/LZ1.h | 4 RcppShark-3.1.1/RcppShark/inst/include/shark/ObjectiveFunctions/Benchmarks/LZ2.h | 4 RcppShark-3.1.1/RcppShark/inst/include/shark/ObjectiveFunctions/Benchmarks/LZ3.h | 4 RcppShark-3.1.1/RcppShark/inst/include/shark/ObjectiveFunctions/Benchmarks/LZ4.h | 4 RcppShark-3.1.1/RcppShark/inst/include/shark/ObjectiveFunctions/Benchmarks/LZ5.h | 4 RcppShark-3.1.1/RcppShark/inst/include/shark/ObjectiveFunctions/Benchmarks/LZ6.h | 4 RcppShark-3.1.1/RcppShark/inst/include/shark/ObjectiveFunctions/Benchmarks/LZ7.h | 4 RcppShark-3.1.1/RcppShark/inst/include/shark/ObjectiveFunctions/Benchmarks/LZ8.h | 4 RcppShark-3.1.1/RcppShark/inst/include/shark/ObjectiveFunctions/Benchmarks/LZ9.h | 4 RcppShark-3.1.1/RcppShark/inst/include/shark/ObjectiveFunctions/Benchmarks/MarkovPole.h | 4 RcppShark-3.1.1/RcppShark/inst/include/shark/ObjectiveFunctions/Benchmarks/MultiObjectiveBenchmark.h | 4 RcppShark-3.1.1/RcppShark/inst/include/shark/ObjectiveFunctions/Benchmarks/NonMarkovPole.h | 5 RcppShark-3.1.1/RcppShark/inst/include/shark/ObjectiveFunctions/Benchmarks/PoleSimulators/DoublePole.h | 4 RcppShark-3.1.1/RcppShark/inst/include/shark/ObjectiveFunctions/Benchmarks/PoleSimulators/SinglePole.h | 4 RcppShark-3.1.1/RcppShark/inst/include/shark/ObjectiveFunctions/Benchmarks/Rosenbrock.h | 4 RcppShark-3.1.1/RcppShark/inst/include/shark/ObjectiveFunctions/Benchmarks/RotatedErrorFunction.h | 4 RcppShark-3.1.1/RcppShark/inst/include/shark/ObjectiveFunctions/Benchmarks/Schwefel.h | 4 RcppShark-3.1.1/RcppShark/inst/include/shark/ObjectiveFunctions/Benchmarks/Sphere.h | 4 RcppShark-3.1.1/RcppShark/inst/include/shark/ObjectiveFunctions/Benchmarks/ZDT1.h | 4 RcppShark-3.1.1/RcppShark/inst/include/shark/ObjectiveFunctions/Benchmarks/ZDT2.h | 4 RcppShark-3.1.1/RcppShark/inst/include/shark/ObjectiveFunctions/Benchmarks/ZDT3.h | 4 RcppShark-3.1.1/RcppShark/inst/include/shark/ObjectiveFunctions/Benchmarks/ZDT4.h | 4 RcppShark-3.1.1/RcppShark/inst/include/shark/ObjectiveFunctions/Benchmarks/ZDT6.h | 4 RcppShark-3.1.1/RcppShark/inst/include/shark/ObjectiveFunctions/BoxConstraintHandler.h | 5 RcppShark-3.1.1/RcppShark/inst/include/shark/ObjectiveFunctions/CombinedObjectiveFunction.h | 4 RcppShark-3.1.1/RcppShark/inst/include/shark/ObjectiveFunctions/CrossValidationError.h | 4 RcppShark-3.1.1/RcppShark/inst/include/shark/ObjectiveFunctions/ErrorFunction.h | 5 RcppShark-3.1.1/RcppShark/inst/include/shark/ObjectiveFunctions/EvaluationArchive.h | 4 RcppShark-3.1.1/RcppShark/inst/include/shark/ObjectiveFunctions/Impl/ErrorFunction.inl | 5 RcppShark-3.1.1/RcppShark/inst/include/shark/ObjectiveFunctions/Impl/FunctionWrapperBase.h | 4 RcppShark-3.1.1/RcppShark/inst/include/shark/ObjectiveFunctions/Impl/NoisyErrorFunction.inl | 5 RcppShark-3.1.1/RcppShark/inst/include/shark/ObjectiveFunctions/Impl/SparseAutoencoderError.inl | 5 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 RcppShark-3.1.1/RcppShark/inst/include/shark/ObjectiveFunctions/Loss/DiscreteLoss.h | 4 RcppShark-3.1.1/RcppShark/inst/include/shark/ObjectiveFunctions/Loss/EpsilonHingeLoss.h | 4 RcppShark-3.1.1/RcppShark/inst/include/shark/ObjectiveFunctions/Loss/HingeLoss.h | 4 RcppShark-3.1.1/RcppShark/inst/include/shark/ObjectiveFunctions/Loss/HuberLoss.h | 4 RcppShark-3.1.1/RcppShark/inst/include/shark/ObjectiveFunctions/Loss/SquaredEpsilonHingeLoss.h | 4 RcppShark-3.1.1/RcppShark/inst/include/shark/ObjectiveFunctions/Loss/SquaredHingeLoss.h | 4 RcppShark-3.1.1/RcppShark/inst/include/shark/ObjectiveFunctions/Loss/SquaredLoss.h | 4 RcppShark-3.1.1/RcppShark/inst/include/shark/ObjectiveFunctions/Loss/TukeyBiweightLoss.h | 4 RcppShark-3.1.1/RcppShark/inst/include/shark/ObjectiveFunctions/Loss/ZeroOneLoss.h | 4 RcppShark-3.1.1/RcppShark/inst/include/shark/ObjectiveFunctions/NegativeAUC.h | 4 RcppShark-3.1.1/RcppShark/inst/include/shark/ObjectiveFunctions/NegativeGaussianProcessEvidence.h | 38 RcppShark-3.1.1/RcppShark/inst/include/shark/ObjectiveFunctions/NegativeLogLikelihood.h | 5 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 RcppShark-3.1.1/RcppShark/inst/include/shark/Statistics/Distributions/MultiNomialDistribution.h | 4 RcppShark-3.1.1/RcppShark/inst/include/shark/Statistics/Distributions/MultiVariateNormalDistribution.h | 44 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 RcppShark-3.1.1/RcppShark/inst/include/shark/Unsupervised/RBM/BipolarRBM.h | 4 RcppShark-3.1.1/RcppShark/inst/include/shark/Unsupervised/RBM/ConvolutionalBinaryRBM.h | 4 RcppShark-3.1.1/RcppShark/inst/include/shark/Unsupervised/RBM/ConvolutionalRBM.h | 5 RcppShark-3.1.1/RcppShark/inst/include/shark/Unsupervised/RBM/Energy.h | 4 RcppShark-3.1.1/RcppShark/inst/include/shark/Unsupervised/RBM/GaussianBinaryRBM.h | 4 RcppShark-3.1.1/RcppShark/inst/include/shark/Unsupervised/RBM/GradientApproximations/ContrastiveDivergence.h | 4 RcppShark-3.1.1/RcppShark/inst/include/shark/Unsupervised/RBM/GradientApproximations/ExactGradient.h | 4 RcppShark-3.1.1/RcppShark/inst/include/shark/Unsupervised/RBM/GradientApproximations/Impl/DataEvaluator.h | 4 RcppShark-3.1.1/RcppShark/inst/include/shark/Unsupervised/RBM/GradientApproximations/MultiChainApproximator.h | 4 RcppShark-3.1.1/RcppShark/inst/include/shark/Unsupervised/RBM/GradientApproximations/SingleChainApproximator.h | 4 RcppShark-3.1.1/RcppShark/inst/include/shark/Unsupervised/RBM/Impl/AverageEnergyGradient.h | 5 RcppShark-3.1.1/RcppShark/inst/include/shark/Unsupervised/RBM/Impl/ConvolutionalEnergyGradient.h | 5 RcppShark-3.1.1/RcppShark/inst/include/shark/Unsupervised/RBM/Impl/analytics.h | 5 RcppShark-3.1.1/RcppShark/inst/include/shark/Unsupervised/RBM/Neuronlayers/BinaryLayer.h | 4 RcppShark-3.1.1/RcppShark/inst/include/shark/Unsupervised/RBM/Neuronlayers/BipolarLayer.h | 4 RcppShark-3.1.1/RcppShark/inst/include/shark/Unsupervised/RBM/Neuronlayers/GaussianLayer.h | 4 RcppShark-3.1.1/RcppShark/inst/include/shark/Unsupervised/RBM/Neuronlayers/TruncatedExponentialLayer.h | 4 RcppShark-3.1.1/RcppShark/inst/include/shark/Unsupervised/RBM/Problems/BarsAndStripes.h | 4 RcppShark-3.1.1/RcppShark/inst/include/shark/Unsupervised/RBM/Problems/DistantModes.h | 4 RcppShark-3.1.1/RcppShark/inst/include/shark/Unsupervised/RBM/Problems/MNIST.h | 4 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 RcppShark-3.1.1/RcppShark/inst/include/shark/Unsupervised/RBM/Sampling/EnergyStoringTemperedMarkovChain.h | 4 RcppShark-3.1.1/RcppShark/inst/include/shark/Unsupervised/RBM/Sampling/GibbsOperator.h | 4 RcppShark-3.1.1/RcppShark/inst/include/shark/Unsupervised/RBM/Sampling/Impl/SampleTypes.h | 5 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 RcppShark-3.1.1/RcppShark/inst/include/shark/Unsupervised/RBM/StateSpaces/RealSpace.h | 5 RcppShark-3.1.1/RcppShark/inst/include/shark/Unsupervised/RBM/StateSpaces/TwoStateSpace.h | 4 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 RcppShark-3.1.1/RcppShark/src/shark/Algorithms/DirectSearch/Operators/Domination/DCNonDominatedSort.h | 6 RcppShark-3.1.1/RcppShark/src/shark/Algorithms/DirectSearch/Operators/Domination/FastNonDominatedSort.h | 4 RcppShark-3.1.1/RcppShark/src/shark/Algorithms/DirectSearch/Operators/Domination/NonDominatedSort.h | 4 RcppShark-3.1.1/RcppShark/src/shark/Algorithms/DirectSearch/Operators/Domination/ParetoDominance.h | 4 RcppShark-3.1.1/RcppShark/src/shark/Algorithms/DirectSearch/Operators/Evaluation/PenalizingEvaluator.h | 29 RcppShark-3.1.1/RcppShark/src/shark/Algorithms/DirectSearch/Operators/Hypervolume/HVContrApproximator.h | 110 RcppShark-3.1.1/RcppShark/src/shark/Algorithms/DirectSearch/Operators/Hypervolume/HypervolumeApproximator.h | 5 RcppShark-3.1.1/RcppShark/src/shark/Algorithms/DirectSearch/Operators/Hypervolume/HypervolumeCalculator.h | 18 RcppShark-3.1.1/RcppShark/src/shark/Algorithms/DirectSearch/Operators/Hypervolume/HypervolumeCalculator2D.h | 5 RcppShark-3.1.1/RcppShark/src/shark/Algorithms/DirectSearch/Operators/Hypervolume/HypervolumeCalculator3D.h | 97 RcppShark-3.1.1/RcppShark/src/shark/Algorithms/DirectSearch/Operators/Hypervolume/HypervolumeCalculatorMDHOY.h |only RcppShark-3.1.1/RcppShark/src/shark/Algorithms/DirectSearch/Operators/Hypervolume/HypervolumeCalculatorMDWFG.h |only RcppShark-3.1.1/RcppShark/src/shark/Algorithms/DirectSearch/Operators/Hypervolume/HypervolumeContribution.h | 5 RcppShark-3.1.1/RcppShark/src/shark/Algorithms/DirectSearch/Operators/Hypervolume/HypervolumeContribution2D.h | 11 RcppShark-3.1.1/RcppShark/src/shark/Algorithms/DirectSearch/Operators/Hypervolume/HypervolumeContribution3D.h | 5 RcppShark-3.1.1/RcppShark/src/shark/Algorithms/DirectSearch/Operators/Hypervolume/HypervolumeContributionMD.h | 90 RcppShark-3.1.1/RcppShark/src/shark/Algorithms/DirectSearch/Operators/Hypervolume/HypervolumeSubsetSelection2D.h | 5 RcppShark-3.1.1/RcppShark/src/shark/Algorithms/DirectSearch/Operators/Indicators/AdditiveEpsilonIndicator.h | 4 RcppShark-3.1.1/RcppShark/src/shark/Algorithms/DirectSearch/Operators/Indicators/HypervolumeIndicator.h | 4 RcppShark-3.1.1/RcppShark/src/shark/Algorithms/DirectSearch/Operators/Mutation/BitflipMutator.h | 4 RcppShark-3.1.1/RcppShark/src/shark/Algorithms/DirectSearch/Operators/Mutation/PolynomialMutation.h | 4 RcppShark-3.1.1/RcppShark/src/shark/Algorithms/DirectSearch/Operators/PopulationBasedStepSizeAdaptation.h | 5 RcppShark-3.1.1/RcppShark/src/shark/Algorithms/DirectSearch/Operators/Recombination/OnePointCrossover.h | 4 RcppShark-3.1.1/RcppShark/src/shark/Algorithms/DirectSearch/Operators/Recombination/SimulatedBinaryCrossover.h | 4 RcppShark-3.1.1/RcppShark/src/shark/Algorithms/DirectSearch/Operators/Recombination/UniformCrossover.h | 4 RcppShark-3.1.1/RcppShark/src/shark/Algorithms/DirectSearch/Operators/Selection/EPTournamentSelection.h | 4 RcppShark-3.1.1/RcppShark/src/shark/Algorithms/DirectSearch/Operators/Selection/ElitistSelection.h | 4 RcppShark-3.1.1/RcppShark/src/shark/Algorithms/DirectSearch/Operators/Selection/IndicatorBasedSelection.h | 4 RcppShark-3.1.1/RcppShark/src/shark/Algorithms/DirectSearch/Operators/Selection/LinearRanking.h | 4 RcppShark-3.1.1/RcppShark/src/shark/Algorithms/DirectSearch/Operators/Selection/RouletteWheelSelection.h | 5 RcppShark-3.1.1/RcppShark/src/shark/Algorithms/DirectSearch/Operators/Selection/TournamentSelection.h | 5 RcppShark-3.1.1/RcppShark/src/shark/Algorithms/DirectSearch/Operators/Selection/UniformRanking.h | 4 RcppShark-3.1.1/RcppShark/src/shark/Algorithms/DirectSearch/Operators/TwoPointStepSizeAdaptation.h | 5 RcppShark-3.1.1/RcppShark/src/shark/Algorithms/DirectSearch/RealCodedNSGAII.h | 4 RcppShark-3.1.1/RcppShark/src/shark/Algorithms/DirectSearch/SMS-EMOA.h | 4 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 RcppShark-3.1.1/RcppShark/src/shark/Algorithms/StoppingCriteria/AbstractStoppingCriterion.h | 4 RcppShark-3.1.1/RcppShark/src/shark/Algorithms/StoppingCriteria/GeneralizationLoss.h | 6 RcppShark-3.1.1/RcppShark/src/shark/Algorithms/StoppingCriteria/GeneralizationQuotient.h | 6 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 RcppShark-3.1.1/RcppShark/src/shark/Algorithms/StoppingCriteria/ValidatedStoppingCriterion.h | 6 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 RcppShark-3.1.1/RcppShark/src/shark/Algorithms/Trainers/Budgeted/AbstractBudgetMaintenanceStrategy.h | 4 RcppShark-3.1.1/RcppShark/src/shark/Algorithms/Trainers/Budgeted/KernelBudgetedSGDTrainer.h | 4 RcppShark-3.1.1/RcppShark/src/shark/Algorithms/Trainers/Budgeted/MergeBudgetMaintenanceStrategy.h | 4 RcppShark-3.1.1/RcppShark/src/shark/Algorithms/Trainers/Budgeted/ProjectBudgetMaintenanceStrategy.h | 4 RcppShark-3.1.1/RcppShark/src/shark/Algorithms/Trainers/Budgeted/RemoveBudgetMaintenanceStrategy.h | 4 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 RcppShark-3.1.1/RcppShark/src/shark/Algorithms/Trainers/Distribution/GenericDistTrainer.h | 4 RcppShark-3.1.1/RcppShark/src/shark/Algorithms/Trainers/Distribution/NormalTrainer.h | 5 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 RcppShark-3.1.1/RcppShark/src/shark/Algorithms/Trainers/MissingFeatureSvmTrainer.h | 4 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(-)