[mlpack] 01/13: merge upstream/2.0.0 carrying along only debian/*
Barak A. Pearlmutter
barak+git at pearlmutter.net
Mon Jan 18 16:07:53 UTC 2016
This is an automated email from the git hooks/post-receive script.
bap pushed a commit to branch master
in repository mlpack.
commit 00b964c2392371386c8e9aabcd930349bf4a3a10
Merge: f15744f 0539869
Author: Barak A. Pearlmutter <barak+git at pearlmutter.net>
Date: Mon Jan 18 15:01:40 2016 +0000
merge upstream/2.0.0 carrying along only debian/*
.gitignore | 1 -
CMake/ARMA_FindARPACK.cmake | 78 +-
CMake/CXX11.cmake | 48 +
CMake/CompilerFlags.cmake | 16 -
CMake/CreateArmaConfigInfo.cmake | 83 +
CMake/CreateGitVersionHeader.cmake | 29 +
CMake/CreateSVNVersionHeader.cmake | 25 -
CMake/FindArmadillo.cmake | 23 +-
CMake/FindBacktrace.cmake | 106 +
CMake/FindPackageHandleStandardArgs.cmake | 296 --
CMake/GenerateDoxyfile.cmake | 9 +-
CMakeLists.txt | 299 +-
COPYRIGHT.txt | 15 +-
Doxyfile | 9 +-
HISTORY.txt => HISTORY.md | 185 +-
README.md | 225 ++
README.txt | 216 --
UPDATING.txt | 35 +
doc/guide/build.hpp | 62 +-
doc/guide/iodoc.hpp | 19 +-
doc/guide/matrices.hpp | 10 +-
doc/guide/sample.hpp | 6 +-
doc/guide/timer.hpp | 9 +-
doc/guide/version.hpp | 2 +-
doc/policies/kernels.hpp | 167 +
doc/policies/metrics.hpp | 113 +
doc/policies/trees.hpp | 901 +++++
doc/tutorials/README.md | 20 +
doc/tutorials/amf/amf.txt | 108 +-
doc/tutorials/cf/cf.txt | 470 +++
doc/tutorials/det/det.txt | 129 +-
doc/tutorials/emst/emst.txt | 28 +-
doc/tutorials/fastmks/fastmks.txt | 126 +-
doc/tutorials/kmeans/kmeans.txt | 205 +-
.../linear_regression/linear_regression.txt | 190 +-
doc/tutorials/neighbor_search/neighbor_search.txt | 188 +-
doc/tutorials/range_search/range_search.txt | 190 +-
doc/tutorials/tutorials.txt | 10 +-
src/mlpack/CMakeLists.txt | 14 +-
src/mlpack/core.hpp | 118 +-
src/mlpack/core/CMakeLists.txt | 1 +
src/mlpack/core/arma_extend/CMakeLists.txt | 5 +-
src/mlpack/core/arma_extend/Mat_extra_bones.hpp | 4 +
src/mlpack/core/arma_extend/Mat_extra_meat.hpp | 35 +
src/mlpack/core/arma_extend/SpMat_extra_bones.hpp | 6 +-
src/mlpack/core/arma_extend/SpMat_extra_meat.hpp | 34 +-
src/mlpack/core/arma_extend/arma_extend.hpp | 17 +
src/mlpack/core/arma_extend/fn_ccov.hpp | 24 +-
src/mlpack/core/arma_extend/fn_inplace_reshape.hpp | 16 -
src/mlpack/core/arma_extend/glue_ccov_meat.hpp | 30 +-
src/mlpack/core/arma_extend/glue_ccov_proto.hpp | 21 +-
src/mlpack/core/arma_extend/op_ccov_meat.hpp | 34 +-
src/mlpack/core/arma_extend/op_ccov_proto.hpp | 22 +-
src/mlpack/core/arma_extend/operator_minus.hpp | 25 +
.../core/{data => boost_backport}/CMakeLists.txt | 13 +-
src/mlpack/core/boost_backport/README.md | 3 +
.../unordered_collections_load_imp.hpp | 74 +
.../unordered_collections_save_imp.hpp | 86 +
src/mlpack/core/boost_backport/unordered_map.hpp | 231 ++
src/mlpack/core/data/CMakeLists.txt | 11 +-
src/mlpack/core/data/dataset_info.hpp | 104 +
src/mlpack/core/data/dataset_info_impl.hpp | 115 +
src/mlpack/core/data/extension.hpp | 48 +
src/mlpack/core/data/format.hpp | 41 +
src/mlpack/core/data/load.hpp | 118 +-
src/mlpack/core/data/load_arff.hpp | 71 +
src/mlpack/core/data/load_arff_impl.hpp | 221 ++
src/mlpack/core/data/load_impl.hpp | 428 ++-
src/mlpack/core/data/normalize_labels.hpp | 32 +-
src/mlpack/core/data/normalize_labels_impl.hpp | 32 +-
src/mlpack/core/data/save.hpp | 68 +-
src/mlpack/core/data/save_impl.hpp | 130 +-
src/mlpack/core/data/serialization_shim.hpp | 520 +++
src/mlpack/core/dists/CMakeLists.txt | 6 +-
src/mlpack/core/dists/discrete_distribution.cpp | 44 +-
src/mlpack/core/dists/discrete_distribution.hpp | 61 +-
src/mlpack/core/dists/gaussian_distribution.cpp | 116 +-
src/mlpack/core/dists/gaussian_distribution.hpp | 154 +-
src/mlpack/core/dists/laplace_distribution.cpp | 40 +-
src/mlpack/core/dists/laplace_distribution.hpp | 55 +-
src/mlpack/core/dists/regression_distribution.cpp | 75 +
src/mlpack/core/dists/regression_distribution.hpp | 140 +
src/mlpack/core/kernels/CMakeLists.txt | 4 +-
src/mlpack/core/kernels/cosine_distance.hpp | 41 +-
src/mlpack/core/kernels/cosine_distance_impl.hpp | 26 +-
src/mlpack/core/kernels/epanechnikov_kernel.cpp | 58 +-
src/mlpack/core/kernels/epanechnikov_kernel.hpp | 57 +-
.../core/kernels/epanechnikov_kernel_impl.hpp | 47 +-
src/mlpack/core/kernels/example_kernel.hpp | 80 +-
src/mlpack/core/kernels/gaussian_kernel.hpp | 75 +-
.../core/kernels/hyperbolic_tangent_kernel.hpp | 42 +-
src/mlpack/core/kernels/kernel_traits.hpp | 27 +-
src/mlpack/core/kernels/laplacian_kernel.hpp | 56 +-
src/mlpack/core/kernels/linear_kernel.hpp | 40 +-
src/mlpack/core/kernels/polynomial_kernel.hpp | 42 +-
.../core/kernels/pspectrum_string_kernel.cpp | 18 +-
.../core/kernels/pspectrum_string_kernel.hpp | 38 +-
.../core/kernels/pspectrum_string_kernel_impl.hpp | 22 +-
src/mlpack/core/kernels/spherical_kernel.hpp | 98 +-
src/mlpack/core/kernels/triangular_kernel.hpp | 57 +-
src/mlpack/core/math/CMakeLists.txt | 9 +-
src/mlpack/core/math/clamp.hpp | 22 +-
src/mlpack/core/math/columns_to_blocks.cpp | 109 +
src/mlpack/core/math/columns_to_blocks.hpp | 237 ++
src/mlpack/core/math/lin_alg.cpp | 105 +-
src/mlpack/core/math/lin_alg.hpp | 68 +-
src/mlpack/core/math/lin_alg_impl.hpp | 38 +
src/mlpack/core/math/random.cpp | 55 +-
src/mlpack/core/math/random.hpp | 81 +-
src/mlpack/core/math/random_basis.cpp | 59 +
src/mlpack/core/math/random_basis.hpp | 42 +
src/mlpack/core/math/range.hpp | 28 +-
src/mlpack/core/math/range_impl.hpp | 35 +-
src/mlpack/core/math/round.hpp | 18 +-
src/mlpack/core/metrics/CMakeLists.txt | 4 +-
src/mlpack/core/metrics/ip_metric.hpp | 65 +-
src/mlpack/core/metrics/ip_metric_impl.hpp | 55 +-
src/mlpack/core/metrics/lmetric.hpp | 62 +-
src/mlpack/core/metrics/lmetric_impl.hpp | 67 +-
src/mlpack/core/metrics/mahalanobis_distance.hpp | 34 +-
.../core/metrics/mahalanobis_distance_impl.hpp | 59 +-
src/mlpack/core/optimizers/CMakeLists.txt | 2 +-
.../optimizers/aug_lagrangian/aug_lagrangian.hpp | 25 +-
.../aug_lagrangian/aug_lagrangian_function.hpp | 25 +-
.../aug_lagrangian_function_impl.hpp | 34 +-
.../aug_lagrangian/aug_lagrangian_impl.hpp | 49 +-
.../aug_lagrangian_test_functions.cpp | 49 +-
.../aug_lagrangian_test_functions.hpp | 25 +-
src/mlpack/core/optimizers/lbfgs/lbfgs.hpp | 37 +-
src/mlpack/core/optimizers/lbfgs/lbfgs_impl.hpp | 84 +-
.../core/optimizers/lbfgs/test_functions.cpp | 18 +-
.../core/optimizers/lbfgs/test_functions.hpp | 24 +-
src/mlpack/core/optimizers/lrsdp/CMakeLists.txt | 13 -
src/mlpack/core/optimizers/lrsdp/lrsdp.cpp | 42 -
src/mlpack/core/optimizers/lrsdp/lrsdp.hpp | 111 -
.../core/optimizers/lrsdp/lrsdp_function.cpp | 176 -
.../core/optimizers/lrsdp/lrsdp_function.hpp | 119 -
.../core/optimizers/sa/exponential_schedule.hpp | 22 +-
src/mlpack/core/optimizers/sa/sa.hpp | 24 +-
src/mlpack/core/optimizers/sa/sa_impl.hpp | 46 +-
src/mlpack/core/optimizers/sdp/CMakeLists.txt | 17 +
src/mlpack/core/optimizers/sdp/lrsdp.hpp | 104 +
src/mlpack/core/optimizers/sdp/lrsdp_function.hpp | 136 +
.../core/optimizers/sdp/lrsdp_function_impl.hpp | 227 ++
src/mlpack/core/optimizers/sdp/lrsdp_impl.hpp | 51 +
src/mlpack/core/optimizers/sdp/primal_dual.hpp | 148 +
.../core/optimizers/sdp/primal_dual_impl.hpp | 473 +++
src/mlpack/core/optimizers/sdp/sdp.hpp | 153 +
src/mlpack/core/optimizers/sdp/sdp_impl.hpp | 86 +
src/mlpack/core/optimizers/sgd/sgd.hpp | 25 +-
src/mlpack/core/optimizers/sgd/sgd_impl.hpp | 39 +-
src/mlpack/core/optimizers/sgd/test_function.cpp | 18 +-
src/mlpack/core/optimizers/sgd/test_function.hpp | 24 +-
src/mlpack/core/tree/CMakeLists.txt | 32 +-
src/mlpack/core/tree/TREE_EXPLANATION.txt | 2 +-
src/mlpack/core/tree/ballbound.hpp | 62 +-
src/mlpack/core/tree/ballbound_impl.hpp | 67 +-
src/mlpack/core/tree/binary_space_tree.hpp | 24 +-
.../tree/binary_space_tree/binary_space_tree.hpp | 317 +-
.../binary_space_tree/binary_space_tree_impl.hpp | 794 ++--
.../breadth_first_dual_tree_traverser.hpp | 125 +
.../breadth_first_dual_tree_traverser_impl.hpp | 220 ++
.../tree/binary_space_tree/dual_tree_traverser.hpp | 32 +-
.../binary_space_tree/dual_tree_traverser_impl.hpp | 53 +-
.../core/tree/binary_space_tree/mean_split.hpp | 24 +-
.../tree/binary_space_tree/mean_split_impl.hpp | 147 +-
.../{mean_split.hpp => midpoint_split.hpp} | 41 +-
.../tree/binary_space_tree/midpoint_split_impl.hpp | 276 ++
.../binary_space_tree/single_tree_traverser.hpp | 32 +-
.../single_tree_traverser_impl.hpp | 141 +-
src/mlpack/core/tree/binary_space_tree/traits.hpp | 37 +-
src/mlpack/core/tree/binary_space_tree/typedef.hpp | 156 +
src/mlpack/core/tree/bound_traits.hpp | 47 +
src/mlpack/core/tree/bounds.hpp | 19 +-
src/mlpack/core/tree/cosine_tree/cosine_tree.cpp | 24 +-
src/mlpack/core/tree/cosine_tree/cosine_tree.hpp | 43 +-
src/mlpack/core/tree/cover_tree.hpp | 22 +-
src/mlpack/core/tree/cover_tree/cover_tree.hpp | 124 +-
.../core/tree/cover_tree/cover_tree_impl.hpp | 729 +++-
.../core/tree/cover_tree/dual_tree_traverser.hpp | 35 +-
.../tree/cover_tree/dual_tree_traverser_impl.hpp | 86 +-
.../core/tree/cover_tree/first_point_is_root.hpp | 25 +-
.../core/tree/cover_tree/single_tree_traverser.hpp | 32 +-
.../tree/cover_tree/single_tree_traverser_impl.hpp | 57 +-
src/mlpack/core/tree/cover_tree/traits.hpp | 34 +-
src/mlpack/core/tree/cover_tree/typedef.hpp | 57 +
src/mlpack/core/tree/example_tree.hpp | 22 +-
src/mlpack/core/tree/hrectbound.hpp | 87 +-
src/mlpack/core/tree/hrectbound_impl.hpp | 221 +-
src/mlpack/core/tree/mrkd_statistic.cpp | 50 -
src/mlpack/core/tree/mrkd_statistic.hpp | 105 -
src/mlpack/core/tree/mrkd_statistic_impl.hpp | 100 -
src/mlpack/core/tree/rectangle_tree.hpp | 30 +-
.../dual_tree_traverser.hpp | 72 +-
.../rectangle_tree/dual_tree_traverser_impl.hpp | 181 +
.../tree/rectangle_tree/hilbert_r_tree_split.hpp | 19 +
.../rectangle_tree/hilbert_r_tree_split_impl.hpp | 19 +
.../r_star_tree_descent_heuristic.hpp | 63 +
.../r_star_tree_descent_heuristic_impl.hpp | 215 ++
.../core/tree/rectangle_tree/r_star_tree_split.hpp | 85 +
.../tree/rectangle_tree/r_star_tree_split_impl.hpp | 694 ++++
.../rectangle_tree/r_tree_descent_heuristic.hpp | 73 +
.../r_tree_descent_heuristic_impl.hpp | 118 +
.../core/tree/rectangle_tree/r_tree_split.hpp | 101 +
.../core/tree/rectangle_tree/r_tree_split_impl.hpp | 540 +++
.../core/tree/rectangle_tree/rectangle_tree.hpp | 629 ++++
.../tree/rectangle_tree/rectangle_tree_impl.hpp | 1060 ++++++
.../tree/rectangle_tree/single_tree_traverser.hpp | 91 +
.../rectangle_tree/single_tree_traverser_impl.hpp | 99 +
src/mlpack/core/tree/rectangle_tree/traits.hpp | 76 +
src/mlpack/core/tree/rectangle_tree/typedef.hpp | 99 +
.../core/tree/rectangle_tree/x_tree_split.hpp | 96 +
.../core/tree/rectangle_tree/x_tree_split_impl.hpp | 847 +++++
src/mlpack/core/tree/statistic.hpp | 34 +-
src/mlpack/core/tree/traversal_info.hpp | 18 +-
src/mlpack/core/tree/tree_traits.hpp | 38 +-
src/mlpack/core/util/CMakeLists.txt | 9 +-
src/mlpack/core/util/arma_config_check.hpp | 49 +
src/mlpack/core/util/arma_traits.hpp | 20 +-
src/mlpack/core/util/cli.cpp | 45 +-
src/mlpack/core/util/cli.hpp | 48 +-
src/mlpack/core/util/cli_deleter.cpp | 18 +-
src/mlpack/core/util/cli_deleter.hpp | 22 +-
src/mlpack/core/util/cli_impl.hpp | 20 +-
src/mlpack/core/util/log.cpp | 45 +-
src/mlpack/core/util/log.hpp | 18 +-
src/mlpack/core/util/nulloutstream.hpp | 18 +-
src/mlpack/core/util/option.cpp | 18 +-
src/mlpack/core/util/option.hpp | 22 +-
src/mlpack/core/util/option_impl.hpp | 22 +-
src/mlpack/core/util/prefixedoutstream.cpp | 18 +-
src/mlpack/core/util/prefixedoutstream.hpp | 61 +-
src/mlpack/core/util/prefixedoutstream_impl.hpp | 67 +-
src/mlpack/core/util/save_restore_utility.cpp | 213 --
src/mlpack/core/util/save_restore_utility.hpp | 129 -
src/mlpack/core/util/save_restore_utility_impl.hpp | 100 -
src/mlpack/core/util/sfinae_utility.hpp | 21 +-
src/mlpack/core/util/string_util.cpp | 18 +-
src/mlpack/core/util/string_util.hpp | 22 +-
src/mlpack/core/util/timers.cpp | 86 +-
src/mlpack/core/util/timers.hpp | 48 +-
src/mlpack/core/util/version.cpp | 26 +-
src/mlpack/core/util/version.hpp | 34 +-
src/mlpack/methods/CMakeLists.txt | 8 +-
.../{decision_stump => adaboost}/CMakeLists.txt | 17 +-
src/mlpack/methods/adaboost/adaboost.hpp | 195 +
src/mlpack/methods/adaboost/adaboost_impl.hpp | 266 ++
src/mlpack/methods/adaboost/adaboost_main.cpp | 376 ++
src/mlpack/methods/amf/CMakeLists.txt | 4 +-
src/mlpack/methods/amf/amf.hpp | 163 +-
src/mlpack/methods/amf/amf_impl.hpp | 26 +-
src/mlpack/methods/amf/amf_main.cpp | 146 -
src/mlpack/methods/amf/init_rules/CMakeLists.txt | 6 +-
src/mlpack/methods/amf/init_rules/average_init.hpp | 75 +-
.../methods/amf/init_rules/random_acol_init.hpp | 64 +-
src/mlpack/methods/amf/init_rules/random_init.hpp | 44 +-
.../amf/termination_policies/CMakeLists.txt | 5 +-
.../complete_incremental_termination.hpp | 129 +-
.../incomplete_incremental_termination.hpp | 104 +-
.../max_iteration_termination.hpp | 95 +
.../simple_residue_termination.hpp | 32 +-
.../simple_tolerance_termination.hpp | 24 +-
.../validation_RMSE_termination.hpp | 125 +-
src/mlpack/methods/amf/update_rules/CMakeLists.txt | 4 +-
src/mlpack/methods/amf/update_rules/nmf_als.hpp | 82 +-
.../methods/amf/update_rules/nmf_mult_dist.hpp | 74 +-
.../methods/amf/update_rules/nmf_mult_div.hpp | 79 +-
.../amf/update_rules/svd_batch_learning.hpp | 191 +-
.../svd_complete_incremental_learning.hpp | 174 +-
.../svd_incomplete_incremental_learning.hpp | 155 +-
src/mlpack/methods/cf/CMakeLists.txt | 13 +-
src/mlpack/methods/cf/cf.cpp | 298 ++
src/mlpack/methods/cf/cf.hpp | 179 +-
src/mlpack/methods/cf/cf_impl.hpp | 293 +-
src/mlpack/methods/cf/cf_main.cpp | 335 +-
src/mlpack/methods/cf/svd_wrapper.hpp | 101 +
src/mlpack/methods/cf/svd_wrapper_impl.hpp | 142 +
src/mlpack/methods/decision_stump/CMakeLists.txt | 11 +-
.../methods/decision_stump/decision_stump.hpp | 174 +-
.../methods/decision_stump/decision_stump_impl.hpp | 302 +-
.../methods/decision_stump/decision_stump_main.cpp | 240 +-
src/mlpack/methods/det/CMakeLists.txt | 8 +-
src/mlpack/methods/det/det_main.cpp | 258 +-
src/mlpack/methods/det/dt_utils.cpp | 75 +-
src/mlpack/methods/det/dt_utils.hpp | 22 +-
src/mlpack/methods/det/dtree.cpp | 81 +-
src/mlpack/methods/det/dtree.hpp | 56 +-
src/mlpack/methods/emst/CMakeLists.txt | 10 +-
src/mlpack/methods/emst/dtb.hpp | 67 +-
src/mlpack/methods/emst/dtb_impl.hpp | 172 +-
src/mlpack/methods/emst/dtb_rules.hpp | 18 +-
src/mlpack/methods/emst/dtb_rules_impl.hpp | 24 +-
src/mlpack/methods/emst/dtb_stat.hpp | 24 +-
src/mlpack/methods/emst/edge_pair.hpp | 22 +-
src/mlpack/methods/emst/emst_main.cpp | 25 +-
src/mlpack/methods/emst/union_find.hpp | 22 +-
src/mlpack/methods/fastmks/CMakeLists.txt | 14 +-
src/mlpack/methods/fastmks/fastmks.hpp | 237 +-
src/mlpack/methods/fastmks/fastmks_impl.hpp | 726 ++--
src/mlpack/methods/fastmks/fastmks_main.cpp | 339 +-
src/mlpack/methods/fastmks/fastmks_model.cpp | 218 ++
src/mlpack/methods/fastmks/fastmks_model.hpp | 155 +
src/mlpack/methods/fastmks/fastmks_model_impl.hpp | 230 ++
src/mlpack/methods/fastmks/fastmks_rules.hpp | 30 +-
src/mlpack/methods/fastmks/fastmks_rules_impl.hpp | 99 +-
src/mlpack/methods/fastmks/fastmks_stat.hpp | 47 +-
src/mlpack/methods/gmm/CMakeLists.txt | 34 +-
src/mlpack/methods/gmm/diagonal_constraint.hpp | 26 +-
.../methods/gmm/eigenvalue_ratio_constraint.hpp | 39 +-
src/mlpack/methods/gmm/em_fit.hpp | 42 +-
src/mlpack/methods/gmm/em_fit_impl.hpp | 146 +-
src/mlpack/methods/gmm/gmm.cpp | 167 +
src/mlpack/methods/gmm/gmm.hpp | 225 +-
src/mlpack/methods/gmm/gmm_generate_main.cpp | 67 +
src/mlpack/methods/gmm/gmm_impl.hpp | 436 +--
src/mlpack/methods/gmm/gmm_probability_main.cpp | 60 +
.../gmm/{gmm_main.cpp => gmm_train_main.cpp} | 134 +-
src/mlpack/methods/gmm/no_constraint.hpp | 26 +-
src/mlpack/methods/gmm/phi.hpp | 154 -
.../methods/gmm/positive_definite_constraint.hpp | 63 +-
src/mlpack/methods/hmm/CMakeLists.txt | 28 +-
src/mlpack/methods/hmm/hmm.hpp | 90 +-
src/mlpack/methods/hmm/hmm_generate_main.cpp | 129 +-
src/mlpack/methods/hmm/hmm_impl.hpp | 132 +-
src/mlpack/methods/hmm/hmm_loglik_main.cpp | 114 +-
src/mlpack/methods/hmm/hmm_regression.hpp | 350 ++
src/mlpack/methods/hmm/hmm_regression_impl.hpp | 206 ++
src/mlpack/methods/hmm/hmm_train_main.cpp | 411 ++-
src/mlpack/methods/hmm/hmm_util.hpp | 63 +-
src/mlpack/methods/hmm/hmm_util_impl.hpp | 333 +-
src/mlpack/methods/hmm/hmm_viterbi_main.cpp | 107 +-
src/mlpack/methods/hoeffding_trees/CMakeLists.txt | 35 +
.../hoeffding_trees/binary_numeric_split.hpp | 146 +
.../hoeffding_trees/binary_numeric_split_impl.hpp | 196 +
.../hoeffding_trees/binary_numeric_split_info.hpp | 59 +
.../hoeffding_trees/categorical_split_info.hpp | 51 +
.../methods/hoeffding_trees/gini_impurity.hpp | 99 +
.../hoeffding_categorical_split.hpp | 139 +
.../hoeffding_categorical_split_impl.hpp | 110 +
.../hoeffding_trees/hoeffding_numeric_split.hpp | 166 +
.../hoeffding_numeric_split_impl.hpp | 264 ++
.../methods/hoeffding_trees/hoeffding_tree.hpp | 332 ++
.../hoeffding_trees/hoeffding_tree_impl.hpp | 731 ++++
.../hoeffding_trees/hoeffding_tree_main.cpp | 343 ++
.../methods/hoeffding_trees/information_gain.hpp | 106 +
.../methods/hoeffding_trees/numeric_split_info.hpp | 63 +
src/mlpack/methods/hoeffding_trees/typedef.hpp | 36 +
src/mlpack/methods/kernel_pca/CMakeLists.txt | 10 +-
src/mlpack/methods/kernel_pca/kernel_pca.hpp | 25 +-
src/mlpack/methods/kernel_pca/kernel_pca_impl.hpp | 35 +-
src/mlpack/methods/kernel_pca/kernel_pca_main.cpp | 34 +-
.../methods/kernel_pca/kernel_rules/CMakeLists.txt | 4 +-
.../kernel_pca/kernel_rules/naive_method.hpp | 28 +-
.../kernel_pca/kernel_rules/nystroem_method.hpp | 50 +-
src/mlpack/methods/kmeans/CMakeLists.txt | 26 +-
src/mlpack/methods/kmeans/allow_empty_clusters.hpp | 47 +-
src/mlpack/methods/kmeans/dual_tree_kmeans.hpp | 187 +
.../methods/kmeans/dual_tree_kmeans_impl.hpp | 706 ++++
.../methods/kmeans/dual_tree_kmeans_rules.hpp | 97 +
.../methods/kmeans/dual_tree_kmeans_rules_impl.hpp | 349 ++
.../methods/kmeans/dual_tree_kmeans_statistic.hpp | 133 +
src/mlpack/methods/kmeans/elkan_kmeans.hpp | 80 +
src/mlpack/methods/kmeans/elkan_kmeans_impl.hpp | 201 ++
src/mlpack/methods/kmeans/hamerly_kmeans.hpp | 78 +
src/mlpack/methods/kmeans/hamerly_kmeans_impl.hpp | 190 +
src/mlpack/methods/kmeans/kmeans.hpp | 129 +-
src/mlpack/methods/kmeans/kmeans_impl.hpp | 440 +--
src/mlpack/methods/kmeans/kmeans_main.cpp | 314 +-
.../methods/kmeans/max_variance_new_cluster.hpp | 62 +-
.../kmeans/max_variance_new_cluster_impl.hpp | 144 +-
src/mlpack/methods/kmeans/naive_kmeans.hpp | 80 +
src/mlpack/methods/kmeans/naive_kmeans_impl.hpp | 99 +
src/mlpack/methods/kmeans/pelleg_moore_kmeans.hpp | 105 +
.../methods/kmeans/pelleg_moore_kmeans_impl.hpp | 98 +
.../methods/kmeans/pelleg_moore_kmeans_rules.hpp | 122 +
.../kmeans/pelleg_moore_kmeans_rules_impl.hpp | 193 +
.../kmeans/pelleg_moore_kmeans_statistic.hpp | 86 +
src/mlpack/methods/kmeans/random_partition.hpp | 30 +-
src/mlpack/methods/kmeans/refined_start.hpp | 32 +-
src/mlpack/methods/kmeans/refined_start_impl.hpp | 29 +-
src/mlpack/methods/lars/CMakeLists.txt | 13 +-
src/mlpack/methods/lars/lars.cpp | 71 +-
src/mlpack/methods/lars/lars.hpp | 63 +-
src/mlpack/methods/lars/lars_impl.hpp | 68 +
src/mlpack/methods/lars/lars_main.cpp | 179 +-
.../methods/linear_regression/CMakeLists.txt | 8 +-
.../linear_regression/linear_regression.cpp | 70 +-
.../linear_regression/linear_regression.hpp | 83 +-
.../linear_regression/linear_regression_main.cpp | 57 +-
.../methods/local_coordinate_coding/CMakeLists.txt | 16 +-
.../{lcc_impl.hpp => lcc.cpp} | 146 +-
src/mlpack/methods/local_coordinate_coding/lcc.hpp | 127 +-
.../methods/local_coordinate_coding/lcc_impl.hpp | 299 +-
.../methods/local_coordinate_coding/lcc_main.cpp | 225 +-
.../methods/logistic_regression/CMakeLists.txt | 10 +-
.../logistic_regression/logistic_regression.hpp | 132 +-
.../logistic_regression_function.hpp | 42 +-
...n.cpp => logistic_regression_function_impl.hpp} | 87 +-
.../logistic_regression_impl.hpp | 160 +-
.../logistic_regression_main.cpp | 296 +-
src/mlpack/methods/lsh/CMakeLists.txt | 13 +-
src/mlpack/methods/lsh/lsh_main.cpp | 157 +-
src/mlpack/methods/lsh/lsh_search.hpp | 220 +-
src/mlpack/methods/lsh/lsh_search_impl.hpp | 356 +-
.../{quic_svd => matrix_completion}/CMakeLists.txt | 8 +-
.../matrix_completion/matrix_completion.cpp | 124 +
.../matrix_completion/matrix_completion.hpp | 155 +
src/mlpack/methods/mean_shift/CMakeLists.txt | 24 +
src/mlpack/methods/mean_shift/mean_shift.hpp | 183 +
src/mlpack/methods/mean_shift/mean_shift_impl.hpp | 285 ++
src/mlpack/methods/mean_shift/mean_shift_main.cpp | 126 +
src/mlpack/methods/mvu/CMakeLists.txt | 23 -
src/mlpack/methods/mvu/mvu.cpp | 114 -
src/mlpack/methods/mvu/mvu.hpp | 50 -
src/mlpack/methods/mvu/mvu_main.cpp | 78 -
src/mlpack/methods/naive_bayes/CMakeLists.txt | 10 +-
.../methods/naive_bayes/naive_bayes_classifier.hpp | 98 +-
.../naive_bayes/naive_bayes_classifier_impl.hpp | 122 +-
src/mlpack/methods/naive_bayes/nbc_main.cpp | 227 +-
src/mlpack/methods/nca/CMakeLists.txt | 10 +-
src/mlpack/methods/nca/nca.hpp | 31 +-
src/mlpack/methods/nca/nca_impl.hpp | 37 +-
src/mlpack/methods/nca/nca_main.cpp | 30 +-
.../methods/nca/nca_softmax_error_function.hpp | 31 +-
.../nca/nca_softmax_error_function_impl.hpp | 38 +-
src/mlpack/methods/neighbor_search/CMakeLists.txt | 16 +-
src/mlpack/methods/neighbor_search/allkfn_main.cpp | 317 +-
src/mlpack/methods/neighbor_search/allknn_main.cpp | 403 +--
.../methods/neighbor_search/neighbor_search.hpp | 290 +-
.../neighbor_search/neighbor_search_impl.hpp | 838 +++--
.../neighbor_search/neighbor_search_rules.hpp | 30 +-
.../neighbor_search/neighbor_search_rules_impl.hpp | 34 +-
.../neighbor_search/neighbor_search_stat.hpp | 40 +-
src/mlpack/methods/neighbor_search/ns_model.hpp | 153 +
.../methods/neighbor_search/ns_model_impl.hpp | 492 +++
.../methods/neighbor_search/ns_traversal_info.hpp | 22 +-
.../sort_policies/furthest_neighbor_sort.cpp | 18 +-
.../sort_policies/furthest_neighbor_sort.hpp | 22 +-
.../sort_policies/furthest_neighbor_sort_impl.hpp | 22 +-
.../sort_policies/nearest_neighbor_sort.cpp | 18 +-
.../sort_policies/nearest_neighbor_sort.hpp | 22 +-
.../sort_policies/nearest_neighbor_sort_impl.hpp | 22 +-
src/mlpack/methods/neighbor_search/typedef.hpp | 22 +-
src/mlpack/methods/neighbor_search/unmap.cpp | 22 +-
src/mlpack/methods/neighbor_search/unmap.hpp | 22 +-
src/mlpack/methods/nmf/CMakeLists.txt | 6 +-
src/mlpack/methods/nmf/nmf_main.cpp | 24 +-
src/mlpack/methods/nystroem_method/CMakeLists.txt | 4 +-
.../methods/nystroem_method/kmeans_selection.hpp | 36 +-
.../methods/nystroem_method/nystroem_method.hpp | 30 +-
.../nystroem_method/nystroem_method_impl.hpp | 28 +-
.../methods/nystroem_method/ordered_selection.hpp | 22 +-
.../methods/nystroem_method/random_selection.hpp | 22 +-
src/mlpack/methods/pca/CMakeLists.txt | 10 +-
src/mlpack/methods/pca/pca.cpp | 28 +-
src/mlpack/methods/pca/pca.hpp | 27 +-
src/mlpack/methods/pca/pca_main.cpp | 18 +-
src/mlpack/methods/perceptron/CMakeLists.txt | 10 +-
.../initialization_methods/CMakeLists.txt | 4 +-
.../initialization_methods/random_init.hpp | 36 +-
.../initialization_methods/zero_init.hpp | 39 +-
.../perceptron/learning_policies/CMakeLists.txt | 4 +-
.../learning_policies/simple_weight_update.hpp | 65 +-
src/mlpack/methods/perceptron/perceptron.hpp | 137 +-
src/mlpack/methods/perceptron/perceptron_impl.hpp | 211 +-
src/mlpack/methods/perceptron/perceptron_main.cpp | 316 +-
src/mlpack/methods/quic_svd/CMakeLists.txt | 4 +-
src/mlpack/methods/quic_svd/quic_svd.hpp | 59 +-
src/mlpack/methods/quic_svd/quic_svd_impl.hpp | 26 +-
src/mlpack/methods/radical/CMakeLists.txt | 8 +-
src/mlpack/methods/radical/radical.cpp | 30 +-
src/mlpack/methods/radical/radical.hpp | 25 +-
src/mlpack/methods/radical/radical_main.cpp | 18 +-
src/mlpack/methods/range_search/CMakeLists.txt | 13 +-
src/mlpack/methods/range_search/range_search.hpp | 314 +-
.../methods/range_search/range_search_impl.hpp | 721 +++-
.../methods/range_search/range_search_main.cpp | 438 ++-
.../methods/range_search/range_search_rules.hpp | 40 +-
.../range_search/range_search_rules_impl.hpp | 35 +-
.../methods/range_search/range_search_stat.hpp | 38 +-
src/mlpack/methods/range_search/rs_model.cpp | 319 ++
src/mlpack/methods/range_search/rs_model.hpp | 186 +
src/mlpack/methods/range_search/rs_model_impl.hpp | 153 +
src/mlpack/methods/rann/CMakeLists.txt | 19 +-
src/mlpack/methods/rann/allkrann_main.cpp | 405 +--
src/mlpack/methods/rann/ra_model.hpp | 187 +
src/mlpack/methods/rann/ra_model_impl.hpp | 573 +++
src/mlpack/methods/rann/ra_query_stat.hpp | 31 +-
src/mlpack/methods/rann/ra_search.hpp | 468 ++-
src/mlpack/methods/rann/ra_search_impl.hpp | 798 +++--
src/mlpack/methods/rann/ra_search_rules.hpp | 77 +-
src/mlpack/methods/rann/ra_search_rules_impl.hpp | 259 +-
src/mlpack/methods/rann/ra_typedef.hpp | 22 +-
src/mlpack/methods/rann/ra_util.cpp | 197 +
src/mlpack/methods/rann/ra_util.hpp | 79 +
src/mlpack/methods/regularized_svd/CMakeLists.txt | 4 +-
.../methods/regularized_svd/regularized_svd.hpp | 107 +-
.../regularized_svd/regularized_svd_function.cpp | 44 +-
.../regularized_svd/regularized_svd_function.hpp | 50 +-
.../regularized_svd/regularized_svd_impl.hpp | 63 +-
.../methods/softmax_regression/CMakeLists.txt | 25 +
.../softmax_regression/softmax_regression.hpp | 215 ++
.../softmax_regression_function.cpp | 217 ++
.../softmax_regression_function.hpp | 163 +
.../softmax_regression/softmax_regression_impl.hpp | 182 +
.../softmax_regression/softmax_regression_main.cpp | 303 ++
.../methods/sparse_autoencoder/CMakeLists.txt | 6 +-
.../methods/sparse_autoencoder/maximal_inputs.cpp | 56 +
.../methods/sparse_autoencoder/maximal_inputs.hpp | 106 +
.../sparse_autoencoder/sparse_autoencoder.hpp | 22 +-
.../sparse_autoencoder_function.cpp | 18 +-
.../sparse_autoencoder_function.hpp | 24 +-
.../sparse_autoencoder/sparse_autoencoder_impl.hpp | 22 +-
src/mlpack/methods/sparse_coding/CMakeLists.txt | 9 +-
.../data_dependent_random_initializer.hpp | 22 +-
.../methods/sparse_coding/nothing_initializer.hpp | 22 +-
.../methods/sparse_coding/random_initializer.hpp | 22 +-
.../{sparse_coding_impl.hpp => sparse_coding.cpp} | 166 +-
src/mlpack/methods/sparse_coding/sparse_coding.hpp | 168 +-
.../methods/sparse_coding/sparse_coding_impl.hpp | 334 +-
.../methods/sparse_coding/sparse_coding_main.cpp | 263 +-
src/mlpack/prereqs.hpp | 44 +-
src/mlpack/tests/CMakeLists.txt | 19 +-
src/mlpack/tests/adaboost_test.cpp | 896 +++++
src/mlpack/tests/allkfn_test.cpp | 167 +-
src/mlpack/tests/allknn_test.cpp | 550 ++-
src/mlpack/tests/allkrann_search_test.cpp | 311 +-
src/mlpack/tests/arma_extend_test.cpp | 214 +-
src/mlpack/tests/armadillo_svd_test.cpp | 67 +
src/mlpack/tests/aug_lagrangian_test.cpp | 18 +-
src/mlpack/tests/cf_test.cpp | 417 ++-
src/mlpack/tests/cli_test.cpp | 32 +-
src/mlpack/tests/cosine_tree_test.cpp | 30 +-
src/mlpack/tests/data/completion_X.csv | 20 +
src/mlpack/tests/data/completion_indices.csv | 2 +
src/mlpack/tests/data/erdosrenyi-n100.csv | 1440 ++++++++
src/mlpack/tests/data/{iris.txt => iris.csv} | 0
src/mlpack/tests/data/iris_labels.txt | 2 +-
src/mlpack/tests/data/iris_test.csv | 63 +
src/mlpack/tests/data/iris_test_labels.csv | 63 +
src/mlpack/tests/data/iris_train.csv | 87 +
.../{iris_labels.txt => iris_train_labels.csv} | 63 -
src/mlpack/tests/data/r10.txt | 10 +
src/mlpack/tests/data/sensing_A.csv | 200 ++
src/mlpack/tests/data/sensing_X.csv | 20 +
src/mlpack/tests/data/test_labels_nonlinsep.txt | 600 ++++
src/mlpack/tests/data/test_nonlinsep.txt | 600 ++++
src/mlpack/tests/data/thyroid_test.csv | 3428 ++++++++++++++++++
src/mlpack/tests/data/thyroid_train.csv | 3772 ++++++++++++++++++++
src/mlpack/tests/data/train_labels_nonlinsep.txt | 1200 +++++++
src/mlpack/tests/data/train_nonlinsep.txt | 1200 +++++++
src/mlpack/tests/data/vc2.csv | 207 ++
.../tests/data/{iris_labels.txt => vc2_labels.txt} | 77 +-
src/mlpack/tests/data/vc2_test.csv | 67 +
src/mlpack/tests/data/vc2_test_labels.txt | 67 +
src/mlpack/tests/decision_stump_test.cpp | 86 +-
src/mlpack/tests/det_test.cpp | 18 +-
src/mlpack/tests/distribution_test.cpp | 182 +-
src/mlpack/tests/emst_test.cpp | 30 +-
src/mlpack/tests/fastmks_test.cpp | 856 ++++-
src/mlpack/tests/gmm_test.cpp | 388 +-
src/mlpack/tests/hmm_test.cpp | 383 +-
src/mlpack/tests/hoeffding_tree_test.cpp | 1001 ++++++
src/mlpack/tests/kernel_pca_test.cpp | 18 +-
src/mlpack/tests/kernel_test.cpp | 18 +-
src/mlpack/tests/kernel_traits_test.cpp | 18 +-
src/mlpack/tests/kmeans_test.cpp | 298 +-
src/mlpack/tests/lars_test.cpp | 156 +-
src/mlpack/tests/layer_traits_test.cpp | 83 +
src/mlpack/tests/lbfgs_test.cpp | 18 +-
src/mlpack/tests/lin_alg_test.cpp | 117 +-
src/mlpack/tests/linear_regression_test.cpp | 39 +-
src/mlpack/tests/load_save_test.cpp | 785 +++-
src/mlpack/tests/local_coordinate_coding_test.cpp | 91 +-
src/mlpack/tests/log_test.cpp | 53 +
src/mlpack/tests/logistic_regression_test.cpp | 219 +-
src/mlpack/tests/lrsdp_test.cpp | 226 +-
src/mlpack/tests/lsh_test.cpp | 69 +-
src/mlpack/tests/math_test.cpp | 18 +-
src/mlpack/tests/matrix_completion_test.cpp | 77 +
src/mlpack/tests/maximal_inputs_test.cpp | 96 +
src/mlpack/tests/mean_shift_test.cpp | 161 +
src/mlpack/tests/metric_test.cpp | 18 +-
src/mlpack/tests/mlpack_test.cpp | 57 +-
src/mlpack/tests/nbc_test.cpp | 189 +-
src/mlpack/tests/nca_test.cpp | 38 +-
src/mlpack/tests/nmf_test.cpp | 30 +-
src/mlpack/tests/nystroem_method_test.cpp | 23 +-
src/mlpack/tests/old_boost_test_definitions.hpp | 18 +-
src/mlpack/tests/pca_test.cpp | 18 +-
src/mlpack/tests/perceptron_test.cpp | 34 +-
src/mlpack/tests/quic_svd_test.cpp | 51 +-
src/mlpack/tests/radical_test.cpp | 18 +-
src/mlpack/tests/range_search_test.cpp | 598 +++-
src/mlpack/tests/rectangle_tree_test.cpp | 853 +++++
src/mlpack/tests/regularized_svd_test.cpp | 18 +-
src/mlpack/tests/sa_test.cpp | 19 +-
src/mlpack/tests/save_restore_utility_test.cpp | 181 -
src/mlpack/tests/sdp_primal_dual_test.cpp | 638 ++++
src/mlpack/tests/serialization.cpp | 91 +
src/mlpack/tests/serialization.hpp | 214 ++
src/mlpack/tests/serialization_test.cpp | 1673 +++++++++
src/mlpack/tests/sgd_test.cpp | 18 +-
src/mlpack/tests/softmax_regression_test.cpp | 426 +++
src/mlpack/tests/sort_policy_test.cpp | 50 +-
src/mlpack/tests/sparse_autoencoder_test.cpp | 18 +-
src/mlpack/tests/sparse_coding_test.cpp | 92 +-
src/mlpack/tests/svd_batch_test.cpp | 105 +-
src/mlpack/tests/svd_incremental_test.cpp | 104 +-
src/mlpack/tests/termination_policy_test.cpp | 76 +
src/mlpack/tests/to_string_test.cpp | 508 ---
src/mlpack/tests/tree_test.cpp | 506 ++-
src/mlpack/tests/tree_traits_test.cpp | 58 +-
src/mlpack/tests/union_find_test.cpp | 18 +-
614 files changed, 70038 insertions(+), 17002 deletions(-)
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