[mlpack-git] master: Merge remote-tracking branch 'upstream/master' into ubtree (fe5f7e9)
gitdub at mlpack.org
gitdub at mlpack.org
Mon Aug 29 12:02:19 EDT 2016
Repository : https://github.com/mlpack/mlpack
On branch : master
Link : https://github.com/mlpack/mlpack/compare/1797a49c8f76d65814fec4a122d0d2fea01fc2d9...9e5cd0ac9c5cde9ac141bc84e7327bd11e19d42e
>---------------------------------------------------------------
commit fe5f7e99f96bad6de668332c0210588d911dc19c
Merge: 2930a75 b12e151
Author: Mikhail Lozhnikov <lozhnikovma at gmail.com>
Date: Mon Aug 1 18:10:19 2016 +0300
Merge remote-tracking branch 'upstream/master' into ubtree
>---------------------------------------------------------------
fe5f7e99f96bad6de668332c0210588d911dc19c
CMake/mlpack_coverage.in | 125 ++
CMakeLists.txt | 62 +-
README.md | 2 +-
doc/guide/build.hpp | 4 +-
doc/tutorials/kmeans/kmeans.txt | 18 +-
src/mlpack/CMakeLists.txt | 3 +
src/mlpack/core.hpp | 1 +
src/mlpack/core/boost_backport/README.md | 14 +-
src/mlpack/core/boost_backport/bernoulli.hpp | 176 +++
src/mlpack/core/boost_backport/boost_backport.hpp | 42 +
.../boost_backport/detail/bernoulli_details.hpp | 660 ++++++++
.../core/boost_backport/detail/polygamma.hpp | 558 +++++++
.../boost_backport/detail/unchecked_bernoulli.hpp | 700 +++++++++
src/mlpack/core/boost_backport/math_fwd.hpp | 1586 ++++++++++++++++++++
src/mlpack/core/boost_backport/policy.hpp | 1042 +++++++++++++
src/mlpack/core/boost_backport/polygamma.hpp | 94 ++
src/mlpack/core/boost_backport/trigamma.hpp | 469 ++++++
src/mlpack/core/data/CMakeLists.txt | 5 +-
src/mlpack/core/data/dataset_info.hpp | 114 --
src/mlpack/core/data/dataset_info_impl.hpp | 100 --
src/mlpack/core/data/dataset_mapper.hpp | 164 ++
src/mlpack/core/data/dataset_mapper_impl.hpp | 151 ++
.../data/imputation_methods}/CMakeLists.txt | 6 +-
.../data/imputation_methods/custom_imputation.hpp | 77 +
.../data/imputation_methods/listwise_deletion.hpp | 69 +
.../data/imputation_methods/mean_imputation.hpp | 99 ++
.../data/imputation_methods/median_imputation.hpp | 88 ++
src/mlpack/core/data/imputer.hpp | 90 ++
src/mlpack/core/data/load.hpp | 18 +-
src/mlpack/core/data/load_arff.hpp | 4 +-
src/mlpack/core/data/load_arff_impl.hpp | 6 +-
src/mlpack/core/data/load_impl.hpp | 51 +-
.../data/map_policies}/CMakeLists.txt | 4 +-
src/mlpack/core/data/map_policies/datatype.hpp | 28 +
.../core/data/map_policies/increment_policy.hpp | 131 ++
.../core/data/map_policies/missing_policy.hpp | 151 ++
src/mlpack/core/dists/CMakeLists.txt | 2 +
src/mlpack/core/dists/gamma_distribution.cpp | 90 ++
src/mlpack/core/dists/gamma_distribution.hpp | 119 ++
.../tree/binary_space_tree/midpoint_split_impl.hpp | 28 +-
src/mlpack/core/util/cli.cpp | 126 +-
src/mlpack/core/util/cli.hpp | 351 +----
src/mlpack/core/util/cli_impl.hpp | 21 +-
src/mlpack/core/util/option.hpp | 20 +-
src/mlpack/core/util/option_impl.hpp | 11 +-
src/mlpack/core/util/param.hpp | 426 ++++++
src/mlpack/methods/CMakeLists.txt | 1 +
src/mlpack/methods/adaboost/adaboost_main.cpp | 37 +-
src/mlpack/methods/ann/layer/pooling_layer.hpp | 37 +-
src/mlpack/methods/cf/cf.cpp | 73 +-
src/mlpack/methods/cf/cf.hpp | 24 +-
src/mlpack/methods/cf/cf_main.cpp | 44 +-
.../methods/decision_stump/decision_stump_main.cpp | 23 +-
src/mlpack/methods/det/det_main.cpp | 37 +-
src/mlpack/methods/emst/emst_main.cpp | 20 +-
src/mlpack/methods/fastmks/fastmks.hpp | 21 +-
src/mlpack/methods/fastmks/fastmks_impl.hpp | 107 +-
src/mlpack/methods/fastmks/fastmks_main.cpp | 33 +-
src/mlpack/methods/fastmks/fastmks_rules.hpp | 69 +-
src/mlpack/methods/fastmks/fastmks_rules_impl.hpp | 101 +-
src/mlpack/methods/gmm/gmm_generate_main.cpp | 15 +-
src/mlpack/methods/gmm/gmm_probability_main.cpp | 21 +-
src/mlpack/methods/gmm/gmm_train_main.cpp | 26 +-
src/mlpack/methods/hmm/hmm_generate_main.cpp | 23 +-
src/mlpack/methods/hmm/hmm_loglik_main.cpp | 8 +-
src/mlpack/methods/hmm/hmm_train_main.cpp | 21 +-
src/mlpack/methods/hmm/hmm_viterbi_main.cpp | 10 +-
.../hoeffding_trees/hoeffding_tree_main.cpp | 36 +-
src/mlpack/methods/kernel_pca/kernel_pca_main.cpp | 31 +-
src/mlpack/methods/kmeans/kmeans_main.cpp | 37 +-
src/mlpack/methods/lars/lars_main.cpp | 61 +-
.../linear_regression/linear_regression_main.cpp | 63 +-
.../local_coordinate_coding_main.cpp | 32 +-
.../logistic_regression_main.cpp | 48 +-
src/mlpack/methods/lsh/lsh_main.cpp | 45 +-
src/mlpack/methods/lsh/lsh_search.hpp | 42 +-
src/mlpack/methods/lsh/lsh_search_impl.hpp | 100 +-
src/mlpack/methods/mean_shift/mean_shift_main.cpp | 80 +-
src/mlpack/methods/mvu/mvu_main.cpp | 10 +-
src/mlpack/methods/naive_bayes/nbc_main.cpp | 17 +-
src/mlpack/methods/nca/nca_main.cpp | 49 +-
src/mlpack/methods/neighbor_search/CMakeLists.txt | 2 -
src/mlpack/methods/neighbor_search/kfn_main.cpp | 40 +-
src/mlpack/methods/neighbor_search/knn_main.cpp | 27 +-
.../neighbor_search/neighbor_search_impl.hpp | 35 +-
.../neighbor_search/neighbor_search_rules.hpp | 66 +-
.../neighbor_search/neighbor_search_rules_impl.hpp | 83 +-
.../sort_policies/furthest_neighbor_sort.cpp | 27 -
.../sort_policies/furthest_neighbor_sort.hpp | 18 -
.../sort_policies/nearest_neighbor_sort.cpp | 27 -
.../sort_policies/nearest_neighbor_sort.hpp | 18 -
src/mlpack/methods/nmf/nmf_main.cpp | 36 +-
src/mlpack/methods/pca/pca_main.cpp | 27 +-
src/mlpack/methods/perceptron/perceptron_main.cpp | 34 +-
src/mlpack/methods/preprocess/CMakeLists.txt | 2 +-
.../preprocess/preprocess_binarize_main.cpp | 18 +-
.../methods/preprocess/preprocess_imputer_main.cpp | 174 +++
.../methods/preprocess/preprocess_split_main.cpp | 64 +-
src/mlpack/methods/radical/radical_main.cpp | 65 +-
.../methods/range_search/range_search_impl.hpp | 2 +-
.../methods/range_search/range_search_main.cpp | 27 +-
.../methods/range_search/range_search_rules.hpp | 8 +-
src/mlpack/methods/rann/krann_main.cpp | 31 +-
src/mlpack/methods/rann/ra_search_impl.hpp | 42 +-
src/mlpack/methods/rann/ra_search_rules.hpp | 76 +-
src/mlpack/methods/rann/ra_search_rules_impl.hpp | 92 +-
src/mlpack/methods/rmva/rmva_main.cpp | 37 +-
.../softmax_regression/softmax_regression_main.cpp | 35 +-
.../methods/sparse_coding/sparse_coding_main.cpp | 56 +-
src/mlpack/prereqs.hpp | 8 +-
src/mlpack/tests/CMakeLists.txt | 1 +
src/mlpack/tests/cli_test.cpp | 2 +-
src/mlpack/tests/distribution_test.cpp | 146 +-
src/mlpack/tests/imputation_test.cpp | 266 ++++
src/mlpack/tests/krann_search_test.cpp | 2 +-
src/mlpack/tests/load_save_test.cpp | 2 +
src/mlpack/tests/pca_test.cpp | 26 +-
src/mlpack/tests/sort_policy_test.cpp | 72 -
118 files changed, 9365 insertions(+), 1837 deletions(-)
diff --cc src/mlpack/methods/neighbor_search/kfn_main.cpp
index 3eb8239,fac28b5..1bb34a3
--- a/src/mlpack/methods/neighbor_search/kfn_main.cpp
+++ b/src/mlpack/methods/neighbor_search/kfn_main.cpp
@@@ -61,14 -61,14 +61,14 @@@ PARAM_INT_IN("k", "Number of furthest n
// The user may specify the type of tree to use, and a few pararmeters for tree
// building.
- PARAM_STRING("tree_type", "Type of tree to use: 'kd', 'ub', 'cover', 'r', "
-PARAM_STRING_IN("tree_type", "Type of tree to use: 'kd', 'cover', 'r', "
++PARAM_STRING_IN("tree_type", "Type of tree to use: 'kd', 'ub', 'cover', 'r', "
"'r-star', 'x', 'ball', 'hilbert-r', 'r-plus', 'r-plus-plus'.", "t", "kd");
- PARAM_INT("leaf_size", "Leaf size for tree building (used for kd-trees, "
-PARAM_INT_IN("leaf_size", "Leaf size for tree building (used for kd-trees, R "
- "trees, R* trees, X trees, Hilbert R trees, R+ trees and R++ trees).", "l",
- 20);
++PARAM_INT_IN("leaf_size", "Leaf size for tree building (used for kd-trees, "
+ "UB-trees, R trees, R* trees, X trees, Hilbert R trees, R+ trees and "
+ "R++ trees).", "l", 20);
PARAM_FLAG("random_basis", "Before tree-building, project the data onto a "
"random orthogonal basis.", "R");
- PARAM_INT("seed", "Random seed (if 0, std::time(NULL) is used).", "s", 0);
+ PARAM_INT_IN("seed", "Random seed (if 0, std::time(NULL) is used).", "s", 0);
// Search settings.
PARAM_FLAG("naive", "If true, O(n^2) naive mode is used for computation.", "N");
diff --cc src/mlpack/methods/neighbor_search/knn_main.cpp
index 1167ff2,14e07db..5251ad1
--- a/src/mlpack/methods/neighbor_search/knn_main.cpp
+++ b/src/mlpack/methods/neighbor_search/knn_main.cpp
@@@ -62,14 -63,14 +63,14 @@@ PARAM_INT_IN("k", "Number of nearest ne
// The user may specify the type of tree to use, and a few parameters for tree
// building.
- PARAM_STRING("tree_type", "Type of tree to use: 'kd', 'ub', 'cover', 'r', "
-PARAM_STRING_IN("tree_type", "Type of tree to use: 'kd', 'cover', 'r', "
++PARAM_STRING_IN("tree_type", "Type of tree to use: 'kd', 'ub', 'cover', 'r', "
"'r-star', 'x', 'ball', 'hilbert-r', 'r-plus', 'r-plus-plus'.", "t", "kd");
- PARAM_INT("leaf_size", "Leaf size for tree building (used for kd-trees, "
-PARAM_INT_IN("leaf_size", "Leaf size for tree building (used for kd-trees, R "
- "trees, R* trees, X trees, Hilbert R trees, R+ trees and R++ trees).", "l",
- 20);
++PARAM_INT_IN("leaf_size", "Leaf size for tree building (used for kd-trees, "
+ "UB -trees, R trees, R* trees, X trees, Hilbert R trees, R+ trees and "
+ "R++ trees).", "l", 20);
PARAM_FLAG("random_basis", "Before tree-building, project the data onto a "
"random orthogonal basis.", "R");
- PARAM_INT("seed", "Random seed (if 0, std::time(NULL) is used).", "s", 0);
+ PARAM_INT_IN("seed", "Random seed (if 0, std::time(NULL) is used).", "s", 0);
// Search settings.
PARAM_FLAG("naive", "If true, O(n^2) naive mode is used for computation.", "N");
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