isotree 0.3.0 → 0.3.1

checksums.yaml

@@ -1,7 +1,7 @@
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data/CHANGELOG.md

@@ -1,3 +1,7 @@
+## 0.3.1 (2023-12-19)
+
+- Updated IsoTree to 0.5.25
+
 ## 0.3.0 (2022-06-13)
 
 - Updated IsoTree to 0.5.16

data/LICENSE.txt

@@ -1,7 +1,7 @@
 BSD 2-Clause License
 
-Copyright (c) 2020-2022, David Cortes
-Copyright (c) 2020-2022, Andrew Kane
+Copyright (c) 2019-2023, David Cortes
+Copyright (c) 2020-2023, Andrew Kane
 All rights reserved.
 
 Redistribution and use in source and binary forms, with or without

data/lib/isotree/version.rb

@@ -1,3 +1,3 @@
 module IsoTree
-  VERSION = "0.3.0"
+  VERSION = "0.3.1"
 end

data/vendor/isotree/LICENSE

@@ -1,6 +1,6 @@
 BSD 2-Clause License
 
-Copyright (c) 2019-2022, David Cortes
+Copyright (c) 2019-2023, David Cortes
 All rights reserved.
 
 Redistribution and use in source and binary forms, with or without

data/vendor/isotree/README.md

@@ -117,6 +117,8 @@ There's already many available implementations of isolation forests for both Pyt
 
 * R:
 
+**Note:** This package benefits from extra optimizations that aren't enabled by default for R packages. See [this guide](https://github.com/david-cortes/installing-optimized-libraries) for instructions on how to enable them.
+
 ```r
 install.packages("isotree")
 ```
@@ -125,6 +127,8 @@ install.packages("isotree")
 
 * Python:
 
+**Note:** requires C/C++ compilers configured for Python. See [this guide](https://github.com/david-cortes/installing-optimized-libraries) for instructions.
+
 ```
 pip install isotree
 ```
@@ -138,7 +142,7 @@ pip install --no-use-pep517 isotree
 ```
 brew install libomp
 ```
-And then reinstall this package: `pip install --force-reinstall isotree`.
+And then reinstall this package: `pip install --upgrade --no-deps --force-reinstall isotree`.
 
 ** *
 **IMPORTANT:** the setup script will try to add compilation flag `-march=native`. This instructs the compiler to tune the package for the CPU in which it is being installed (by e.g. using AVX instructions if available), but the result might not be usable in other computers. If building a binary wheel of this package or putting it into a docker image which will be used in different machines, this can be overriden either by (a) defining an environment variable `DONT_SET_MARCH=1`, or by (b) manually supplying compilation `CFLAGS` as an environment variable with something related to architecture. For maximum compatibility (but slowest speed), it's possible to do something like this:
@@ -289,10 +293,6 @@ cmake -DNO_TEMPLATED_VERSIONS=1 ..
 (this option is not available for the Python build system)
 
 
-# Help wanted
-
-The package does not currenly have any functionality for visualizing trees. Pull requests adding such functionality would be welcome.
-
 # References
 
 * Liu, Fei Tony, Kai Ming Ting, and Zhi-Hua Zhou. "Isolation forest." 2008 Eighth IEEE International Conference on Data Mining. IEEE, 2008.

data/vendor/isotree/include/isotree.hpp

@@ -62,9 +62,12 @@
 */
 
 /* Standard headers */
+#include <cmath>
 #include <cstddef>
 #include <cstdint>
 #include <vector>
+#include <cstdio>
+#include <iostream>
 using std::size_t;
 
 /*  The library has overloaded functions supporting different input types.
@@ -164,6 +167,7 @@ typedef struct IsoForest {
     NewCategAction    new_cat_action;
     CategSplit        cat_split_type;
     MissingAction     missing_action;
+    ScoringMetric     scoring_metric;
     double            exp_avg_depth;
     double            exp_avg_sep;
     size_t            orig_sample_size;
@@ -176,6 +180,7 @@ typedef struct ExtIsoForest {
     NewCategAction    new_cat_action;
     CategSplit        cat_split_type;
     MissingAction     missing_action;
+    ScoringMetric     scoring_metric;
     double            exp_avg_depth;
     double            exp_avg_sep;
     size_t            orig_sample_size;

data/vendor/isotree/inst/COPYRIGHTS

@@ -60,3 +60,73 @@ DATA, OR PROFITS; OR BUSINESS INTERRUPTION) HOWEVER CAUSED AND ON ANY
 THEORY OF LIABILITY, WHETHER IN CONTRACT, STRICT LIABILITY, OR TORT
 (INCLUDING NEGLIGENCE OR OTHERWISE) ARISING IN ANY WAY OUT OF THE USE
 OF THIS SOFTWARE, EVEN IF ADVISED OF THE POSSIBILITY OF SUCH DAMAGE.
+
+----------------
+
+For the digamma function (file "src/digamma.hpp"):
+
+Copyright (c) 2001-2002 Enthought, Inc. 2003-2023, SciPy Developers.
+All rights reserved.
+
+Redistribution and use in source and binary forms, with or without
+modification, are permitted provided that the following conditions
+are met:
+
+1. Redistributions of source code must retain the above copyright
+   notice, this list of conditions and the following disclaimer.
+
+2. Redistributions in binary form must reproduce the above
+   copyright notice, this list of conditions and the following
+   disclaimer in the documentation and/or other materials provided
+   with the distribution.
+
+3. Neither the name of the copyright holder nor the names of its
+   contributors may be used to endorse or promote products derived
+   from this software without specific prior written permission.
+
+THIS SOFTWARE IS PROVIDED BY THE COPYRIGHT HOLDERS AND CONTRIBUTORS
+"AS IS" AND ANY EXPRESS OR IMPLIED WARRANTIES, INCLUDING, BUT NOT
+LIMITED TO, THE IMPLIED WARRANTIES OF MERCHANTABILITY AND FITNESS FOR
+A PARTICULAR PURPOSE ARE DISCLAIMED. IN NO EVENT SHALL THE COPYRIGHT
+OWNER OR CONTRIBUTORS BE LIABLE FOR ANY DIRECT, INDIRECT, INCIDENTAL,
+SPECIAL, EXEMPLARY, OR CONSEQUENTIAL DAMAGES (INCLUDING, BUT NOT
+LIMITED TO, PROCUREMENT OF SUBSTITUTE GOODS OR SERVICES; LOSS OF USE,
+DATA, OR PROFITS; OR BUSINESS INTERRUPTION) HOWEVER CAUSED AND ON ANY
+THEORY OF LIABILITY, WHETHER IN CONTRACT, STRICT LIABILITY, OR TORT
+(INCLUDING NEGLIGENCE OR OTHERWISE) ARISING IN ANY WAY OUT OF THE USE
+OF THIS SOFTWARE, EVEN IF ADVISED OF THE POSSIBILITY OF SUCH DAMAGE.
+
+Distributed under 3-clause BSD license with permission from the author,
+see https://lists.debian.org/debian-legal/2004/12/msg00295.html
+
+------------------------------------------------------------------
+
+Cephes Math Library Release 2.8:  June, 2000
+Copyright 1984, 1995, 2000 by Stephen L. Moshier
+
+This software is derived from the Cephes Math Library and is
+incorporated herein by permission of the author.
+
+All rights reserved.
+
+Redistribution and use in source and binary forms, with or without
+modification, are permitted provided that the following conditions are met:
+  * Redistributions of source code must retain the above copyright
+    notice, this list of conditions and the following disclaimer.
+  * Redistributions in binary form must reproduce the above copyright
+    notice, this list of conditions and the following disclaimer in the
+    documentation and/or other materials provided with the distribution.
+  * Neither the name of the <organization> nor the
+    names of its contributors may be used to endorse or promote products
+    derived from this software without specific prior written permission.
+
+THIS SOFTWARE IS PROVIDED BY THE COPYRIGHT HOLDERS AND CONTRIBUTORS "AS IS" AND
+ANY EXPRESS OR IMPLIED WARRANTIES, INCLUDING, BUT NOT LIMITED TO, THE IMPLIED
+WARRANTIES OF MERCHANTABILITY AND FITNESS FOR A PARTICULAR PURPOSE ARE
+DISCLAIMED. IN NO EVENT SHALL <COPYRIGHT HOLDER> BE LIABLE FOR ANY
+DIRECT, INDIRECT, INCIDENTAL, SPECIAL, EXEMPLARY, OR CONSEQUENTIAL DAMAGES
+(INCLUDING, BUT NOT LIMITED TO, PROCUREMENT OF SUBSTITUTE GOODS OR SERVICES;
+LOSS OF USE, DATA, OR PROFITS; OR BUSINESS INTERRUPTION) HOWEVER CAUSED AND
+ON ANY THEORY OF LIABILITY, WHETHER IN CONTRACT, STRICT LIABILITY, OR TORT
+(INCLUDING NEGLIGENCE OR OTHERWISE) ARISING IN ANY WAY OUT OF THE USE OF THIS
+SOFTWARE, EVEN IF ADVISED OF THE POSSIBILITY OF SUCH DAMAGE.

data/vendor/isotree/src/RcppExports.cpp

@@ -50,19 +50,59 @@ BEGIN_RCPP
     return rcpp_result_gen;
 END_RCPP
 }
-// check_null_ptr_model
-Rcpp::LogicalVector check_null_ptr_model(SEXP ptr_model);
-RcppExport SEXP _isotree_check_null_ptr_model(SEXP ptr_modelSEXP) {
+// serialize_IsoForest_from_ptr
+SEXP serialize_IsoForest_from_ptr(SEXP R_ptr);
+RcppExport SEXP _isotree_serialize_IsoForest_from_ptr(SEXP R_ptrSEXP) {
+BEGIN_RCPP
+    Rcpp::RObject rcpp_result_gen;
+    Rcpp::traits::input_parameter< SEXP >::type R_ptr(R_ptrSEXP);
+    rcpp_result_gen = Rcpp::wrap(serialize_IsoForest_from_ptr(R_ptr));
+    return rcpp_result_gen;
+END_RCPP
+}
+// serialize_ExtIsoForest_from_ptr
+SEXP serialize_ExtIsoForest_from_ptr(SEXP R_ptr);
+RcppExport SEXP _isotree_serialize_ExtIsoForest_from_ptr(SEXP R_ptrSEXP) {
+BEGIN_RCPP
+    Rcpp::RObject rcpp_result_gen;
+    Rcpp::traits::input_parameter< SEXP >::type R_ptr(R_ptrSEXP);
+    rcpp_result_gen = Rcpp::wrap(serialize_ExtIsoForest_from_ptr(R_ptr));
+    return rcpp_result_gen;
+END_RCPP
+}
+// serialize_Imputer_from_ptr
+SEXP serialize_Imputer_from_ptr(SEXP R_ptr);
+RcppExport SEXP _isotree_serialize_Imputer_from_ptr(SEXP R_ptrSEXP) {
+BEGIN_RCPP
+    Rcpp::RObject rcpp_result_gen;
+    Rcpp::traits::input_parameter< SEXP >::type R_ptr(R_ptrSEXP);
+    rcpp_result_gen = Rcpp::wrap(serialize_Imputer_from_ptr(R_ptr));
+    return rcpp_result_gen;
+END_RCPP
+}
+// serialize_Indexer_from_ptr
+SEXP serialize_Indexer_from_ptr(SEXP R_ptr);
+RcppExport SEXP _isotree_serialize_Indexer_from_ptr(SEXP R_ptrSEXP) {
+BEGIN_RCPP
+    Rcpp::RObject rcpp_result_gen;
+    Rcpp::traits::input_parameter< SEXP >::type R_ptr(R_ptrSEXP);
+    rcpp_result_gen = Rcpp::wrap(serialize_Indexer_from_ptr(R_ptr));
+    return rcpp_result_gen;
+END_RCPP
+}
+// check_null_ptr_model_internal
+Rcpp::LogicalVector check_null_ptr_model_internal(SEXP ptr_model);
+RcppExport SEXP _isotree_check_null_ptr_model_internal(SEXP ptr_modelSEXP) {
 BEGIN_RCPP
     Rcpp::RObject rcpp_result_gen;
     Rcpp::traits::input_parameter< SEXP >::type ptr_model(ptr_modelSEXP);
-    rcpp_result_gen = Rcpp::wrap(check_null_ptr_model(ptr_model));
+    rcpp_result_gen = Rcpp::wrap(check_null_ptr_model_internal(ptr_model));
     return rcpp_result_gen;
 END_RCPP
 }
 // fit_model
-Rcpp::List fit_model(Rcpp::NumericVector X_num, Rcpp::IntegerVector X_cat, Rcpp::IntegerVector ncat, Rcpp::NumericVector Xc, Rcpp::IntegerVector Xc_ind, Rcpp::IntegerVector Xc_indptr, Rcpp::NumericVector sample_weights, Rcpp::NumericVector col_weights, size_t nrows, size_t ncols_numeric, size_t ncols_categ, size_t ndim, size_t ntry, Rcpp::CharacterVector coef_type, bool coef_by_prop, bool with_replacement, bool weight_as_sample, size_t sample_size, size_t ntrees, size_t max_depth, size_t ncols_per_tree, bool limit_depth, bool penalize_range, bool standardize_data, Rcpp::CharacterVector scoring_metric, bool fast_bratio, bool calc_dist, bool standardize_dist, bool sq_dist, bool calc_depth, bool standardize_depth, bool weigh_by_kurt, double prob_pick_by_gain_pl, double prob_pick_by_gain_avg, double prob_pick_by_full_gain, double prob_pick_by_dens, double prob_pick_col_by_range, double prob_pick_col_by_var, double prob_pick_col_by_kurt, double min_gain, Rcpp::CharacterVector cat_split_type, Rcpp::CharacterVector new_cat_action, Rcpp::CharacterVector missing_action, bool all_perm, bool build_imputer, bool output_imputations, size_t min_imp_obs, Rcpp::CharacterVector depth_imp, Rcpp::CharacterVector weigh_imp_rows, int random_seed, bool use_long_double, int nthreads);
-RcppExport SEXP _isotree_fit_model(SEXP X_numSEXP, SEXP X_catSEXP, SEXP ncatSEXP, SEXP XcSEXP, SEXP Xc_indSEXP, SEXP Xc_indptrSEXP, SEXP sample_weightsSEXP, SEXP col_weightsSEXP, SEXP nrowsSEXP, SEXP ncols_numericSEXP, SEXP ncols_categSEXP, SEXP ndimSEXP, SEXP ntrySEXP, SEXP coef_typeSEXP, SEXP coef_by_propSEXP, SEXP with_replacementSEXP, SEXP weight_as_sampleSEXP, SEXP sample_sizeSEXP, SEXP ntreesSEXP, SEXP max_depthSEXP, SEXP ncols_per_treeSEXP, SEXP limit_depthSEXP, SEXP penalize_rangeSEXP, SEXP standardize_dataSEXP, SEXP scoring_metricSEXP, SEXP fast_bratioSEXP, SEXP calc_distSEXP, SEXP standardize_distSEXP, SEXP sq_distSEXP, SEXP calc_depthSEXP, SEXP standardize_depthSEXP, SEXP weigh_by_kurtSEXP, SEXP prob_pick_by_gain_plSEXP, SEXP prob_pick_by_gain_avgSEXP, SEXP prob_pick_by_full_gainSEXP, SEXP prob_pick_by_densSEXP, SEXP prob_pick_col_by_rangeSEXP, SEXP prob_pick_col_by_varSEXP, SEXP prob_pick_col_by_kurtSEXP, SEXP min_gainSEXP, SEXP cat_split_typeSEXP, SEXP new_cat_actionSEXP, SEXP missing_actionSEXP, SEXP all_permSEXP, SEXP build_imputerSEXP, SEXP output_imputationsSEXP, SEXP min_imp_obsSEXP, SEXP depth_impSEXP, SEXP weigh_imp_rowsSEXP, SEXP random_seedSEXP, SEXP use_long_doubleSEXP, SEXP nthreadsSEXP) {
+Rcpp::List fit_model(Rcpp::NumericVector X_num, Rcpp::IntegerVector X_cat, Rcpp::IntegerVector ncat, Rcpp::NumericVector Xc, Rcpp::IntegerVector Xc_ind, Rcpp::IntegerVector Xc_indptr, Rcpp::NumericVector sample_weights, Rcpp::NumericVector col_weights, size_t nrows, size_t ncols_numeric, size_t ncols_categ, size_t ndim, size_t ntry, Rcpp::CharacterVector coef_type, bool coef_by_prop, bool with_replacement, bool weight_as_sample, size_t sample_size, size_t ntrees, size_t max_depth, size_t ncols_per_tree, bool limit_depth, bool penalize_range, bool standardize_data, Rcpp::CharacterVector scoring_metric, bool fast_bratio, bool calc_dist, bool standardize_dist, bool sq_dist, bool calc_depth, bool standardize_depth, bool weigh_by_kurt, double prob_pick_by_gain_pl, double prob_pick_by_gain_avg, double prob_pick_by_full_gain, double prob_pick_by_dens, double prob_pick_col_by_range, double prob_pick_col_by_var, double prob_pick_col_by_kurt, double min_gain, Rcpp::CharacterVector cat_split_type, Rcpp::CharacterVector new_cat_action, Rcpp::CharacterVector missing_action, bool all_perm, bool build_imputer, bool output_imputations, size_t min_imp_obs, Rcpp::CharacterVector depth_imp, Rcpp::CharacterVector weigh_imp_rows, int random_seed, bool use_long_double, int nthreads, bool lazy_serialization);
+RcppExport SEXP _isotree_fit_model(SEXP X_numSEXP, SEXP X_catSEXP, SEXP ncatSEXP, SEXP XcSEXP, SEXP Xc_indSEXP, SEXP Xc_indptrSEXP, SEXP sample_weightsSEXP, SEXP col_weightsSEXP, SEXP nrowsSEXP, SEXP ncols_numericSEXP, SEXP ncols_categSEXP, SEXP ndimSEXP, SEXP ntrySEXP, SEXP coef_typeSEXP, SEXP coef_by_propSEXP, SEXP with_replacementSEXP, SEXP weight_as_sampleSEXP, SEXP sample_sizeSEXP, SEXP ntreesSEXP, SEXP max_depthSEXP, SEXP ncols_per_treeSEXP, SEXP limit_depthSEXP, SEXP penalize_rangeSEXP, SEXP standardize_dataSEXP, SEXP scoring_metricSEXP, SEXP fast_bratioSEXP, SEXP calc_distSEXP, SEXP standardize_distSEXP, SEXP sq_distSEXP, SEXP calc_depthSEXP, SEXP standardize_depthSEXP, SEXP weigh_by_kurtSEXP, SEXP prob_pick_by_gain_plSEXP, SEXP prob_pick_by_gain_avgSEXP, SEXP prob_pick_by_full_gainSEXP, SEXP prob_pick_by_densSEXP, SEXP prob_pick_col_by_rangeSEXP, SEXP prob_pick_col_by_varSEXP, SEXP prob_pick_col_by_kurtSEXP, SEXP min_gainSEXP, SEXP cat_split_typeSEXP, SEXP new_cat_actionSEXP, SEXP missing_actionSEXP, SEXP all_permSEXP, SEXP build_imputerSEXP, SEXP output_imputationsSEXP, SEXP min_imp_obsSEXP, SEXP depth_impSEXP, SEXP weigh_imp_rowsSEXP, SEXP random_seedSEXP, SEXP use_long_doubleSEXP, SEXP nthreadsSEXP, SEXP lazy_serializationSEXP) {
 BEGIN_RCPP
     Rcpp::RObject rcpp_result_gen;
     Rcpp::traits::input_parameter< Rcpp::NumericVector >::type X_num(X_numSEXP);
@@ -117,13 +157,14 @@ BEGIN_RCPP
     Rcpp::traits::input_parameter< int >::type random_seed(random_seedSEXP);
     Rcpp::traits::input_parameter< bool >::type use_long_double(use_long_doubleSEXP);
     Rcpp::traits::input_parameter< int >::type nthreads(nthreadsSEXP);
-    rcpp_result_gen = Rcpp::wrap(fit_model(X_num, X_cat, ncat, Xc, Xc_ind, Xc_indptr, sample_weights, col_weights, nrows, ncols_numeric, ncols_categ, ndim, ntry, coef_type, coef_by_prop, with_replacement, weight_as_sample, sample_size, ntrees, max_depth, ncols_per_tree, limit_depth, penalize_range, standardize_data, scoring_metric, fast_bratio, calc_dist, standardize_dist, sq_dist, calc_depth, standardize_depth, weigh_by_kurt, prob_pick_by_gain_pl, prob_pick_by_gain_avg, prob_pick_by_full_gain, prob_pick_by_dens, prob_pick_col_by_range, prob_pick_col_by_var, prob_pick_col_by_kurt, min_gain, cat_split_type, new_cat_action, missing_action, all_perm, build_imputer, output_imputations, min_imp_obs, depth_imp, weigh_imp_rows, random_seed, use_long_double, nthreads));
+    Rcpp::traits::input_parameter< bool >::type lazy_serialization(lazy_serializationSEXP);
+    rcpp_result_gen = Rcpp::wrap(fit_model(X_num, X_cat, ncat, Xc, Xc_ind, Xc_indptr, sample_weights, col_weights, nrows, ncols_numeric, ncols_categ, ndim, ntry, coef_type, coef_by_prop, with_replacement, weight_as_sample, sample_size, ntrees, max_depth, ncols_per_tree, limit_depth, penalize_range, standardize_data, scoring_metric, fast_bratio, calc_dist, standardize_dist, sq_dist, calc_depth, standardize_depth, weigh_by_kurt, prob_pick_by_gain_pl, prob_pick_by_gain_avg, prob_pick_by_full_gain, prob_pick_by_dens, prob_pick_col_by_range, prob_pick_col_by_var, prob_pick_col_by_kurt, min_gain, cat_split_type, new_cat_action, missing_action, all_perm, build_imputer, output_imputations, min_imp_obs, depth_imp, weigh_imp_rows, random_seed, use_long_double, nthreads, lazy_serialization));
     return rcpp_result_gen;
 END_RCPP
 }
 // fit_tree
-void fit_tree(SEXP model_R_ptr, Rcpp::RawVector serialized_obj, Rcpp::RawVector serialized_imputer, SEXP indexer_R_ptr, Rcpp::RawVector serialized_indexer, Rcpp::NumericVector X_num, Rcpp::IntegerVector X_cat, Rcpp::IntegerVector ncat, Rcpp::NumericVector Xc, Rcpp::IntegerVector Xc_ind, Rcpp::IntegerVector Xc_indptr, Rcpp::NumericVector sample_weights, Rcpp::NumericVector col_weights, size_t nrows, size_t ncols_numeric, size_t ncols_categ, size_t ndim, size_t ntry, Rcpp::CharacterVector coef_type, bool coef_by_prop, size_t max_depth, size_t ncols_per_tree, bool limit_depth, bool penalize_range, bool standardize_data, bool fast_bratio, bool weigh_by_kurt, double prob_pick_by_gain_pl, double prob_pick_by_gain_avg, double prob_pick_by_full_gain, double prob_pick_by_dens, double prob_pick_col_by_range, double prob_pick_col_by_var, double prob_pick_col_by_kurt, double min_gain, Rcpp::CharacterVector cat_split_type, Rcpp::CharacterVector new_cat_action, Rcpp::CharacterVector missing_action, bool build_imputer, size_t min_imp_obs, SEXP imp_R_ptr, Rcpp::CharacterVector depth_imp, Rcpp::CharacterVector weigh_imp_rows, bool all_perm, Rcpp::NumericVector ref_X_num, Rcpp::IntegerVector ref_X_cat, Rcpp::NumericVector ref_Xc, Rcpp::IntegerVector ref_Xc_ind, Rcpp::IntegerVector ref_Xc_indptr, uint64_t random_seed, bool use_long_double, Rcpp::List& model_cpp_obj_update, Rcpp::List& model_params_update);
-RcppExport SEXP _isotree_fit_tree(SEXP model_R_ptrSEXP, SEXP serialized_objSEXP, SEXP serialized_imputerSEXP, SEXP indexer_R_ptrSEXP, SEXP serialized_indexerSEXP, SEXP X_numSEXP, SEXP X_catSEXP, SEXP ncatSEXP, SEXP XcSEXP, SEXP Xc_indSEXP, SEXP Xc_indptrSEXP, SEXP sample_weightsSEXP, SEXP col_weightsSEXP, SEXP nrowsSEXP, SEXP ncols_numericSEXP, SEXP ncols_categSEXP, SEXP ndimSEXP, SEXP ntrySEXP, SEXP coef_typeSEXP, SEXP coef_by_propSEXP, SEXP max_depthSEXP, SEXP ncols_per_treeSEXP, SEXP limit_depthSEXP, SEXP penalize_rangeSEXP, SEXP standardize_dataSEXP, SEXP fast_bratioSEXP, SEXP weigh_by_kurtSEXP, SEXP prob_pick_by_gain_plSEXP, SEXP prob_pick_by_gain_avgSEXP, SEXP prob_pick_by_full_gainSEXP, SEXP prob_pick_by_densSEXP, SEXP prob_pick_col_by_rangeSEXP, SEXP prob_pick_col_by_varSEXP, SEXP prob_pick_col_by_kurtSEXP, SEXP min_gainSEXP, SEXP cat_split_typeSEXP, SEXP new_cat_actionSEXP, SEXP missing_actionSEXP, SEXP build_imputerSEXP, SEXP min_imp_obsSEXP, SEXP imp_R_ptrSEXP, SEXP depth_impSEXP, SEXP weigh_imp_rowsSEXP, SEXP all_permSEXP, SEXP ref_X_numSEXP, SEXP ref_X_catSEXP, SEXP ref_XcSEXP, SEXP ref_Xc_indSEXP, SEXP ref_Xc_indptrSEXP, SEXP random_seedSEXP, SEXP use_long_doubleSEXP, SEXP model_cpp_obj_updateSEXP, SEXP model_params_updateSEXP) {
+void fit_tree(SEXP model_R_ptr, Rcpp::RawVector serialized_obj, Rcpp::RawVector serialized_imputer, SEXP indexer_R_ptr, Rcpp::RawVector serialized_indexer, Rcpp::NumericVector X_num, Rcpp::IntegerVector X_cat, Rcpp::IntegerVector ncat, Rcpp::NumericVector Xc, Rcpp::IntegerVector Xc_ind, Rcpp::IntegerVector Xc_indptr, Rcpp::NumericVector sample_weights, Rcpp::NumericVector col_weights, size_t nrows, size_t ncols_numeric, size_t ncols_categ, size_t ndim, size_t ntry, Rcpp::CharacterVector coef_type, bool coef_by_prop, size_t max_depth, size_t ncols_per_tree, bool limit_depth, bool penalize_range, bool standardize_data, bool fast_bratio, bool weigh_by_kurt, double prob_pick_by_gain_pl, double prob_pick_by_gain_avg, double prob_pick_by_full_gain, double prob_pick_by_dens, double prob_pick_col_by_range, double prob_pick_col_by_var, double prob_pick_col_by_kurt, double min_gain, Rcpp::CharacterVector cat_split_type, Rcpp::CharacterVector new_cat_action, Rcpp::CharacterVector missing_action, bool build_imputer, size_t min_imp_obs, SEXP imp_R_ptr, Rcpp::CharacterVector depth_imp, Rcpp::CharacterVector weigh_imp_rows, bool all_perm, Rcpp::NumericVector ref_X_num, Rcpp::IntegerVector ref_X_cat, Rcpp::NumericVector ref_Xc, Rcpp::IntegerVector ref_Xc_ind, Rcpp::IntegerVector ref_Xc_indptr, uint64_t random_seed, bool use_long_double, Rcpp::List& model_cpp_obj_update, Rcpp::List& model_params_update, bool is_altrepped);
+RcppExport SEXP _isotree_fit_tree(SEXP model_R_ptrSEXP, SEXP serialized_objSEXP, SEXP serialized_imputerSEXP, SEXP indexer_R_ptrSEXP, SEXP serialized_indexerSEXP, SEXP X_numSEXP, SEXP X_catSEXP, SEXP ncatSEXP, SEXP XcSEXP, SEXP Xc_indSEXP, SEXP Xc_indptrSEXP, SEXP sample_weightsSEXP, SEXP col_weightsSEXP, SEXP nrowsSEXP, SEXP ncols_numericSEXP, SEXP ncols_categSEXP, SEXP ndimSEXP, SEXP ntrySEXP, SEXP coef_typeSEXP, SEXP coef_by_propSEXP, SEXP max_depthSEXP, SEXP ncols_per_treeSEXP, SEXP limit_depthSEXP, SEXP penalize_rangeSEXP, SEXP standardize_dataSEXP, SEXP fast_bratioSEXP, SEXP weigh_by_kurtSEXP, SEXP prob_pick_by_gain_plSEXP, SEXP prob_pick_by_gain_avgSEXP, SEXP prob_pick_by_full_gainSEXP, SEXP prob_pick_by_densSEXP, SEXP prob_pick_col_by_rangeSEXP, SEXP prob_pick_col_by_varSEXP, SEXP prob_pick_col_by_kurtSEXP, SEXP min_gainSEXP, SEXP cat_split_typeSEXP, SEXP new_cat_actionSEXP, SEXP missing_actionSEXP, SEXP build_imputerSEXP, SEXP min_imp_obsSEXP, SEXP imp_R_ptrSEXP, SEXP depth_impSEXP, SEXP weigh_imp_rowsSEXP, SEXP all_permSEXP, SEXP ref_X_numSEXP, SEXP ref_X_catSEXP, SEXP ref_XcSEXP, SEXP ref_Xc_indSEXP, SEXP ref_Xc_indptrSEXP, SEXP random_seedSEXP, SEXP use_long_doubleSEXP, SEXP model_cpp_obj_updateSEXP, SEXP model_params_updateSEXP, SEXP is_altreppedSEXP) {
 BEGIN_RCPP
     Rcpp::traits::input_parameter< SEXP >::type model_R_ptr(model_R_ptrSEXP);
     Rcpp::traits::input_parameter< Rcpp::RawVector >::type serialized_obj(serialized_objSEXP);
@@ -178,7 +219,8 @@ BEGIN_RCPP
     Rcpp::traits::input_parameter< bool >::type use_long_double(use_long_doubleSEXP);
     Rcpp::traits::input_parameter< Rcpp::List& >::type model_cpp_obj_update(model_cpp_obj_updateSEXP);
     Rcpp::traits::input_parameter< Rcpp::List& >::type model_params_update(model_params_updateSEXP);
-    fit_tree(model_R_ptr, serialized_obj, serialized_imputer, indexer_R_ptr, serialized_indexer, X_num, X_cat, ncat, Xc, Xc_ind, Xc_indptr, sample_weights, col_weights, nrows, ncols_numeric, ncols_categ, ndim, ntry, coef_type, coef_by_prop, max_depth, ncols_per_tree, limit_depth, penalize_range, standardize_data, fast_bratio, weigh_by_kurt, prob_pick_by_gain_pl, prob_pick_by_gain_avg, prob_pick_by_full_gain, prob_pick_by_dens, prob_pick_col_by_range, prob_pick_col_by_var, prob_pick_col_by_kurt, min_gain, cat_split_type, new_cat_action, missing_action, build_imputer, min_imp_obs, imp_R_ptr, depth_imp, weigh_imp_rows, all_perm, ref_X_num, ref_X_cat, ref_Xc, ref_Xc_ind, ref_Xc_indptr, random_seed, use_long_double, model_cpp_obj_update, model_params_update);
+    Rcpp::traits::input_parameter< bool >::type is_altrepped(is_altreppedSEXP);
+    fit_tree(model_R_ptr, serialized_obj, serialized_imputer, indexer_R_ptr, serialized_indexer, X_num, X_cat, ncat, Xc, Xc_ind, Xc_indptr, sample_weights, col_weights, nrows, ncols_numeric, ncols_categ, ndim, ntry, coef_type, coef_by_prop, max_depth, ncols_per_tree, limit_depth, penalize_range, standardize_data, fast_bratio, weigh_by_kurt, prob_pick_by_gain_pl, prob_pick_by_gain_avg, prob_pick_by_full_gain, prob_pick_by_dens, prob_pick_col_by_range, prob_pick_col_by_var, prob_pick_col_by_kurt, min_gain, cat_split_type, new_cat_action, missing_action, build_imputer, min_imp_obs, imp_R_ptr, depth_imp, weigh_imp_rows, all_perm, ref_X_num, ref_X_cat, ref_Xc, ref_Xc_ind, ref_Xc_indptr, random_seed, use_long_double, model_cpp_obj_update, model_params_update, is_altrepped);
     return R_NilValue;
 END_RCPP
 }
@@ -256,47 +298,55 @@ BEGIN_RCPP
 END_RCPP
 }
 // drop_imputer
-void drop_imputer(Rcpp::List lst_modify, Rcpp::List lst_modify2);
-RcppExport SEXP _isotree_drop_imputer(SEXP lst_modifySEXP, SEXP lst_modify2SEXP) {
-BEGIN_RCPP
-    Rcpp::traits::input_parameter< Rcpp::List >::type lst_modify(lst_modifySEXP);
-    Rcpp::traits::input_parameter< Rcpp::List >::type lst_modify2(lst_modify2SEXP);
-    drop_imputer(lst_modify, lst_modify2);
+void drop_imputer(bool is_altrepped, bool free_cpp, SEXP lst_imputer, Rcpp::List lst_cpp_objects, Rcpp::List lst_params);
+RcppExport SEXP _isotree_drop_imputer(SEXP is_altreppedSEXP, SEXP free_cppSEXP, SEXP lst_imputerSEXP, SEXP lst_cpp_objectsSEXP, SEXP lst_paramsSEXP) {
+BEGIN_RCPP
+    Rcpp::traits::input_parameter< bool >::type is_altrepped(is_altreppedSEXP);
+    Rcpp::traits::input_parameter< bool >::type free_cpp(free_cppSEXP);
+    Rcpp::traits::input_parameter< SEXP >::type lst_imputer(lst_imputerSEXP);
+    Rcpp::traits::input_parameter< Rcpp::List >::type lst_cpp_objects(lst_cpp_objectsSEXP);
+    Rcpp::traits::input_parameter< Rcpp::List >::type lst_params(lst_paramsSEXP);
+    drop_imputer(is_altrepped, free_cpp, lst_imputer, lst_cpp_objects, lst_params);
     return R_NilValue;
 END_RCPP
 }
 // drop_indexer
-void drop_indexer(Rcpp::List lst_modify, Rcpp::List lst_modify2);
-RcppExport SEXP _isotree_drop_indexer(SEXP lst_modifySEXP, SEXP lst_modify2SEXP) {
-BEGIN_RCPP
-    Rcpp::traits::input_parameter< Rcpp::List >::type lst_modify(lst_modifySEXP);
-    Rcpp::traits::input_parameter< Rcpp::List >::type lst_modify2(lst_modify2SEXP);
-    drop_indexer(lst_modify, lst_modify2);
+void drop_indexer(bool is_altrepped, bool free_cpp, SEXP lst_indexer, Rcpp::List lst_cpp_objects, Rcpp::List lst_metadata);
+RcppExport SEXP _isotree_drop_indexer(SEXP is_altreppedSEXP, SEXP free_cppSEXP, SEXP lst_indexerSEXP, SEXP lst_cpp_objectsSEXP, SEXP lst_metadataSEXP) {
+BEGIN_RCPP
+    Rcpp::traits::input_parameter< bool >::type is_altrepped(is_altreppedSEXP);
+    Rcpp::traits::input_parameter< bool >::type free_cpp(free_cppSEXP);
+    Rcpp::traits::input_parameter< SEXP >::type lst_indexer(lst_indexerSEXP);
+    Rcpp::traits::input_parameter< Rcpp::List >::type lst_cpp_objects(lst_cpp_objectsSEXP);
+    Rcpp::traits::input_parameter< Rcpp::List >::type lst_metadata(lst_metadataSEXP);
+    drop_indexer(is_altrepped, free_cpp, lst_indexer, lst_cpp_objects, lst_metadata);
     return R_NilValue;
 END_RCPP
 }
 // drop_reference_points
-void drop_reference_points(Rcpp::List lst_modify, Rcpp::List lst_modify2);
-RcppExport SEXP _isotree_drop_reference_points(SEXP lst_modifySEXP, SEXP lst_modify2SEXP) {
-BEGIN_RCPP
-    Rcpp::traits::input_parameter< Rcpp::List >::type lst_modify(lst_modifySEXP);
-    Rcpp::traits::input_parameter< Rcpp::List >::type lst_modify2(lst_modify2SEXP);
-    drop_reference_points(lst_modify, lst_modify2);
+void drop_reference_points(bool is_altrepped, SEXP lst_indexer, Rcpp::List lst_cpp_objects, Rcpp::List lst_metadata);
+RcppExport SEXP _isotree_drop_reference_points(SEXP is_altreppedSEXP, SEXP lst_indexerSEXP, SEXP lst_cpp_objectsSEXP, SEXP lst_metadataSEXP) {
+BEGIN_RCPP
+    Rcpp::traits::input_parameter< bool >::type is_altrepped(is_altreppedSEXP);
+    Rcpp::traits::input_parameter< SEXP >::type lst_indexer(lst_indexerSEXP);
+    Rcpp::traits::input_parameter< Rcpp::List >::type lst_cpp_objects(lst_cpp_objectsSEXP);
+    Rcpp::traits::input_parameter< Rcpp::List >::type lst_metadata(lst_metadataSEXP);
+    drop_reference_points(is_altrepped, lst_indexer, lst_cpp_objects, lst_metadata);
     return R_NilValue;
 END_RCPP
 }
 // subset_trees
-Rcpp::List subset_trees(SEXP model_R_ptr, SEXP imputer_R_ptr, SEXP indexer_R_ptr, bool is_extended, bool has_imputer, Rcpp::IntegerVector trees_take);
-RcppExport SEXP _isotree_subset_trees(SEXP model_R_ptrSEXP, SEXP imputer_R_ptrSEXP, SEXP indexer_R_ptrSEXP, SEXP is_extendedSEXP, SEXP has_imputerSEXP, SEXP trees_takeSEXP) {
+Rcpp::List subset_trees(SEXP model_R_ptr, SEXP imputer_R_ptr, SEXP indexer_R_ptr, bool is_extended, bool is_altrepped, Rcpp::IntegerVector trees_take);
+RcppExport SEXP _isotree_subset_trees(SEXP model_R_ptrSEXP, SEXP imputer_R_ptrSEXP, SEXP indexer_R_ptrSEXP, SEXP is_extendedSEXP, SEXP is_altreppedSEXP, SEXP trees_takeSEXP) {
 BEGIN_RCPP
     Rcpp::RObject rcpp_result_gen;
     Rcpp::traits::input_parameter< SEXP >::type model_R_ptr(model_R_ptrSEXP);
     Rcpp::traits::input_parameter< SEXP >::type imputer_R_ptr(imputer_R_ptrSEXP);
     Rcpp::traits::input_parameter< SEXP >::type indexer_R_ptr(indexer_R_ptrSEXP);
     Rcpp::traits::input_parameter< bool >::type is_extended(is_extendedSEXP);
-    Rcpp::traits::input_parameter< bool >::type has_imputer(has_imputerSEXP);
+    Rcpp::traits::input_parameter< bool >::type is_altrepped(is_altreppedSEXP);
     Rcpp::traits::input_parameter< Rcpp::IntegerVector >::type trees_take(trees_takeSEXP);
-    rcpp_result_gen = Rcpp::wrap(subset_trees(model_R_ptr, imputer_R_ptr, indexer_R_ptr, is_extended, has_imputer, trees_take));
+    rcpp_result_gen = Rcpp::wrap(subset_trees(model_R_ptr, imputer_R_ptr, indexer_R_ptr, is_extended, is_altrepped, trees_take));
     return rcpp_result_gen;
 END_RCPP
 }
@@ -322,8 +372,8 @@ BEGIN_RCPP
 END_RCPP
 }
 // append_trees_from_other
-void append_trees_from_other(SEXP model_R_ptr, SEXP other_R_ptr, SEXP imp_R_ptr, SEXP oimp_R_ptr, SEXP ind_R_ptr, SEXP oind_R_ptr, bool is_extended, Rcpp::RawVector serialized_obj, Rcpp::RawVector serialized_imputer, Rcpp::RawVector serialized_indexer, Rcpp::List& model_cpp_obj_update, Rcpp::List& model_params_update);
-RcppExport SEXP _isotree_append_trees_from_other(SEXP model_R_ptrSEXP, SEXP other_R_ptrSEXP, SEXP imp_R_ptrSEXP, SEXP oimp_R_ptrSEXP, SEXP ind_R_ptrSEXP, SEXP oind_R_ptrSEXP, SEXP is_extendedSEXP, SEXP serialized_objSEXP, SEXP serialized_imputerSEXP, SEXP serialized_indexerSEXP, SEXP model_cpp_obj_updateSEXP, SEXP model_params_updateSEXP) {
+void append_trees_from_other(SEXP model_R_ptr, SEXP other_R_ptr, SEXP imp_R_ptr, SEXP oimp_R_ptr, SEXP ind_R_ptr, SEXP oind_R_ptr, bool is_extended, Rcpp::RawVector serialized_obj, Rcpp::RawVector serialized_imputer, Rcpp::RawVector serialized_indexer, Rcpp::List& model_cpp_obj_update, Rcpp::List& model_params_update, bool is_altrepped);
+RcppExport SEXP _isotree_append_trees_from_other(SEXP model_R_ptrSEXP, SEXP other_R_ptrSEXP, SEXP imp_R_ptrSEXP, SEXP oimp_R_ptrSEXP, SEXP ind_R_ptrSEXP, SEXP oind_R_ptrSEXP, SEXP is_extendedSEXP, SEXP serialized_objSEXP, SEXP serialized_imputerSEXP, SEXP serialized_indexerSEXP, SEXP model_cpp_obj_updateSEXP, SEXP model_params_updateSEXP, SEXP is_altreppedSEXP) {
 BEGIN_RCPP
     Rcpp::traits::input_parameter< SEXP >::type model_R_ptr(model_R_ptrSEXP);
     Rcpp::traits::input_parameter< SEXP >::type other_R_ptr(other_R_ptrSEXP);
@@ -337,7 +387,8 @@ BEGIN_RCPP
     Rcpp::traits::input_parameter< Rcpp::RawVector >::type serialized_indexer(serialized_indexerSEXP);
     Rcpp::traits::input_parameter< Rcpp::List& >::type model_cpp_obj_update(model_cpp_obj_updateSEXP);
     Rcpp::traits::input_parameter< Rcpp::List& >::type model_params_update(model_params_updateSEXP);
-    append_trees_from_other(model_R_ptr, other_R_ptr, imp_R_ptr, oimp_R_ptr, ind_R_ptr, oind_R_ptr, is_extended, serialized_obj, serialized_imputer, serialized_indexer, model_cpp_obj_update, model_params_update);
+    Rcpp::traits::input_parameter< bool >::type is_altrepped(is_altreppedSEXP);
+    append_trees_from_other(model_R_ptr, other_R_ptr, imp_R_ptr, oimp_R_ptr, ind_R_ptr, oind_R_ptr, is_extended, serialized_obj, serialized_imputer, serialized_indexer, model_cpp_obj_update, model_params_update, is_altrepped);
     return R_NilValue;
 END_RCPP
 }
@@ -377,28 +428,30 @@ BEGIN_RCPP
 END_RCPP
 }
 // copy_cpp_objects
-Rcpp::List copy_cpp_objects(SEXP model_R_ptr, bool is_extended, SEXP imp_R_ptr, bool has_imputer, SEXP ind_R_ptr);
-RcppExport SEXP _isotree_copy_cpp_objects(SEXP model_R_ptrSEXP, SEXP is_extendedSEXP, SEXP imp_R_ptrSEXP, SEXP has_imputerSEXP, SEXP ind_R_ptrSEXP) {
+Rcpp::List copy_cpp_objects(SEXP model_R_ptr, bool is_extended, SEXP imp_R_ptr, SEXP ind_R_ptr, bool lazy_serialization);
+RcppExport SEXP _isotree_copy_cpp_objects(SEXP model_R_ptrSEXP, SEXP is_extendedSEXP, SEXP imp_R_ptrSEXP, SEXP ind_R_ptrSEXP, SEXP lazy_serializationSEXP) {
 BEGIN_RCPP
     Rcpp::RObject rcpp_result_gen;
     Rcpp::traits::input_parameter< SEXP >::type model_R_ptr(model_R_ptrSEXP);
     Rcpp::traits::input_parameter< bool >::type is_extended(is_extendedSEXP);
     Rcpp::traits::input_parameter< SEXP >::type imp_R_ptr(imp_R_ptrSEXP);
-    Rcpp::traits::input_parameter< bool >::type has_imputer(has_imputerSEXP);
     Rcpp::traits::input_parameter< SEXP >::type ind_R_ptr(ind_R_ptrSEXP);
-    rcpp_result_gen = Rcpp::wrap(copy_cpp_objects(model_R_ptr, is_extended, imp_R_ptr, has_imputer, ind_R_ptr));
+    Rcpp::traits::input_parameter< bool >::type lazy_serialization(lazy_serializationSEXP);
+    rcpp_result_gen = Rcpp::wrap(copy_cpp_objects(model_R_ptr, is_extended, imp_R_ptr, ind_R_ptr, lazy_serialization));
     return rcpp_result_gen;
 END_RCPP
 }
 // build_tree_indices
-void build_tree_indices(Rcpp::List lst_modify, bool is_extended, bool with_distances, int nthreads);
-RcppExport SEXP _isotree_build_tree_indices(SEXP lst_modifySEXP, SEXP is_extendedSEXP, SEXP with_distancesSEXP, SEXP nthreadsSEXP) {
+void build_tree_indices(Rcpp::List lst_cpp_objects, SEXP ptr_model, bool is_altrepped, bool is_extended, bool with_distances, int nthreads);
+RcppExport SEXP _isotree_build_tree_indices(SEXP lst_cpp_objectsSEXP, SEXP ptr_modelSEXP, SEXP is_altreppedSEXP, SEXP is_extendedSEXP, SEXP with_distancesSEXP, SEXP nthreadsSEXP) {
 BEGIN_RCPP
-    Rcpp::traits::input_parameter< Rcpp::List >::type lst_modify(lst_modifySEXP);
+    Rcpp::traits::input_parameter< Rcpp::List >::type lst_cpp_objects(lst_cpp_objectsSEXP);
+    Rcpp::traits::input_parameter< SEXP >::type ptr_model(ptr_modelSEXP);
+    Rcpp::traits::input_parameter< bool >::type is_altrepped(is_altreppedSEXP);
     Rcpp::traits::input_parameter< bool >::type is_extended(is_extendedSEXP);
     Rcpp::traits::input_parameter< bool >::type with_distances(with_distancesSEXP);
     Rcpp::traits::input_parameter< int >::type nthreads(nthreadsSEXP);
-    build_tree_indices(lst_modify, is_extended, with_distances, nthreads);
+    build_tree_indices(lst_cpp_objects, ptr_model, is_altrepped, is_extended, with_distances, nthreads);
     return R_NilValue;
 END_RCPP
 }
@@ -413,11 +466,14 @@ BEGIN_RCPP
 END_RCPP
 }
 // set_reference_points
-void set_reference_points(Rcpp::List lst_modify, Rcpp::List lst_modify2, SEXP rnames, bool is_extended, Rcpp::NumericVector X_num, Rcpp::IntegerVector X_cat, Rcpp::NumericVector Xc, Rcpp::IntegerVector Xc_ind, Rcpp::IntegerVector Xc_indptr, size_t nrows, int nthreads, bool with_distances);
-RcppExport SEXP _isotree_set_reference_points(SEXP lst_modifySEXP, SEXP lst_modify2SEXP, SEXP rnamesSEXP, SEXP is_extendedSEXP, SEXP X_numSEXP, SEXP X_catSEXP, SEXP XcSEXP, SEXP Xc_indSEXP, SEXP Xc_indptrSEXP, SEXP nrowsSEXP, SEXP nthreadsSEXP, SEXP with_distancesSEXP) {
+void set_reference_points(Rcpp::List lst_cpp_objects, SEXP ptr_model, SEXP ind_R_ptr, bool is_altrepped, Rcpp::List lst_metadata, SEXP rnames, bool is_extended, Rcpp::NumericVector X_num, Rcpp::IntegerVector X_cat, Rcpp::NumericVector Xc, Rcpp::IntegerVector Xc_ind, Rcpp::IntegerVector Xc_indptr, size_t nrows, int nthreads, bool with_distances);
+RcppExport SEXP _isotree_set_reference_points(SEXP lst_cpp_objectsSEXP, SEXP ptr_modelSEXP, SEXP ind_R_ptrSEXP, SEXP is_altreppedSEXP, SEXP lst_metadataSEXP, SEXP rnamesSEXP, SEXP is_extendedSEXP, SEXP X_numSEXP, SEXP X_catSEXP, SEXP XcSEXP, SEXP Xc_indSEXP, SEXP Xc_indptrSEXP, SEXP nrowsSEXP, SEXP nthreadsSEXP, SEXP with_distancesSEXP) {
 BEGIN_RCPP
-    Rcpp::traits::input_parameter< Rcpp::List >::type lst_modify(lst_modifySEXP);
-    Rcpp::traits::input_parameter< Rcpp::List >::type lst_modify2(lst_modify2SEXP);
+    Rcpp::traits::input_parameter< Rcpp::List >::type lst_cpp_objects(lst_cpp_objectsSEXP);
+    Rcpp::traits::input_parameter< SEXP >::type ptr_model(ptr_modelSEXP);
+    Rcpp::traits::input_parameter< SEXP >::type ind_R_ptr(ind_R_ptrSEXP);
+    Rcpp::traits::input_parameter< bool >::type is_altrepped(is_altreppedSEXP);
+    Rcpp::traits::input_parameter< Rcpp::List >::type lst_metadata(lst_metadataSEXP);
     Rcpp::traits::input_parameter< SEXP >::type rnames(rnamesSEXP);
     Rcpp::traits::input_parameter< bool >::type is_extended(is_extendedSEXP);
     Rcpp::traits::input_parameter< Rcpp::NumericVector >::type X_num(X_numSEXP);
@@ -428,7 +484,7 @@ BEGIN_RCPP
     Rcpp::traits::input_parameter< size_t >::type nrows(nrowsSEXP);
     Rcpp::traits::input_parameter< int >::type nthreads(nthreadsSEXP);
     Rcpp::traits::input_parameter< bool >::type with_distances(with_distancesSEXP);
-    set_reference_points(lst_modify, lst_modify2, rnames, is_extended, X_num, X_cat, Xc, Xc_ind, Xc_indptr, nrows, nthreads, with_distances);
+    set_reference_points(lst_cpp_objects, ptr_model, ind_R_ptr, is_altrepped, lst_metadata, rnames, is_extended, X_num, X_cat, Xc, Xc_ind, Xc_indptr, nrows, nthreads, with_distances);
     return R_NilValue;
 END_RCPP
 }
@@ -452,12 +508,13 @@ BEGIN_RCPP
     return rcpp_result_gen;
 END_RCPP
 }
-// get_null_R_pointer
-SEXP get_null_R_pointer();
-RcppExport SEXP _isotree_get_null_R_pointer() {
+// get_null_R_pointer_internal
+SEXP get_null_R_pointer_internal(bool altrepped);
+RcppExport SEXP _isotree_get_null_R_pointer_internal(SEXP altreppedSEXP) {
 BEGIN_RCPP
     Rcpp::RObject rcpp_result_gen;
-    rcpp_result_gen = Rcpp::wrap(get_null_R_pointer());
+    Rcpp::traits::input_parameter< bool >::type altrepped(altreppedSEXP);
+    rcpp_result_gen = Rcpp::wrap(get_null_R_pointer_internal(altrepped));
     return rcpp_result_gen;
 END_RCPP
 }
@@ -477,13 +534,14 @@ BEGIN_RCPP
 END_RCPP
 }
 // deserialize_from_file
-Rcpp::List deserialize_from_file(Rcpp::CharacterVector fname);
-RcppExport SEXP _isotree_deserialize_from_file(SEXP fnameSEXP) {
+Rcpp::List deserialize_from_file(Rcpp::CharacterVector fname, bool lazy_serialization);
+RcppExport SEXP _isotree_deserialize_from_file(SEXP fnameSEXP, SEXP lazy_serializationSEXP) {
 BEGIN_RCPP
     Rcpp::RObject rcpp_result_gen;
     Rcpp::RNGScope rcpp_rngScope_gen;
     Rcpp::traits::input_parameter< Rcpp::CharacterVector >::type fname(fnameSEXP);
-    rcpp_result_gen = Rcpp::wrap(deserialize_from_file(fname));
+    Rcpp::traits::input_parameter< bool >::type lazy_serialization(lazy_serializationSEXP);
+    rcpp_result_gen = Rcpp::wrap(deserialize_from_file(fname, lazy_serialization));
     return rcpp_result_gen;
 END_RCPP
 }
@@ -728,30 +786,34 @@ static const R_CallMethodDef CallEntries[] = {
     {"_isotree_deserialize_ExtIsoForest", (DL_FUNC) &_isotree_deserialize_ExtIsoForest, 1},
     {"_isotree_deserialize_Imputer", (DL_FUNC) &_isotree_deserialize_Imputer, 1},
     {"_isotree_deserialize_Indexer", (DL_FUNC) &_isotree_deserialize_Indexer, 1},
-    {"_isotree_check_null_ptr_model", (DL_FUNC) &_isotree_check_null_ptr_model, 1},
-    {"_isotree_fit_model", (DL_FUNC) &_isotree_fit_model, 52},
-    {"_isotree_fit_tree", (DL_FUNC) &_isotree_fit_tree, 53},
+    {"_isotree_serialize_IsoForest_from_ptr", (DL_FUNC) &_isotree_serialize_IsoForest_from_ptr, 1},
+    {"_isotree_serialize_ExtIsoForest_from_ptr", (DL_FUNC) &_isotree_serialize_ExtIsoForest_from_ptr, 1},
+    {"_isotree_serialize_Imputer_from_ptr", (DL_FUNC) &_isotree_serialize_Imputer_from_ptr, 1},
+    {"_isotree_serialize_Indexer_from_ptr", (DL_FUNC) &_isotree_serialize_Indexer_from_ptr, 1},
+    {"_isotree_check_null_ptr_model_internal", (DL_FUNC) &_isotree_check_null_ptr_model_internal, 1},
+    {"_isotree_fit_model", (DL_FUNC) &_isotree_fit_model, 53},
+    {"_isotree_fit_tree", (DL_FUNC) &_isotree_fit_tree, 54},
     {"_isotree_predict_iso", (DL_FUNC) &_isotree_predict_iso, 17},
     {"_isotree_dist_iso", (DL_FUNC) &_isotree_dist_iso, 20},
     {"_isotree_impute_iso", (DL_FUNC) &_isotree_impute_iso, 11},
-    {"_isotree_drop_imputer", (DL_FUNC) &_isotree_drop_imputer, 2},
-    {"_isotree_drop_indexer", (DL_FUNC) &_isotree_drop_indexer, 2},
-    {"_isotree_drop_reference_points", (DL_FUNC) &_isotree_drop_reference_points, 2},
+    {"_isotree_drop_imputer", (DL_FUNC) &_isotree_drop_imputer, 5},
+    {"_isotree_drop_indexer", (DL_FUNC) &_isotree_drop_indexer, 5},
+    {"_isotree_drop_reference_points", (DL_FUNC) &_isotree_drop_reference_points, 4},
     {"_isotree_subset_trees", (DL_FUNC) &_isotree_subset_trees, 6},
     {"_isotree_inplace_set_to_zero", (DL_FUNC) &_isotree_inplace_set_to_zero, 1},
     {"_isotree_get_n_nodes", (DL_FUNC) &_isotree_get_n_nodes, 3},
-    {"_isotree_append_trees_from_other", (DL_FUNC) &_isotree_append_trees_from_other, 12},
+    {"_isotree_append_trees_from_other", (DL_FUNC) &_isotree_append_trees_from_other, 13},
     {"_isotree_model_to_sql", (DL_FUNC) &_isotree_model_to_sql, 9},
     {"_isotree_model_to_sql_with_select_from", (DL_FUNC) &_isotree_model_to_sql_with_select_from, 8},
     {"_isotree_copy_cpp_objects", (DL_FUNC) &_isotree_copy_cpp_objects, 5},
-    {"_isotree_build_tree_indices", (DL_FUNC) &_isotree_build_tree_indices, 4},
+    {"_isotree_build_tree_indices", (DL_FUNC) &_isotree_build_tree_indices, 6},
     {"_isotree_check_node_indexer_has_distances", (DL_FUNC) &_isotree_check_node_indexer_has_distances, 1},
-    {"_isotree_set_reference_points", (DL_FUNC) &_isotree_set_reference_points, 12},
+    {"_isotree_set_reference_points", (DL_FUNC) &_isotree_set_reference_points, 15},
     {"_isotree_check_node_indexer_has_references", (DL_FUNC) &_isotree_check_node_indexer_has_references, 1},
     {"_isotree_get_num_references", (DL_FUNC) &_isotree_get_num_references, 1},
-    {"_isotree_get_null_R_pointer", (DL_FUNC) &_isotree_get_null_R_pointer, 0},
+    {"_isotree_get_null_R_pointer_internal", (DL_FUNC) &_isotree_get_null_R_pointer_internal, 1},
     {"_isotree_serialize_to_file", (DL_FUNC) &_isotree_serialize_to_file, 6},
-    {"_isotree_deserialize_from_file", (DL_FUNC) &_isotree_deserialize_from_file, 1},
+    {"_isotree_deserialize_from_file", (DL_FUNC) &_isotree_deserialize_from_file, 2},
     {"_isotree_call_sort_csc_indices", (DL_FUNC) &_isotree_call_sort_csc_indices, 3},
     {"_isotree_call_reconstruct_csr_sliced", (DL_FUNC) &_isotree_call_reconstruct_csr_sliced, 5},
     {"_isotree_call_reconstruct_csr_with_categ", (DL_FUNC) &_isotree_call_reconstruct_csr_with_categ, 11},
@@ -774,7 +836,9 @@ static const R_CallMethodDef CallEntries[] = {
     {NULL, NULL, 0}
 };
 
+void init_altrepped_vectors(DllInfo* dll);
 RcppExport void R_init_isotree(DllInfo *dll) {
     R_registerRoutines(dll, NULL, CallEntries, NULL, NULL);
     R_useDynamicSymbols(dll, FALSE);
+    init_altrepped_vectors(dll);
 }