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Merge pull request #17 from ropensci/oop
object oriented re-write
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| ^Rmd/ | ||
| lastMiKTeXException | ||
| ^\.zenodo\.json$ | ||
| ^scratch\.R$ | ||
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| @@ -1,67 +1,27 @@ | ||
| # Generated by using Rcpp::compileAttributes() -> do not edit by hand | ||
| # Generator token: 10BE3573-1514-4C36-9D1C-5A225CD40393 | ||
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| std_setdiff <- function(x, y) { | ||
| .Call(`_aorsf_std_setdiff`, x, y) | ||
| coxph_fit_exported <- function(x_node, y_node, w_node, method, cph_eps, cph_iter_max) { | ||
| .Call(`_aorsf_coxph_fit_exported`, x_node, y_node, w_node, method, cph_eps, cph_iter_max) | ||
| } | ||
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| x_node_scale_exported <- function(x_, w_) { | ||
| .Call(`_aorsf_x_node_scale_exported`, x_, w_) | ||
| compute_cstat_exported_vec <- function(y, w, p, pred_is_risklike) { | ||
| .Call(`_aorsf_compute_cstat_exported_vec`, y, w, p, pred_is_risklike) | ||
| } | ||
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| leaf_kaplan_testthat <- function(y, w) { | ||
| .Call(`_aorsf_leaf_kaplan_testthat`, y, w) | ||
| compute_cstat_exported_uvec <- function(y, w, g, pred_is_risklike) { | ||
| .Call(`_aorsf_compute_cstat_exported_uvec`, y, w, g, pred_is_risklike) | ||
| } | ||
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| newtraph_cph_testthat <- function(x_in, y_in, w_in, method, cph_eps_, iter_max) { | ||
| .Call(`_aorsf_newtraph_cph_testthat`, x_in, y_in, w_in, method, cph_eps_, iter_max) | ||
| compute_logrank_exported <- function(y, w, g) { | ||
| .Call(`_aorsf_compute_logrank_exported`, y, w, g) | ||
| } | ||
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| lrt_multi_testthat <- function(y_node_, w_node_, XB_, n_split_, leaf_min_events_, leaf_min_obs_) { | ||
| .Call(`_aorsf_lrt_multi_testthat`, y_node_, w_node_, XB_, n_split_, leaf_min_events_, leaf_min_obs_) | ||
| cph_scale <- function(x, w) { | ||
| .Call(`_aorsf_cph_scale`, x, w) | ||
| } | ||
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| oobag_c_harrell_testthat <- function(y_mat, s_vec) { | ||
| .Call(`_aorsf_oobag_c_harrell_testthat`, y_mat, s_vec) | ||
| } | ||
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| ostree_pred_leaf_testthat <- function(tree, x_pred_) { | ||
| .Call(`_aorsf_ostree_pred_leaf_testthat`, tree, x_pred_) | ||
| } | ||
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| orsf_fit <- function(x, y, weights, n_tree, n_split_, mtry_, leaf_min_events_, leaf_min_obs_, split_min_events_, split_min_obs_, split_min_stat_, cph_method_, cph_eps_, cph_iter_max_, cph_do_scale_, net_alpha_, net_df_target_, oobag_pred_, oobag_pred_type_, oobag_pred_horizon_, oobag_eval_every_, oobag_importance_, oobag_importance_type_, tree_seeds, max_retry_, f_beta, type_beta_, f_oobag_eval, type_oobag_eval_, verbose_progress) { | ||
| .Call(`_aorsf_orsf_fit`, x, y, weights, n_tree, n_split_, mtry_, leaf_min_events_, leaf_min_obs_, split_min_events_, split_min_obs_, split_min_stat_, cph_method_, cph_eps_, cph_iter_max_, cph_do_scale_, net_alpha_, net_df_target_, oobag_pred_, oobag_pred_type_, oobag_pred_horizon_, oobag_eval_every_, oobag_importance_, oobag_importance_type_, tree_seeds, max_retry_, f_beta, type_beta_, f_oobag_eval, type_oobag_eval_, verbose_progress) | ||
| } | ||
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| orsf_oob_negate_vi <- function(x, y, forest, last_eval_stat, time_pred_, f_oobag_eval, pred_type_, type_oobag_eval_) { | ||
| .Call(`_aorsf_orsf_oob_negate_vi`, x, y, forest, last_eval_stat, time_pred_, f_oobag_eval, pred_type_, type_oobag_eval_) | ||
| } | ||
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| orsf_oob_permute_vi <- function(x, y, forest, last_eval_stat, time_pred_, f_oobag_eval, pred_type_, type_oobag_eval_) { | ||
| .Call(`_aorsf_orsf_oob_permute_vi`, x, y, forest, last_eval_stat, time_pred_, f_oobag_eval, pred_type_, type_oobag_eval_) | ||
| } | ||
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| orsf_pred_uni <- function(forest, x_new, time_dbl, pred_type) { | ||
| .Call(`_aorsf_orsf_pred_uni`, forest, x_new, time_dbl, pred_type) | ||
| } | ||
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| orsf_pred_multi <- function(forest, x_new, time_vec, pred_type) { | ||
| .Call(`_aorsf_orsf_pred_multi`, forest, x_new, time_vec, pred_type) | ||
| } | ||
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| pd_new_smry <- function(forest, x_new_, x_cols_, x_vals_, probs_, time_dbl, pred_type) { | ||
| .Call(`_aorsf_pd_new_smry`, forest, x_new_, x_cols_, x_vals_, probs_, time_dbl, pred_type) | ||
| } | ||
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| pd_oob_smry <- function(forest, x_new_, x_cols_, x_vals_, probs_, time_dbl, pred_type) { | ||
| .Call(`_aorsf_pd_oob_smry`, forest, x_new_, x_cols_, x_vals_, probs_, time_dbl, pred_type) | ||
| } | ||
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| pd_new_ice <- function(forest, x_new_, x_cols_, x_vals_, probs_, time_dbl, pred_type) { | ||
| .Call(`_aorsf_pd_new_ice`, forest, x_new_, x_cols_, x_vals_, probs_, time_dbl, pred_type) | ||
| } | ||
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| pd_oob_ice <- function(forest, x_new_, x_cols_, x_vals_, probs_, time_dbl, pred_type) { | ||
| .Call(`_aorsf_pd_oob_ice`, forest, x_new_, x_cols_, x_vals_, probs_, time_dbl, pred_type) | ||
| orsf_cpp <- function(x, y, w, tree_type_R, tree_seeds, loaded_forest, lincomb_R_function, oobag_R_function, n_tree, mtry, sample_with_replacement, sample_fraction, vi_type_R, vi_max_pvalue, leaf_min_events, leaf_min_obs, split_rule_R, split_min_events, split_min_obs, split_min_stat, split_max_cuts, split_max_retry, lincomb_type_R, lincomb_eps, lincomb_iter_max, lincomb_scale, lincomb_alpha, lincomb_df_target, lincomb_ties_method, pred_mode, pred_type_R, pred_horizon, pred_aggregate, oobag, oobag_eval_type_R, oobag_eval_every, pd_type_R, pd_x_vals, pd_x_cols, pd_probs, n_thread, write_forest, run_forest, verbosity) { | ||
| .Call(`_aorsf_orsf_cpp`, x, y, w, tree_type_R, tree_seeds, loaded_forest, lincomb_R_function, oobag_R_function, n_tree, mtry, sample_with_replacement, sample_fraction, vi_type_R, vi_max_pvalue, leaf_min_events, leaf_min_obs, split_rule_R, split_min_events, split_min_obs, split_min_stat, split_max_cuts, split_max_retry, lincomb_type_R, lincomb_eps, lincomb_iter_max, lincomb_scale, lincomb_alpha, lincomb_df_target, lincomb_ties_method, pred_mode, pred_type_R, pred_horizon, pred_aggregate, oobag, oobag_eval_type_R, oobag_eval_every, pd_type_R, pd_x_vals, pd_x_cols, pd_probs, n_thread, write_forest, run_forest, verbosity) | ||
| } | ||
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| Original file line number | Diff line number | Diff line change |
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| @@ -0,0 +1,15 @@ | ||
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| compute_mean_leaves <- function(forest){ | ||
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| if(is.null(forest$leaf_summary)){ | ||
| return(0) | ||
| } | ||
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| collapse::fmean( | ||
| vapply(forest$leaf_summary, | ||
| function(leaf_smry) sum(leaf_smry != 0), | ||
| FUN.VALUE = integer(1)) | ||
| ) | ||
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| } |
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