From f755ea9348acecf92f8dd7d140d3a4b2d3c49388 Mon Sep 17 00:00:00 2001
From: bcjaeger <byron.jaeger@gmail.com>
Date: Sat, 7 Oct 2023 20:02:43 -0400
Subject: [PATCH] drop global verbosity

---
 src/ForestSurvival.cpp        |  2 +-
 src/Tree.cpp                  | 42 ++++++++++++++---------------------
 src/globals.h                 |  2 --
 tests/testthat/test-oobag.R   |  6 ++---
 tests/testthat/test-orsf_pd.R | 16 +++++++++++++
 5 files changed, 36 insertions(+), 32 deletions(-)

diff --git a/src/ForestSurvival.cpp b/src/ForestSurvival.cpp
index 93291546..9b9335f6 100644
--- a/src/ForestSurvival.cpp
+++ b/src/ForestSurvival.cpp
@@ -49,7 +49,7 @@ void ForestSurvival::load(
  this->pd_x_cols = pd_x_cols;
  this->pd_probs  = pd_probs;
 
- if(VERBOSITY > 0){
+ if(verbosity > 2){
   Rcout << "---- loading forest from input list ----";
   Rcout << std::endl << std::endl;
  }
diff --git a/src/Tree.cpp b/src/Tree.cpp
index 1fe8426d..98528d4a 100644
--- a/src/Tree.cpp
+++ b/src/Tree.cpp
@@ -315,12 +315,12 @@
 
   }
 
-  if(VERBOSITY > 1){
+  if(verbosity > 4){
 
    mat x_print = x_inbag.rows(rows_node);
-   Rcout << "Column " << j << " was sampled but ";
-   Rcout << "unique values of column " << j << " are ";
-   Rcout << unique(x_print.col(j)) << std::endl;
+   Rcout << "   -- Column " << j << " was sampled but ";
+   Rcout << "its unique values are " << unique(x_print.col(j));
+   Rcout << std::endl;
 
   }
 
@@ -371,10 +371,6 @@
 
   double n_obs = 0;
 
-  if(VERBOSITY > 1){
-   Rcout << "----- finding lower bound for cut-points -----" << std::endl;
-  }
-
   // stop at end-1 b/c we access it+1 in lincomb_sort
   for(it = lincomb_sort.begin(); it < lincomb_sort.end()-1; ++it){
 
@@ -388,10 +384,10 @@
 
     if(n_obs >= leaf_min_obs) {
 
-     if(VERBOSITY > 0){
+     if(verbosity > 3){
       Rcout << std::endl;
-      Rcout << "lower cutpoint: "         << lincomb(*it) << std::endl;
-      Rcout << " - n_obs, left node:   " << n_obs   << std::endl;
+      Rcout << "   -- lower cutpoint: " << lincomb(*it) << std::endl;
+      Rcout << "      - n_obs, left node:   " << n_obs   << std::endl;
       Rcout << std::endl;
      }
 
@@ -407,8 +403,8 @@
 
   if(it == lincomb_sort.end()-1) {
 
-   if(VERBOSITY > 1){
-    Rcout << "Could not find a valid cut-point" << std::endl;
+   if(verbosity > 3){
+    Rcout << "   -- Could not find a valid cut-point" << std::endl;
    }
 
    return;
@@ -421,10 +417,6 @@
   // reset before finding the upper limit
   n_obs=0;
 
-  if(VERBOSITY > 1){
-   Rcout << "----- finding upper bound for cut-points -----" << std::endl;
-  }
-
   // stop at beginning+1 b/c we access it-1 in lincomb_sort
   for(it = lincomb_sort.end()-1; it >= lincomb_sort.begin()+1; --it){
 
@@ -444,10 +436,10 @@
 
      --it;
 
-     if(VERBOSITY > 0){
+     if(verbosity > 3){
       Rcout << std::endl;
-      Rcout << "upper cutpoint: " << lincomb(*it) << std::endl;
-      Rcout << " - n_obs, right node:   " << n_obs << std::endl;
+      Rcout << "   -- upper cutpoint: " << lincomb(*it) << std::endl;
+      Rcout << "      - n_obs, right node:   " << n_obs << std::endl;
       Rcout << std::endl;
      }
 
@@ -466,8 +458,8 @@
 
   if(j > k){
 
-   if(VERBOSITY > 0) {
-    Rcout << "Could not find valid cut-points" << std::endl;
+   if(verbosity > 2) {
+    Rcout << "   -- Could not find valid cut-points" << std::endl;
    }
 
    return;
@@ -698,10 +690,10 @@
 
     double accuracy_permuted = compute_prediction_accuracy(pred_values);
 
-    if(VERBOSITY>1){
-     Rcout << "prediction accuracy after noising " << pred_col << ": ";
+    if(verbosity > 3){
+     Rcout << "   -- prediction accuracy after noising " << pred_col << ": ";
      Rcout << accuracy_permuted << std::endl;
-     Rcout << "  - mean leaf pred: ";
+     Rcout << "      - mean leaf pred: ";
      Rcout << mean(conv_to<vec>::from(pred_leaf));
      Rcout << std::endl << std::endl;
     }
diff --git a/src/globals.h b/src/globals.h
index c684b813..22c68d30 100644
--- a/src/globals.h
+++ b/src/globals.h
@@ -97,8 +97,6 @@
 
  const PredType DEFAULT_PRED_TYPE = PRED_RISK;
 
- const int VERBOSITY = 0;
-
  // Interval to print progress in seconds
  const double STATUS_INTERVAL = 1.0;
 
diff --git a/tests/testthat/test-oobag.R b/tests/testthat/test-oobag.R
index db96150a..2d876c21 100644
--- a/tests/testthat/test-oobag.R
+++ b/tests/testthat/test-oobag.R
@@ -3,14 +3,12 @@ fit_custom_oobag <- orsf(pbc_orsf,
                          formula = Surv(time, status) ~ . - id,
                          n_tree = 100,
                          oobag_fun = oobag_c_survival,
-                         tree_seeds = 1:100,
-                         verbose_progress = 0)
+                         tree_seeds = 1:100)
 
 fit_standard_oobag <- orsf(pbc_orsf,
                            formula = Surv(time, status) ~ . - id,
                            n_tree = 100,
-                           tree_seeds = 1:100,
-                           verbose_progress = 0)
+                           tree_seeds = 1:100)
 
 testthat::expect_equal(
  fit_custom_oobag$forest$rows_oobag,
diff --git a/tests/testthat/test-orsf_pd.R b/tests/testthat/test-orsf_pd.R
index 9a219b6e..2a8393c4 100644
--- a/tests/testthat/test-orsf_pd.R
+++ b/tests/testthat/test-orsf_pd.R
@@ -209,5 +209,21 @@ test_that(
 #  }
 # )
 
+# bili_seq <- seq(1, 5, length.out=20)
+#
+# microbenchmark::microbenchmark(
+#  pd_reference = partial(fit,
+#                         pred.var = "bili",
+#                         pred.grid = data.frame(bili = bili_seq),
+#                         pred.fun = pred_aorsf,
+#                         plot = FALSE,
+#                         ice = TRUE,
+#                         train = pbc_orsf),
+#  pd_aorsf = orsf_ice_new(fit,
+#                          new_data = pbc_orsf,
+#                          pred_spec = list(bili=bili_seq),
+#                          pred_horizon = 1000,
+#                          expand_grid = TRUE)
+# )