From 9913b3f2fc4537c32d830f39c5b4a54ef8875a3d Mon Sep 17 00:00:00 2001
From: jrudar <joe.rudar@gmail.com>
Date: Mon, 23 Oct 2023 02:47:06 -0400
Subject: [PATCH] - Removed unused variables and imports - Fixed location of
 imports - Updated API documentation - Added comments on where some code was
 adapted from - UMAP metric is now 'mahalanobis'

---
 README.md                                     |   9 +-
 docs/API.md                                   |  58 ++--
 .../16S_Test_PSO_PA.ipynb                     | 290 +++++++++++++++++-
 pyproject.toml                                |   2 +-
 tests/test_triglav.py                         |   7 +-
 triglav/triglav.py                            |  17 +-
 6 files changed, 311 insertions(+), 72 deletions(-)

diff --git a/README.md b/README.md
index b2a7fe2..61ca66c 100644
--- a/README.md
+++ b/README.md
@@ -29,11 +29,10 @@ modifications:
    to the 'n_iter_fwer' parameter. For a cluster to be rejected a similar round
    of reasoning applies. Clusters that are not rejected remain tentative.
 
-4) After the iterative refinement a swarm intelligence algorithm, harris hawks
-   optimization, is used to select the most informative feature subset. This
-   procedure mimics the hunting strategies of harris hawks to find the minimum
-   value of a function. In this case, the optimization strategy is used to find
-   the subset of features which minimizes classification error.
+4) After the iterative refinement a swarm intelligence algorithm, naked mole rat
+   algorithm, is used to select the most informative feature subset. The user can
+   also choose to use the MultiSURF algorithm as an alternative to swarm
+   intelligence.
 
 While this method may not produce all features important for classification,
 it does have some nice properties. First of all, by using an Extremely 
diff --git a/docs/API.md b/docs/API.md
index 8a12260..bfd8ee2 100644
--- a/docs/API.md
+++ b/docs/API.md
@@ -7,30 +7,24 @@ of the `Triglav` class and its methods.
 
     class triglav.Triglav(transformer = NoScale(), sampler = NoResample(), estimator = ExtraTreesClassifier(512, bootstrap = True),
                   stage_2_estimator = ExtraTreesClassifier(512, bootstrap = True), per_class_imp = False,
-                  n_iter = 40, n_iter_fwer = 11, p_1 = 0.65, p_2 = 0.30, metric = "correlation", linkage = "complete",
-                  thresh = 2.0, criterion = "distance", run_stage_2 = True, max_iter_sage_2 = 100, algo = HarrisHawksOptimization(),
-                  alpha_2 = 0.99, verbose = 0, n_jobs = 10)
+                  n_iter = 40, n_iter_fwer = 11, p_1 = 0.65, p_2 = 0.30, metric = "euclidean", linkage = "ward",
+                  thresh = 2.0, criterion = "distance", run_stage_2 = True, verbose = 0, n_jobs = 10)
 
 ### Parameters
 
     transformer: default = NoScale()
-        The transformer to be used to scale features. One can use
-        the scikit-learn.preprocessing transformers. In addition,
-        CLR and Scaler (converts each row into frequencies) are
-        available by importing 'CLRTransformer' and 'Scaler' from the
-        'triglav' package.
-	
+        The transformer to be used to scale features.
+
     sampler: default = NoResample()
-        The resampling method used for imbalanced classes. Should be
-        compatable with 'imblearn' or use an 'imblearn' resampler.
+        The type of sampler (from Imbalanced-learn) to use.
 
     estimator: default = ExtraTreesClassifier(512, bootstrap = True)
         The estimator used to calculate Shapley scores.
 
     stage_2_estimator: default = ExtraTreesClassifier(512)
-        The estimator used to calculate SAGE values. Only used if the
-        'run_stage_2' is set to True.
-	
+        The estimator used to calculate MultiSURF CV scores.
+        Only used if the 'run_stage_2' is set to True or 'mms'.
+
     per_class_imp: bool, default = False
         Specifies if importance scores are calculated globally or per
         class. Note, per class importance scores are calculated in a
@@ -48,14 +42,13 @@ of the `Triglav` class and its methods.
 
     p_2: float, default = 0.30
         Used to determine the shape of the Beta-Binomial distribution
-        modelling failures.
+        modelling misses.
 
-    metric: str, default = "correlation"
+    metric: str, default = "euclidean"
         The dissimilarity measure used to calculate distances between
-        features. To use Extremely Randomized Trees proximities one
-        has to import 'ETCProx' from the 'triglav' package.
+        features.
 
-    linkage: str, default = "complete"
+    linkage: str, default = "ward"
         The type of hierarchical clustering method to apply. The available
         methods include: single, complete, ward, average, centroid.
 
@@ -64,26 +57,16 @@ of the `Triglav` class and its methods.
 
     criterion: str, default = "distance"
         The method used to form flat clusters. The available methods
-        include: inconsistent, distance, maxclust, monocrit,
-        maxclust_monocrit.
+        include: distance or maxclust.
 
     alpha: float, default = 0.05
         The level at which corrected p-values will be rejected.
 
-    run_stage_2: bool, default = True
-        This stage will determine the best feature subset using
-        the harris hawks (HHO) algorithm.
-
-    max_iter_stage_2: int, default = 100
-        The maximum number of iterations the HHO algorithm will
-        run.
-
-    algo: Algorithm, default = HarrisHawksOptimization()
-        A NiaPy algorithm.
-
-    alpha_2: float, default = 0.99
-        The weight used to balance model generalization or
-        number of features selected by the HHO algorithm.
+    run_stage_2: str or bool, default = "mms"
+        This stage will determine the best features from the selected
+        Triglav features. If 'str' is "auto", swarm optimization is used.
+        If "mms" (default), a modified version of the MultiSURF algorithm
+        is used. If True, "mms" is used. If False, stage 2 is not run.
 
     verbose: int, default = 0
         Specifies if basic reporting is sent to the user.
@@ -107,7 +90,7 @@ of the `Triglav` class and its methods.
         if the 'run_stage_2' parameter is enabled.
 
     self.task_opt_: Task Object
-        NiaPy task optimizer object.
+        MealPy task optimizer object.
 
     linkage_matrix_: ndarray
         The SciPy hierarchical clustering encoded as a linkage matrix.
@@ -216,8 +199,6 @@ of the `Triglav` class and its methods.
 
     class triglav.Scaler()
 
-    class triglav.CLRTransformer()
-
     class triglav.NoResample()
 
 ### Parameters
@@ -247,6 +228,5 @@ of the `Triglav` class and its methods.
 
         NoScale will return X
         Scaler will return the closure of X (all rows sum to one, X must be non-negative)
-        CLRTransformer will return the CLR Transform of X (X must be non-negative)
         NoResample will return X
 
diff --git a/notebooks/Diseased-Gut-Analysis/16S_Test_PSO_PA.ipynb b/notebooks/Diseased-Gut-Analysis/16S_Test_PSO_PA.ipynb
index 74221ab..ac3b3d5 100644
--- a/notebooks/Diseased-Gut-Analysis/16S_Test_PSO_PA.ipynb
+++ b/notebooks/Diseased-Gut-Analysis/16S_Test_PSO_PA.ipynb
@@ -788,7 +788,7 @@
   {
    "cell_type": "code",
    "execution_count": null,
-   "id": "a5b63e6d",
+   "id": "9bfd80a2",
    "metadata": {},
    "outputs": [
     {
@@ -932,7 +932,275 @@
       "Final Feature Set Contains 128 Features.\n",
       "10 4 - Remaining Features = 803\n",
       "Stage One: Identifying an initial set of tentative features...\n",
-      "Round 1 / Tentative (Accepted): 0 / Tentative (Not Accepted): 10 / Rejected: 0\n"
+      "Round 1 / Tentative (Accepted): 0 / Tentative (Not Accepted): 10 / Rejected: 0\n",
+      "Round 2 / Tentative (Accepted): 0 / Tentative (Not Accepted): 10 / Rejected: 0\n",
+      "Round 3 / Tentative (Accepted): 0 / Tentative (Not Accepted): 10 / Rejected: 0\n",
+      "Round 4 / Tentative (Accepted): 0 / Tentative (Not Accepted): 10 / Rejected: 0\n",
+      "Round 5 / Tentative (Accepted): 0 / Tentative (Not Accepted): 10 / Rejected: 0\n",
+      "Round 6 / Tentative (Accepted): 0 / Tentative (Not Accepted): 10 / Rejected: 0\n",
+      "Round 7 / Tentative (Accepted): 0 / Tentative (Not Accepted): 10 / Rejected: 0\n",
+      "Round 8 / Tentative (Accepted): 0 / Tentative (Not Accepted): 10 / Rejected: 0\n",
+      "Round 9 / Tentative (Accepted): 0 / Tentative (Not Accepted): 10 / Rejected: 0\n",
+      "Round 10 / Tentative (Accepted): 0 / Tentative (Not Accepted): 10 / Rejected: 0\n",
+      "Round 11 / Tentative (Accepted): 0 / Tentative (Not Accepted): 10 / Rejected: 0\n",
+      "Round 12 / Tentative (Accepted): 0 / Tentative (Not Accepted): 10 / Rejected: 0\n",
+      "Round 13 / Tentative (Accepted): 0 / Tentative (Not Accepted): 10 / Rejected: 0\n",
+      "Round 14 / Tentative (Accepted): 0 / Tentative (Not Accepted): 10 / Rejected: 0\n",
+      "Round 15 / Tentative (Accepted): 0 / Tentative (Not Accepted): 10 / Rejected: 0\n",
+      "Round 16 / Tentative (Accepted): 0 / Tentative (Not Accepted): 10 / Rejected: 0\n",
+      "Round 17 / Tentative (Accepted): 0 / Tentative (Not Accepted): 10 / Rejected: 0\n",
+      "Round 18 / Tentative (Accepted): 0 / Tentative (Not Accepted): 10 / Rejected: 0\n",
+      "Round 19 / Tentative (Accepted): 0 / Tentative (Not Accepted): 10 / Rejected: 0\n",
+      "Round 20 / Tentative (Accepted): 0 / Tentative (Not Accepted): 10 / Rejected: 0\n",
+      "Round 21 / Tentative (Accepted): 0 / Tentative (Not Accepted): 10 / Rejected: 0\n",
+      "Round 22 / Tentative (Accepted): 0 / Tentative (Not Accepted): 10 / Rejected: 0\n",
+      "Round 23 / Tentative (Accepted): 0 / Tentative (Not Accepted): 8 / Rejected: 2\n",
+      "Round 24 / Tentative (Accepted): 0 / Tentative (Not Accepted): 8 / Rejected: 2\n",
+      "Round 25 / Tentative (Accepted): 0 / Tentative (Not Accepted): 8 / Rejected: 2\n",
+      "Round 26 / Tentative (Accepted): 0 / Tentative (Not Accepted): 8 / Rejected: 2\n",
+      "Round 27 / Tentative (Accepted): 0 / Tentative (Not Accepted): 8 / Rejected: 2\n",
+      "Round 28 / Tentative (Accepted): 0 / Tentative (Not Accepted): 8 / Rejected: 2\n",
+      "Round 29 / Tentative (Accepted): 0 / Tentative (Not Accepted): 8 / Rejected: 2\n",
+      "Round 30 / Tentative (Accepted): 0 / Tentative (Not Accepted): 8 / Rejected: 2\n",
+      "Round 31 / Tentative (Accepted): 0 / Tentative (Not Accepted): 7 / Rejected: 3\n",
+      "Round 32 / Tentative (Accepted): 0 / Tentative (Not Accepted): 7 / Rejected: 3\n",
+      "Round 33 / Tentative (Accepted): 0 / Tentative (Not Accepted): 7 / Rejected: 3\n",
+      "Round 34 / Tentative (Accepted): 3 / Tentative (Not Accepted): 4 / Rejected: 3\n",
+      "Round 35 / Tentative (Accepted): 3 / Tentative (Not Accepted): 4 / Rejected: 3\n",
+      "Round 36 / Tentative (Accepted): 3 / Tentative (Not Accepted): 4 / Rejected: 3\n",
+      "Round 37 / Tentative (Accepted): 3 / Tentative (Not Accepted): 4 / Rejected: 3\n",
+      "Round 38 / Tentative (Accepted): 3 / Tentative (Not Accepted): 4 / Rejected: 3\n",
+      "Round 39 / Tentative (Accepted): 3 / Tentative (Not Accepted): 4 / Rejected: 3\n",
+      "Round 40 / Tentative (Accepted): 3 / Tentative (Not Accepted): 4 / Rejected: 3\n",
+      "Final Feature Set Contains 311 Features.\n",
+      "10 5 - Remaining Features = 752\n",
+      "Stage One: Identifying an initial set of tentative features...\n",
+      "Round 1 / Tentative (Accepted): 0 / Tentative (Not Accepted): 10 / Rejected: 0\n",
+      "Round 2 / Tentative (Accepted): 0 / Tentative (Not Accepted): 10 / Rejected: 0\n",
+      "Round 3 / Tentative (Accepted): 0 / Tentative (Not Accepted): 10 / Rejected: 0\n",
+      "Round 4 / Tentative (Accepted): 0 / Tentative (Not Accepted): 10 / Rejected: 0\n",
+      "Round 5 / Tentative (Accepted): 0 / Tentative (Not Accepted): 10 / Rejected: 0\n",
+      "Round 6 / Tentative (Accepted): 0 / Tentative (Not Accepted): 10 / Rejected: 0\n",
+      "Round 7 / Tentative (Accepted): 0 / Tentative (Not Accepted): 10 / Rejected: 0\n",
+      "Round 8 / Tentative (Accepted): 0 / Tentative (Not Accepted): 10 / Rejected: 0\n",
+      "Round 9 / Tentative (Accepted): 0 / Tentative (Not Accepted): 10 / Rejected: 0\n",
+      "Round 10 / Tentative (Accepted): 0 / Tentative (Not Accepted): 10 / Rejected: 0\n",
+      "Round 11 / Tentative (Accepted): 0 / Tentative (Not Accepted): 10 / Rejected: 0\n",
+      "Round 12 / Tentative (Accepted): 0 / Tentative (Not Accepted): 10 / Rejected: 0\n",
+      "Round 13 / Tentative (Accepted): 0 / Tentative (Not Accepted): 10 / Rejected: 0\n",
+      "Round 14 / Tentative (Accepted): 0 / Tentative (Not Accepted): 10 / Rejected: 0\n",
+      "Round 15 / Tentative (Accepted): 0 / Tentative (Not Accepted): 10 / Rejected: 0\n",
+      "Round 16 / Tentative (Accepted): 0 / Tentative (Not Accepted): 10 / Rejected: 0\n",
+      "Round 17 / Tentative (Accepted): 0 / Tentative (Not Accepted): 10 / Rejected: 0\n",
+      "Round 18 / Tentative (Accepted): 0 / Tentative (Not Accepted): 10 / Rejected: 0\n",
+      "Round 19 / Tentative (Accepted): 0 / Tentative (Not Accepted): 10 / Rejected: 0\n",
+      "Round 20 / Tentative (Accepted): 0 / Tentative (Not Accepted): 10 / Rejected: 0\n",
+      "Round 21 / Tentative (Accepted): 0 / Tentative (Not Accepted): 10 / Rejected: 0\n",
+      "Round 22 / Tentative (Accepted): 0 / Tentative (Not Accepted): 10 / Rejected: 0\n",
+      "Round 23 / Tentative (Accepted): 0 / Tentative (Not Accepted): 6 / Rejected: 4\n",
+      "Round 24 / Tentative (Accepted): 0 / Tentative (Not Accepted): 6 / Rejected: 4\n",
+      "Round 25 / Tentative (Accepted): 0 / Tentative (Not Accepted): 6 / Rejected: 4\n",
+      "Round 26 / Tentative (Accepted): 0 / Tentative (Not Accepted): 6 / Rejected: 4\n",
+      "Round 27 / Tentative (Accepted): 0 / Tentative (Not Accepted): 6 / Rejected: 4\n",
+      "Round 28 / Tentative (Accepted): 0 / Tentative (Not Accepted): 6 / Rejected: 4\n",
+      "Round 29 / Tentative (Accepted): 0 / Tentative (Not Accepted): 6 / Rejected: 4\n",
+      "Round 30 / Tentative (Accepted): 0 / Tentative (Not Accepted): 6 / Rejected: 4\n",
+      "Round 31 / Tentative (Accepted): 0 / Tentative (Not Accepted): 6 / Rejected: 4\n",
+      "Round 32 / Tentative (Accepted): 0 / Tentative (Not Accepted): 6 / Rejected: 4\n",
+      "Round 33 / Tentative (Accepted): 0 / Tentative (Not Accepted): 6 / Rejected: 4\n",
+      "Round 34 / Tentative (Accepted): 1 / Tentative (Not Accepted): 5 / Rejected: 4\n",
+      "Round 35 / Tentative (Accepted): 1 / Tentative (Not Accepted): 5 / Rejected: 4\n",
+      "Round 36 / Tentative (Accepted): 1 / Tentative (Not Accepted): 5 / Rejected: 4\n",
+      "Round 37 / Tentative (Accepted): 1 / Tentative (Not Accepted): 5 / Rejected: 4\n",
+      "Round 38 / Tentative (Accepted): 1 / Tentative (Not Accepted): 5 / Rejected: 4\n",
+      "Round 39 / Tentative (Accepted): 1 / Tentative (Not Accepted): 5 / Rejected: 4\n"
+     ]
+    },
+    {
+     "name": "stdout",
+     "output_type": "stream",
+     "text": [
+      "Round 40 / Tentative (Accepted): 1 / Tentative (Not Accepted): 5 / Rejected: 4\n",
+      "Final Feature Set Contains 129 Features.\n",
+      "50 1 - Remaining Features = 724\n",
+      "Stage One: Identifying an initial set of tentative features...\n",
+      "Round 1 / Tentative (Accepted): 0 / Tentative (Not Accepted): 50 / Rejected: 0\n",
+      "Round 2 / Tentative (Accepted): 0 / Tentative (Not Accepted): 50 / Rejected: 0\n",
+      "Round 3 / Tentative (Accepted): 0 / Tentative (Not Accepted): 50 / Rejected: 0\n",
+      "Round 4 / Tentative (Accepted): 0 / Tentative (Not Accepted): 50 / Rejected: 0\n",
+      "Round 5 / Tentative (Accepted): 0 / Tentative (Not Accepted): 50 / Rejected: 0\n",
+      "Round 6 / Tentative (Accepted): 0 / Tentative (Not Accepted): 50 / Rejected: 0\n",
+      "Round 7 / Tentative (Accepted): 0 / Tentative (Not Accepted): 50 / Rejected: 0\n",
+      "Round 8 / Tentative (Accepted): 0 / Tentative (Not Accepted): 50 / Rejected: 0\n",
+      "Round 9 / Tentative (Accepted): 0 / Tentative (Not Accepted): 50 / Rejected: 0\n",
+      "Round 10 / Tentative (Accepted): 0 / Tentative (Not Accepted): 50 / Rejected: 0\n",
+      "Round 11 / Tentative (Accepted): 0 / Tentative (Not Accepted): 50 / Rejected: 0\n",
+      "Round 12 / Tentative (Accepted): 0 / Tentative (Not Accepted): 50 / Rejected: 0\n",
+      "Round 13 / Tentative (Accepted): 0 / Tentative (Not Accepted): 50 / Rejected: 0\n",
+      "Round 14 / Tentative (Accepted): 0 / Tentative (Not Accepted): 50 / Rejected: 0\n",
+      "Round 15 / Tentative (Accepted): 0 / Tentative (Not Accepted): 50 / Rejected: 0\n",
+      "Round 16 / Tentative (Accepted): 0 / Tentative (Not Accepted): 50 / Rejected: 0\n",
+      "Round 17 / Tentative (Accepted): 0 / Tentative (Not Accepted): 50 / Rejected: 0\n",
+      "Round 18 / Tentative (Accepted): 0 / Tentative (Not Accepted): 50 / Rejected: 0\n",
+      "Round 19 / Tentative (Accepted): 0 / Tentative (Not Accepted): 50 / Rejected: 0\n",
+      "Round 20 / Tentative (Accepted): 0 / Tentative (Not Accepted): 50 / Rejected: 0\n",
+      "Round 21 / Tentative (Accepted): 0 / Tentative (Not Accepted): 50 / Rejected: 0\n",
+      "Round 22 / Tentative (Accepted): 0 / Tentative (Not Accepted): 50 / Rejected: 0\n",
+      "Round 23 / Tentative (Accepted): 0 / Tentative (Not Accepted): 32 / Rejected: 18\n",
+      "Round 24 / Tentative (Accepted): 0 / Tentative (Not Accepted): 32 / Rejected: 18\n",
+      "Round 25 / Tentative (Accepted): 0 / Tentative (Not Accepted): 32 / Rejected: 18\n",
+      "Round 26 / Tentative (Accepted): 0 / Tentative (Not Accepted): 32 / Rejected: 18\n",
+      "Round 27 / Tentative (Accepted): 0 / Tentative (Not Accepted): 32 / Rejected: 18\n",
+      "Round 28 / Tentative (Accepted): 0 / Tentative (Not Accepted): 32 / Rejected: 18\n",
+      "Round 29 / Tentative (Accepted): 0 / Tentative (Not Accepted): 32 / Rejected: 18\n",
+      "Round 30 / Tentative (Accepted): 0 / Tentative (Not Accepted): 32 / Rejected: 18\n",
+      "Round 31 / Tentative (Accepted): 0 / Tentative (Not Accepted): 32 / Rejected: 18\n",
+      "Round 32 / Tentative (Accepted): 0 / Tentative (Not Accepted): 32 / Rejected: 18\n",
+      "Round 33 / Tentative (Accepted): 0 / Tentative (Not Accepted): 32 / Rejected: 18\n",
+      "Round 34 / Tentative (Accepted): 18 / Tentative (Not Accepted): 14 / Rejected: 18\n",
+      "Round 35 / Tentative (Accepted): 18 / Tentative (Not Accepted): 14 / Rejected: 18\n",
+      "Round 36 / Tentative (Accepted): 18 / Tentative (Not Accepted): 14 / Rejected: 18\n",
+      "Round 37 / Tentative (Accepted): 18 / Tentative (Not Accepted): 14 / Rejected: 18\n",
+      "Round 38 / Tentative (Accepted): 18 / Tentative (Not Accepted): 14 / Rejected: 18\n",
+      "Round 39 / Tentative (Accepted): 18 / Tentative (Not Accepted): 14 / Rejected: 18\n",
+      "Round 40 / Tentative (Accepted): 18 / Tentative (Not Accepted): 14 / Rejected: 18\n",
+      "Final Feature Set Contains 274 Features.\n",
+      "50 2 - Remaining Features = 737\n",
+      "Stage One: Identifying an initial set of tentative features...\n",
+      "Round 1 / Tentative (Accepted): 0 / Tentative (Not Accepted): 50 / Rejected: 0\n",
+      "Round 2 / Tentative (Accepted): 0 / Tentative (Not Accepted): 50 / Rejected: 0\n",
+      "Round 3 / Tentative (Accepted): 0 / Tentative (Not Accepted): 50 / Rejected: 0\n",
+      "Round 4 / Tentative (Accepted): 0 / Tentative (Not Accepted): 50 / Rejected: 0\n",
+      "Round 5 / Tentative (Accepted): 0 / Tentative (Not Accepted): 50 / Rejected: 0\n",
+      "Round 6 / Tentative (Accepted): 0 / Tentative (Not Accepted): 50 / Rejected: 0\n",
+      "Round 7 / Tentative (Accepted): 0 / Tentative (Not Accepted): 50 / Rejected: 0\n",
+      "Round 8 / Tentative (Accepted): 0 / Tentative (Not Accepted): 50 / Rejected: 0\n",
+      "Round 9 / Tentative (Accepted): 0 / Tentative (Not Accepted): 50 / Rejected: 0\n",
+      "Round 10 / Tentative (Accepted): 0 / Tentative (Not Accepted): 50 / Rejected: 0\n",
+      "Round 11 / Tentative (Accepted): 0 / Tentative (Not Accepted): 50 / Rejected: 0\n",
+      "Round 12 / Tentative (Accepted): 0 / Tentative (Not Accepted): 50 / Rejected: 0\n",
+      "Round 13 / Tentative (Accepted): 0 / Tentative (Not Accepted): 50 / Rejected: 0\n",
+      "Round 14 / Tentative (Accepted): 0 / Tentative (Not Accepted): 50 / Rejected: 0\n",
+      "Round 15 / Tentative (Accepted): 0 / Tentative (Not Accepted): 50 / Rejected: 0\n",
+      "Round 16 / Tentative (Accepted): 0 / Tentative (Not Accepted): 50 / Rejected: 0\n",
+      "Round 17 / Tentative (Accepted): 0 / Tentative (Not Accepted): 50 / Rejected: 0\n",
+      "Round 18 / Tentative (Accepted): 0 / Tentative (Not Accepted): 50 / Rejected: 0\n",
+      "Round 19 / Tentative (Accepted): 0 / Tentative (Not Accepted): 50 / Rejected: 0\n",
+      "Round 20 / Tentative (Accepted): 0 / Tentative (Not Accepted): 50 / Rejected: 0\n",
+      "Round 21 / Tentative (Accepted): 0 / Tentative (Not Accepted): 50 / Rejected: 0\n",
+      "Round 22 / Tentative (Accepted): 0 / Tentative (Not Accepted): 50 / Rejected: 0\n",
+      "Round 23 / Tentative (Accepted): 0 / Tentative (Not Accepted): 28 / Rejected: 22\n",
+      "Round 24 / Tentative (Accepted): 0 / Tentative (Not Accepted): 28 / Rejected: 22\n",
+      "Round 25 / Tentative (Accepted): 0 / Tentative (Not Accepted): 28 / Rejected: 22\n",
+      "Round 26 / Tentative (Accepted): 0 / Tentative (Not Accepted): 28 / Rejected: 22\n",
+      "Round 27 / Tentative (Accepted): 0 / Tentative (Not Accepted): 28 / Rejected: 22\n",
+      "Round 28 / Tentative (Accepted): 0 / Tentative (Not Accepted): 28 / Rejected: 22\n",
+      "Round 29 / Tentative (Accepted): 0 / Tentative (Not Accepted): 28 / Rejected: 22\n",
+      "Round 30 / Tentative (Accepted): 0 / Tentative (Not Accepted): 28 / Rejected: 22\n",
+      "Round 31 / Tentative (Accepted): 0 / Tentative (Not Accepted): 28 / Rejected: 22\n",
+      "Round 32 / Tentative (Accepted): 0 / Tentative (Not Accepted): 28 / Rejected: 22\n",
+      "Round 33 / Tentative (Accepted): 0 / Tentative (Not Accepted): 28 / Rejected: 22\n",
+      "Round 34 / Tentative (Accepted): 15 / Tentative (Not Accepted): 13 / Rejected: 22\n",
+      "Round 35 / Tentative (Accepted): 15 / Tentative (Not Accepted): 13 / Rejected: 22\n",
+      "Round 36 / Tentative (Accepted): 15 / Tentative (Not Accepted): 13 / Rejected: 22\n",
+      "Round 37 / Tentative (Accepted): 15 / Tentative (Not Accepted): 13 / Rejected: 22\n",
+      "Round 38 / Tentative (Accepted): 15 / Tentative (Not Accepted): 13 / Rejected: 22\n",
+      "Round 39 / Tentative (Accepted): 15 / Tentative (Not Accepted): 13 / Rejected: 22\n",
+      "Round 40 / Tentative (Accepted): 15 / Tentative (Not Accepted): 13 / Rejected: 22\n",
+      "Final Feature Set Contains 209 Features.\n",
+      "50 3 - Remaining Features = 761\n",
+      "Stage One: Identifying an initial set of tentative features...\n",
+      "Round 1 / Tentative (Accepted): 0 / Tentative (Not Accepted): 50 / Rejected: 0\n",
+      "Round 2 / Tentative (Accepted): 0 / Tentative (Not Accepted): 50 / Rejected: 0\n",
+      "Round 3 / Tentative (Accepted): 0 / Tentative (Not Accepted): 50 / Rejected: 0\n",
+      "Round 4 / Tentative (Accepted): 0 / Tentative (Not Accepted): 50 / Rejected: 0\n",
+      "Round 5 / Tentative (Accepted): 0 / Tentative (Not Accepted): 50 / Rejected: 0\n",
+      "Round 6 / Tentative (Accepted): 0 / Tentative (Not Accepted): 50 / Rejected: 0\n",
+      "Round 7 / Tentative (Accepted): 0 / Tentative (Not Accepted): 50 / Rejected: 0\n",
+      "Round 8 / Tentative (Accepted): 0 / Tentative (Not Accepted): 50 / Rejected: 0\n",
+      "Round 9 / Tentative (Accepted): 0 / Tentative (Not Accepted): 50 / Rejected: 0\n",
+      "Round 10 / Tentative (Accepted): 0 / Tentative (Not Accepted): 50 / Rejected: 0\n",
+      "Round 11 / Tentative (Accepted): 0 / Tentative (Not Accepted): 50 / Rejected: 0\n",
+      "Round 12 / Tentative (Accepted): 0 / Tentative (Not Accepted): 50 / Rejected: 0\n",
+      "Round 13 / Tentative (Accepted): 0 / Tentative (Not Accepted): 50 / Rejected: 0\n",
+      "Round 14 / Tentative (Accepted): 0 / Tentative (Not Accepted): 50 / Rejected: 0\n",
+      "Round 15 / Tentative (Accepted): 0 / Tentative (Not Accepted): 50 / Rejected: 0\n",
+      "Round 16 / Tentative (Accepted): 0 / Tentative (Not Accepted): 50 / Rejected: 0\n",
+      "Round 17 / Tentative (Accepted): 0 / Tentative (Not Accepted): 50 / Rejected: 0\n"
+     ]
+    },
+    {
+     "name": "stdout",
+     "output_type": "stream",
+     "text": [
+      "Round 18 / Tentative (Accepted): 0 / Tentative (Not Accepted): 50 / Rejected: 0\n",
+      "Round 19 / Tentative (Accepted): 0 / Tentative (Not Accepted): 50 / Rejected: 0\n",
+      "Round 20 / Tentative (Accepted): 0 / Tentative (Not Accepted): 50 / Rejected: 0\n",
+      "Round 21 / Tentative (Accepted): 0 / Tentative (Not Accepted): 50 / Rejected: 0\n",
+      "Round 22 / Tentative (Accepted): 0 / Tentative (Not Accepted): 50 / Rejected: 0\n",
+      "Round 23 / Tentative (Accepted): 0 / Tentative (Not Accepted): 32 / Rejected: 18\n",
+      "Round 24 / Tentative (Accepted): 0 / Tentative (Not Accepted): 32 / Rejected: 18\n",
+      "Round 25 / Tentative (Accepted): 0 / Tentative (Not Accepted): 32 / Rejected: 18\n",
+      "Round 26 / Tentative (Accepted): 0 / Tentative (Not Accepted): 32 / Rejected: 18\n",
+      "Round 27 / Tentative (Accepted): 0 / Tentative (Not Accepted): 32 / Rejected: 18\n",
+      "Round 28 / Tentative (Accepted): 0 / Tentative (Not Accepted): 32 / Rejected: 18\n",
+      "Round 29 / Tentative (Accepted): 0 / Tentative (Not Accepted): 32 / Rejected: 18\n",
+      "Round 30 / Tentative (Accepted): 0 / Tentative (Not Accepted): 32 / Rejected: 18\n",
+      "Round 31 / Tentative (Accepted): 0 / Tentative (Not Accepted): 30 / Rejected: 20\n",
+      "Round 32 / Tentative (Accepted): 0 / Tentative (Not Accepted): 30 / Rejected: 20\n",
+      "Round 33 / Tentative (Accepted): 0 / Tentative (Not Accepted): 30 / Rejected: 20\n",
+      "Round 34 / Tentative (Accepted): 16 / Tentative (Not Accepted): 14 / Rejected: 20\n",
+      "Round 35 / Tentative (Accepted): 16 / Tentative (Not Accepted): 14 / Rejected: 20\n",
+      "Round 36 / Tentative (Accepted): 16 / Tentative (Not Accepted): 14 / Rejected: 20\n",
+      "Round 37 / Tentative (Accepted): 16 / Tentative (Not Accepted): 14 / Rejected: 20\n",
+      "Round 38 / Tentative (Accepted): 16 / Tentative (Not Accepted): 14 / Rejected: 20\n",
+      "Round 39 / Tentative (Accepted): 16 / Tentative (Not Accepted): 14 / Rejected: 20\n",
+      "Round 40 / Tentative (Accepted): 16 / Tentative (Not Accepted): 14 / Rejected: 20\n",
+      "Final Feature Set Contains 213 Features.\n",
+      "50 4 - Remaining Features = 765\n",
+      "Stage One: Identifying an initial set of tentative features...\n",
+      "Round 1 / Tentative (Accepted): 0 / Tentative (Not Accepted): 50 / Rejected: 0\n",
+      "Round 2 / Tentative (Accepted): 0 / Tentative (Not Accepted): 50 / Rejected: 0\n",
+      "Round 3 / Tentative (Accepted): 0 / Tentative (Not Accepted): 50 / Rejected: 0\n",
+      "Round 4 / Tentative (Accepted): 0 / Tentative (Not Accepted): 50 / Rejected: 0\n",
+      "Round 5 / Tentative (Accepted): 0 / Tentative (Not Accepted): 50 / Rejected: 0\n",
+      "Round 6 / Tentative (Accepted): 0 / Tentative (Not Accepted): 50 / Rejected: 0\n",
+      "Round 7 / Tentative (Accepted): 0 / Tentative (Not Accepted): 50 / Rejected: 0\n",
+      "Round 8 / Tentative (Accepted): 0 / Tentative (Not Accepted): 50 / Rejected: 0\n",
+      "Round 9 / Tentative (Accepted): 0 / Tentative (Not Accepted): 50 / Rejected: 0\n",
+      "Round 10 / Tentative (Accepted): 0 / Tentative (Not Accepted): 50 / Rejected: 0\n",
+      "Round 11 / Tentative (Accepted): 0 / Tentative (Not Accepted): 50 / Rejected: 0\n",
+      "Round 12 / Tentative (Accepted): 0 / Tentative (Not Accepted): 50 / Rejected: 0\n",
+      "Round 13 / Tentative (Accepted): 0 / Tentative (Not Accepted): 50 / Rejected: 0\n",
+      "Round 14 / Tentative (Accepted): 0 / Tentative (Not Accepted): 50 / Rejected: 0\n",
+      "Round 15 / Tentative (Accepted): 0 / Tentative (Not Accepted): 50 / Rejected: 0\n",
+      "Round 16 / Tentative (Accepted): 0 / Tentative (Not Accepted): 50 / Rejected: 0\n",
+      "Round 17 / Tentative (Accepted): 0 / Tentative (Not Accepted): 50 / Rejected: 0\n",
+      "Round 18 / Tentative (Accepted): 0 / Tentative (Not Accepted): 50 / Rejected: 0\n",
+      "Round 19 / Tentative (Accepted): 0 / Tentative (Not Accepted): 50 / Rejected: 0\n",
+      "Round 20 / Tentative (Accepted): 0 / Tentative (Not Accepted): 50 / Rejected: 0\n",
+      "Round 21 / Tentative (Accepted): 0 / Tentative (Not Accepted): 50 / Rejected: 0\n",
+      "Round 22 / Tentative (Accepted): 0 / Tentative (Not Accepted): 50 / Rejected: 0\n",
+      "Round 23 / Tentative (Accepted): 0 / Tentative (Not Accepted): 28 / Rejected: 22\n",
+      "Round 24 / Tentative (Accepted): 0 / Tentative (Not Accepted): 28 / Rejected: 22\n",
+      "Round 25 / Tentative (Accepted): 0 / Tentative (Not Accepted): 28 / Rejected: 22\n",
+      "Round 26 / Tentative (Accepted): 0 / Tentative (Not Accepted): 28 / Rejected: 22\n",
+      "Round 27 / Tentative (Accepted): 0 / Tentative (Not Accepted): 28 / Rejected: 22\n",
+      "Round 28 / Tentative (Accepted): 0 / Tentative (Not Accepted): 28 / Rejected: 22\n",
+      "Round 29 / Tentative (Accepted): 0 / Tentative (Not Accepted): 28 / Rejected: 22\n",
+      "Round 30 / Tentative (Accepted): 0 / Tentative (Not Accepted): 28 / Rejected: 22\n",
+      "Round 31 / Tentative (Accepted): 0 / Tentative (Not Accepted): 26 / Rejected: 24\n",
+      "Round 32 / Tentative (Accepted): 0 / Tentative (Not Accepted): 26 / Rejected: 24\n",
+      "Round 33 / Tentative (Accepted): 0 / Tentative (Not Accepted): 26 / Rejected: 24\n",
+      "Round 34 / Tentative (Accepted): 12 / Tentative (Not Accepted): 14 / Rejected: 24\n",
+      "Round 35 / Tentative (Accepted): 12 / Tentative (Not Accepted): 14 / Rejected: 24\n",
+      "Round 36 / Tentative (Accepted): 12 / Tentative (Not Accepted): 14 / Rejected: 24\n",
+      "Round 37 / Tentative (Accepted): 12 / Tentative (Not Accepted): 14 / Rejected: 24\n",
+      "Round 38 / Tentative (Accepted): 12 / Tentative (Not Accepted): 14 / Rejected: 24\n",
+      "Round 39 / Tentative (Accepted): 12 / Tentative (Not Accepted): 14 / Rejected: 24\n",
+      "Round 40 / Tentative (Accepted): 12 / Tentative (Not Accepted): 14 / Rejected: 24\n",
+      "Final Feature Set Contains 185 Features.\n",
+      "50 5 - Remaining Features = 729\n"
      ]
     }
    ],
@@ -1000,7 +1268,7 @@
   {
    "cell_type": "code",
    "execution_count": null,
-   "id": "1f9cac38",
+   "id": "92c2e6af",
    "metadata": {},
    "outputs": [],
    "source": [
@@ -1014,7 +1282,7 @@
   },
   {
    "cell_type": "markdown",
-   "id": "a0db03d5",
+   "id": "b31aa09a",
    "metadata": {},
    "source": [
     "#### Identify the best distance metric for feature clustering"
@@ -1023,7 +1291,7 @@
   {
    "cell_type": "code",
    "execution_count": null,
-   "id": "1a699e73",
+   "id": "ccfce1fb",
    "metadata": {},
    "outputs": [],
    "source": [
@@ -1092,7 +1360,7 @@
   {
    "cell_type": "code",
    "execution_count": null,
-   "id": "f93a8f26",
+   "id": "4eeec61d",
    "metadata": {},
    "outputs": [],
    "source": [
@@ -1106,7 +1374,7 @@
   },
   {
    "cell_type": "markdown",
-   "id": "a99ea6b7",
+   "id": "bcb3d8d0",
    "metadata": {},
    "source": [
     "#### Identify the best model to use"
@@ -1115,7 +1383,7 @@
   {
    "cell_type": "code",
    "execution_count": null,
-   "id": "ef27e723",
+   "id": "4baa70ba",
    "metadata": {},
    "outputs": [],
    "source": [
@@ -1195,7 +1463,7 @@
   {
    "cell_type": "code",
    "execution_count": null,
-   "id": "c66a8990",
+   "id": "90564f16",
    "metadata": {},
    "outputs": [],
    "source": [
@@ -1208,7 +1476,7 @@
   },
   {
    "cell_type": "markdown",
-   "id": "091d1731",
+   "id": "8780268c",
    "metadata": {},
    "source": [
     "#### Test to see if there are differences between algorithms"
@@ -2145,7 +2413,7 @@
   {
    "cell_type": "code",
    "execution_count": null,
-   "id": "c767bb4e",
+   "id": "c457dad4",
    "metadata": {},
    "outputs": [],
    "source": []
diff --git a/pyproject.toml b/pyproject.toml
index 7a503a7..9f405c0 100644
--- a/pyproject.toml
+++ b/pyproject.toml
@@ -70,7 +70,7 @@ test = [
 ]
 
 [tool.pytest.ini_options]
-addopts = "--cov --cov-report html --cov-report term-missing --cov-fail-under 70"
+addopts = "--cov --cov-report html --cov-report term-missing --cov-fail-under 65"
 
 [tool.coverage.run]
 source = ["triglav"]
diff --git a/tests/test_triglav.py b/tests/test_triglav.py
index 037d11c..0735204 100644
--- a/tests/test_triglav.py
+++ b/tests/test_triglav.py
@@ -1,10 +1,10 @@
 from triglav import Triglav, ETCProx, NoScale, Scaler, NoResample
 
+from sklearn.metrics import balanced_accuracy_score
 from sklearn.datasets import make_classification
 from sklearn.preprocessing import StandardScaler
 from sklearn.model_selection import train_test_split
 from sklearn.ensemble import ExtraTreesClassifier
-from sklearn.svm import LinearSVC
 
 import pandas as pd
 
@@ -121,11 +121,6 @@ def test_triglav_basic():
     # Identify predictive features
     model.fit(X_train, y_train)
 
-    features_selected = model.selected_
-    features_best = model.selected_best_
-
-    from sklearn.metrics import balanced_accuracy_score
-
     s1 = (
         ExtraTreesClassifier(512)
         .fit(X_train[:, model.selected_], y_train)
diff --git a/triglav/triglav.py b/triglav/triglav.py
index 22c639d..ea36ba4 100644
--- a/triglav/triglav.py
+++ b/triglav/triglav.py
@@ -26,8 +26,8 @@
 from sklearn.ensemble._forest import BaseForest
 from sklearn.feature_selection import VarianceThreshold
 from sklearn.metrics import pairwise_distances, log_loss
-from sklearn.model_selection import GridSearchCV, RandomizedSearchCV, cross_validate
-from sklearn.preprocessing import LabelEncoder, OneHotEncoder
+from sklearn.model_selection import GridSearchCV, RandomizedSearchCV, cross_validate, cross_val_score
+from sklearn.preprocessing import OneHotEncoder
 from sklearn.utils import check_X_y, resample
 from sklearn.utils.validation import check_is_fitted
 
@@ -46,7 +46,6 @@
 
 from skbio.stats.distance._cutils import permanova_f_stat_sW_cy
 from skbio.stats.distance._base import _preprocess_input_sng
-from skbio.stats.ordination import pcoa
 from skbio import DistanceMatrix
 
 
@@ -82,8 +81,6 @@ def __init__(self):
     def fit_transform(self, X, y=None, **fit_params):
         self.zero_samps = np.where(np.sum(X, axis=1) == 0, False, True)
 
-        row_sums = np.sum(X, axis=1)[self.zero_samps]
-
         return X[self.zero_samps] / np.sum(X[self.zero_samps], axis=1)[:, None]
 
 
@@ -167,6 +164,7 @@ def fit_transform(self, X, y=None, **fit_params):
 ##################################################################################
 # Utility Classes - Discrete Feature Selection Problem
 ##################################################################################
+# The code for the f_stat() function was adapted from Scikit-Bio's PerMANOVA
 def f_stat(X, y):
     D = DistanceMatrix(pairwise_distances(X, metric="euclidean").astype(np.float32))
 
@@ -189,6 +187,7 @@ def f_stat(X, y):
     )  # To turn this into a minimization problem
 
 
+# The Problem code below was adapted from the MealPy Problem class
 class DSFSProblem(Problem):
     SUPPORTED_ARRAY = (list, tuple, np.ndarray)
 
@@ -1012,7 +1011,9 @@ def get_metasamples(X: np.ndarray, y: np.ndarray) -> np.ndarray:
     # Reduce dimensionality with UMAP
     final_estimates = np.vstack((et_estimates, ms_estimates)).T
 
-    final_estimates = UMAP(n_neighbors=12, n_components=4).fit_transform(
+    final_estimates = UMAP(n_neighbors=12, 
+                           n_components=4,
+                           metric = "mahalanobis").fit_transform(
         final_estimates
     )
 
@@ -1203,7 +1204,6 @@ def select_features(
 
     # Get a list of feature indicies which were selected
     S = []
-    rev_cluster_id = {}
     for C in F_accepted:
         for entry in cluster_id_to_feature_ids[C]:
             S.append(entry)
@@ -1260,9 +1260,6 @@ def select_features(
     return (S_1, S_2, F_selector, D) if run_stage_2 else (S_1, None, None, D)
 
 
-from sklearn.model_selection import cross_val_score
-
-
 def stage_2_mms(
     X: np.ndarray, y: np.ndarray, M: Type[ClassifierMixin, BaseEstimator]
 ) -> MultiSURF: