feat : Braun-Blanquet-similarity added #349

sepandhaghighi · Aug 10, 2022 · 5328cd5 · 5328cd5
1 parent db48191
commit 5328cd5
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Showing 3 changed files with 26 additions and 4 deletions.
diff --git a/pycm/pycm_class_func.py b/pycm/pycm_class_func.py
@@ -104,6 +104,24 @@ def OC_calc(TP, TOP, P):
     except (ZeroDivisionError, TypeError):
         return "None"
 
+def BB_calc(TP, TOP, P):
+    """
+    Calculate Braun-Blanquet similarity (BB).
+
+    :param TP: true positive
+    :type TP: int
+    :param TOP: number of positives in predict vector
+    :type TOP: int
+    :param P: number of actual positives
+    :type P: int
+    :return: BB as float
+    """
+    try:
+        BB = TP / max(TOP, P)
+        return BB
+    except (ZeroDivisionError, TypeError):
+        return "None"
+
 
 def AGF_calc(TP, FP, FN, TN):
     """
@@ -790,6 +808,7 @@ def class_statistics(TP, TN, FP, FN, classes, table):
         result["MCCI"][i] = MCC_analysis(result["MCC"][i])
         result["AGF"][i] = AGF_calc(TP[i], FP[i], FN[i], TN[i])
         result["OC"][i] = OC_calc(TP[i], result["TOP"][i], result["P"][i])
+        result["BB"][i] = BB_calc(TP[i], result["TOP"][i], result["P"][i])
         result["OOC"][i] = OOC_calc(TP[i], result["TOP"][i], result["P"][i])
         result["AUPR"][i] = AUC_calc(result["PPV"][i], result["TPR"][i])
         result["ICSI"][i] = MK_BM_calc(result["PPV"][i], result["TPR"][i])

diff --git a/pycm/pycm_handler.py b/pycm/pycm_handler.py
@@ -77,7 +77,7 @@ def __class_stat_init__(cm):
     cm.AUPR = cm.class_stat["AUPR"]
     cm.ICSI = cm.class_stat["ICSI"]
     cm.HD = cm.class_stat["HD"]
-
+    cm.BB = cm.class_stat["BB"]
 
 def __overall_stat_init__(cm):
     """

diff --git a/pycm/pycm_param.py b/pycm/pycm_param.py
@@ -171,7 +171,8 @@
     "AUPR",
     "ICSI",
     "QI",
-    "HD"]
+    "HD",
+    "BB"]
 
 SUMMARY_OVERALL = [
     "ACC Macro",
@@ -455,7 +456,8 @@
     "OOC": "Otsuka-Ochiai coefficient",
     "AUPR": "Area under the PR curve",
     "ICSI": "Individual classification success index",
-    "HD": "Hamming distance"}
+    "HD": "Hamming distance",
+    "BB": "Braun-Blanquet similarity"}
 
 PARAMS_LINK = {
     "TPR": "TPR-(True-positive-rate)",
@@ -582,7 +584,8 @@
     "ARI": "ARI-(Adjusted-Rand-index)",
     "Bangdiwala B": "Bangdiwala's-B",
     "Krippendorff Alpha": "Krippendorff's-alpha",
-    "HD": "HD-(Hamming-distance)"}
+    "HD": "HD-(Hamming-distance)",
+    "BB": "BB-(Braun-Blanquet-similarity)"}
 
 CAPITALIZE_FILTER = ["BCD", "AUCI", "Q", "AGF", "OOC", "AUPR", "AUC", "QI"]