displacing "Lower Confidence Limit of Proportional Reporting Ratio"

docs/SymptomsCausedByVaccines/js/PrrByKeyTable.js

@@ -80,7 +80,7 @@ class PrrByKeyTable {
     }
 
     #markRowIfPrrTooHigh({ prr, row }) {
-        if (prr > 1.0) {
+        if (prr >= 2.0) {
             $(row).addClass('prrTooHigh');
         }
     }

docs/SymptomsCausedByVaccines/js/PrrBySymptomTableView.js

@@ -18,7 +18,7 @@ class PrrBySymptomTableView {
         return new PrrByKeyTable({
             tableElement: tableElement,
             keyColumnName: 'Symptom',
-            prrColumnName: 'Proportional Reporting Ratio > 1',
+            prrColumnName: 'Lower Confidence Limit of Proportional Reporting Ratio >= 2',
             shallMarkRowIfPrrTooHigh: false
         });
     }

docs/SymptomsCausedByVaccines/js/PrrByVaccineTableView.js

@@ -18,7 +18,7 @@ class PrrByVaccineTableView {
         return new PrrByKeyTable({
             tableElement: tableElement,
             keyColumnName: 'Vaccine',
-            prrColumnName: 'Proportional Reporting Ratio',
+            prrColumnName: 'Lower Confidence Limit of Proportional Reporting Ratio',
             shallMarkRowIfPrrTooHigh: true
         });
     }

src/HowBadIsMyBatch.ipynb

@@ -449,13 +449,14 @@
   {
    "cell_type": "code",
    "execution_count": null,
-   "id": "eaf8fe21",
    "metadata": {},
    "outputs": [],
    "source": [
     "prrByVaccineAndSymptom = pd.read_csv(\n",
-    "    'data/safety-signal-sym.csv',\n",
-    "    index_col = 'VACCINE')\n",
+    "    'data/tLCI.csv',\n",
+    "    usecols = lambda x: x != \"Unnamed: 0\",\n",
+    "    index_col = 'VAX_TYPE')\n",
+    "prrByVaccineAndSymptom.index.name = 'VACCINE'\n",
     "prrByVaccineAndSymptom"
    ]
   },
@@ -499,7 +500,7 @@
    "metadata": {},
    "outputs": [],
    "source": [
-    "prrBySymptomByVaccineWithHighPrrs = PrrSeriesTransformer.filterByHighPrrs(prrBySymptomByVaccine)\n",
+    "prrBySymptomByVaccineWithHighPrrs = PrrSeriesTransformer.filterPrrs(prrBySymptomByVaccine, lambda prr: prr >= 2)\n",
     "prrBySymptomByVaccineWithHighPrrs"
    ]
   },
@@ -604,7 +605,7 @@
    "metadata": {},
    "outputs": [],
    "source": [
-    "prrBySymptomByLotWithHighPrrs = PrrSeriesTransformer.filterByHighPrrs(prrBySymptomByLot)\n",
+    "prrBySymptomByLotWithHighPrrs = PrrSeriesTransformer.filterPrrs(prrBySymptomByLot, lambda prr: prr > 1)\n",
     "prrBySymptomByLotWithHighPrrs"
    ]
   },

src/SymptomsCausedByVaccines/PrrSeriesTransformer.py

@@ -2,17 +2,11 @@ class PrrSeriesTransformer:
 
     @staticmethod
     def filterByNonZeroPrrs(prrByVaccineBySymptom):
-        return PrrSeriesTransformer._filterPrrsBy(
+        return PrrSeriesTransformer.filterPrrs(
             prrByVaccineBySymptom,
             lambda prr: prr != 0)
 
     @staticmethod
-    def filterByHighPrrs(prrBySymptomByVaccine):
-        return PrrSeriesTransformer._filterPrrsBy(
-            prrBySymptomByVaccine,
-            lambda prr: prr > 1)
-
-    @staticmethod
-    def _filterPrrsBy(prrByKeyByOtherKey, prrFilter):
+    def filterPrrs(prrByKeyByOtherKey, prrFilter):
         return prrByKeyByOtherKey.map(
             lambda prrByKey: {key: prr for key, prr in prrByKey.items() if prrFilter(prr)})

src/SymptomsCausedByVaccines/PrrSeriesTransformerTest.py

@@ -25,22 +25,22 @@ class PrrSeriesTransformerTest(unittest.TestCase):
                     '17-hydroxyprogesterone': {'6VAX-F': 1.5}
                 }))
 
-    def test_filterByHighPrrs(self):
+    def test_filterPrrs(self):
         # Given
         prrBySymptomByVaccine = pd.Series(
                 {
-                    '6VAX-F': {'11-beta-hydroxylase deficiency': 0.6, '17-hydroxyprogesterone': 1.5},
-                    'ADEN':   {'11-beta-hydroxylase deficiency': 1.3, '17-hydroxyprogesterone': 0.9}
+                    '6VAX-F': {'11-beta-hydroxylase deficiency': 2.6, '17-hydroxyprogesterone': 1.5},
+                    'ADEN':   {'11-beta-hydroxylase deficiency': 1.3, '17-hydroxyprogesterone': 2.9}
                 })
         
         # When
-        prrBySymptomByVaccineWithHighPrrs = PrrSeriesTransformer.filterByHighPrrs(prrBySymptomByVaccine)
+        prrBySymptomByVaccineWithHighPrrs = PrrSeriesTransformer.filterPrrs(prrBySymptomByVaccine, lambda prr: prr >= 2)
         
         # Then
         assert_series_equal(
             prrBySymptomByVaccineWithHighPrrs,
             pd.Series(
                 {
-                    '6VAX-F': {'17-hydroxyprogesterone': 1.5},
-                    'ADEN':   {'11-beta-hydroxylase deficiency': 1.3}
+                    '6VAX-F': {'11-beta-hydroxylase deficiency': 2.6},
+                    'ADEN':   {'17-hydroxyprogesterone': 2.9}
                 }))