adding saveNthDoseTable()

HowBadIsMyBatch.ipynb

@@ -219,16 +219,24 @@
    "source": [
     "class DoseAnalysis:\n",
     "    \n",
+    "    @staticmethod\n",
     "    def getNthDoseTable(dataFrame, dose):\n",
-    "        nthDoseDataFrame = DataFrameFilter(dataFrame).filterBy(dose = dose)\n",
-    "        dict = {\n",
-    "            'Total reports': len(nthDoseDataFrame.index),\n",
-    "            'Deaths': len(nthDoseDataFrame[nthDoseDataFrame['DIED'] == 'Y']),\n",
-    "            'Disabilities': len(nthDoseDataFrame[nthDoseDataFrame['DISABLE'] == 'Y']),\n",
-    "            'Life Threatening Illnesses': len(nthDoseDataFrame[nthDoseDataFrame['L_THREAT'] == 'Y'])\n",
+    "        return pd.Series(DoseAnalysis._getNthDoseDict(DataFrameFilter(dataFrame).filterBy(dose = dose)))\n",
+    "\n",
+    "    @staticmethod\n",
+    "    def _getNthDoseDict(df):\n",
+    "        nthDoseDict = {\n",
+    "            'Total reports': len(df.index),\n",
+    "            'Deaths': DoseAnalysis._count(df, 'DIED'),\n",
+    "            'Disabilities': DoseAnalysis._count(df, 'DISABLE'),\n",
+    "            'Life Threatening Illnesses': DoseAnalysis._count(df, 'L_THREAT')\n",
     "        }\n",
-    "        dict['Severe reports'] =  (dict['Deaths'] + dict['Disabilities'] + dict['Life Threatening Illnesses'])/dict['Total reports'] * 100\n",
-    "        return pd.Series(dict)"
+    "        nthDoseDict['Severe reports'] = (nthDoseDict['Deaths'] + nthDoseDict['Disabilities'] + nthDoseDict['Life Threatening Illnesses']) / nthDoseDict['Total reports'] * 100\n",
+    "        return nthDoseDict\n",
+    "\n",
+    "    @staticmethod\n",
+    "    def _count(dataFrame, column):\n",
+    "        return len(dataFrame[dataFrame[column] == 'Y'])\n"
    ]
   },
   {
@@ -512,7 +520,7 @@
     "\n",
     "    def test_createBatchCodeTable(self):\n",
     "        dataFrame = VaersDescr2DataFrameConverter.createDataFrameFromDescrs(\n",
-    "            VaersDescrReader(\"test/VAERS\").readAllVaersDescrs())\n",
+    "            VaersDescrReader(dataDir = \"test/VAERS\").readAllVaersDescrs())\n",
     "        self._test_createBatchCodeTable(dataFrame, \"MODERNA\", '1')\n",
     "\n",
     "    def _test_createBatchCodeTable(self, dataFrame, manufacturer, dose):\n",
@@ -618,10 +626,10 @@
    "outputs": [],
    "source": [
     "def saveBatchCodeTable(manufacturer, excelFile):\n",
-    "    vaersDescrs = VaersDescrReader(\"VAERS\").readAllVaersDescrs()\n",
+    "    vaersDescrs = VaersDescrReader(dataDir = \"VAERS\").readAllVaersDescrs()\n",
     "    dataFrame = VaersDescr2DataFrameConverter.createDataFrameFromDescrs(vaersDescrs)\n",
     "    batchCodeTable = BatchCodeTableFactory.createBatchCodeTable(dataFrame, manufacturer = manufacturer, dose = '1')\n",
-    "    display(manufacturer, batchCodeTable)\n",
+    "    display(manufacturer + ':', batchCodeTable)\n",
     "    batchCodeTable.to_excel(excelFile)"
    ]
   },
@@ -645,10 +653,10 @@
    "outputs": [],
    "source": [
     "def saveSevereEffectsBatchCodeTable(excelFile):\n",
-    "    vaersDescrs = VaersDescrReader(\"VAERS\").readAllVaersDescrs()\n",
+    "    vaersDescrs = VaersDescrReader(dataDir = \"VAERS\").readAllVaersDescrs()\n",
     "    dataFrame = VaersDescr2DataFrameConverter.createDataFrameFromDescrs(vaersDescrs)\n",
     "    severeEffectsBatchCodeTable = BatchCodeTableFactory.createSevereEffectsBatchCodeTable(dataFrame, dose = '1')\n",
-    "    display('severeEffectsBatchCodeTable', severeEffectsBatchCodeTable)\n",
+    "    display('severeEffectsBatchCodeTable:', severeEffectsBatchCodeTable)\n",
     "    severeEffectsBatchCodeTable.to_excel(excelFile)"
    ]
   },
@@ -671,12 +679,49 @@
    ]
   },
   {
-   "cell_type": "markdown",
+   "cell_type": "code",
+   "execution_count": null,
    "id": "202f7c3f",
    "metadata": {},
+   "outputs": [],
    "source": [
-    "see https://www.howbadismybatch.com/firstsecond.html"
+    "# https://www.howbadismybatch.com/firstsecond.html\n",
+    "\n",
+    "def saveNthDoseTable(dose, excelFile):\n",
+    "    vaersDescrs = VaersDescrReader(dataDir = \"VAERS\").readAllVaersDescrs()\n",
+    "    dataFrame = VaersDescr2DataFrameConverter.createDataFrameFromDescrs(vaersDescrs)\n",
+    "    doseTable = DoseAnalysis.getNthDoseTable(dataFrame, dose)\n",
+    "    display(f'doseTable(dose = {dose}):', doseTable)\n",
+    "    doseTable.to_excel(excelFile)\n"
    ]
+  },
+  {
+   "cell_type": "code",
+   "execution_count": null,
+   "id": "394fa19d",
+   "metadata": {},
+   "outputs": [],
+   "source": [
+    "saveNthDoseTable(dose = '1', excelFile = 'results/firstDoseTable.xlsx')"
+   ]
+  },
+  {
+   "cell_type": "code",
+   "execution_count": null,
+   "id": "686d4ddf",
+   "metadata": {},
+   "outputs": [],
+   "source": [
+    "saveNthDoseTable(dose = '2', excelFile = 'results/secondDoseTable.xlsx')"
+   ]
+  },
+  {
+   "cell_type": "code",
+   "execution_count": null,
+   "id": "e6bc676b",
+   "metadata": {},
+   "outputs": [],
+   "source": []
   }
  ],
  "metadata": {