adding getDoseByMonthTable()

HowBadIsMyBatch.ipynb

@@ -64,7 +64,9 @@
     "    def _readVAERSDATA(self, file):\n",
     "        VAERSDATA = self._read_csv(\n",
     "            file = file,\n",
-    "            usecols = ['VAERS_ID', 'DIED', 'L_THREAT', 'DISABLE', 'HOSPITAL', 'ER_VISIT'])\n",
+    "            usecols = ['VAERS_ID', 'RECVDATE', 'DIED', 'L_THREAT', 'DISABLE', 'HOSPITAL', 'ER_VISIT'],\n",
+    "            parse_dates = ['RECVDATE'],\n",
+    "            date_parser = lambda dateStr: pd.to_datetime(dateStr, format = \"%m/%d/%Y\"))\n",
     "        DataFrameConverter.convertColumnsOfDataFrameToNumerics(\n",
     "            VAERSDATA,\n",
     "            ['DIED', 'L_THREAT', 'DISABLE', 'HOSPITAL', 'ER_VISIT'])\n",
@@ -274,6 +276,33 @@
     "            })\n",
     "        doseTable = doseTable[['Total reports', 'Deaths', 'Disabilities', 'Life Threatening Illnesses']]\n",
     "        doseTable['Severe reports (%)'] = (doseTable['Deaths'] + doseTable['Disabilities'] + doseTable['Life Threatening Illnesses']) / doseTable['Total reports'] * 100\n",
+    "        return doseTable\n",
+    "\n",
+    "    @staticmethod\n",
+    "    def getDoseByMonthTable(dataFrame):\n",
+    "        # https://stackoverflow.com/questions/61879166/pandas-groupby-month-and-year-date-as-datetime64ns-and-summarized-by-count\n",
+    "        grouped = dataFrame.groupby(\n",
+    "            [\n",
+    "                dataFrame['RECVDATE'].dt.year.rename('year'),\n",
+    "                dataFrame['RECVDATE'].dt.month.rename('month'),\n",
+    "                dataFrame['VAX_DOSE_SERIES']\n",
+    "            ])\n",
+    "        # FK-TODO: DRY with getDoseTable()\n",
+    "        doseTable = AggregationHelper.aggregateAndFlattenColumnsAndRenameColumns(\n",
+    "            dataFrame = grouped,\n",
+    "            aggFunctionsByColumn = {\n",
+    "                'DIED': ['sum', 'size'],\n",
+    "                'L_THREAT': 'sum',\n",
+    "                'DISABLE': 'sum'\n",
+    "            },\n",
+    "            columnNameMappingsDict = {\n",
+    "                \"DIED_size\": \"Total reports\",\n",
+    "                \"DIED_sum\": \"Deaths\",\n",
+    "                \"L_THREAT_sum\": \"Life Threatening Illnesses\",\n",
+    "                \"DISABLE_sum\": \"Disabilities\"\n",
+    "            })\n",
+    "        doseTable = doseTable[['Total reports', 'Deaths', 'Disabilities', 'Life Threatening Illnesses']]\n",
+    "        doseTable['Severe reports (%)'] = (doseTable['Deaths'] + doseTable['Disabilities'] + doseTable['Life Threatening Illnesses']) / doseTable['Total reports'] * 100\n",
     "        return doseTable\n"
    ]
   },
@@ -620,6 +649,42 @@
     "                },\n",
     "                index = pd.Index(['1', '2'], dtype = \"string\", name = 'VAX_DOSE_SERIES')))\n",
     "                \n",
+    "    def test_getDoseByMonthTable(self):\n",
+    "        # Given\n",
+    "        parseDate = lambda dateStr: pd.to_datetime(dateStr, format = \"%m/%d/%Y\")\n",
+    "        dataFrame = self.createDataFrame(\n",
+    "            columns = ['RECVDATE',             'DIED', 'L_THREAT', 'DISABLE', 'VAX_TYPE', 'VAX_MANU', 'VAX_LOT', 'VAX_DOSE_SERIES'],\n",
+    "            data = [  [parseDate('01/01/2021'), 1,     0,          0,         'COVID19',  'MODERNA',  '016M20A', '2'],\n",
+    "                      [parseDate('01/01/2021'), 1,     0,          0,         'COVID19',  'MODERNA',  '030L20A', '1'],\n",
+    "                      [parseDate('01/01/2021'), 1,     1,          1,         'COVID19',  'MODERNA',  '030L20B', '1']],\n",
+    "            index = [\n",
+    "                \"1048786\",\n",
+    "                \"1048786\",\n",
+    "                \"4711\"],\n",
+    "            dtypes = {'VAX_DOSE_SERIES': \"string\"})\n",
+    "        \n",
+    "        # When\n",
+    "        doseByMonthTable = DoseAnalysis.getDoseByMonthTable(dataFrame)\n",
+    "\n",
+    "        # Then\n",
+    "        assert_frame_equal(\n",
+    "            doseByMonthTable,\n",
+    "            pd.DataFrame(\n",
+    "                data = {\n",
+    "                    'Total reports':              [2,                   1],\n",
+    "                    'Deaths':                     [2,                   1],\n",
+    "                    'Disabilities':               [1,                   0],\n",
+    "                    'Life Threatening Illnesses': [1,                   0],\n",
+    "                    'Severe reports (%)':         [(2 + 1 + 1)/2 * 100, (1 + 0 + 0)/1 * 100]\n",
+    "                },\n",
+    "                index = pd.MultiIndex.from_tuples(\n",
+    "                    [\n",
+    "                        (2021,  1, '1'),\n",
+    "                        (2021,  1, '2'),\n",
+    "                    ],\n",
+    "                names = ('year', 'month', 'VAX_DOSE_SERIES'))),\n",
+    "                check_index_type = False)\n",
+    "\n",
     "    def createDataFrame(self, index, columns, data, dtypes = {}):\n",
     "        return pd.DataFrame(index = index, columns = columns, data = data).astype(dtypes)\n"
    ]
@@ -706,7 +771,12 @@
     "def getDoseTable():\n",
     "    vaersDescrs = VaersDescrReader(dataDir = \"VAERS\").readAllVaersDescrs()\n",
     "    dataFrame = VaersDescr2DataFrameConverter.createDataFrameFromDescrs(vaersDescrs)\n",
-    "    return DoseAnalysis.getDoseTable(dataFrame)"
+    "    return DoseAnalysis.getDoseTable(dataFrame)\n",
+    "\n",
+    "def getDoseByMonthTable():\n",
+    "    vaersDescrs = VaersDescrReader(dataDir = \"VAERS\").readAllVaersDescrs()\n",
+    "    dataFrame = VaersDescr2DataFrameConverter.createDataFrameFromDescrs(vaersDescrs)\n",
+    "    return DoseAnalysis.getDoseByMonthTable(dataFrame)"
    ]
   },
   {
@@ -718,6 +788,18 @@
    "source": [
     "getDoseTable()"
    ]
+  },
+  {
+   "cell_type": "code",
+   "execution_count": null,
+   "id": "b333e5fb",
+   "metadata": {},
+   "outputs": [],
+   "source": [
+    "doseByMonthTable = getDoseByMonthTable()\n",
+    "doseByMonthTable.to_excel('results/doseByMonthTable.xlsx')\n",
+    "doseByMonthTable"
+   ]
   }
  ],
  "metadata": {