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refactoring

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frankknoll
2022-02-04 01:25:07 +01:00
parent 2ac84d32fe
commit 0d7a976612
1 changed files with 59 additions and 52 deletions
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111
HowBadIsMyBatch.ipynb
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@@ -40,7 +40,6 @@
" 'VAERSDATA':\n",
" self._read_csv(\n",
" folder + year + \"VAERSDATA.csv\",\n",
" # FK-TODO: use Column enum\n",
" ['VAERS_ID', 'DIED', 'L_THREAT', 'DISABLE', 'HOSPITAL', 'ER_VISIT']),\n",
" 'VAERSVAX':\n",
" self._read_csv(\n",
@@ -129,55 +128,56 @@
" \n",
" def __init__(self, dataFrame : pd.DataFrame):\n",
" self.dataFrame = dataFrame \n",
" self._convertColumnOfDataFrameToNumeric('DIED')\n",
" self._convertColumnOfDataFrameToNumeric('L_THREAT')\n",
" self._convertColumnOfDataFrameToNumeric('DISABLE')\n",
" self._convertColumnOfDataFrameToNumeric('HOSPITAL')\n",
" self._convertColumnOfDataFrameToNumeric('ER_VISIT')\n",
"\n",
" def createBatchCodeTable(self):\n",
" return self._asDataFrame(\n",
" batchCodeTable = self.dataFrame.groupby('VAX_LOT').agg(\n",
" {\n",
" 'ADRs': self._getADRs(),\n",
" 'DEATHS': self._getDEATHS(),\n",
" 'DISABILITIES': self._getDISABILITIES(),\n",
" 'LIFE THREATENING ILLNESSES': self._getLIFE_THREATENING_ILLNESSES()\n",
" 'DIED': ['sum', 'size'],\n",
" 'L_THREAT': 'sum',\n",
" 'DISABLE': 'sum'\n",
" })\n",
" self._flattenColumns(batchCodeTable)\n",
" batchCodeTable = batchCodeTable.rename(\n",
" columns =\n",
" {\n",
" \"DIED_size\": \"ADRs\",\n",
" \"DIED_sum\": \"DEATHS\",\n",
" \"L_THREAT_sum\": \"LIFE THREATENING ILLNESSES\",\n",
" \"DISABLE_sum\": \"DISABILITIES\"\n",
" })[['ADRs', 'DEATHS', 'DISABILITIES', 'LIFE THREATENING ILLNESSES']]\n",
" return batchCodeTable.sort_values(by = 'ADRs', ascending = False)\n",
"\n",
" # create table from https://www.howbadismybatch.com/combined.html\n",
" def createSevereEffectsBatchCodeTable(self):\n",
" batchCodeTable = self.dataFrame.groupby('VAX_LOT').agg(\n",
" {\n",
" 'DIED': ['sum', 'size'],\n",
" 'L_THREAT': 'sum',\n",
" 'DISABLE': 'sum',\n",
" 'HOSPITAL': 'sum',\n",
" 'ER_VISIT': 'sum'\n",
" })\n",
" self._flattenColumns(batchCodeTable)\n",
" batchCodeTable = batchCodeTable.rename(\n",
" columns =\n",
" {\n",
" \"DIED_size\": \"ADRs\",\n",
" \"DIED_sum\": \"DEATHS\",\n",
" \"L_THREAT_sum\": \"LIFE THREATENING ILLNESSES\",\n",
" \"DISABLE_sum\": \"DISABILITIES\",\n",
" 'HOSPITAL_sum': 'HOSPITALISATIONS',\n",
" 'ER_VISIT_sum': 'EMERGENCY ROOM OR DOCTOR VISITS'\n",
" })[['ADRs', 'DEATHS', 'DISABILITIES', 'LIFE THREATENING ILLNESSES', 'HOSPITALISATIONS', 'EMERGENCY ROOM OR DOCTOR VISITS']]\n",
" batchCodeTable = batchCodeTable.sort_values(by = 'ADRs', ascending = False)\n",
" return self._addCompanyColumn(\n",
" self._asDataFrame(\n",
" {\n",
" 'ADRs': self._getADRs(),\n",
" 'DEATHS': self._getDEATHS(),\n",
" 'DISABILITIES': self._getDISABILITIES(),\n",
" 'LIFE THREATENING ILLNESSES': self._getLIFE_THREATENING_ILLNESSES(),\n",
" 'HOSPITALISATIONS': self._getHOSPITALISATIONS(),\n",
" 'EMERGENCY ROOM OR DOCTOR VISITS': self._getER_VISITs()\n",
" }),\n",
" batchCodeTable,\n",
" self._createCompanyByBatchCodeTable())\n",
"\n",
" def _getADRs(self):\n",
" return self.dataFrame['VAX_LOT'].value_counts()\n",
"\n",
" def _getDEATHS(self):\n",
" return self._countValues('DIED')\n",
"\n",
" def _getDISABILITIES(self):\n",
" return self._countValues('DISABLE')\n",
"\n",
" def _getLIFE_THREATENING_ILLNESSES(self):\n",
" return self._countValues('L_THREAT')\n",
"\n",
" def _getHOSPITALISATIONS(self):\n",
" return self._countValues('HOSPITAL')\n",
"\n",
" def _getER_VISITs(self):\n",
" return self._countValues('ER_VISIT')\n",
"\n",
" def _countValues(self, column):\n",
" return self.dataFrame[self.dataFrame[column] == 'Y']['VAX_LOT'].value_counts()\n",
"\n",
" def _asDataFrame(self, dict):\n",
" dataFrame = pd.concat(dict, axis = 'columns')\n",
" dataFrame.index.name = 'VAX_LOT'\n",
" return dataFrame.replace(to_replace = np.nan, value = 0)\n",
"\n",
" def _addCompanyColumn(self, batchCodeTable, companyByBatchCodeTable):\n",
" return pd.merge(\n",
@@ -196,6 +196,13 @@
" manufacturerByBatchCodeTable = manufacturerByBatchCodeTable.drop_duplicates(subset = ['VAX_LOT'])\n",
" return manufacturerByBatchCodeTable.set_index('VAX_LOT')\n",
"\n",
" def _convertColumnOfDataFrameToNumeric(self, column):\n",
" self.dataFrame[column] = np.where(self.dataFrame[column] == 'Y', 1, 0)\n",
"\n",
" def _flattenColumns(self, batchCodeTable):\n",
" batchCodeTable.columns = [\"_\".join(a) for a in batchCodeTable.columns.to_flat_index()]\n",
"\n",
"\n",
"class BatchCodeTableFactory:\n",
"\n",
" @staticmethod\n",
@@ -468,14 +475,14 @@
" batchCodeTableExpected = pd.DataFrame(\n",
" data = {\n",
" 'ADRs': [1, 1],\n",
" 'DEATHS': [1, 0],\n",
" 'DISABILITIES': [0, 1],\n",
" 'LIFE THREATENING ILLNESSES': [1, 0],\n",
" 'HOSPITALISATIONS': [1, 0],\n",
" 'DEATHS': [0, 1],\n",
" 'DISABILITIES': [1, 0],\n",
" 'LIFE THREATENING ILLNESSES': [0, 1],\n",
" 'HOSPITALISATIONS': [0, 1],\n",
" 'EMERGENCY ROOM OR DOCTOR VISITS': [1, 1],\n",
" 'COMPANY': ['MODERNA', 'PFIZER\\BIONTECH']\n",
" 'COMPANY': ['PFIZER\\BIONTECH', 'MODERNA']\n",
" },\n",
" index = pd.Index(['037K20A', '025L20A'], name='VAX_LOT'))\n",
" index = pd.Index(['025L20A', '037K20A'], name = 'VAX_LOT'))\n",
" assert_frame_equal(batchCodeTable, batchCodeTableExpected, check_dtype = False)\n",
"\n",
" def test_createBatchCodeTable2(self):\n",
@@ -483,9 +490,9 @@
" [\n",
" {\n",
" 'VAERSDATA': self.createDataFrame(\n",
" columns = ['DIED', 'L_THREAT', 'DISABLE'],\n",
" data = [ ['Y', np.NaN, np.NaN],\n",
" [np.NaN, np.NaN, 'Y']],\n",
" columns = ['DIED', 'L_THREAT', 'DISABLE', 'HOSPITAL', 'ER_VISIT'],\n",
" data = [ ['Y', np.NaN, np.NaN, np.NaN, np.NaN],\n",
" [np.NaN, np.NaN, 'Y', np.NaN, np.NaN]],\n",
" index = [\n",
" \"0916600\",\n",
" \"0916601\"]),\n",
@@ -500,9 +507,9 @@
" },\n",
" {\n",
" 'VAERSDATA': self.createDataFrame(\n",
" columns = ['DIED', 'L_THREAT', 'DISABLE'],\n",
" data = [ [np.NaN, np.NaN, np.NaN],\n",
" [np.NaN, np.NaN, 'Y']],\n",
" columns = ['DIED', 'L_THREAT', 'DISABLE', 'HOSPITAL', 'ER_VISIT'],\n",
" data = [ [np.NaN, np.NaN, np.NaN, np.NaN, np.NaN],\n",
" [np.NaN, np.NaN, 'Y', np.NaN, np.NaN]],\n",
" index = [\n",
" \"1996873\",\n",
" \"1996874\"]),\n",