1261 lines
47 KiB
Plaintext
1261 lines
47 KiB
Plaintext
{
|
||
"cells": [
|
||
{
|
||
"cell_type": "code",
|
||
"execution_count": 1,
|
||
"id": "9de5907f-18f5-4cb1-903e-26028ff1fa03",
|
||
"metadata": {},
|
||
"outputs": [],
|
||
"source": [
|
||
"import numpy as np\n",
|
||
"import pandas as pd\n",
|
||
"\n",
|
||
"pd.set_option('display.max_rows', 100)\n",
|
||
"pd.set_option('display.max_columns', None)"
|
||
]
|
||
},
|
||
{
|
||
"cell_type": "code",
|
||
"execution_count": 2,
|
||
"id": "a271254b",
|
||
"metadata": {},
|
||
"outputs": [],
|
||
"source": [
|
||
"import pandas as pd\n",
|
||
"\n",
|
||
"class VaersDescrReader:\n",
|
||
" \n",
|
||
" def __init__(self, dataDir):\n",
|
||
" self.dataDir = dataDir \n",
|
||
"\n",
|
||
" def readAllVaersDescrs(self):\n",
|
||
" return self.readVaersDescrs([\"2021\", \"2022\"])\n",
|
||
" \n",
|
||
" def readVaersDescrs(self, years):\n",
|
||
" return [self.readVaersDescr(year) for year in years]\n",
|
||
"\n",
|
||
" def readVaersDescr(self, year):\n",
|
||
" folder = self.dataDir + \"/\" + year + \"VAERSData/\"\n",
|
||
" return {\n",
|
||
" 'VAERSDATA':\n",
|
||
" self._read_csv(\n",
|
||
" folder + year + \"VAERSDATA.csv\",\n",
|
||
" ['VAERS_ID', 'DIED', 'L_THREAT', 'DISABLE', 'HOSPITAL', 'ER_VISIT']),\n",
|
||
" 'VAERSVAX':\n",
|
||
" self._read_csv(\n",
|
||
" folder + year + \"VAERSVAX.csv\",\n",
|
||
" ['VAERS_ID', 'VAX_DOSE_SERIES', 'VAX_TYPE', 'VAX_MANU', 'VAX_LOT'],\n",
|
||
" dtype = {\"VAX_DOSE_SERIES\": \"string\"})\n",
|
||
" }\n",
|
||
"\n",
|
||
" def _read_csv(self, file, usecols, dtype = {}):\n",
|
||
" return pd.read_csv(\n",
|
||
" file,\n",
|
||
" index_col = 'VAERS_ID',\n",
|
||
" encoding = 'latin1',\n",
|
||
" low_memory = False,\n",
|
||
" usecols = usecols,\n",
|
||
" dtype = dtype)\n"
|
||
]
|
||
},
|
||
{
|
||
"cell_type": "code",
|
||
"execution_count": 3,
|
||
"id": "7b5d6df0",
|
||
"metadata": {},
|
||
"outputs": [],
|
||
"source": [
|
||
"import pandas as pd\n",
|
||
"\n",
|
||
"class VaersDescr2DataFrameConverter:\n",
|
||
"\n",
|
||
" @staticmethod\n",
|
||
" def createDataFrameFromDescr(vaersDescr):\n",
|
||
" return pd.merge(\n",
|
||
" vaersDescr['VAERSDATA'],\n",
|
||
" vaersDescr['VAERSVAX'],\n",
|
||
" how = 'left',\n",
|
||
" left_index = True,\n",
|
||
" right_index = True,\n",
|
||
" validate = 'one_to_many')\n",
|
||
"\n",
|
||
" @staticmethod\n",
|
||
" def createDataFrameFromDescrs(vaersDescrs):\n",
|
||
" dataFrames = [VaersDescr2DataFrameConverter.createDataFrameFromDescr(vaersDescr) for vaersDescr in vaersDescrs]\n",
|
||
" return pd.concat(dataFrames)\n"
|
||
]
|
||
},
|
||
{
|
||
"cell_type": "code",
|
||
"execution_count": 4,
|
||
"id": "3ebcba86",
|
||
"metadata": {},
|
||
"outputs": [],
|
||
"source": [
|
||
"import pandas as pd\n",
|
||
"\n",
|
||
"class DataFrameFilter:\n",
|
||
" \n",
|
||
" @staticmethod\n",
|
||
" def filterDataFrame(df, manufacturer = None, dose = None):\n",
|
||
" isCovid19 = df[\"VAX_TYPE\"] == \"COVID19\"\n",
|
||
" isManufacturer = df[\"VAX_MANU\"] == manufacturer if manufacturer is not None else True\n",
|
||
" isDose = df[\"VAX_DOSE_SERIES\"].str.contains(dose) if dose is not None else True\n",
|
||
" return df[isCovid19 & isManufacturer & isDose]\n",
|
||
"\n",
|
||
" @staticmethod\n",
|
||
" def filterDataFrameForSevereEffects(df, dose):\n",
|
||
" return DataFrameFilter.filterDataFrame(df, dose = dose)\n"
|
||
]
|
||
},
|
||
{
|
||
"cell_type": "code",
|
||
"execution_count": 5,
|
||
"id": "99945ca8",
|
||
"metadata": {},
|
||
"outputs": [],
|
||
"source": [
|
||
"def createBatchCodeTable(df : pd.DataFrame):\n",
|
||
" def filterDataFrame(df, col):\n",
|
||
" return df[df[col] == 'Y'][['VAX_LOT']]\n",
|
||
"\n",
|
||
" batchCodeTableDict = {\n",
|
||
" 'ADRs': df[['VAX_LOT']].value_counts(),\n",
|
||
" 'DEATHS': filterDataFrame(df, 'DIED').value_counts(),\n",
|
||
" 'DISABILITIES': filterDataFrame(df, 'DISABLE').value_counts(),\n",
|
||
" 'LIFE THREATENING ILLNESSES': filterDataFrame(df, 'L_THREAT').value_counts()\n",
|
||
" }\n",
|
||
" return pd.concat(batchCodeTableDict, axis = 'columns').replace(to_replace = np.nan, value = 0)\n",
|
||
"\n",
|
||
"def createManufacturerByBatchCodeTable(df):\n",
|
||
" manufacturerByBatchCodeTable = df[['VAX_LOT', 'VAX_MANU']]\n",
|
||
" manufacturerByBatchCodeTable = manufacturerByBatchCodeTable.drop_duplicates(subset = ['VAX_LOT'])\n",
|
||
" return manufacturerByBatchCodeTable.set_index('VAX_LOT')\n",
|
||
"\n",
|
||
"def createCompanyByBatchCodeTable(df):\n",
|
||
" return createManufacturerByBatchCodeTable(df).rename(columns = {\"VAX_MANU\": \"COMPANY\"})\n",
|
||
"\n",
|
||
"# create table from https://www.howbadismybatch.com/combined.html\n",
|
||
"# FK-TODO: DRY with createBatchCodeTable()\n",
|
||
"def createSevereEffectsBatchCodeTable(df):\n",
|
||
" def filterDataFrame(df, col):\n",
|
||
" return df[df[col] == 'Y']['VAX_LOT']\n",
|
||
"\n",
|
||
" batchCodeTableDict = {\n",
|
||
" 'ADRs': df['VAX_LOT'].value_counts(),\n",
|
||
" 'DEATHS': filterDataFrame(df, 'DIED').value_counts(),\n",
|
||
" 'DISABILITIES': filterDataFrame(df, 'DISABLE').value_counts(),\n",
|
||
" 'LIFE THREATENING ILLNESSES': filterDataFrame(df, 'L_THREAT').value_counts(),\n",
|
||
" 'HOSPITALISATIONS': filterDataFrame(df, 'HOSPITAL').value_counts(),\n",
|
||
" 'EMERGENCY ROOM OR DOCTOR VISITS': filterDataFrame(df, 'ER_VISIT').value_counts()\n",
|
||
" }\n",
|
||
" batchCodeTable = pd.concat(batchCodeTableDict, axis = 'columns')\n",
|
||
" batchCodeTable.index.name = 'VAX_LOT'\n",
|
||
" # add Company column:\n",
|
||
" batchCodeTable = pd.merge(\n",
|
||
" batchCodeTable,\n",
|
||
" createCompanyByBatchCodeTable(df),\n",
|
||
" how = 'left',\n",
|
||
" left_index = True,\n",
|
||
" right_index = True,\n",
|
||
" validate = 'one_to_one')\n",
|
||
" return batchCodeTable.replace(to_replace = np.nan, value = 0)\n"
|
||
]
|
||
},
|
||
{
|
||
"cell_type": "code",
|
||
"execution_count": 6,
|
||
"id": "3dacedfd",
|
||
"metadata": {},
|
||
"outputs": [],
|
||
"source": [
|
||
"import unittest"
|
||
]
|
||
},
|
||
{
|
||
"cell_type": "code",
|
||
"execution_count": 7,
|
||
"id": "e59a1825",
|
||
"metadata": {},
|
||
"outputs": [],
|
||
"source": [
|
||
"from pandas.testing import assert_frame_equal\n",
|
||
"\n",
|
||
"class CreateAndFilterDataFrameTest(unittest.TestCase):\n",
|
||
"\n",
|
||
" def test_createAndFilterDataFrameFromDescrs(self):\n",
|
||
" # Given\n",
|
||
" vaersDescrs = [\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",
|
||
" index = [\n",
|
||
" \"0916600\",\n",
|
||
" \"0916601\"]),\n",
|
||
" 'VAERSVAX': self.createDataFrame(\n",
|
||
" columns = ['VAX_TYPE', 'VAX_MANU', 'VAX_LOT', 'VAX_DOSE_SERIES'],\n",
|
||
" data = [ ['COVID19', 'MODERNA', '037K20A', '1'],\n",
|
||
" ['COVID19', 'MODERNA', '025L20A', '1']],\n",
|
||
" index = [\n",
|
||
" \"0916600\",\n",
|
||
" \"0916601\"],\n",
|
||
" dtypes = {'VAX_DOSE_SERIES': \"string\"})\n",
|
||
" },\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",
|
||
" index = [\n",
|
||
" \"1996873\",\n",
|
||
" \"1996874\"]),\n",
|
||
" 'VAERSVAX': self.createDataFrame(\n",
|
||
" columns = ['VAX_TYPE', 'VAX_MANU', 'VAX_LOT', 'VAX_DOSE_SERIES'],\n",
|
||
" data = [ ['HPV9', 'MERCK & CO. INC.', 'R017624', 'UNK'],\n",
|
||
" ['COVID19', 'MODERNA', '025L20A', '1']],\n",
|
||
" index = [\n",
|
||
" \"1996873\",\n",
|
||
" \"1996874\"],\n",
|
||
" dtypes = {'VAX_DOSE_SERIES': \"string\"})\n",
|
||
" }\n",
|
||
" ]\n",
|
||
" dataFrame = VaersDescr2DataFrameConverter.createDataFrameFromDescrs(vaersDescrs)\n",
|
||
" \n",
|
||
" # When\n",
|
||
" dataFrame = DataFrameFilter.filterDataFrame(dataFrame, manufacturer = \"MODERNA\", dose = '1')\n",
|
||
" \n",
|
||
" # Then\n",
|
||
" dataFrameExpected = self.createDataFrame(\n",
|
||
" columns = ['DIED', 'L_THREAT', 'DISABLE', 'VAX_TYPE', 'VAX_MANU', 'VAX_LOT', 'VAX_DOSE_SERIES'],\n",
|
||
" data = [ ['Y', np.NaN, np.NaN, 'COVID19', 'MODERNA', '037K20A', '1'],\n",
|
||
" [np.NaN, np.NaN, 'Y', 'COVID19', 'MODERNA', '025L20A', '1'],\n",
|
||
" [np.NaN, np.NaN, 'Y', 'COVID19', 'MODERNA', '025L20A', '1']],\n",
|
||
" index = [\n",
|
||
" \"0916600\",\n",
|
||
" \"0916601\",\n",
|
||
" \"1996874\"],\n",
|
||
" dtypes = {'VAX_DOSE_SERIES': \"string\"})\n",
|
||
" assert_frame_equal(dataFrame, dataFrameExpected, check_dtype = False)\n",
|
||
"\n",
|
||
" def test_createDataFrameFromForSevereEffects(self):\n",
|
||
" # Given\n",
|
||
" vaersDescrs = [\n",
|
||
" {\n",
|
||
" 'VAERSDATA': self.createDataFrame(\n",
|
||
" columns = ['DIED', 'L_THREAT', 'DISABLE', 'HOSPITAL', 'ER_VISIT'],\n",
|
||
" data = [ ['Y', 'Y', np.NaN, 'Y', 'Y'],\n",
|
||
" [np.NaN, np.NaN, 'Y', np.NaN, 'Y']],\n",
|
||
" index = [\n",
|
||
" \"0916600\",\n",
|
||
" \"0916601\"]),\n",
|
||
" 'VAERSVAX': self.createDataFrame(\n",
|
||
" columns = ['VAX_TYPE', 'VAX_MANU', 'VAX_LOT', 'VAX_DOSE_SERIES'],\n",
|
||
" data = [ ['COVID19', 'MODERNA', '037K20A', '1'],\n",
|
||
" ['COVID19', 'PFIZER\\BIONTECH', '025L20A', '1']],\n",
|
||
" index = [\n",
|
||
" \"0916600\",\n",
|
||
" \"0916601\"],\n",
|
||
" dtypes = {'VAX_DOSE_SERIES': \"string\"})\n",
|
||
" }\n",
|
||
" ]\n",
|
||
" dataFrame = VaersDescr2DataFrameConverter.createDataFrameFromDescrs(vaersDescrs)\n",
|
||
" \n",
|
||
" # When\n",
|
||
" dataFrame = DataFrameFilter.filterDataFrameForSevereEffects(dataFrame, dose = '1')\n",
|
||
" \n",
|
||
" # Then\n",
|
||
" dataFrameExpected = self.createDataFrame(\n",
|
||
" columns = ['DIED', 'L_THREAT', 'DISABLE', 'HOSPITAL', 'ER_VISIT', 'VAX_TYPE', 'VAX_MANU', 'VAX_LOT', 'VAX_DOSE_SERIES'],\n",
|
||
" data = [ ['Y', 'Y', np.NaN, 'Y', 'Y', 'COVID19', 'MODERNA', '037K20A', '1'],\n",
|
||
" [np.NaN, np.NaN, 'Y', np.NaN, 'Y', 'COVID19', 'PFIZER\\BIONTECH', '025L20A', '1']],\n",
|
||
" index = [\n",
|
||
" \"0916600\",\n",
|
||
" \"0916601\"],\n",
|
||
" dtypes = {'VAX_DOSE_SERIES': \"string\"})\n",
|
||
" assert_frame_equal(dataFrame, dataFrameExpected, check_dtype = False)\n",
|
||
"\n",
|
||
" def test_createAndFilterDataFrameFromDescrsWithFirstDose(self):\n",
|
||
" # Given\n",
|
||
" vaersDescrs = [\n",
|
||
" {\n",
|
||
" 'VAERSDATA': self.createDataFrame(\n",
|
||
" columns = ['DIED', 'L_THREAT', 'DISABLE'],\n",
|
||
" data = [ ['Y', np.NaN, np.NaN]],\n",
|
||
" index = [\n",
|
||
" \"1048786\"]),\n",
|
||
" 'VAERSVAX': self.createDataFrame(\n",
|
||
" columns = ['VAX_TYPE', 'VAX_MANU', 'VAX_LOT', 'VAX_DOSE_SERIES'],\n",
|
||
" data = [ ['COVID19', 'MODERNA', '016M20A', '2'],\n",
|
||
" ['COVID19', 'MODERNA', '030L20A', '1']],\n",
|
||
" index = [\n",
|
||
" \"1048786\",\n",
|
||
" \"1048786\"],\n",
|
||
" dtypes = {'VAX_DOSE_SERIES': \"string\"})\n",
|
||
" }\n",
|
||
" ]\n",
|
||
" dataFrame = VaersDescr2DataFrameConverter.createDataFrameFromDescrs(vaersDescrs)\n",
|
||
" \n",
|
||
" # When\n",
|
||
" dataFrame = DataFrameFilter.filterDataFrame(dataFrame, manufacturer = \"MODERNA\", dose = '1')\n",
|
||
" \n",
|
||
" # Then\n",
|
||
" dataFrameExpected = self.createDataFrame(\n",
|
||
" columns = ['DIED', 'L_THREAT', 'DISABLE', 'VAX_TYPE', 'VAX_MANU', 'VAX_LOT', 'VAX_DOSE_SERIES'],\n",
|
||
" data = [ ['Y', np.NaN, np.NaN, 'COVID19', 'MODERNA', '030L20A', '1']],\n",
|
||
" index = [\n",
|
||
" \"1048786\"],\n",
|
||
" dtypes = {'VAX_DOSE_SERIES': \"string\"})\n",
|
||
" assert_frame_equal(dataFrame, dataFrameExpected, check_dtype = False)\n",
|
||
"\n",
|
||
" def test_createAndFilterDataFrameFromDescrsWithSecondDose(self):\n",
|
||
" # Given\n",
|
||
" vaersDescrs = [\n",
|
||
" {\n",
|
||
" 'VAERSDATA': self.createDataFrame(\n",
|
||
" columns = ['DIED', 'L_THREAT', 'DISABLE'],\n",
|
||
" data = [ ['Y', np.NaN, np.NaN]],\n",
|
||
" index = [\n",
|
||
" \"1048786\"]),\n",
|
||
" 'VAERSVAX': self.createDataFrame(\n",
|
||
" columns = ['VAX_TYPE', 'VAX_MANU', 'VAX_LOT', 'VAX_DOSE_SERIES'],\n",
|
||
" data = [ ['COVID19', 'MODERNA', '016M20A', '2'],\n",
|
||
" ['COVID19', 'MODERNA', '030L20A', '1']],\n",
|
||
" index = [\n",
|
||
" \"1048786\",\n",
|
||
" \"1048786\"],\n",
|
||
" dtypes = {'VAX_DOSE_SERIES': \"string\"})\n",
|
||
" }\n",
|
||
" ]\n",
|
||
" dataFrame = VaersDescr2DataFrameConverter.createDataFrameFromDescrs(vaersDescrs)\n",
|
||
" \n",
|
||
" # When\n",
|
||
" dataFrame = DataFrameFilter.filterDataFrame(dataFrame, manufacturer = \"MODERNA\", dose = '2')\n",
|
||
" \n",
|
||
" # Then\n",
|
||
" dataFrameExpected = self.createDataFrame(\n",
|
||
" columns = ['DIED', 'L_THREAT', 'DISABLE', 'VAX_TYPE', 'VAX_MANU', 'VAX_LOT', 'VAX_DOSE_SERIES'],\n",
|
||
" data = [ ['Y', np.NaN, np.NaN, 'COVID19', 'MODERNA', '016M20A', '2']],\n",
|
||
" index = [\n",
|
||
" \"1048786\"],\n",
|
||
" dtypes = {'VAX_DOSE_SERIES': \"string\"})\n",
|
||
" assert_frame_equal(dataFrame, dataFrameExpected, check_dtype = False)\n",
|
||
"\n",
|
||
" def createDataFrame(self, index, columns, data, dtypes = {}):\n",
|
||
" return pd.DataFrame(index = index, columns = columns, data = data).astype(dtypes)\n"
|
||
]
|
||
},
|
||
{
|
||
"cell_type": "code",
|
||
"execution_count": 8,
|
||
"id": "e14465d7",
|
||
"metadata": {},
|
||
"outputs": [],
|
||
"source": [
|
||
"from pandas.testing import assert_frame_equal\n",
|
||
"\n",
|
||
"class BatchCodeTableTest(unittest.TestCase):\n",
|
||
"\n",
|
||
" def test_createBatchCodeTable2(self):\n",
|
||
" dataFrame = VaersDescr2DataFrameConverter.createDataFrameFromDescrs(\n",
|
||
" [\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",
|
||
" index = [\n",
|
||
" \"0916600\",\n",
|
||
" \"0916601\"]),\n",
|
||
" 'VAERSVAX': self.createDataFrame(\n",
|
||
" columns = ['VAX_TYPE', 'VAX_MANU', 'VAX_LOT', 'VAX_DOSE_SERIES'],\n",
|
||
" data = [ ['COVID19', 'MODERNA', '037K20A', '1'],\n",
|
||
" ['COVID19', 'MODERNA', '025L20A', '1']],\n",
|
||
" index = [\n",
|
||
" \"0916600\",\n",
|
||
" \"0916601\"],\n",
|
||
" dtypes = {'VAX_DOSE_SERIES': \"string\"})\n",
|
||
" },\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",
|
||
" index = [\n",
|
||
" \"1996873\",\n",
|
||
" \"1996874\"]),\n",
|
||
" 'VAERSVAX': self.createDataFrame(\n",
|
||
" columns = ['VAX_TYPE', 'VAX_MANU', 'VAX_LOT', 'VAX_DOSE_SERIES'],\n",
|
||
" data = [ ['HPV9', 'MERCK & CO. INC.', 'R017624', 'UNK'],\n",
|
||
" ['COVID19', 'MODERNA', '025L20A', '1']],\n",
|
||
" index = [\n",
|
||
" \"1996873\",\n",
|
||
" \"1996874\"],\n",
|
||
" dtypes = {'VAX_DOSE_SERIES': \"string\"})\n",
|
||
" }\n",
|
||
" ])\n",
|
||
" dataFrame = DataFrameFilter.filterDataFrame(dataFrame, manufacturer = \"MODERNA\", dose = '1')\n",
|
||
" self._test_createBatchCodeTable(dataFrame);\n",
|
||
"\n",
|
||
" def test_createBatchCodeTable(self):\n",
|
||
" self._test_createBatchCodeTable(\n",
|
||
" DataFrameFilter.filterDataFrame(\n",
|
||
" VaersDescr2DataFrameConverter.createDataFrameFromDescrs(\n",
|
||
" VaersDescrReader(\"test/VAERS\").readAllVaersDescrs()),\n",
|
||
" manufacturer = \"MODERNA\",\n",
|
||
" dose = '1'))\n",
|
||
"\n",
|
||
" def _test_createBatchCodeTable(self, dataFrame):\n",
|
||
" # When\n",
|
||
" batchCodeTable = createBatchCodeTable(dataFrame)\n",
|
||
"\n",
|
||
" # Then\n",
|
||
" batchCodeTableExpected = pd.DataFrame(\n",
|
||
" data = {\n",
|
||
" 'ADRs': [2, 1],\n",
|
||
" 'DEATHS': [0, 1],\n",
|
||
" 'DISABILITIES': [2, 0],\n",
|
||
" 'LIFE THREATENING ILLNESSES': [0, 0]\n",
|
||
" },\n",
|
||
" index = pd.MultiIndex.from_arrays([['025L20A', '037K20A']], names = ('VAX_LOT',)))\n",
|
||
" assert_frame_equal(batchCodeTable, batchCodeTableExpected, check_dtype = False)\n",
|
||
"\n",
|
||
" def createDataFrame(self, index, columns, data, dtypes = {}):\n",
|
||
" return pd.DataFrame(index = index, columns = columns, data = data).astype(dtypes)\n"
|
||
]
|
||
},
|
||
{
|
||
"cell_type": "code",
|
||
"execution_count": 9,
|
||
"id": "ded70c87",
|
||
"metadata": {},
|
||
"outputs": [],
|
||
"source": [
|
||
"from pandas.testing import assert_frame_equal\n",
|
||
"\n",
|
||
"class SevereEffectsBatchCodeTableTest(unittest.TestCase):\n",
|
||
"\n",
|
||
" def test_createSevereEffectsBatchCodeTable(self):\n",
|
||
" # Given\n",
|
||
" dataFrame = VaersDescr2DataFrameConverter.createDataFrameFromDescrs(\n",
|
||
" [\n",
|
||
" {\n",
|
||
" 'VAERSDATA': self.createDataFrame(\n",
|
||
" columns = ['DIED', 'L_THREAT', 'DISABLE', 'HOSPITAL', 'ER_VISIT'],\n",
|
||
" data = [ ['Y', 'Y', np.NaN, 'Y', 'Y'],\n",
|
||
" [np.NaN, np.NaN, 'Y', np.NaN, 'Y']],\n",
|
||
" index = [\n",
|
||
" \"0916600\",\n",
|
||
" \"0916601\"]),\n",
|
||
" 'VAERSVAX': self.createDataFrame(\n",
|
||
" columns = ['VAX_TYPE', 'VAX_MANU', 'VAX_LOT', 'VAX_DOSE_SERIES'],\n",
|
||
" data = [ ['COVID19', 'MODERNA', '037K20A', '1'],\n",
|
||
" ['COVID19', 'PFIZER\\BIONTECH', '025L20A', '1']],\n",
|
||
" index = [\n",
|
||
" \"0916600\",\n",
|
||
" \"0916601\"],\n",
|
||
" dtypes = {'VAX_DOSE_SERIES': \"string\"})\n",
|
||
" }\n",
|
||
" ]\n",
|
||
" )\n",
|
||
" dataFrame = DataFrameFilter.filterDataFrameForSevereEffects(dataFrame, dose = '1')\n",
|
||
"\n",
|
||
" # When\n",
|
||
" batchCodeTable = createSevereEffectsBatchCodeTable(dataFrame)\n",
|
||
"\n",
|
||
" # Then\n",
|
||
" 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",
|
||
" 'EMERGENCY ROOM OR DOCTOR VISITS': [1, 1],\n",
|
||
" 'COMPANY': ['MODERNA', 'PFIZER\\BIONTECH']\n",
|
||
" },\n",
|
||
" index = pd.Index(['037K20A', '025L20A'], name='VAX_LOT'))\n",
|
||
" assert_frame_equal(batchCodeTable, batchCodeTableExpected, check_dtype = False)\n",
|
||
"\n",
|
||
" def createDataFrame(self, index, columns, data, dtypes = {}):\n",
|
||
" return pd.DataFrame(index = index, columns = columns, data = data).astype(dtypes)\n"
|
||
]
|
||
},
|
||
{
|
||
"cell_type": "code",
|
||
"execution_count": 10,
|
||
"id": "5a8bff1b",
|
||
"metadata": {},
|
||
"outputs": [
|
||
{
|
||
"name": "stderr",
|
||
"output_type": "stream",
|
||
"text": [
|
||
"test_createBatchCodeTable (__main__.BatchCodeTableTest) ... ok\n",
|
||
"test_createBatchCodeTable2 (__main__.BatchCodeTableTest) ... ok\n",
|
||
"test_createAndFilterDataFrameFromDescrs (__main__.CreateAndFilterDataFrameTest) ... ok\n",
|
||
"test_createAndFilterDataFrameFromDescrsWithFirstDose (__main__.CreateAndFilterDataFrameTest) ... ok\n",
|
||
"test_createAndFilterDataFrameFromDescrsWithSecondDose (__main__.CreateAndFilterDataFrameTest) ... ok\n",
|
||
"test_createDataFrameFromForSevereEffects (__main__.CreateAndFilterDataFrameTest) ... ok\n",
|
||
"test_createSevereEffectsBatchCodeTable (__main__.SevereEffectsBatchCodeTableTest) ... ok\n",
|
||
"\n",
|
||
"----------------------------------------------------------------------\n",
|
||
"Ran 7 tests in 0.156s\n",
|
||
"\n",
|
||
"OK\n"
|
||
]
|
||
},
|
||
{
|
||
"data": {
|
||
"text/plain": [
|
||
"<unittest.main.TestProgram at 0x7f8aa7824220>"
|
||
]
|
||
},
|
||
"execution_count": 10,
|
||
"metadata": {},
|
||
"output_type": "execute_result"
|
||
}
|
||
],
|
||
"source": [
|
||
"unittest.main(argv = [''], verbosity = 2, exit = False)"
|
||
]
|
||
},
|
||
{
|
||
"cell_type": "code",
|
||
"execution_count": 11,
|
||
"id": "86e0e4f2",
|
||
"metadata": {},
|
||
"outputs": [],
|
||
"source": [
|
||
"def saveBatchCodeTable(manufacturer, excelFile):\n",
|
||
" batchCodeTable = createBatchCodeTable(\n",
|
||
" DataFrameFilter.filterDataFrame(\n",
|
||
" VaersDescr2DataFrameConverter.createDataFrameFromDescrs(\n",
|
||
" VaersDescrReader(\"VAERS\").readAllVaersDescrs()),\n",
|
||
" manufacturer = manufacturer,\n",
|
||
" dose = '1'))\n",
|
||
" display(manufacturer, batchCodeTable)\n",
|
||
" batchCodeTable.to_excel(excelFile)"
|
||
]
|
||
},
|
||
{
|
||
"cell_type": "code",
|
||
"execution_count": 12,
|
||
"id": "ab170c16",
|
||
"metadata": {},
|
||
"outputs": [
|
||
{
|
||
"data": {
|
||
"text/plain": [
|
||
"'MODERNA'"
|
||
]
|
||
},
|
||
"metadata": {},
|
||
"output_type": "display_data"
|
||
},
|
||
{
|
||
"data": {
|
||
"text/html": [
|
||
"<div>\n",
|
||
"<style scoped>\n",
|
||
" .dataframe tbody tr th:only-of-type {\n",
|
||
" vertical-align: middle;\n",
|
||
" }\n",
|
||
"\n",
|
||
" .dataframe tbody tr th {\n",
|
||
" vertical-align: top;\n",
|
||
" }\n",
|
||
"\n",
|
||
" .dataframe thead th {\n",
|
||
" text-align: right;\n",
|
||
" }\n",
|
||
"</style>\n",
|
||
"<table border=\"1\" class=\"dataframe\">\n",
|
||
" <thead>\n",
|
||
" <tr style=\"text-align: right;\">\n",
|
||
" <th></th>\n",
|
||
" <th>ADRs</th>\n",
|
||
" <th>DEATHS</th>\n",
|
||
" <th>DISABILITIES</th>\n",
|
||
" <th>LIFE THREATENING ILLNESSES</th>\n",
|
||
" </tr>\n",
|
||
" <tr>\n",
|
||
" <th>VAX_LOT</th>\n",
|
||
" <th></th>\n",
|
||
" <th></th>\n",
|
||
" <th></th>\n",
|
||
" <th></th>\n",
|
||
" </tr>\n",
|
||
" </thead>\n",
|
||
" <tbody>\n",
|
||
" <tr>\n",
|
||
" <th>039K20A</th>\n",
|
||
" <td>3330</td>\n",
|
||
" <td>67.0</td>\n",
|
||
" <td>22.0</td>\n",
|
||
" <td>29.0</td>\n",
|
||
" </tr>\n",
|
||
" <tr>\n",
|
||
" <th>026L20A</th>\n",
|
||
" <td>3327</td>\n",
|
||
" <td>25.0</td>\n",
|
||
" <td>24.0</td>\n",
|
||
" <td>21.0</td>\n",
|
||
" </tr>\n",
|
||
" <tr>\n",
|
||
" <th>011J20A</th>\n",
|
||
" <td>3072</td>\n",
|
||
" <td>33.0</td>\n",
|
||
" <td>27.0</td>\n",
|
||
" <td>26.0</td>\n",
|
||
" </tr>\n",
|
||
" <tr>\n",
|
||
" <th>025L20A</th>\n",
|
||
" <td>2391</td>\n",
|
||
" <td>42.0</td>\n",
|
||
" <td>16.0</td>\n",
|
||
" <td>26.0</td>\n",
|
||
" </tr>\n",
|
||
" <tr>\n",
|
||
" <th>012L20A</th>\n",
|
||
" <td>2352</td>\n",
|
||
" <td>57.0</td>\n",
|
||
" <td>28.0</td>\n",
|
||
" <td>22.0</td>\n",
|
||
" </tr>\n",
|
||
" <tr>\n",
|
||
" <th>...</th>\n",
|
||
" <td>...</td>\n",
|
||
" <td>...</td>\n",
|
||
" <td>...</td>\n",
|
||
" <td>...</td>\n",
|
||
" </tr>\n",
|
||
" <tr>\n",
|
||
" <th>028-20A</th>\n",
|
||
" <td>1</td>\n",
|
||
" <td>0.0</td>\n",
|
||
" <td>0.0</td>\n",
|
||
" <td>0.0</td>\n",
|
||
" </tr>\n",
|
||
" <tr>\n",
|
||
" <th>028(L or Z?)20A</th>\n",
|
||
" <td>1</td>\n",
|
||
" <td>0.0</td>\n",
|
||
" <td>0.0</td>\n",
|
||
" <td>0.0</td>\n",
|
||
" </tr>\n",
|
||
" <tr>\n",
|
||
" <th>028 L20A</th>\n",
|
||
" <td>1</td>\n",
|
||
" <td>0.0</td>\n",
|
||
" <td>0.0</td>\n",
|
||
" <td>0.0</td>\n",
|
||
" </tr>\n",
|
||
" <tr>\n",
|
||
" <th>028 L 20A</th>\n",
|
||
" <td>1</td>\n",
|
||
" <td>0.0</td>\n",
|
||
" <td>0.0</td>\n",
|
||
" <td>0.0</td>\n",
|
||
" </tr>\n",
|
||
" <tr>\n",
|
||
" <th>xx3A21A</th>\n",
|
||
" <td>1</td>\n",
|
||
" <td>0.0</td>\n",
|
||
" <td>0.0</td>\n",
|
||
" <td>0.0</td>\n",
|
||
" </tr>\n",
|
||
" </tbody>\n",
|
||
"</table>\n",
|
||
"<p>10248 rows × 4 columns</p>\n",
|
||
"</div>"
|
||
],
|
||
"text/plain": [
|
||
" ADRs DEATHS DISABILITIES LIFE THREATENING ILLNESSES\n",
|
||
"VAX_LOT \n",
|
||
"039K20A 3330 67.0 22.0 29.0\n",
|
||
"026L20A 3327 25.0 24.0 21.0\n",
|
||
"011J20A 3072 33.0 27.0 26.0\n",
|
||
"025L20A 2391 42.0 16.0 26.0\n",
|
||
"012L20A 2352 57.0 28.0 22.0\n",
|
||
"... ... ... ... ...\n",
|
||
"028-20A 1 0.0 0.0 0.0\n",
|
||
"028(L or Z?)20A 1 0.0 0.0 0.0\n",
|
||
"028 L20A 1 0.0 0.0 0.0\n",
|
||
"028 L 20A 1 0.0 0.0 0.0\n",
|
||
"xx3A21A 1 0.0 0.0 0.0\n",
|
||
"\n",
|
||
"[10248 rows x 4 columns]"
|
||
]
|
||
},
|
||
"metadata": {},
|
||
"output_type": "display_data"
|
||
},
|
||
{
|
||
"data": {
|
||
"text/plain": [
|
||
"'PFIZER\\\\BIONTECH'"
|
||
]
|
||
},
|
||
"metadata": {},
|
||
"output_type": "display_data"
|
||
},
|
||
{
|
||
"data": {
|
||
"text/html": [
|
||
"<div>\n",
|
||
"<style scoped>\n",
|
||
" .dataframe tbody tr th:only-of-type {\n",
|
||
" vertical-align: middle;\n",
|
||
" }\n",
|
||
"\n",
|
||
" .dataframe tbody tr th {\n",
|
||
" vertical-align: top;\n",
|
||
" }\n",
|
||
"\n",
|
||
" .dataframe thead th {\n",
|
||
" text-align: right;\n",
|
||
" }\n",
|
||
"</style>\n",
|
||
"<table border=\"1\" class=\"dataframe\">\n",
|
||
" <thead>\n",
|
||
" <tr style=\"text-align: right;\">\n",
|
||
" <th></th>\n",
|
||
" <th>ADRs</th>\n",
|
||
" <th>DEATHS</th>\n",
|
||
" <th>DISABILITIES</th>\n",
|
||
" <th>LIFE THREATENING ILLNESSES</th>\n",
|
||
" </tr>\n",
|
||
" <tr>\n",
|
||
" <th>VAX_LOT</th>\n",
|
||
" <th></th>\n",
|
||
" <th></th>\n",
|
||
" <th></th>\n",
|
||
" <th></th>\n",
|
||
" </tr>\n",
|
||
" </thead>\n",
|
||
" <tbody>\n",
|
||
" <tr>\n",
|
||
" <th>EK5730</th>\n",
|
||
" <td>1741</td>\n",
|
||
" <td>18.0</td>\n",
|
||
" <td>25.0</td>\n",
|
||
" <td>16.0</td>\n",
|
||
" </tr>\n",
|
||
" <tr>\n",
|
||
" <th>EK9231</th>\n",
|
||
" <td>1631</td>\n",
|
||
" <td>37.0</td>\n",
|
||
" <td>19.0</td>\n",
|
||
" <td>21.0</td>\n",
|
||
" </tr>\n",
|
||
" <tr>\n",
|
||
" <th>EH9899</th>\n",
|
||
" <td>1570</td>\n",
|
||
" <td>14.0</td>\n",
|
||
" <td>36.0</td>\n",
|
||
" <td>18.0</td>\n",
|
||
" </tr>\n",
|
||
" <tr>\n",
|
||
" <th>EN6205</th>\n",
|
||
" <td>1487</td>\n",
|
||
" <td>25.0</td>\n",
|
||
" <td>37.0</td>\n",
|
||
" <td>31.0</td>\n",
|
||
" </tr>\n",
|
||
" <tr>\n",
|
||
" <th>EN6208</th>\n",
|
||
" <td>1475</td>\n",
|
||
" <td>33.0</td>\n",
|
||
" <td>27.0</td>\n",
|
||
" <td>25.0</td>\n",
|
||
" </tr>\n",
|
||
" <tr>\n",
|
||
" <th>...</th>\n",
|
||
" <td>...</td>\n",
|
||
" <td>...</td>\n",
|
||
" <td>...</td>\n",
|
||
" <td>...</td>\n",
|
||
" </tr>\n",
|
||
" <tr>\n",
|
||
" <th>EN6266</th>\n",
|
||
" <td>1</td>\n",
|
||
" <td>0.0</td>\n",
|
||
" <td>0.0</td>\n",
|
||
" <td>0.0</td>\n",
|
||
" </tr>\n",
|
||
" <tr>\n",
|
||
" <th>EN626207</th>\n",
|
||
" <td>1</td>\n",
|
||
" <td>0.0</td>\n",
|
||
" <td>0.0</td>\n",
|
||
" <td>0.0</td>\n",
|
||
" </tr>\n",
|
||
" <tr>\n",
|
||
" <th>EN6262</th>\n",
|
||
" <td>1</td>\n",
|
||
" <td>0.0</td>\n",
|
||
" <td>0.0</td>\n",
|
||
" <td>0.0</td>\n",
|
||
" </tr>\n",
|
||
" <tr>\n",
|
||
" <th>EN6251</th>\n",
|
||
" <td>1</td>\n",
|
||
" <td>0.0</td>\n",
|
||
" <td>0.0</td>\n",
|
||
" <td>0.0</td>\n",
|
||
" </tr>\n",
|
||
" <tr>\n",
|
||
" <th>zw0151</th>\n",
|
||
" <td>1</td>\n",
|
||
" <td>0.0</td>\n",
|
||
" <td>1.0</td>\n",
|
||
" <td>0.0</td>\n",
|
||
" </tr>\n",
|
||
" </tbody>\n",
|
||
"</table>\n",
|
||
"<p>6765 rows × 4 columns</p>\n",
|
||
"</div>"
|
||
],
|
||
"text/plain": [
|
||
" ADRs DEATHS DISABILITIES LIFE THREATENING ILLNESSES\n",
|
||
"VAX_LOT \n",
|
||
"EK5730 1741 18.0 25.0 16.0\n",
|
||
"EK9231 1631 37.0 19.0 21.0\n",
|
||
"EH9899 1570 14.0 36.0 18.0\n",
|
||
"EN6205 1487 25.0 37.0 31.0\n",
|
||
"EN6208 1475 33.0 27.0 25.0\n",
|
||
"... ... ... ... ...\n",
|
||
"EN6266 1 0.0 0.0 0.0\n",
|
||
"EN626207 1 0.0 0.0 0.0\n",
|
||
"EN6262 1 0.0 0.0 0.0\n",
|
||
"EN6251 1 0.0 0.0 0.0\n",
|
||
"zw0151 1 0.0 1.0 0.0\n",
|
||
"\n",
|
||
"[6765 rows x 4 columns]"
|
||
]
|
||
},
|
||
"metadata": {},
|
||
"output_type": "display_data"
|
||
},
|
||
{
|
||
"data": {
|
||
"text/plain": [
|
||
"'JANSSEN'"
|
||
]
|
||
},
|
||
"metadata": {},
|
||
"output_type": "display_data"
|
||
},
|
||
{
|
||
"data": {
|
||
"text/html": [
|
||
"<div>\n",
|
||
"<style scoped>\n",
|
||
" .dataframe tbody tr th:only-of-type {\n",
|
||
" vertical-align: middle;\n",
|
||
" }\n",
|
||
"\n",
|
||
" .dataframe tbody tr th {\n",
|
||
" vertical-align: top;\n",
|
||
" }\n",
|
||
"\n",
|
||
" .dataframe thead th {\n",
|
||
" text-align: right;\n",
|
||
" }\n",
|
||
"</style>\n",
|
||
"<table border=\"1\" class=\"dataframe\">\n",
|
||
" <thead>\n",
|
||
" <tr style=\"text-align: right;\">\n",
|
||
" <th></th>\n",
|
||
" <th>ADRs</th>\n",
|
||
" <th>DEATHS</th>\n",
|
||
" <th>DISABILITIES</th>\n",
|
||
" <th>LIFE THREATENING ILLNESSES</th>\n",
|
||
" </tr>\n",
|
||
" <tr>\n",
|
||
" <th>VAX_LOT</th>\n",
|
||
" <th></th>\n",
|
||
" <th></th>\n",
|
||
" <th></th>\n",
|
||
" <th></th>\n",
|
||
" </tr>\n",
|
||
" </thead>\n",
|
||
" <tbody>\n",
|
||
" <tr>\n",
|
||
" <th>043A21A</th>\n",
|
||
" <td>1692</td>\n",
|
||
" <td>28.0</td>\n",
|
||
" <td>29.0</td>\n",
|
||
" <td>37.0</td>\n",
|
||
" </tr>\n",
|
||
" <tr>\n",
|
||
" <th>042A21A</th>\n",
|
||
" <td>1461</td>\n",
|
||
" <td>43.0</td>\n",
|
||
" <td>33.0</td>\n",
|
||
" <td>35.0</td>\n",
|
||
" </tr>\n",
|
||
" <tr>\n",
|
||
" <th>202A21A</th>\n",
|
||
" <td>1159</td>\n",
|
||
" <td>22.0</td>\n",
|
||
" <td>16.0</td>\n",
|
||
" <td>21.0</td>\n",
|
||
" </tr>\n",
|
||
" <tr>\n",
|
||
" <th>1805018</th>\n",
|
||
" <td>1129</td>\n",
|
||
" <td>32.0</td>\n",
|
||
" <td>30.0</td>\n",
|
||
" <td>39.0</td>\n",
|
||
" </tr>\n",
|
||
" <tr>\n",
|
||
" <th>201A21A</th>\n",
|
||
" <td>1129</td>\n",
|
||
" <td>15.0</td>\n",
|
||
" <td>27.0</td>\n",
|
||
" <td>24.0</td>\n",
|
||
" </tr>\n",
|
||
" <tr>\n",
|
||
" <th>...</th>\n",
|
||
" <td>...</td>\n",
|
||
" <td>...</td>\n",
|
||
" <td>...</td>\n",
|
||
" <td>...</td>\n",
|
||
" </tr>\n",
|
||
" <tr>\n",
|
||
" <th>1808998</th>\n",
|
||
" <td>1</td>\n",
|
||
" <td>0.0</td>\n",
|
||
" <td>0.0</td>\n",
|
||
" <td>0.0</td>\n",
|
||
" </tr>\n",
|
||
" <tr>\n",
|
||
" <th>1808996</th>\n",
|
||
" <td>1</td>\n",
|
||
" <td>0.0</td>\n",
|
||
" <td>0.0</td>\n",
|
||
" <td>0.0</td>\n",
|
||
" </tr>\n",
|
||
" <tr>\n",
|
||
" <th>1808992</th>\n",
|
||
" <td>1</td>\n",
|
||
" <td>0.0</td>\n",
|
||
" <td>0.0</td>\n",
|
||
" <td>0.0</td>\n",
|
||
" </tr>\n",
|
||
" <tr>\n",
|
||
" <th>180898le</th>\n",
|
||
" <td>1</td>\n",
|
||
" <td>0.0</td>\n",
|
||
" <td>0.0</td>\n",
|
||
" <td>0.0</td>\n",
|
||
" </tr>\n",
|
||
" <tr>\n",
|
||
" <th>z03az1a</th>\n",
|
||
" <td>1</td>\n",
|
||
" <td>0.0</td>\n",
|
||
" <td>0.0</td>\n",
|
||
" <td>0.0</td>\n",
|
||
" </tr>\n",
|
||
" </tbody>\n",
|
||
"</table>\n",
|
||
"<p>1797 rows × 4 columns</p>\n",
|
||
"</div>"
|
||
],
|
||
"text/plain": [
|
||
" ADRs DEATHS DISABILITIES LIFE THREATENING ILLNESSES\n",
|
||
"VAX_LOT \n",
|
||
"043A21A 1692 28.0 29.0 37.0\n",
|
||
"042A21A 1461 43.0 33.0 35.0\n",
|
||
"202A21A 1159 22.0 16.0 21.0\n",
|
||
"1805018 1129 32.0 30.0 39.0\n",
|
||
"201A21A 1129 15.0 27.0 24.0\n",
|
||
"... ... ... ... ...\n",
|
||
"1808998 1 0.0 0.0 0.0\n",
|
||
"1808996 1 0.0 0.0 0.0\n",
|
||
"1808992 1 0.0 0.0 0.0\n",
|
||
"180898le 1 0.0 0.0 0.0\n",
|
||
"z03az1a 1 0.0 0.0 0.0\n",
|
||
"\n",
|
||
"[1797 rows x 4 columns]"
|
||
]
|
||
},
|
||
"metadata": {},
|
||
"output_type": "display_data"
|
||
}
|
||
],
|
||
"source": [
|
||
"saveBatchCodeTable(\"MODERNA\", \"results/moderna.xlsx\")\n",
|
||
"saveBatchCodeTable(\"PFIZER\\BIONTECH\", \"results/pfizer.xlsx\")\n",
|
||
"saveBatchCodeTable(\"JANSSEN\", \"results/janssen.xlsx\")"
|
||
]
|
||
},
|
||
{
|
||
"cell_type": "code",
|
||
"execution_count": 13,
|
||
"id": "bc56831d",
|
||
"metadata": {},
|
||
"outputs": [],
|
||
"source": [
|
||
"def saveSevereEffectsBatchCodeTable(excelFile):\n",
|
||
" severeEffectsBatchCodeTable = createSevereEffectsBatchCodeTable(\n",
|
||
" DataFrameFilter.filterDataFrameForSevereEffects(\n",
|
||
" VaersDescr2DataFrameConverter.createDataFrameFromDescrs(\n",
|
||
" VaersDescrReader(\"VAERS\").readAllVaersDescrs()),\n",
|
||
" dose = '1'))\n",
|
||
" display('severeEffectsBatchCodeTable', severeEffectsBatchCodeTable)\n",
|
||
" severeEffectsBatchCodeTable.to_excel(excelFile)"
|
||
]
|
||
},
|
||
{
|
||
"cell_type": "code",
|
||
"execution_count": 14,
|
||
"id": "ace3fed9",
|
||
"metadata": {},
|
||
"outputs": [
|
||
{
|
||
"data": {
|
||
"text/plain": [
|
||
"'severeEffectsBatchCodeTable'"
|
||
]
|
||
},
|
||
"metadata": {},
|
||
"output_type": "display_data"
|
||
},
|
||
{
|
||
"data": {
|
||
"text/html": [
|
||
"<div>\n",
|
||
"<style scoped>\n",
|
||
" .dataframe tbody tr th:only-of-type {\n",
|
||
" vertical-align: middle;\n",
|
||
" }\n",
|
||
"\n",
|
||
" .dataframe tbody tr th {\n",
|
||
" vertical-align: top;\n",
|
||
" }\n",
|
||
"\n",
|
||
" .dataframe thead th {\n",
|
||
" text-align: right;\n",
|
||
" }\n",
|
||
"</style>\n",
|
||
"<table border=\"1\" class=\"dataframe\">\n",
|
||
" <thead>\n",
|
||
" <tr style=\"text-align: right;\">\n",
|
||
" <th></th>\n",
|
||
" <th>ADRs</th>\n",
|
||
" <th>DEATHS</th>\n",
|
||
" <th>DISABILITIES</th>\n",
|
||
" <th>LIFE THREATENING ILLNESSES</th>\n",
|
||
" <th>HOSPITALISATIONS</th>\n",
|
||
" <th>EMERGENCY ROOM OR DOCTOR VISITS</th>\n",
|
||
" <th>COMPANY</th>\n",
|
||
" </tr>\n",
|
||
" <tr>\n",
|
||
" <th>VAX_LOT</th>\n",
|
||
" <th></th>\n",
|
||
" <th></th>\n",
|
||
" <th></th>\n",
|
||
" <th></th>\n",
|
||
" <th></th>\n",
|
||
" <th></th>\n",
|
||
" <th></th>\n",
|
||
" </tr>\n",
|
||
" </thead>\n",
|
||
" <tbody>\n",
|
||
" <tr>\n",
|
||
" <th>026L20A</th>\n",
|
||
" <td>3335</td>\n",
|
||
" <td>25.0</td>\n",
|
||
" <td>24.0</td>\n",
|
||
" <td>21.0</td>\n",
|
||
" <td>125.0</td>\n",
|
||
" <td>0.0</td>\n",
|
||
" <td>MODERNA</td>\n",
|
||
" </tr>\n",
|
||
" <tr>\n",
|
||
" <th>039K20A</th>\n",
|
||
" <td>3335</td>\n",
|
||
" <td>67.0</td>\n",
|
||
" <td>22.0</td>\n",
|
||
" <td>29.0</td>\n",
|
||
" <td>134.0</td>\n",
|
||
" <td>0.0</td>\n",
|
||
" <td>MODERNA</td>\n",
|
||
" </tr>\n",
|
||
" <tr>\n",
|
||
" <th>011J20A</th>\n",
|
||
" <td>3078</td>\n",
|
||
" <td>34.0</td>\n",
|
||
" <td>27.0</td>\n",
|
||
" <td>26.0</td>\n",
|
||
" <td>106.0</td>\n",
|
||
" <td>0.0</td>\n",
|
||
" <td>MODERNA</td>\n",
|
||
" </tr>\n",
|
||
" <tr>\n",
|
||
" <th>025L20A</th>\n",
|
||
" <td>2397</td>\n",
|
||
" <td>42.0</td>\n",
|
||
" <td>16.0</td>\n",
|
||
" <td>26.0</td>\n",
|
||
" <td>83.0</td>\n",
|
||
" <td>0.0</td>\n",
|
||
" <td>MODERNA</td>\n",
|
||
" </tr>\n",
|
||
" <tr>\n",
|
||
" <th>012L20A</th>\n",
|
||
" <td>2357</td>\n",
|
||
" <td>57.0</td>\n",
|
||
" <td>29.0</td>\n",
|
||
" <td>22.0</td>\n",
|
||
" <td>135.0</td>\n",
|
||
" <td>1.0</td>\n",
|
||
" <td>MODERNA</td>\n",
|
||
" </tr>\n",
|
||
" <tr>\n",
|
||
" <th>...</th>\n",
|
||
" <td>...</td>\n",
|
||
" <td>...</td>\n",
|
||
" <td>...</td>\n",
|
||
" <td>...</td>\n",
|
||
" <td>...</td>\n",
|
||
" <td>...</td>\n",
|
||
" <td>...</td>\n",
|
||
" </tr>\n",
|
||
" <tr>\n",
|
||
" <th>EN6207-</th>\n",
|
||
" <td>1</td>\n",
|
||
" <td>0.0</td>\n",
|
||
" <td>0.0</td>\n",
|
||
" <td>0.0</td>\n",
|
||
" <td>0.0</td>\n",
|
||
" <td>0.0</td>\n",
|
||
" <td>PFIZER\\BIONTECH</td>\n",
|
||
" </tr>\n",
|
||
" <tr>\n",
|
||
" <th>039820A</th>\n",
|
||
" <td>1</td>\n",
|
||
" <td>0.0</td>\n",
|
||
" <td>0.0</td>\n",
|
||
" <td>0.0</td>\n",
|
||
" <td>0.0</td>\n",
|
||
" <td>0.0</td>\n",
|
||
" <td>MODERNA</td>\n",
|
||
" </tr>\n",
|
||
" <tr>\n",
|
||
" <th>Blue-218</th>\n",
|
||
" <td>1</td>\n",
|
||
" <td>0.0</td>\n",
|
||
" <td>0.0</td>\n",
|
||
" <td>0.0</td>\n",
|
||
" <td>0.0</td>\n",
|
||
" <td>0.0</td>\n",
|
||
" <td>MODERNA</td>\n",
|
||
" </tr>\n",
|
||
" <tr>\n",
|
||
" <th>1808973</th>\n",
|
||
" <td>1</td>\n",
|
||
" <td>0.0</td>\n",
|
||
" <td>0.0</td>\n",
|
||
" <td>0.0</td>\n",
|
||
" <td>0.0</td>\n",
|
||
" <td>0.0</td>\n",
|
||
" <td>UNKNOWN MANUFACTURER</td>\n",
|
||
" </tr>\n",
|
||
" <tr>\n",
|
||
" <th>FJ1161</th>\n",
|
||
" <td>1</td>\n",
|
||
" <td>0.0</td>\n",
|
||
" <td>0.0</td>\n",
|
||
" <td>0.0</td>\n",
|
||
" <td>0.0</td>\n",
|
||
" <td>0.0</td>\n",
|
||
" <td>PFIZER\\BIONTECH</td>\n",
|
||
" </tr>\n",
|
||
" </tbody>\n",
|
||
"</table>\n",
|
||
"<p>18428 rows × 7 columns</p>\n",
|
||
"</div>"
|
||
],
|
||
"text/plain": [
|
||
" ADRs DEATHS DISABILITIES LIFE THREATENING ILLNESSES \\\n",
|
||
"VAX_LOT \n",
|
||
"026L20A 3335 25.0 24.0 21.0 \n",
|
||
"039K20A 3335 67.0 22.0 29.0 \n",
|
||
"011J20A 3078 34.0 27.0 26.0 \n",
|
||
"025L20A 2397 42.0 16.0 26.0 \n",
|
||
"012L20A 2357 57.0 29.0 22.0 \n",
|
||
"... ... ... ... ... \n",
|
||
"EN6207- 1 0.0 0.0 0.0 \n",
|
||
"039820A 1 0.0 0.0 0.0 \n",
|
||
"Blue-218 1 0.0 0.0 0.0 \n",
|
||
"1808973 1 0.0 0.0 0.0 \n",
|
||
"FJ1161 1 0.0 0.0 0.0 \n",
|
||
"\n",
|
||
" HOSPITALISATIONS EMERGENCY ROOM OR DOCTOR VISITS \\\n",
|
||
"VAX_LOT \n",
|
||
"026L20A 125.0 0.0 \n",
|
||
"039K20A 134.0 0.0 \n",
|
||
"011J20A 106.0 0.0 \n",
|
||
"025L20A 83.0 0.0 \n",
|
||
"012L20A 135.0 1.0 \n",
|
||
"... ... ... \n",
|
||
"EN6207- 0.0 0.0 \n",
|
||
"039820A 0.0 0.0 \n",
|
||
"Blue-218 0.0 0.0 \n",
|
||
"1808973 0.0 0.0 \n",
|
||
"FJ1161 0.0 0.0 \n",
|
||
"\n",
|
||
" COMPANY \n",
|
||
"VAX_LOT \n",
|
||
"026L20A MODERNA \n",
|
||
"039K20A MODERNA \n",
|
||
"011J20A MODERNA \n",
|
||
"025L20A MODERNA \n",
|
||
"012L20A MODERNA \n",
|
||
"... ... \n",
|
||
"EN6207- PFIZER\\BIONTECH \n",
|
||
"039820A MODERNA \n",
|
||
"Blue-218 MODERNA \n",
|
||
"1808973 UNKNOWN MANUFACTURER \n",
|
||
"FJ1161 PFIZER\\BIONTECH \n",
|
||
"\n",
|
||
"[18428 rows x 7 columns]"
|
||
]
|
||
},
|
||
"metadata": {},
|
||
"output_type": "display_data"
|
||
}
|
||
],
|
||
"source": [
|
||
"saveSevereEffectsBatchCodeTable('results/severeEffects.xlsx')"
|
||
]
|
||
}
|
||
],
|
||
"metadata": {
|
||
"kernelspec": {
|
||
"display_name": "Python 3 (ipykernel)",
|
||
"language": "python",
|
||
"name": "python3"
|
||
},
|
||
"language_info": {
|
||
"codemirror_mode": {
|
||
"name": "ipython",
|
||
"version": 3
|
||
},
|
||
"file_extension": ".py",
|
||
"mimetype": "text/x-python",
|
||
"name": "python",
|
||
"nbconvert_exporter": "python",
|
||
"pygments_lexer": "ipython3",
|
||
"version": "3.9.7"
|
||
}
|
||
},
|
||
"nbformat": 4,
|
||
"nbformat_minor": 5
|
||
}
|