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adding "Lethality (%)" column

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frankknoll
2022-02-15 02:36:32 +01:00
parent 68669b1543
commit d574c1a6b7
3 changed files with 43 additions and 10 deletions
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44
src/HowBadIsMyBatch.ipynb
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@@ -230,19 +230,46 @@
" def createBatchCodeTable(dataFrame : pd.DataFrame, dose):\n",
" dataFrame = DataFrameFilter().filterByCovid19(dataFrame)\n",
" dataFrame = DataFrameFilter().filterBy(dataFrame, dose = dose)\n",
" return BatchCodeTableFactory._createSummationTableByVAX_LOT(dataFrame)[['Total Number of Adverse Reaction Reports', 'Deaths', 'Disabilities', 'Life Threatening Illnesses', 'Company']]\n",
" return BatchCodeTableFactory._createSummationTableByVAX_LOT(dataFrame)[\n",
" [\n",
" 'Total Number of Adverse Reaction Reports',\n",
" 'Deaths',\n",
" 'Disabilities',\n",
" 'Life Threatening Illnesses',\n",
" 'Company',\n",
" 'Lethality (%)'\n",
" ]]\n",
"\n",
" # create table from https://www.howbadismybatch.com/combined.html\n",
" @staticmethod\n",
" def createSevereEffectsBatchCodeTable(dataFrame : pd.DataFrame, dose):\n",
" dataFrame = DataFrameFilter().filterByCovid19(dataFrame)\n",
" dataFrame = DataFrameFilter().filterBy(dataFrame, dose = dose)\n",
" return BatchCodeTableFactory._createSummationTableByVAX_LOT(dataFrame)\n",
" return BatchCodeTableFactory._createSummationTableByVAX_LOT(dataFrame)[\n",
" [\n",
" 'Total Number of Adverse Reaction Reports', \n",
" 'Deaths',\n",
" 'Disabilities',\n",
" 'Life Threatening Illnesses',\n",
" 'Hospitalisations',\n",
" 'Emergency Room or Doctor Visits',\n",
" 'Company'\n",
" ]]\n",
"\n",
" @staticmethod\n",
" def _createSummationTableByVAX_LOT(dataFrame):\n",
" batchCodeTable = SummationTableFactory.createSummationTable(dataFrame.groupby('VAX_LOT'))\n",
" batchCodeTable = batchCodeTable[['Total Number of Adverse Reaction Reports', 'Deaths', 'Disabilities', 'Life Threatening Illnesses', 'Hospitalisations', 'Emergency Room or Doctor Visits']]\n",
" batchCodeTable['Lethality (%)'] = batchCodeTable['Deaths'] / batchCodeTable['Total Number of Adverse Reaction Reports'] * 100\n",
" batchCodeTable = batchCodeTable[\n",
" [\n",
" 'Total Number of Adverse Reaction Reports',\n",
" 'Deaths',\n",
" 'Disabilities',\n",
" 'Life Threatening Illnesses',\n",
" 'Hospitalisations',\n",
" 'Emergency Room or Doctor Visits',\n",
" 'Lethality (%)'\n",
" ]]\n",
" batchCodeTable = batchCodeTable.sort_values(by = 'Total Number of Adverse Reaction Reports', ascending = False)\n",
" return BatchCodeTableFactory._addCompanyColumn(batchCodeTable, BatchCodeTableFactory._createCompanyByBatchCodeTable(dataFrame))\n",
"\n",
@@ -754,11 +781,12 @@
" # Then\n",
" batchCodeTableExpected = pd.DataFrame(\n",
" data = {\n",
" 'Total Number of Adverse Reaction Reports': [2, 1],\n",
" 'Deaths': [0, 1],\n",
" 'Disabilities': [2, 0],\n",
" 'Life Threatening Illnesses': [0, 0],\n",
" 'Company': ['MODERNA', 'MODERNA']\n",
" 'Total Number of Adverse Reaction Reports': [2, 1],\n",
" 'Deaths': [0, 1],\n",
" 'Disabilities': [2, 0],\n",
" 'Life Threatening Illnesses': [0, 0],\n",
" 'Company': ['MODERNA', 'MODERNA'],\n",
" 'Lethality (%)': [0/2 * 100, 1/1 * 100]\n",
" },\n",
" index = pd.Index(['025L20A', '037K20A'], name = 'VAX_LOT'))\n",
" assert_frame_equal(batchCodeTable, batchCodeTableExpected, check_dtype = False)\n"