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adding Lethality column

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frankknoll
2022-02-19 16:16:46 +01:00
parent c9764d09a5
commit 2563fde5d3
14 changed files with 41 additions and 28 deletions
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34
src/HowBadIsMyBatch.ipynb
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@@ -213,7 +213,16 @@
" \"SEVERE_sum\": \"Severities\"\n",
" })\n",
" summationTable['Severe reports'] = summationTable['Severities'] / summationTable['Total Number of Adverse Reaction Reports'] * 100\n",
" summationTable = summationTable[['Total Number of Adverse Reaction Reports', 'Deaths', 'Disabilities', 'Life Threatening Illnesses', 'Severe reports']]\n",
" summationTable['Lethality'] = summationTable['Deaths'] / summationTable['Total Number of Adverse Reaction Reports'] * 100\n",
" summationTable = summationTable[\n",
" [\n",
" 'Total Number of Adverse Reaction Reports',\n",
" 'Deaths',\n",
" 'Disabilities',\n",
" 'Life Threatening Illnesses',\n",
" 'Severe reports',\n",
" 'Lethality'\n",
" ]]\n",
" return summationTable\n",
"\n",
" @staticmethod\n",
@@ -1005,7 +1014,8 @@
" 'Deaths': [2, 1],\n",
" 'Disabilities': [1, 0],\n",
" 'Life Threatening Illnesses': [1, 0],\n",
" 'Severe reports': [2/2 * 100, 1/1 * 100]\n",
" 'Severe reports': [2/2 * 100, 1/1 * 100],\n",
" 'Lethality': [2/2 * 100, 1/1 * 100]\n",
" },\n",
" index = pd.Index(['1', '2'], dtype = \"string\", name = 'Dose')))\n",
" \n",
@@ -1036,7 +1046,8 @@
" 'Deaths': [2, 1],\n",
" 'Disabilities': [1, 0],\n",
" 'Life Threatening Illnesses': [1, 0],\n",
" 'Severe reports': [2/2 * 100, 1/1 * 100]\n",
" 'Severe reports': [2/2 * 100, 1/1 * 100],\n",
" 'Lethality': [2/2 * 100, 1/1 * 100]\n",
" },\n",
" index = pd.MultiIndex.from_tuples(\n",
" [\n",
@@ -1082,10 +1093,10 @@
" assert_frame_equal(\n",
" internationalLotTable,\n",
" TestHelper.createDataFrame(\n",
" columns = ['Total Number of Adverse Reaction Reports', 'Deaths', 'Disabilities', 'Life Threatening Illnesses', 'Severe reports'],\n",
" data = [ [2, 2, 1, 1, 2/2 * 100],\n",
" [1, 1, 0, 0, 1/1 * 100],\n",
" [2, 0, 0, 0, 0/2 * 100]],\n",
" columns = ['Total Number of Adverse Reaction Reports', 'Deaths', 'Disabilities', 'Life Threatening Illnesses', 'Severe reports', 'Lethality'],\n",
" data = [ [2, 2, 1, 1, 2/2 * 100, 2/2 * 100],\n",
" [1, 1, 0, 0, 1/1 * 100, 1/1 * 100],\n",
" [2, 0, 0, 0, 0/2 * 100, 0/2 * 100]],\n",
" index = pd.Index(\n",
" [\n",
" 'France',\n",
@@ -1117,9 +1128,9 @@
" assert_frame_equal(\n",
" batchCodeTable,\n",
" TestHelper.createDataFrame(\n",
" columns = ['Total Number of Adverse Reaction Reports', 'Deaths', 'Disabilities', 'Life Threatening Illnesses', 'Severe reports'],\n",
" data = [ [2, 1, 2, 2, 2/2 * 100],\n",
" [1, 0, 0, 0, 0/1 * 100]],\n",
" columns = ['Total Number of Adverse Reaction Reports', 'Deaths', 'Disabilities', 'Life Threatening Illnesses', 'Severe reports', 'Lethality'],\n",
" data = [ [2, 1, 2, 2, 2/2 * 100, 1/2 * 100],\n",
" [1, 0, 0, 0, 0/1 * 100, 0/1 * 100]],\n",
" index = pd.Index(\n",
" [\n",
" '030L20B',\n",
@@ -1353,12 +1364,11 @@
"outputs": [],
"source": [
"def createAndSaveAndDisplayBatchCodeTableByCountry(nonDomesticVaers, country, minADRsForLethality = None):\n",
" # FK-TODO: add Lethality column\n",
" # FK-TODO: add Company column\n",
" batchCodeTable = InternationalLotTableFactory.createBatchCodeTableByCountry(nonDomesticVaers, country)\n",
" batchCodeTable.index.set_names(\"Batch\", inplace = True)\n",
" if minADRsForLethality is not None:\n",
" batchCodeTable.loc[batchCodeTable['Total Number of Adverse Reaction Reports'] < minADRsForLethality, 'Severe reports'] = np.nan\n",
" batchCodeTable.loc[batchCodeTable['Total Number of Adverse Reaction Reports'] < minADRsForLethality, ['Severe reports', 'Lethality']] = [np.nan, np.nan]\n",
" IOUtils.saveDataFrame(batchCodeTable, '../data/' + country)\n",
" display(country + \":\", batchCodeTable)\n",
"\n",