francois/HowBadIsMyBatch
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renaming a column

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frankknoll
2022-02-19 15:48:55 +01:00
parent 608f268a84
commit c9764d09a5
15 changed files with 29 additions and 25 deletions
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src/HowBadIsMyBatch.ipynb
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@@ -212,8 +212,8 @@
" \"DISABLE_sum\": \"Disabilities\",\n",
" \"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['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",
" return summationTable\n",
"\n",
" @staticmethod\n",
@@ -392,13 +392,13 @@
" def createInternationalLotTable(dataFrame):\n",
" dataFrame = DataFrameFilter().filterByCovid19(dataFrame)\n",
" internationalLotTable = InternationalLotTableFactory._createInternationalLotTable(dataFrame)\n",
" return internationalLotTable.sort_values(by = 'Severe reports (%)', ascending = False)\n",
" return internationalLotTable.sort_values(by = 'Severe reports', ascending = False)\n",
"\n",
" @staticmethod\n",
" def createBatchCodeTableByCountry(dataFrame : pd.DataFrame, country):\n",
" dataFrame = DataFrameFilter().filterByCovid19(dataFrame)\n",
" batchCodeTable = InternationalLotTableFactory._createBatchCodeTableByCountry(dataFrame, country)\n",
" return batchCodeTable.sort_values(by = 'Severe reports (%)', ascending = False)\n",
" return batchCodeTable.sort_values(by = 'Severe reports', ascending = False)\n",
"\n",
" @staticmethod\n",
" def _createInternationalLotTable(dataFrame):\n",
@@ -1005,7 +1005,7 @@
" '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",
" },\n",
" index = pd.Index(['1', '2'], dtype = \"string\", name = 'Dose')))\n",
" \n",
@@ -1036,7 +1036,7 @@
" '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",
" },\n",
" index = pd.MultiIndex.from_tuples(\n",
" [\n",
@@ -1082,7 +1082,7 @@
" assert_frame_equal(\n",
" internationalLotTable,\n",
" TestHelper.createDataFrame(\n",
" columns = ['Total Number of Adverse Reaction Reports', 'Deaths', 'Disabilities', 'Life Threatening Illnesses', 'Severe reports (%)'],\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",
@@ -1117,7 +1117,7 @@
" assert_frame_equal(\n",
" batchCodeTable,\n",
" TestHelper.createDataFrame(\n",
" columns = ['Total Number of Adverse Reaction Reports', 'Deaths', 'Disabilities', 'Life Threatening Illnesses', 'Severe reports (%)'],\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",
" index = pd.Index(\n",
@@ -1353,10 +1353,12 @@
"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'] = np.nan\n",
" IOUtils.saveDataFrame(batchCodeTable, '../data/' + country)\n",
" display(country + \":\", batchCodeTable)\n",
"\n",
@@ -1374,6 +1376,7 @@
"source": [
"createAndSaveAndDisplayBatchCodeTablesByCountry(\n",
" nonDomesticVaers,\n",
" # FK-TODO: create BatchCodeTables for all available countries\n",
" [\n",
" 'United Kingdom',\n",
" 'France',\n",