diff --git a/src/HowBadIsMyBatch.ipynb b/src/HowBadIsMyBatch.ipynb index fa16e57ea61..2feb0b0ffc2 100644 --- a/src/HowBadIsMyBatch.ipynb +++ b/src/HowBadIsMyBatch.ipynb @@ -202,13 +202,13 @@ " summationTable = SummationTableFactory.createSummationTable(\n", " dataFrame,\n", " columnNameMappingsDict = {\n", - " \"DIED_size\": \"Total reports\",\n", + " \"DIED_size\": \"Total Number of Adverse Reaction Reports\",\n", " \"DIED_sum\": \"Deaths\",\n", " \"L_THREAT_sum\": \"Life Threatening Illnesses\",\n", " \"DISABLE_sum\": \"Disabilities\"\n", " })\n", - " summationTable['Severe reports (%)'] = (summationTable['Deaths'] + summationTable['Disabilities'] + summationTable['Life Threatening Illnesses']) / summationTable['Total reports'] * 100\n", - " summationTable = summationTable[['Total reports', 'Deaths', 'Disabilities', 'Life Threatening Illnesses', 'Severe reports (%)']]\n", + " summationTable['Severe reports (%)'] = (summationTable['Deaths'] + summationTable['Disabilities'] + summationTable['Life Threatening Illnesses']) / 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", @@ -797,11 +797,11 @@ " doseTable,\n", " pd.DataFrame(\n", " data = {\n", - " 'Total reports': [2, 1],\n", - " 'Deaths': [2, 1],\n", - " 'Disabilities': [1, 0],\n", - " 'Life Threatening Illnesses': [1, 0],\n", - " 'Severe reports (%)': [(2 + 1 + 1)/2 * 100, (1 + 0 + 0)/1 * 100]\n", + " 'Total Number of Adverse Reaction Reports': [2, 1],\n", + " 'Deaths': [2, 1],\n", + " 'Disabilities': [1, 0],\n", + " 'Life Threatening Illnesses': [1, 0],\n", + " 'Severe reports (%)': [(2 + 1 + 1)/2 * 100, (1 + 0 + 0)/1 * 100]\n", " },\n", " index = pd.Index(['1', '2'], dtype = \"string\", name = 'Dose')))\n", " \n", @@ -827,11 +827,11 @@ " doseByMonthTable,\n", " pd.DataFrame(\n", " data = {\n", - " 'Total reports': [2, 1],\n", - " 'Deaths': [2, 1],\n", - " 'Disabilities': [1, 0],\n", - " 'Life Threatening Illnesses': [1, 0],\n", - " 'Severe reports (%)': [(2 + 1 + 1)/2 * 100, (1 + 0 + 0)/1 * 100]\n", + " 'Total Number of Adverse Reaction Reports': [2, 1],\n", + " 'Deaths': [2, 1],\n", + " 'Disabilities': [1, 0],\n", + " 'Life Threatening Illnesses': [1, 0],\n", + " 'Severe reports (%)': [(2 + 1 + 1)/2 * 100, (1 + 0 + 0)/1 * 100]\n", " },\n", " index = pd.MultiIndex.from_tuples(\n", " [\n", @@ -876,10 +876,10 @@ " assert_frame_equal(\n", " internationalLotTable,\n", " TestHelper.createDataFrame(\n", - " columns = ['Total reports', 'Deaths', 'Disabilities', 'Life Threatening Illnesses', 'Severe reports (%)'],\n", - " data = [ [2, 2, 1, 1, (2 + 1 + 1) / 2 * 100],\n", - " [1, 1, 0, 0, (1 + 0 + 0) / 1 * 100],\n", - " [2, 0, 0, 0, (0 + 0 + 0) / 2 * 100]],\n", + " columns = ['Total Number of Adverse Reaction Reports', 'Deaths', 'Disabilities', 'Life Threatening Illnesses', 'Severe reports (%)'],\n", + " data = [ [2, 2, 1, 1, (2 + 1 + 1) / 2 * 100],\n", + " [1, 1, 0, 0, (1 + 0 + 0) / 1 * 100],\n", + " [2, 0, 0, 0, (0 + 0 + 0) / 2 * 100]],\n", " index = pd.Index(\n", " [\n", " 'France',\n", @@ -910,9 +910,9 @@ " assert_frame_equal(\n", " batchCodeTable,\n", " TestHelper.createDataFrame(\n", - " columns = ['Total reports', 'Deaths', 'Disabilities', 'Life Threatening Illnesses', 'Severe reports (%)'],\n", - " data = [ [2, 1, 2, 2, (1 + 2 + 2) / 2 * 100],\n", - " [1, 1, 0, 0, (1 + 0 + 0) / 1 * 100]],\n", + " columns = ['Total Number of Adverse Reaction Reports', 'Deaths', 'Disabilities', 'Life Threatening Illnesses', 'Severe reports (%)'],\n", + " data = [ [2, 1, 2, 2, (1 + 2 + 2) / 2 * 100],\n", + " [1, 1, 0, 0, (1 + 0 + 0) / 1 * 100]],\n", " index = pd.Index(\n", " [\n", " '030L20B',\n", @@ -1115,7 +1115,7 @@ "metadata": {}, "outputs": [], "source": [ - "internationalLotTable = internationalLotTable[internationalLotTable['Total reports'] > 50]\n", + "internationalLotTable = internationalLotTable[internationalLotTable['Total Number of Adverse Reaction Reports'] > 50]\n", "IOUtils.saveDataFrame(internationalLotTable, 'results/international/International_Deadly_Lots')\n", "internationalLotTable" ] @@ -1129,7 +1129,7 @@ "source": [ "def createAndSaveAndDisplayBatchCodeTableByCountry(nonDomesticVaers, country):\n", " batchCodeTable = InternationalLotTableFactory.createBatchCodeTableByCountry(nonDomesticVaers, country)\n", - " batchCodeTable = batchCodeTable[batchCodeTable['Total reports'] > 50]\n", + " batchCodeTable = batchCodeTable[batchCodeTable['Total Number of Adverse Reaction Reports'] > 50]\n", " IOUtils.saveDataFrame(batchCodeTable, 'results/international/' + country)\n", " display(country + \":\", batchCodeTable)\n", "\n",