francois/HowBadIsMyBatch
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renaming columns

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frankknoll
2022-02-13 23:48:36 +01:00
parent 7a2c136cd5
commit 1c3e207168
1 changed files with 22 additions and 22 deletions
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src/HowBadIsMyBatch.ipynb
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@@ -202,13 +202,13 @@
" summationTable = SummationTableFactory.createSummationTable(\n", " summationTable = SummationTableFactory.createSummationTable(\n",
" dataFrame,\n", " dataFrame,\n",
" columnNameMappingsDict = {\n", " columnNameMappingsDict = {\n",
" \"DIED_size\": \"Total reports\",\n", " \"DIED_size\": \"Total Number of Adverse Reaction Reports\",\n",
" \"DIED_sum\": \"Deaths\",\n", " \"DIED_sum\": \"Deaths\",\n",
" \"L_THREAT_sum\": \"Life Threatening Illnesses\",\n", " \"L_THREAT_sum\": \"Life Threatening Illnesses\",\n",
" \"DISABLE_sum\": \"Disabilities\"\n", " \"DISABLE_sum\": \"Disabilities\"\n",
" })\n", " })\n",
" summationTable['Severe reports (%)'] = (summationTable['Deaths'] + summationTable['Disabilities'] + summationTable['Life Threatening Illnesses']) / summationTable['Total reports'] * 100\n", " summationTable['Severe reports (%)'] = (summationTable['Deaths'] + summationTable['Disabilities'] + summationTable['Life Threatening Illnesses']) / summationTable['Total Number of Adverse Reaction Reports'] * 100\n",
" summationTable = summationTable[['Total reports', 'Deaths', 'Disabilities', 'Life Threatening Illnesses', 'Severe reports (%)']]\n", " summationTable = summationTable[['Total Number of Adverse Reaction Reports', 'Deaths', 'Disabilities', 'Life Threatening Illnesses', 'Severe reports (%)']]\n",
" return summationTable\n", " return summationTable\n",
"\n", "\n",
" @staticmethod\n", " @staticmethod\n",
@@ -797,11 +797,11 @@
" doseTable,\n", " doseTable,\n",
" pd.DataFrame(\n", " pd.DataFrame(\n",
" data = {\n", " data = {\n",
" 'Total reports': [2, 1],\n", " 'Total Number of Adverse Reaction Reports': [2, 1],\n",
" 'Deaths': [2, 1],\n", " 'Deaths': [2, 1],\n",
" 'Disabilities': [1, 0],\n", " 'Disabilities': [1, 0],\n",
" 'Life Threatening Illnesses': [1, 0],\n", " 'Life Threatening Illnesses': [1, 0],\n",
" 'Severe reports (%)': [(2 + 1 + 1)/2 * 100, (1 + 0 + 0)/1 * 100]\n", " 'Severe reports (%)': [(2 + 1 + 1)/2 * 100, (1 + 0 + 0)/1 * 100]\n",
" },\n", " },\n",
" index = pd.Index(['1', '2'], dtype = \"string\", name = 'Dose')))\n", " index = pd.Index(['1', '2'], dtype = \"string\", name = 'Dose')))\n",
" \n", " \n",
@@ -827,11 +827,11 @@
" doseByMonthTable,\n", " doseByMonthTable,\n",
" pd.DataFrame(\n", " pd.DataFrame(\n",
" data = {\n", " data = {\n",
" 'Total reports': [2, 1],\n", " 'Total Number of Adverse Reaction Reports': [2, 1],\n",
" 'Deaths': [2, 1],\n", " 'Deaths': [2, 1],\n",
" 'Disabilities': [1, 0],\n", " 'Disabilities': [1, 0],\n",
" 'Life Threatening Illnesses': [1, 0],\n", " 'Life Threatening Illnesses': [1, 0],\n",
" 'Severe reports (%)': [(2 + 1 + 1)/2 * 100, (1 + 0 + 0)/1 * 100]\n", " 'Severe reports (%)': [(2 + 1 + 1)/2 * 100, (1 + 0 + 0)/1 * 100]\n",
" },\n", " },\n",
" index = pd.MultiIndex.from_tuples(\n", " index = pd.MultiIndex.from_tuples(\n",
" [\n", " [\n",
@@ -876,10 +876,10 @@
" assert_frame_equal(\n", " assert_frame_equal(\n",
" internationalLotTable,\n", " internationalLotTable,\n",
" TestHelper.createDataFrame(\n", " TestHelper.createDataFrame(\n",
" columns = ['Total 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 + 1 + 1) / 2 * 100],\n", " data = [ [2, 2, 1, 1, (2 + 1 + 1) / 2 * 100],\n",
" [1, 1, 0, 0, (1 + 0 + 0) / 1 * 100],\n", " [1, 1, 0, 0, (1 + 0 + 0) / 1 * 100],\n",
" [2, 0, 0, 0, (0 + 0 + 0) / 2 * 100]],\n", " [2, 0, 0, 0, (0 + 0 + 0) / 2 * 100]],\n",
" index = pd.Index(\n", " index = pd.Index(\n",
" [\n", " [\n",
" 'France',\n", " 'France',\n",
@@ -910,9 +910,9 @@
" assert_frame_equal(\n", " assert_frame_equal(\n",
" batchCodeTable,\n", " batchCodeTable,\n",
" TestHelper.createDataFrame(\n", " TestHelper.createDataFrame(\n",
" columns = ['Total 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, (1 + 2 + 2) / 2 * 100],\n", " data = [ [2, 1, 2, 2, (1 + 2 + 2) / 2 * 100],\n",
" [1, 1, 0, 0, (1 + 0 + 0) / 1 * 100]],\n", " [1, 1, 0, 0, (1 + 0 + 0) / 1 * 100]],\n",
" index = pd.Index(\n", " index = pd.Index(\n",
" [\n", " [\n",
" '030L20B',\n", " '030L20B',\n",
@@ -1115,7 +1115,7 @@
"metadata": {}, "metadata": {},
"outputs": [], "outputs": [],
"source": [ "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", "IOUtils.saveDataFrame(internationalLotTable, 'results/international/International_Deadly_Lots')\n",
"internationalLotTable" "internationalLotTable"
] ]
@@ -1129,7 +1129,7 @@
"source": [ "source": [
"def createAndSaveAndDisplayBatchCodeTableByCountry(nonDomesticVaers, country):\n", "def createAndSaveAndDisplayBatchCodeTableByCountry(nonDomesticVaers, country):\n",
" batchCodeTable = InternationalLotTableFactory.createBatchCodeTableByCountry(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", " IOUtils.saveDataFrame(batchCodeTable, 'results/international/' + country)\n",
" display(country + \":\", batchCodeTable)\n", " display(country + \":\", batchCodeTable)\n",
"\n", "\n",