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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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data/Australia.json
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{"columns":["Batch","Total Number of Adverse Reaction Reports","Deaths","Disabilities","Life Threatening Illnesses","Severe reports"],"data":[["3002188",1,0,0,1,null],["EX2405",1,0,1,0,null],["FL350",1,0,1,0,null],["FF3438",1,0,1,0,null],["FE8163",2,0,2,0,null],["FF4222",1,0,1,0,null],["EP2163 SERIAL 1",1,1,0,0,null],["FF4206",2,0,1,0,null],["NO BATCH NUMBER",33,4,0,0,null],["UNKNOWN",58,1,4,2,null],["FA7338",1,0,0,0,null],["FE3712",1,0,0,0,null],["ER7449",1,0,0,0,null],["3006325",1,0,0,0,null],["FG1657",1,0,0,0,null],["FG3712",1,0,0,0,null],["FG7372",1,0,0,0,null],["FH3219",1,0,0,0,null],["EJ8516",1,0,0,0,null],["FL3560",1,0,0,0,null],["FN0565",1,0,0,0,null],["UNSURE",1,0,0,0,null]]} {"columns":["Batch","Total Number of Adverse Reaction Reports","Deaths","Disabilities","Life Threatening Illnesses","Severe reports","Lethality"],"data":[["3002188",1,0,0,1,null,null],["EX2405",1,0,1,0,null,null],["FL350",1,0,1,0,null,null],["FF3438",1,0,1,0,null,null],["FE8163",2,0,2,0,null,null],["FF4222",1,0,1,0,null,null],["EP2163 SERIAL 1",1,1,0,0,null,null],["FF4206",2,0,1,0,null,null],["NO BATCH NUMBER",33,4,0,0,null,null],["UNKNOWN",58,1,4,2,null,null],["FA7338",1,0,0,0,null,null],["FE3712",1,0,0,0,null,null],["ER7449",1,0,0,0,null,null],["3006325",1,0,0,0,null,null],["FG1657",1,0,0,0,null,null],["FG3712",1,0,0,0,null,null],["FG7372",1,0,0,0,null,null],["FH3219",1,0,0,0,null,null],["EJ8516",1,0,0,0,null,null],["FL3560",1,0,0,0,null,null],["FN0565",1,0,0,0,null,null],["UNSURE",1,0,0,0,null,null]]}
data/Austria.json
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data/Belgium.json
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data/France.json
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data/Germany.json
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data/Italy.json
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data/Japan.json
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data/Netherlands.json
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data/Portugal.json
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data/Spain.json
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data/Sweden.json
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data/United Kingdom.json
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internationalBatchCodeTables.html
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@@ -20,6 +20,7 @@
'Disabilities': 3, 'Disabilities': 3,
'Life Threatening Illnesses': 4, 'Life Threatening Illnesses': 4,
'Severe reports': 5, 'Severe reports': 5,
'Lethality': 6
}; };
return $('#batchCodeTable').DataTable( return $('#batchCodeTable').DataTable(
{ {
@@ -43,15 +44,16 @@
columnIndex['Deaths'], columnIndex['Deaths'],
columnIndex['Disabilities'], columnIndex['Disabilities'],
columnIndex['Life Threatening Illnesses'], columnIndex['Life Threatening Illnesses'],
columnIndex['Severe reports'] columnIndex['Severe reports'],
columnIndex['Lethality']
] ]
}, },
{ {
render: (data, type, row) => { render: (data, type, row) => {
const severeReports = parseFloat(data); const numberInPercent = parseFloat(data);
return !isNaN(severeReports) ? severeReports.toFixed(2) + " %" : ''; return !isNaN(numberInPercent) ? numberInPercent.toFixed(2) + " %" : '';
}, },
targets: [columnIndex['Severe reports']] targets: [columnIndex['Severe reports'], columnIndex['Lethality']]
} }
] ]
}); });
@@ -113,6 +115,7 @@
<th>Disabilities</th> <th>Disabilities</th>
<th>Life Threatening Illnesses</th> <th>Life Threatening Illnesses</th>
<th>Severe reports</th> <th>Severe reports</th>
<th>Lethality</th>
</tr> </tr>
</thead> </thead>
</table> </table>
src/HowBadIsMyBatch.ipynb
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@@ -213,7 +213,16 @@
" \"SEVERE_sum\": \"Severities\"\n", " \"SEVERE_sum\": \"Severities\"\n",
" })\n", " })\n",
" summationTable['Severe reports'] = summationTable['Severities'] / summationTable['Total Number of Adverse Reaction Reports'] * 100\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", " return summationTable\n",
"\n", "\n",
" @staticmethod\n", " @staticmethod\n",
@@ -1005,7 +1014,8 @@
" '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': [2/2 * 100, 1/1 * 100]\n", " 'Severe reports': [2/2 * 100, 1/1 * 100],\n",
" 'Lethality': [2/2 * 100, 1/1 * 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",
@@ -1036,7 +1046,8 @@
" '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': [2/2 * 100, 1/1 * 100]\n", " 'Severe reports': [2/2 * 100, 1/1 * 100],\n",
" 'Lethality': [2/2 * 100, 1/1 * 100]\n",
" },\n", " },\n",
" index = pd.MultiIndex.from_tuples(\n", " index = pd.MultiIndex.from_tuples(\n",
" [\n", " [\n",
@@ -1082,10 +1093,10 @@
" assert_frame_equal(\n", " assert_frame_equal(\n",
" internationalLotTable,\n", " internationalLotTable,\n",
" TestHelper.createDataFrame(\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', 'Lethality'],\n",
" data = [ [2, 2, 1, 1, 2/2 * 100],\n", " data = [ [2, 2, 1, 1, 2/2 * 100, 2/2 * 100],\n",
" [1, 1, 0, 0, 1/1 * 100],\n", " [1, 1, 0, 0, 1/1 * 100, 1/1 * 100],\n",
" [2, 0, 0, 0, 0/2 * 100]],\n", " [2, 0, 0, 0, 0/2 * 100, 0/2 * 100]],\n",
" index = pd.Index(\n", " index = pd.Index(\n",
" [\n", " [\n",
" 'France',\n", " 'France',\n",
@@ -1117,9 +1128,9 @@
" assert_frame_equal(\n", " assert_frame_equal(\n",
" batchCodeTable,\n", " batchCodeTable,\n",
" TestHelper.createDataFrame(\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', 'Lethality'],\n",
" data = [ [2, 1, 2, 2, 2/2 * 100],\n", " data = [ [2, 1, 2, 2, 2/2 * 100, 1/2 * 100],\n",
" [1, 0, 0, 0, 0/1 * 100]],\n", " [1, 0, 0, 0, 0/1 * 100, 0/1 * 100]],\n",
" index = pd.Index(\n", " index = pd.Index(\n",
" [\n", " [\n",
" '030L20B',\n", " '030L20B',\n",
@@ -1353,12 +1364,11 @@
"outputs": [], "outputs": [],
"source": [ "source": [
"def createAndSaveAndDisplayBatchCodeTableByCountry(nonDomesticVaers, country, minADRsForLethality = None):\n", "def createAndSaveAndDisplayBatchCodeTableByCountry(nonDomesticVaers, country, minADRsForLethality = None):\n",
" # FK-TODO: add Lethality column\n",
" # FK-TODO: add Company column\n", " # FK-TODO: add Company column\n",
" batchCodeTable = InternationalLotTableFactory.createBatchCodeTableByCountry(nonDomesticVaers, country)\n", " batchCodeTable = InternationalLotTableFactory.createBatchCodeTableByCountry(nonDomesticVaers, country)\n",
" batchCodeTable.index.set_names(\"Batch\", inplace = True)\n", " batchCodeTable.index.set_names(\"Batch\", inplace = True)\n",
" if minADRsForLethality is not None:\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", " IOUtils.saveDataFrame(batchCodeTable, '../data/' + country)\n",
" display(country + \":\", batchCodeTable)\n", " display(country + \":\", batchCodeTable)\n",
"\n", "\n",