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andymithamclarke/💉 VAERS 2021 | Cleaning & Joining.ipynb

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A notebook documenting the way a team at Graphext cleaned and joined data from the 2021 VAERS wave.
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💉 VAERS 2021 | Cleaning & Joining.ipynb
{
"cells": [
{
"cell_type": "markdown",
"source": "# 💉 VAERS 2021 | Cleaning & Joining",
"metadata": {
"cell_id": "00000-ec22fe00-94f1-4bd1-a363-9ab31b7b74b0",
"deepnote_cell_type": "markdown"
}
},
{
"cell_type": "markdown",
"source": "<a style='text-decoration:none;line-height:16px;display:flex;color:#5B5B62;padding:10px;justify-content:end;' href='https://www.graphext.com/post/conspiracies-complexity-and-clustering-investigating-reports-of-adverse-covid-19-vaccine-effects' target=\"_blank\">Explore the Graphext project we created with<span style='font-weight:600;margin-left:4px;'> VAERS 2021 data</span></a>",
"metadata": {
"cell_id": "00001-654a7e7e-5293-4f8e-b2a7-223c5c4f75fe",
"deepnote_cell_type": "markdown"
}
},
{
"cell_type": "markdown",
"source": "In this notebook we clean and join the three CSV files provided by VAERS on Vaccine Adverse Events reported in the USA.\n> __VAERS DATA__ - Contains information about the person, their medical history, their symptoms alongside other information included in the report that they submitted to VAERS.\n\n> __VAERS SYMPTOMS__ - Contains more precise information about the symptoms suffered.\n\n> __VAERS VAX__ - Contains information about the vaccination dose given to the person.",
"metadata": {
"cell_id": "00002-4e01f594-dceb-4ead-a501-65a9786fc12f",
"deepnote_cell_type": "markdown"
}
},
{
"cell_type": "markdown",
"source": "<a style='text-decoration:none;line-height:16px;display:flex;color:#5B5B62;padding:10px;justify-content:end;' href='https://vaers.hhs.gov/data.html' target=\"_blank\">Download the data for yourself <span style='font-weight:600;margin-left:4px;'> here</span></a>",
"metadata": {
"cell_id": "00003-530de53d-5dd8-4911-8c5e-7694f859ffc6",
"deepnote_cell_type": "markdown"
}
},
{
"cell_type": "code",
"metadata": {
"cell_id": "00004-e2e5f80d-f200-4bc9-86d7-a3f9ea7043f6",
"deepnote_to_be_reexecuted": false,
"source_hash": "ddcf1604",
"execution_start": 1621950274995,
"execution_millis": 0,
"deepnote_cell_type": "code"
},
"source": "# Module Imports \nimport pandas as pd",
"execution_count": 1,
"outputs": []
},
{
"cell_type": "code",
"metadata": {
"cell_id": "00005-a2216329-b55d-494f-80f9-d431be1d434a",
"deepnote_to_be_reexecuted": false,
"source_hash": "8d968c9",
"execution_start": 1621950274995,
"execution_millis": 1,
"deepnote_cell_type": "code"
},
"source": "# Configure pandas to display all rows and columns in a data frame\npd.set_option('display.max_rows', None)\npd.set_option('display.max_columns', None)",
"execution_count": 2,
"outputs": []
},
{
"cell_type": "code",
"metadata": {
"cell_id": "00006-5d7050b9-2393-4f82-9c21-0a0c0e8e4db7",
"deepnote_to_be_reexecuted": false,
"source_hash": "590e7e21",
"execution_start": 1621950274996,
"execution_millis": 6750,
"deepnote_cell_type": "code"
},
"source": "# Read all data files\ndf_data = pd.read_csv('2021VAERSData_Update.csv', engine='python') \ndf_symps = pd.read_csv('2021VAERSSYMPTOMS_UPDATE.csv', engine='python') \ndf_vax = pd.read_csv('2021VAERSVAX_UPDATE.csv', engine='python') ",
"execution_count": 3,
"outputs": []
},
{
"cell_type": "code",
"metadata": {
"cell_id": "00007-be271112-b955-4fba-9e0e-406119ec1f63",
"deepnote_to_be_reexecuted": false,
"source_hash": "492a0b94",
"execution_start": 1621950281802,
"execution_millis": 53,
"deepnote_cell_type": "code"
},
"source": "# Inspect the VAERS DATA data frame \ndf_data.head()",
"execution_count": 4,
"outputs": [
{
"output_type": "execute_result",
"execution_count": 4,
"data": {
"application/vnd.deepnote.dataframe.v2+json": {
"row_count": 5,
"column_count": 35,
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"name": "VAERS_ID",
"dtype": "int64",
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]
}
},
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"name": "RECVDATE",
"dtype": "object",
"stats": {
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"nan_count": 0,
"categories": [
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"count": 5
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}
},
{
"name": "STATE",
"dtype": "object",
"stats": {
"unique_count": 3,
"nan_count": 0,
"categories": [
{
"name": "TX",
"count": 2
},
{
"name": "WA",
"count": 2
},
{
"name": "CA",
"count": 1
}
]
}
},
{
"name": "AGE_YRS",
"dtype": "float64",
"stats": {
"unique_count": 5,
"nan_count": 0,
"min": "23.0",
"max": "73.0",
"histogram": [
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]
}
},
{
"name": "CAGE_MO",
"dtype": "float64",
"stats": {
"unique_count": 0,
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"min": null,
"max": null,
"histogram": [
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}
]
}
},
{
"name": "SEX",
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"stats": {
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"categories": [
{
"name": "F",
"count": 5
}
]
}
},
{
"name": "RPT_DATE",
"dtype": "object",
"stats": {
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"nan_count": 5,
"categories": [
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]
}
},
{
"name": "SYMPTOM_TEXT",
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"categories": [
{
"name": "Right side of epiglottis swelled up and hinder swallowing pictures taken Benadryl Tylenol taken",
"count": 1
},
{
"name": "Approximately 30 min post vaccination administration patient demonstrated SOB and anxiousness. Assessed at time of event: Heart sounds normal, Lung sounds clear. Vitals within normal limits for patient. O2 91% on 3 liters NC Continuous flow. 2 consecutive nebulized albuterol treatments were administered. At approximately 1.5 hours post reaction, patients' SOB and anxiousness had subsided and the patient stated that they were feel \"much better\".",
"count": 1
},
{
"name": "3 others",
"count": 3
}
]
}
},
{
"name": "DIED",
"dtype": "object",
"stats": {
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"categories": [
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]
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},
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"name": "DATEDIED",
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"stats": {
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"categories": [
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]
}
},
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"name": "L_THREAT",
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"categories": [
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]
}
},
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"categories": [
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},
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},
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]
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},
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{
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{
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]
}
},
{
"name": "ONSET_DATE",
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},
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},
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}
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},
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]
}
},
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}
},
{
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],
"rows_top": [
{
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"RECVDATE": "01/01/2021",
"STATE": "TX",
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"CAGE_YR": 33,
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"LAB_DATA": "None",
"V_ADMINBY": "PVT",
"V_FUNDBY": "nan",
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"HISTORY": "None",
"PRIOR_VAX": "nan",
"SPLTTYPE": "nan",
"FORM_VERS": 2,
"TODAYS_DATE": "01/01/2021",
"BIRTH_DEFECT": "nan",
"OFC_VISIT": "Y",
"ER_ED_VISIT": "nan",
"ALLERGIES": "Pcn and bee venom",
"_deepnote_index_column": 0
},
{
"VAERS_ID": 916601,
"RECVDATE": "01/01/2021",
"STATE": "CA",
"AGE_YRS": 73,
"CAGE_YR": 73,
"CAGE_MO": "nan",
"SEX": "F",
"RPT_DATE": "nan",
"SYMPTOM_TEXT": "Approximately 30 min post vaccination administration patient demonstrated SOB and anxiousness. Assessed at time of event: Heart sounds normal, Lung sounds clear. Vitals within normal limits for patient. O2 91% on 3 liters NC Continuous flow. 2 consecutive nebulized albuterol treatments were administered. At approximately 1.5 hours post reaction, patients' SOB and anxiousness had subsided and the patient stated that they were feel \"much better\".",
"DIED": "nan",
"DATEDIED": "nan",
"L_THREAT": "nan",
"ER_VISIT": "nan",
"HOSPITAL": "nan",
"HOSPDAYS": "nan",
"X_STAY": "nan",
"DISABLE": "nan",
"RECOVD": "Y",
"VAX_DATE": "12/31/2020",
"ONSET_DATE": "12/31/2020",
"NUMDAYS": 0,
"LAB_DATA": "nan",
"V_ADMINBY": "SEN",
"V_FUNDBY": "nan",
"OTHER_MEDS": "Patient residing at nursing facility. See patients chart.",
"CUR_ILL": "Patient residing at nursing facility. See patients chart.",
"HISTORY": "Patient residing at nursing facility. See patients chart.",
"PRIOR_VAX": "nan",
"SPLTTYPE": "nan",
"FORM_VERS": 2,
"TODAYS_DATE": "01/01/2021",
"BIRTH_DEFECT": "nan",
"OFC_VISIT": "Y",
"ER_ED_VISIT": "nan",
"ALLERGIES": "\"Dairy\"",
"_deepnote_index_column": 1
},
{
"VAERS_ID": 916602,
"RECVDATE": "01/01/2021",
"STATE": "WA",
"AGE_YRS": 23,
"CAGE_YR": 23,
"CAGE_MO": "nan",
"SEX": "F",
"RPT_DATE": "nan",
"SYMPTOM_TEXT": "About 15 minutes after receiving the vaccine, the patient complained about her left arm hurting. She also complained of chest tightness and difficulty swallowing. Patient also had vision changes. We gave the patient 1 tablet of Benadryl 25 mg and called EMS services. EMS checked her out and we advised the patient to go to the ER to be observed and given more Benadryl. Patient was able to walk out of facility herself.",
"DIED": "nan",
"DATEDIED": "nan",
"L_THREAT": "nan",
"ER_VISIT": "nan",
"HOSPITAL": "nan",
"HOSPDAYS": "nan",
"X_STAY": "nan",
"DISABLE": "nan",
"RECOVD": "U",
"VAX_DATE": "12/31/2020",
"ONSET_DATE": "12/31/2020",
"NUMDAYS": 0,
"LAB_DATA": "nan",
"V_ADMINBY": "SEN",
"V_FUNDBY": "nan",
"OTHER_MEDS": "None",
"CUR_ILL": "None",
"HISTORY": "None",
"PRIOR_VAX": "nan",
"SPLTTYPE": "nan",
"FORM_VERS": 2,
"TODAYS_DATE": "01/01/2021",
"BIRTH_DEFECT": "nan",
"OFC_VISIT": "nan",
"ER_ED_VISIT": "Y",
"ALLERGIES": "Shellfish",
"_deepnote_index_column": 2
},
{
"VAERS_ID": 916603,
"RECVDATE": "01/01/2021",
"STATE": "WA",
"AGE_YRS": 58,
"CAGE_YR": 58,
"CAGE_MO": "nan",
"SEX": "F",
"RPT_DATE": "nan",
"SYMPTOM_TEXT": "extreme fatigue, dizziness,. could not lift my left arm for 72 hours",
"DIED": "nan",
"DATEDIED": "nan",
"L_THREAT": "nan",
"ER_VISIT": "nan",
"HOSPITAL": "nan",
"HOSPDAYS": "nan",
"X_STAY": "nan",
"DISABLE": "nan",
"RECOVD": "Y",
"VAX_DATE": "12/23/2020",
"ONSET_DATE": "12/23/2020",
"NUMDAYS": 0,
"LAB_DATA": "none",
"V_ADMINBY": "WRK",
"V_FUNDBY": "nan",
"OTHER_MEDS": "none",
"CUR_ILL": "kidney infection",
"HISTORY": "diverticulitis, mitral valve prolapse, osteoarthritis",
"PRIOR_VAX": "got measles from measel shot, mums from mumps shot, headaches and nausea from flu shot",
"SPLTTYPE": "nan",
"FORM_VERS": 2,
"TODAYS_DATE": "01/01/2021",
"BIRTH_DEFECT": "nan",
"OFC_VISIT": "nan",
"ER_ED_VISIT": "nan",
"ALLERGIES": "Diclofenac, novacaine, lidocaine, pickles, tomatoes, milk",
"_deepnote_index_column": 3
},
{
"VAERS_ID": 916604,
"RECVDATE": "01/01/2021",
"STATE": "TX",
"AGE_YRS": 47,
"CAGE_YR": 47,
"CAGE_MO": "nan",
"SEX": "F",
"RPT_DATE": "nan",
"SYMPTOM_TEXT": "Injection site swelling, redness, warm to the touch and itchy",
"DIED": "nan",
"DATEDIED": "nan",
"L_THREAT": "nan",
"ER_VISIT": "nan",
"HOSPITAL": "nan",
"HOSPDAYS": "nan",
"X_STAY": "nan",
"DISABLE": "nan",
"RECOVD": "N",
"VAX_DATE": "12/22/2020",
"ONSET_DATE": "12/29/2020",
"NUMDAYS": 7,
"LAB_DATA": "nan",
"V_ADMINBY": "PUB",
"V_FUNDBY": "nan",
"OTHER_MEDS": "Na",
"CUR_ILL": "Na",
"HISTORY": "nan",
"PRIOR_VAX": "nan",
"SPLTTYPE": "nan",
"FORM_VERS": 2,
"TODAYS_DATE": "01/01/2021",
"BIRTH_DEFECT": "nan",
"OFC_VISIT": "nan",
"ER_ED_VISIT": "nan",
"ALLERGIES": "Na",
"_deepnote_index_column": 4
}
],
"rows_bottom": null
},
"text/plain": " VAERS_ID RECVDATE STATE AGE_YRS CAGE_YR CAGE_MO SEX RPT_DATE \\\n0 916600 01/01/2021 TX 33.0 33.0 NaN F NaN \n1 916601 01/01/2021 CA 73.0 73.0 NaN F NaN \n2 916602 01/01/2021 WA 23.0 23.0 NaN F NaN \n3 916603 01/01/2021 WA 58.0 58.0 NaN F NaN \n4 916604 01/01/2021 TX 47.0 47.0 NaN F NaN \n\n SYMPTOM_TEXT DIED DATEDIED L_THREAT \\\n0 Right side of epiglottis swelled up and hinder... NaN NaN NaN \n1 Approximately 30 min post vaccination administ... NaN NaN NaN \n2 About 15 minutes after receiving the vaccine, ... NaN NaN NaN \n3 extreme fatigue, dizziness,. could not lift my... NaN NaN NaN \n4 Injection site swelling, redness, warm to the ... NaN NaN NaN \n\n ER_VISIT HOSPITAL HOSPDAYS X_STAY DISABLE RECOVD VAX_DATE ONSET_DATE \\\n0 NaN NaN NaN NaN NaN Y 12/28/2020 12/30/2020 \n1 NaN NaN NaN NaN NaN Y 12/31/2020 12/31/2020 \n2 NaN NaN NaN NaN NaN U 12/31/2020 12/31/2020 \n3 NaN NaN NaN NaN NaN Y 12/23/2020 12/23/2020 \n4 NaN NaN NaN NaN NaN N 12/22/2020 12/29/2020 \n\n NUMDAYS LAB_DATA V_ADMINBY V_FUNDBY \\\n0 2.0 None PVT NaN \n1 0.0 NaN SEN NaN \n2 0.0 NaN SEN NaN \n3 0.0 none WRK NaN \n4 7.0 NaN PUB NaN \n\n OTHER_MEDS \\\n0 None \n1 Patient residing at nursing facility. See pati... \n2 None \n3 none \n4 Na \n\n CUR_ILL \\\n0 None \n1 Patient residing at nursing facility. See pati... \n2 None \n3 kidney infection \n4 Na \n\n HISTORY \\\n0 None \n1 Patient residing at nursing facility. See pati... \n2 None \n3 diverticulitis, mitral valve prolapse, osteoar... \n4 NaN \n\n PRIOR_VAX SPLTTYPE FORM_VERS \\\n0 NaN NaN 2 \n1 NaN NaN 2 \n2 NaN NaN 2 \n3 got measles from measel shot, mums from mumps ... NaN 2 \n4 NaN NaN 2 \n\n TODAYS_DATE BIRTH_DEFECT OFC_VISIT ER_ED_VISIT \\\n0 01/01/2021 NaN Y NaN \n1 01/01/2021 NaN Y NaN \n2 01/01/2021 NaN NaN Y \n3 01/01/2021 NaN NaN NaN \n4 01/01/2021 NaN NaN NaN \n\n ALLERGIES \n0 Pcn and bee venom \n1 \"Dairy\" \n2 Shellfish \n3 Diclofenac, novacaine, lidocaine, pickles, tom... \n4 Na ",
"text/html": "<div>\n<style scoped>\n .dataframe tbody tr th:only-of-type {\n vertical-align: middle;\n }\n\n .dataframe tbody tr th {\n vertical-align: top;\n }\n\n .dataframe thead th {\n text-align: right;\n }\n</style>\n<table border=\"1\" class=\"dataframe\">\n <thead>\n <tr style=\"text-align: right;\">\n <th></th>\n <th>VAERS_ID</th>\n <th>RECVDATE</th>\n <th>STATE</th>\n <th>AGE_YRS</th>\n <th>CAGE_YR</th>\n <th>CAGE_MO</th>\n <th>SEX</th>\n <th>RPT_DATE</th>\n <th>SYMPTOM_TEXT</th>\n <th>DIED</th>\n <th>DATEDIED</th>\n <th>L_THREAT</th>\n <th>ER_VISIT</th>\n <th>HOSPITAL</th>\n <th>HOSPDAYS</th>\n <th>X_STAY</th>\n <th>DISABLE</th>\n <th>RECOVD</th>\n <th>VAX_DATE</th>\n <th>ONSET_DATE</th>\n <th>NUMDAYS</th>\n <th>LAB_DATA</th>\n <th>V_ADMINBY</th>\n <th>V_FUNDBY</th>\n <th>OTHER_MEDS</th>\n <th>CUR_ILL</th>\n <th>HISTORY</th>\n <th>PRIOR_VAX</th>\n <th>SPLTTYPE</th>\n <th>FORM_VERS</th>\n <th>TODAYS_DATE</th>\n <th>BIRTH_DEFECT</th>\n <th>OFC_VISIT</th>\n <th>ER_ED_VISIT</th>\n <th>ALLERGIES</th>\n </tr>\n </thead>\n <tbody>\n <tr>\n <th>0</th>\n <td>916600</td>\n <td>01/01/2021</td>\n <td>TX</td>\n <td>33.0</td>\n <td>33.0</td>\n <td>NaN</td>\n <td>F</td>\n <td>NaN</td>\n <td>Right side of epiglottis swelled up and hinder...</td>\n <td>NaN</td>\n <td>NaN</td>\n <td>NaN</td>\n <td>NaN</td>\n <td>NaN</td>\n <td>NaN</td>\n <td>NaN</td>\n <td>NaN</td>\n <td>Y</td>\n <td>12/28/2020</td>\n <td>12/30/2020</td>\n <td>2.0</td>\n <td>None</td>\n <td>PVT</td>\n <td>NaN</td>\n <td>None</td>\n <td>None</td>\n <td>None</td>\n <td>NaN</td>\n <td>NaN</td>\n <td>2</td>\n <td>01/01/2021</td>\n <td>NaN</td>\n <td>Y</td>\n <td>NaN</td>\n <td>Pcn and bee venom</td>\n </tr>\n <tr>\n <th>1</th>\n <td>916601</td>\n <td>01/01/2021</td>\n <td>CA</td>\n <td>73.0</td>\n <td>73.0</td>\n <td>NaN</td>\n <td>F</td>\n <td>NaN</td>\n <td>Approximately 30 min post vaccination administ...</td>\n <td>NaN</td>\n <td>NaN</td>\n <td>NaN</td>\n <td>NaN</td>\n <td>NaN</td>\n <td>NaN</td>\n <td>NaN</td>\n <td>NaN</td>\n <td>Y</td>\n <td>12/31/2020</td>\n <td>12/31/2020</td>\n <td>0.0</td>\n <td>NaN</td>\n <td>SEN</td>\n <td>NaN</td>\n <td>Patient residing at nursing facility. See pati...</td>\n <td>Patient residing at nursing facility. See pati...</td>\n <td>Patient residing at nursing facility. See pati...</td>\n <td>NaN</td>\n <td>NaN</td>\n <td>2</td>\n <td>01/01/2021</td>\n <td>NaN</td>\n <td>Y</td>\n <td>NaN</td>\n <td>\"Dairy\"</td>\n </tr>\n <tr>\n <th>2</th>\n <td>916602</td>\n <td>01/01/2021</td>\n <td>WA</td>\n <td>23.0</td>\n <td>23.0</td>\n <td>NaN</td>\n <td>F</td>\n <td>NaN</td>\n <td>About 15 minutes after receiving the vaccine, ...</td>\n <td>NaN</td>\n <td>NaN</td>\n <td>NaN</td>\n <td>NaN</td>\n <td>NaN</td>\n <td>NaN</td>\n <td>NaN</td>\n <td>NaN</td>\n <td>U</td>\n <td>12/31/2020</td>\n <td>12/31/2020</td>\n <td>0.0</td>\n <td>NaN</td>\n <td>SEN</td>\n <td>NaN</td>\n <td>None</td>\n <td>None</td>\n <td>None</td>\n <td>NaN</td>\n <td>NaN</td>\n <td>2</td>\n <td>01/01/2021</td>\n <td>NaN</td>\n <td>NaN</td>\n <td>Y</td>\n <td>Shellfish</td>\n </tr>\n <tr>\n <th>3</th>\n <td>916603</td>\n <td>01/01/2021</td>\n <td>WA</td>\n <td>58.0</td>\n <td>58.0</td>\n <td>NaN</td>\n <td>F</td>\n <td>NaN</td>\n <td>extreme fatigue, dizziness,. could not lift my...</td>\n <td>NaN</td>\n <td>NaN</td>\n <td>NaN</td>\n <td>NaN</td>\n <td>NaN</td>\n <td>NaN</td>\n <td>NaN</td>\n <td>NaN</td>\n <td>Y</td>\n <td>12/23/2020</td>\n <td>12/23/2020</td>\n <td>0.0</td>\n <td>none</td>\n <td>WRK</td>\n <td>NaN</td>\n <td>none</td>\n <td>kidney infection</td>\n <td>diverticulitis, mitral valve prolapse, osteoar...</td>\n <td>got measles from measel shot, mums from mumps ...</td>\n <td>NaN</td>\n <td>2</td>\n <td>01/01/2021</td>\n <td>NaN</td>\n <td>NaN</td>\n <td>NaN</td>\n <td>Diclofenac, novacaine, lidocaine, pickles, tom...</td>\n </tr>\n <tr>\n <th>4</th>\n <td>916604</td>\n <td>01/01/2021</td>\n <td>TX</td>\n <td>47.0</td>\n <td>47.0</td>\n <td>NaN</td>\n <td>F</td>\n <td>NaN</td>\n <td>Injection site swelling, redness, warm to the ...</td>\n <td>NaN</td>\n <td>NaN</td>\n <td>NaN</td>\n <td>NaN</td>\n <td>NaN</td>\n <td>NaN</td>\n <td>NaN</td>\n <td>NaN</td>\n <td>N</td>\n <td>12/22/2020</td>\n <td>12/29/2020</td>\n <td>7.0</td>\n <td>NaN</td>\n <td>PUB</td>\n <td>NaN</td>\n <td>Na</td>\n <td>Na</td>\n <td>NaN</td>\n <td>NaN</td>\n <td>NaN</td>\n <td>2</td>\n <td>01/01/2021</td>\n <td>NaN</td>\n <td>NaN</td>\n <td>NaN</td>\n <td>Na</td>\n </tr>\n </tbody>\n</table>\n</div>"
},
"metadata": {}
}
]
},
{
"cell_type": "code",
"metadata": {
"cell_id": "00008-d5eec822-ccd0-47fc-b476-9f2640849a36",
"deepnote_to_be_reexecuted": false,
"source_hash": "518d4b55",
"execution_start": 1621950281885,
"execution_millis": 8,
"deepnote_cell_type": "code"
},
"source": "# Inspect the VAERS SYMPTOMS data frame \ndf_symps.head()",
"execution_count": 5,
"outputs": [
{
"output_type": "execute_result",
"execution_count": 5,
"data": {
"application/vnd.deepnote.dataframe.v2+json": {
"row_count": 5,
"column_count": 11,
"columns": [
{
"name": "VAERS_ID",
"dtype": "int64",
"stats": {
"unique_count": 5,
"nan_count": 0,
"min": "916600",
"max": "916604",
"histogram": [
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"count": 1
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"count": 0
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"count": 1
}
]
}
},
{
"name": "SYMPTOM1",
"dtype": "object",
"stats": {
"unique_count": 5,
"nan_count": 0,
"categories": [
{
"name": "Dysphagia",
"count": 1
},
{
"name": "Anxiety",
"count": 1
},
{
"name": "3 others",
"count": 3
}
]
}
},
{
"name": "SYMPTOMVERSION1",
"dtype": "float64",
"stats": {
"unique_count": 1,
"nan_count": 0,
"min": "23.1",
"max": "23.1",
"histogram": [
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"count": 0
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"count": 5
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"count": 0
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"count": 0
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]
}
},
{
"name": "SYMPTOM2",
"dtype": "object",
"stats": {
"unique_count": 5,
"nan_count": 0,
"categories": [
{
"name": "Epiglottitis",
"count": 1
},
{
"name": "Dyspnoea",
"count": 1
},
{
"name": "3 others",
"count": 3
}
]
}
},
{
"name": "SYMPTOMVERSION2",
"dtype": "float64",
"stats": {
"unique_count": 1,
"nan_count": 0,
"min": "23.1",
"max": "23.1",
"histogram": [
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"count": 0
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"count": 5
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"count": 0
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]
}
},
{
"name": "SYMPTOM3",
"dtype": "object",
"stats": {
"unique_count": 3,
"nan_count": 2,
"categories": [
{
"name": "Pain in extremity",
"count": 1
},
{
"name": "2 others",
"count": 2
},
{
"name": "Missing",
"count": 2
}
]
}
},
{
"name": "SYMPTOMVERSION3",
"dtype": "float64",
"stats": {
"unique_count": 1,
"nan_count": 2,
"min": "23.1",
"max": "23.1",
"histogram": [
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"bin_end": 22.700000000000003,
"count": 0
},
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"count": 0
},
{
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"count": 0
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"count": 0
},
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"count": 0
},
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"count": 3
},
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},
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]
}
},
{
"name": "SYMPTOM4",
"dtype": "object",
"stats": {
"unique_count": 2,
"nan_count": 3,
"categories": [
{
"name": "Visual impairment",
"count": 1
},
{
"name": "Injection site warmth",
"count": 1
},
{
"name": "Missing",
"count": 3
}
]
}
},
{
"name": "SYMPTOMVERSION4",
"dtype": "float64",
"stats": {
"unique_count": 1,
"nan_count": 3,
"min": "23.1",
"max": "23.1",
"histogram": [
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"bin_end": 22.700000000000003,
"count": 0
},
{
"bin_start": 22.700000000000003,
"bin_end": 22.8,
"count": 0
},
{
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"bin_end": 22.900000000000002,
"count": 0
},
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"bin_end": 23,
"count": 0
},
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"count": 0
},
{
"bin_start": 23.1,
"bin_end": 23.200000000000003,
"count": 2
},
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"count": 0
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"count": 0
},
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"count": 0
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]
}
},
{
"name": "SYMPTOM5",
"dtype": "object",
"stats": {
"unique_count": 0,
"nan_count": 5,
"categories": [
{
"name": "Missing",
"count": 5
}
]
}
},
{
"name": "SYMPTOMVERSION5",
"dtype": "float64",
"stats": {
"unique_count": 0,
"nan_count": 5,
"min": null,
"max": null,
"histogram": [
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"count": 0
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}
]
}
},
{
"name": "_deepnote_index_column",
"dtype": "int64"
}
],
"rows_top": [
{
"VAERS_ID": 916600,
"SYMPTOM1": "Dysphagia",
"SYMPTOMVERSION1": 23.1,
"SYMPTOM2": "Epiglottitis",
"SYMPTOMVERSION2": 23.1,
"SYMPTOM3": "nan",
"SYMPTOMVERSION3": "nan",
"SYMPTOM4": "nan",
"SYMPTOMVERSION4": "nan",
"SYMPTOM5": "nan",
"SYMPTOMVERSION5": "nan",
"_deepnote_index_column": 0
},
{
"VAERS_ID": 916601,
"SYMPTOM1": "Anxiety",
"SYMPTOMVERSION1": 23.1,
"SYMPTOM2": "Dyspnoea",
"SYMPTOMVERSION2": 23.1,
"SYMPTOM3": "nan",
"SYMPTOMVERSION3": "nan",
"SYMPTOM4": "nan",
"SYMPTOMVERSION4": "nan",
"SYMPTOM5": "nan",
"SYMPTOMVERSION5": "nan",
"_deepnote_index_column": 1
},
{
"VAERS_ID": 916602,
"SYMPTOM1": "Chest discomfort",
"SYMPTOMVERSION1": 23.1,
"SYMPTOM2": "Dysphagia",
"SYMPTOMVERSION2": 23.1,
"SYMPTOM3": "Pain in extremity",
"SYMPTOMVERSION3": "23.1",
"SYMPTOM4": "Visual impairment",
"SYMPTOMVERSION4": "23.1",
"SYMPTOM5": "nan",
"SYMPTOMVERSION5": "nan",
"_deepnote_index_column": 2
},
{
"VAERS_ID": 916603,
"SYMPTOM1": "Dizziness",
"SYMPTOMVERSION1": 23.1,
"SYMPTOM2": "Fatigue",
"SYMPTOMVERSION2": 23.1,
"SYMPTOM3": "Mobility decreased",
"SYMPTOMVERSION3": "23.1",
"SYMPTOM4": "nan",
"SYMPTOMVERSION4": "nan",
"SYMPTOM5": "nan",
"SYMPTOMVERSION5": "nan",
"_deepnote_index_column": 3
},
{
"VAERS_ID": 916604,
"SYMPTOM1": "Injection site erythema",
"SYMPTOMVERSION1": 23.1,
"SYMPTOM2": "Injection site pruritus",
"SYMPTOMVERSION2": 23.1,
"SYMPTOM3": "Injection site swelling",
"SYMPTOMVERSION3": "23.1",
"SYMPTOM4": "Injection site warmth",
"SYMPTOMVERSION4": "23.1",
"SYMPTOM5": "nan",
"SYMPTOMVERSION5": "nan",
"_deepnote_index_column": 4
}
],
"rows_bottom": null
},
"text/plain": " VAERS_ID SYMPTOM1 SYMPTOMVERSION1 \\\n0 916600 Dysphagia 23.1 \n1 916601 Anxiety 23.1 \n2 916602 Chest discomfort 23.1 \n3 916603 Dizziness 23.1 \n4 916604 Injection site erythema 23.1 \n\n SYMPTOM2 SYMPTOMVERSION2 SYMPTOM3 \\\n0 Epiglottitis 23.1 NaN \n1 Dyspnoea 23.1 NaN \n2 Dysphagia 23.1 Pain in extremity \n3 Fatigue 23.1 Mobility decreased \n4 Injection site pruritus 23.1 Injection site swelling \n\n SYMPTOMVERSION3 SYMPTOM4 SYMPTOMVERSION4 SYMPTOM5 \\\n0 NaN NaN NaN NaN \n1 NaN NaN NaN NaN \n2 23.1 Visual impairment 23.1 NaN \n3 23.1 NaN NaN NaN \n4 23.1 Injection site warmth 23.1 NaN \n\n SYMPTOMVERSION5 \n0 NaN \n1 NaN \n2 NaN \n3 NaN \n4 NaN ",
"text/html": "<div>\n<style scoped>\n .dataframe tbody tr th:only-of-type {\n vertical-align: middle;\n }\n\n .dataframe tbody tr th {\n vertical-align: top;\n }\n\n .dataframe thead th {\n text-align: right;\n }\n</style>\n<table border=\"1\" class=\"dataframe\">\n <thead>\n <tr style=\"text-align: right;\">\n <th></th>\n <th>VAERS_ID</th>\n <th>SYMPTOM1</th>\n <th>SYMPTOMVERSION1</th>\n <th>SYMPTOM2</th>\n <th>SYMPTOMVERSION2</th>\n <th>SYMPTOM3</th>\n <th>SYMPTOMVERSION3</th>\n <th>SYMPTOM4</th>\n <th>SYMPTOMVERSION4</th>\n <th>SYMPTOM5</th>\n <th>SYMPTOMVERSION5</th>\n </tr>\n </thead>\n <tbody>\n <tr>\n <th>0</th>\n <td>916600</td>\n <td>Dysphagia</td>\n <td>23.1</td>\n <td>Epiglottitis</td>\n <td>23.1</td>\n <td>NaN</td>\n <td>NaN</td>\n <td>NaN</td>\n <td>NaN</td>\n <td>NaN</td>\n <td>NaN</td>\n </tr>\n <tr>\n <th>1</th>\n <td>916601</td>\n <td>Anxiety</td>\n <td>23.1</td>\n <td>Dyspnoea</td>\n <td>23.1</td>\n <td>NaN</td>\n <td>NaN</td>\n <td>NaN</td>\n <td>NaN</td>\n <td>NaN</td>\n <td>NaN</td>\n </tr>\n <tr>\n <th>2</th>\n <td>916602</td>\n <td>Chest discomfort</td>\n <td>23.1</td>\n <td>Dysphagia</td>\n <td>23.1</td>\n <td>Pain in extremity</td>\n <td>23.1</td>\n <td>Visual impairment</td>\n <td>23.1</td>\n <td>NaN</td>\n <td>NaN</td>\n </tr>\n <tr>\n <th>3</th>\n <td>916603</td>\n <td>Dizziness</td>\n <td>23.1</td>\n <td>Fatigue</td>\n <td>23.1</td>\n <td>Mobility decreased</td>\n <td>23.1</td>\n <td>NaN</td>\n <td>NaN</td>\n <td>NaN</td>\n <td>NaN</td>\n </tr>\n <tr>\n <th>4</th>\n <td>916604</td>\n <td>Injection site erythema</td>\n <td>23.1</td>\n <td>Injection site pruritus</td>\n <td>23.1</td>\n <td>Injection site swelling</td>\n <td>23.1</td>\n <td>Injection site warmth</td>\n <td>23.1</td>\n <td>NaN</td>\n <td>NaN</td>\n </tr>\n </tbody>\n</table>\n</div>"
},
"metadata": {}
}
]
},
{
"cell_type": "code",
"metadata": {
"cell_id": "00009-b8fa5103-3e3d-4e43-95c0-377f66e16286",
"deepnote_to_be_reexecuted": false,
"source_hash": "9e58a8a4",
"execution_start": 1621950281913,
"execution_millis": 41,
"deepnote_cell_type": "code"
},
"source": "# Inspect the VAERS VAX data frame \ndf_vax.head()",
"execution_count": 6,
"outputs": [
{
"output_type": "execute_result",
"execution_count": 6,
"data": {
"application/vnd.deepnote.dataframe.v2+json": {
"row_count": 5,
"column_count": 8,
"columns": [
{
"name": "VAERS_ID",
"dtype": "int64",
"stats": {
"unique_count": 5,
"nan_count": 0,
"min": "916600",
"max": "916604",
"histogram": [
{
"bin_start": 916600,
"bin_end": 916600.4,
"count": 1
},
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"bin_start": 916600.4,
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"count": 0
},
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"bin_start": 916600.8,
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"count": 1
},
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"bin_start": 916601.2,
"bin_end": 916601.6,
"count": 0
},
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"bin_end": 916602,
"count": 0
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"bin_start": 916602,
"bin_end": 916602.4,
"count": 1
},
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"bin_end": 916602.8,
"count": 0
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"bin_end": 916603.2,
"count": 1
},
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"bin_start": 916603.2,
"bin_end": 916603.6,
"count": 0
},
{
"bin_start": 916603.6,
"bin_end": 916604,
"count": 1
}
]
}
},
{
"name": "VAX_TYPE",
"dtype": "object",
"stats": {
"unique_count": 1,
"nan_count": 0,
"categories": [
{
"name": "COVID19",
"count": 5
}
]
}
},
{
"name": "VAX_MANU",
"dtype": "object",
"stats": {
"unique_count": 2,
"nan_count": 0,
"categories": [
{
"name": "MODERNA",
"count": 4
},
{
"name": "PFIZER\\BIONTECH",
"count": 1
}
]
}
},
{
"name": "VAX_LOT",
"dtype": "object",
"stats": {
"unique_count": 4,
"nan_count": 1,
"categories": [
{
"name": "037K20A",
"count": 1
},
{
"name": "3 others",
"count": 3
},
{
"name": "Missing",
"count": 1
}
]
}
},
{
"name": "VAX_DOSE_SERIES",
"dtype": "object",
"stats": {
"unique_count": 2,
"nan_count": 0,
"categories": [
{
"name": "1",
"count": 4
},
{
"name": "UNK",
"count": 1
}
]
}
},
{
"name": "VAX_ROUTE",
"dtype": "object",
"stats": {
"unique_count": 1,
"nan_count": 1,
"categories": [
{
"name": "IM",
"count": 4
},
{
"name": "Missing",
"count": 1
}
]
}
},
{
"name": "VAX_SITE",
"dtype": "object",
"stats": {
"unique_count": 2,
"nan_count": 1,
"categories": [
{
"name": "LA",
"count": 3
},
{
"name": "RA",
"count": 1
},
{
"name": "Missing",
"count": 1
}
]
}
},
{
"name": "VAX_NAME",
"dtype": "object",
"stats": {
"unique_count": 2,
"nan_count": 0,
"categories": [
{
"name": "COVID19 (COVID19 (MODERNA))",
"count": 4
},
{
"name": "COVID19 (COVID19 (PFIZER-BIONTECH))",
"count": 1
}
]
}
},
{
"name": "_deepnote_index_column",
"dtype": "int64"
}
],
"rows_top": [
{
"VAERS_ID": 916600,
"VAX_TYPE": "COVID19",
"VAX_MANU": "MODERNA",
"VAX_LOT": "037K20A",
"VAX_DOSE_SERIES": "1",
"VAX_ROUTE": "IM",
"VAX_SITE": "LA",
"VAX_NAME": "COVID19 (COVID19 (MODERNA))",
"_deepnote_index_column": 0
},
{
"VAERS_ID": 916601,
"VAX_TYPE": "COVID19",
"VAX_MANU": "MODERNA",
"VAX_LOT": "025L20A",
"VAX_DOSE_SERIES": "1",
"VAX_ROUTE": "IM",
"VAX_SITE": "RA",
"VAX_NAME": "COVID19 (COVID19 (MODERNA))",
"_deepnote_index_column": 1
},
{
"VAERS_ID": 916602,
"VAX_TYPE": "COVID19",
"VAX_MANU": "PFIZER\\BIONTECH",
"VAX_LOT": "EL1284",
"VAX_DOSE_SERIES": "1",
"VAX_ROUTE": "IM",
"VAX_SITE": "LA",
"VAX_NAME": "COVID19 (COVID19 (PFIZER-BIONTECH))",
"_deepnote_index_column": 2
},
{
"VAERS_ID": 916603,
"VAX_TYPE": "COVID19",
"VAX_MANU": "MODERNA",
"VAX_LOT": "unknown",
"VAX_DOSE_SERIES": "UNK",
"VAX_ROUTE": "nan",
"VAX_SITE": "nan",
"VAX_NAME": "COVID19 (COVID19 (MODERNA))",
"_deepnote_index_column": 3
},
{
"VAERS_ID": 916604,
"VAX_TYPE": "COVID19",
"VAX_MANU": "MODERNA",
"VAX_LOT": "nan",
"VAX_DOSE_SERIES": "1",
"VAX_ROUTE": "IM",
"VAX_SITE": "LA",
"VAX_NAME": "COVID19 (COVID19 (MODERNA))",
"_deepnote_index_column": 4
}
],
"rows_bottom": null
},
"text/plain": " VAERS_ID VAX_TYPE VAX_MANU VAX_LOT VAX_DOSE_SERIES VAX_ROUTE \\\n0 916600 COVID19 MODERNA 037K20A 1 IM \n1 916601 COVID19 MODERNA 025L20A 1 IM \n2 916602 COVID19 PFIZER\\BIONTECH EL1284 1 IM \n3 916603 COVID19 MODERNA unknown UNK NaN \n4 916604 COVID19 MODERNA NaN 1 IM \n\n VAX_SITE VAX_NAME \n0 LA COVID19 (COVID19 (MODERNA)) \n1 RA COVID19 (COVID19 (MODERNA)) \n2 LA COVID19 (COVID19 (PFIZER-BIONTECH)) \n3 NaN COVID19 (COVID19 (MODERNA)) \n4 LA COVID19 (COVID19 (MODERNA)) ",
"text/html": "<div>\n<style scoped>\n .dataframe tbody tr th:only-of-type {\n vertical-align: middle;\n }\n\n .dataframe tbody tr th {\n vertical-align: top;\n }\n\n .dataframe thead th {\n text-align: right;\n }\n</style>\n<table border=\"1\" class=\"dataframe\">\n <thead>\n <tr style=\"text-align: right;\">\n <th></th>\n <th>VAERS_ID</th>\n <th>VAX_TYPE</th>\n <th>VAX_MANU</th>\n <th>VAX_LOT</th>\n <th>VAX_DOSE_SERIES</th>\n <th>VAX_ROUTE</th>\n <th>VAX_SITE</th>\n <th>VAX_NAME</th>\n </tr>\n </thead>\n <tbody>\n <tr>\n <th>0</th>\n <td>916600</td>\n <td>COVID19</td>\n <td>MODERNA</td>\n <td>037K20A</td>\n <td>1</td>\n <td>IM</td>\n <td>LA</td>\n <td>COVID19 (COVID19 (MODERNA))</td>\n </tr>\n <tr>\n <th>1</th>\n <td>916601</td>\n <td>COVID19</td>\n <td>MODERNA</td>\n <td>025L20A</td>\n <td>1</td>\n <td>IM</td>\n <td>RA</td>\n <td>COVID19 (COVID19 (MODERNA))</td>\n </tr>\n <tr>\n <th>2</th>\n <td>916602</td>\n <td>COVID19</td>\n <td>PFIZER\\BIONTECH</td>\n <td>EL1284</td>\n <td>1</td>\n <td>IM</td>\n <td>LA</td>\n <td>COVID19 (COVID19 (PFIZER-BIONTECH))</td>\n </tr>\n <tr>\n <th>3</th>\n <td>916603</td>\n <td>COVID19</td>\n <td>MODERNA</td>\n <td>unknown</td>\n <td>UNK</td>\n <td>NaN</td>\n <td>NaN</td>\n <td>COVID19 (COVID19 (MODERNA))</td>\n </tr>\n <tr>\n <th>4</th>\n <td>916604</td>\n <td>COVID19</td>\n <td>MODERNA</td>\n <td>NaN</td>\n <td>1</td>\n <td>IM</td>\n <td>LA</td>\n <td>COVID19 (COVID19 (MODERNA))</td>\n </tr>\n </tbody>\n</table>\n</div>"
},
"metadata": {}
}
]
},
{
"cell_type": "markdown",
"source": "## 🧹 Cleaning Symptoms ",
"metadata": {
"cell_id": "00010-f175d200-f9fe-4439-b389-00dfb84da5ce",
"deepnote_cell_type": "markdown"
}
},
{
"cell_type": "code",
"metadata": {
"cell_id": "00011-57da80ca-cc87-4416-a21c-9f109691ae8e",
"deepnote_to_be_reexecuted": false,
"source_hash": "be5b4f3c",
"execution_start": 1621950281921,
"execution_millis": 10,
"deepnote_cell_type": "code"
},
"source": "# Drop `Version` columns from dataframe\ndf_symps = df_symps.drop(['SYMPTOMVERSION1', 'SYMPTOMVERSION2', 'SYMPTOMVERSION3', 'SYMPTOMVERSION4', 'SYMPTOMVERSION5'], axis=1)",
"execution_count": 7,
"outputs": []
},
{
"cell_type": "code",
"metadata": {
"cell_id": "00012-30270254-a51b-4a04-9e90-5b500b094e25",
"deepnote_to_be_reexecuted": false,
"source_hash": "3b9149c5",
"execution_start": 1621950281986,
"execution_millis": 29201,
"deepnote_cell_type": "code"
},
"source": "# Populate a dictionary with every symptom belonging to a specific VAERS ID\nsymps_dict = {}\n\nfor k, v in df_symps.iterrows():\n \n if v['VAERS_ID'] in symps_dict:\n pass\n else: \n symps_dict[v['VAERS_ID']] = []\n \n if str(v['SYMPTOM1']) != 'nan':\n symps_dict[v['VAERS_ID']].append(v['SYMPTOM1'])\n \n if str(v['SYMPTOM2']) != 'nan':\n symps_dict[v['VAERS_ID']].append(v['SYMPTOM2'])\n \n if str(v['SYMPTOM3']) != 'nan':\n symps_dict[v['VAERS_ID']].append(v['SYMPTOM3'])\n \n if str(v['SYMPTOM4']) != 'nan':\n symps_dict[v['VAERS_ID']].append(v['SYMPTOM4'])\n \n if str(v['SYMPTOM5']) != 'nan':\n symps_dict[v['VAERS_ID']].append(v['SYMPTOM5'])\n",
"execution_count": 8,
"outputs": []
},
{
"cell_type": "code",
"metadata": {
"cell_id": "00013-41ae5f2a-59e4-42f8-9306-a45a746d4eac",
"deepnote_to_be_reexecuted": false,
"source_hash": "52cefa0a",
"execution_start": 1621950311393,
"execution_millis": 89,
"deepnote_cell_type": "code"
},
"source": "# Create and inspect data frame of cleaned symptoms\ndf_symps_clean = pd.DataFrame(symps_dict.items(), columns=['VAERS_ID', 'Symptoms'])\ndf_symps_clean.head()",
"execution_count": 9,
"outputs": [
{
"output_type": "execute_result",
"execution_count": 9,
"data": {
"application/vnd.deepnote.dataframe.v2+json": {
"row_count": 5,
"column_count": 2,
"columns": [
{
"name": "VAERS_ID",
"dtype": "int64",
"stats": {
"unique_count": 5,
"nan_count": 0,
"min": "916600",
"max": "916604",
"histogram": [
{
"bin_start": 916600,
"bin_end": 916600.4,
"count": 1
},
{
"bin_start": 916600.4,
"bin_end": 916600.8,
"count": 0
},
{
"bin_start": 916600.8,
"bin_end": 916601.2,
"count": 1
},
{
"bin_start": 916601.2,
"bin_end": 916601.6,
"count": 0
},
{
"bin_start": 916601.6,
"bin_end": 916602,
"count": 0
},
{
"bin_start": 916602,
"bin_end": 916602.4,
"count": 1
},
{
"bin_start": 916602.4,
"bin_end": 916602.8,
"count": 0
},
{
"bin_start": 916602.8,
"bin_end": 916603.2,
"count": 1
},
{
"bin_start": 916603.2,
"bin_end": 916603.6,
"count": 0
},
{
"bin_start": 916603.6,
"bin_end": 916604,
"count": 1
}
]
}
},
{
"name": "Symptoms",
"dtype": "object",
"stats": {
"unique_count": 5,
"nan_count": 0,
"categories": [
{
"name": "['Dysphagia', 'Epiglottitis']",
"count": 1
},
{
"name": "['Anxiety', 'Dyspnoea']",
"count": 1
},
{
"name": "3 others",
"count": 3
}
]
}
},
{
"name": "_deepnote_index_column",
"dtype": "int64"
}
],
"rows_top": [
{
"VAERS_ID": 916600,
"Symptoms": "['Dysphagia', 'Epiglottitis']",
"_deepnote_index_column": 0
},
{
"VAERS_ID": 916601,
"Symptoms": "['Anxiety', 'Dyspnoea']",
"_deepnote_index_column": 1
},
{
"VAERS_ID": 916602,
"Symptoms": "['Chest discomfort', 'Dysphagia', 'Pain in extremity', 'Visual impairment']",
"_deepnote_index_column": 2
},
{
"VAERS_ID": 916603,
"Symptoms": "['Dizziness', 'Fatigue', 'Mobility decreased']",
"_deepnote_index_column": 3
},
{
"VAERS_ID": 916604,
"Symptoms": "['Injection site erythema', 'Injection site pruritus', 'Injection site swelling', 'Injection site warmth']",
"_deepnote_index_column": 4
}
],
"rows_bottom": null
},
"text/plain": " VAERS_ID Symptoms\n0 916600 [Dysphagia, Epiglottitis]\n1 916601 [Anxiety, Dyspnoea]\n2 916602 [Chest discomfort, Dysphagia, Pain in extremit...\n3 916603 [Dizziness, Fatigue, Mobility decreased]\n4 916604 [Injection site erythema, Injection site pruri...",
"text/html": "<div>\n<style scoped>\n .dataframe tbody tr th:only-of-type {\n vertical-align: middle;\n }\n\n .dataframe tbody tr th {\n vertical-align: top;\n }\n\n .dataframe thead th {\n text-align: right;\n }\n</style>\n<table border=\"1\" class=\"dataframe\">\n <thead>\n <tr style=\"text-align: right;\">\n <th></th>\n <th>VAERS_ID</th>\n <th>Symptoms</th>\n </tr>\n </thead>\n <tbody>\n <tr>\n <th>0</th>\n <td>916600</td>\n <td>[Dysphagia, Epiglottitis]</td>\n </tr>\n <tr>\n <th>1</th>\n <td>916601</td>\n <td>[Anxiety, Dyspnoea]</td>\n </tr>\n <tr>\n <th>2</th>\n <td>916602</td>\n <td>[Chest discomfort, Dysphagia, Pain in extremit...</td>\n </tr>\n <tr>\n <th>3</th>\n <td>916603</td>\n <td>[Dizziness, Fatigue, Mobility decreased]</td>\n </tr>\n <tr>\n <th>4</th>\n <td>916604</td>\n <td>[Injection site erythema, Injection site pruri...</td>\n </tr>\n </tbody>\n</table>\n</div>"
},
"metadata": {}
}
]
},
{
"cell_type": "markdown",
"source": "## 🗜️ Join Symptoms with Data",
"metadata": {
"cell_id": "00014-b91b7c96-8d05-47b5-af23-a573f65b09ef",
"deepnote_cell_type": "markdown"
}
},
{
"cell_type": "code",
"metadata": {
"cell_id": "00015-623bd078-b0c0-415d-a982-543021732bd5",
"deepnote_to_be_reexecuted": false,
"source_hash": "dba7c70d",
"execution_start": 1621950311464,
"execution_millis": 545,
"deepnote_cell_type": "code"
},
"source": "# Merge data with symptoms\njoined_one = pd.merge(df_data, df_symps_clean, on='VAERS_ID', how='left')",
"execution_count": 10,
"outputs": []
},
{
"cell_type": "markdown",
"source": "## 🧪 Extract Dose Numbers from VAX data",
"metadata": {
"cell_id": "00016-6c09aac6-e844-4cc3-9c81-d1e538c724e4",
"deepnote_cell_type": "markdown"
}
},
{
"cell_type": "code",
"metadata": {
"cell_id": "00017-ee34292a-76c0-46b4-8422-e349097aa49f",
"deepnote_to_be_reexecuted": false,
"source_hash": "54151bb2",
"execution_start": 1621950312019,
"execution_millis": 15967,
"deepnote_cell_type": "code"
},
"source": "# Populate a dictionary with every dose number belonging to a specific VAERS ID\nvax_dose_dict = {}\n\nfor k, v in df_vax.iterrows():\n \n if v['VAERS_ID'] in vax_dose_dict:\n pass\n else: \n vax_dose_dict[v['VAERS_ID']] = []\n \n if str(v['VAX_MANU']) != 'nan':\n vax_dose_dict[v['VAERS_ID']] = v['VAX_DOSE_SERIES']",
"execution_count": 11,
"outputs": []
},
{
"cell_type": "code",
"metadata": {
"cell_id": "00018-5c4f492f-9453-4690-8f02-75e2b24a9dc0",
"deepnote_to_be_reexecuted": false,
"source_hash": "bde6bc00",
"execution_start": 1621950328009,
"execution_millis": 64,
"deepnote_cell_type": "code"
},
"source": "# Create and inspect data frame of cleaned dose numbers\ndf_vax_dose = pd.DataFrame(vax_dose_dict.items(), columns=['VAERS_ID', 'Dose Number'])\ndf_vax_dose.head()",
"execution_count": 12,
"outputs": [
{
"output_type": "execute_result",
"execution_count": 12,
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"text/plain": " VAERS_ID Dose Number\n0 916600 1\n1 916601 1\n2 916602 1\n3 916603 UNK\n4 916604 1",
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},
"metadata": {}
}
]
},
{
"cell_type": "markdown",
"source": "## 🗜️ Join Dose Numbers with Data",
"metadata": {
"cell_id": "00019-c4b41882-e7df-47f8-8a2a-d116e3c14603",
"deepnote_cell_type": "markdown"
}
},
{
"cell_type": "code",
"metadata": {
"cell_id": "00020-1952667f-9942-42d4-8128-b12b16119683",
"deepnote_to_be_reexecuted": false,
"source_hash": "3001530b",
"execution_start": 1621950328071,
"execution_millis": 146,
"deepnote_cell_type": "code"
},
"source": "# Merge data with dose numbers\njoined_2 = pd.merge(joined_one, df_vax_dose, on='VAERS_ID', how='left')",
"execution_count": 13,
"outputs": []
},
{
"cell_type": "markdown",
"source": "## 🥼 Extract Manufacturer from VAX data",
"metadata": {
"cell_id": "00021-b13b7033-ebc6-4f7c-86f8-74d63d285286",
"deepnote_cell_type": "markdown"
}
},
{
"cell_type": "code",
"metadata": {
"cell_id": "00022-9d5f1d69-e98f-403c-9e4a-0e14a304f106",
"deepnote_to_be_reexecuted": false,
"source_hash": "3238d7ad",
"execution_start": 1621950328231,
"execution_millis": 16005,
"deepnote_cell_type": "code"
},
"source": "# Populate a dictionary with every manufacturer of a dose belonging to a specific VAERS ID\n\nvax_man_dict = {}\n\nfor k, v in df_vax.iterrows():\n \n if v['VAERS_ID'] in vax_man_dict:\n pass\n else: \n vax_man_dict[v['VAERS_ID']] = []\n \n if str(v['VAX_MANU']) != 'nan':\n vax_man_dict[v['VAERS_ID']] = v['VAX_MANU']",
"execution_count": 14,
"outputs": []
},
{
"cell_type": "code",
"metadata": {
"cell_id": "00023-aa09fd8a-0569-42ea-ad1d-78b030eac37a",
"deepnote_to_be_reexecuted": false,
"source_hash": "591afe4",
"execution_start": 1621950344265,
"execution_millis": 62,
"deepnote_cell_type": "code"
},
"source": "# Create and inspect data frame of cleaned vax manufacturers\ndf_vax_man = pd.DataFrame(vax_man_dict.items(), columns=['VAERS_ID', 'Manufacturer'])\ndf_vax_man.head()",
"execution_count": 15,
"outputs": [
{
"output_type": "execute_result",
"execution_count": 15,
"data": {
"application/vnd.deepnote.dataframe.v2+json": {
"row_count": 5,
"column_count": 2,
"columns": [
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"name": "VAERS_ID",
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"text/plain": " VAERS_ID Manufacturer\n0 916600 MODERNA\n1 916601 MODERNA\n2 916602 PFIZER\\BIONTECH\n3 916603 MODERNA\n4 916604 MODERNA",
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},
"metadata": {}
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},
{
"cell_type": "markdown",
"source": "## 🗜️ Join Manufacturers with Data",
"metadata": {
"cell_id": "00024-cadb7ad0-5b81-46f9-b254-8c4c67191252",
"deepnote_cell_type": "markdown"
}
},
{
"cell_type": "code",
"metadata": {
"cell_id": "00025-ec5910c7-0058-44ed-8b6d-58343586e07c",
"deepnote_to_be_reexecuted": false,
"source_hash": "ec2b80f5",
"execution_start": 1621950344323,
"execution_millis": 121,
"deepnote_cell_type": "code"
},
"source": "joined_3 = pd.merge(joined_2, df_vax_man, on='VAERS_ID', how='left')",
"execution_count": 16,
"outputs": []
},
{
"cell_type": "markdown",
"source": "## 💊 Extract Route Method from VAX data",
"metadata": {
"cell_id": "00026-4703c8cc-d086-4661-b6f6-680cb598cd61",
"deepnote_cell_type": "markdown"
}
},
{
"cell_type": "code",
"metadata": {
"cell_id": "00027-1d260ad0-7186-49e5-97d7-a61ea001ae89",
"deepnote_to_be_reexecuted": false,
"source_hash": "c64092f0",
"execution_start": 1621950344454,
"execution_millis": 16067,
"deepnote_cell_type": "code"
},
"source": "# Populate a dictionary with every route method of a dose belonging to a specific VAERS ID\n\nvax_how_dict = {}\n\nfor k, v in df_vax.iterrows():\n \n if v['VAERS_ID'] in vax_how_dict:\n pass\n else: \n vax_how_dict[v['VAERS_ID']] = []\n \n if str(v['VAX_MANU']) != 'nan':\n vax_how_dict[v['VAERS_ID']] = v['VAX_ROUTE']",
"execution_count": 17,
"outputs": []
},
{
"cell_type": "code",
"metadata": {
"cell_id": "00028-51b9ab02-7bbe-48f5-b861-a081f72be895",
"deepnote_to_be_reexecuted": false,
"source_hash": "2ce32ba2",
"execution_start": 1621950360568,
"execution_millis": 42,
"deepnote_cell_type": "code"
},
"source": "# Create and inspect data frame of cleaned route methods\ndf_vax_how = pd.DataFrame(vax_how_dict.items(), columns=['VAERS_ID', 'Route'])\ndf_vax_how.head()",
"execution_count": 18,
"outputs": [
{
"output_type": "execute_result",
"execution_count": 18,
"data": {
"application/vnd.deepnote.dataframe.v2+json": {
"row_count": 5,
"column_count": 2,
"columns": [
{
"name": "VAERS_ID",
"dtype": "int64",
"stats": {
"unique_count": 5,
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"min": "916600",
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"histogram": [
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}
},
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"name": "Route",
"dtype": "object",
"stats": {
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"categories": [
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"name": "IM",
"count": 4
},
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"count": 1
}
]
}
},
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"dtype": "int64"
}
],
"rows_top": [
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"VAERS_ID": 916600,
"Route": "IM",
"_deepnote_index_column": 0
},
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"VAERS_ID": 916601,
"Route": "IM",
"_deepnote_index_column": 1
},
{
"VAERS_ID": 916602,
"Route": "IM",
"_deepnote_index_column": 2
},
{
"VAERS_ID": 916603,
"Route": "nan",
"_deepnote_index_column": 3
},
{
"VAERS_ID": 916604,
"Route": "IM",
"_deepnote_index_column": 4
}
],
"rows_bottom": null
},
"text/plain": " VAERS_ID Route\n0 916600 IM\n1 916601 IM\n2 916602 IM\n3 916603 NaN\n4 916604 IM",
"text/html": "<div>\n<style scoped>\n .dataframe tbody tr th:only-of-type {\n vertical-align: middle;\n }\n\n .dataframe tbody tr th {\n vertical-align: top;\n }\n\n .dataframe thead th {\n text-align: right;\n }\n</style>\n<table border=\"1\" class=\"dataframe\">\n <thead>\n <tr style=\"text-align: right;\">\n <th></th>\n <th>VAERS_ID</th>\n <th>Route</th>\n </tr>\n </thead>\n <tbody>\n <tr>\n <th>0</th>\n <td>916600</td>\n <td>IM</td>\n </tr>\n <tr>\n <th>1</th>\n <td>916601</td>\n <td>IM</td>\n </tr>\n <tr>\n <th>2</th>\n <td>916602</td>\n <td>IM</td>\n </tr>\n <tr>\n <th>3</th>\n <td>916603</td>\n <td>NaN</td>\n </tr>\n <tr>\n <th>4</th>\n <td>916604</td>\n <td>IM</td>\n </tr>\n </tbody>\n</table>\n</div>"
},
"metadata": {}
}
]
},
{
"cell_type": "markdown",
"source": "## 🗜️ Join Route Methods with Data",
"metadata": {
"cell_id": "00029-2dd4f166-288f-4052-82b6-0843211c6d7d",
"deepnote_cell_type": "markdown"
}
},
{
"cell_type": "code",
"metadata": {
"cell_id": "00030-551b6659-91be-4a0b-b275-a8a7923eca52",
"deepnote_to_be_reexecuted": false,
"source_hash": "d763d02a",
"execution_start": 1621950360607,
"execution_millis": 126,
"deepnote_cell_type": "code"
},
"source": "joined_4 = pd.merge(joined_3, df_vax_how, on='VAERS_ID', how='left')",
"execution_count": 19,
"outputs": []
},
{
"cell_type": "markdown",
"source": "## 🧽 Drop & Rename Columns",
"metadata": {
"cell_id": "00031-5c96fa59-e22f-44fa-8a3e-5b93d892f859",
"deepnote_cell_type": "markdown"
}
},
{
"cell_type": "code",
"metadata": {
"cell_id": "00032-c2cb8f30-1a23-4c31-b090-9999643338db",
"deepnote_to_be_reexecuted": false,
"source_hash": "a9d00715",
"execution_start": 1621950360741,
"execution_millis": 188,
"deepnote_cell_type": "code"
},
"source": "# Save cleaned data frame by dropping extraneous columns \ndf_clean = joined_4.drop(['RECVDATE', 'CAGE_YR', 'CAGE_MO', 'RPT_DATE', 'ER_VISIT', 'X_STAY', 'LAB_DATA', 'SPLTTYPE', 'FORM_VERS', 'TODAYS_DATE', 'BIRTH_DEFECT', 'OFC_VISIT', 'ER_ED_VISIT', 'V_FUNDBY'], axis=1)",
"execution_count": 20,
"outputs": []
},
{
"cell_type": "code",
"metadata": {
"cell_id": "00033-7a6ae7fc-7cfb-43bc-99c3-76fe8e2bca1c",
"deepnote_to_be_reexecuted": false,
"source_hash": "8c7947e3",
"execution_start": 1621950360935,
"execution_millis": 59,
"deepnote_cell_type": "code"
},
"source": "# Rename remaining columns\ndf_clean = df_clean.rename(columns={'VAERS_ID':'ID', \"STATE\": \"State\", \"AGE_YRS\": \"Age\", \"SEX\": 'Sex', \"SYMPTOM_TEXT\": \"Symptom Description\", \"DIED\": \"Died\", \"DATEDIED\": \"Date of Death\", \"L_THREAT\": \"Life-Threatening Illness\", \"HOSPITAL\": \"Hospitalized\", \"HOSPDAYS\": \"Days in Hospital\", \"DISABLE\": \"Disabled\", \"RECOVD\": \"Recovered\", \"VAX_DATE\": \"Vaccination Date\", \"ONSET_DATE\": \"Symptom Onset Date\", \"NUMDAYS\": \"Days Between Vax - Symptoms\", 'V_ADMINBY': \"Facility Type\", \"OTHER_MEDS\": \"Other Medication\", \"CUR_ILL\": \"Current Illnesses\", \"HISTORY\": \"Medical History Notes\", \"PRIOR_VAX\": \"Prior Vaccinations\", \"ALLERGIES\": \"Allergies\"})",
"execution_count": 21,
"outputs": []
},
{
"cell_type": "code",
"metadata": {
"cell_id": "00034-f154781c-337f-4a24-97c1-d17a735a2df8",
"deepnote_to_be_reexecuted": false,
"source_hash": "3d024c1",
"execution_start": 1621950360999,
"execution_millis": 80,
"deepnote_cell_type": "code"
},
"source": "# Inspect data frame\ndf_clean.tail()",
"execution_count": 22,
"outputs": [
{
"output_type": "execute_result",
"execution_count": 22,
"data": {
"application/vnd.deepnote.dataframe.v2+json": {
"row_count": 5,
"column_count": 25,
"columns": [
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"name": "ID",
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}
},
{
"name": "State",
"dtype": "object",
"stats": {
"unique_count": 2,
"nan_count": 3,
"categories": [
{
"name": "HI",
"count": 1
},
{
"name": "IL",
"count": 1
},
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"Symptom Description": "BAD FLARE UP IN EYE (SCLERITIS); Rheumatoid arthritis flare up; Cold sores; This spontaneous case was reported by a consumer and describes the occurrence of SCLERITIS (BAD FLARE UP IN EYE (SCLERITIS)) and RHEUMATOID ARTHRITIS (Rheumatoid arthritis flare up) in a 50-year-old female patient who received mRNA-1273 (Moderna COVID-19 Vaccine) for COVID-19 vaccination. The occurrence of additional non-serious events is detailed below. Co-suspect product included non-company product UPADACITINIB (RINVOQ) for Rheumatoid arthritis. Concurrent medical conditions included Arthritis. On an unknown date, the patient received second dose of mRNA-1273 (Moderna COVID-19 Vaccine) (Intramuscular) 1 dosage form On an unknown date, received first dose of mRNA-1273 (Moderna COVID-19 Vaccine) (unknown route) dosage was changed to 1 dosage form. and UPADACITINIB (RINVOQ) (Oral) at an unspecified dose. In March 2021, the patient experienced SCLERITIS (BAD FLARE UP IN EYE (SCLERITIS)) (seriousness criterion medically significant), RHEUMATOID ARTHRITIS (Rheumatoid arthritis flare up) (seriousness criterion medically significant) and ORAL HERPES (Cold sores). At the time of the report, SCLERITIS (BAD FLARE UP IN EYE (SCLERITIS)), RHEUMATOID ARTHRITIS (Rheumatoid arthritis flare up) and ORAL HERPES (Cold sores) outcome was unknown. No concomitant medication reported. No treatment information provided. Action taken with respect to mRNA-1273 was not applicable. Company comment: Very limited information regarding these events has been provided at this time. The events are probably related to the patient's comorbidities.; Sender's Comments: Very limited information regarding these events has been provided at this time. The events are probably related to the patient's comorbidities.",
"Died": "nan",
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"Symptom Description": "Heart flutter; Fever; Hurt self in the toilet/broken ribs; This spontaneous case was reported by a consumer (subsequently medically confirmed) and describes the occurrence of CARDIAC FLUTTER (Heart flutter) in a 57-year-old female patient who received mRNA-1273 (Moderna COVID-19 Vaccine) for COVID-19 vaccination. The occurrence of additional non-serious events is detailed below. Concurrent medical conditions included Plaque psoriasis. Concomitant products included RISANKIZUMAB (SKYRIZI [RISANKIZUMAB]) from 01-Mar-2021 to an unknown date for Plaque psoriasis. On 17-Mar-2021, the patient received first dose of mRNA-1273 (Moderna COVID-19 Vaccine) (Intramuscular) 1 dosage form. On 14-Apr-2021, received second dose of mRNA-1273 (Moderna COVID-19 Vaccine) (Intramuscular) dosage was changed to 1 dosage form. On 18-Apr-2021, the patient experienced RIB FRACTURE (Hurt self in the toilet/broken ribs). On an unknown date, the patient experienced CARDIAC FLUTTER (Heart flutter) (seriousness criterion medically significant) and PYREXIA (Fever). At the time of the report, CARDIAC FLUTTER (Heart flutter), RIB FRACTURE (Hurt self in the toilet/broken ribs) and PYREXIA (Fever) outcome was unknown. The patient reported after started Skyrizi, she hurt herself in the toilet. She went to the emergency room on 18-Apr-2021 as she had broken ribs and physician prescribed medication, but she could not recall name. She reported after receiving Moderna vaccine she experienced heart flutter and fever in 2021. Company comment: Very limited information regarding these events has been provided at this time. The events are probably related to the patient's comorbidities. A causal relationship cannot be excluded for the pyrexia event.; Sender's Comments: Very limited information regarding these events has been provided at this time. The events are probably related to the patient's comorbidities. A causal relationship cannot be excluded for the pyrexia event.",
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"Symptom Description": "Death; Based on the current case data, this case has been classified as invalid. This spontaneous case was reported by a consumer and describes the occurrence of DEATH (Death) in a patient of an unknown age and gender who received mRNA-1273 (Moderna COVID-19 Vaccine) for COVID-19 vaccination. No Medical History information was reported. On an unknown date, the patient received first dose of mRNA-1273 (Moderna COVID-19 Vaccine) (unknown route) 1 dosage form. On an unknown date, received second dose of mRNA-1273 (Moderna COVID-19 Vaccine) (unknown route) dosage was changed to 1 dosage form. Death occurred on an unknown date The cause of death was not reported. It is unknown if an autopsy was performed. Concomitant product use was not provided by the reporter. The reporter informed there were 2 deaths of those who had received their second dose of Moderna vaccine, same day, same location who died 2 hours after vaccine administration. Treatment information was not provided. This is a patient who received mRNA-1273 (COVID 19 Vaccine Moderna) (batch no. unk) and died after he received the second dose of vaccine. No Medical History information was reported. Concomitant product use was not provided by the reporter Very limited information has been reported at this time. Further information is expected.; Sender's Comments: This is a patient who received mRNA-1273 (COVID 19 Vaccine Moderna) (batch no. unk) and died after he received the second dose of vaccine. No Medical History information was reported. Concomitant product use was not provided by the reporter Very limited information has been reported at this time. Further information is expected.; Reported Cause(s) of Death: Unknown cause of death",
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"Died": "nan",
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"Other Medication": "I was taken narco 5/325",
"Current Illnesses": "None",
"Medical History Notes": "Back pain from disk issues",
"Prior Vaccinations": "nan",
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"text/plain": " ID State Age Sex \\\n182554 1294839 NaN 50.0 F \n182555 1294840 NaN 57.0 F \n182556 1294841 NaN NaN U \n182557 1294843 HI 34.0 M \n182558 1294855 IL 28.0 M \n\n Symptom Description Died Date of Death \\\n182554 BAD FLARE UP IN EYE (SCLERITIS); Rheumatoid ar... NaN NaN \n182555 Heart flutter; Fever; Hurt self in the toilet/... NaN NaN \n182556 Death; Based on the current case data, this ca... Y NaN \n182557 Within two hours spiked a fever too 102.00 deg... NaN NaN \n182558 Client of a group home requested to be vaccina... NaN NaN \n\n Life-Threatening Illness Hospitalized Days in Hospital Disabled \\\n182554 NaN NaN NaN NaN \n182555 NaN NaN NaN NaN \n182556 NaN NaN NaN NaN \n182557 NaN NaN NaN NaN \n182558 NaN NaN NaN NaN \n\n Recovered Vaccination Date Symptom Onset Date \\\n182554 U NaN 03/01/2021 \n182555 U 03/17/2021 04/18/2021 \n182556 N NaN NaN \n182557 N 05/05/2021 05/05/2021 \n182558 Y 05/06/2021 05/06/2021 \n\n Days Between Vax - Symptoms Facility Type Other Medication \\\n182554 NaN UNK RINVOQ \n182555 32.0 UNK SKYRIZI [RISANKIZUMAB] \n182556 NaN UNK NaN \n182557 0.0 PHM I was taken narco 5/325 \n182558 0.0 OTH NaN \n\n Current Illnesses Medical History Notes Prior Vaccinations \\\n182554 Arthritis NaN NaN \n182555 Plaque psoriasis NaN NaN \n182556 NaN NaN NaN \n182557 None Back pain from disk issues NaN \n182558 NaN NaN NaN \n\n Allergies Symptoms Dose Number \\\n182554 NaN [Oral herpes, Rheumatoid arthritis, Scleritis] 1 \n182555 NaN [Cardiac flutter, Pyrexia, Rib fracture] 2 \n182556 NaN [Death] 2 \n182557 None [Malaise, Pyrexia, Vomiting] 1 \n182558 NaN [Extra dose administered] UNK \n\n Manufacturer Route \n182554 MODERNA OT \n182555 MODERNA OT \n182556 MODERNA OT \n182557 JANSSEN SYR \n182558 JANSSEN IM ",
"text/html": "<div>\n<style scoped>\n .dataframe tbody tr th:only-of-type {\n vertical-align: middle;\n }\n\n .dataframe tbody tr th {\n vertical-align: top;\n }\n\n .dataframe thead th {\n text-align: right;\n }\n</style>\n<table border=\"1\" class=\"dataframe\">\n <thead>\n <tr style=\"text-align: right;\">\n <th></th>\n <th>ID</th>\n <th>State</th>\n <th>Age</th>\n <th>Sex</th>\n <th>Symptom Description</th>\n <th>Died</th>\n <th>Date of Death</th>\n <th>Life-Threatening Illness</th>\n <th>Hospitalized</th>\n <th>Days in Hospital</th>\n <th>Disabled</th>\n <th>Recovered</th>\n <th>Vaccination Date</th>\n <th>Symptom Onset Date</th>\n <th>Days Between Vax - Symptoms</th>\n <th>Facility Type</th>\n <th>Other Medication</th>\n <th>Current Illnesses</th>\n <th>Medical History Notes</th>\n <th>Prior Vaccinations</th>\n <th>Allergies</th>\n <th>Symptoms</th>\n <th>Dose Number</th>\n <th>Manufacturer</th>\n <th>Route</th>\n </tr>\n </thead>\n <tbody>\n <tr>\n <th>182554</th>\n <td>1294839</td>\n <td>NaN</td>\n <td>50.0</td>\n <td>F</td>\n <td>BAD FLARE UP IN EYE (SCLERITIS); Rheumatoid ar...</td>\n <td>NaN</td>\n <td>NaN</td>\n <td>NaN</td>\n <td>NaN</td>\n <td>NaN</td>\n <td>NaN</td>\n <td>U</td>\n <td>NaN</td>\n <td>03/01/2021</td>\n <td>NaN</td>\n <td>UNK</td>\n <td>RINVOQ</td>\n <td>Arthritis</td>\n <td>NaN</td>\n <td>NaN</td>\n <td>NaN</td>\n <td>[Oral herpes, Rheumatoid arthritis, Scleritis]</td>\n <td>1</td>\n <td>MODERNA</td>\n <td>OT</td>\n </tr>\n <tr>\n <th>182555</th>\n <td>1294840</td>\n <td>NaN</td>\n <td>57.0</td>\n <td>F</td>\n <td>Heart flutter; Fever; Hurt self in the toilet/...</td>\n <td>NaN</td>\n <td>NaN</td>\n <td>NaN</td>\n <td>NaN</td>\n <td>NaN</td>\n <td>NaN</td>\n <td>U</td>\n <td>03/17/2021</td>\n <td>04/18/2021</td>\n <td>32.0</td>\n <td>UNK</td>\n <td>SKYRIZI [RISANKIZUMAB]</td>\n <td>Plaque psoriasis</td>\n <td>NaN</td>\n <td>NaN</td>\n <td>NaN</td>\n <td>[Cardiac flutter, Pyrexia, Rib fracture]</td>\n <td>2</td>\n <td>MODERNA</td>\n <td>OT</td>\n </tr>\n <tr>\n <th>182556</th>\n <td>1294841</td>\n <td>NaN</td>\n <td>NaN</td>\n <td>U</td>\n <td>Death; Based on the current case data, this ca...</td>\n <td>Y</td>\n <td>NaN</td>\n <td>NaN</td>\n <td>NaN</td>\n <td>NaN</td>\n <td>NaN</td>\n <td>N</td>\n <td>NaN</td>\n <td>NaN</td>\n <td>NaN</td>\n <td>UNK</td>\n <td>NaN</td>\n <td>NaN</td>\n <td>NaN</td>\n <td>NaN</td>\n <td>NaN</td>\n <td>[Death]</td>\n <td>2</td>\n <td>MODERNA</td>\n <td>OT</td>\n </tr>\n <tr>\n <th>182557</th>\n <td>1294843</td>\n <td>HI</td>\n <td>34.0</td>\n <td>M</td>\n <td>Within two hours spiked a fever too 102.00 deg...</td>\n <td>NaN</td>\n <td>NaN</td>\n <td>NaN</td>\n <td>NaN</td>\n <td>NaN</td>\n <td>NaN</td>\n <td>N</td>\n <td>05/05/2021</td>\n <td>05/05/2021</td>\n <td>0.0</td>\n <td>PHM</td>\n <td>I was taken narco 5/325</td>\n <td>None</td>\n <td>Back pain from disk issues</td>\n <td>NaN</td>\n <td>None</td>\n <td>[Malaise, Pyrexia, Vomiting]</td>\n <td>1</td>\n <td>JANSSEN</td>\n <td>SYR</td>\n </tr>\n <tr>\n <th>182558</th>\n <td>1294855</td>\n <td>IL</td>\n <td>28.0</td>\n <td>M</td>\n <td>Client of a group home requested to be vaccina...</td>\n <td>NaN</td>\n <td>NaN</td>\n <td>NaN</td>\n <td>NaN</td>\n <td>NaN</td>\n <td>NaN</td>\n <td>Y</td>\n <td>05/06/2021</td>\n <td>05/06/2021</td>\n <td>0.0</td>\n <td>OTH</td>\n <td>NaN</td>\n <td>NaN</td>\n <td>NaN</td>\n <td>NaN</td>\n <td>NaN</td>\n <td>[Extra dose administered]</td>\n <td>UNK</td>\n <td>JANSSEN</td>\n <td>IM</td>\n </tr>\n </tbody>\n</table>\n</div>"
},
"metadata": {}
}
]
},
{
"cell_type": "markdown",
"source": "## 🚰 Fill Columns with Empty Boolean Values",
"metadata": {
"cell_id": "00035-30f46901-af9f-43f9-8a38-ff516e9fcbbf",
"deepnote_cell_type": "markdown"
}
},
{
"cell_type": "code",
"metadata": {
"cell_id": "00036-cfb2e51b-1665-4723-a8dd-1b3985493038",
"deepnote_to_be_reexecuted": false,
"source_hash": "92336e39",
"execution_start": 1621950361070,
"execution_millis": 1,
"deepnote_cell_type": "code"
},
"source": "# Define function to fill values in boolean columns\n# Yes - Y value already given in column\n# Not Reported - No value given in column\n\ndef boolean_clean(x):\n if str(x) == \"Y\":\n return \"Yes\"\n else:\n return \"Not Reported\"",
"execution_count": 23,
"outputs": []
},
{
"cell_type": "code",
"metadata": {
"cell_id": "00037-cbfc492c-003b-4618-951d-0dfac40d4864",
"deepnote_to_be_reexecuted": false,
"source_hash": "9b706327",
"execution_start": 1621950361075,
"execution_millis": 230,
"deepnote_cell_type": "code"
},
"source": "# Apply boolean_clean function to relevant columns\ndf_clean['Died'] = df_clean['Died'].apply(boolean_clean)\ndf_clean['Hospitalized'] = df_clean['Hospitalized'].apply(boolean_clean)\ndf_clean['Life-Threatening Illness'] = df_clean['Life-Threatening Illness'].apply(boolean_clean)\ndf_clean['Disabled'] = df_clean['Disabled'].apply(boolean_clean)",
"execution_count": 24,
"outputs": []
},
{
"cell_type": "code",
"metadata": {
"cell_id": "00038-8c7a8aa8-3b4a-4b2f-a3b0-2536969f887c",
"deepnote_to_be_reexecuted": false,
"source_hash": "b443e3b5",
"execution_start": 1621950361309,
"execution_millis": 3818,
"deepnote_cell_type": "code"
},
"source": "# Export data as CSV file\ndf_clean.to_csv(\"VAERS-Cleaned-Data.csv\", index=None)",
"execution_count": 25,
"outputs": []
},
{
"cell_type": "code",
"metadata": {
"cell_id": "00039-91d8bcc1-83cf-4144-acd6-b6fa342954fd",
"deepnote_to_be_reexecuted": false,
"source_hash": "d3706706",
"execution_start": 1621950365167,
"execution_millis": 44,
"deepnote_cell_type": "code"
},
"source": "# Inspect final dataframe\ndf_clean.head()",
"execution_count": 26,
"outputs": [
{
"output_type": "execute_result",
"execution_count": 26,
"data": {
"application/vnd.deepnote.dataframe.v2+json": {
"row_count": 5,
"column_count": 25,
"columns": [
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"name": "ID",
"dtype": "int64",
"stats": {
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"histogram": [
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]
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},
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"name": "State",
"dtype": "object",
"stats": {
"unique_count": 3,
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"categories": [
{
"name": "TX",
"count": 2
},
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]
}
},
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"name": "Age",
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"min": "23.0",
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},
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"name": "Sex",
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"stats": {
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"name": "Approximately 30 min post vaccination administration patient demonstrated SOB and anxiousness. Assessed at time of event: Heart sounds normal, Lung sounds clear. Vitals within normal limits for patient. O2 91% on 3 liters NC Continuous flow. 2 consecutive nebulized albuterol treatments were administered. At approximately 1.5 hours post reaction, patients' SOB and anxiousness had subsided and the patient stated that they were feel \"much better\".",
"count": 1
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{
"name": "3 others",
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},
{
"name": "Died",
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},
{
"name": "Date of Death",
"dtype": "object",
"stats": {
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"nan_count": 5,
"categories": [
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"name": "Missing",
"count": 5
}
]
}
},
{
"name": "Life-Threatening Illness",
"dtype": "object",
"stats": {
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"categories": [
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"name": "Not Reported",
"count": 5
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]
}
},
{
"name": "Hospitalized",
"dtype": "object",
"stats": {
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"nan_count": 0,
"categories": [
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"name": "Not Reported",
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]
}
},
{
"name": "Days in Hospital",
"dtype": "float64",
"stats": {
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},
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"count": 0
},
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"bin_start": 0.2,
"bin_end": 0.30000000000000004,
"count": 0
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"count": 0
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]
}
},
{
"name": "Disabled",
"dtype": "object",
"stats": {
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"categories": [
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"name": "Not Reported",
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}
]
}
},
{
"name": "Recovered",
"dtype": "object",
"stats": {
"unique_count": 3,
"nan_count": 0,
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"name": "Y",
"count": 3
},
{
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"count": 1
},
{
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}
]
}
},
{
"name": "Vaccination Date",
"dtype": "object",
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},
{
"name": "Symptom Onset Date",
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]
}
},
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"name": "Facility Type",
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"stats": {
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{
"name": "SEN",
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},
{
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"count": 1
},
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"name": "2 others",
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}
]
}
},
{
"name": "Other Medication",
"dtype": "object",
"stats": {
"unique_count": 4,
"nan_count": 0,
"categories": [
{
"name": "None",
"count": 2
},
{
"name": "Patient residing at nursing facility. See patients chart.",
"count": 1
},
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}
]
}
},
{
"name": "Current Illnesses",
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]
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"name": "Allergies",
"dtype": "object",
"stats": {
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"name": "Pcn and bee venom",
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"name": "\"Dairy\"",
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},
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],
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"Sex": "F",
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"Died": "Not Reported",
"Date of Death": "nan",
"Life-Threatening Illness": "Not Reported",
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"Prior Vaccinations": "nan",
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"Symptoms": "['Dysphagia', 'Epiglottitis']",
"Dose Number": "1",
"Manufacturer": "MODERNA",
"Route": "IM",
"_deepnote_index_column": 0
},
{
"ID": 916601,
"State": "CA",
"Age": 73,
"Sex": "F",
"Symptom Description": "Approximately 30 min post vaccination administration patient demonstrated SOB and anxiousness. Assessed at time of event: Heart sounds normal, Lung sounds clear. Vitals within normal limits for patient. O2 91% on 3 liters NC Continuous flow. 2 consecutive nebulized albuterol treatments were administered. At approximately 1.5 hours post reaction, patients' SOB and anxiousness had subsided and the patient stated that they were feel \"much better\".",
"Died": "Not Reported",
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"Facility Type": "SEN",
"Other Medication": "Patient residing at nursing facility. See patients chart.",
"Current Illnesses": "Patient residing at nursing facility. See patients chart.",
"Medical History Notes": "Patient residing at nursing facility. See patients chart.",
"Prior Vaccinations": "nan",
"Allergies": "\"Dairy\"",
"Symptoms": "['Anxiety', 'Dyspnoea']",
"Dose Number": "1",
"Manufacturer": "MODERNA",
"Route": "IM",
"_deepnote_index_column": 1
},
{
"ID": 916602,
"State": "WA",
"Age": 23,
"Sex": "F",
"Symptom Description": "About 15 minutes after receiving the vaccine, the patient complained about her left arm hurting. She also complained of chest tightness and difficulty swallowing. Patient also had vision changes. We gave the patient 1 tablet of Benadryl 25 mg and called EMS services. EMS checked her out and we advised the patient to go to the ER to be observed and given more Benadryl. Patient was able to walk out of facility herself.",
"Died": "Not Reported",
"Date of Death": "nan",
"Life-Threatening Illness": "Not Reported",
"Hospitalized": "Not Reported",
"Days in Hospital": "nan",
"Disabled": "Not Reported",
"Recovered": "U",
"Vaccination Date": "12/31/2020",
"Symptom Onset Date": "12/31/2020",
"Days Between Vax - Symptoms": 0,
"Facility Type": "SEN",
"Other Medication": "None",
"Current Illnesses": "None",
"Medical History Notes": "None",
"Prior Vaccinations": "nan",
"Allergies": "Shellfish",
"Symptoms": "['Chest discomfort', 'Dysphagia', 'Pain in extremity', 'Visual impairment']",
"Dose Number": "1",
"Manufacturer": "PFIZER\\BIONTECH",
"Route": "IM",
"_deepnote_index_column": 2
},
{
"ID": 916603,
"State": "WA",
"Age": 58,
"Sex": "F",
"Symptom Description": "extreme fatigue, dizziness,. could not lift my left arm for 72 hours",
"Died": "Not Reported",
"Date of Death": "nan",
"Life-Threatening Illness": "Not Reported",
"Hospitalized": "Not Reported",
"Days in Hospital": "nan",
"Disabled": "Not Reported",
"Recovered": "Y",
"Vaccination Date": "12/23/2020",
"Symptom Onset Date": "12/23/2020",
"Days Between Vax - Symptoms": 0,
"Facility Type": "WRK",
"Other Medication": "none",
"Current Illnesses": "kidney infection",
"Medical History Notes": "diverticulitis, mitral valve prolapse, osteoarthritis",
"Prior Vaccinations": "got measles from measel shot, mums from mumps shot, headaches and nausea from flu shot",
"Allergies": "Diclofenac, novacaine, lidocaine, pickles, tomatoes, milk",
"Symptoms": "['Dizziness', 'Fatigue', 'Mobility decreased']",
"Dose Number": "UNK",
"Manufacturer": "MODERNA",
"Route": "nan",
"_deepnote_index_column": 3
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{
"ID": 916604,
"State": "TX",
"Age": 47,
"Sex": "F",
"Symptom Description": "Injection site swelling, redness, warm to the touch and itchy",
"Died": "Not Reported",
"Date of Death": "nan",
"Life-Threatening Illness": "Not Reported",
"Hospitalized": "Not Reported",
"Days in Hospital": "nan",
"Disabled": "Not Reported",
"Recovered": "N",
"Vaccination Date": "12/22/2020",
"Symptom Onset Date": "12/29/2020",
"Days Between Vax - Symptoms": 7,
"Facility Type": "PUB",
"Other Medication": "Na",
"Current Illnesses": "Na",
"Medical History Notes": "nan",
"Prior Vaccinations": "nan",
"Allergies": "Na",
"Symptoms": "['Injection site erythema', 'Injection site pruritus', 'Injection site swelling', 'Injection site warmth']",
"Dose Number": "1",
"Manufacturer": "MODERNA",
"Route": "IM",
"_deepnote_index_column": 4
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"text/plain": " ID State Age Sex Symptom Description \\\n0 916600 TX 33.0 F Right side of epiglottis swelled up and hinder... \n1 916601 CA 73.0 F Approximately 30 min post vaccination administ... \n2 916602 WA 23.0 F About 15 minutes after receiving the vaccine, ... \n3 916603 WA 58.0 F extreme fatigue, dizziness,. could not lift my... \n4 916604 TX 47.0 F Injection site swelling, redness, warm to the ... \n\n Died Date of Death Life-Threatening Illness Hospitalized \\\n0 Not Reported NaN Not Reported Not Reported \n1 Not Reported NaN Not Reported Not Reported \n2 Not Reported NaN Not Reported Not Reported \n3 Not Reported NaN Not Reported Not Reported \n4 Not Reported NaN Not Reported Not Reported \n\n Days in Hospital Disabled Recovered Vaccination Date \\\n0 NaN Not Reported Y 12/28/2020 \n1 NaN Not Reported Y 12/31/2020 \n2 NaN Not Reported U 12/31/2020 \n3 NaN Not Reported Y 12/23/2020 \n4 NaN Not Reported N 12/22/2020 \n\n Symptom Onset Date Days Between Vax - Symptoms Facility Type \\\n0 12/30/2020 2.0 PVT \n1 12/31/2020 0.0 SEN \n2 12/31/2020 0.0 SEN \n3 12/23/2020 0.0 WRK \n4 12/29/2020 7.0 PUB \n\n Other Medication \\\n0 None \n1 Patient residing at nursing facility. See pati... \n2 None \n3 none \n4 Na \n\n Current Illnesses \\\n0 None \n1 Patient residing at nursing facility. See pati... \n2 None \n3 kidney infection \n4 Na \n\n Medical History Notes \\\n0 None \n1 Patient residing at nursing facility. See pati... \n2 None \n3 diverticulitis, mitral valve prolapse, osteoar... \n4 NaN \n\n Prior Vaccinations \\\n0 NaN \n1 NaN \n2 NaN \n3 got measles from measel shot, mums from mumps ... \n4 NaN \n\n Allergies \\\n0 Pcn and bee venom \n1 \"Dairy\" \n2 Shellfish \n3 Diclofenac, novacaine, lidocaine, pickles, tom... \n4 Na \n\n Symptoms Dose Number \\\n0 [Dysphagia, Epiglottitis] 1 \n1 [Anxiety, Dyspnoea] 1 \n2 [Chest discomfort, Dysphagia, Pain in extremit... 1 \n3 [Dizziness, Fatigue, Mobility decreased] UNK \n4 [Injection site erythema, Injection site pruri... 1 \n\n Manufacturer Route \n0 MODERNA IM \n1 MODERNA IM \n2 PFIZER\\BIONTECH IM \n3 MODERNA NaN \n4 MODERNA IM ",
"text/html": "<div>\n<style scoped>\n .dataframe tbody tr th:only-of-type {\n vertical-align: middle;\n }\n\n .dataframe tbody tr th {\n vertical-align: top;\n }\n\n .dataframe thead th {\n text-align: right;\n }\n</style>\n<table border=\"1\" class=\"dataframe\">\n <thead>\n <tr style=\"text-align: right;\">\n <th></th>\n <th>ID</th>\n <th>State</th>\n <th>Age</th>\n <th>Sex</th>\n <th>Symptom Description</th>\n <th>Died</th>\n <th>Date of Death</th>\n <th>Life-Threatening Illness</th>\n <th>Hospitalized</th>\n <th>Days in Hospital</th>\n <th>Disabled</th>\n <th>Recovered</th>\n <th>Vaccination Date</th>\n <th>Symptom Onset Date</th>\n <th>Days Between Vax - Symptoms</th>\n <th>Facility Type</th>\n <th>Other Medication</th>\n <th>Current Illnesses</th>\n <th>Medical History Notes</th>\n <th>Prior Vaccinations</th>\n <th>Allergies</th>\n <th>Symptoms</th>\n <th>Dose Number</th>\n <th>Manufacturer</th>\n <th>Route</th>\n </tr>\n </thead>\n <tbody>\n <tr>\n <th>0</th>\n <td>916600</td>\n <td>TX</td>\n <td>33.0</td>\n <td>F</td>\n <td>Right side of epiglottis swelled up and hinder...</td>\n <td>Not Reported</td>\n <td>NaN</td>\n <td>Not Reported</td>\n <td>Not Reported</td>\n <td>NaN</td>\n <td>Not Reported</td>\n <td>Y</td>\n <td>12/28/2020</td>\n <td>12/30/2020</td>\n <td>2.0</td>\n <td>PVT</td>\n <td>None</td>\n <td>None</td>\n <td>None</td>\n <td>NaN</td>\n <td>Pcn and bee venom</td>\n <td>[Dysphagia, Epiglottitis]</td>\n <td>1</td>\n <td>MODERNA</td>\n <td>IM</td>\n </tr>\n <tr>\n <th>1</th>\n <td>916601</td>\n <td>CA</td>\n <td>73.0</td>\n <td>F</td>\n <td>Approximately 30 min post vaccination administ...</td>\n <td>Not Reported</td>\n <td>NaN</td>\n <td>Not Reported</td>\n <td>Not Reported</td>\n <td>NaN</td>\n <td>Not Reported</td>\n <td>Y</td>\n <td>12/31/2020</td>\n <td>12/31/2020</td>\n <td>0.0</td>\n <td>SEN</td>\n <td>Patient residing at nursing facility. See pati...</td>\n <td>Patient residing at nursing facility. See pati...</td>\n <td>Patient residing at nursing facility. See pati...</td>\n <td>NaN</td>\n <td>\"Dairy\"</td>\n <td>[Anxiety, Dyspnoea]</td>\n <td>1</td>\n <td>MODERNA</td>\n <td>IM</td>\n </tr>\n <tr>\n <th>2</th>\n <td>916602</td>\n <td>WA</td>\n <td>23.0</td>\n <td>F</td>\n <td>About 15 minutes after receiving the vaccine, ...</td>\n <td>Not Reported</td>\n <td>NaN</td>\n <td>Not Reported</td>\n <td>Not Reported</td>\n <td>NaN</td>\n <td>Not Reported</td>\n <td>U</td>\n <td>12/31/2020</td>\n <td>12/31/2020</td>\n <td>0.0</td>\n <td>SEN</td>\n <td>None</td>\n <td>None</td>\n <td>None</td>\n <td>NaN</td>\n <td>Shellfish</td>\n <td>[Chest discomfort, Dysphagia, Pain in extremit...</td>\n <td>1</td>\n <td>PFIZER\\BIONTECH</td>\n <td>IM</td>\n </tr>\n <tr>\n <th>3</th>\n <td>916603</td>\n <td>WA</td>\n <td>58.0</td>\n <td>F</td>\n <td>extreme fatigue, dizziness,. could not lift my...</td>\n <td>Not Reported</td>\n <td>NaN</td>\n <td>Not Reported</td>\n <td>Not Reported</td>\n <td>NaN</td>\n <td>Not Reported</td>\n <td>Y</td>\n <td>12/23/2020</td>\n <td>12/23/2020</td>\n <td>0.0</td>\n <td>WRK</td>\n <td>none</td>\n <td>kidney infection</td>\n <td>diverticulitis, mitral valve prolapse, osteoar...</td>\n <td>got measles from measel shot, mums from mumps ...</td>\n <td>Diclofenac, novacaine, lidocaine, pickles, tom...</td>\n <td>[Dizziness, Fatigue, Mobility decreased]</td>\n <td>UNK</td>\n <td>MODERNA</td>\n <td>NaN</td>\n </tr>\n <tr>\n <th>4</th>\n <td>916604</td>\n <td>TX</td>\n <td>47.0</td>\n <td>F</td>\n <td>Injection site swelling, redness, warm to the ...</td>\n <td>Not Reported</td>\n <td>NaN</td>\n <td>Not Reported</td>\n <td>Not Reported</td>\n <td>NaN</td>\n <td>Not Reported</td>\n <td>N</td>\n <td>12/22/2020</td>\n <td>12/29/2020</td>\n <td>7.0</td>\n <td>PUB</td>\n <td>Na</td>\n <td>Na</td>\n <td>NaN</td>\n <td>NaN</td>\n <td>Na</td>\n <td>[Injection site erythema, Injection site pruri...</td>\n <td>1</td>\n <td>MODERNA</td>\n <td>IM</td>\n </tr>\n </tbody>\n</table>\n</div>"
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