diff --git a/.gitignore b/.gitignore new file mode 100644 index 00000000000..14e15ff4fc7 --- /dev/null +++ b/.gitignore @@ -0,0 +1,2 @@ +VAERS/ +.ipynb_checkpoints/ \ No newline at end of file diff --git a/HowBadIsMyBatch.ipynb b/HowBadIsMyBatch.ipynb index c5e3db712b7..c24b568f82e 100644 --- a/HowBadIsMyBatch.ipynb +++ b/HowBadIsMyBatch.ipynb @@ -2,20 +2,20 @@ "cells": [ { "cell_type": "code", - "execution_count": 3, + "execution_count": null, "id": "9de5907f-18f5-4cb1-903e-26028ff1fa03", "metadata": {}, "outputs": [], "source": [ "import numpy as np\n", "import pandas as pd\n", - "pd.set_option('display.max_rows', 10)\n", + "pd.set_option('display.max_rows', 100)\n", "pd.set_option('display.max_columns', None)" ] }, { "cell_type": "code", - "execution_count": 4, + "execution_count": null, "id": "ad0e6044", "metadata": {}, "outputs": [], @@ -25,680 +25,10 @@ }, { "cell_type": "code", - "execution_count": 5, + "execution_count": null, "id": "4472e902", "metadata": {}, - "outputs": [ - { - "data": { - "text/html": [ - "
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RECVDATESTATEAGE_YRSCAGE_YRCAGE_MOSEXRPT_DATESYMPTOM_TEXTDIEDDATEDIEDL_THREATER_VISITHOSPITALHOSPDAYSX_STAYDISABLERECOVDVAX_DATEONSET_DATENUMDAYSLAB_DATAV_ADMINBYV_FUNDBYOTHER_MEDSCUR_ILLHISTORYPRIOR_VAXSPLTTYPEFORM_VERSTODAYS_DATEBIRTH_DEFECTOFC_VISITER_ED_VISITALLERGIES
VAERS_ID
91660001/01/2021TX33.033.0NaNFNaNRight side of epiglottis swelled up and hinder...NaNNaNNaNNaNNaNNaNNaNNaNY12/28/202012/30/20202.0NonePVTNaNNoneNoneNoneNaNNaN201/01/2021NaNYNaNPcn and bee venom
91660101/01/2021CA73.073.0NaNFNaNApproximately 30 min post vaccination administ...NaNNaNNaNNaNNaNNaNNaNNaNY12/31/202012/31/20200.0NaNSENNaNPatient residing at nursing facility. See pati...Patient residing at nursing facility. See pati...Patient residing at nursing facility. See pati...NaNNaN201/01/2021NaNYNaN\"Dairy\"
91660201/01/2021WA23.023.0NaNFNaNAbout 15 minutes after receiving the vaccine, ...NaNNaNNaNNaNNaNNaNNaNNaNU12/31/202012/31/20200.0NaNSENNaNNoneNoneNoneNaNNaN201/01/2021NaNNaNYShellfish
91660301/01/2021WA58.058.0NaNFNaNextreme fatigue, dizziness,. could not lift my...NaNNaNNaNNaNNaNNaNNaNNaNY12/23/202012/23/20200.0noneWRKNaNnonekidney infectiondiverticulitis, mitral valve prolapse, osteoar...got measles from measel shot, mums from mumps ...NaN201/01/2021NaNNaNNaNDiclofenac, novacaine, lidocaine, pickles, tom...
91660401/01/2021TX47.047.0NaNFNaNInjection site swelling, redness, warm to the ...NaNNaNNaNNaNNaNNaNNaNNaNN12/22/202012/29/20207.0NaNPUBNaNNaNaNaNNaNNaN201/01/2021NaNNaNNaNNa
.........................................................................................................
199712012/31/2021ID56.056.0NaNMNaNI had symptoms of low level un-diagnosed kidn...NaNNaNNaNNaNNaNNaNNaNNaNY11/28/202111/30/20212.0lab test for UTIUNKNaNnoneun-diagnosed kidney infectionnoneNaNNaN212/31/2021NaNYNaNnone
199712112/31/2021OH69.069.0NaNMNaNI got very bad eczema after first shot. Then i...NaNNaNNaNNaNNaNNaNNaNNaNN02/26/202103/04/20216.0went to my doctor he said I have eczema. Gave...PHMNaNb12 and d3 vitaminsNaNhypothyroidNaNNaN212/31/2021NaNNaNNaNpenicillin, statin drugs, codeine
199712212/31/2021NV50.050.0NaNMNaNHives all over the body and swelling of the li...NaNNaNNaNNaNNaNNaNNaNNaNU09/04/202110/01/202127.0NaNPHMNaNNaNNoneNoneNaNNaN212/31/2021NaNNaNNaNNone
199866812/31/2021SCNaNNaNNaNFNaNArm tendernessNaNNaNNaNNaNNaNNaNNaNNaNYNaNNaNNaNNaNPVTNaNNaNNaNNaNNaNNaN212/31/2021NaNNaNNaNNaN
199866912/31/2021CA59.059.0NaNMNaNCan't get up, all joints hurt States he is in ...NaNNaNNaNNaNNaNNaNNaNNaNN04/29/202105/05/20216.0Blood test.PVTNaNNaNNaNNaNNaNNaN207/07/2021NaNYNaNNKA
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749067 rows × 34 columns

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" - ], - "text/plain": [ - " RECVDATE STATE AGE_YRS CAGE_YR CAGE_MO SEX RPT_DATE \\\n", - "VAERS_ID \n", - "916600 01/01/2021 TX 33.0 33.0 NaN F NaN \n", - "916601 01/01/2021 CA 73.0 73.0 NaN F NaN \n", - "916602 01/01/2021 WA 23.0 23.0 NaN F NaN \n", - "916603 01/01/2021 WA 58.0 58.0 NaN F NaN \n", - "916604 01/01/2021 TX 47.0 47.0 NaN F NaN \n", - "... ... ... ... ... ... .. ... \n", - "1997120 12/31/2021 ID 56.0 56.0 NaN M NaN \n", - "1997121 12/31/2021 OH 69.0 69.0 NaN M NaN \n", - "1997122 12/31/2021 NV 50.0 50.0 NaN M NaN \n", - "1998668 12/31/2021 SC NaN NaN NaN F NaN \n", - "1998669 12/31/2021 CA 59.0 59.0 NaN M NaN \n", - "\n", - " SYMPTOM_TEXT DIED DATEDIED \\\n", - "VAERS_ID \n", - "916600 Right side of epiglottis swelled up and hinder... NaN NaN \n", - "916601 Approximately 30 min post vaccination administ... NaN NaN \n", - "916602 About 15 minutes after receiving the vaccine, ... NaN NaN \n", - "916603 extreme fatigue, dizziness,. could not lift my... NaN NaN \n", - "916604 Injection site swelling, redness, warm to the ... NaN NaN \n", - "... ... ... ... \n", - "1997120 I had symptoms of low level un-diagnosed kidn... NaN NaN \n", - "1997121 I got very bad eczema after first shot. Then i... NaN NaN \n", - "1997122 Hives all over the body and swelling of the li... NaN NaN \n", - "1998668 Arm tenderness NaN NaN \n", - "1998669 Can't get up, all joints hurt States he is in ... NaN NaN \n", - "\n", - " L_THREAT ER_VISIT HOSPITAL HOSPDAYS X_STAY DISABLE RECOVD \\\n", - "VAERS_ID \n", - "916600 NaN NaN NaN NaN NaN NaN Y \n", - "916601 NaN NaN NaN NaN NaN NaN Y \n", - "916602 NaN NaN NaN NaN NaN NaN U \n", - "916603 NaN NaN NaN NaN NaN NaN Y \n", - "916604 NaN NaN NaN NaN NaN NaN N \n", - "... ... ... ... ... ... ... ... \n", - "1997120 NaN NaN NaN NaN NaN NaN Y \n", - "1997121 NaN NaN NaN NaN NaN NaN N \n", - "1997122 NaN NaN NaN NaN NaN NaN U \n", - "1998668 NaN NaN NaN NaN NaN NaN Y \n", - "1998669 NaN NaN NaN NaN NaN NaN N \n", - "\n", - " VAX_DATE ONSET_DATE NUMDAYS \\\n", - "VAERS_ID \n", - "916600 12/28/2020 12/30/2020 2.0 \n", - "916601 12/31/2020 12/31/2020 0.0 \n", - "916602 12/31/2020 12/31/2020 0.0 \n", - "916603 12/23/2020 12/23/2020 0.0 \n", - "916604 12/22/2020 12/29/2020 7.0 \n", - "... ... ... ... \n", - "1997120 11/28/2021 11/30/2021 2.0 \n", - "1997121 02/26/2021 03/04/2021 6.0 \n", - "1997122 09/04/2021 10/01/2021 27.0 \n", - "1998668 NaN NaN NaN \n", - "1998669 04/29/2021 05/05/2021 6.0 \n", - "\n", - " LAB_DATA V_ADMINBY \\\n", - "VAERS_ID \n", - "916600 None PVT \n", - "916601 NaN SEN \n", - "916602 NaN SEN \n", - "916603 none WRK \n", - "916604 NaN PUB \n", - "... ... ... \n", - "1997120 lab test for UTI UNK \n", - "1997121 went to my doctor he said I have eczema. Gave... PHM \n", - "1997122 NaN PHM \n", - "1998668 NaN PVT \n", - "1998669 Blood test. PVT \n", - "\n", - " V_FUNDBY OTHER_MEDS \\\n", - "VAERS_ID \n", - "916600 NaN None \n", - "916601 NaN Patient residing at nursing facility. See pati... \n", - "916602 NaN None \n", - "916603 NaN none \n", - "916604 NaN Na \n", - "... ... ... \n", - "1997120 NaN none \n", - "1997121 NaN b12 and d3 vitamins \n", - "1997122 NaN NaN \n", - "1998668 NaN NaN \n", - "1998669 NaN NaN \n", - "\n", - " CUR_ILL \\\n", - "VAERS_ID \n", - "916600 None \n", - "916601 Patient residing at nursing facility. See pati... \n", - "916602 None \n", - "916603 kidney infection \n", - "916604 Na \n", - "... ... \n", - "1997120 un-diagnosed kidney infection \n", - "1997121 NaN \n", - "1997122 None \n", - "1998668 NaN \n", - "1998669 NaN \n", - "\n", - " HISTORY \\\n", - "VAERS_ID \n", - "916600 None \n", - "916601 Patient residing at nursing facility. See pati... \n", - "916602 None \n", - "916603 diverticulitis, mitral valve prolapse, osteoar... \n", - "916604 NaN \n", - "... ... \n", - "1997120 none \n", - "1997121 hypothyroid \n", - "1997122 None \n", - "1998668 NaN \n", - "1998669 NaN \n", - "\n", - " PRIOR_VAX SPLTTYPE \\\n", - "VAERS_ID \n", - "916600 NaN NaN \n", - "916601 NaN NaN \n", - "916602 NaN NaN \n", - "916603 got measles from measel shot, mums from mumps ... NaN \n", - "916604 NaN NaN \n", - "... ... ... \n", - "1997120 NaN NaN \n", - "1997121 NaN NaN \n", - "1997122 NaN NaN \n", - "1998668 NaN NaN \n", - "1998669 NaN NaN \n", - "\n", - " FORM_VERS TODAYS_DATE BIRTH_DEFECT OFC_VISIT ER_ED_VISIT \\\n", - "VAERS_ID \n", - "916600 2 01/01/2021 NaN Y NaN \n", - "916601 2 01/01/2021 NaN Y NaN \n", - "916602 2 01/01/2021 NaN NaN Y \n", - "916603 2 01/01/2021 NaN NaN NaN \n", - "916604 2 01/01/2021 NaN NaN NaN \n", - "... ... ... ... ... ... \n", - "1997120 2 12/31/2021 NaN Y NaN \n", - "1997121 2 12/31/2021 NaN NaN NaN \n", - "1997122 2 12/31/2021 NaN NaN NaN \n", - "1998668 2 12/31/2021 NaN NaN NaN \n", - "1998669 2 07/07/2021 NaN Y NaN \n", - "\n", - " ALLERGIES \n", - "VAERS_ID \n", - "916600 Pcn and bee venom \n", - "916601 \"Dairy\" \n", - "916602 Shellfish \n", - "916603 Diclofenac, novacaine, lidocaine, pickles, tom... \n", - "916604 Na \n", - "... ... \n", - "1997120 none \n", - "1997121 penicillin, statin drugs, codeine \n", - "1997122 None \n", - "1998668 NaN \n", - "1998669 NKA \n", - "\n", - "[749067 rows x 34 columns]" - ] - }, - "execution_count": 5, - "metadata": {}, - "output_type": "execute_result" - } - ], + "outputs": [], "source": [ "df_patients_22.index\n", "df_patients_22" @@ -706,7 +36,7 @@ }, { "cell_type": "code", - "execution_count": 6, + "execution_count": null, "id": "fb54ec47", "metadata": {}, "outputs": [], @@ -716,212 +46,19 @@ }, { "cell_type": "code", - "execution_count": 7, + "execution_count": null, "id": "d8942466", "metadata": { - "scrolled": false + "scrolled": true }, - "outputs": [ - { - "data": { - "text/html": [ - "
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VAX_TYPEVAX_MANUVAX_LOTVAX_DOSE_SERIESVAX_ROUTEVAX_SITEVAX_NAME
VAERS_ID
916600COVID19MODERNA037K20A1IMLACOVID19 (COVID19 (MODERNA))
916601COVID19MODERNA025L20A1IMRACOVID19 (COVID19 (MODERNA))
916602COVID19PFIZER\\BIONTECHEL12841IMLACOVID19 (COVID19 (PFIZER-BIONTECH))
916603COVID19MODERNAunknownUNKNaNNaNCOVID19 (COVID19 (MODERNA))
916604COVID19MODERNANaN1IMLACOVID19 (COVID19 (MODERNA))
........................
2013746HIBVMERCK & CO. INC.T026960UNKIMLLHIB (PEDVAXHIB)
2013746PNC13PFIZER\\WYETHDR1779UNKIMLLPNEUMO (PREVNAR13)
2013746RV5MERCK & CO. INC.1742458UNKPOMOROTAVIRUS (ROTATEQ)
2013757DTAPIPVGLAXOSMITHKLINE BIOLOGICALS7P5J51IMLADTAP + IPV (KINRIX)
2013757MMRVMERCK & CO. INC.T0271111SCLAMEASLES + MUMPS + RUBELLA + VARICELLA (PROQUAD)
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793346 rows × 7 columns

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916600COVID19MODERNA037K20A1IMLACOVID19 (COVID19 (MODERNA))
916601COVID19MODERNA025L20A1IMRACOVID19 (COVID19 (MODERNA))
916602COVID19PFIZER\\BIONTECHEL12841IMLACOVID19 (COVID19 (PFIZER-BIONTECH))
916603COVID19MODERNAunknownUNKNaNNaNCOVID19 (COVID19 (MODERNA))
916604COVID19MODERNANaN1IMLACOVID19 (COVID19 (MODERNA))
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2005264COVID19PFIZER\\BIONTECHEN6208UNKNaNNaNCOVID19 (COVID19 (PFIZER-BIONTECH))
2005274COVID19MODERNA028L20AUNKIMLACOVID19 (COVID19 (MODERNA))
2005274COVID19MODERNA014M20AUNKIMLACOVID19 (COVID19 (MODERNA))
2005290COVID19JANSSEN1805020UNKIMNaNCOVID19 (COVID19 (JANSSEN))
2009884COVID19MODERNANaN2IMLACOVID19 (COVID19 (MODERNA))
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91660201/01/2021WA23.023.0NaNFNaNAbout 15 minutes after receiving the vaccine, ...NaNNaNNaNNaNNaNNaNNaNNaNU12/31/202012/31/20200.0NaNSENNaNNoneNoneNoneNaNNaN201/01/2021NaNNaNYShellfishCOVID19PFIZER\\BIONTECHEL12841IMLACOVID19 (COVID19 (PFIZER-BIONTECH))
91660301/01/2021WA58.058.0NaNFNaNextreme fatigue, dizziness,. could not lift my...NaNNaNNaNNaNNaNNaNNaNNaNY12/23/202012/23/20200.0noneWRKNaNnonekidney infectiondiverticulitis, mitral valve prolapse, osteoar...got measles from measel shot, mums from mumps ...NaN201/01/2021NaNNaNNaNDiclofenac, novacaine, lidocaine, pickles, tom...COVID19MODERNAunknownUNKNaNNaNCOVID19 (COVID19 (MODERNA))
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200527404/26/2021NC65.065.0NaNFNaNNew onset nasal herpes simplex coming up about...NaNNaNNaNNaNNaNNaNNaNNaNNaN03/01/202103/10/20219.0NaNPVTNaNNaNNaNNaNNaNNaN204/24/2021NaNYNaNNaNCOVID19MODERNA028L20AUNKIMLACOVID19 (COVID19 (MODERNA))
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200529004/21/2021MI44.044.0NaNMNaN5 weeks daily; Sweats, Nausea, Light headed, L...NaNNaNNaNNaNNaNNaNNaNNaNN03/17/202103/18/20211.0unremarkable; CBC, Comp Panel, Sed rate, D-dim...PHMNaNsee listNaNinsulin dependant diabetes, hypertension, obes...NaNNaN204/26/2021NaNYNaNBactrim, cephalexin, penicillinCOVID19JANSSEN1805020UNKIMNaNCOVID19 (COVID19 (JANSSEN))
200988404/26/2021NaN62.061.0NaNMNaNCoughWheeze Chills, night sweats, arm sore, ey...NaNNaNNaNNaNNaNNaNNaNNaNY04/21/202104/22/20211.0NaNOTHNaNNaNNaNNaNNaNNaN204/26/2021NaNNaNNaNNaNCOVID19MODERNANaN2IMLACOVID19 (COVID19 (MODERNA))
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737971 rows × 41 columns

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NaN NaN \n", - "916604 Injection site swelling, redness, warm to the ... NaN NaN \n", - "... ... ... ... \n", - "2005264 None NaN NaN \n", - "2005274 New onset nasal herpes simplex coming up about... NaN NaN \n", - "2005274 New onset nasal herpes simplex coming up about... NaN NaN \n", - "2005290 5 weeks daily; Sweats, Nausea, Light headed, L... NaN NaN \n", - "2009884 CoughWheeze Chills, night sweats, arm sore, ey... NaN NaN \n", - "\n", - " L_THREAT ER_VISIT HOSPITAL HOSPDAYS X_STAY DISABLE RECOVD \\\n", - "VAERS_ID \n", - "916600 NaN NaN NaN NaN NaN NaN Y \n", - "916601 NaN NaN NaN NaN NaN NaN Y \n", - "916602 NaN NaN NaN NaN NaN NaN U \n", - "916603 NaN NaN NaN NaN NaN NaN Y \n", - "916604 NaN NaN NaN NaN NaN NaN N \n", - "... ... ... ... ... ... ... ... \n", - "2005264 NaN NaN NaN NaN NaN NaN Y \n", - "2005274 NaN NaN NaN NaN NaN NaN NaN \n", - "2005274 NaN NaN NaN NaN NaN NaN NaN \n", - "2005290 NaN NaN NaN NaN NaN NaN N \n", - "2009884 NaN NaN NaN NaN NaN NaN Y \n", - "\n", - " VAX_DATE ONSET_DATE NUMDAYS \\\n", - "VAERS_ID \n", - "916600 12/28/2020 12/30/2020 2.0 \n", - "916601 12/31/2020 12/31/2020 0.0 \n", - "916602 12/31/2020 12/31/2020 0.0 \n", - "916603 12/23/2020 12/23/2020 0.0 \n", - "916604 12/22/2020 12/29/2020 7.0 \n", - "... ... ... ... \n", - "2005264 NaN NaN NaN \n", - "2005274 03/01/2021 03/10/2021 9.0 \n", - "2005274 03/01/2021 03/10/2021 9.0 \n", - "2005290 03/17/2021 03/18/2021 1.0 \n", - "2009884 04/21/2021 04/22/2021 1.0 \n", - "\n", - " LAB_DATA V_ADMINBY \\\n", - "VAERS_ID \n", - "916600 None PVT \n", - "916601 NaN SEN \n", - "916602 NaN SEN \n", - "916603 none WRK \n", - "916604 NaN PUB \n", - "... ... ... \n", - "2005264 NaN PVT \n", - "2005274 NaN PVT \n", - "2005274 NaN PVT \n", - "2005290 unremarkable; CBC, Comp Panel, Sed rate, D-dim... PHM \n", - "2009884 NaN OTH \n", - "\n", - " V_FUNDBY OTHER_MEDS \\\n", - "VAERS_ID \n", - "916600 NaN None \n", - "916601 NaN Patient residing at nursing facility. See pati... \n", - "916602 NaN None \n", - "916603 NaN none \n", - "916604 NaN Na \n", - "... ... ... \n", - "2005264 NaN NaN \n", - "2005274 NaN NaN \n", - "2005274 NaN NaN \n", - "2005290 NaN see list \n", - "2009884 NaN NaN \n", - "\n", - " CUR_ILL \\\n", - "VAERS_ID \n", - "916600 None \n", - "916601 Patient residing at nursing facility. See pati... \n", - "916602 None \n", - "916603 kidney infection \n", - "916604 Na \n", - "... ... \n", - "2005264 NaN \n", - "2005274 NaN \n", - "2005274 NaN \n", - "2005290 NaN \n", - "2009884 NaN \n", - "\n", - " HISTORY \\\n", - "VAERS_ID \n", - "916600 None \n", - "916601 Patient residing at nursing facility. See pati... \n", - "916602 None \n", - "916603 diverticulitis, mitral valve prolapse, osteoar... \n", - "916604 NaN \n", - "... ... \n", - "2005264 NaN \n", - "2005274 NaN \n", - "2005274 NaN \n", - "2005290 insulin dependant diabetes, hypertension, obes... \n", - "2009884 NaN \n", - "\n", - " PRIOR_VAX SPLTTYPE \\\n", - "VAERS_ID \n", - "916600 NaN NaN \n", - "916601 NaN NaN \n", - "916602 NaN NaN \n", - "916603 got measles from measel shot, mums from mumps ... NaN \n", - "916604 NaN NaN \n", - "... ... ... \n", - "2005264 NaN NaN \n", - "2005274 NaN NaN \n", - "2005274 NaN NaN \n", - "2005290 NaN NaN \n", - "2009884 NaN NaN \n", - "\n", - " FORM_VERS TODAYS_DATE BIRTH_DEFECT OFC_VISIT ER_ED_VISIT \\\n", - "VAERS_ID \n", - "916600 2 01/01/2021 NaN Y NaN \n", - "916601 2 01/01/2021 NaN Y NaN \n", - "916602 2 01/01/2021 NaN NaN Y \n", - "916603 2 01/01/2021 NaN NaN NaN \n", - "916604 2 01/01/2021 NaN NaN NaN \n", - "... ... ... ... ... ... \n", - "2005264 2 04/24/2021 NaN NaN NaN \n", - "2005274 2 04/24/2021 NaN Y NaN \n", - "2005274 2 04/24/2021 NaN Y NaN \n", - "2005290 2 04/26/2021 NaN Y NaN \n", - "2009884 2 04/26/2021 NaN NaN NaN \n", - "\n", - " ALLERGIES VAX_TYPE \\\n", - "VAERS_ID \n", - "916600 Pcn and bee venom COVID19 \n", - "916601 \"Dairy\" COVID19 \n", - "916602 Shellfish COVID19 \n", - "916603 Diclofenac, novacaine, lidocaine, pickles, tom... COVID19 \n", - "916604 Na COVID19 \n", - "... ... ... \n", - "2005264 NaN COVID19 \n", - "2005274 NaN COVID19 \n", - "2005274 NaN COVID19 \n", - "2005290 Bactrim, cephalexin, penicillin COVID19 \n", - "2009884 NaN COVID19 \n", - "\n", - " VAX_MANU VAX_LOT VAX_DOSE_SERIES VAX_ROUTE VAX_SITE \\\n", - "VAERS_ID \n", - "916600 MODERNA 037K20A 1 IM LA \n", - "916601 MODERNA 025L20A 1 IM RA \n", - "916602 PFIZER\\BIONTECH EL1284 1 IM LA \n", - "916603 MODERNA unknown UNK NaN NaN \n", - "916604 MODERNA NaN 1 IM LA \n", - "... ... ... ... ... ... \n", - "2005264 PFIZER\\BIONTECH EN6208 UNK NaN NaN \n", - "2005274 MODERNA 028L20A UNK IM LA \n", - "2005274 MODERNA 014M20A UNK IM LA \n", - "2005290 JANSSEN 1805020 UNK IM NaN \n", - "2009884 MODERNA NaN 2 IM LA \n", - "\n", - " VAX_NAME \n", - "VAERS_ID \n", - "916600 COVID19 (COVID19 (MODERNA)) \n", - "916601 COVID19 (COVID19 (MODERNA)) \n", - "916602 COVID19 (COVID19 (PFIZER-BIONTECH)) \n", - "916603 COVID19 (COVID19 (MODERNA)) \n", - "916604 COVID19 (COVID19 (MODERNA)) \n", - "... ... \n", - "2005264 COVID19 (COVID19 (PFIZER-BIONTECH)) \n", - "2005274 COVID19 (COVID19 (MODERNA)) \n", - "2005274 COVID19 (COVID19 (MODERNA)) \n", - "2005290 COVID19 (COVID19 (JANSSEN)) \n", - "2009884 COVID19 (COVID19 (MODERNA)) \n", - "\n", - "[737971 rows x 41 columns]" - ] - }, - "execution_count": 12, - "metadata": {}, - "output_type": "execute_result" - } - ], + "outputs": [], "source": [ "# pd.set_option('display.max_rows', 100)\n", "df_patients_COVID19" @@ -1969,7 +113,7 @@ }, { "cell_type": "code", - "execution_count": 13, + "execution_count": null, "id": "233bc590", "metadata": {}, "outputs": [], @@ -1979,72 +123,27 @@ }, { "cell_type": "code", - "execution_count": 14, + "execution_count": null, + "id": "e41885a8", + "metadata": {}, + "outputs": [], + "source": [ + "df_PFIZER_BIONTECH" + ] + }, + { + "cell_type": "code", + "execution_count": null, "id": "86e0e4f2", "metadata": {}, - "outputs": [ - { - "name": "stdout", - "output_type": "stream", - "text": [ - "\n", - "Int64Index: 339877 entries, 916600 to 2009884\n", - "Data columns (total 41 columns):\n", - " # Column Non-Null Count Dtype \n", - "--- ------ -------------- ----- \n", - " 0 RECVDATE 339877 non-null object \n", - " 1 STATE 302148 non-null object \n", - " 2 AGE_YRS 309475 non-null float64\n", - " 3 CAGE_YR 302392 non-null float64\n", - " 4 CAGE_MO 561 non-null float64\n", - " 5 SEX 339877 non-null object \n", - " 6 RPT_DATE 271 non-null object \n", - " 7 SYMPTOM_TEXT 339774 non-null object \n", - " 8 DIED 4694 non-null object \n", - " 9 DATEDIED 4392 non-null object \n", - " 10 L_THREAT 4753 non-null object \n", - " 11 ER_VISIT 26 non-null object \n", - " 12 HOSPITAL 20841 non-null object \n", - " 13 HOSPDAYS 13803 non-null float64\n", - " 14 X_STAY 152 non-null object \n", - " 15 DISABLE 4875 non-null object \n", - " 16 RECOVD 308614 non-null object \n", - " 17 VAX_DATE 323994 non-null object \n", - " 18 ONSET_DATE 311854 non-null object \n", - " 19 NUMDAYS 306537 non-null float64\n", - " 20 LAB_DATA 127507 non-null object \n", - " 21 V_ADMINBY 339877 non-null object \n", - " 22 V_FUNDBY 284 non-null object \n", - " 23 OTHER_MEDS 200657 non-null object \n", - " 24 CUR_ILL 163361 non-null object \n", - " 25 HISTORY 203490 non-null object \n", - " 26 PRIOR_VAX 18047 non-null object \n", - " 27 SPLTTYPE 97511 non-null object \n", - " 28 FORM_VERS 339877 non-null int64 \n", - " 29 TODAYS_DATE 337268 non-null object \n", - " 30 BIRTH_DEFECT 191 non-null object \n", - " 31 OFC_VISIT 61181 non-null object \n", - " 32 ER_ED_VISIT 34734 non-null object \n", - " 33 ALLERGIES 178840 non-null object \n", - " 34 VAX_TYPE 339877 non-null object \n", - " 35 VAX_MANU 339877 non-null object \n", - " 36 VAX_LOT 236149 non-null object \n", - " 37 VAX_DOSE_SERIES 339478 non-null object \n", - " 38 VAX_ROUTE 301519 non-null object \n", - " 39 VAX_SITE 246947 non-null object \n", - " 40 VAX_NAME 339877 non-null object \n", - "dtypes: float64(5), int64(1), object(35)\n", - "memory usage: 108.9+ MB\n" - ] - } - ], + "outputs": [], "source": [ "df_PFIZER_BIONTECH.info()" ] }, { "cell_type": "code", - "execution_count": 15, + "execution_count": null, "id": "4b3cb943", "metadata": {}, "outputs": [], @@ -2054,788 +153,132 @@ }, { "cell_type": "code", - "execution_count": 16, - "id": "349da946", - "metadata": { - "scrolled": false - }, - "outputs": [ - { - "data": { - "text/html": [ - "
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"#pd.set_option('display.max_rows', None)\n", - "#print(df2)\n", - "pd.set_option('display.max_rows', None)\n", - "df.value_counts()" + "pd.set_option('display.max_rows', None)" ] }, { "cell_type": "code", "execution_count": null, - "id": "eff80ae1", + "id": "349da946", + "metadata": { + "scrolled": true + }, + "outputs": [], + "source": [ + "df_DIED = df_PFIZER_BIONTECH[df_PFIZER_BIONTECH['DIED']=='Y'][['VAX_LOT']]\n", + "df_DIED" + ] + }, + { + "cell_type": "code", + "execution_count": null, + "id": "9c5ff2fd", + "metadata": { + "scrolled": false + }, + "outputs": [], + "source": [ + "# df = df.groupby(['VAX_LOT']).count()\n", + "#df2 = df.sort_values(by=['DIED'], ascending=False)\n", + "#pd.set_option('display.max_rows', None)\n", + "#print(df2)\n", + "df_DIED.value_counts()" + ] + }, + { + "cell_type": "code", + "execution_count": null, + "id": "2f660707", + "metadata": { + "scrolled": false + }, + "outputs": [], + "source": [ + "df_DISABLE = df_PFIZER_BIONTECH[df_PFIZER_BIONTECH['DISABLE']=='Y'][['VAX_LOT']]\n", + "df_DISABLE" + ] + }, + { + "cell_type": "code", + "execution_count": null, + "id": "3d782392", + "metadata": {}, + "outputs": [], + "source": [ + "df_DISABLE.value_counts()" + ] + }, + { + "cell_type": "code", + "execution_count": null, + "id": "9f537710", + "metadata": { + "scrolled": false + }, + "outputs": [], + "source": [ + "df_L_THREAT = df_PFIZER_BIONTECH[df_PFIZER_BIONTECH['L_THREAT']=='Y'][['VAX_LOT']]\n", + "df_L_THREAT" + ] + }, + { + "cell_type": "code", + "execution_count": null, + "id": "1a629007", + "metadata": { + "scrolled": false + }, + "outputs": [], + "source": [ + "df_L_THREAT.value_counts()" + ] + }, + { + "cell_type": "code", + "execution_count": null, + "id": "f675fcfe", + "metadata": { + "scrolled": false + }, + "outputs": [], + "source": [ + "df_ADR = df_PFIZER_BIONTECH[['VAX_LOT']]\n", + "df_ADR" + ] + }, + { + "cell_type": "code", + "execution_count": null, + "id": "7b3005db", + "metadata": { + "scrolled": false + }, + "outputs": [], + "source": [ + "df_ADR_valueCounts = df_ADR.value_counts()" + ] + }, + { + "cell_type": "code", + "execution_count": null, + "id": "07c93e74", + "metadata": { + "scrolled": false + }, + "outputs": [], + "source": [ + "df_ADR_valueCounts" + ] + }, + { + "cell_type": "code", + "execution_count": null, + "id": "1244c494", "metadata": {}, "outputs": [], "source": [] diff --git a/README.md b/README.md index e604f3739dd..70db6b98e8a 100644 --- a/README.md +++ b/README.md @@ -1,3 +1,30 @@ # HowBadIsMyBatch jupyter notebook + +FK-TODO: +- VAX_LOT-Spalte normalisieren, d.h. toUpperCase(), Format des jeweiligen Herstellers berücksichtigen und "verschmutzte" Einträge Säubern, denn sie stellen alle dieselbe Charge dar: +039k20a +MOD039K20A +#039K20A +039K20A-MODERNA +039K20A-2A +039K20A or 039L +Moderna/039K20A +MODERNA 039K20A +MODERNA039K20A +Modena 039k20A +L039K20A +M039K20A +MOD; 039K20A +m0039k20A +u039k20a +6/21 039K20A +2039K20A +013L20A 039K20A#039K20A +#039K +039K20A 12-31- +039K20A & 031M2 +039K20A and 032 +039K20A, 011L20 +