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covid-montefiore

Analysis of Covid patients in the Bronx at Montefiore Medical Center

Contents:

Analyses

Usage

You must have a file called COVID19_RETROSPECTIVE_DATA5.15.xlsx in the folder data/raw

*** Note: This file contains confidential patient information and is not available in the public source for this paper. ***

To load the dataset (into python)

from covidmonte import get_retrospective_data
df = get_retrospective_data()

The first time you do this, the 'cleaned' dataset will be generated and stored as a CSV file in data/confidential. Afterwards, this dataset will be loaded.

To load the dataset (other languages)

Follow the instructions above for python to generate the processed CSV file (or get it from someone). Then load that CSV file into the tool of your choice.

Additional utilities (Python)

There is a context manager called Plotter which generates a matplotlib ax and automatically saves the resulting figure on exit. Here's an example:

df = get_retrospective_data()
with Plotter('histogram.svg', show=False) as ax:
  df.hist('age', ax=ax)
  ax.set_title("Distribution of Patient Ages")

This will generate the following histogram saved as histogram.svg:

histogram

This is a very wide dataset with 182 columns. To make this easier to work with, you can extract a subset of the data using predefined lists of columns in the covidmonte package:

  • demographic_columns
  • date_columns
  • status_columns
  • symptoms_columns
  • vitals_columns
  • categorical_events_columns
  • radiology_columns
  • comorbidities_columns
  • treatments_columns
  • labs_columns

Dataset Cleaning

The script scripts/clean_dataset.py converts the raw data stored in data/raw/COVID19_RETROSPECTIVE_5.15.csv to a DataFrame with the columns cleaned up as described below. The raw data is in .gitignore, so you will have to get it yourself and put it inside your version of the repo.

Whenever a column name is changed in the cleaned version of the dataset, its new name is listed after an arrow (->). All columns in the cleaned version are lower-case.

Identifying Columns

  • Patient_study_ID -> id
  • MRN -> mrn
  • Patient_study_ID.1 -> id2

Demographic Columns

  • Date of Birth -> dob
  • Age
  • Sex (Female=1. Male=0) -> sex
  • Ethnicity (1="Hispanic/Latino". 0= "NOT hispanic/latino. . = unknown/missing) -> ethnicity
  • Race (1=Black. 2=white. 3=other. = unknown/missing) -> race
  • Place of residence (nursing home/assisted living = 1. home=0. 2=other. . = unknown) -> residence
  • HCW (1=Y. 0=N. .=unknown) -> hcw
  • Smoking- Former or current (0=No. 1= Yes. . unkn) -> smoking
  • BMI

Date Columns

  • Presentationdate1
  • Dischargedate1
  • Admissiondate2
  • Dischargedate2
  • ICUadmissiondate1
  • ICUadmissiondate2
  • ICUdischargedate2
  • SARS-CoV-2collectiondate1
  • SARS-CoV-2resultdate1
  • SARS-CoV-2collectiondate2
  • SARS-CoV-2resultdate2
  • SARS-CoV-2collectiondate3
  • SARS-CoV-2resultdate3
  • Intubationdate1
  • Extubationdate1
  • Intubationdate2
  • Extubationdate2
  • Deathdate
  • wbcadmdateac
  • cradmdateac
  • bunadmdateac
  • astadmdateac
  • ldhadmdateac
  • crpadmdateac
  • ddimeradmdateac
  • inradmdateac
  • fibrinoaddatemac
  • ferritadmdateac
  • pttadmdateac
  • CD4date

Admission Status Info

  • Admitted or Outpt/ED (outpatient=0. ED=1. admit=2) -> admission
  • DischargeDispo1 (0=home. 1=nursing home/assisted living/rehab 2=deceased. 3=other. .=unknown) -> discharge_destination1
  • DischargeDispo2 (0=home. 1=nursing home/assisted living/rehab 2=deceased. 3=other. .=unknown) -> discharge_destination2
  • DaysOfSymptomsBefore1stAdmission (unknown .. otherwise number) -> days_of_symptoms_before_1st_admission
  • stillinpatient

Symptoms

  • Fever (Yes=1. No=0. unknown=.) -> fever
  • Cough
  • SOB
  • Fatigue
  • Sore throat
  • Chills
  • Headache
  • Diarrhea
  • Othersymptoms
  • Fever duration (days)- (>100.4 days) -> fever_duration

Vitals

  • TempF - initial temp (or date of test collection) -> initial_temp
  • TempF - max temp during admission -> max_temp
  • Systolic BP - first recorded -> 1stsystolic_bp
  • Diastolic BP - first recorded -> 1stdiastolic_bp
  • RR - initial -> initial_rr
  • SaO2 (please write as NUMBER) -> sao2
  • Lung exam results (wheezing. rales.rhonchi. egophony) -> lung_exam

Categorical Events

These are events that took place but are not associated with a date.

  • Antipiretics- (Yes=1. No=0. unknown=.) -> antipyretics
  • Received oral medications in first 24 hours (Yes=1. No=0. unknown = .) -> oral_medication_in_1st_24hr
  • On oxygen at presentation (Yes=1. No=0. unknown=.) -> on_o2_at_presentation
  • Altered Mental Status (Yes=1. No=0. unknown=.) -> altered_mental_status
  • Intubations (0=No. 1=Yes. Unknown= 0) -> intubated
  • Hi-flow (0=no. 1=yes. Unk= 0) -> hiflow
  • NonRebreather Mask (N=no. 1=yes. Unk= 0) -> non_rebreather_mask
  • CPAP/BPAP) (1/0) -> cpap
  • nasal cannula (1/0) -> nasal_cannula
  • AKI (Yes=1. No=0. unknown=.) -> aki
  • Concurrent pathogen infection (describe in free text) (bacterial. viral. fungal. etc) -> concurrent_pathogen_infection
  • Sepsis/septic shock? -> sepsis
  • Cardiogenic shock -> cardiogenic_shock
  • Myocarditis -> myocarditis
  • Cardiac arrest (Yes=1. No=0. unknown=.) -> cardiac_arrest
  • ARDS (Yes=1.No=0. unknown=.) -> ards
  • ECMO (Yes=1. No=0. unknown=.) -> ecmo
  • Other Complications free text (stroke. heart failure. renal failure. pulmonary embolism. etc) -> other_complications
  • readmission
  • qsofaams
  • qsofabp
  • qsofarr
  • qsofa
  • composite
  • death

Radiology

  • Admission x-ray (paste text) -> admission_cxr
  • CXR-BilatOpacities -> cxr_bilateral_opacities
  • CXR-Interstitial -> cxr_interstitial
  • CXR-UnilatOpacities -> cxr_unilateral_opacities
  • POCUSlunginitial Free text -> poc_us_lung_initial
  • POCUSheartinitial free text -> poc_us_heart_initial

Comorbidities

  • COPD (0=No. 1= Yes. 999=unknown) -> copd
  • Asthma (0=No. 1= Yes. 999=unknown) -> asthma
  • Hypertension(0=No. 1= Yes. .=Unknown) -> htn
  • Diabetes (complicated by CKD. PVD. CHF/ischemic cardiomyopathy. OR uncomplicated)(0=No. 1= Yes. 999=Unknown) -> diabetes
  • Pulmonary disease (COPD. asthma. emphysema. bronchiectasis. pulmonary hypertension)(0=No. 1= Yes. 999=Unknown) -> pulmonary_dx
  • Heart disease (CAD. hx of CABG or PCI. CHF. AICD -> heart_dx
  • Malignancy (within 2 years or receiving immunosuppressive treatment)(0=No. 1= Yes. 999=Unknown) -> malignancy
  • Chronic kidney disease(0=No. 1= Yes. 999=Unknown) -> ckd
  • HD (Yes=1. No=0. unknown=.) -> hd
  • Immunocompromised state (eg: steroids. monoclonal antibod1 tx for asthma/RA. transplant)(0=No. 1= Yes. 999=Unknown) -> immunocompromised
  • HIV(0=No. 1= Yes. 999=Unknown) -> hiv
  • Other comorbidity(0=No. 1= Yes. 999=Unknown) -> other_comorbidity
  • Other comorbidity- free text -> other_comorbidity_text
  • ACE (1=yes. 0=no. .=unknown) -> ace
  • ARB (1=yes. 0=no. .=unknown) -> arb

Labs

  • A1C%
  • CD4count_mostrecent
  • CD4%_mostrecent
  • wbcadmac
  • wbcpeakac
  • wbcnadirac
  • crpeakac
  • cradmac
  • bunadmac
  • neutadmac
  • neutnadirac
  • lymphadmac
  • lymphnadirac
  • pltpeakac
  • pltnadirac
  • pltadmac
  • astpeakac
  • astadmac
  • altpeakac
  • altadmac
  • ldhpeakac
  • ldhadmac
  • procalpeakac
  • procaladmac
  • crppeakac
  • crpadmac
  • ddimeradmac
  • ddimerpeakac
  • inradmac
  • inrpeakac
  • fibrinoadmac
  • fibrinopeakac
  • ferritadmac
  • ferritpeakac
  • pttadmdateac
  • pttadmac
  • pttpeakac
  • ptadmac
  • ptpeakac
  • alkpadmac
  • alkppeakac
  • albadmac
  • il6initac
  • il6peakac
  • eosadmac
  • g6pd-def1-norml0-inter2
  • bpsystac
  • bpdiastac
  • tempinitac
  • tempmaxac
  • rrinitac
  • pulseoxinitac
  • readmission
  • qsofaams
  • qsofabp
  • qsofarr
  • qsofa

Treatments

  • Chloroquinedays -> chloroquine_days
  • Hydroxychloroquinedays -> hydroxychloroquine_days
  • Kaletra (Lopinavir/Ritonavir) days -> kaletra_days
  • Remdesivir-compastionate days -> remdesivir_compassionate_days
  • Remdesivir- clinical trial days -> remdesivir_clinical_trial_days
  • OtherTrial_free text -> other_trial
  • Pressors days -> pressors_days
  • pronation (Y=1. N=0. unknown=.) - search in notes -> pronation
  • Other IV antibiotics (new columns?) -> other_iv_abx
  • Azithromycindays
  • Glucose-6 (Yes=1. No=0. missing/unknown=.)
  • Glucocorticoids_freetext
  • NSAID (Yes=1. No=0. unknown=.)