Explorative Data Analysis of the National Pandemic Cohort Network (NAPKON) Public Data Set¶

Welcome! The following statistics provide some visusal insights into NAPKON Public Data Set. The Public Data Set constitutes patient data from the NAPKON after a data cleaning process and includes data from patients documented until September 28, 2023. The NAPKON Public Data Set is originating from the NAPKON SecuTrial. The data anonymization pipeline is described by Jakob et al. in "Design and evaluation of a data anonymization pipeline to promote Open Science on COVID-19". The public data is anonymized using our "data protection concept". The anonymization process was carried out with the "ARX software"

Copyright: This work is licensed under the Creative Commons Attribution Non-Commercial 4.0 License. With the use of this data you agree to include a proper acknowledgement of the NAPKON study group in any work based on the data set. By working with this notebook you agree to maintain the confidentiality of the data set at all times and to not attempt to compromise or otherwise violate the privacy of the patients described. To view a copy of the license, visit https://creativecommons.org/licenses/by-nc/4.0/.

If you have any comments on the notebook, please drop us a message at support@napkon.de.

Data Set Structure¶

Here we provide information on the basic structure of the NAPKON Public Data Set.

The data set consists of 5988 patients and 16 variables. A row represents anonymized data of a single patient.

The columns are described by the variables:

age (categorial): age group
gender (categorial): gender
month_first_diagnosis (categorical): quartile of first confirmed diagnosis of COVID-19
year_first_diagnosis (categorical): year of first confirmed diagnosis of COVID-19
cohort (categorical): Selection of the respective cohort in which the patient was included
mild_disease_phase (categorical): yes if patient was in the Mild Phase*
moderate_disease_phase (categorical): yes if patient was in the Moderate Phase*
severe_disease_phase (categorical): yes if patient was in the Severe Phase*
patient_status_at_end_of_acute_phase (categorial): status of the patient at the end of acute phase of SARS-CoV-2
hospitalization_during_acute_phase (categorial): patient hospitalized during acute phase of SARS-CoV-2
intensive_care_treatment (categorial): patient with intensive care treatment during acute phase of SARS-CoV-2
inv_ventilation (categorial): patient with invasive ventilation during acute phase of SARS-CoV-2
availability_3month_followup (categorial): completion of the 3-month follow-up
ability_to_work_3MFU (categorial): patient is able to work at the time of 3-month follow-up
any_symptom_3MFU (categorial): patient has any symptoms at the 3-month follow-up

For further information regarding the variables please refer to: https://cloud.idcohorts.net/s/ELRzpzgBkKb5ejY and https://cloud.napkon.de/s/W2PQpmqzoRkjABL

*The Clinical Phases are defined according to the WHO clinical progression scale:

To get to know the Public Data Set better, the values of variables are shown below according to the used data set. Please be aware that the Public Data Set is only a part of the complete NAPKON data set. Anonymization processes may lead to variables having less values than in the complete NAPKON data set. For example the variable 'gender' can also have the value 'diverse', but there is no patient with this gender in the Public Data Set.

age:
18 - 39 years, 40 - 59 years, 60 - 79 years, >= 80 years

gender:
female, male

quarter_first_diagnosis:
Q1, Q2, Q3, Q4, unknown/missing

year_first_diagnosis:
2020, 2021, 2022, 2023, unknown/missing

cohort:
HAP, POP, SUEP

mild_phase:
no, yes

moderate_phase:
no, yes

severe_phase:
no, unknown/missing, yes

patient_status_end_acute_phase:
ambulant, dead, discharged, referral/transfer, unknown/missing

hospitalisation:
no, yes

intensive_care_treatment:
no, yes

inv_ventilation:
no, unknown/missing, yes

availability_3month_followup:
no/not yet, yes

ability_to_work_3MFU:
n/a, no, unknown/missing, yes

any_symptom_3MFU:
n/a, no, unknown/missing, yes

n/a: In cases where the patient was not in the respective phase a variable refers to, the variable has been given the value 'Not applicable (N/a)'. If for example a patient has never been in the completion of the 3-month follow-up, 'any symptoms at the 3-month follow-up' is a variable which is not applicable to this patient.

1. Descriptive Analysis¶

The following descriptive statistics are computed in this section:

Cohort Distribution
Date of diagnosis Distribution by Cohort
Gender Distribution by Cohort
Age Distribution by Cohort
Age - Gender Distribution by Cohort

Number of patients from HAP is lower than from SUEP and POP. Therefore please pay attention to difference in scaling especially in HAP.