Man pages for ISARICDataPlatform/CovidClinicalDataProcessor
Data Import and Processing for ISARIC COVID-19 Hospital Data
| admission.symptoms | Heat admission.symptoms |
| admission.to.icu.prep | Aggregate data for hospital admission to ICU admission |
| age.pyramid.prep | Data for the report summary |
| comorbidity.prep | Prepare Table4. comorbidities |
| comorbidity.prevalence.prep | Aggregate data for comorbidity prevalence plot |
| comorbidity.upset.prep | Aggregate data for comorbidities upset plot |
| date_pull | Shared pre-processing of input CSV files |
| func_plot_comorbid_asthma | Comorbidities by age |
| func_plot_lab_crp | Box and whisker plots for laboratory results at hospital... |
| func_plots_vs_resp | vital signs |
| func_plot_symptoms_history_of_fever | symptoms by age |
| icu.treatment.use.proportion.prep | Aggregate data for treatment ICU use proportion plot |
| import.demographic.data | Import demographic data |
| import.microb.data | Import microb data |
| import.symptom.and.comorbidity.data | Import data on symptoms and comorbidities |
| key.times.prep | Prepare Table6. key times variable |
| length.of.stay.age.prep | Aggregate data for hospital stay plot by age |
| length.of.stay.icu.prep | Aggregate data for length of stay within ICU |
| length.of.stay.sex.prep | Aggregate data for hospital stay plot by sex |
| outcome.admission.date.prep | Aggregate data for outcome by admission date plot |
| outcome.age.sex.prep | Prepare Table2. Outcome by age and sex |
| patient.by.case.def.prep | Case definitions data From christiana's paper |
| patient.by.country.map.prep | Map data |
| patient.by.country.prep | Aggregate data for patient by country |
| patient.characteristic.prep | Prepare Table1. Patient characteristics |
| patient.site.time.map.prep | Aggregate data for case enrolment over time by site |
| process.all.data | Fully process data |
| process.common.treatment.data | Process data on the most common treatments |
| process.comorbidity.data | Process data on comorbidities |
| process.ICU.data | Process data on ICU admission |
| process.IMV.NIV.data | Process dates on IMV and NIV |
| process.laboratory.data | Process data on laboratory |
| process.outcome.data | Process data on outcomes |
| process.pregnancy.data | Process data on pregnancy (as comorbidity) |
| process.symptom.data | Process data on symptoms |
| process.treatment.data | Process data on treatments |
| process.treatment.icu.data | Process data on the most common icu treatments |
| process.vital.sign.data | Process data on vital sign |
| randomization | Generate a randomized dataset based on a real wide dataset... |
| status.by.time.after.admission.prep | Aggregate data for timeline plot |
| summary.input.overall.prep | Data for the report summary |
| summary.input.prep | Aggregate data for the summary and flowchart |
| symptom.heatmap | Plot pairwise symptom prevalance. |
| symptom.prevalence.prep | Aggregate data for symptom prevalence plot |
| symptoms.prep | Prepare Table3. symptoms |
| symptom.upset.prep | Aggregate data for symptoms upset plot |
| synthesise | Generate a basic synthetic dataset based on a dataset... |
| treatment.icu.upset.prep | Aggregate data for ICU treatments upset plot |
| treatments.prep | Prepare Table5. Prevalence of treatments |
| treatment.upset.prep | Aggregate data for treatments upset plot |
| treatment.use.proportion.prep | Aggregate data for treatment use proportion plot |
