CRISSPAC
This is the repositoryCoronary artery disease RIsk-stratification Syntax Score Predictive Algorithm Calculator
Description
CRISSPAC: Coronary artery disease RIsk-stratification Syntax Score Predictive Algorithm Calculator
Installation
The development of the platform is based on the open-source statistical programming language R and the R shiny framework. Users will need to download R in order to use CRISSPAC and we suggest the use of RStudio. All required code can be found in this GitHub repository.
Required software
- R version (minimal version 4.1.1)
- Rstudio (minimal version 2021.09.0 Build 351) (optional)
List of required R packages (with their dependencies)
| R package | Version |
|---|---|
| dplyr | 1.0.7 |
| DT | 0.19 |
| Formula | 1.2-4 |
| ggbeeswarm | 0.6.0 |
| ggExtra | 0.9 |
| ggplot2 | 3.3.6 |
| ggthemes | 4.2.4 |
| Hmisc | 4.5-0 |
| lattice | 0.20-44 |
| psych | 2.1.9 |
| randomForest | 4.6-14 |
| readxl | 1.3.1 |
| reshape2 | 1.4.4 |
| shiny | 1.6.0 |
| shinydashboard | 0.7.1 |
| shinyjs | 2.0.0 |
| survival | 3.2-11 |
| tidyr | 1.1.3 |
Input
CRISSPAC uses the Electronic Health Records (EHRs) collected during the GESS study (GESS trial, ClinicalTrials.gov Identifier: NCT03150680). Regarding this, five types of EHRs (see Appendix) with seventy-two measured risk factors are the main input of the platform.
Usage
To initiate CRISSPAC, simply run the file server.R from Rstudio (or RGUI). Minimal data are contained in the source code of the package. For more detailed examples please have a look at the journal publication.
Reference
Mittas, N., Chatzopoulou, F., Kyritsis, K. A., Papagiannopoulos, C. I., Theodoroula, N. F., Papazoglou, A. S., ... & Vizirianakis, I. S. (2021). A Risk-Stratification Machine Learning Framework for the Prediction of Coronary Artery Disease Severity: Insights from the GESS Trial. Frontiers in cardiovascular medicine, 8.
Appendix
| Electronic Health Record | Risk factor | Description | Type | Levels |
|---|---|---|---|---|
| History | HYPERTENSION | History of hypertension | Categorical | No/Yes |
| History | DIABETES MELLITUS | History of diabetes mellitus | Categorical | No/Yes |
| History | DYSLIPIDAEMIA | History of dyslipidaemia | Categorical | No/Yes |
| History | (+) FAMILY HISTORY | Positive (+) family history of CAD | Categorical | No/Yes |
| History | SMOKING | History of smoking | Categorical | No/Yes |
| History | PREVIOUS STROKE | Previous stroke | Categorical | No/Yes |
| History | CHRONIC KIDNEY FAILURE | History of chronic kidney disease | Categorical | No/Yes |
| History | PERIPHERAL VASCULAR DISEASE | History of peripheral vascular disease | Categorical | No/Yes |
| History | AORTIC ANEURYSMS | History of aortic aneurysms | Categorical | No/Yes |
| History | CHRONIC PULMONARY OBSTRUCTIVE DISEASE | History of chronic pulmonary obstructive disease | Categorical | No/Yes |
| History | AUTOIMMUNE DISEASE | History of any autoimmune disease | Categorical | No/Yes |
| History | ATRIAL FIBRILLATION | History of atrial fibrillation | Categorical | No/Yes |
| History | AGE | Age of patient (in years) | Numeric | - |
| Entry | CHEST PAIN | Chest pain | Categorical | No/Yes |
| Entry | DYSPNEA | Dyspnea | Categorical | No/Yes |
| Entry | EASY FATIGUE | Easy fatigue | Categorical | No/Yes |
| Entry | ST-T CHANGES | ST-T changes | Categorical | No/Yes |
| Entry | Q wave in ECG | Q wave on the electrocardiogram | Categorical | No/Yes |
| Entry | BMI | Body mass index (kg/m2) | Numeric | - |
| Entry | BPM | Beats per minute (heart rate) | Numeric | - |
| Entry | SAP | Systolic arterial pressure (SAP) (mmHg) | Numeric | - |
| Entry | DAP | Diastolic arterial pressure (DAP) (mmHg) | Numeric | - |
| Entry | CRUSADE SCORE | Crusade score | Categorical | No/Yes |
| Entry | GRACE SCORE | Grace score | Categorical | No/Yes |
| Entry | QRS DURATION ms | Body mass index (kg/m2) | Numeric | - |
| Biochemical | GFR | Glomerular filtration rate by CKD-EPI (mL/min/1.73m2) | Numeric | - |
| Biochemical | GLU | Glucose (mg/dL) | Numeric | - |
| Biochemical | UREA | Urea (mg/dL) | Numeric | - |
| Biochemical | CREATININE | Creatinine (mg/dL) | Numeric | - |
| Biochemical | URIC ACID | Uric acid (mg/dL) | Numeric | - |
| Biochemical | CHOL | Total cholesterol (mg/dL) | Numeric | - |
| Biochemical | TG | Triglycerides (mg/dL) | Numeric | - |
| Biochemical | HDL | High density lipoprotein cholesterol (mg/dL) | Numeric | - |
| Biochemical | LDL | Low density lipoprotein cholesterol (mg/dL) | Numeric | - |
| Biochemical | TNT-HS | High sensitivity cardiac troponin (ng/L) | Numeric | - |
| Biochemical | SGOT | Aspartate aminotransferase (units/L) | Numeric | - |
| Biochemical | SGPT | Alanine aminotransferase (units/L) | Numeric | - |
| Biochemical | LDH | Lactic acid dehydrogenase (units/L) | Numeric | - |
| Biochemical | CPK | Creatine phosphokinase (units/L) | Numeric | - |
| Biochemical | NA | Sodium (mEq/L) | Numeric | - |
| Biochemical | K | Potassium (mmol/L) | Numeric | - |
| Biochemical | INR | International normalized ratio | Numeric | - |
| Complete Blood Count | WBC | White blood cells (*1000) | Numeric | - |
| Complete Blood Count | NEU% | Neutrophils percentage | Numeric | - |
| Complete Blood Count | LYM% | Lymphocytes percentage | Numeric | - |
| Complete Blood Count | MONO% | Monocytes percentage | Numeric | - |
| Complete Blood Count | EOS% | Eosinophils percentage | Numeric | - |
| Complete Blood Count | BASO% | Basophils percentage | Numeric | - |
| Complete Blood Count | RBC | Red blood cells (*1000000) | Numeric | - |
| Complete Blood Count | HGB | Hemoglobin (g/dL) | Numeric | - |
| Complete Blood Count | HCT | Hematocrit percentage | Numeric | - |
| Complete Blood Count | MCV | Mean corpuscular volume (fl) | Numeric | - |
| Complete Blood Count | MCH | Mean corpuscular hemoglobin (pg) | Numeric | - |
| Complete Blood Count | MCHC | Mean corpuscular hemoglobin concentration (g/dL) | Numeric | - |
| Complete Blood Count | RDW-CV | Red blood cell distribution width- coefficient of variation (percentage) | Numeric | - |
| Complete Blood Count | RDW-SD | Red blood cell distribution width- standard deviation (percentage) | Numeric | - |
| Complete Blood Count | PLT | Platelets (1000) | Numeric | - |
| Complete Blood Count | MPV | Mean platelet volume (fl) | Numeric | - |
| Complete Blood Count | PDW | Platelet distribution width (percentage) | Numeric | - |
| Complete Blood Count | PCT | Plateletcrit (percentage) | Numeric | - |
| Complete Blood Count | P-LCR | Platelet-large cell ratio | Numeric | - |
| Differential | ACS | Acute coronary syndrome | Categorical | No/Yes |
| Differential | NSTEMI | Non-ST-elevated myocardial infarction | Categorical | No/Yes |
| Differential | STEMI | ST-elevated myocardial infraction | Categorical | No/Yes |
| Differential | UNSTABLE ANGINA | Unstable angina | Categorical | No/Yes |
| Differential | STABLE ANGINA | Stable angina | Categorical | No/Yes |
| Differential | SPECT | Pathological single-photon emission computerized tomography results | Categorical | No/Yes |
| Differential | CCTA | Pathological coronary computed tomography angiography results | Categorical | No/Yes |
| Differential | THORACIC PAIN | Thoracic pain | Categorical | No/Yes |
| Differential | CHRONIC CORONARY SYNDROME | Chronic coronary syndrome | Categorical | No/Yes |
| Differential | AORTIC VALVE STENOSIS | Severe aortic stenosis | Categorical | No/Yes |
| Differential | HEART FAILURE | Heart failure | Categorical | No/Yes |