README.md

riskModel

The riskModel pkg is developed based on several publicly available packages and codes for developing risk prediction models using survival data.

Collections of risk prediction models

1. BMJ series papers

• 2024

  • Part 1. Evaluation of clinical prediction models: from development to external validation, R code

  • Part 2. Evaluation of clinical prediction models: how to undertake an external validation study

  • Part 3. Evaluation of clinical prediction models: calculating the sample size required for an external validation study, R code

• 2023

  • Transparent reporting of multivariable prediction models developed or validated using clustered data (TRIPOD-Cluster): explanation and elaboration

  • Transparent reporting of multivariable prediction models developed or validated using clustered data: TRIPOD-Cluster checklist

  • Development and internal-external validation of statistical and machine learning models for breast cancer prognostication: cohort study

• Before 2023

  • 2022 Validation of prediction models in the presence of competing risks: a guide through modern methods, R code

  • 2020 Calculating the sample size required for developing a clinical prediction model, R code

  • 2019 Guide to presenting clinical prediction models for use in clinical settings, R code

  • 2019 When and how to use data from randomised trials to develop or validate prognostic models

  • 2016 Adding tests to risk based guidelines: evaluating improvements in prediction for an intermediate risk group

  • 2015 How to develop a more accurate risk prediction model when there are few events

  • 2012 Comparing risk prediction models

  • 2012 Heart Part 1. Risk prediction models: I. Development, internal validation, and assessing the incremental value of a new biomarker

  • 2012 Heart Part 2. Risk prediction models: II. External validation, model updating, and impact assessment

2. Methodological papers

• 2022 Int J Epidemiol Lessons learnt when accounting for competing events in the external validation of time-to-event prognostic models, R code

• 2022 Ann Intern Med Assessing Performance and Clinical Usefulness in Prediction Models With Survival Outcomes: Practical Guidance for Cox Proportional Hazards Models, R code

• 2016 J Clin Oncol Assessing the clinical impact of risk prediction models with decision curves: guidance for correct interpretation and appropriate Use, R code

• 2014 Ann Intern Med Net reclassification improvement: compuataion, interpretation, and controversies

• 2010 Epidemiology Assessing the performance of prediction models: A framework for traditional and novel measures, R code 1, R code 2

• 2003 J Clin Epidemiol Internal and external validation of predictive models: a simulation study of bias and precision in small samples

• 2001 J Clin Epidemiol Internal validation of predictive models: efficiency of some procedures for logistic regression analysis

3. Advanced topics

3.1 Predictors selections

• 2023 J Clin Epidemiol Practical guide to the typical analysis of prognostic factors and biomarkers without the use of P-values

• 2021 J Stat Softw glmulti: An R package for easy automated model selection with (Generalized) linear models, R code

3.2 Super learner

• 2018 Epidemiology Using super learner prediction modeling to improve high-dimensional propensity score estimation, R code 1; R code 2

3.3 Dynamic prediction

• 2021 Am J Epidemiol Dynamical modeling as a tool for inferring causation

• 2021 R Journal JMcmprsk: An R Package for Joint Modelling of Longitudinal and Survival Data with Competing Risks, R code

• 2020 Int J Epidemiol Reflections on modern methods: Dynamic prediction using joint models of longitudinal and time-to-event data, R code

• 2015 Int J Epidemiol Joint modelling of repeated measurement and time-to-event data: an introductory tutorial, R code

• 2013 Biometrics Dynamic pseudo-observations: a robust approach to dynamic prediction in competing risks, R code

3.4 Prediction of counterfactual risk

• 2022 Eur J Epidemiol Predicting counterfactual risks under hypothetical treatment strategies: an application to HIV

• 2022 Eur J Epidemiol A structural characterization of shortcut features for prediction

• 2020 Eur J Epidemiol Counterfactual prediction is not only for causal inference

• 2020 Eur J Epidemiol Prediction meets causal inference: the role of treatment in clinical prediction models

3.5 Lifetime risk

• 2021 Eur J Epidemiol A comparison of statistical methods to predict the residual lifetime risk, R code

• 2000 Stat Med Computing estimates of incidence, including lifetime risk: Alzheimer’s disease in the framingham study. the practical incidence estimators (pie) macro

3.6 Multistate model

• 2016 Circ Heart Fail Multistate model to predict heart failure hospitalizations and all-cause mortality in outpatients with heart failure with reduced ejection fraction: Model derivation and external validation

3.7 Deep learning

• 2024 arXiv Deep learning for survival analysis: A review, R code

• 2017 arXiv Machine Learning for Survival Analysis: A Survey, R code

3.8 Automatic machine learning

• 2022 BMC Med Res Methodol Survival prediction models: an introduction to discrete-time modeling, R code

3.9 Risk model presentations

• 2004 Stat Med Presentation of multivariate data for clinical use: The Framingham Study risk score functions

• 2016 Korean J Radiol How to Develop, Validate, and Compare Clinical Prediction Models Involving Radiological Parameters: Study Design and Statistical Methods

4 Well-established risk prediction models

4.1 Framingham Heart Study risk scores

• 1988 Circulation Original FHS CHD score Prediction of coronary heart disease using risk factor categories

• 1999 Lancet Lifetime risk of developing coronary heart disease

• 2006 Circulation USA-PRC Estimation of 10-year risk of fatal and nonfatal ischemic cardiovascular diseases in Chinese adults

• 2009 Circulation FHS 30-year CVD risk prediction model Predicting the 30-year risk of cardiovascular disease: The Framingham Heart Study

4.2 QRISK

• 2007 BMJ QRISK Derivation and validation of QRISK, a new cardiovascular disease risk score for the United Kingdom: prospective open cohort study

• 2008 BMJ QRISK2 Predicting cardiovascular risk in England and Wales: prospective derivation and validation of QRISK2

• 2010 BMJ QRISK-lifetime risk Derivation, validation, and evaluation of a new QRISK model to estimate lifetime risk of cardiovascular disease: cohort study using QResearch database

• 2017 BMJ QRISK3 Development and validation of QRISK3 risk prediction algorithms to estimate future risk of cardiovascular disease: prospective cohort study

• 2024 Eur J Prev Cardiol QRISK2-PRS A polygenic risk score added to a QRISK®2 cardiovascular disease risk calculator demonstrated robust clinical acceptance and clinical utility in the primary care setting

4.3 CMCS Risk prediction models

• 2003 中华心血管病杂志 中国35~64岁人群心血管病危险因素与发病危险因素预测模型的前瞻性研究

• 2004 JAMA FHS CHD score in Chinese population Predictive Value for the Chinese Population of the Framingham CHD Risk Assessment Tool Compared With the Chinese Multi-provincial Cohort Study

• 2013 Eur J Prev Cardiol CMCS CVD lifetime risk Lifetime risk for cardiovascular disease in a Chinese population: the Chinese Multi-Provincial Cohort Study

• 2016 J Hypertens Lifetime risk of stroke in young-aged and middle-aged Chinese population: the Chinese Multi-Provincial Cohort Study

• 2018 中华心血管病杂志 中国动脉粥样硬化性心血管病发病危险评估的新方案

• 2023 CVIA Addition of Risk-enhancing Factors Improves Risk Assessment of Atherosclerotic Cardiovascular Disease in Middle-aged and Older Chinese Adults: Findings from the Chinese Multi-provincial Cohort Study

4.4 Pooled Cohort ASCVD Risk Equations ASCVD Risk Calculator

• 2013 Circulation PCE 2013 ACC/AHA guideline on the assessment of cardiovascular risk: a report of the American College of Cardiology/American Heart Association Task Force on Practice Guidelines

• 2013 J Am Coll Cardiol PCE 2013 ACC/AHA guideline on the treatment of blood cholesterol to reduce atherosclerotic cardiovascular risk in adults: a report of the American College of Cardiology/American Heart Association Task Force on Practice Guidelines

• 2017 Circulation PCE lifetime risk Estimating Longitudinal Risks and Benefits From Cardiovascular Preventive Therapies Among Medicare Patients: The Million Hearts Longitudinal ASCVD Risk Assessment Tool: A Special Report From the American Heart Association and American College of Cardiology

• 2020 JAMA Netw Open PCE by BMI Performance of the Pooled Cohort Equations to Estimate Atherosclerotic Cardiovascular Disease Risk by Body Mass Index

• 2021 JAMA Cardiol PCE by self-reported physical activity Performance of the American Heart Association/American College of Cardiology Pooled Cohort Equations to Estimate Atherosclerotic Cardiovascular Disease Risk by Self-reported Physical Activity Levels

4.5 China-PAR, 心脑血管风险评估网站

• 2016 Circulation China-PAR ASCVD risk Predicting the 10-Year Risks of Atherosclerotic Cardiovascular Disease in Chinese Population: The China-PAR Project (Prediction for ASCVD Risk in China)

• 2016 Chronic Dis Transl Med China-PAR ASCVD risk stratification Risk stratification of atherosclerotic cardiovascular disease in Chinese adults

• 2018 Sci Bull (Beijing) China-PAR ASCVD lifetime risk Predicting lifetime risk for developing atherosclerotic cardiovascular disease in Chinese population: the China-PAR project

• 2022 Eur Heart J China-PAR PRS A polygenic risk score improves risk stratification of coronary artery disease: a large-scale prospective Chinese cohort study

• 2019 中国循环杂志 中国心血管病风险评估和管理指南

4.6 SCORE project

• 2003 Eur Heart J SCORE Estimation of ten-year risk of fatal cardiovascular disease in Europe: the SCORE project

• 2021 Eur Heart J SCORE2 risk prediction algorithms: new models to estimate 10-year risk of cardiovascular disease in Europe

• 2021 Eur Heart J SCORE2-OP risk prediction algorithms: estimating incident cardiovascular event risk in older persons in four geographical risk regions

4.7 Others

• 2016 Eur Heart J CHD GRS Genomic prediction of coronary heart disease

• 2019 Lancet Glob Health WHO CVD Risk Charts World Health Organization cardiovascular disease risk charts: revised models to estimate risk in 21 global regions

• 2020 Eur Heart J LIFE-CVD Prediction of individualized lifetime benefit from cholesterol lowering, blood pressure lowering, antithrombotic therapy, and smoking cessation in apparently healthy people

• 2023 Chin Med J (Engl) CKB PRS Minimal improvement in coronary artery disease risk prediction in Chinese population using polygenic risk scores: evidence from the China Kadoorie Biobank

• 2024 Eur Heart J CVD risk communication Cardiovascular disease risk communication and prevention: a meta-analysis