SC.06

SC.06 Extension of survival models for correlated data: joint frailty models with recurrent events,

Sunday, 5 July 2020  |  9:00 - 17:00 | Location: TBD

Instructors:
  • Virginie Rondeau
  • Denis Rustand


Summary:

Event history analysis may be particularly complex because of correlated event times, such as clustered or recurrent events. Extensions of simple shared frailty models, in the field of joint models for correlated data have been recently developed and applied for recurrent or clustered survival data in the literature, however even present in publications they are not well developed in classical software. We are aiming at filling this gap by considering different extensions of joint frailty models and by presenting an implementation of these models using the R package frailtypack on real datasets. A particular interest will be devoted to joint frailty models to analysis recurrent events such as cancer relapses and a terminal event, models for two survival outcomes for clustered data, models for two types of recurrent events and a terminal event, models for a longitudinal biomarker and a terminal event and models for a longitudinal biomarker, recurrent events and a terminal event (death or lost to follow-up).The estimation of these models and predictive dynamic tools that can be derived from them will be exposed, with methods to evaluate their predictive accuracy.

Emphasis is given, via examples on real and simulated data, of the ability of extended frailty models to describe a very broad range of practical situations. Real life examples are used, and there is time for practical use. Each lecture is complemented by a practical session implementing the methods using the R package frailtypack.

Krol, C. Tournigaud, S. Michiels, and V. Rondeau. Multivariate joint frailty model for the analysis of nonlinear tumor kinetics and dynamic predictions of death. Statistics in Medicine, 2018.
Krol, A. Mauguen, Y. Mazroui, A. Laurent, S. Michiels, and V. Rondeau. Tutorial in joint modeling and prediction: A statistical software for correlated longitudinal outcomes, recurrent events and a terminal event. Journal of Statistical Software, 81(3), 2017.
Krol, L. Ferrer, JP. Pignon, C. Proust-Lima, M. Ducreux, O. Bouché, S. Michiels, and V. Rondeau. Joint model for left-censored longitudinal data, recurrent events and terminal event: Predictive abilities of tumor burden for cancer evolution with application to the ffcd 2000-05 trial. Biometrics, 72(3) :907–16, 2016.
Ferrer, V. Rondeau, J. Dignam, T. Pickles, H. Jacqmin-Gadda, and Proust-Lima C. Joint modelling of longitudinal and multi-state processes: application to clinical progressions in prostate cancer. Statistics in Medicine, 35(22) :3933–48, 2016
Commenges, H. Jacqmin-Gadda, A. Amadou, P. Joly, B. Liquet, C. Proust-Lima, V. Rondeau, and R. Thiébaut. Dynamical Biostatistical Models, volume 86. CRC Press,2015.
Mazroui, A. Mauguen, S. Mathoulin-Pélissier, G. MacGrogan, V. Brouste, and V. Rondeau. Time-varying coefficients in a multivariate frailty model: Application to breast cancer recurrences of several types and death. Lifetime data analysis, pages 1–25, 2015.
Rondeau, A. Mauguen, A. Laurent, C. Berr, and C. Helmer. Dynamic prediction models for clustered and interval-censored outcomes: Investigating the intra-couple correlation in the risk of dementia. Statistical methods in medical research, 2015.
Mauguen, B. Rachet, S. Mathoulin-Pélissier, G. MacGrogan, and V. Rondeau. Dynamic prediction of risk of death using history of cancer recurrences in joint frailty models. Statistics in Medicine, 32(30) :5366–5380, 2013
Mazroui, S. Mathoulin-Pelissier, P. Soubeyran, and V. Rondeau. General joint frailty model for recurrent event data with a dependent terminal event: application to follicular lymphoma data. Statistics in medicine, 31(11-12) :1162–1176, 2012.
Rondeau, Y. Mazroui, and J.R. Gonzalez. frailtypack: An R package for the analysis of correlated survival data with frailty models using penalized likelihood estimation or parametrical estimation. Journal Of Statistical Software, 47(4) :1–28, 2012
Rondeau, S. Mathoulin-Pelissier, H. Jacqmin-Gadda, V. Brouste, and P. Soubeyran. Joint frailty models for recurring events and death using maximum penalized likelihood estimation: application on cancer events. Biostatistics, 8(4) :708–721, 2007.
Rondeau and J.R. Gonzalez. frailtypack: A computer program for the analysis of correlated failure time data using penalized likelihood estimation. Computer Methods and Programs in Biomedicine, 80(2) :154–164, 2005
Rondeau, D. Commenges, and P. Joly. Maximum penalized likelihood estimation in a gamma-frailty model. Lifetime Data Analysis, 9(2) :139–153, 2003.


Prerequisites:
A knowledge of survival analysis is required.
Good, basic knowledge in the R programming is preferable. 


Outline:

Different models and methods of estimation (parametric and semi-parametric) with goodness of fit methods will be presented. These models cover a wide field of event history analysis from survival models for truncated and/or censored data, with or without interval-censoring. Both parametric and semi-parametric penalized likelihood approaches were implemented. Dynamic predictive tools and evaluation of predictive accuracy that can be derived from these models will be exposed. Each concept will be illustrated through implementation of these models on real dataset using the R package frailtypack.

PART 1: Introduction to correlated survival data and heterogeneity

PART 2: Introduction to shared frailty models

PART 3: Joint frailty models with recurrent events

  • Joint frailty models for recurrent events and a terminal event
  • Joint models for two types of recurrent events and a terminal event

PART 4: Joint frailty models with a longitudinal biomarker

  • Joint models for a longitudinal biomarker and a terminal event
  • Joint models for a longitudinal biomarker, recurrent events and a terminal event

PART 5: Joint frailty models for clustered data

  • Joint frailty models for two survival outcomes for clustered data
  • Joint models for clustered longitudinal biomarker and a terminal event


Learning Outcomes:

After this one-day course the attendees will be able to:

  • decide which joint modelling is the most appropriate, with which correlated structure of the data when faced with recurrent events, a longitudinal biomarker and a terminal event
  • fit these joint models with R packages
  • assess their statistical assumptions
  • interpret their results

About the Instructors:

Virginie Rondeau is researcher since 2001 and director of research since 2014 in the department of Biostatistics at the National Health and Medical Research Institute of the Bordeaux University. Dr. Rondeau‘s interests include statistical modeling, survival analysis, correlated survival data, prognostic models. She has been heavily involved in collaborations in the areas of cancer recurrences and environmental health effects.

  1. Rondeau is well-suited for this course for different reasons:
  • she already gave this kind of international course at the Karolinska Institutet (with Agnieszka Krol) in 2016 and also in 2014 at the ISCB conference (in Vienna).
  • She as solid track record as principal investigator and co-investigator of many French government agency funded statistical methods and clinical research studies with >70 publications
  • She has major contributions to the development of joint statistical models for recurrent event data in the presence of competing events, including statistical software development (e.g. R statistical package “Frailtypack”since 2005
  • She has the ability to successfully collaborate with local and international clinical and statistical researchers (e.g. Sebastien Haneuse and Ina Jazic from Haward, Boston, USA; Bernard Rachet, from the London school of Hygiene and Tropical Medicine, London, UK; Takeshi Emura, from the National Central University, Taoyuan, Taiwan; Laurent Briollais, from the Dalla Lana School of Public Health, Ontario).
  • She has ongoing participation in professional statistical societies, including (International Biometric Society, International Society for Clinical Biostatistics).

Joint Models for recurrent events and competing risks (e.g. death)

Development of joint models for multiple longitudinal markers and/or multiple times-to-event.This research axis focuses mainly on the development of models for time-to-event data taking account of incomplete and/or correlated observations. These models cover a wide field of event history analysis from survival models for truncated and/or censored data, with or without interval-censoring. Both parametric and semi-parametric penalized likelihood approaches were implemented. The developed methods were mainly applied to study recurrences of cancer. I supervised several PhD students on this topic and initiated new international collaborations for that (e.g., Laurent Briollais, from the Dalla Lana School of Public Health, Ontario).

Prognostic survival models and validation

Using estimated parameter from joint models it is quite easy to compute prediction probabilities to meet a health event in a window of prediction. However, a major step in the development of dynamic prognostic tools is the validation of model assumptions and the assessment of predictive performances. These steps are much more challenging with joint models and complex censoring schemes and extensions of existing approaches need to be considered. I supervised different PhD students on this topic and initiated new international collaborations for that (e.g., Bernard Rachet from the London School of Hygiene and Tropical Medicine).

Statistical software development for correlated survival data, including joint models for recurrent events with competing risks or terminating events (e.g. death).  R statistical software “Frailtypack”

I wanted to invest a great effort in the dissemination of these statistical methods for biostatisticians but also for epidemiologists and clinicians. This is why I worked on their implementation in the R-package “FRAILTYPACK”. Furthermore, I work on the organization of short courses in several conferences, publication of didactic papers in journals of epidemiology or medical specialties and participating in the writing of a book.

Denis Rustand 

Recommendations for the Course:

A laptop is highly recommended for applications with R and Rstudio.