Special Issue about Competing Risks and Multi-State Models

There is a clear growing interest, at least in the statistical literature, in competing risks and multi-state models. With the rising interest in competing risks and multi-state models a number of software packages have been developed for the analysis of such models. The present special issue of the Journal of Statistical Software introduces a selection of R packages devoted to competing risks and multi-state models. This introduction to the special issue contains some background and highlights the contents of the contributions.

Efficient estimation of Banach parameters in semiparametric models

Consider a semiparametric model with a Euclidean parameter and an infinite-dimensional parameter, to be called a Banach parameter. Assume: (a) There exists an efficient estimator of the Euclidean parameter. (b) When the value of the Euclidean parameter is known, there exists an estimator of the Banach parameter, which depends on this value and is efficient within this restricted model. Substituting the efficient estimator of the Euclidean parameter for the value of this parameter in the estimator of the Banach parameter, one obtains an efficient estimator of the Banach parameter for the full semiparametric model with the Euclidean parameter unknown. This hereditary property of efficiency completes estimation in semiparametric models in which the Euclidean parameter has been estimated efficiently. Typically, estimation of both the Euclidean and the Banach parameter is necessary in order to describe the random phenomenon under study to a sufficient extent. Since efficient estimators are asymptotically linear, the above substitution method is a particular case of substituting asymptotically linear estimators of a Euclidean parameter into estimators that are asymptotically linear themselves and that depend on this Euclidean parameter. This more general substitution case is studied for its own sake as well, and a hereditary property for asymptotic linearity is proved.Comment: Published at http://dx.doi.org/10.1214/009053604000000913 in the Annals of Statistics (http://www.imstat.org/aos/) by the Institute of Mathematical Statistics (http://www.imstat.org

mstate: An R Package for the Analysis of Competing Risks and Multi-State Models

Multi-state models are a very useful tool to answer a wide range of questions in survival analysis that cannot, or only in a more complicated way, be answered by classical models. They are suitable for both biomedical and other applications in which time-to-event variables are analyzed. However, they are still not frequently applied. So far, an important reason for this has been the lack of available software. To overcome this problem, we have developed the mstate package in R for the analysis of multi-state models. The package covers all steps of the analysis of multi-state models, from model building and data preparation to estimation and graphical representation of the results. It can be applied to non- and semi-parametric (Cox) models. The package is also suitable for competing risks models, as they are a special category of multi-state models. This article offers guidelines for the actual use of the software by means of an elaborate multi-state analysis of data describing post-transplant events of patients with blood cancer. The data have been provided by the EBMT (the European Group for Blood and Marrow Transplantation). Special attention will be paid to the modeling of different covariate effects (the same for all transitions or transition-specific) and different baseline hazard assumptions (different for all transitions or equal for some).

The population-attributable fraction for time-dependent exposures using dynamic prediction and landmarking

The public health impact of a harmful exposure can be quantified by the population-attributable fraction (PAF). The PAF describes the attributable risk due to an exposure and is often interpreted as the proportion of preventable cases if the exposure could be extinct. Difficulties in the definition and interpretation of the PAF arise when the exposure of interest depends on time. Then, the definition of exposed and unexposed individuals is not straightforward. We propose dynamic prediction and landmarking to define and estimate a PAF in this data situation. Two estimands are discussed which are based on two hypothetical interventions that could prevent the exposure in different ways. Considering the first estimand, at each landmark the estimation problem is reduced to a time-independent setting. Then, estimation is simply performed by using a generalized-linear model accounting for the current exposure state and further (time-varying) covariates. The second estimand is based on counterfactual outcomes, estimation can be performed using pseudo-values or inverse-probability weights. The approach is explored in a simulation study and applied on two data examples. First, we study a large French database of intensive care unit patients to estimate the population-benefit of a pathogen-specific intervention that could prevent ventilator-associated pneumonia caused by the pathogen Pseudomonas aeruginosa. Moreover, we quantify the population-attributable burden of locoregional and distant recurrence in breast cancer patients.Comment: A revised version has been submitte

Special Issue about Competing Risks and Multi-State Models

There is a clear growing interest, at least in the statistical literature, in competing risks and multi-state models. With the rising interest in competing risks and multi-state models a number of software packages have been developed for the analysis of such models. The present special issue of the Journal of Statistical Software introduces a selection of R packages devoted to competing risks and multi-state models. This introduction to the special issue contains some background and highlights the contents of the contributions

Impact of chemotherapy-induced nausea and vomiting on quality of life in indonesian patients with gynecologic cancer.

Patients reported a negative impact on the QoL of delayed emesis after chemotherapy. Poor prophylaxis of patients' nausea and vomiting after chemotherapy interferes with patients' QoL. Medical and behavioral interventions may help to alleviate the negative consequences of chemotherapeutic treatment in patients with gynecologic cancers treated with suboptimal antiemetics

Maximum likelihood estimation in the additive hazards model

The additive hazards model specifies the effect of covariates on the hazard in an additive way, in contrast to the popular Cox model, in which it is multiplicative. As non-parametric model, it offers a very flexible way of modeling time-varying covariate effects. It is most commonly estimated by ordinary least squares. In this paper we consider the case where covariates are bounded, and derive the maximum likelihood estimator under the constraint that the hazard is non-negative for all covariate values in their domain. We describe an efficient algorithm to find the maximum likelihood estimator. The method is contrasted with the ordinary least squares approach in a simulation study, and the method is illustrated on a realistic data set

Individual frailty excess hazard models in cancer epidemiology

Unobserved individual heterogeneity is a common challenge in population cancer survival studies. This heterogeneity is usually associated with the combination of model misspecification and the failure to record truly relevant variables. We investigate the effects of unobserved individual heterogeneity in the context of excess hazard models, one of the main tools in cancer epidemiology. We propose an individual excess hazard frailty model to account for individual heterogeneity. This represents an extension of frailty modeling to the relative survival framework. In order to facilitate the inference on the parameters of the proposed model, we select frailty distributions which produce closed-form expressions of the marginal hazard and survival functions. The resulting model allows for an intuitive interpretation, in which the frailties induce a selection of the healthier individuals among survivors. We model the excess hazard using a flexible parametric model with a general hazard structure which facilitates the inclusion of time-dependent effects. We illustrate the performance of the proposed methodology through a simulation study. We present a real-data example using data from lung cancer patients diagnosed in England, and discuss the impact of not accounting for unobserved heterogeneity on the estimation of net survival. The methodology is implemented in the R package IFNS

SUrvival Control Chart EStimation Software in R: the success package

Monitoring the quality of statistical processes has been of great importance, mostly in industrial applications. Control charts are widely used for this purpose, but often lack the possibility to monitor survival outcomes. Recently, inspecting survival outcomes has become of interest, especially in medical settings where outcomes often depend on risk factors of patients. For this reason many new survival control charts have been devised and existing ones have been extended to incorporate survival outcomes. The R package success allows users to construct risk-adjusted control charts for survival data. Functions to determine control chart parameters are included, which can be used even without expert knowledge on the subject of control charts. The package allows to create static as well as interactive charts, which are built using ggplot2 (Wickham 2016) and plotly (Sievert 2020).Comment: 29 pages, 10 figures, guide for the R package success, see https://cran.r-project.org/package=succes