Semi-Parametric Joint Modeling of Survival and Longitudinal Data: The R Package JSM

This paper is devoted to the R package JSM which performs joint statistical modeling of survival and longitudinal data. In biomedical studies it has been increasingly common to collect both baseline and longitudinal covariates along with a possibly censored survival time. Instead of analyzing the survival and longitudinal outcomes separately, joint modeling approaches have attracted substantive attention in the recent literature and have been shown to correct biases from separate modeling approaches and enhance information. Most existing approaches adopt a linear mixed effects model for the longitudinal component and the Cox proportional hazards model for the survival component. We extend the Cox model to a more general class of transformation models for the survival process, where the baseline hazard function is completely unspecified leading to semiparametric survival models. We also offer a non-parametric multiplicative random effects model for the longitudinal process in JSM in addition to the linear mixed effects model. In this paper, we present the joint modeling framework that is implemented in JSM, as well as the standard error estimation methods, and illustrate the package with two real data examples: a liver cirrhosis data and a Mayo Clinic primary biliary cirrhosis data

Unifying Amplitude and Phase Analysis: A Compositional Data Approach to Functional Multivariate Mixed-Effects Modeling of Mandarin Chinese

Mandarin Chinese is characterized by being a tonal language; the pitch (or $F_0$) of its utterances carries considerable linguistic information. However, speech samples from different individuals are subject to changes in amplitude and phase which must be accounted for in any analysis which attempts to provide a linguistically meaningful description of the language. A joint model for amplitude, phase and duration is presented which combines elements from Functional Data Analysis, Compositional Data Analysis and Linear Mixed Effects Models. By decomposing functions via a functional principal component analysis, and connecting registration functions to compositional data analysis, a joint multivariate mixed effect model can be formulated which gives insights into the relationship between the different modes of variation as well as their dependence on linguistic and non-linguistic covariates. The model is applied to the COSPRO-1 data set, a comprehensive database of spoken Taiwanese Mandarin, containing approximately 50 thousand phonetically diverse sample $F_0$ contours (syllables), and reveals that phonetic information is jointly carried by both amplitude and phase variation.Comment: 49 pages, 13 figures, small changes to discussio

Functional principal component analysis for identifying multivariate patterns and archetypes of growth, and their association with long-term cognitive development

For longitudinal studies with multivariate observations, we propose statistical methods to identify clusters of archetypal subjects by using techniques from functional data analysis and to relate longitudinal patterns to outcomes. We demonstrate how this approach can be applied to examine associations between multiple time-varying exposures and subsequent health outcomes, where the former are recorded sparsely and irregularly in time, with emphasis on the utility of multiple longitudinal observations in the framework of dimension reduction techniques. In applications to children's growth data, we investigate archetypes of infant growth patterns and identify subgroups that are related to cognitive development in childhood. Specifically, "Stunting" and "Faltering" time-dynamic patterns of head circumference, body length and weight in the first 12 months are associated with lower levels of long-term cognitive development in comparison to "Generally Large" and "Catch-up" growth. Our findings provide evidence for the statistical association between multivariate growth patterns in infancy and long-term cognitive development

Functional principal component analysis for identifying multivariate patterns and archetypes of growth, and their association with long-term cognitive development.

For longitudinal studies with multivariate observations, we propose statistical methods to identify clusters of archetypal subjects by using techniques from functional data analysis and to relate longitudinal patterns to outcomes. We demonstrate how this approach can be applied to examine associations between multiple time-varying exposures and subsequent health outcomes, where the former are recorded sparsely and irregularly in time, with emphasis on the utility of multiple longitudinal observations in the framework of dimension reduction techniques. In applications to children's growth data, we investigate archetypes of infant growth patterns and identify subgroups that are related to cognitive development in childhood. Specifically, "Stunting" and "Faltering" time-dynamic patterns of head circumference, body length and weight in the first 12 months are associated with lower levels of long-term cognitive development in comparison to "Generally Large" and "Catch-up" growth. Our findings provide evidence for the statistical association between multivariate growth patterns in infancy and long-term cognitive development