When considering functional principal component analysis for sparsely observed longitudinal data that take values on a nonlinear manifold, a major challenge is how to handle the sparse and irregular observations that are commonly encountered in longitudinal studies. Addressing this challenge, we provide theory and implementations for a manifold version of the principal analysis by conditional expectation (PACE) procedure that produces representations intrinsic to the manifold, extending a well-established version of functional principal component analysis targeting sparsely sampled longitudinal data in linear spaces. Key steps are local linear smoothing methods for the estimation of a Frechet mean curve, mapping the observed manifold-valued longitudinal data to tangent spaces around the estimated mean curve, and applying smoothing methods to obtain the covariance structure of the mapped data. Dimension reduction is achieved via representations based on the first few leading principal components. A finitely truncated representation of the original manifold-valued data is then obtained by mapping these tangent space representations to the manifold. We show that the proposed estimates of mean curve and covariance structure achieve state-of-the-art convergence rates. For longitudinal emotional well-being data for unemployed workers as an example of time-dynamic compositional data that are located on a sphere, we demonstrate that our methods lead to interpretable eigenfunctions and principal component scores. In a second example, we analyze the body shapes of wallabies by mapping the relative size of their body parts onto a spherical pre-shape space. Compared to standard functional principal component analysis, which is based on Euclidean geometry, the proposed approach leads to improved trajectory recovery for sparsely sampled data on nonlinear manifolds.
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