A gentle tutorial on accelerated parameter and confidence interval estimation for hidden Markov models using Template Model Builder

Many modern estimators require bootstrapping to calculate confidence intervals because either no analytic standard error is available or the distribution of the parameter of interest is nonsymmetric. It remains however unclear how to obtain valid bootstrap inference when dealing with multiple imputation to address missing data. We present 4 methods that are intuitively appealing, easy to implement, and combine bootstrap estimation with multiple imputation. We show that 3 of the 4 approaches yield valid inference, but that the performance of the methods varies with respect to the number of imputed data sets and the extent of missingness. Simulation studies reveal the behavior of our approaches in finite samples. A topical analysis from HIV treatment research, which determines the optimal timing of antiretroviral treatment initiation in young children, demonstrates the practical implications of the 4 methods in a sophisticated and realistic setting. This analysis suffers from missing dat …

While likelihood-based derivatives and related facilities are available in R for many types of statistical models, the facilities are notably lacking for models estimated via lme4. This is because the necessary statistical output, including the Hessian, Fisher information and casewise contributions to the model gradient, is not immediately available from lme4 and is not trivial to obtain. In this article, we describe merDeriv, an R package which supplies new functions to obtain analytic output from Gaussian mixed models. We discuss the theoretical results implemented in the code, focusing on calculation of robust standard errors via package sandwich. We also use the sleepstudy data to illustrate the package and to compare it to a benchmark from package lavaan.

Assessing sampling uncertainty in extremum estimation can be challenging when the asymptotic variance is not analytically tractable. Bootstrap inference offers a feasible solution but can be computationally costly especially when the model is complex. This paper uses iterates of a specially designed stochastic optimization algorithm as draws from which both point estimates and bootstrap standard errors can be computed in a single run. The draws are generated by the gradient and Hessian computed from batches of data that are resampled at each iteration. We show that these draws yield consistent estimates and asymptotically valid frequentist inference for a large class of regular problems. The algorithm provides accurate standard errors in simulation examples and empirical applications at low computational costs. The draws from the algorithm also provide a convenient way to detect data irregularities.

In non-linear estimations, it is common to assess sampling uncertainty by bootstrap inference. For complex models, this can be computationally intensive. This paper combines optimization with resampling: turning stochastic optimization into a fast resampling device. Two methods are introduced: a resampled Newton-Raphson (rNR) and a resampled quasi-Newton (rqN) algorithm. Both produce draws that can be used to compute consistent estimates, confidence intervals, and standard errors in a single run. The draws are generated by a gradient and Hessian (or an approximation) computed from batches of data that are resampled at each iteration. The proposed methods transition quickly from optimization to resampling when the objective is smooth and strictly convex. Simulated and empirical applications illustrate the properties of the methods on large scale and computationally intensive problems. Comparisons with frequentist and Bayesian methods highlight the features of the algorithms.

Linear mixed-effects models are commonly used to analyze clustered data structures. There are numerous packages to fit these models in R and conduct likelihood-based inference. The implementation of resampling-based procedures for inference are more limited. In this paper, we introduce the lmeresampler package for bootstrapping nested linear mixed-effects models fit via lme4 or nlme. Bootstrap estimation allows for bias correction, adjusted standard errors and confidence intervals for small samples sizes and when distributional assumptions break down. We will also illustrate how bootstrap resampling can be used to diagnose this model class. In addition, lmeresampler makes it easy to construct interval estimates of functions of model parameters.