Markov Chain Monte Carlo

Estimating Causal Effects from Panel Data with Dynamic Multivariate Panel Models

Abstract Panel data are ubiquitous in scientific domains such as sociology and econometrics. Various modeling approaches have been presented for the causal inference based on such data, including Markov models, cross-lagged panel models, and their extensions. Existing panel data modeling approaches typically impose some restrictive assumptions on the data-generating process, such as Gaussian responses, effects that are constant in time, and ability to consider only short-term causal effects.

Spatio-temporal modeling of co-dynamics of smallpox, measles and pertussis in pre-healthcare Finland

Abstract Infections are known to interact as previous infections may have an effect on risk of succumbing to a new infection. The co-dynamics can be mediated by immunosuppression or -modulation, shared environmental or climatic drivers, or competition for susceptible hosts. Research and statistical methods in epidemiology often concentrate on large pooled datasets, or high quality data from cities, leaving rural areas underrepresented in literature. Data considering rural populations are typically sparse and scarce, especially in the case of historical data sources, which may introduce considerable methodological challenges.

dynamite: An R Package for Dynamic Multivariate Panel Models

Abstract dynamite is an R package for Bayesian inference of intensive panel (time series) data comprising of multiple measurements per multiple individuals measured in time. The package supports joint modeling of multiple response variables, time-varying and time-invariant effects, a wide range of discrete and continuous distributions, group-specific random effects, latent factors, and customization of prior distributions of the model parameters. Models in the package are defined via a user-friendly formula interface, and estimation of the posterior distribution of the model parameters takes advantage of state-of-the-art Markov chain Monte Carlo methods.

A Bayesian spatio-temporal analysis of markets during the Finnish 1860s famine

Abstract We develop a Bayesian spatio-temporal model to study pre-industrial grain market integration during the Finnish famine of the 1860s. Our model takes into account several problematic features often present when analysing multiple spatially interdependent time series. For example, compared with the error correction methodology commonly applied in econometrics, our approach allows simultaneous modelling of multiple interdependent time series avoiding cumbersome statistical testing needed to predetermine the market leader as a point of reference.

Efficient Bayesian generalized linear models with time-varying coefficients: The walker package in R

Abstract The R package walker extends standard Bayesian general linear models to the case where the effects of the explanatory variables can vary in time. This allows, for example, to model the effects of interventions such as changes in tax policy which gradually increases their effect over time. The Markov chain Monte Carlo algorithms powering the Bayesian inference are based on Hamiltonian Monte Carlo provided by Stan software, using a state space representation of the model to marginalise over the regression coefficients for efficient low-dimensional sampling.

bssm: Bayesian Inference of Non-linear and Non-Gaussian State Space Models in R

Abstract We present an R package bssm for Bayesian non-linear/non-Gaussian state space modelling. Unlike the existing packages, bssm allows for easy-to-use approximate inference for the latent states based on Gaussian approximations such as the Laplace approximation and the extended Kalman filter. The package accommodates also discretised diffusion latent state processes. The inference is based on fully automatic, adaptive Markov chain Monte Carlo (MCMC) on the hyperparameters, with optional importance sampling post-correction to eliminate any approximation bias.

bssm: Bayesian Inference of Non-linear and Non-Gaussian State Space Models in R

Efficient methods for Bayesian inference of state space models via particle Markov chain Monte Carlo (MCMC) and MCMC based on parallel importance sampling type weighted estimators (Vihola, Helske, and Franks, 2020, doi:10.1111/sjos.12492). Gaussian, Poisson, binomial, negative binomial, and Gamma observation densities and basic stochastic volatility models with linear-Gaussian state dynamics, as well as general non-linear Gaussian models and discretised diffusion models are supported.

Importance sampling type estimators based on approximate marginal Markov chain Monte Carlo

Abstract We consider importance sampling (IS) type weighted estimators based on Markov chain Monte Carlo (MCMC) targeting an approximate marginal of the target distribution. In the context of Bayesian latent variable models, the MCMC typically operates on the hyper parameters, and the subsequent weighting may be based on IS or sequential Monte Carlo (SMC), but allows for multilevel techniques as well. The IS approach provides a natural alternative to delayed acceptance (DA) pseudo-marginal/particle MCMC, and has many advantages over DA, including a straightforward parallelisation and additional flexibility in MCMC implementation.

ramcmc: Robust Adaptive Metropolis Algorithm

Function for adapting the shape of the random walk Metropolis proposal as specified by robust adaptive Metropolis algorithm by Vihola (2012) doi:10.1007/s11222-011-9269-5. The package also includes fast functions for rank-one Cholesky update and downdate. These functions can be used directly from R or the corresponding C++ header files can be easily linked to other R packages.