bssm: Bayesian Inference of State Space Models

In bssm: Bayesian Inference of Non-Linear and Non-Gaussian State Space Models

Bayesian Inference of State Space Models

Description

This package contains functions for efficient Bayesian inference of state space models (SSMs). For details, see the package vignette and the R Journal paper.

Details

The model is assumed to be either

• Exponential family state space model, where the state equation is linear Gaussian, and the conditional observation density is either Gaussian, Poisson, binomial, negative binomial or Gamma density.

• Basic stochastic volatility model.

• General non-linear model with Gaussian noise terms.

• Model with continuous SDE dynamics.

Missing values in response series are allowed as per SSM theory and can be automatically predicted, but there can be no missing values in the system matrices of the model.

The package contains multiple functions for building the model:

• bsm_lg for basic univariate structural time series model (BSM), ar1 for univariate noisy AR(1) process, and ssm_ulg and ssm_mlg for arbitrary linear gaussian model with univariate/multivariate observations.

• The non-Gaussian versions (where observations are non-Gaussian) of the above models can be constructed using the functions bsm_ng, ar1_ng, ssm_ung and ssm_mng.

• An univariate stochastic volatility model can be defined using a function svm.

• For non-linear models, user must define the model using C++ snippets and the the function ssm_nlg. See details in the growth_model vignette.

• Diffusion models can be defined with the function ssm_sde, again using the C++ snippets. See sde_model vignette for details.

See the corresponding functions for some examples and details.

After building the model, the model can be estimated via run_mcmc function. The documentation of this function gives some examples. The bssm package includes several MCMC sampling and sequential Monte Carlo methods for models outside classic linear-Gaussian framework. For definitions of the currently supported models and methods, usage of the package as well as some theory behind the novel IS-MCMC and \psi-APF algorithms, see Helske and Vihola (2021), Vihola, Helske, Franks (2020), and the package vignettes.

The output of the run_mcmc can be analysed by extracting the posterior samples of the latent states and hyperparameters using as.data.frame, as_draws, expand_sample, and summary methods, as well as fitted and predict methods. Some MCMC diagnostics checks are available via check_diagnostics function, some of which are also provided via the print method of the run_mcmc output. Functionality of the ggplot2 and bayesplot, can be used to visualize the posterior draws or their summary statistics, and further diagnostics checks can be performed with the help of the posterior and coda packages.

References

Helske J, Vihola M (2021). bssm: Bayesian Inference of Non-linear and Non-Gaussian State Space Models in R. The R Journal (2021) 13:2, 578-589. https://doi.org/10.32614/RJ-2021-103

Vihola, M, Helske, J, Franks, J. (2020). Importance sampling type estimators based on approximate marginal Markov chain Monte Carlo. Scand J Statist. 1-38. https://doi.org/10.1111/sjos.12492

H. Wickham. ggplot2: Elegant Graphics for Data Analysis. Springer-Verlag New York, 2016.

Gabry J, Mahr T (2022). “bayesplot: Plotting for Bayesian Models.” R package version 1.9.0, https://mc-stan.org/bayesplot.

Bürkner P, Gabry J, Kay M, Vehtari A (2022). “posterior: Tools for Working with Posterior Distributions.” R package version 1.2.1, https://mc-stan.org/posterior.

Martyn Plummer, Nicky Best, Kate Cowles and Karen Vines (2006). CODA: Convergence Diagnosis and Output Analysis for MCMC, R News, vol 6, 7-11.

Examples

# Create a local level model (latent random walk + noise) to the Nile
# dataset using the bsm_lg function:
model <- bsm_lg(Nile,
  sd_y = tnormal(init = 100, mean = 100, sd = 100, min = 0),
  sd_level = tnormal(init = 50, mean = 50, sd = 100, min = 0),
  a1 = 1000, P1 = 500^2)

# the priors for the unknown paramters sd_y and sd_level were defined
# as trunctated normal distributions, see ?bssm_prior for details

# Run the MCMC for 2000 iterations (notice the small number of iterations to
# comply with the CRAN's check requirements)
fit <- run_mcmc(model, iter = 2000)

# Some diagnostics checks:
check_diagnostics(fit)

# print some summary information:
fit

# traceplots:
plot(fit)

# extract the summary statistics for state variable
sumr <- summary(fit,variable = "states")

# visualize
library("ggplot2")
ggplot(sumr, aes(time, Mean)) +
    geom_ribbon(aes(ymin = `2.5%`, ymax = `97.5%`),alpha = 0.25) +
    geom_line() +
    theme_bw()

bssm documentation built on Nov. 2, 2023, 6:25 p.m.