KFAS - Kalman Filter and Smoother for Exponential Family State Space Models

State space modelling is an efficient and flexible framework for statistical inference of a broad class of time series and other data. KFAS includes computationally efficient functions for Kalman filtering, smoothing, forecasting, and simulation of multivariate exponential family state space models, with observations from Gaussian, Poisson, binomial, negative binomial, and gamma distributions. See the paper by Helske (2017) <doi:10.18637/jss.v078.i10> for details.

Last updated 2 months ago

dynamic-linear-modelexponential-familyfortrangaussian-modelsstate-spacetime-series

10.83 score 64 stars 16 packages 205 scripts 13k downloads

seqHMM - Mixture Hidden Markov Models for Social Sequence Data and Other Multivariate, Multichannel Categorical Time Series

Designed for fitting hidden (latent) Markov models and mixture hidden Markov models for social sequence data and other categorical time series. Also some more restricted versions of these type of models are available: Markov models, mixture Markov models, and latent class models. The package supports models for one or multiple subjects with one or multiple parallel sequences (channels). External covariates can be added to explain cluster membership in mixture models. The package provides functions for evaluating and comparing models, as well as functions for visualizing of multichannel sequence data and hidden Markov models. Models are estimated using maximum likelihood via the EM algorithm and/or direct numerical maximization with analytical gradients. All main algorithms are written in C++ with support for parallel computation. Documentation is available via several vignettes in this page, and the paper by Helske and Helske (2019, <doi:10.18637/jss.v088.i03>).

Last updated 1 years ago

categorical-dataem-algorithmhidden-markov-modelshmmmixture-markov-modelstime-series

8.51 score 96 stars 1 packages 93 scripts 480 downloads

walker - Bayesian Generalized Linear Models with Time-Varying Coefficients

Efficient Bayesian generalized linear models with time-varying coefficients as in Helske (2022, <doi:10.1016/j.softx.2022.101016>). Gaussian, Poisson, and binomial observations are supported. The Markov chain Monte Carlo (MCMC) computations are done using Hamiltonian Monte Carlo provided by Stan, using a state space representation of the model in order to marginalise over the coefficients for efficient sampling. For non-Gaussian models, the package uses the importance sampling type estimators based on approximate marginal MCMC as in Vihola, Helske, Franks (2020, <doi:10.1111/sjos.12492>).

Last updated 3 months ago

bayesiangeneralized-linear-modelsmcmcstantime-series

6.43 score 45 stars 15 scripts 399 downloads

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

Efficient methods for Bayesian inference of state space models via Markov chain Monte Carlo (MCMC) based on parallel importance sampling type weighted estimators (Vihola, Helske, and Franks, 2020, <doi:10.1111/sjos.12492>), particle MCMC, and its delayed acceptance version. 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. See Helske and Vihola (2021, <doi:10.32614/RJ-2021-103>) for details.

Last updated 2 months ago

bayesian-inferencecppmarkov-chain-monte-carloparticle-filterstate-spacetime-series

6.43 score 40 stars 11 scripts 1.5k downloads

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.

Last updated 3 years ago

6.22 score 6 stars 12 packages 8 scripts 1.5k downloads

Rlibeemd - Ensemble Empirical Mode Decomposition (EEMD) and Its Complete Variant (CEEMDAN)

An R interface for libeemd (Luukko, Helske, Räsänen, 2016) <doi:10.1007/s00180-015-0603-9>, a C library of highly efficient parallelizable functions for performing the ensemble empirical mode decomposition (EEMD), its complete variant (CEEMDAN), the regular empirical mode decomposition (EMD), and bivariate EMD (BEMD). Due to the possible portability issues CRAN version no longer supports OpenMP, you can install OpenMP-supported version from GitHub: <https://github.com/helske/Rlibeemd/>.

Last updated 1 years ago

cdecompositioneemdemdtime-series

6.06 score 37 stars 13 packages 16 scripts 596 downloads

changer - Change R Package Name

Changing the name of an existing R package is annoying but common task especially in the early stages of package development. This package (mostly) automates this task.

Last updated 3 years ago

4.38 score 48 stars 2 scripts 195 downloads

diagis - Diagnostic Plot and Multivariate Summary Statistics of Weighted Samples from Importance Sampling

Fast functions for effective sample size, weighted multivariate mean, variance, and quantile computation, and weight diagnostic plot for generic importance sampling type or other probability weighted samples.

Last updated 1 years ago

cppimportance-samplingweighted-samples

4.29 score 1 stars 1 packages 13 scripts 878 downloads

tsPI - Improved Prediction Intervals for ARIMA Processes and Structural Time Series

Prediction intervals for ARIMA and structural time series models using importance sampling approach with uninformative priors for model parameters, leading to more accurate coverage probabilities in frequentist sense. Instead of sampling the future observations and hidden states of the state space representation of the model, only model parameters are sampled, and the method is based solving the equations corresponding to the conditional coverage probability of the prediction intervals. This makes method relatively fast compared to for example MCMC methods, and standard errors of prediction limits can also be computed straightforwardly.

Last updated 1 years ago

3.60 score 8 stars 6 scripts 209 downloads

ggstudent - Continuous Confidence Interval Plots using t-Distribution

Provides an extension to 'ggplot2' (Wickham, 2016, <doi:10.1007/978-3-319-24277-4>) for creating two types of continuous confidence interval plots (Violin CI and Gradient CI plots), typically for the sample mean. These plots contain multiple user-defined confidence areas with varying colours, defined by the underlying t-distribution used to compute standard confidence intervals for the mean of the normal distribution when the variance is unknown. Two types of plots are available, a gradient plot with rectangular areas, and a violin plot where the shape (horizontal width) is defined by the probability density function of the t-distribution.

Last updated 3 years ago

2.70 score 127 downloads

particlefield - Sequential Monte Carlo for Latent Conditional Autoregressive Model

Functions for replicating the results of the latent Gaussian Markov random field experiment of Lindsten, Helske, Vihola (2018), XX. Contains also functions for performing particle Markov chain Monte Carlo estimation of the model parameters.

Last updated 3 years ago

2.18 score 3 stars 4 scripts