pomp
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Pomp
Description
Tools for data analysis with partially observed Markov process (POMP) models (also known as stochastic dynamical systems, hidden Markov models, and nonlinear, non-Gaussian, state-space models). The package provides facilities for implementing POMP models, simulating them, and fitting them to time series data by a variety of frequentist and Bayesian methods. It is also a versatile platform for implementation of inference methods for general POMP models.
Cited in
(only showing first 100 items - show all)- Time series analysis via mechanistic models
- tsiR
- pder
- dynamite
- epimdr2
- Estimating reducible stochastic differential equations by conversion to a least-squares problem
- Direct likelihood-based inference for discretely observed stochastic compartmental models of infectious disease
- Sequential Bayesian inference for static parameters in dynamic state space models
- deSolve
- dlm
- MSBVAR
- Coupling stochastic EM and approximate Bayesian computation for parameter inference in state-space models
- A second-order iterated smoothing algorithm
- Modeling spatial invasion of Ebola in West Africa
- Modelling the skip-and-resurgence of Japanese encephalitis epidemics in Hong Kong
- Design and analysis of infectious disease studies. Abstracts from the workshop held February 18--24, 2018
- DEDiscover
- Optimal control for estimation in partially observed elliptic and hypoelliptic linear stochastic differential equations
- R package for statistical inference in dynamical systems using kernel based gradient matching: KGode
- Inference of the generalized-growth model via maximum likelihood estimation: a reflection on the impact of overdispersion
- mcmcse
- depmix
- Time-scale analysis and parameter fitting for vector-borne diseases with spatial dynamics
- Markov genealogy processes
- A mathematical model to study the 2014--2015 large-scale dengue epidemics in Kaohsiung and Tainan cities in Taiwan, China
- Mechanistic modelling of the large-scale Lassa fever epidemics in Nigeria from 2016 to 2019
- Modeling the 2014--2015 Ebola virus disease outbreaks in Sierra Leone, Guinea, and Liberia with effect of high- and low-risk susceptible individuals
- Modelling the effects of the contaminated environments on tuberculosis in Jiangsu, China
- Stochastic epidemic models inference and diagnosis with Poisson random measure data augmentation
- Inference for partially observed epidemic dynamics guided by Kalman filtering techniques
- RHmm
- emdbook
- Composable models for online Bayesian analysis of streaming data
- scaRabee
- smfsb
- On idiosyncratic stochasticity of financial leverage effects
- PLAS
- gputools
- CollocInfer
- Adaptive particle allocation in iterated sequential Monte Carlo via approximating meta-models
- smcUtils
- KFAS
- FKF
- Disentangling how multiple traits drive 2 strain frequencies in SIS dynamics with coinfection
- Delaporte
- ctsem
- Be-CoDiS
- phybreak
- adaptivetau
- bayesImageS
- incidence
- Inference for dynamic and latent variable models via iterated perturbed Bayes maps
- The elements of financial econometrics
- dynr
- Stochastic modelling for systems biology.
- stochvol
- LibBi
- Biips
- vSMC
- SMCTC
- PBSddesolve
- POET
- episode
- glarma
- MARSS
- tsintermittent
- gamlss.util
- acp
- epiABC
- R0
- is2
- EpiEstim
- SurvStat@RKI
- DeCo
- DR-ABC
- dse
- simode
- deGradInfer
- treespace
- panelPomp
- phyloscanner
- socialmixr
- Nextstrain
- epimdr
- Comparison of the performance of particle filter algorithms applied to tracking of a disease epidemic
- Bootstrap maximum likelihood for quasi-stationary distributions
- Epidemics. Models and data using R
- Particle Markov Chain Monte Carlo Methods
- walker
- torchsde
- Bivariate models for time series of counts: a comparison study between PBINAR models and dynamic factor models
- Panel Data Analysis via Mechanistic Models
- KGode
- FENmlm
- stlh
- Gaussian process emulators for spatial individual-level models of infectious disease
- dynamichazard
- BayesEstDiffusion.jl
- Time series analysis for the state-space model with R/Stan
- Discussion of ``Feature matching in time series modeling by Y. Xia and H. Tong
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