R package pmhtutorial available from CRAN.
Zipkin, E.F., Sillett, T.S., Grant, E.H.C., Chandler, R.B., and Royle, J.A. (2014) Inferences from count data using multi-state population models: a comparison to capture-recapture approaches. Ecology and Evolution. 4: 417-426.
State-space models for statistical mortality projections
An R package for fitting state-space models to repeated measures of multiple individuals with covariates
Himes Boor, G.K., T.L. McGuire, A.J. Warlick, R.L. Taylor, S.J. Converse, J.R. McClung, A.D. Stephens. 2022. Estimating reproductive rates and juvenile survival when offspring ages are uncertain: a novel multievent mark-recapture model applied to an endangered beluga whale population. Methods in Ecology and Evolution
a helper package for pomp
Create Multivariate Autoregressive State-Space Models with the MARSS R package
Bayesian State-Space Modeling of Mouse-Tracking Experiments via Stan
Modeling the COVID-19 Infection Rates by Regime Switching Unobserved Components Models
An age-based state-space stock assessment model for the stock of American plaice on the Grand Bank of Newfoundland.
Source code and data for the tutorial: "Getting started with particle Metropolis-Hastings for inference in nonlinear models"
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