Bayesian capture-recapture inference with hidden Markov models

A two-day workshop with R and Nimble

What: This is a workshop on Bayesian inference of animal demography. Hopefully, you will learn about how to infer demographic parameters (e.g. survival, dispersal). Our hope is to provide you with what you need to go your own path. The event is free of charge, and video-recorded.

For whom: This is a workshop for ecologists. No previous experience with Nimble or Bayesian statistics is assumed, but knowledge of R is required.

How: Through a combination of lectures and live demonstrations, you will get acquainted with the Bayesian approach, MCMC methods and the R Nimble package to fit single-site, multi-site, multi-state and multi-event models to capture-recapture data within the hidden Markov modeling (HMM) framework.

Who: O. Gimenez, C. R. Nater, S. Cubaynes, P. de Valpine, M. Quéroué

When: May 17-18, 2021

Where: Online via Zoom/Slack


All times are Paris time UTC+2

  1. Welcoming words (9am-9:30am)
  2. Crash course on Bayesian statistics and MCMC algorithms (9:30am-11am)
  3. Free the modeler in you: Introduction to Nimble (11:30am-12:30pm)
  4. What you see is not what you get: Hidden Markov models and capture-recapture data (2pm-3:30pm)
  5. Dead or alive: Survival estimation - part 1 (4pm-5pm)
  1. Dead or alive: Survival estimation - part 2 (9am-10:30am)
  2. On the move: Transition estimation (11am-12:30pm)
  3. Known knowns, unknown knowns and unknowns: Uncertainty in state assignment (2pm-3:30pm)
  4. Skip your coffee break: Speed up MCMC convergence (4pm-5pm)
  5. Take-home messages (5pm-5:30pm)


To-do list


Text and figures are licensed under Creative Commons Attribution CC BY 4.0. Any computer code (R, HTML, CSS, etc.) in slides and worksheets, including in slide and worksheet sources, is also licensed under MIT.


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