index.Rmd

---
title: "Bayesian analysis of capture-recapture data with hidden Markov models"
subtitle: "Theory and case studies in R and NIMBLE"
author: "Olivier Gimenez"
date: "`r Sys.Date()`"
documentclass: krantz
bibliography: [book.bib]
#biblio-style: apalike
link-citations: yes
colorlinks: yes
lot: yes
lof: yes
fontsize: 12pt
site: bookdown::bookdown_site
description: "This is a textbook on the analysis of capture-recapture data with hidden Markov models (HMM) implemented in the Bayesian framework with R and NIMBLE."
url: 'https://oliviergimenez.github.io/banana-book/'
github-repo: oliviergimenez/banana-book
header-includes: 
  - \usepackage{tikz}
  - \usepackage{pgfplots}
  - \usepackage{blkarray}
  - \pgfplotsset{compat=1.18} 
  - \usepackage{tcolorbox}
  - \usepackage{arydshln}
  - \newtcolorbox{blackbox}{
    colback=white,
    colframe=purple,
    coltext=black,
    boxsep=5pt,
    arc=4pt}
  - \usepackage{subfig}
# Warning: Package pgfplots Warning: running in backwards compatibility mode (unsuitable tick labels; missing features). Consider writing \pgfplotsset{compat=1.18} into your preamble.
---

```{r setup, include=FALSE}
options(
#  htmltools.dir.version = FALSE, 
  formatR.indent = 2,
  width = 55, 
  digits = 4, 
  warnPartialMatchAttr = FALSE, 
  warnPartialMatchDollar = FALSE
)
```

# Welcome {-}

<!-- bookdown::render_book("index.Rmd", "bookdown::pdf_book") -->

Welcome to the online version of the book *Bayesian analysis of capture-recapture data with hidden Markov models: Theory and case studies in R and NIMBLE*. <!-- The book is also available in [PDF format](https://github.com/oliviergimenez/banana-book/raw/master/docs/bayesHMMcapturerecapture.pdf). -->  Here, I write about three of my favorite research topics -- capture-recapture, hidden Markov models and Bayesian statistics -- let's enjoy this great cocktail together `r emo::ji("tropical_drink")`

I'm currently writing this book, and I welcome any feedback. You may raise an issue [here](https://github.com/oliviergimenez/banana-book/issues), amend directly the R Markdown file that generated the page you're reading by clicking on the 'Edit this page' icon in the right panel, or [email me](mailto:olivier.gimenez@cefe.cnrs.fr). Many thanks!

<!-- The PDF of the book can be downloaded [here](banana-book.pdf). I still need to fix lots of issues.  -->

Olivier Gimenez. Written in Montpellier, France and Athens, Greece. 
Last updated: `r Sys.setlocale("LC_TIME", "C"); format(Sys.Date(), "%B %d, %Y")`

## License {-}

The online version of this book is licensed under the [Creative Commons Attribution-NonCommercial-NoDerivatives 4.0 International License](http://creativecommons.org/licenses/by-nc-nd/4.0/). 

The code is public domain, licensed under [Creative Commons CC0 1.0 Universal (CC0 1.0)](https://creativecommons.org/publicdomain/zero/1.0/).