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index.Rmd
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---
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:[email protected]). 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/).