index.Rmd

---
title: "How to fit an animal model"
subtitle: "An ecologist guide"
author: 
  - Julien Martin^[Univeristy of Ottawa, julien.martin@uottawa.ca]
  - Matthieu Videlier^[UQAM, videlier.mathieu@courrier.uqam.ca]
date: "`r format(Sys.Date(), '%d-%m-%Y')`"
site: bookdown::bookdown_site
documentclass: book
bibliography: [book.bib, packages.bib]
biblio-style: apalike
link-citations: yes
fontsize: 12pt
monofontoptions: "Scale=0.7"
description: "Updated and extended tutorials from An ecologist guide to animal model [@wilson2010]"
github-repo: "JulienGAMartin/wam_tuto"
cover-image: "images/missing.png"
params:
  echo_sol: true
  fit_all: false
  html_pdf: false
---

# Preface {-}

This book is a collection of tutorial from the excellent paper by [@wilson2010].
Instead of just copy pasting the tutorial in a bookdown format, the tutorials have been updated to work with the newest version of the softwares and extended to present other softwares.
**However, this is still a work in progress.**

```{block2, type = "rmdwarning"}
Do not take anything in this manual as gospel.
```

### Contributors {-}

List of people who contributed to update and extend tutorials:

- Eric Postma updated the previous tutorial from asreml-r 3 to asreml-r 4
- Julien Martin developed and maintains the site
- Mathieu Videlier added (and continues to add) more details in the document

```{r include=FALSE}
# automatically create a bib database for R packages
knitr::write_bib(c(
  .packages(), "bookdown", "knitr", "rmarkdown", "MCMCglmm", "asreml",
  "gremlin", "brms", "rstan"
), 'packages.bib')

#check 
files_rda <- list.files("data/", pattern = ".rda")


htmlT_pdfF <- ifelse(params$html_pdf == TRUE, TRUE, FALSE)
htmlF_pdfT <- ifelse(params$html_pdf == TRUE, FALSE, TRUE)

library(lme4)
library(rptR)
library(visreg)
library(asreml)
library(MCMCglmm)
library(brms)
library(mvtnorm)
library(ggplot2)
library(gridExtra)
library(nadiv)
```