Bayesian Data Analysis in Ecology with R and Stan

This repository mainly contains the files to produce the online book "Data Analysis in Ecology with R and Stan".

Content

1. Top level of the repository

   The top level of the repository mainly contains the files that are used by bookdown to build the online book. These mainly include the .yml files for different settings of the book and the .Rmd files that contain the content of the book with one such file for each chapter of the book.

2. admin-Folder

   Contains administrative notes.

3. docs-Folder

   This folder contains all the files that are used to produced the page that ist published under https://tobiasroth.github.io/BDAEcology. Note that if the book is locally built using bookdown the resulting files for the html version are saved in the folder docs_local . Whenever we added new content that we are happy with, we manually copy the content of docs_local to docs and thus publish the new content. As a consequence, https://tobiasroth.github.io/BDAEcology may correspond alder versions of the .Rmd files at the top level of the repository.

4. future_chapters-Folder

   This folder contains the .Rmd files for chapters that we may eventually include into the book. Currently, these chapters are mostly under construction.

5. images

   Contains pictures that are used in the book. Note that this folder does not include the figures produced by the .Rmd files.

6. RData-Folder

   This folder contains some of the data that we use in the book. The data files are storred as .RData files that can be directly loaded into R using the funtion load(). By convention the name of the file is also the name of the R-object that will be loaded. E.g. using load("RData/elevation.RData") will load a tibble named elevation. Note, that most of the data-files that we use in the book are instead available from the R-package blmeco.

7. references-Folder

   Contains the .bib files that contain the data-base of references that we partly used in the book. The file References_fk.bib is the export of the data-base maintained by Fränzi. This file should not be changed. Additional references or references that you like to improve you should add to References_new.bib.

8. settings-Folder

9. stanmodels-Folder

   Contains the stan model description for all the models used in the book.

How to contribute

In order to contribute you need to join GitHub.

You can contribute in several ways:

• To make a general comment or add a wish for new content you can add an issue.

• The second way is to contribute content directly through the edit button at the top of the page (i.e. a symbol showing a pencil in a square). That button is linked to the rmarkdown source file of each page. You can correct typos or add new text and then submit a GitHub pull request.

• You can download the entire repository to your local computer, improve the text or R code, run the code to test and as soon you are happy with the improvement submit the entire change as a pull request.

We try to respond to you as quickly as possible. We are looking forward to your contribution!

Contributors

Thank a lot to the people that contributed to this book. We also like to acknowledge the following people that used other means than GitHub to contribute to this book:

• Ruben Garcia

Dependencies

• The main data files we use as examples in the book are contained in the R-Package blmeco available from cran or from https://github.com/fraenzi/blmeco.