In order to compile the website, a few things are needed:

1. The most recent R version
2. The Rstudio IDE
3. The Rmarkdown package
4. The knitcitations package
5. This script to run the content of the website:
   • install.packages(c("poppr", "mmod", "genetics", "magrittr"))
6. perl
7. The Roman perl module

Once all things are installed, you can edit the *.Rmd files and then run:

make all

If everything is installed correctly, the website should compile perfectly and you can view it by opening index.html.

If you want to add a new page to the website, there are a couple of steps needed:

1. Add your page in Rmarkdown format (*.Rmd).
2. Add the basename of the new page to toc.txt in the appropriate place (preface, body, or appendix).
3. Add the proper HTML list tag to include/before_body.html.

For example, if you wanted to add a new chapter called "Mantel Tests" after the Population Structure chapter, you would do the following:

• Name the file Mantel_Test.Rmd
• In toc.txt, add the name of the file (Note, Arrows added for emphasis. Do not add them in like this):

prefix:
start:i
Preface

prefix:
start:1
Introduction
Getting_ready_to_use_R
Data_Preparation
First_Steps
Population_Hierarchies
Locus_Stats
Genotypic_EvenRichDiv
Linkage_disequilibrium
Pop_Structure
>>> Mantel_Test <<<
AMOVA
DAPC

prefix:A
start:1
Data_sets
Function_Glossary
Intro_to_R

• Modify include/before_body.html and run make all:

<!-- Some stuff up here -->
               <li><a href="Linkage_disequilibrium.html">8. Linkage disequilibrium</a></li>
               <li><a href="Pop_Structure.html">9. Population structure</a></li>
<!-- HERE >--> <li><a href="Mantel_Test.html">9. Mantel Tests</a></li> <!-- <<<<<<<< HERE -->
               <li><a href="AMOVA.html">10. AMOVA</a></li>
<!-- more stuff down here -->

Note that you don't need to change the number, when you run make all, the perl script update_toc.pl will automatically update the HTML from the table of contents.