There is a thesis template at https://github.com/robjhyndman/monashthesis which can be forked or cloned.
The MonashEBSTemplates package (https://github.com/robjhyndman/monashebstemplates) contains additional templates for working papers, letters, exams, and presentations. This package adds templates to RStudio's Rmarkdown template menu.
All five templates are designed for output to pdf only, and meet Monash University's formatting requirements.