index.Rmd

---
#
# Required Information --------------------------------------------------------
#
doctype: 'Dissertation' 
title: 'Development and Application of Tools for Genetic Analysis of Clonal Populations'
author: 'Zhian N. Kamvar'
date: 'December 6, 2016'
commencement: '2017'    
degree: 'Doctor of Philosophy'
major: 'Botany and Plant Pathology'
depttype: 'Department'
depthead: 'Head'
department: 'Botany and Plant Pathology'
advisor: 'Niklaus J. Grünwald'
#
# Rendering Options -----------------------------------------------------------
#
knit: "bookdown::render_book"
site: bookdown::bookdown_site
output: 
  # beaverdown::thesis_pdf: default
  beaverdown::thesis_gitbook: default
  # beaverdown::thesis_word: default
#  beaverdown::thesis_epub: default
# If you are creating a PDF you'll need to write your preliminary content here 
# or use code similar to the line below for the files.  If you are producing in 
# a different format than PDF, you can delete or ignore the following lines in 
# this YAML header.
bibliography: ['bib/main_bibliography.bib']
# Download your specific bibliography database file and refer to it in the line above.
# csl: csl/frontiers.csl
csl: csl/apa.csl
# csl: csl/american-phytopathological-society.csl
# Download your specific csl file and refer to it in the line above.
link-citations: yes
# For citations at the end of every chapter in the gitbook and linked citations
# in the PDF document.
# header-includes:
# - \renewcommand{\familydefault}{\sfdefault}
#
# Pretext sections ------------------------------------------------------------
#
abstract: >
  `r if(knitr:::is_latex_output()) beaverdown::inc("pre/00-abstract.Rmd")`
# If you'd rather include the preliminary content in files instead of inline
# like below, use a command like that for the abstract above.  Note that a tab is 
# needed on the line after the >.
acknowledgements: |
  `r if(knitr:::is_latex_output()) beaverdown::inc("pre/00-acknowledgements.Rmd")`
contributors: | 
  `r if(knitr:::is_latex_output()) beaverdown::inc("pre/00-contributors.Rmd")`
dedication: |
  This dissertation is dedicated to my mother, Jane H. Kamvar and the memory of
  my grandfather, Franklin R. Hepner. 
# preface: >  
#  Uncomment the above to include a preface. Again, this can be rendered much
#  like the files above.
---


```{r, setup, include = FALSE}
# evaluate fig.cap after a chunk is evaluated
knitr::opts_knit$set(eval.after = c('fig.cap', 'fig.scap'))
knitr::opts_chunk$set(message = FALSE, warning = FALSE)
LATEX <- knitr::opts_knit$get("rmarkdown.pandoc.to") == "latex"
TO <- if (LATEX) "latex" else "markdown"
```