initial commit

_bookdown_files/thesis-dissertaion_cache/latex/__packages

+base
+tidyverse
+ggplot2
+tibble
+tidyr
+readr
+purrr
+dplyr
+stringr
+forcats
+kableExtra

_output.yml

+bookdown::pdf_book:
+  latex_engine: xelatex
+  includes:
+      in_header: tex-files/preamble.tex
+      keep_tex: yes
+      citation_package: natbib
+      fig_caption: yes
+      fontsize: 11pt
+      linestretch: 1.5
+      toc-depth: 1
+      secnumdepth: 1
+      biblio-style: apalike
\ No newline at end of file

appendix.Rmd

+# (APPENDIX) Appendix {-}
\ No newline at end of file

bib/packages.bib

+@Manual{R-base,
+  title = {R: A Language and Environment for Statistical Computing},
+  author = {{R Core Team}},
+  organization = {R Foundation for Statistical Computing},
+  address = {Vienna, Austria},
+  year = {2018},
+  url = {https://www.R-project.org/},
+}
+@Manual{R-bookdown,
+  title = {bookdown: Authoring Books and Technical Documents with R Markdown},
+  author = {Yihui Xie},
+  year = {2018},
+  note = {R package version 0.7},
+  url = {https://CRAN.R-project.org/package=bookdown},
+}
+@Manual{R-knitr,
+  title = {knitr: A General-Purpose Package for Dynamic Report Generation in R},
+  author = {Yihui Xie},
+  year = {2018},
+  note = {R package version 1.20},
+  url = {https://CRAN.R-project.org/package=knitr},
+}
+@Manual{R-rmarkdown,
+  title = {rmarkdown: Dynamic Documents for R},
+  author = {JJ Allaire and Yihui Xie and Jonathan McPherson and Javier Luraschi and Kevin Ushey and Aron Atkins and Hadley Wickham and Joe Cheng and Winston Chang},
+  year = {2018},
+  note = {R package version 1.10},
+  url = {https://CRAN.R-project.org/package=rmarkdown},
+}
+@Manual{R-PepTools,
+  title = {PepTools - An R-package for making immunoinformatics accessible},
+  author = {Leon Eyrich Jessen},
+  year = {2018},
+  note = {R package version 0.1.0},
+  url = {https://github.com/leonjessen/PepTools},
+}

index.Rmd

+--- 
+# YAML for thesis template
+site: bookdown::bookdown_site
+documentclass: book
+bibliography: [bib/packages.bib, bib/papers.bib] # Changes to reference bib files as needed
+biblio-style: apalike
+toc: False # Table of contents supplied from tex files
+lof: False # List of figures supplied from tex files
+lot: False # List of tables supplied from text files
+link-citations: yes
+geometry: "left=2.5cm, right=2.5cm, top=2.5cm, bottom=2.5cm" # Change to margins required
+---
+
+```{r include=FALSE, cache=TRUE}
+# Load libraries and data here, and cache the data
+library(tidyverse)
+library(kableExtra)
+```