Completed PDF version

.Rbuildignore

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+^.*\.Rproj$
+^\.Rproj\.user$

.gitignore

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+.Rproj.user
+.Rhistory
+.RData

DESCRIPTION

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+Package: thesisdown
+Title: An updated R Markdown thesis template using the bookdown package
+Version: 0.0.1
+Authors@R: person("Chester", "Ismay", email = "chester.ismay@gmail.com", role = c("aut", "cre"))
+Description: Using the bookdown package and LaTeX and Word thesis templates from
+    Reed College, this package aims to encourage reproducible research using
+    simple Markdown syntax while embedding all of the R code to produce plots
+    and analyses as well.
+Depends:
+    R (>= 3.3.0),
+    devtools,
+    dplyr,
+    ggplot2,
+    bookdown,
+    knitr
+License: MIT
+Encoding: UTF-8
+LazyData: true
+RoxygenNote: 5.0.1

NAMESPACE

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+# Generated by roxygen2: do not edit by hand
+
+export(thesis_pdf)

R/thesis.R

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+#' Creates an R Markdown PDF Thesis document
+#'
+#' This is a function called in output in the YAML of the driver Rmd file
+#' to specify using the Reed College Senior Thesis LaTeX template and cls files.
+#'
+#' @export
+#' @param toc A Boolean (TRUE or FALSE) specifying where table of contents should be created
+#' @param toc_depth A positive integer
+#' @return A modified \code{pdf_document} based on the Reed Senior Thesis LaTeX
+#'   template
+#' @examples
+#' \dontrun{
+#'  output: thesisdown::thesis_pdf
+#' }
+thesis_pdf <- function(toc = TRUE, toc_depth = 3){
+  #template <- system.file("template.tex", package = )
+
+  base <- bookdown::pdf_book(template = "template.tex",
+    toc = toc,
+    toc_depth = toc_depth,
+    highlight = "pygments",
+    keep_tex = TRUE,
+    pandoc_args = "--chapters")
+
+  # Mostly copied from knitr::render_sweave
+  base$knitr$opts_chunk$comment <- NA
+  base$knitr$opts_chunk$fig.align <- "center"
+  base$knitr$knit_hooks$plot <- knitr:::hook_plot_tex
+
+  base
+  #  }
+
+}

R/thesisdown.R

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+#' thesisdown: A package for creating undergraduate, Masters, and PhD theses
+#'using R Markdown
+#'
+#' The reedtemplates package provides three important functions:
+#' reed_thesis, label, and ref.
+#'
+#' @section thesis_gitbook:
+#' Creates an R Markdown thesis template as a webpage
+#' @section thesis_pdf:
+#' Creates an R Markdown thesis template as a PDF
+#' @section thesis_word:
+#' Creates an R Markdown thesis template as a Microsoft Word document
+#' @docType package
+#' @name thesisdown
+NULL

inst/rmarkdown/templates/thesis/skeleton/_book/thesis.log

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+This is pdfTeX, Version 3.14159265-2.6-1.40.17 (TeX Live 2016) (preloaded format=pdflatex 2016.5.22)  16 AUG 2016 13:40
+entering extended mode
+ \write18 enabled.
+ %&-line parsing enabled.
+**thesis.tex
+(./thesis.tex
+LaTeX2e <2016/03/31>
+Babel <3.9r> and hyphenation patterns for 83 language(s) loaded.
+
+! LaTeX Error: File `reedthesis.cls' not found.
+
+Type X to quit or <RETURN> to proceed,
+or enter new name. (Default extension: cls)
+
+Enter file name: 
+! Emergency stop.
+<read *> 
+
+l.33 \usepackage
+                {graphicx,latexsym}^^M
+*** (cannot \read from terminal in nonstop modes)
+
+
+Here is how much of TeX's memory you used:
+ 10 strings out of 493014
+ 192 string characters out of 6133351
+ 53601 words of memory out of 5000000
+ 3651 multiletter control sequences out of 15000+600000
+ 3640 words of font info for 14 fonts, out of 8000000 for 9000
+ 1141 hyphenation exceptions out of 8191
+ 10i,0n,7p,81b,8s stack positions out of 5000i,500n,10000p,200000b,80000s
+!  ==> Fatal error occurred, no output PDF file produced!