Merge pull request #21 from jhollway/develop

Adding chapter_pdf()

DESCRIPTION

@@ -1,7 +1,7 @@
 Package: iheiddown
 Title: A RMarkdown class for IHEID documents
-Date: 2020-08-10
-Version: 0.6.0
+Date: 2020-09-14
+Version: 0.7.0
 Authors@R: 
     c(person(given = "James",
            family = "Hollway",
@@ -13,10 +13,10 @@ Description: This package supports writing dissertations, theses, and syllabi
     according to the Graduate Institute of International and Development Studies 
     regulations.
 License: MIT
-Imports: bookdown, tidyverse, roxygen2, citr, covr
+Imports: bookdown, tidyverse, roxygen2, citr, covr, ggplot2
 Encoding: UTF-8
 LazyData: true
 Roxygen: list(markdown = TRUE)
 RoxygenNote: 7.1.1
 Suggests: 
-    testthat
+    testthat, kableExtra

NAMESPACE

@@ -1,6 +1,8 @@
 # Generated by roxygen2: do not edit by hand
 
 export(advdate)
+export(bookdown_profile)
+export(chapter_pdf)
 export(syllabus_pdf)
 export(thesis_pdf)
 importFrom(utils,file.edit)

NEWS.md

@@ -1,3 +1,20 @@
+# iheiddown 0.7.0
+
+## Thesis
+
+* Added `chapter_pdf()` knit function for previewing chapters (closes #19)
+* Added `bookdown_profile` addin for RStudio to improve access to the bookdown profile
+* Overhaul of chapter 4 of skeleton:
+  * More detail and figure on code chunks
+  * More detail on including external graphics
+  * More detail on loading, exploring, and summarising data
+  * Added detail on presenting tables of inferential results (closes #18)
+
+## Syllabus
+
+* Added 'geneva-syllabus.csl' to support in-text full citations (fixes #20)
+* Added 'tightlist' framework to syllabus template
+
 # iheiddown 0.6.0
 
 * Set up `testthat` for package

R/bookdown_profile.R

@@ -0,0 +1,17 @@
+#' Manage iheiddown profile
+#'
+#' @description This RStudio Addin opens up the ~/_bookdown.yml file for
+#' users to edit. If the file doesn't exists, it will create one.
+#' 
+#' @importFrom utils file.edit
+#' @export
+bookdown_profile <- function() {
+  profile_file <- getOption("_bookdown.yml", "~/_bookdown.yml")
+  if (!file.exists(profile_file)) {
+    file.copy(
+      from = system.file("_bookdown.yml", package = "iheiddown"),
+      to = profile_file
+    )
+  }
+  file.edit(profile_file)
+}

R/thesis_pdf.R

@@ -19,3 +19,24 @@ thesis_pdf <- function(...){
                                                         template = system.file('rmarkdown', 'templates', 'thesis_pdf', 'resources', 'template.tex',
                                                                                package = 'iheiddown')))
 }
+
+#' Creates an R Markdown PDF Thesis chapter
+#'
+#' This function can be used in the header of each constituent chapter of an IHEID thesis
+#' to output a draft version of the chapter for proofreading or sending to your supervisor.
+#'
+#' @export
+#'
+#' @return A modified \code{pdf_document} based on the IHEID Thesis LaTeX
+#'   template
+#' @examples
+#' \dontrun{
+#' knit: iheiddown::chapter_pdf
+#' }
+chapter_pdf <- function(...){
+  bookdown::preview_chapter(...,
+                        output_file = paste0("Chapter_", Sys.Date()), 
+                        output_format = rmarkdown::pdf_document(latex_engine = "xelatex",
+                                                           template = system.file('rmarkdown', 'templates', 'chapter_pdf', 'resources', 'template.tex',
+                                                                                  package = 'iheiddown')))
+}

inst/_bookdown.yml

@@ -0,0 +1,19 @@
+# If you specify a sub directory with rmd_subdir, then bookdown will search through this
+# folder too
+rmd_subdir: ["front-matter","chapters"]
+# Make sure to start any acknowledgements and/or abstract Rmd files with 
+# an underscore, e.g. _abstract.Rmd. 
+# Otherwise bookdown will start to merge the abstract in to the body text which almost 
+# certainly isn't what you want
+# Alternatively, you can comment out rmd_subdir and specify manually what files to include with rmd_files
+# rmd_files: ["Untitled.Rmd", "chapters/01-basics.Rmd", "back-matter/99-references.Rmd"]
+
+# The following can be changed to another folder if you wish
+output_dir: "versions"
+
+# Please suggest and submit changes to the source .Rmd files here:
+edit: https://github.com/jhollway/iheiddown/tree/master/%s
+
+# If this is set to true, then you don't have to manually delete the merged _main.Rmd file 
+# if something goes wrong when you try to build
+delete_merged_file: true

inst/rmarkdown/templates/chapter_pdf/resources/template.tex

@@ -0,0 +1,195 @@
+%%%%%%%%%%%%%%%%%%%%%%%%%%%
+%% IHEID CHAPTER TEMPLATE %%
+%%%%%%%%%%%%%%%%%%%%%%%%%%%
+
+%%%% PAGE LAYOUT
+% Pass this in from YAML
+\documentclass[a4paper, oneside]{report}
+\usepackage[includehead,hmargin={3.1cm, 3.1cm}, vmargin={2.5cm,2.7cm}, headsep=.8cm,footskip=1.2cm]{geometry}
+
+\usepackage{fancyhdr}
+\setlength{\headheight}{15pt}
+\fancyhf{} % clear the header and footers
+\pagestyle{fancy}
+\renewcommand{\chaptermark}[1]{\markboth{\thechapter. #1}{\thechapter. #1}}
+\renewcommand{\sectionmark}[1]{\markright{\thesection. #1}} 
+\renewcommand{\headrulewidth}{0pt}
+\fancyhead[LO]{\emph{\leftmark}}
+
+\fancypagestyle{plain}{\fancyhf{}\fancyfoot[C]{\emph{\thepage}}}
+
+% This adds a "DRAFT" footer to every normal page.  (The first page of each chapter is not a "normal" page.)
+\fancyfoot[C]{\emph{DRAFT from \today}}
+
+%%%%% FONTS
+\RequirePackage[T1]{fontenc} % requires XeLatex or LuaTex (remove to use pdfLaTex)
+%\RequirePackage[utf8]{inputenc} % ignored when using XeLaTex or LuaTex (uncomment when using pdfLaTex)
+\RequirePackage{microtype} % this makes fonts almost imperceptibly smoother
+\RequirePackage{fontspec} % requires XeLatex or LuaTex (remove to use pdfLaTex)
+% For the headings we will use Helvetica
+\RequirePackage{helvet}
+\usepackage[immediate]{silence}
+\WarningFilter[temp]{latex}{Command} % silence the warning
+\usepackage{sectsty}
+\DeactivateWarningFilters[temp] % So nothing unrelated gets silenced
+\allsectionsfont{\sffamily}
+% For the main text and equations we will use Baskerville and Palatino
+\RequirePackage{mathpazo}
+\RequirePackage{baskervald}
+% For formatting code or package names, we will use Lucida Console
+\RequirePackage{zi4}
+% Enable strikethrough
+\usepackage[normalem]{ulem}
+
+% This highlights (in blue) corrections marked with (for words) \mccorrect{blah} or (for whole
+% paragraphs) \begin{mccorrection} . . . \end{mccorrection}.  This can be useful for sending a PDF of
+% your corrected thesis to your examiners for review.  Turn it off, and the blue disappears.
+% $if(params.corrections)$
+% \correctionstrue
+% $endif$
+
+% UL 30 Nov 2018 pandoc puts lists in 'tightlist' command when no space between bullet points in Rmd file
+\providecommand{\tightlist}{%
+  \setlength{\itemsep}{0pt}\setlength{\parskip}{0pt}}
+
+%UL 15 Oct 2019, enable link highlighting to be turned off from YAML
+% \usepackage[dvipsnames]{color}
+% \usepackage[colorlinks=true,pdfpagelabels,hidelinks=$hidelinks$]{hyperref}
+\RequirePackage[colorlinks=true,linkcolor=red,
+citecolor=red,filecolor=red,urlcolor=black]{hyperref} % uses IHEID red for external links
+% \hypersetup{citecolor=red}
+
+%%%%% BIBLIOGRAPHY SETUP
+% Note that your bibliography will require some tweaking depending on your department, preferred format, etc.
+% The options included below are just very basic "sciencey" and "humanitiesey" options to get started.
+% If you've not used LaTeX before, I recommend reading a little about biblatex/biber and getting started with it.
+% If you're already a LaTeX pro and are used to natbib or something, modify as necessary.
+% Either way, you'll have to choose and configure an appropriate bibliography format...
+
+% The science-type option: numerical in-text citation with references in order of appearance.
+% \usepackage[style=numeric-comp, sorting=none, backend=biber, doi=false, isbn=false]{biblatex}
+% \newcommand*{\bibtitle}{References}
+
+% The humanities-type option: author-year in-text citation with an alphabetical works cited.
+% \usepackage[style=authoryear, sorting=nyt, backend=biber, maxcitenames=2, useprefix, doi=false, isbn=false]{biblatex}
+% \newcommand*{\bibtitle}{Works Cited}
+
+%UL 3 Dec 2018: set this from YAML in index.Rmd
+% $if(bib-humanities)$
+% \usepackage[style=authoryear, sorting=nyt, backend=biber, maxcitenames=2, useprefix, 
+% doi=$if(doi-in-bibliography)$$doi-in-bibliography$$else$false$endif$, isbn=false, uniquename=false]{biblatex}
+% \newcommand*{\bibtitle}{$bibliography-heading-in-pdf$}
+% $else$
+% \usepackage[style=numeric-comp, sorting=none, backend=biber, doi=$doi-in-bibliography$, isbn=false]{biblatex}
+% \newcommand*{\bibtitle}{$bibliography-heading-in-pdf$}
+% $endif$
+
+% This makes the bibliography left-aligned (not 'justified') and slightly smaller font.
+% \renewcommand*{\bibfont}{\raggedright\small}
+
+% Change this to the name of your .bib file (usually exported from a citation manager like Zotero or EndNote).
+% \addbibresource{$bibliography$}
+
+% Uncomment this if you want equation numbers per section (2.3.12), instead of per chapter (2.18):
+%\numberwithin{equation}{subsection}
+
+
+%%%%% THESIS / TITLE PAGE INFORMATION
+% Everybody needs to complete the following:
+% \title{$title$}
+% \author{$author$}
+
+% JEM: Lengths for single spacing (ie separate abstract, captions), front matter (abstract,
+%   acknowledgements, table of contents, etc), and main body text.
+\newlength{\singlebaselineskip}
+\newlength{\frontmatterbaselineskip}
+\newlength{\textbaselineskip}
+
+\setlength{\singlebaselineskip}{\baselineskip}
+\setlength{\frontmatterbaselineskip}{17pt plus1pt minus1pt}
+\setlength{\textbaselineskip}{22pt plus2pt}
+
+%
+% Environments
+%
+
+\usepackage[nohints,tight]{minitoc} 
+	\setcounter{minitocdepth}{2} 
+	% Generates mini tables of contents per chapter
+
+% For the abbreviations
+\usepackage{enumitem}
+\newlist{abbrv}{itemize}{1}
+\setlist[abbrv,1]{label=,labelwidth=1in,align=parleft,itemsep=0.1\baselineskip,leftmargin=!}
+
+\usepackage{nicefrac}
+\usepackage{amsmath}
+\usepackage{amssymb}
+\usepackage{textcomp}
+
+\usepackage{longtable} 
+	% Allows tables to span multiple pages (this package must be called before hyperref)
+
+\usepackage[font=small,labelfont=bf]{caption} 
+	% Nicer captions
+
+\usepackage{multicol,multirow,array} 
+	% Used to make multiple columns for the indices and for creating columns that span multiple rows in tables
+
+\usepackage{rotating} 
+	% To allow tables in landscape mode
+
+\usepackage{booktabs} 
+	% For better looking tables
+
+\usepackage{pdfpages} 
+	% Allows multi-page pdfs to be inserted as graphics
+
+\usepackage{graphicx}
+\graphicspath{{../figures/}{_bookdown_files/}}
+
+\usepackage{xfrac}
+
+%%%%%%%%%%%%%%%%%%%%%%%%%%%
+%% ACTUAL DOCUMENT HERE  %%
+%%%%%%%%%%%%%%%%%%%%%%%%%%%
+\begin{document}
+
+%%%%% CHOOSE YOUR LINE SPACING HERE
+% This is the official option.  Use it for your submission copy and library copy:
+\setlength{\textbaselineskip}{22pt plus2pt}
+% This is closer spacing (about 1.5-spaced) that you might prefer for your personal copies:
+%\setlength{\textbaselineskip}{18pt plus2pt minus1pt}
+
+% You can set the spacing here for the roman-numbered pages (acknowledgements, table of contents, etc.)
+\setlength{\frontmatterbaselineskip}{17pt plus1pt minus1pt}
+
+% UL: You can set the general paragraph spacing here - I've set it to 2pt (was 0) so
+% it's less claustrophobic
+\setlength{\parskip}{2pt plus 1pt}
+
+% Leave this line alone; it gets things started for the real document.
+\setlength{\baselineskip}{\textbaselineskip}
+
+%%%%% CHAPTERS
+% Add or remove any chapters you'd like here, by file name (excluding '.tex'):
+\flushbottom
+
+% all your chapters and appendices will appear here
+$body$
+
+
+%%%%% REFERENCES
+
+% JEM: Quote for the top of references (just like a chapter quote if you're using them).  Comment to skip.
+% \begin{savequote}[8cm]
+% The first kind of intellectual and artistic personality belongs to the hedgehogs, the second to the foxes \dots
+%   \qauthor{--- Sir Isaiah Berlin \cite{berlin_hedgehog_2013}}
+% \end{savequote}
+
+% \setlength{\baselineskip}{0pt} % JEM: Single-space References
+% 
+% {\renewcommand*\MakeUppercase[1]{#1}%
+% \printbibliography[heading=bibintoc,title={References}]}
+
+\end{document}