update (#88)

* Add hadamardown template (#67) * Add hadamardown * Update documentation * Update DESCRIPTION * Switch to PDF by default * Update README.md * Update README.md * updates README.md (#78) * updates README.md * changes dependencies from devtools to remotes. * Update template.tex (#79) * Add link to amsterdown pkg in README (#80) * Fixed broken URLs and added few more (#85) * Fixed broken URLs and added few more * Reversed a URL change for markdown cheatsheet I moved the Rmakrdown Cheatsheet under R Markdown and reversed the modification of the Markdown Cheatsheet. * Allow user to change bookdown::gitbook() options (#84) * Add ... * Allow user to change "before" and "after" toc arguments * Pass all type of option and sub-options to bookdown::gitbook Co-authored-by: Antoine Bichat <30300749+abichat@users.noreply.github.com> Co-authored-by: Leon Reteig <35737105+lcreteig@users.noreply.github.com> Co-authored-by: Mehrad Mahmoudian <m.mahmoudian@gmail.com>
ismayc · May 25, 2020 · f358802 · f358802
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diff --git a/DESCRIPTION b/DESCRIPTION
@@ -11,7 +11,7 @@ Description: Using the bookdown package and LaTeX and Word thesis templates from
 Maintainer: Chester Ismay <chester.ismay@gmail.com>
 Depends:
     R (>= 3.2.0),
-    devtools,
+    remotes,
     dplyr,
     ggplot2,
     bookdown,

diff --git a/R/thesis.R b/R/thesis.R
@@ -53,14 +53,36 @@ thesis_pdf <- function(toc = TRUE, toc_depth = 3, highlight = "default", ...){
 #' }
 thesis_gitbook <- function(...){
 
-  base <- bookdown::gitbook(
-    split_by = "chapter+number",
-    config = list(toc = list(collapse = "section",
-      before = '<li><a href="./"></a></li>',
-      after = '<li><a href="https://github.com/rstudio/bookdown" target="blank">Published with bookdown</a></li>',
-      ...)
-    )
-  )
+  config_default <- list(
+    toc = list(collapse = "section",
+               before = '<li><a href="./"></a></li>',
+               after = '<li><a href="https://github.com/rstudio/bookdown" target="blank">Published with bookdown</a></li>'))
+
+  listarg <- list(...)
+
+  if (!"split_by" %in% names(listarg)) {
+    listarg$split_by <- "chapter+number"
+  }
+
+  if (!"config" %in% names(listarg)) {
+    listarg$config <- config_default
+  } else {
+    if (!"toc" %in% names(listarg$config)) {
+      listarg$config$toc <- config_default$toc
+    } else {
+      if (!"collapse" %in% names(listarg$config$toc)) {
+        listarg$config$toc$collapse <- config_default$toc$collapse
+      }
+      if (!"before" %in% names(listarg$config$toc)) {
+        listarg$config$toc$before <- config_default$toc$before
+      }
+      if (!"after" %in% names(listarg$config$toc)) {
+        listarg$config$toc$after <- config_default$toc$after
+      }
+    }
+  }
+
+  base <- do.call(bookdown::gitbook, listarg)
 
   # Mostly copied from knitr::render_sweave
   base$knitr$opts_chunk$comment <- NA

diff --git a/README.md b/README.md
@@ -49,6 +49,8 @@ Have you created a thesisdown template for your institution and would like to ha
 |University of Washington                |[benmarwick/huskydown](https://github.com/benmarwick/huskydown)                               |[ismayc/thesisdown](https://github.com/ismayc/thesisdown)       |
 |TU Wien                                 |[ben-schwen/robotdown](https://github.com/ben-schwen/robotdown)                               |[ismayc/thesisdown](https://github.com/ismayc/thesisdown)       |
 |University of Bristol                                 |[mattlee821/bristolthesis](https://github.com/mattlee821/bristolthesis)                               |[ismayc/thesisdown](https://github.com/ismayc/thesisdown)       |
+|Universidade Federal de Santa Catarina  | [lfpdroubi/ufscdown](https://github.com/lfpdroubi/ufscdown)                                  |[ismayc/thesisdown](https://github.com/ismayc/thesisdown)       |
+|Universiteit van Amsterdam              | [lcreteig/amsterdown](https://github.com/lcreteig/amsterdown)                                |[benmarwick/huskydown](https://github.com/benmarwick/huskydown) |
 
 ### Using thesisdown from Chester's GitHub
 
@@ -63,13 +65,17 @@ tinytex::install_tinytex()
 tinytex:::is_tinytex() 
 ```
 
-You may need to install a few extra LaTeX packages on your first attempt to knit as well. 
+You may need to install a few extra LaTeX packages on your first attempt to knit as well. Here is one such example of how to do so:
+
+```{r}
+tinytex::tlmgr_install("babel-portuges")
+```
 
 To use **thesisdown** from [RStudio](http://www.rstudio.com/products/rstudio/download/):
 
 1) Ensure that you have already installed LaTeX and the fonts described above, and are using the latest version of [RStudio](http://www.rstudio.com/products/rstudio/download/). You can use `thesisdown` without RStudio. For example, you can write the Rmd files in your favourite text editor (e.g. [Atom](https://atom.io/), [Notepad++](https://notepad-plus-plus.org/)). But RStudio is probably the easiest tool for writing both R code and text in your thesis. It also provides a nice way to build your thesis while editing. We'll proceed assuming that you have decided to use the RStudio workflow.
 
-2) Install the **bookdown** and **thesisdown** packages: 
+2) Install the **bookdown** and **thesisdown** packages. Note that **thesisdown** is not available on CRAN at the moment and that's why `install.packages("thesisdown")` won't work. Use `remotes::install_github()` as shown below instead to install the package.
 
 ```r
 if (!require("remotes")) install.packages("remotes", repos = "http://cran.rstudio.org")

diff --git a/inst/rmarkdown/templates/thesis/skeleton/01-chap1.Rmd b/inst/rmarkdown/templates/thesis/skeleton/01-chap1.Rmd
@@ -176,8 +176,17 @@ flights %>% filter(month == 3, day == 3) %>%
 
 - _Markdown_ Cheatsheet - <https://github.com/adam-p/markdown-here/wiki/Markdown-Cheatsheet>
 
-- _R Markdown_ Reference Guide - <https://www.rstudio.com/wp-content/uploads/2015/03/rmarkdown-reference.pdf>
+- _R Markdown_
+    - Reference Guide - <https://www.rstudio.com/wp-content/uploads/2015/03/rmarkdown-reference.pdf>
+    - Cheatsheet - <https://github.com/rstudio/cheatsheets/raw/master/rmarkdown-2.0.pdf>
 
-- Introduction to `dplyr` - <https://cran.rstudio.com/web/packages/dplyr/vignettes/introduction.html>
+- _RStudio IDE_
+    - Cheatsheet - <https://github.com/rstudio/cheatsheets/raw/master/rstudio-ide.pdf>
+    - Official website - <https://rstudio.com/products/rstudio/>
+
+- Introduction to `dplyr` - <https://cran.rstudio.com/web/packages/dplyr/vignettes/dplyr.html>
+
+- `ggplot2`
+    - Documentation - <https://ggplot2.tidyverse.org/>
+    - Cheatsheet - <https://github.com/rstudio/cheatsheets/raw/master/data-visualization-2.1.pdf>
 
-- `ggplot2` Documentation - <http://docs.ggplot2.org/current/>
diff --git a/inst/rmarkdown/templates/thesis/skeleton/skeleton.Rmd b/inst/rmarkdown/templates/thesis/skeleton/skeleton.Rmd
@@ -12,8 +12,8 @@ title: 'My Final College Paper'
 knit: "bookdown::render_book"
 site: bookdown::bookdown_site
 output: 
-#  thesisdown::thesis_pdf: default
-  thesisdown::thesis_gitbook: default
+  thesisdown::thesis_pdf: default
+#  thesisdown::thesis_gitbook: default
 #  thesisdown::thesis_word: default
 #  thesisdown::thesis_epub: default
 # If you are creating a PDF you'll need to write your preliminary content (e.g., abstract, acknowledgements) here or

diff --git a/inst/rmarkdown/templates/thesis/skeleton/template.tex b/inst/rmarkdown/templates/thesis/skeleton/template.tex
@@ -113,6 +113,16 @@
 }
 \makeatother
 
+%Added by @MyKo101, code provided by @GerbrichFerdinands
+$if(csl-refs)$
+\newlength{\cslhangindent}
+\setlength{\cslhangindent}{1.5em}
+\newenvironment{cslreferences}%
+  {$if(csl-hanging-indent)$\setlength{\parindent}{0pt}%
+  \everypar{\setlength{\hangindent}{\cslhangindent}}\ignorespaces$endif$}%
+  {\par}
+$endif$
+
 \renewcommand{\contentsname}{Table of Contents}
 % End of CII addition