diff --git a/README.Rmd b/README.Rmd
index 85718ecb..12379f56 100644
--- a/README.Rmd
+++ b/README.Rmd
@@ -10,72 +10,76 @@ knitr::opts_chunk$set(
)
```
-
-# thesisdown 
+# thesisdown
This project was inspired by the [bookdown](https://github.com/rstudio/bookdown) package and is an updated version of my Senior Thesis template in the `reedtemplates` package [here](https://github.com/ismayc/reedtemplates). It was originally designed to only work with the Reed College LaTeX template, but has since been adapted to work with many different institutions by many different individuals. Check out the [**Customizing thesisdown to your institution**](https://github.com/ismayc/thesisdown#customizing-thesisdown-to-your-institution) section below for examples.
-Currently, the PDF and gitbook versions are fully-functional. The word and epub versions are developmental, have no templates behind them, and are essentially calls to the appropriate functions in bookdown.
+Currently, the PDF and gitbook versions are fully-functional. The word and epub versions are developmental, have no templates behind them, and are essentially calls to the appropriate functions in bookdown.
If you are new to working with `bookdown`/`rmarkdown`, please read over the documentation available in the `gitbook` template at .
The current output for the four versions is here:
-- [PDF](https://github.com/ismayc/thesisdown_book/blob/master/thesis.pdf) (Generating LaTeX file is available [here](https://github.com/ismayc/thesisdown_book/blob/master/thesis.tex) with other files in the [book directory](https://github.com/ismayc/thesisdown_book/tree/master).)
-- [Word](https://github.com/ismayc/thesisdown_book/blob/master/thesis.docx)
-- [ePub](https://github.com/ismayc/thesisdown_book/blob/master/thesis.epub)
-- [gitbook](https://ismayc.github.io/thesisdown_book)
+- [PDF](https://github.com/ismayc/thesisdown_book/blob/master/thesis.pdf) (Generating LaTeX file is available [here](https://github.com/ismayc/thesisdown_book/blob/master/thesis.tex) with other files in the [book directory](https://github.com/ismayc/thesisdown_book/tree/master).)
+- [Word](https://github.com/ismayc/thesisdown_book/blob/master/thesis.docx)
+- [ePub](https://github.com/ismayc/thesisdown_book/blob/master/thesis.epub)
+- [gitbook](https://ismayc.github.io/thesisdown_book)
Under the hood, the Reed College LaTeX template is used to ensure that documents conform precisely to submission standards. At the same time, composition and formatting can be done using lightweight [markdown](https://rmarkdown.rstudio.com/authoring_basics.html) syntax, and **R** code and its output can be seamlessly included using [rmarkdown](https://rmarkdown.rstudio.com).
## Customizing thesisdown to your institution
-In an ideal world, this package would support a variety of different LaTeX templates from a wide range of institutions and we'd love to get it there at some point. Until that time, realize that this was designed to only work with the Reed College LaTeX template but others have adapted it to work with their institutions. Here are some that have customized it to fit their needs. It is recommended you review how they changed the files by comparing their repositories to this one and then make tweaks to yours as needed. Feel free to file an issue on this repo if you have questions/troubles.
+In an ideal world, this package would support a variety of different LaTeX templates from a wide range of institutions and we'd love to get it there at some point. Until that time, realize that this was designed to only work with the Reed College LaTeX template but others have adapted it to work with their institutions. Here are some that have customized it to fit their needs. It is recommended you review how they changed the files by comparing their repositories to this one and then make tweaks to yours as needed. Feel free to file an issue on this repo if you have questions/troubles.
Have you created a thesisdown template for your institution and would like to have it included here? Make a PR [similar to the commit done to include `jayhawkdown`](https://github.com/ismayc/thesisdown/commit/760113a076767cf67b6e22339e398bd3f15305c5). I'll review it and merge it in. Let's keep the list going!
-
-|College/University |Repository |Based on |
-|:---------------------------------------|:---------------------------------------------------------------------------------------------|:---------------------------------------------------------------|
-|American University |[SimonHeuberger/eagledown](https://github.com/SimonHeuberger/eagledown) |[benmarwick/huskydown](https://github.com/benmarwick/huskydown) |
-|Boğaziçi University, the Institute of Graduate Studies in Social Sciences |[serhatcevikel/boundown](https://github.com/serhatcevikel/boundown) |[ismayc/thesisdown](https://github.com/ismayc/thesisdown) |
-|Brock University |[brentthorne/brockdown](https://github.com/brentthorne/brockdown) |[zkamvar/beaverdown](https://github.com/zkamvar/beaverdown) |
-|Coventry University |[tomislavmedak/coventrydown](https://github.com/tomislavmedak/coventrydown) |[ulyngs/oxforddown](https://github.com/ulyngs/oxforddown) |
-|École Doctorale de Mathématiques Hadamard |[abichat/hadamardown](https://github.com/abichat/hadamardown) |[ismayc/thesisdown](https://github.com/ismayc/thesisdown) |
-|Drexel University |[tbradley1013/dragondown](https://github.com/tbradley1013/dragondown) |[ismayc/thesisdown](https://github.com/ismayc/thesisdown) |
-|Duke University |[mine-cetinkaya-rundel/thesisdowndss](https://github.com/mine-cetinkaya-rundel/thesisdowndss) |[ismayc/thesisdown](https://github.com/ismayc/thesisdown) |
-|Graduate Institute of International and Development Studies |[jhollway/iheiddown](https://github.com/jhollway/iheiddown) |[ulyngs/oxforddown](https://github.com/ulyngs/oxforddown) |
-|Heidelberg University, Faculty of Biosciences |[nkurzaw/heididown](https://github.com/nkurzaw/heididown) |[phister/huwiwidown](https://github.com/phister/huwiwidown) |
-|Humboldt University of Berlin |[phister/huwiwidown](https://github.com/phister/huwiwidown) |[ismayc/thesisdown](https://github.com/ismayc/thesisdown) |
-|Kansas State University |[emraher/wildcatdown](https://github.com/emraher/wildcatdown) |[benmarwick/huskydown](https://github.com/benmarwick/huskydown) |
-|McMaster University | [paezha/macdown](https://github.com/paezha/macdown) |[ismayc/thesisdown](https://github.com/ismayc/thesisdown)|
-|Massachusetts Institute of Technology |[ratatstats/manusdown](https://github.com/ratatstats/manusdown) |[ismayc/thesisdown](https://github.com/ismayc/thesisdown) |
-|Oregon State University |[zkamvar/beaverdown](https://github.com/zkamvar/beaverdown) |[ismayc/thesisdown](https://github.com/ismayc/thesisdown) |
-|Oxford University |[davidplans/oxdown](https://github.com/davidplans/oxdown) |[ismayc/thesisdown](https://github.com/ismayc/thesisdown) |
-|Smith College |[SmithCollege-SDS/pioneerdown](https://github.com/SmithCollege-SDS/pioneerdown) |[ismayc/thesisdown](https://github.com/ismayc/thesisdown) |
-|Southampton University |[dr-harper/sotonthesis](https://github.com/dr-harper/sotonthesis) |[ismayc/thesisdown](https://github.com/ismayc/thesisdown) |
-|Stanford University |[mhtess/treedown](https://github.com/mhtess/treedown) |[ismayc/thesisdown](https://github.com/ismayc/thesisdown) |
-|Universidade Federal do Rio de Janeiro |[COPPE-UFRJ/coppedown](https://github.com/COPPE-UFRJ/coppedown) |[ismayc/thesisdown](https://github.com/ismayc/thesisdown) |
-|Université Paris-Saclay |[abichat/hadamardown](https://github.com/abichat/hadamardown) |[ismayc/thesisdown](https://github.com/ismayc/thesisdown) |
-|University College London |[benyohaiphysics/thesisdownUCL](https://github.com/benyohaiphysics/thesisdownUCL) |[ismayc/thesisdown](https://github.com/ismayc/thesisdown) |
-| University of Arizona | [kelseygonzalez/beardown](https://github.com/kelseygonzalez/beardown) |[ismayc/thesisdown](https://github.com/ismayc/thesisdown) |
-|University of California, Davis |[ryanpeek/aggiedown](https://github.com/ryanpeek/aggiedown) |[DanOvando/gauchodown](https://github.com/DanOvando/gauchodown) |
-|University of California, Santa Barbara |[DanOvando/gauchodown](https://github.com/DanOvando/gauchodown) |[benmarwick/huskydown](https://github.com/benmarwick/huskydown) |
-|University of Florida |[ksauby/thesisdownufl](https://github.com/ksauby/thesisdownufl) |[ismayc/thesisdown](https://github.com/ismayc/thesisdown) |
-|University of Freiburg |[vivekbhr/doctorRbite](https://github.com/vivekbhr/doctorRbite) |[ismayc/thesisdown](https://github.com/ismayc/thesisdown) |
-|University of Guelph |[sebsciarra/guelphdown](https://github.com/sebsciarra/guelphdown) |[ismayc/thesisdown](https://github.com/ismayc/thesisdown) |
-|University of Kansas |[wjakethompson/jayhawkdown](https://github.com/wjakethompson/jayhawkdown) |[ismayc/thesisdown](https://github.com/ismayc/thesisdown) |
-|University of Manchester |[juliov/uomthesisdown](https://github.com/JulioV/uomthesisdown) |[ismayc/thesisdown](https://github.com/ismayc/thesisdown) |
-|University of Minnesota |[zief0002/gopherdown](https://github.com/zief0002/gopherdown) |[wjakethompson/jayhawkdown](https://github.com/wjakethompson/jayhawkdown) |
-|University of New South Wales |[rensa/unswthesisdown](https://github.com/rensa/unswthesisdown) |[ismayc/thesisdown](https://github.com/ismayc/thesisdown) |
-|University of Salzburg |[irmingard/salzburgthesisdown](https://github.com/irmingard/salzburgthesisdown) |[ismayc/thesisdown](https://github.com/ismayc/thesisdown) |
-|University of Toronto |[mattwarkentin/torontodown](https://github.com/mattwarkentin/torontodown) |[zkamvar/beaverdown](https://github.com/zkamvar/beaverdown) |
-|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) |
-
+|College/University |Repository |Based on |
+|:-------------------------------------------------------------------------|:-----------------------------------|:-----------------------------------|
+|American University |[SimonHeuberger/eagledown](https://github.com/SimonHeuberger/eagledown)|[benmarwick/huskydown](https://github.com/benmarwick/huskydown)|
+|Boğaziçi University, the Institute of Graduate Studies in Social Sciences |[serhatcevikel/boundown](https://github.com/serhatcevikel/boundown)|[ismayc/thesisdown](https://github.com/ismayc/thesisdown)|
+|Brock University |[brentthorne/brockdown](https://github.com/brentthorne/brockdown)|[zkamvar/beaverdown](https://github.com/zkamvar/beaverdown)|
+|Coventry University |[tomislavmedak/coventrydown](https://github.com/tomislavmedak/coventrydown)|[ulyngs/oxforddown](https://github.com/ulyngs/oxforddown)|
+|Drexel University |[tbradley1013/dragondown](https://github.com/tbradley1013/dragondown)|[ismayc/thesisdown](https://github.com/ismayc/thesisdown)|
+|Duke University |[mine-cetinkaya-rundel/thesisdowndss](https://github.com/mine-cetinkaya-rundel/thesisdowndss)|[ismayc/thesisdown](https://github.com/ismayc/thesisdown)|
+|École Doctorale de Mathématiques Hadamard |[abichat/hadamardown](https://github.com/abichat/hadamardown)|[ismayc/thesisdown](https://github.com/ismayc/thesisdown)|
+|Graduate Institute of International and Development Studies |[jhollway/iheiddown](https://github.com/jhollway/iheiddown)|[ulyngs/oxforddown](https://github.com/ulyngs/oxforddown)|
+|Heidelberg University, Faculty of Biosciences |[nkurzaw/heididown](https://github.com/nkurzaw/heididown)|[phister/huwiwidown](https://github.com/phister/huwiwidown)|
+|Humboldt University of Berlin |[phister/huwiwidown](https://github.com/phister/huwiwidown)|[ismayc/thesisdown](https://github.com/ismayc/thesisdown)|
+|Kansas State University |[emraher/wildcatdown](https://github.com/emraher/wildcatdown)|[benmarwick/huskydown](https://github.com/benmarwick/huskydown)|
+|Macquarie University |[thomas-fung/thesisdownmq](https://github.com/thomas-fung/thesisdownmq)|[mine-cetinkaya-rundel/thesisdowndss](https://github.com/mine-cetinkaya-rundel/thesisdowndss)|
+|Massachusetts Institute of Technology |[ratatstats/manusdown](https://github.com/ratatstats/manusdown)|[ismayc/thesisdown](https://github.com/ismayc/thesisdown)|
+|McMaster University |[paezha/macdown](https://github.com/paezha/macdown)|[ismayc/thesisdown](https://github.com/ismayc/thesisdown)|
+|Monash University |[masiraji/monashthesisdown](https://github.com/masiraji/monashthesisdown)|[ismayc/thesisdown](https://github.com/ismayc/thesisdown)|
+|Oregon State University |[zkamvar/beaverdown](https://github.com/zkamvar/beaverdown)|[ismayc/thesisdown](https://github.com/ismayc/thesisdown)|
+|Oxford University |[davidplans/oxdown](https://github.com/davidplans/oxdown)|[ismayc/thesisdown](https://github.com/ismayc/thesisdown)|
+|Queen's University |[eugenesit/gaelsdown](https://github.com/eugenesit/gaelsdown)|[ismayc/thesisdown](https://github.com/ismayc/thesisdown)|
+|Smith College |[SmithCollege-SDS/pioneerdown](https://github.com/SmithCollege-SDS/pioneerdown)|[ismayc/thesisdown](https://github.com/ismayc/thesisdown)|
+|Southampton University |[dr-harper/sotonthesis](https://github.com/dr-harper/sotonthesis)|[ismayc/thesisdown](https://github.com/ismayc/thesisdown)|
+|Stanford University |[mhtess/treedown](https://github.com/mhtess/treedown)|[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)|
+|Universidade Federal de Santa Catarina |[lfpdroubi/ufscdown](https://github.com/lfpdroubi/ufscdown)|[ismayc/thesisdown](https://github.com/ismayc/thesisdown)|
+|Universidade Federal do Ceará |[damarals/ufcdown](https://github.com/damarals/ufcdown)|[ismayc/thesisdown](https://github.com/ismayc/thesisdown)|
+|Universidade Federal do Rio de Janeiro |[COPPE-UFRJ/coppedown](https://github.com/COPPE-UFRJ/coppedown)|[ismayc/thesisdown](https://github.com/ismayc/thesisdown)|
+|Universiteit van Amsterdam |[lcreteig/amsterdown](https://github.com/lcreteig/amsterdown)|[benmarwick/huskydown](https://github.com/benmarwick/huskydown)|
+|University College London |[benyohaiphysics/thesisdownUCL](https://github.com/benyohaiphysics/thesisdownUCL)|[ismayc/thesisdown](https://github.com/ismayc/thesisdown)|
+|University of Arizona |[kelseygonzalez/beardown](https://github.com/kelseygonzalez/beardown)|[ismayc/thesisdown](https://github.com/ismayc/thesisdown)|
+|University of Auckland |[d-scanzi/UOAdown](https://github.com/d-scanzi/UOAdown)|[ismayc/thesisdown](https://github.com/ismayc/thesisdown)|
+|University of Bristol |[mattlee821/bristolthesis](https://github.com/mattlee821/bristolthesis)|[ismayc/thesisdown](https://github.com/ismayc/thesisdown)|
+|University of California, Davis |[ryanpeek/aggiedown](https://github.com/ryanpeek/aggiedown)|[DanOvando/gauchodown](https://github.com/DanOvando/gauchodown)|
+|University of California, Santa Barbara |[DanOvando/gauchodown](https://github.com/DanOvando/gauchodown)|[benmarwick/huskydown](https://github.com/benmarwick/huskydown)|
+|University of Florida |[ksauby/thesisdownufl](https://github.com/ksauby/thesisdownufl)|[ismayc/thesisdown](https://github.com/ismayc/thesisdown)|
+|University of Freiburg |[vivekbhr/doctorRbite](https://github.com/vivekbhr/doctorRbite)|[ismayc/thesisdown](https://github.com/ismayc/thesisdown)|
+|University of Guelph |[sebsciarra/guelphdown](https://github.com/sebsciarra/guelphdown)|[ismayc/thesisdown](https://github.com/ismayc/thesisdown)|
+|University of Kansas |[wjakethompson/jayhawkdown](https://github.com/wjakethompson/jayhawkdown)|[ismayc/thesisdown](https://github.com/ismayc/thesisdown)|
+|University of Manchester |[juliov/uomthesisdown](https://github.com/JulioV/uomthesisdown)|[ismayc/thesisdown](https://github.com/ismayc/thesisdown)|
+|University of Maryland, College Park |[ImNotaGit/thesisdown](https://github.com/ImNotaGit/thesisdown/tree/umd)|[ismayc/thesisdown](https://github.com/ismayc/thesisdown)|
+|University of Minnesota |[zief0002/gopherdown](https://github.com/zief0002/gopherdown)|[wjakethompson/jayhawkdown](https://github.com/wjakethompson/jayhawkdown)|
+|University of New South Wales |[rensa/unswthesisdown](https://github.com/rensa/unswthesisdown)|[ismayc/thesisdown](https://github.com/ismayc/thesisdown)|
+|University of Salzburg |[irmingard/salzburgthesisdown](https://github.com/irmingard/salzburgthesisdown)|[ismayc/thesisdown](https://github.com/ismayc/thesisdown)|
+|University of Toronto |[mattwarkentin/torontodown](https://github.com/mattwarkentin/torontodown)|[zkamvar/beaverdown](https://github.com/zkamvar/beaverdown)|
+|University of Washington |[benmarwick/huskydown](https://github.com/benmarwick/huskydown)|[ismayc/thesisdown](https://github.com/ismayc/thesisdown)|
+|Université Paris-Saclay |[abichat/hadamardown](https://github.com/abichat/hadamardown)|[ismayc/thesisdown](https://github.com/ismayc/thesisdown)|
+|Youngstown State University |[gjkerns/penguindown](https://github.com/gjkerns/penguindown)|[ismayc/thesisdown](https://github.com/ismayc/thesisdown)|
### Using thesisdown from Chester's GitHub
@@ -83,7 +87,7 @@ Special thanks to [Ben Marwick](https://github.com/benmarwick) for helping to ad
Using {thesisdown} has some prerequisites which are described below. To compile PDF documents using **R**, you are going to need to have LaTeX installed. By far the easiest way to install LaTeX on any platform is with the [tinytex](https://yihui.name/tinytex/) R package:
-```r
+``` r
install.packages(c('tinytex', 'rmarkdown'))
tinytex::install_tinytex()
# after restarting RStudio, confirm that you have LaTeX with
@@ -92,60 +96,46 @@ tinytex:::is_tinytex()
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
+``` r
tinytex::tlmgr_install("babel-portuges")
```
To use {thesisdown} from [RStudio](https://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](https://www.rstudio.com/products/rstudio/download/). You can use `thesisdown` without RStudio. For example, you can write the Rmd files in your favorite 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.
+1. Ensure that you have already installed LaTeX and the fonts described above, and are using the latest version of [RStudio](https://www.rstudio.com/products/rstudio/download/). You can use `thesisdown` without RStudio. For example, you can write the Rmd files in your favorite 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. 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.
+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
+ ``` r
if (!require("remotes"))
install.packages("remotes", repos = "https://cran.rstudio.org")
remotes::install_github("rstudio/bookdown")
remotes::install_github("ismayc/thesisdown")
```
-
- Note that you may need to restart RStudio at this point for the following dialog to show up.
-3. Get started with the {thesisdown} template. There are two
-options for doing so.
+ Note that you may need to restart RStudio at this point for the following dialog to show up.
+
+3. Get started with the {thesisdown} template. There are two options for doing so.
-- 3a) **RECOMMENDED** Create a new RStudio project with a
-{thesisdown} template.
+- 3a) **RECOMMENDED** Create a new RStudio project with a {thesisdown} template.
- In RStudio, click on **File** > **New Project** >
-**New Directory**. Then select
-**Thesis Project using thesisdown** from the dropdown that
-will look something like the image below. You'll see the
-graduation cap as the icon on the left for the appropriate
-project type.
+ In RStudio, click on **File** \> **New Project** \> **New Directory**. Then select **Thesis Project using thesisdown** from the dropdown that will look something like the image below. You'll see the graduation cap as the icon on the left for the appropriate project type.
- 
+ 
- Next, give your project a name and specify where you'd like
-the files to appear. In the screenshot below, the project
-name is `my_thesis` and it will appear as a new folder
-on my Desktop.
+ Next, give your project a name and specify where you'd like the files to appear. In the screenshot below, the project name is `my_thesis` and it will appear as a new folder on my Desktop.
- 
+ 
- If you got this far, skip over step 3b which is the older
-version of getting the template. It might force you to
-change some of the directories to get knitting to work
-and has some other limitations as well. That's why step 3a
-is recommended.
+ If you got this far, skip over step 3b which is the older version of getting the template. It might force you to change some of the directories to get knitting to work and has some other limitations as well. That's why step 3a is recommended.
-- 3b) Use the **New R Markdown** dialog to select **Thesis**:
+- 3b) Use the **New R Markdown** dialog to select **Thesis**:
- 
+ 
- Note that this will currently only **Knit** if you name the directory `index` as shown above. This guarantees that `index.html` is generated correctly for the Gitbook version of the thesis.
+ Note that this will currently only **Knit** if you name the directory `index` as shown above. This guarantees that `index.html` is generated correctly for the Gitbook version of the thesis.
-4. After choosing which type of output you'd like in the YAML at the top of `index.Rmd`, **Knit** the `index.Rmd` file to get the book in PDF or HTML formats.
+4. After choosing which type of output you'd like in the YAML at the top of `index.Rmd`, **Knit** the `index.Rmd` file to get the book in PDF or HTML formats.
### Day-to-day writing of your thesis
@@ -167,8 +157,7 @@ This is the main configuration file for your thesis. You can change the name of
### `index.Rmd`
-This file contains all the meta information that goes at the beginning of your
-document. You'll need to edit the top portion of this file (the YAML) to put your name on the first page, the title of your thesis, etc. Note that you need to have at least one chapter start in the `index.Rmd` file for the build to work. For the template, this is done with `# Introduction` in the example from the template.
+This file contains all the meta information that goes at the beginning of your document. You'll need to edit the top portion of this file (the YAML) to put your name on the first page, the title of your thesis, etc. Note that you need to have at least one chapter start in the `index.Rmd` file for the build to work. For the template, this is done with `# Introduction` in the example from the template.
### `01-chap1.Rmd`, `02-chap2.Rmd`, etc.
@@ -180,8 +169,7 @@ Store your bibliography (as bibtex files) here. We recommend using the [citr add
### `csl/`
-Specific style files for bibliographies should be stored here. A good source for
-citation styles is https://github.com/citation-style-language/styles#readme.
+Specific style files for bibliographies should be stored here. A good source for citation styles is .
### `figure/` and `data/`
diff --git a/README.md b/README.md
index 1b2e0427..3fd41a37 100644
--- a/README.md
+++ b/README.md
@@ -1,7 +1,7 @@
-# thesisdown
+# thesisdown
This project was inspired by the
[bookdown](https://github.com/rstudio/bookdown) package and is an
@@ -24,14 +24,14 @@ the documentation available in the `gitbook` template at
The current output for the four versions is here:
-- [PDF](https://github.com/ismayc/thesisdown_book/blob/master/thesis.pdf)
- (Generating LaTeX file is available
- [here](https://github.com/ismayc/thesisdown_book/blob/master/thesis.tex)
- with other files in the [book
- directory](https://github.com/ismayc/thesisdown_book/tree/master).)
-- [Word](https://github.com/ismayc/thesisdown_book/blob/master/thesis.docx)
-- [ePub](https://github.com/ismayc/thesisdown_book/blob/master/thesis.epub)
-- [gitbook](https://ismayc.github.io/thesisdown_book)
+- [PDF](https://github.com/ismayc/thesisdown_book/blob/master/thesis.pdf)
+ (Generating LaTeX file is available
+ [here](https://github.com/ismayc/thesisdown_book/blob/master/thesis.tex)
+ with other files in the [book
+ directory](https://github.com/ismayc/thesisdown_book/tree/master).)
+- [Word](https://github.com/ismayc/thesisdown_book/blob/master/thesis.docx)
+- [ePub](https://github.com/ismayc/thesisdown_book/blob/master/thesis.epub)
+- [gitbook](https://ismayc.github.io/thesisdown_book)
Under the hood, the Reed College LaTeX template is used to ensure that
documents conform precisely to submission standards. At the same time,
@@ -58,50 +58,53 @@ include
`jayhawkdown`](https://github.com/ismayc/thesisdown/commit/760113a076767cf67b6e22339e398bd3f15305c5).
I’ll review it and merge it in. Let’s keep the list going!
-| College/University | Repository | Based on |
-|:------------------------------------------------------------|:----------------------------------------------------------------------------------------------|:----------------------------------------------------------------|
-| American University | [SimonHeuberger/eagledown](https://github.com/SimonHeuberger/eagledown) | [benmarwick/huskydown](https://github.com/benmarwick/huskydown) |
-| Brock University | [brentthorne/brockdown](https://github.com/brentthorne/brockdown) | [zkamvar/beaverdown](https://github.com/zkamvar/beaverdown) |
-| École Doctorale de Mathématiques Hadamard | [abichat/hadamardown](https://github.com/abichat/hadamardown) | [ismayc/thesisdown](https://github.com/ismayc/thesisdown) |
-| Drexel University | [tbradley1013/dragondown](https://github.com/tbradley1013/dragondown) | [ismayc/thesisdown](https://github.com/ismayc/thesisdown) |
-| Duke University | [mine-cetinkaya-rundel/thesisdowndss](https://github.com/mine-cetinkaya-rundel/thesisdowndss) | [ismayc/thesisdown](https://github.com/ismayc/thesisdown) |
-| Graduate Institute of International and Development Studies | [jhollway/iheiddown](https://github.com/jhollway/iheiddown) | [ulyngs/oxforddown](https://github.com/ulyngs/oxforddown) |
-| Heidelberg University, Faculty of Biosciences | [nkurzaw/heididown](https://github.com/nkurzaw/heididown) | [phister/huwiwidown](https://github.com/phister/huwiwidown) |
-| Humboldt University of Berlin | [phister/huwiwidown](https://github.com/phister/huwiwidown) | [ismayc/thesisdown](https://github.com/ismayc/thesisdown) |
-| Kansas State University | [emraher/wildcatdown](https://github.com/emraher/wildcatdown) | [benmarwick/huskydown](https://github.com/benmarwick/huskydown) |
-| McMaster University | [paezha/macdown](https://github.com/paezha/macdown) | [ismayc/thesisdown](https://github.com/ismayc/thesisdown) |
-| Massachusetts Institute of Technology | [ratatstats/manusdown](https://github.com/ratatstats/manusdown) | [ismayc/thesisdown](https://github.com/ismayc/thesisdown) |
-| Monash University | [masiraji/monashthesisdown](https://github.com/masiraji/monashthesisdown) | [ismayc/thesisdown](https://github.com/ismayc/thesisdown) |
-| Oregon State University | [zkamvar/beaverdown](https://github.com/zkamvar/beaverdown) | [ismayc/thesisdown](https://github.com/ismayc/thesisdown) |
-| Oxford University | [davidplans/oxdown](https://github.com/davidplans/oxdown) | [ismayc/thesisdown](https://github.com/ismayc/thesisdown) |
-| Queen's University | [eugenesit/gaelsdown](https://github.com/eugenesit/gaelsdown)| [ismayc/thesisdown](https://github.com/ismayc/thesisdown) |
-| Smith College | [SmithCollege-SDS/pioneerdown](https://github.com/SmithCollege-SDS/pioneerdown) | [ismayc/thesisdown](https://github.com/ismayc/thesisdown) |
-| Southampton University | [dr-harper/sotonthesis](https://github.com/dr-harper/sotonthesis) | [ismayc/thesisdown](https://github.com/ismayc/thesisdown) |
-| Stanford University | [mhtess/treedown](https://github.com/mhtess/treedown) | [ismayc/thesisdown](https://github.com/ismayc/thesisdown) |
-| Universidade Federal do Ceará | [damarals/ufcdown](https://github.com/damarals/ufcdown) | [ismayc/thesisdown](https://github.com/ismayc/thesisdown) |
-| Universidade Federal do Rio de Janeiro | [COPPE-UFRJ/coppedown](https://github.com/COPPE-UFRJ/coppedown) | [ismayc/thesisdown](https://github.com/ismayc/thesisdown) |
-| Université Paris-Saclay | [abichat/hadamardown](https://github.com/abichat/hadamardown) | [ismayc/thesisdown](https://github.com/ismayc/thesisdown) |
-| University College London | [benyohaiphysics/thesisdownUCL](https://github.com/benyohaiphysics/thesisdownUCL) | [ismayc/thesisdown](https://github.com/ismayc/thesisdown) |
-| University of Arizona | [kelseygonzalez/beardown](https://github.com/kelseygonzalez/beardown) | [ismayc/thesisdown](https://github.com/ismayc/thesisdown) |
-| University of Auckland | [d-scanzi/UOAdown](https://github.com/d-scanzi/UOAdown) | [ismayc/thesisdown](https://github.com/ismayc/thesisdown) |
-| University of California, Davis | [ryanpeek/aggiedown](https://github.com/ryanpeek/aggiedown) | [DanOvando/gauchodown](https://github.com/DanOvando/gauchodown) |
-| University of California, Santa Barbara | [DanOvando/gauchodown](https://github.com/DanOvando/gauchodown) | [benmarwick/huskydown](https://github.com/benmarwick/huskydown) |
-| University of Florida | [ksauby/thesisdownufl](https://github.com/ksauby/thesisdownufl) | [ismayc/thesisdown](https://github.com/ismayc/thesisdown) |
-| University of Freiburg | [vivekbhr/doctorRbite](https://github.com/vivekbhr/doctorRbite) | [ismayc/thesisdown](https://github.com/ismayc/thesisdown) |
-University of Guelph |[sebsciarra/guelphdown](https://github.com/sebsciarra/guelphdown) |[ismayc/thesisdown](https://github.com/ismayc/thesisdown) |
-| University of Kansas | [wjakethompson/jayhawkdown](https://github.com/wjakethompson/jayhawkdown) | [ismayc/thesisdown](https://github.com/ismayc/thesisdown) |
-| University of Manchester | [juliov/uomthesisdown](https://github.com/JulioV/uomthesisdown) | [ismayc/thesisdown](https://github.com/ismayc/thesisdown) |
-| University of Maryland, College Park | [ImNotaGit/thesisdown](https://github.com/ImNotaGit/thesisdown/tree/umd) | [ismayc/thesisdown](https://github.com/ismayc/thesisdown) |
-|University of Minnesota |[zief0002/gopherdown](https://github.com/zief0002/gopherdown) |[wjakethompson/jayhawkdown](https://github.com/wjakethompson/jayhawkdown) |
-| University of New South Wales | [rensa/unswthesisdown](https://github.com/rensa/unswthesisdown) | [ismayc/thesisdown](https://github.com/ismayc/thesisdown) |
-| University of Salzburg | [irmingard/salzburgthesisdown](https://github.com/irmingard/salzburgthesisdown) | [ismayc/thesisdown](https://github.com/ismayc/thesisdown) |
-| University of Toronto | [mattwarkentin/torontodown](https://github.com/mattwarkentin/torontodown) | [zkamvar/beaverdown](https://github.com/zkamvar/beaverdown) |
-| 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) |
-| Youngstown State University | [gjkerns/penguindown](https://github.com/gjkerns/penguindown) | [ismayc/thesisdown](https://github.com/ismayc/thesisdown) |
+|College/University |Repository |Based on |
+|:-------------------------------------------------------------------------|:-----------------------------------|:-----------------------------------|
+|American University |[SimonHeuberger/eagledown](https://github.com/SimonHeuberger/eagledown)|[benmarwick/huskydown](https://github.com/benmarwick/huskydown)|
+|Boğaziçi University, the Institute of Graduate Studies in Social Sciences |[serhatcevikel/boundown](https://github.com/serhatcevikel/boundown)|[ismayc/thesisdown](https://github.com/ismayc/thesisdown)|
+|Brock University |[brentthorne/brockdown](https://github.com/brentthorne/brockdown)|[zkamvar/beaverdown](https://github.com/zkamvar/beaverdown)|
+|Coventry University |[tomislavmedak/coventrydown](https://github.com/tomislavmedak/coventrydown)|[ulyngs/oxforddown](https://github.com/ulyngs/oxforddown)|
+|Drexel University |[tbradley1013/dragondown](https://github.com/tbradley1013/dragondown)|[ismayc/thesisdown](https://github.com/ismayc/thesisdown)|
+|Duke University |[mine-cetinkaya-rundel/thesisdowndss](https://github.com/mine-cetinkaya-rundel/thesisdowndss)|[ismayc/thesisdown](https://github.com/ismayc/thesisdown)|
+|École Doctorale de Mathématiques Hadamard |[abichat/hadamardown](https://github.com/abichat/hadamardown)|[ismayc/thesisdown](https://github.com/ismayc/thesisdown)|
+|Graduate Institute of International and Development Studies |[jhollway/iheiddown](https://github.com/jhollway/iheiddown)|[ulyngs/oxforddown](https://github.com/ulyngs/oxforddown)|
+|Heidelberg University, Faculty of Biosciences |[nkurzaw/heididown](https://github.com/nkurzaw/heididown)|[phister/huwiwidown](https://github.com/phister/huwiwidown)|
+|Humboldt University of Berlin |[phister/huwiwidown](https://github.com/phister/huwiwidown)|[ismayc/thesisdown](https://github.com/ismayc/thesisdown)|
+|Kansas State University |[emraher/wildcatdown](https://github.com/emraher/wildcatdown)|[benmarwick/huskydown](https://github.com/benmarwick/huskydown)|
+|Macquarie University |[thomas-fung/thesisdownmq](https://github.com/thomas-fung/thesisdownmq)|[mine-cetinkaya-rundel/thesisdowndss](https://github.com/mine-cetinkaya-rundel/thesisdowndss)|
+|Massachusetts Institute of Technology |[ratatstats/manusdown](https://github.com/ratatstats/manusdown)|[ismayc/thesisdown](https://github.com/ismayc/thesisdown)|
+|McMaster University |[paezha/macdown](https://github.com/paezha/macdown)|[ismayc/thesisdown](https://github.com/ismayc/thesisdown)|
+|Monash University |[masiraji/monashthesisdown](https://github.com/masiraji/monashthesisdown)|[ismayc/thesisdown](https://github.com/ismayc/thesisdown)|
+|Oregon State University |[zkamvar/beaverdown](https://github.com/zkamvar/beaverdown)|[ismayc/thesisdown](https://github.com/ismayc/thesisdown)|
+|Oxford University |[davidplans/oxdown](https://github.com/davidplans/oxdown)|[ismayc/thesisdown](https://github.com/ismayc/thesisdown)|
+|Queen's University |[eugenesit/gaelsdown](https://github.com/eugenesit/gaelsdown)|[ismayc/thesisdown](https://github.com/ismayc/thesisdown)|
+|Smith College |[SmithCollege-SDS/pioneerdown](https://github.com/SmithCollege-SDS/pioneerdown)|[ismayc/thesisdown](https://github.com/ismayc/thesisdown)|
+|Southampton University |[dr-harper/sotonthesis](https://github.com/dr-harper/sotonthesis)|[ismayc/thesisdown](https://github.com/ismayc/thesisdown)|
+|Stanford University |[mhtess/treedown](https://github.com/mhtess/treedown)|[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)|
+|Universidade Federal de Santa Catarina |[lfpdroubi/ufscdown](https://github.com/lfpdroubi/ufscdown)|[ismayc/thesisdown](https://github.com/ismayc/thesisdown)|
+|Universidade Federal do Ceará |[damarals/ufcdown](https://github.com/damarals/ufcdown)|[ismayc/thesisdown](https://github.com/ismayc/thesisdown)|
+|Universidade Federal do Rio de Janeiro |[COPPE-UFRJ/coppedown](https://github.com/COPPE-UFRJ/coppedown)|[ismayc/thesisdown](https://github.com/ismayc/thesisdown)|
+|Universiteit van Amsterdam |[lcreteig/amsterdown](https://github.com/lcreteig/amsterdown)|[benmarwick/huskydown](https://github.com/benmarwick/huskydown)|
+|University College London |[benyohaiphysics/thesisdownUCL](https://github.com/benyohaiphysics/thesisdownUCL)|[ismayc/thesisdown](https://github.com/ismayc/thesisdown)|
+|University of Arizona |[kelseygonzalez/beardown](https://github.com/kelseygonzalez/beardown)|[ismayc/thesisdown](https://github.com/ismayc/thesisdown)|
+|University of Auckland |[d-scanzi/UOAdown](https://github.com/d-scanzi/UOAdown)|[ismayc/thesisdown](https://github.com/ismayc/thesisdown)|
+|University of Bristol |[mattlee821/bristolthesis](https://github.com/mattlee821/bristolthesis)|[ismayc/thesisdown](https://github.com/ismayc/thesisdown)|
+|University of California, Davis |[ryanpeek/aggiedown](https://github.com/ryanpeek/aggiedown)|[DanOvando/gauchodown](https://github.com/DanOvando/gauchodown)|
+|University of California, Santa Barbara |[DanOvando/gauchodown](https://github.com/DanOvando/gauchodown)|[benmarwick/huskydown](https://github.com/benmarwick/huskydown)|
+|University of Florida |[ksauby/thesisdownufl](https://github.com/ksauby/thesisdownufl)|[ismayc/thesisdown](https://github.com/ismayc/thesisdown)|
+|University of Freiburg |[vivekbhr/doctorRbite](https://github.com/vivekbhr/doctorRbite)|[ismayc/thesisdown](https://github.com/ismayc/thesisdown)|
+|University of Guelph |[sebsciarra/guelphdown](https://github.com/sebsciarra/guelphdown)|[ismayc/thesisdown](https://github.com/ismayc/thesisdown)|
+|University of Kansas |[wjakethompson/jayhawkdown](https://github.com/wjakethompson/jayhawkdown)|[ismayc/thesisdown](https://github.com/ismayc/thesisdown)|
+|University of Manchester |[juliov/uomthesisdown](https://github.com/JulioV/uomthesisdown)|[ismayc/thesisdown](https://github.com/ismayc/thesisdown)|
+|University of Maryland, College Park |[ImNotaGit/thesisdown](https://github.com/ImNotaGit/thesisdown/tree/umd)|[ismayc/thesisdown](https://github.com/ismayc/thesisdown)|
+|University of Minnesota |[zief0002/gopherdown](https://github.com/zief0002/gopherdown)|[wjakethompson/jayhawkdown](https://github.com/wjakethompson/jayhawkdown)|
+|University of New South Wales |[rensa/unswthesisdown](https://github.com/rensa/unswthesisdown)|[ismayc/thesisdown](https://github.com/ismayc/thesisdown)|
+|University of Salzburg |[irmingard/salzburgthesisdown](https://github.com/irmingard/salzburgthesisdown)|[ismayc/thesisdown](https://github.com/ismayc/thesisdown)|
+|University of Toronto |[mattwarkentin/torontodown](https://github.com/mattwarkentin/torontodown)|[zkamvar/beaverdown](https://github.com/zkamvar/beaverdown)|
+|University of Washington |[benmarwick/huskydown](https://github.com/benmarwick/huskydown)|[ismayc/thesisdown](https://github.com/ismayc/thesisdown)|
+|Université Paris-Saclay |[abichat/hadamardown](https://github.com/abichat/hadamardown)|[ismayc/thesisdown](https://github.com/ismayc/thesisdown)|
+|Youngstown State University |[gjkerns/penguindown](https://github.com/gjkerns/penguindown)|[ismayc/thesisdown](https://github.com/ismayc/thesisdown)|
### Using thesisdown from Chester’s GitHub
@@ -163,35 +166,34 @@ the following dialog to show up.
3. Get started with the {thesisdown} template. There are two options
for doing so.
-- 3a) **RECOMMENDED** Create a new RStudio project with a {thesisdown}
- template.
+- 3a) **RECOMMENDED** Create a new RStudio project with a {thesisdown}
+ template.
- In RStudio, click on **File** > **New Project** > **New Directory**.
- Then select **Thesis Project using thesisdown** from the dropdown
- that will look something like the image below. You’ll see the
- graduation cap as the icon on the left for the appropriate project
- type.
+ In RStudio, click on **File** \> **New Project** \> **New Directory**.
+ Then select **Thesis Project using thesisdown** from the dropdown that
+ will look something like the image below. You’ll see the graduation
+ cap as the icon on the left for the appropriate project type.
- 
+ 
- Next, give your project a name and specify where you’d like the
- files to appear. In the screenshot below, the project name is
- `my_thesis` and it will appear as a new folder on my Desktop.
+ Next, give your project a name and specify where you’d like the files
+ to appear. In the screenshot below, the project name is `my_thesis`
+ and it will appear as a new folder on my Desktop.
- 
+ 
- If you got this far, skip over step 3b which is the older version of
- getting the template. It might force you to change some of the
- directories to get knitting to work and has some other limitations
- as well. That’s why step 3a is recommended.
+ If you got this far, skip over step 3b which is the older version of
+ getting the template. It might force you to change some of the
+ directories to get knitting to work and has some other limitations as
+ well. That’s why step 3a is recommended.
-- 3b) Use the **New R Markdown** dialog to select **Thesis**:
+- 3b) Use the **New R Markdown** dialog to select **Thesis**:
- 
+ 
- Note that this will currently only **Knit** if you name the
- directory `index` as shown above. This guarantees that `index.html`
- is generated correctly for the Gitbook version of the thesis.
+ Note that this will currently only **Knit** if you name the directory
+ `index` as shown above. This guarantees that `index.html` is generated
+ correctly for the Gitbook version of the thesis.
4. After choosing which type of output you’d like in the YAML at the
top of `index.Rmd`, **Knit** the `index.Rmd` file to get the book in