ismayc · ismayc · May 27, 2020 · Jan 27, 2020 · Jan 27, 2020 · May 25, 2020
diff --git a/.Rbuildignore b/.Rbuildignore
@@ -1,2 +1,8 @@
 ^.*\.Rproj$
 ^\.Rproj\.user$
+R/.setup.R
+^_pkgdown\.yml$
+^docs$
+^pkgdown$
+^images$
+^LICENSE\.md$
diff --git a/DESCRIPTION b/DESCRIPTION
@@ -10,15 +10,18 @@ Description: Using the bookdown package and LaTeX and Word thesis templates from
     and analyses as well.
 Maintainer: Chester Ismay <[email protected]>
 Depends:
-    R (>= 3.2.0),
-    remotes,
+    R (>= 3.2.0)
+Imports: 
     dplyr,
     ggplot2,
     bookdown,
     knitr,
     here
-License: MIT
+Suggests:
+    remotes,
+    usethis
+License: MIT + file LICENSE
 Encoding: UTF-8
 LazyData: true
-SystemRequirements: pandoc (>= 1.18) - http://pandoc.org
+SystemRequirements: pandoc (>= 1.18) - https://pandoc.org
 RoxygenNote: 7.1.0
diff --git a/LICENSE b/LICENSE
@@ -1,21 +1,2 @@
-MIT License
-
-Copyright (c) 2016 Chester Ismay
-
-Permission is hereby granted, free of charge, to any person obtaining a copy
-of this software and associated documentation files (the "Software"), to deal
-in the Software without restriction, including without limitation the rights
-to use, copy, modify, merge, publish, distribute, sublicense, and/or sell
-copies of the Software, and to permit persons to whom the Software is
-furnished to do so, subject to the following conditions:
-
-The above copyright notice and this permission notice shall be included in all
-copies or substantial portions of the Software.
-
-THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND, EXPRESS OR
-IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES OF MERCHANTABILITY,
-FITNESS FOR A PARTICULAR PURPOSE AND NONINFRINGEMENT. IN NO EVENT SHALL THE
-AUTHORS OR COPYRIGHT HOLDERS BE LIABLE FOR ANY CLAIM, DAMAGES OR OTHER
-LIABILITY, WHETHER IN AN ACTION OF CONTRACT, TORT OR OTHERWISE, ARISING FROM,
-OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE USE OR OTHER DEALINGS IN THE
-SOFTWARE.
+YEAR: 2020
+COPYRIGHT HOLDER: Chester Ismay
diff --git a/LICENSE.md b/LICENSE.md
@@ -0,0 +1,21 @@
+# MIT License
+
+Copyright (c) 2020 Chester Ismay
+
+Permission is hereby granted, free of charge, to any person obtaining a copy
+of this software and associated documentation files (the "Software"), to deal
+in the Software without restriction, including without limitation the rights
+to use, copy, modify, merge, publish, distribute, sublicense, and/or sell
+copies of the Software, and to permit persons to whom the Software is
+furnished to do so, subject to the following conditions:
+
+The above copyright notice and this permission notice shall be included in all
+copies or substantial portions of the Software.
+
+THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND, EXPRESS OR
+IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES OF MERCHANTABILITY,
+FITNESS FOR A PARTICULAR PURPOSE AND NONINFRINGEMENT. IN NO EVENT SHALL THE
+AUTHORS OR COPYRIGHT HOLDERS BE LIABLE FOR ANY CLAIM, DAMAGES OR OTHER
+LIABILITY, WHETHER IN AN ACTION OF CONTRACT, TORT OR OTHERWISE, ARISING FROM,
+OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE USE OR OTHER DEALINGS IN THE
+SOFTWARE.
diff --git a/NEWS.md b/NEWS.md
@@ -1,3 +1,12 @@
+# thesisdown 0.1.0
+
+- Fixed issue ((#86)[https://github.com/ismayc/thesisdown/issues/86]) with references not showing in Gitbook version
+- Added support for customizing of thesisdown::gitbook ((#84)[https://github.com/ismayc/thesisdown/pull/84])
+- Added hex sticker ([1](https://github.com/ismayc/thesisdown/commit/ababba5437ee2fe0632c74d5428fed35b911c751) and [2](https://github.com/ismayc/thesisdown/commit/d556073c94ae5069d4373fc73811b3115905c56f))
+- [Converted http to https throughout Rmd files](https://github.com/ismayc/thesisdown/commit/aa4bac89ab7cf91d7898d9b52d737b00e6b6f71a)
+- [Reduced `flights.csv` included data](https://github.com/ismayc/thesisdown/commit/0a6bf0c5d6bdb75be4e09a58b588feeaff778af0) to prepare for sending to CRAN
+- [Created {pkgdown} site](https://github.com/ismayc/thesisdown/commit/7febd70b98ae6e8d104bf1080e066468d030b968)
+
 # thesisdown 0.0.2
 
 - Changed default filename (in directions) to be `index` instead of `skeleton` to match with gitbook requirements

diff --git a/R/.setup.R b/R/.setup.R
@@ -0,0 +1,7 @@
+import_pkgs <- c("bookdown", "dplyr", "ggplot2", "here", "knitr")
+invisible(lapply(import_pkgs, usethis::use_package, type = "Imports"))
+suggest_pkgs <- c("remotes", "usethis")
+invisible(lapply(suggest_pkgs, usethis::use_package, type = "Suggests"))
+
+usethis::use_pkgdown()
+usethis::use_mit_license(name = "Chester Ismay")
diff --git a/R/thesisdown.R b/R/thesisdown.R
@@ -12,4 +12,4 @@
 #' Creates an R Markdown thesis template as an ebook
 #' @docType package
 #' @name thesisdown
-NULL
+"_PACKAGE"
diff --git a/README.md b/README.md
@@ -1,4 +1,4 @@
-# thesisdown
+# thesisdown <img src="man/figures/thesisdown_hex.png" align="right" width=200 />
 
 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.
 
@@ -7,7 +7,7 @@ Currently, the PDF and gitbook versions are fully-functional.  The word and epub
 If you are new to working with `bookdown`/`rmarkdown`, please read over the documentation available in the `gitbook` template at https://thesisdown.netlify.com/.  This is also available below at https://ismayc.github.io/thesisdown_book.
 
 The current output for the four versions is here:
-- [PDF](https://github.com/ismayc/thesisdown_book/blob/gh-pages/thesis.pdf) (Generating LaTeX file is available [here](https://github.com/ismayc/thesisdown_book/blob/gh-pages/thesis.tex) with other files at in the [book directory](https://github.com/ismayc/thesisdown_book/tree/gh-pages).)
+- [PDF](https://github.com/ismayc/thesisdown_book/blob/gh-pages/thesis.pdf) (Generating LaTeX file is available [here](https://github.com/ismayc/thesisdown_book/blob/gh-pages/thesis.tex) with other files in the [book directory](https://github.com/ismayc/thesisdown_book/tree/gh-pages).)
 - [Word](https://github.com/ismayc/thesisdown_book/blob/gh-pages/thesis.docx)
 - [ePub](https://github.com/ismayc/thesisdown_book/blob/gh-pages/thesis.epub)
 - [gitbook](https://ismayc.github.io/thesisdown_book)
@@ -71,14 +71,14 @@ You may need to install a few extra LaTeX packages on your first attempt to knit
 tinytex::tlmgr_install("babel-portuges")
 ```
 
-To use **thesisdown** from [RStudio](http://www.rstudio.com/products/rstudio/download/):
+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](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.
+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 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. 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")
+if (!require("remotes")) install.packages("remotes", repos = "https://cran.rstudio.org")
 remotes::install_github("rstudio/bookdown")
 remotes::install_github("ismayc/thesisdown")
 ```
@@ -87,15 +87,15 @@ Note that you may need to restart RStudio at this point for the following dialog
 
 3) Use the **New R Markdown** dialog to select **Thesis**:
 
-    ![New R Markdown](thesis_rmd.png)
+  ![New R Markdown](images/thesis_rmd.png)
 
-    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.
 
 ### Day-to-day writing of your thesis 
 
-You need to edit the individual chapter R Markdown files to write your thesis. It's recommended that you version control your thesis using GitHub if possible. RStudio can also easily sync up with GitHub to make the process easier. While writing, you should `git commit` your work frequently, after every major activity on your thesis. For example, every few paragraphs or section of text, and after major step of analysis development. You should `git push` at the end of each work session before you leave your computer or change tasks. For a gentle, novice-friendly guide to getting starting with using Git with R and RStudio, see <http://happygitwithr.com/>.
+You need to edit the individual chapter R Markdown files to write your thesis. It's recommended that you version control your thesis using GitHub if possible. RStudio can also easily sync up with GitHub to make the process easier. While writing, you should `git commit` your work frequently, after every major activity on your thesis. For example, every few paragraphs or section of text, and after major step of analysis development. You should `git push` at the end of each work session before you leave your computer or change tasks. For a gentle, novice-friendly guide to getting starting with using Git with R and RStudio, see <https://happygitwithr.com/>.
 
 ## Rendering
 
@@ -127,7 +127,7 @@ 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
+citation styles is https://github.com/citation-style-language/styles#readme.
 
 ### `figure/` and `data/`
 

diff --git a/_pkgdown.yml b/_pkgdown.yml
diff --git a/docs/404.html b/docs/404.html