Develop

DESCRIPTION

@@ -1,6 +1,6 @@
 Package: thesisdown
 Title: An updated R Markdown thesis template using the bookdown package
-Version: 0.0.3
+Version: 0.1.0
 Authors@R: c(
     person("Chester", "Ismay", email = "chester.ismay@gmail.com", role = "cre"),
     person("Nick", "Solomon", email = "nick@nicksolomon.me", role = "aut"))
@@ -15,9 +15,10 @@ Depends:
     dplyr,
     ggplot2,
     bookdown,
-    knitr
+    knitr,
+    here
 License: MIT
 Encoding: UTF-8
 LazyData: true
 SystemRequirements: pandoc (>= 1.18) - http://pandoc.org
-RoxygenNote: 7.0.2
+RoxygenNote: 7.1.0

R/thesis.R

@@ -5,37 +5,40 @@
 #'
 #' @export
 #'
-#' @param toc A Boolean (TRUE or FALSE) specifying whether table of contents should be created
+#' @param toc A Boolean (TRUE or FALSE) specifying whether table of contents
+#'  should be created
 #' @param toc_depth A positive integer
 #' @param ... Further arguments passed to or from other methods.
-#' @param highlight Syntax highlighting style. Supported styles include "default", "tango", "pygments", "kate", "monochrome", "espresso", "zenburn", and "haddock". Pass NULL to prevent syntax highlighting.
+#' @param highlight Syntax highlighting style. Supported styles include
+#' "default", "tango", "pygments", "kate", "monochrome", "espresso", "zenburn",
+#' and "haddock". Pass NULL to prevent syntax highlighting.
 #'
 #' @return A modified \code{pdf_document} based on the Reed Senior Thesis LaTeX
 #'   template
 #' @examples
 #' \dontrun{
-#'  output: thesisdown::thesis_pdf
+#' output:thesisdown::thesis_pdf
 #' }
-thesis_pdf <- function(toc = TRUE, toc_depth = 3, highlight = "default", ...){
-
-  base <- bookdown::pdf_book(template = "template.tex",
+thesis_pdf <- function(toc = TRUE, toc_depth = 3, highlight = "default", ...) {
+  base <- bookdown::pdf_book(
+    template = "template.tex",
     toc = toc,
     toc_depth = toc_depth,
     highlight = highlight,
     keep_tex = TRUE,
     pandoc_args = "--top-level-division=chapter",
-    ...)
+    ...
+  )
 
   # Mostly copied from knitr::render_sweave
   base$knitr$opts_chunk$comment <- NA
-  #base$knitr$opts_chunk$fig.align <- "center"
+  # base$knitr$opts_chunk$fig.align <- "center"
 
   old_opt <- getOption("bookdown.post.latex")
   options(bookdown.post.latex = fix_envs)
   on.exit(options(bookdown.post.late = old_opt))
 
   base
-
 }
 
 #' Creates an R Markdown gitbook Thesis document
@@ -49,14 +52,19 @@ thesis_pdf <- function(toc = TRUE, toc_depth = 3, highlight = "default", ...){
 #' @return A gitbook webpage
 #' @examples
 #' \dontrun{
-#'  output: thesisdown::thesis_gitbook
+#' output:thesisdown::thesis_gitbook
 #' }
-thesis_gitbook <- function(...){
-
+thesis_gitbook <- function(...) {
   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>'))
+    toc = list(
+      collapse = "section",
+      before = '<li><a href="./"></a></li>',
+      after = paste(
+        '<li><a href="https://github.com/rstudio/bookdown',
+        'target="blank">Published with bookdown</a></li>'
+      )
+    )
+  )
 
   listarg <- list(...)
 
@@ -89,7 +97,6 @@ thesis_gitbook <- function(...){
   base$knitr$opts_chunk$fig.align <- "center"
 
   base
-
 }
 
 #' Creates an R Markdown Word Thesis document
@@ -104,18 +111,16 @@ thesis_gitbook <- function(...){
 #' the Reed Senior Thesis Word template
 #' @examples
 #' \dontrun{
-#'  output: thesisdown::thesis_word
+#' output:thesisdown::thesis_word
 #' }
-thesis_word <- function(...){
-
+thesis_word <- function(...) {
   base <- bookdown::word_document2(...)
 
   # Mostly copied from knitr::render_sweave
   base$knitr$opts_chunk$comment <- NA
   base$knitr$opts_chunk$fig.align <- "center"
 
   base
-
 }
 
 #' Creates an R Markdown epub Thesis document
@@ -129,28 +134,31 @@ thesis_word <- function(...){
 #' @return A ebook version of the thesis
 #' @examples
 #' \dontrun{
-#'  output: thesisdown::thesis_epub
+#' output:thesisdown::thesis_epub
 #' }
-thesis_epub <- function(...){
-
+thesis_epub <- function(...) {
   base <- bookdown::epub_book(...)
 
   # Mostly copied from knitr::render_sweave
   base$knitr$opts_chunk$comment <- NA
   base$knitr$opts_chunk$fig.align <- "center"
 
   base
-
 }
 
-fix_envs = function(x){
-  beg_reg <- '^\\s*\\\\begin\\{.*\\}'
-  end_reg <- '^\\s*\\\\end\\{.*\\}'
-  i3 = if (length(i1 <- grep(beg_reg, x))) (i1 - 1)[grepl("^\\s*$", x[i1 - 1])]
+fix_envs <- function(x) {
+  beg_reg <- "^\\s*\\\\begin\\{.*\\}"
+  end_reg <- "^\\s*\\\\end\\{.*\\}"
+  i3 <- if (length(i1 <- grep(beg_reg, x))) {
+    (i1 - 1)[grepl("^\\s*$", x[i1 - 1])]
+  }
 
-  i3 = c(i3,
-         if (length(i2 <- grep(end_reg, x))) (i2 + 1)[grepl("^\\s*$", x[i2 + 1])]
+  i3 <- c(
+    i3,
+    if (length(i2 <- grep(end_reg, x))) {
+      (i2 + 1)[grepl("^\\s*$", x[i2 + 1])]
+    }
   )
-  if (length(i3)) x = x[-i3]
+  if (length(i3)) x <- x[-i3]
   x
 }

R/thesisdown.R

@@ -1,5 +1,5 @@
 #' thesisdown: A package for creating undergraduate, Masters, and PhD theses
-#'using R Markdown
+#' using R Markdown
 #'
 #'
 #' @section thesis_gitbook:

inst/rmarkdown/templates/thesis/skeleton/01-chap1.Rmd

@@ -120,8 +120,9 @@ pkg <- c("dplyr", "ggplot2", "knitr", "bookdown", "devtools")
 new.pkg <- pkg[!(pkg %in% installed.packages())]
 # If there are any packages in the list that aren't installed,
 # install them
-if (length(new.pkg))
+if (length(new.pkg)) {
   install.packages(new.pkg, repos = "http://cran.rstudio.com")
+}
 # Load packages (thesisdown will load all of the packages as well)
 library(thesisdown)
 ```
@@ -135,22 +136,23 @@ The example we show here does the following:
 - Using `flights2`, we determine the largest arrival delay for each of the carriers.
 
 ```{r max_delays}
-flights2 <- flights %>% 
+flights2 <- flights %>%
   select(carrier_name, arr_delay)
-max_delays <- flights2 %>% 
+max_delays <- flights2 %>%
   group_by(carrier_name) %>%
   summarize(max_arr_delay = max(arr_delay, na.rm = TRUE))
 ```
 
 A useful function in the `knitr` package for making nice tables in _R Markdown_ is called `kable`.  It is much easier to use than manually entering values into a table by copying and pasting values into Excel or LaTeX.  This again goes to show how nice reproducible documents can be! (Note the use of `results="asis"`, which will produce the table instead of the code to create the table.)  The `caption.short` argument is used to include a shorter title to appear in the List of Tables.
 
 ```{r maxdelays, results="asis"}
-kable(max_delays, 
-      col.names = c("Airline", "Max Arrival Delay"),
-      caption = "Maximum Delays by Airline",
-      caption.short = "Max Delays by Airline",
-      longtable = TRUE,
-      booktabs = TRUE)
+kable(max_delays,
+  col.names = c("Airline", "Max Arrival Delay"),
+  caption = "Maximum Delays by Airline",
+  caption.short = "Max Delays by Airline",
+  longtable = TRUE,
+  booktabs = TRUE
+)
 ```
 
 The last two options make the table a little easier-to-read.
@@ -159,17 +161,24 @@ We can further look into the properties of the largest value here for American A
 
 
 ```{r max_props}
-flights %>% filter(arr_delay == 1539, 
-                  carrier_name == "American Airlines Inc.") %>%
-  select(-c(month, day, carrier, dest_name, hour, 
-            minute, carrier_name, arr_delay))
+flights %>%
+  filter(
+    arr_delay == 1539,
+    carrier_name == "American Airlines Inc."
+  ) %>%
+  select(-c(
+    month, day, carrier, dest_name, hour,
+    minute, carrier_name, arr_delay
+  ))
 ```
 
 We see that the flight occurred on March 3rd and departed a little after 2 PM on its way to Dallas/Fort Worth.  Lastly, we show how we can visualize the arrival delay of all departing flights from Portland on March 3rd against time of departure.
 
 ```{r march3plot, fig.height=3, fig.width=6}
-flights %>% filter(month == 3, day == 3) %>%
-  ggplot(aes(x = dep_time, y = arr_delay)) + geom_point()
+flights %>%
+  filter(month == 3, day == 3) %>%
+  ggplot(aes(x = dep_time, y = arr_delay)) +
+  geom_point()
 ```
 
 ## Additional resources

inst/rmarkdown/templates/thesis/skeleton/03-chap3.Rmd

@@ -3,18 +3,67 @@
 # installed and loaded. This thesisdown package includes
 # the template files for the thesis and also two functions
 # used for labeling and referencing
-if(!require(devtools))
-  install.packages("devtools", repos = "http://cran.rstudio.com")
-if(!require(dplyr))
-    install.packages("dplyr", repos = "http://cran.rstudio.com")
-if(!require(ggplot2))
-    install.packages("ggplot2", repos = "http://cran.rstudio.com")
-if(!require(ggplot2))
-    install.packages("bookdown", repos = "http://cran.rstudio.com")
-if(!require(thesisdown)){
-  library(devtools)
-  devtools::install_github("ismayc/thesisdown")
+if (!require(remotes)) {
+  if (params$`Install needed packages for {thesisdown}`) {
+    install.packages("remotes", repos = "https://cran.rstudio.com")
+  } else {
+    stop(
+      paste(
+        'You need to run install.packages("remotes")',
+        "first in the Console."
+      )
+    )
   }
+}
+if (!require(dplyr)) {
+  if (params$`Install needed packages for {thesisdown}`) {
+    install.packages("dplyr", repos = "https://cran.rstudio.com")
+  } else {
+    stop(
+      paste(
+        'You need to run install.packages("dplyr")',
+        "first in the Console."
+      )
+    )
+  }
+}
+if (!require(ggplot2)) {
+  if (params$`Install needed packages for {thesisdown}`) {
+    install.packages("ggplot2", repos = "https://cran.rstudio.com")
+  } else {
+    stop(
+      paste(
+        'You need to run install.packages("ggplot2")',
+        "first in the Console."
+      )
+    )
+  }
+}
+if (!require(bookdown)) {
+  if (params$`Install needed packages for {thesisdown}`) {
+    install.packages("bookdown", repos = "https://cran.rstudio.com")
+  } else {
+    stop(
+      paste(
+        'You need to run install.packages("bookdown")',
+        "first in the Console."
+      )
+    )
+  }
+}
+if (!require(thesisdown)) {
+  if (params$`Install needed packages for {thesisdown}`) {
+    remotes::install_github("ismayc/thesisdown")
+  } else {
+    stop(
+      paste(
+        "You need to run",
+        'remotes::install_github("ismayc/thesisdown")',
+        "first in the Console."
+      )
+    )
+  }
+}
 library(thesisdown)
 flights <- read.csv("data/flights.csv")
 ```
@@ -77,7 +126,8 @@ Here is a reference to the Reed logo: Figure \@ref(fig:reedlogo).  Note the use
 Below we will investigate how to save the output of an **R** plot and label it in a way similar to that done above.  Recall the `flights` dataset from Chapter \@ref(rmd-basics).  (Note that we've shown a different way to reference a section or chapter here.)  We will next explore a bar graph with the mean flight departure delays by airline from Portland for 2014.  Note also the use of the `scale` parameter which is discussed on the next page.
 
 ```{r delaysboxplot, warnings=FALSE, messages=FALSE, fig.cap="Mean Delays by Airline", fig.width=6}
-flights %>% group_by(carrier) %>%
+flights %>%
+  group_by(carrier) %>%
   summarize(mean_dep_delay = mean(dep_delay)) %>%
   ggplot(aes(x = carrier, y = mean_dep_delay)) +
   geom_bar(position = "identity", stat = "identity", fill = "red")

inst/rmarkdown/templates/thesis/skeleton/05-appendix.Rmd

@@ -2,13 +2,13 @@
 
 `r if(!knitr:::is_latex_output()) '# (APPENDIX) Appendix {-}'` 
 
+
+# The First Appendix
+
 <!--
 If you feel it necessary to include an appendix, it goes here.
 -->
 
-
-# The First Appendix
-
 This first appendix includes all of the R chunks of code that were hidden throughout the document (using the `include = FALSE` chunk tag) to help with readibility and/or setup.
 
 **In the main Rmd file**

inst/rmarkdown/templates/thesis/skeleton/_bookdown.yml

@@ -1,5 +1,8 @@
 book_filename: "thesis"
 chapter_name: "Chapter "
-rmd_files: ["index.Rmd", "01-chap1.Rmd", "02-chap2.Rmd", "03-chap3.Rmd", "04-conclusion.Rmd", "05-appendix.Rmd", "99-references.Rmd"]
-download: [["thesis.pdf", "PDF"], ["thesis.epub", "EPUB"], ["thesis.docx", "Word"]]
+download: [
+    ["thesis.pdf", "PDF"],
+    ["thesis.epub", "EPUB"],
+    ["thesis.docx", "Word"]
+  ]
 delete_merged_file: true

inst/rmarkdown/templates/thesis/skeleton/reedthesis.cls

@@ -185,8 +185,7 @@
 %\setlength{\oddsidemargin}{.6in}
 %\setlength{\evensidemargin}{0in}
 %\setlength{\textwidth}{5.9in}
-%\setlength\topmargin{0in}
-%\addtolength\headheight{2.5pt}
+\addtolength\headheight{2.5pt}
 %\addtolength\topmargin{-\headheight}
 %\addtolength\topmargin{-\headsep}
 %\addtolength\textheight{1in}