/
thesis_pdf.R
122 lines (121 loc) · 5.45 KB
/
thesis_pdf.R
1
2
3
4
5
6
7
8
9
10
11
12
13
14
15
16
17
18
19
20
21
22
23
24
25
26
27
28
29
30
31
32
33
34
35
36
37
38
39
40
41
42
43
44
45
46
47
48
49
50
51
52
53
54
55
56
57
58
59
60
61
62
63
64
65
66
67
68
69
70
71
72
73
74
75
76
77
78
79
80
81
82
83
84
85
86
87
88
89
90
91
92
93
94
95
96
97
98
99
100
101
102
103
104
105
106
107
108
109
110
111
112
113
114
115
116
117
118
119
120
121
122
#' Creates an R Markdown PDF Thesis document
#'
#' This is a function called in output in the YAML of the driver Rmd file
#' to specify using the IHEID Thesis LaTeX template file.
#' @param input Rmd input file that will be processed by the function.
#' @param ... Instructions passed to the function from a correctly specified
#' .Rmd document
#' @return A modified \code{pdf_document} based on the IHEID Thesis LaTeX
#' template
#' @examples
#' \dontrun{
#' knit: iheiddown::thesis_pdf
#' }
#' @importFrom bookdown render_book pdf_book
#' @export
thesis_pdf <- function(input = ".", ...) {
options(bookdown.render.file_scope = FALSE)
author <- readLines(input)
author <- author[grepl("^lastnames:", author)]
author <- strsplit(author, " ")[[1]][2]
bookdown::render_book(...,
output_file =
paste0("Thesis_",
author,
"_",
Sys.Date()),
output_format = bookdown::pdf_book(
latex_engine = "xelatex",
template = system.file("rmarkdown",
"templates",
"thesis_pdf",
"resources",
"template.tex",
package = "iheiddown"),
citation_package = "biblatex"))
file.remove(c(list.files(pattern = ".*.maf", recursive = TRUE),
list.files(pattern = ".*.mtc", recursive = TRUE)))
}
#' 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.
#' @param input Rmd input file that will be processed by the function.
#' @param ... Instructions passed to the function from a correctly specified
#' .Rmd document
#' @importFrom bookdown preview_chapter
#' @importFrom rmarkdown pdf_document
#' @import crayon
#' @return A modified \code{pdf_document} based on the IHEID Thesis LaTeX
#' template
#' @examples
#' \dontrun{
#' knit: iheiddown::chapter_pdf
#' }
#' @export
chapter_pdf <- function(input, ...) {
# Extract metadata to check whether to knit in context or not.
in_context <- readLines(input)
in_context <- in_context[grepl("^in_context:", in_context)]
in_context <- strsplit(in_context, " ")[[1]][2]
if (in_context) {
# Extract metadata to name output file without running into annoying
# bookdown error
author <- readLines(input)
author <- author[grepl("^author:", author)]
author <- strsplit(author, " ")[[1]][2]
chapter <- readLines(input)
chapter <- chapter[grepl("^chapter:", chapter)]
chapter <- strsplit(chapter, " ")[[1]][2]
message("In-context rendering")
#Render chapter
bookdown::preview_chapter(input = input, ...,
output_file =
paste0("versions/",
author, "_",
"Chapter_",
chapter, "_",
Sys.Date()),
output_format =
rmarkdown::pdf_document(
latex_engine = "xelatex",
template =
system.file("rmarkdown",
"templates",
"chapter_pdf",
"resources",
"template.tex",
package = "iheiddown")))
file.remove(c(list.files(pattern = ".*.maf", recursive = TRUE),
list.files(pattern = ".*.mtc", recursive = TRUE)))
} else {
# Extract metadata to name output file without running into annoying
# bookdown error
author <- readLines(input)
author <- author[grepl("^author:", author)]
author <- strsplit(author, " ")[[1]][2]
chapter <- readLines(input)
chapter <- chapter[grepl("^chapter:", chapter)]
chapter <- strsplit(chapter, " ")[[1]][2]
message("Out of context rendering")
#Render chapter
rmarkdown::render(input, ...,
output_file = paste0("versions/",
author, "_",
"Chapter_",
chapter,
"_",
Sys.Date()),
output_format =
rmarkdown::pdf_document(latex_engine = "xelatex",
template =
system.file("rmarkdown",
"templates",
"chapter_pdf",
"resources",
"template.tex",
package =
"iheiddown")))
}
}