doc: style write* functions

R/write_authors.R

@@ -1,71 +1,82 @@
 #' Compile Authors Names in YAML Form
 #'
-#' Write a file to the disk with all authors and their affiliations
-#' using the yaml form for inclusion in the stock assessment.
+#' Write a file to the disk with all authors and their affiliations using the
+#' yaml form for inclusion in the stock assessment.
 #'
 #' @template authors
 #' @template fileout
 #' @author Kelli F. Johnson
 #' @family write
 #' @export
 #' @examples
-#' # An example with a standard first name middle initial full stop and last name
-#' # then a first initial full stop middle initial full stop and last name and
-#' # last a first name and last name with no middle initial.
+#' # An example with a standard first name middle initial full stop and last
+#' # name then a first initial full stop middle initial full stop and last
+#' # name and last a first name and last name with no middle initial.
 #' eg <- utils::capture.output(
-#' 	write_authors(
-#' 		c("Kelli F. Johnson", "E. J. Dick", "Qi Lee"),
-#' 		fileout = ""
-#' 	)
+#'   write_authors(
+#'     c("Kelli F. Johnson", "E. J. Dick", "Qi Lee"),
+#'     fileout = ""
+#'   )
 #' )
 #' \dontrun{
 #' print(eg)
 #' }
 write_authors <- function(authors,
-	fileout = "00authors.Rmd") {
-	affil <- get_affiliation(authors)
-	affil_u <- affil[!duplicated(affil)]
-	matches <- match(affil, affil_u)
-	persons <- utils::as.person(authors)
-	first <- vapply(lapply(
-		strsplit(format(persons, include = "given"), "\\s+"),
-		"[[", 1
-	), substr, "character", start = 1, stop = 1)
-	middle <- vapply(gsub("^[A-Z][a-z]*\\.*\\s*", "", format(persons, include = "given")),
-		FUN = substr, FUN.VALUE = "character", start = 1, stop = 1, USE.NAMES = FALSE
-	)
-	initials <- gsub("\\.\\.", "\\.", sprintf("%1$s.%2$s.", first, middle))
-	last <- format(persons, include = "family")
-	citation <- paste(last[1], initials[1], sep = ", ")
-	if (length(last) > 1) {
-		citation <- paste(citation, paste(initials[-1], last[-1],
-			sep = " ", collapse = ", "
-		), sep = ", ")
-	} else {
-		citation <- gsub("\\.*$", "", citation)
-	}
-	address <- sprintf(
-		"^%1$s^%2$s",
-		seq_along(affil[!duplicated(affil)]), affil[!duplicated(affil)]
-	)
+                          fileout = "00authors.Rmd") {
+  affil <- get_affiliation(authors)
+  affil_u <- affil[!duplicated(affil)]
+  matches <- match(affil, affil_u)
+  persons <- utils::as.person(authors)
+  first <- vapply(
+    lapply(strsplit(format(persons, include = "given"), "\\s+"), "[[", 1),
+    substr,
+    "character",
+    start = 1,
+    stop = 1
+  )
+  middle <- vapply(
+    gsub("^[A-Z][a-z]*\\.*\\s*", "", format(persons, include = "given")),
+    FUN = substr,
+    FUN.VALUE = "character",
+    start = 1,
+    stop = 1,
+    USE.NAMES = FALSE
+  )
+  initials <- gsub("\\.\\.", "\\.", sprintf("%1$s.%2$s.", first, middle))
+  last <- format(persons, include = "family")
+  citation <- paste(last[1], initials[1], sep = ", ")
+  if (length(last) > 1) {
+    citation <- paste(citation, paste(initials[-1], last[-1],
+      sep = " ", collapse = ", "
+    ), sep = ", ")
+  } else {
+    citation <- gsub("\\.*$", "", citation)
+  }
+  address <- sprintf(
+    "^%1$s^%2$s",
+    seq_along(affil[!duplicated(affil)]), affil[!duplicated(affil)]
+  )
 
-	xfun::write_utf8(
-		c(
-			"---\n",
-			yaml::as.yaml(column.major = FALSE, indent.mapping.sequence = TRUE, list(
-				author = data.frame(
-					name = authors, code = matches,
-					first = first, middle = middle, family = format(persons, include = "family")
-				),
-				author_list = citation,
-				affiliation = data.frame(
-					code = matches[!duplicated(affil)],
-					address = affil[!duplicated(affil)]
-				),
-				address = address
-			)),
-			"---"
-		),
-		con = fileout, sep = ""
-	)
+  xfun::write_utf8(
+    c(
+      "---\n",
+      yaml::as.yaml(column.major = FALSE, indent.mapping.sequence = TRUE, list(
+        author = data.frame(
+          name = authors,
+          code = matches,
+          first = first,
+          middle = middle,
+          family = format(persons, include = "family")
+        ),
+        author_list = citation,
+        affiliation = data.frame(
+          code = matches[!duplicated(affil)],
+          address = affil[!duplicated(affil)]
+        ),
+        address = address
+      )),
+      "---"
+    ),
+    con = fileout, sep = ""
+  )
 }

R/write_bibliography.R

@@ -1,82 +1,80 @@
 #' Write yaml header for bibliography to its own .Rmd file
 #'
-#' Write the yaml header entry for bibliographies based on
-#' `.bib` files found within the directory (`basedirectory`).
-#' Users can also search through higher-level directories using `up` and
-#' lower-level directories using `recursive`.
-#' This function is helpful when using bookdown because you will often
-#' be sourcing files from multiple levels and have many bibliography files,
-#' which can all be included in a single call within your yaml header.
-#' No need to put all references into a single bib file or specify
-#' the bib files ahead of time. Let us use R for this!
+#' Write the yaml header entry for bibliographies based on `.bib` files found
+#' within the directory (`basedirectory`). Users can also search through
+#' higher-level directories using `up` and lower-level directories using
+#' `recursive`. This function is helpful when using bookdown because you will
+#' often be sourcing files from multiple levels and have many bibliography
+#' files, which can all be included in a single call within your yaml header. No
+#' need to put all references into a single bib file or specify the bib files
+#' ahead of time. Let us use R for this!
 #'
 #' @details
-#' Within this package, note that this function is not currently
-#' called by any other function, which is fine because each template
-#' has its own `.bib` file.
+#' Within this package, note that this function is not currently called by any
+#' other function, which is fine because each template has its own `.bib` file.
 #' You can add `.bib` files later by running this function prior to compiling
-#' your document. Or, you could add it to your index/skeleton.Rmd file
-#' using a code chunk. For example,
-#' `write_bibliography(getwd(), up = 1)` would update the yaml header
-#' every time that you compile, but be aware that you will have to run
-#' [bookdown::render_book] multiple times to get get this to work.
-#' Developers are working on using the code within the yaml to get it
-#' to work instantaneously; so, stay tuned.
+#' your document. Or, you could add it to your index/skeleton.Rmd file using a
+#' code chunk. For example, `write_bibliography(getwd(), up = 1)` would update
+#' the yaml header every time that you compile, but be aware that you will have
+#' to run [bookdown::render_book] multiple times to get get this to work.
+#' Developers are working on using the code within the yaml to get it to work
+#' instantaneously; so, stay tuned.
 #'
 #' @param basedirectory The directory that you want to look for bib files
-#' in. If `up = 0`, then this will be the only directory that is searched.
-#' @param up An integer value specifying how many directory levels you want
-#' to search above `basedirectory`.
-#' The default is to only search the base directory.
+#'   in. If `up = 0`, then this will be the only directory that is searched.
+#' @param up An integer value specifying how many directory levels you want to
+#'   search above `basedirectory`. The default is to only search the base
+#'   directory.
 #' @param recursive A logical value specifying if each directory should be
-#' searched for using recursion. The default is to not search recursively
-#' because you could have other folders higher up that are not relevant.
+#'   searched for using recursion. The default is to not search recursively
+#'   because you could have other folders higher up that are not relevant.
 #' @template fileout
 #'
 #' @author Kelli F. Johnson
 #' @export
-#' @return A yaml header for markdown either printed to a file or
-#' returned to the screen if using `fileout = stdout()`.
+#' @return
+#' A yaml header for markdown either printed to a file or returned to the screen
+#' if using `fileout = stdout()`.
 #' @family write
 #' @examples
 #' # print the output to the screen rather than save to a file
 #' write_bibliography(getwd(), fileout = stdout())
 write_bibliography <- function(basedirectory = getwd(),
-	up = 0,
-	recursive = FALSE,
-	fileout = "00bibliography.Rmd") {
-	changedirectory <- basedirectory
-	bibfiles <- vector()
-	while (up >= 0) {
-		bibfiles <- append(
-			x = bibfiles,
-			after = length(bibfiles),
-			values = dir(
-				path = changedirectory,
-				recursive = recursive,
-				pattern = "\\.bib$",
-				full.names = TRUE
-			)
-		)
-		up <- up - 1
-		changedirectory <- dirname(changedirectory)
-	}
-	relativepaths <- R.utils::getRelativePath(
-		pathname = bibfiles,
-		relativeTo = basedirectory
-	)
-	if (length(bibfiles) == 0) {
-		return()
-	}
+                               up = 0,
+                               recursive = FALSE,
+                               fileout = "00bibliography.Rmd") {
+  changedirectory <- basedirectory
+  bibfiles <- vector()
+  while (up >= 0) {
+    bibfiles <- append(
+      x = bibfiles,
+      after = length(bibfiles),
+      values = dir(
+        path = changedirectory,
+        recursive = recursive,
+        pattern = "\\.bib$",
+        full.names = TRUE
+      )
+    )
+    up <- up - 1
+    changedirectory <- dirname(changedirectory)
+  }
+  relativepaths <- R.utils::getRelativePath(
+    pathname = bibfiles,
+    relativeTo = basedirectory
+  )
+  if (length(bibfiles) == 0) {
+    return()
+  }
 
-	# Format for yaml
-	writeLines(
-		con = fileout,
-		text = utils::capture.output(
-			ymlthis::yml_citations(
-				.yml = ymlthis::yml_empty(),
-				bibliography = relativepaths
-			)
-		)
-	)
+  # Format for yaml
+  writeLines(
+    con = fileout,
+    text = utils::capture.output(
+      ymlthis::yml_citations(
+        .yml = ymlthis::yml_empty(),
+        bibliography = relativepaths
+      )
+    )
+  )
 }

R/write_summary.R

@@ -1,17 +1,17 @@
 #' Write Summary Files
 #'
-#' Write a file to the disk with the title
-#' using the yaml form for inclusion in the stock assessment.
+#' Write a file to the disk with the title using the yaml form for inclusion in
+#' the stock assessment.
 #'
-#' @param type A vector of the type of summaries you want included in the
-#' stock assessment document. Current options are listed in the default
-#' call to \code{write_summary}.
+#' @param type A vector of the type of summaries you want included in the stock
+#'   assessment document. Current options are listed in the default call to
+#'   `write_summary()`.
 #' @template fileout
 #'
 #' @author Kelli F. Johnson
 
 write_summary <- function(type = c("executive", "onepage"),
-	fileout = "01summaries.Rmd") {
-	type <- match.arg(type, several.ok = TRUE)
-	stop("This function is incomplete.")
+                          fileout = "01summaries.Rmd") {
+  type <- match.arg(type, several.ok = TRUE)
+  stop("This function is incomplete.")
 }

R/write_title.R

@@ -1,37 +1,39 @@
 #' Compile Title in YAML format
 #'
-#' Write a file to the disk with the title
-#' using the yaml form for inclusion in the stock assessment.
+#' Write a file to the disk with the title using the yaml form for inclusion in
+#' the stock assessment.
 #'
-#' @details The Latin name as specified in \code{"latin"} argument
-#' will be encased in underscores to facilitate it being italicized.
-#' Using emph is not allowed because the tagging structure
-#' for the creation of the 508 compliant pdf will not render the LaTex
-#' code here. Nevertheless, the use of markdown inside the yaml seems
-#' to work just fine.
+#' @details
+#' The Latin name as specified in \code{"latin"} argument will be encased in
+#' underscores to facilitate it being italicized. Using emph is not allowed
+#' because the tagging structure for the creation of the 508 compliant pdf will
+#' not render the LaTex code here. Nevertheless, the use of markdown inside the
+#' yaml seems to work just fine.
 #'
 #' @template species
 #' @template latin
 #' @template coast
-#' @param year A numeric or character string specifying the year.
-#' The default uses \code{Sys.Date()} to format the year into a four
-#' digit character value.
+#' @param year A numeric or character string specifying the year. The default
+#'   uses [Sys.Date()] to format the year into a four digit character value.
 #' @template fileout
 #'
 #' @author Kelli F. Johnson
 #' @family write
-
 write_title <- function(species,
-	latin,
-	coast,
-	year = format(Sys.Date(), "%Y"),
-	fileout = "00title.Rmd") {
-	xfun::write_utf8(text = c(
-		"---\n",
-		yaml::as.yaml(list(title = paste0(
-			"Status of ", species, " (_", latin, "_)",
-			" along the ", coast, " coast in ", year
-		))),
-		"---"
-	), con = fileout, sep = "")
+                        latin,
+                        coast,
+                        year = format(Sys.Date(), "%Y"),
+                        fileout = "00title.Rmd") {
+  xfun::write_utf8(
+    text = c(
+      "---\n",
+      yaml::as.yaml(list(title = paste0(
+        "Status of ", species, " (_", latin, "_)",
+        " along the ", coast, " coast in ", year
+      ))),
+      "---"
+    ),
+    con = fileout,
+    sep = ""
+  )
 }