Merge pull request #290 from jmbarbone/roxygen2md

Use `roxygen2md`

DESCRIPTION

@@ -91,3 +91,4 @@ Collate:
     'writeDataTable.R'
     'writexlsx.R'
     'zzz.R'
+Roxygen: list(markdown = TRUE)

R/CommentClass.R

@@ -66,13 +66,12 @@ Comment$methods(show = function() {
 #' @description Create a cell Comment object to pass to writeComment()
 #' @param comment Comment text. Character vector.
 #' @param author Author of comment. Character vector of length 1
-#' @param style A Style object or list of style objects the same length as
-#'   comment vector. See \code{\link{createStyle}}.
+#' @param style A Style object or list of style objects the same length as comment vector. See [createStyle()].
 #' @param visible TRUE or FALSE. Is comment visible.
 #' @param width,height Width and height of textbook (in number of cells);
 #'   doubles are rounded with \code{base::round()}
 #' @export
-#' @seealso \code{\link{writeComment}}
+#' @seealso [writeComment()]
 #' @examples
 #' wb <- createWorkbook()
 #' addWorksheet(wb, "Sheet 1")
@@ -127,12 +126,12 @@ createComment <- function(comment,
 #' @param sheet A vector of names or indices of worksheets
 #' @param col Column a column number of letter
 #' @param row A row number.
-#' @param comment A Comment object. See \code{\link{createComment}}.
-#' @param xy An alternative to specifying \code{col} and
-#' \code{row} individually.  A vector of the form
-#' \code{c(col, row)}.
+#' @param comment A Comment object. See [createComment()].
+#' @param xy An alternative to specifying `col` and
+#' `row` individually.  A vector of the form
+#' `c(col, row)`.
 #' @export
-#' @seealso \code{\link{createComment}}
+#' @seealso [createComment()]
 #' @examples
 #' wb <- createWorkbook()
 #' addWorksheet(wb, "Sheet 1")
@@ -205,11 +204,11 @@ writeComment <- function(wb, sheet, col, row, comment, xy = NULL) {
 #' @param sheet A vector of names or indices of worksheets
 #' @param cols Columns to delete comments from
 #' @param rows Rows to delete comments from
-#' @param gridExpand If \code{TRUE}, all data in rectangle min(rows):max(rows) X min(cols):max(cols)
+#' @param gridExpand If `TRUE`, all data in rectangle min(rows):max(rows) X min(cols):max(cols)
 #' will be removed.
 #' @export
-#' @seealso \code{\link{createComment}}
-#' @seealso \code{\link{writeComment}}
+#' @seealso [createComment()]
+#' @seealso [writeComment()]
 removeComment <- function(wb, sheet, cols, rows, gridExpand = TRUE) {
   sheet <- wb$validateSheet(sheet)
 

R/build_workbook.R

@@ -5,18 +5,18 @@
 #' @details 
 #' This function can be used as shortcut to create a workbook object from a 
 #'   data.frame or named list.  If names are available in the list they will be
-#'   used as the worksheet names.  The parameters in \code{...} are collected
-#'   and passed to \code{\link{writeData}} or \code{\link{writeDataTable}} to
+#'   used as the worksheet names.  The parameters in `...` are collected
+#'   and passed to [writeData()] or [writeDataTable()] to
 #'   initially create the Workbook objects then appropriate parameters are 
-#'   passed to \code{\link{setColWidths}}.
+#'   passed to [setColWidths()].
 #' 
 #' @param x A data.frame or a (named) list of objects that can be handled by
-#'   \code{\link{writeData}} or \code{\link{writeDataTable}} to write to file
-#' @param asTable If \code{TRUE} will use \code{\link{writeDataTable}} rather
-#'   than \code{\link{writeData}} to write \code{x} to the file (default: 
-#'   \code{FALSE})
-#' @param ... Additional arguments passed to \code{\link{writeData}}, 
-#'   \code{\link{writeDataTable}}, \code{\link{setColWidths}} (see Optional
+#'   [writeData()] or [writeDataTable()] to write to file
+#' @param asTable If `TRUE` will use [writeDataTable()] rather
+#'   than [writeData()] to write `x` to the file (default: 
+#'   `FALSE`)
+#' @param ... Additional arguments passed to [writeData()], 
+#'   [writeDataTable()], [setColWidths()] (see Optional
 #'   Parameters)
 #' @author Jordan Mark Barbone
 #' @returns A Workbook object
@@ -27,49 +27,49 @@
 #' 
 #' @section Optional Parameters:
 #' 
-#' \bold{createWorkbook Parameters}
+#' **createWorkbook Parameters**
 #' \itemize{
-#'   \item{\bold{creator}}{ A string specifying the workbook author}
+#'   \item{**creator**}{ A string specifying the workbook author}
 #' }
 #'
-#' \bold{addWorksheet Parameters}
+#' **addWorksheet Parameters**
 #' \itemize{
-#'   \item{\bold{sheetName}}{ Name of the worksheet}
-#'   \item{\bold{gridLines}}{ A logical. If \code{FALSE}, the worksheet grid lines will be hidden.}
-#'   \item{\bold{tabColour}}{ Colour of the worksheet tab. A valid colour (belonging to colours())
+#'   \item{**sheetName**}{ Name of the worksheet}
+#'   \item{**gridLines**}{ A logical. If `FALSE`, the worksheet grid lines will be hidden.}
+#'   \item{**tabColour**}{ Colour of the worksheet tab. A valid colour (belonging to colours())
 #'   or a valid hex colour beginning with "#".}
-#'   \item{\bold{zoom}}{ A numeric between 10 and 400. Worksheet zoom level as a percentage.}
+#'   \item{**zoom**}{ A numeric between 10 and 400. Worksheet zoom level as a percentage.}
 #' }
 #'
-#' \bold{writeData/writeDataTable Parameters}
+#' **writeData/writeDataTable Parameters**
 #' \itemize{
-#'   \item{\bold{startCol}}{ A vector specifying the starting column(s) to write df}
-#'   \item{\bold{startRow}}{ A vector specifying the starting row(s) to write df}
-#'   \item{\bold{xy}}{ An alternative to specifying startCol and startRow individually.
+#'   \item{**startCol**}{ A vector specifying the starting column(s) to write df}
+#'   \item{**startRow**}{ A vector specifying the starting row(s) to write df}
+#'   \item{**xy**}{ An alternative to specifying startCol and startRow individually.
 #'  A vector of the form c(startCol, startRow)}
-#'   \item{\bold{colNames or col.names}}{ If \code{TRUE}, column names of x are written.}
-#'   \item{\bold{rowNames or row.names}}{ If \code{TRUE}, row names of x are written.}
-#'   \item{\bold{headerStyle}}{ Custom style to apply to column names.}
-#'   \item{\bold{borders}}{ Either "surrounding", "columns" or "rows" or NULL.  If "surrounding", a border is drawn around the
+#'   \item{**colNames or col.names**}{ If `TRUE`, column names of x are written.}
+#'   \item{**rowNames or row.names**}{ If `TRUE`, row names of x are written.}
+#'   \item{**headerStyle**}{ Custom style to apply to column names.}
+#'   \item{**borders**}{ Either "surrounding", "columns" or "rows" or NULL.  If "surrounding", a border is drawn around the
 #' data.  If "rows", a surrounding border is drawn a border around each row. If "columns", a surrounding border is drawn with a border
-#' between each column.  If "\code{all}" all cell borders are drawn.}
-#'   \item{\bold{borderColour}}{ Colour of cell border}
-#'   \item{\bold{borderStyle}}{ Border line style.}
-#'   \item{\bold{keepNA}} {If \code{TRUE}, NA values are converted to #N/A (or \code{na.string}, if not NULL) in Excel, else NA cells will be empty. Defaults to FALSE.}
-#'   \item{\bold{na.string}} {If not NULL, and if \code{keepNA} is \code{TRUE}, NA values are converted to this string in Excel. Defaults to NULL.}
+#' between each column.  If "`all`" all cell borders are drawn.}
+#'   \item{**borderColour**}{ Colour of cell border}
+#'   \item{**borderStyle**}{ Border line style.}
+#'   \item{**keepNA**} {If `TRUE`, NA values are converted to #N/A (or `na.string`, if not NULL) in Excel, else NA cells will be empty. Defaults to FALSE.}
+#'   \item{**na.string**} {If not NULL, and if `keepNA` is `TRUE`, NA values are converted to this string in Excel. Defaults to NULL.}
 #' }
 #'
-#' \bold{freezePane Parameters}
+#' **freezePane Parameters**
 #' \itemize{
-#'   \item{\bold{firstActiveRow}} {Top row of active region to freeze pane.}
-#'   \item{\bold{firstActiveCol}} {Furthest left column of active region to freeze pane.}
-#'   \item{\bold{firstRow}} {If \code{TRUE}, freezes the first row (equivalent to firstActiveRow = 2)}
-#'   \item{\bold{firstCol}} {If \code{TRUE}, freezes the first column (equivalent to firstActiveCol = 2)}
+#'   \item{**firstActiveRow**} {Top row of active region to freeze pane.}
+#'   \item{**firstActiveCol**} {Furthest left column of active region to freeze pane.}
+#'   \item{**firstRow**} {If `TRUE`, freezes the first row (equivalent to firstActiveRow = 2)}
+#'   \item{**firstCol**} {If `TRUE`, freezes the first column (equivalent to firstActiveCol = 2)}
 #' }
 #'
-#' \bold{colWidths Parameters}
+#' **colWidths Parameters**
 #' \itemize{
-#'   \item{\bold{colWidths}} {May be a single value for all columns (or "auto"), or a list of vectors that will be recycled for each sheet (see examples)}
+#'   \item{**colWidths**} {May be a single value for all columns (or "auto"), or a list of vectors that will be recycled for each sheet (see examples)}
 #' }
 #' 
 #' @examples
@@ -80,7 +80,7 @@
 #' buildWorkbook(y, asTable = TRUE)
 #' buildWorkbook(y, asTable = TRUE, tableStyle = "TableStyleLight8")
 #' 
-#' @seealso \code{\link{write.xlsx}}
+#' @seealso [write.xlsx()]
 #' 
 #' @export
 

R/conditional_formatting.R

@@ -21,7 +21,7 @@
 #'
 #' If type == "expression"
 #' \itemize{
-#'   \item{style is a Style object. See \code{\link{createStyle}}}
+#'   \item{style is a Style object. See [createStyle()]}
 #'   \item{rule is an expression. Valid operators are "<", "<=", ">", ">=", "==", "!=".}
 #' }
 #'
@@ -37,56 +37,56 @@
 #'   \item{rule is a numeric vector specifying the range of the databar colours. Must be equal length to style}
 #'   \item{...
 #'   \itemize{
-#'     \item{\bold{showvalue} If FALSE the cell value is hidden. Default TRUE.}
-#'     \item{\bold{gradient} If FALSE colour gradient is removed. Default TRUE.}
-#'     \item{\bold{border} If FALSE the border around the database is hidden. Default TRUE.}
+#'     \item{**showvalue** If FALSE the cell value is hidden. Default TRUE.}
+#'     \item{**gradient** If FALSE colour gradient is removed. Default TRUE.}
+#'     \item{**border** If FALSE the border around the database is hidden. Default TRUE.}
 #'      }
 #'    }
 #' }
 #'
 #' If type == "duplicates"
 #' \itemize{
-#'   \item{style is a Style object. See \code{\link{createStyle}}}
+#'   \item{style is a Style object. See [createStyle()]}
 #'   \item{rule is ignored.}
 #' }
 #'
 #' If type == "contains"
 #' \itemize{
-#'   \item{style is a Style object. See \code{\link{createStyle}}}
+#'   \item{style is a Style object. See [createStyle()]}
 #'   \item{rule is the text to look for within cells}
 #' }
 #'
 #' If type == "between"
 #' \itemize{
-#'   \item{style is a Style object. See \code{\link{createStyle}}}
+#'   \item{style is a Style object. See [createStyle()]}
 #'   \item{rule is a numeric vector of length 2 specifying lower and upper bound (Inclusive)}
 #' }
 #'
 #' If type == "topN"
 #' \itemize{
-#'   \item{style is a Style object. See \code{\link{createStyle}}}
+#'   \item{style is a Style object. See [createStyle()]}
 #'   \item{rule is ignored}
 #'   \item{...
 #'   \itemize{
-#'     \item{\bold{rank} numeric vector of length 1 indicating number of highest values.}
-#'     \item{\bold{percent} TRUE if you want top N percentage.}
+#'     \item{**rank** numeric vector of length 1 indicating number of highest values.}
+#'     \item{**percent** TRUE if you want top N percentage.}
 #'      }
 #'    }
 #' }
 #' 
 #' If type == "bottomN"
 #' \itemize{
-#'   \item{style is a Style object. See \code{\link{createStyle}}}
+#'   \item{style is a Style object. See [createStyle()]}
 #'   \item{rule is ignored}
 #'   \item{...
 #'   \itemize{
-#'     \item{\bold{rank} numeric vector of length 1 indicating number of lowest values.}
-#'     \item{\bold{percent} TRUE if you want bottom N percentage.}
+#'     \item{**rank** numeric vector of length 1 indicating number of lowest values.}
+#'     \item{**percent** TRUE if you want bottom N percentage.}
 #'      }
 #'    }
 #' }
 #' 
-#' @seealso \code{\link{createStyle}}
+#' @seealso [createStyle()]
 #' @export
 #' @examples
 #' wb <- createWorkbook()

R/helperFunctions.R

@@ -10,7 +10,7 @@
 #' @param col column number of letter for hyperlink to link to
 #' @param text display text
 #' @param file Excel file name to point to. If NULL hyperlink is internal.
-#' @seealso \code{\link{writeFormula}}
+#' @seealso [writeFormula()]
 #' @export makeHyperlinkString
 #' @examples
 #'

R/loadWorkbook.R

@@ -11,7 +11,7 @@
 #' formatting of the original .xlsx file.
 #' @return Workbook object.
 #' @export
-#' @seealso \code{\link{removeWorksheet}}
+#' @seealso [removeWorksheet()]
 #' @examples
 #' ## load existing workbook from package folder
 #' wb <- loadWorkbook(file = system.file("extdata", "loadExample.xlsx", package = "openxlsx"))

R/openXL.R

@@ -8,14 +8,14 @@
 #' In Windows (c) and Mac (c), it uses system default handlers,
 #' given the file type.
 #'
-#' In Linux it searches (via \code{which}) for available xls/xlsx
-#' reader applications (unless \code{options('openxlsx.excelApp')}
+#' In Linux it searches (via `which`) for available xls/xlsx
+#' reader applications (unless `options('openxlsx.excelApp')`
 #' is set to the app bin path), and if it finds anything, sets
-#' \code{options('openxlsx.excelApp')} to the program choosen by
+#' `options('openxlsx.excelApp')` to the program choosen by
 #' the user via a menu (if many are present, otherwise it will
 #' set the only available). Currently searched for apps are
-#' Libreoffice/Openoffice (\code{soffice} bin), Gnumeric
-#' (\code{gnumeric}) and Calligra Sheets (\code{calligrasheets}).
+#' Libreoffice/Openoffice (`soffice` bin), Gnumeric
+#' (`gnumeric`) and Calligra Sheets (`calligrasheets`).
 #'
 #' @param file path to the Excel (xls/xlsx) file or Workbook object.
 #' @usage openXL(file=NULL)

R/openxlsx.R

@@ -11,19 +11,19 @@
 #'
 #' @seealso
 #' \itemize{
-#'    \item{\code{vignette("Introduction", package = "openxlsx")}}
-#'    \item{\code{vignette("formatting", package = "openxlsx")}}
-#'    \item{\code{\link{writeData}}}
-#'    \item{\code{\link{writeDataTable}}}
-#'    \item{\code{\link{write.xlsx}}}
-#'    \item{\code{\link{read.xlsx}}}
-#'    \item{\code{\link{op.openxlsx}}}
+#'    \item{`vignette("Introduction", package = "openxlsx")`}
+#'    \item{`vignette("formatting", package = "openxlsx")`}
+#'    \item{[writeData()]}
+#'    \item{[writeDataTable()]}
+#'    \item{[write.xlsx()]}
+#'    \item{[read.xlsx()]}
+#'    \item{[op.openxlsx()]}
 #'   }
 #' for examples
 #'
 #' @details
 #' The openxlsx package uses global options, most to simplify formatting.  These
-#'   are stored in the \code{op.openxlsx} object.
+#'   are stored in the `op.openxlsx` object.
 #'
 #' \describe{
 #'  \item{openxlsx.bandedCols}{FALSE}
@@ -44,8 +44,8 @@
 #'  \item{openxlsx.tabColour}{"TableStyleLight9"}
 #'  \item{openxlsx.tableStyle}{"TableStyleLight9"}
 #'  \item{openxlsx.withFilter}{NA Whether to write data with or without a 
-#'  filter. If NA will make filters with \code{writeDataTable} and will not for
-#'  \code{writeData}}
+#'  filter. If NA will make filters with `writeDataTable` and will not for
+#'  `writeData`}
 #' }
 #' 
 #' See the Formatting vignette for examples.
@@ -61,13 +61,13 @@
 #' 
 #' @details
 #' 
-#' \code{openxlsx_getOp()} retrieves the \code{"openxlsx"} options found in
-#'   \code{op.openxlsx}.  If none are set (currently `NULL`) retrieves the 
-#'   default option from \code{op.openxlsx}.  This will also check that the
-#'   intended option is a standard option (listed in \code{op.openxlsx}) and
+#' `openxlsx_getOp()` retrieves the `"openxlsx"` options found in
+#'   `op.openxlsx`.  If none are set (currently `NULL`) retrieves the 
+#'   default option from `op.openxlsx`.  This will also check that the
+#'   intended option is a standard option (listed in `op.openxlsx`) and
 #'    will provide a warning otherwise.
 #'   
-#' \code{openxlsx_setOp()} is a safer way to set an option as it will first
+#' `openxlsx_setOp()` is a safer way to set an option as it will first
 #'   check that the option is a standard option (as above) before setting.
 #' 
 #' @examples
@@ -114,8 +114,8 @@ op.openxlsx <- list(
   openxlsx.withFilter       = NULL
 )
 
-#' @param x An option name (\code{"openxlsx."} prefix optional)
-#' @param default A default value if \code{NULL}
+#' @param x An option name (`"openxlsx."` prefix optional)
+#' @param default A default value if `NULL`
 #' @rdname openxlsx_options
 #' @export
 openxlsx_getOp <- function(x, default = NULL) {

R/readWorkbook.R

@@ -9,11 +9,11 @@
 #' @param sheet The name or index of the sheet to read data from.
 #' @param startRow first row to begin looking for data.  Empty rows at the top of a file are always skipped,
 #' regardless of the value of startRow.
-#' @param colNames If \code{TRUE}, the first row of data will be used as column names.
-#' @param skipEmptyRows If \code{TRUE}, empty rows are skipped else empty rows after the first row containing data
+#' @param colNames If `TRUE`, the first row of data will be used as column names.
+#' @param skipEmptyRows If `TRUE`, empty rows are skipped else empty rows after the first row containing data
 #' will return a row of NAs.
-#' @param rowNames If \code{TRUE}, first column of data will be used as row names.
-#' @param detectDates If \code{TRUE}, attempt to recognise dates and perform conversion.
+#' @param rowNames If `TRUE`, first column of data will be used as row names.
+#' @param detectDates If `TRUE`, attempt to recognise dates and perform conversion.
 #' @param cols A numeric vector specifying which columns in the Excel file to read.
 #' If NULL, all columns are read.
 #' @param rows A numeric vector specifying which rows in the Excel file to read.
@@ -24,8 +24,8 @@
 #' @param namedRegion A named region in the Workbook. If not NULL startRow, rows and cols parameters are ignored.
 #' @param na.strings A character vector of strings which are to be interpreted as NA. Blank cells will be returned as NA.
 #' @param fillMergedCells If TRUE, the value in a merged cell is given to all cells within the merge.
-#' @param skipEmptyCols If \code{TRUE}, empty columns are skipped.
-#' @seealso \code{\link{getNamedRegions}}
+#' @param skipEmptyCols If `TRUE`, empty columns are skipped.
+#' @seealso [getNamedRegions()]
 #' @details Formulae written using writeFormula to a Workbook object will not get picked up by read.xlsx().
 #' This is because only the formula is written and left to be evaluated when the file is opened in Excel.
 #' Opening, saving and closing the file with Excel will resolve this.
@@ -561,8 +561,8 @@ read.xlsx.default <- function(
 #' @details Creates a data.frame of all data in worksheet.
 #' @author Alexander Walker
 #' @return data.frame
-#' @seealso \code{\link{getNamedRegions}}
-#' @seealso \code{\link{read.xlsx}}
+#' @seealso [getNamedRegions()]
+#' @seealso [read.xlsx()]
 #' @export
 #' @examples
 #' xlsxFile <- system.file("extdata", "readTest.xlsx", package = "openxlsx")