Generate OM Documentation Report

Usage

OMdoc(
  OM = NULL,
  rmd.source = NULL,
  overwrite = FALSE,
  out.file = NULL,
  inc.plot = TRUE,
  render = TRUE,
  output = "html_document",
  openFile = TRUE,
  quiet = FALSE,
  dir = NULL,
  ...
)

Arguments

OM: An object of class 'OM' or the name of an OM xlsx file
rmd.source: Optional. Name of the source.rmd file corresponding to the 'OM'. Default assumption is that the file is 'OM@Name.Rmd'
overwrite: Logical. Should existing files be overwritten?
out.file: Optional. Character. Name of the output file. Default is the same as the text file.
inc.plot: Logical. Should the plots be included?
render: Logical. Should the document be compiled? May be useful to turn off if there are problems with compiling the Rmd file.
output: Character. Output file type. Default is 'html_document'. 'pdf_document' is available but may require additional software and have some formatting issues.
openFile: Logical. Should the compiled file be opened in web browser?
quiet: TRUE to suppress printing of the pandoc command line.
dir: Optional file path to read the xlsx and rmd files. Default is getwd()
...: Optional additional named arguments provided to runMSE

Value

Creates a Rmarkdown file and compiles a HTML report file in the working directory.

Author

A. Hordyk

Examples

if (FALSE) { # \dontrun{
OMinit('myOM', Stock='Herring', Fleet='Generic_Fleet', Obs='Generic_Obs',
Imp='Perfect_Imp', overwrite=TRUE)
myOM <- XL2OM('myOM.xlsx')
OMdoc(myOM)
} # }