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#' Clinical data format for bookdown report.
#'
#' This function is only meant to set sensitive
#' defaults for gitbook.\cr
#' \code{\link[bookdown]{gitbook}} can be used instead.
#' @param logo String, path to the logo. No logo is printed by default.
#' @param logoHeight String, indicating the logo height; 60px height by default.
#' @param split_by String, how the reports should be split,
#' (see help of the \link[bookdown]{gitbook} function)
#' @param config List with config parameters,
#' by default: no sharing and collapsed by section.
#' (see help of the \link[bookdown]{gitbook} function)
#' @param extra_dependencies NULL by default
#' @param css String, path to the css.
#' @param ... Extra parameters passed to the
#' \link[bookdown]{gitbook} function.
#' @return R Markdown output format to pass to \code{\link[bookdown]{render_book}}.
#' @importFrom bookdown gitbook
#' @author Laure Cougnaud
#' @family clinical data reporting
#' @export
gitbook_clinDataReview_report <- function(
logo = NULL,
logoHeight = '60px',
split_by = 'section+number',
config = list(
sharing = NULL,
toc = list(collapse = 'section')
),
extra_dependencies = NULL,
css = NULL,
...)
{
if(!is.null(logo)) includes <- addLogoGitbook(
logo = logo, logoHeight = logoHeight
) else includes <- list()
file.copy(
from = system.file(
"css", "gitbook.css", package = "clinDataReview"
),
to = "./gitbook.css",
overwrite = TRUE
)
bookdown::gitbook(
...,
css = c("./gitbook.css", css),
split_by = split_by,
config = config,
extra_dependencies = extra_dependencies,
includes = includes
)
}
#' @importFrom htmltools img
#' @importFrom knitr image_uri
addLogoGitbook <- function(logo = NULL, logoHeight = '60px') {
height <- sprintf("height:%s;", logoHeight)
logoStyle <- paste0(
height,
"position:absolute;top:50px; right:1%; padding:10px;z-index:200;"
)
# Create the external file
logoText <- img(
src = image_uri(logo),
alt = 'logo',
style = logoStyle
)
logoText <- paste0('<script>document.write(\'<div class="logos">',
logoText, '</div>\')</script>'
)
logoHtml <- tempfile(fileext = ".html")
cat(logoText, file = logoHtml)
includes <- list()
includes$in_header <- logoHtml
return(includes)
}
#' Clinical data format for rmarkdown report.
#'
#' This function only kept for back-compatibility,
#' \code{\link[rmarkdown]{html_document}}
#' can be used instead.
#' @param extra_dependencies NULL by default.
#' @param ... Extra parameters passed to the
#' \link[rmarkdown]{html_document} function.
#' @return R Markdown output format to pass to \code{\link[rmarkdown]{render}}.
#' @author Laure Cougnaud
#' @family clinical data reporting
#' @importFrom rmarkdown html_document
#' @export
html_clinDataReview_report <- function(
extra_dependencies = NULL,
...){
rmarkdown::html_document(
...,
extra_dependencies = extra_dependencies
)
}
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