#' Create HTML Report
#'
#' Create HTML Report for an \code{occDet} object.
#'
#' @param occDet An object of class occDet
#' @param open Logical, if \code{TRUE} the html report is opened once complete
#' @param output_dir Character, the directory where the html file will be saved,
#' defaults to the working directory.
#' @param output_file (Optional) The file name given to the html file
#' @param ... Additional arguments passed to rmarkdown::render
#'
#' @return Path to html report
#' @import rmarkdown
#'
#' @examples
#'
#' \dontrun{
#' # Create data
#' set.seed(125)
#' n <- 15000 #size of dataset
#' nyr <- 20 # number of years in data
#' nSamples <- 100 # set number of dates
#' nSites <- 50 # set number of sites
#'
#' # Create somes dates
#' first <- as.Date(strptime("1980/01/01", "%Y/%m/%d"))
#' last <- as.Date(strptime(paste(1980+(nyr-1),"/12/31", sep=''), "%Y/%m/%d"))
#' dt <- last-first
#' rDates <- first + (runif(nSamples)*dt)
#'
#' # taxa are set as random letters
#' taxa <- sample(letters, size = n, TRUE)
#'
#' # three sites are visited randomly
#' site <- sample(paste('A', 1:nSites, sep=''), size = n, TRUE)
#'
#' # the date of visit is selected at random from those created earlier
#' survey <- sample(rDates, size = n, TRUE)
#'
#' # run the model with these data for one species
#' # using defaults
#' results <- occDetModel(taxa = taxa,
#' site = site,
#' survey = survey,
#' species_list = 'a',
#' write_results = TRUE,
#' n_iterations = 1000,
#' burnin = 10,
#' thinning = 2)
#'
#' generate summary
#' htmlSummary(results$a)
#'
#' }
#'
#' @export
htmlSummary <- function(occDet,
open = TRUE,
output_dir = getwd(),
output_file = NULL,
...){
html_template <- system.file("templates/Occ_viz_html.Rmd", package = "sparta")
stopifnot(inherits(occDet, 'occDet'))
temp_f <- tempfile()
saveRDS(occDet, file = temp_f)
output_path <- render(html_template,
params = list(dataFile = temp_f),
output_dir = output_dir,
output_file = output_file,
intermediates_dir = tempdir(),
quiet = TRUE,
...)
if(open) browseURL(output_path)
return(output_path)
}
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