R/vis_sim.R

In PaulRegular/SimSurvey: Test Surveys by Simulating Spatially-Correlated Populations

#' Make a flexdashboard for visualizing the simulation
#'
#' Assumes the working directory is the project directory
#'
#' @param sim            Object produced by \code{\link{sim_abundance}}, \code{\link{sim_distribution}},
#'                       \code{\link{sim_survey}} or \code{\link{test_surveys}}.
#' @param ...            Additional arguments to send to \link[rmarkdown]{run}
#'
#' @return No value returned; function produces an interactive dashboard.
#'
#' @examples
#'
#' \donttest{
#'
#' if (interactive()) {
#'
#'   pop <- sim_abundance(ages = 1:20, years = 1:20)
#'   vis_sim(pop)
#'
#'   dist <- sim_distribution(pop, grid = make_grid(res = c(10, 10)))
#'   vis_sim(dist)
#'
#'   ## Run one survey design
#'   survey <- sim_survey(dist, n_sims = 5)
#'   vis_sim(survey)
#'
#'   ## Run several survey designs and assess stratified estimates
#'   ## (Note: total number of simulations are low to decrease computation time for the example)
#'   surveys <- expand_surveys(set_den = c(1, 2) / 1000,
#'                             lengths_cap = c(100, 500),
#'                             ages_cap = c(5, 20))
#'   tests <- test_surveys(dist, surveys = surveys, keep_details = 1,
#'                         n_sims = 5, n_loops = 5, cores = 1)
#'   vis_sim(tests)
#'
#' }
#' }
#'
#' @export
#'

vis_sim <- function(sim, ...) {

  pkg <- c("rmarkdown", "shiny", "flexdashboard", "crosstalk", "plotly", "viridis")
  for (p in pkg) {
    if (!requireNamespace(p, quietly = TRUE)) {
      stop(paste(p, "is needed for vis_fit to work. Please install it."), call. = FALSE)
    }
  }

  rmd_env <- new.env()
  rmd_env$sim <- sim
  rmarkdown::run(file = system.file("rmd", "vis_sim.Rmd", package = "SimSurvey"),
                 render_args = list(envir = rmd_env), ...)

}