write_idea.R

#' Write IDEA4 results and graphs to local disc
#'
#' This function allows the user to write IDEA4 results either as local PNG files or compiled in reports.
#'
#' @param IDEA_plots an IDEA_plots or IDEA_group_plots object from a \code{plot_idea()} call.
#' @param output_directory the desired output directory for the rendered reports and/or plots. Defaults to "IDEATools_output"
#' @param type the type of output to produce. Can be either "report" to produce compiled reports or "local" to write raw plots as PNG files.
#' @param prefix a prefix which will be added to output files names. Typically, the name of the farm. Ignored in the case of a group analysis : The \code{metadata$MTD_01} field will then be used to identify each farm.
#' @param report_format a string indicating the output format if \code{type = "report"}. Can be a single format (e.g \code{"pdf"}) or multiple formats (e.g. \code{c("pdf","xlsx")}). Possible formats are "pdf", "docx", "pptx" and "xlsx"
#' @param dpi ggplot output resolution.
#' @param append If the input is an xlsx format, should the individual output be appended to the original file ?
#' @param input_file_append file path to an xslx IDEA data spreadsheet
#' @param quiet A command to remove console printing.
#'
#' @details This function automatically creates in \code{output_directory} a subdirectory named after the system date for users to use the same output_directory for multiple diagnosis.
#'
#' Inputs of class \code{IDEA_plots} can be generated by a classic \code{read_idea() |> compute_idea() |> plot_idea()} or \code{old_idea() |> plot_idea()} individual analysis pipelines. Inputs of class \code{IDEA_group_plots} can only be generated by a \code{plot_idea()} call in a group analysis conducted by \code{diag_idea}.
#'
#' In the case of an individual analysis, another subdirectory is created with \code{prefix} as a name so that analyses are not mixed up. The user can choose if output should be raw plots (that can be used in custom reports) or pre-compiled reports with a large variety of available formats.
#'
#' In the case of a group analysis, another subdirectory is created with a name like "Groupe_number_of_farms" so that analyses are not mixed up. The user can again choose if output should be raw plots or pre-compiled reports.
#'
#' If the \code{report_format} argument is set to either "docx" or "pptx", the report will be rendered using the rmarkdown package (and officedown/officer packages for the docx output) using a template stored in this package. For "pdf" output, LaTeX will be called with the rmarkdown package. For "xlsx" output, the openxlsx package will be used to sequentially produce Excel worksheets and files, using an internal R function.
#'
#' Please note that an error will be produced if the input object does not contain all three "dimensions","trees" and "radars" entries in the case of an individual analysis and if \code{type = "report"}.
#'
#' @return Reports and/or raw plots in \code{output_directory}.
#' @export
#'
#' @import data.table
#' @importFrom ggplot2 ggsave
#' @importFrom rmarkdown render
#' @importFrom tibble tibble
#' @importFrom pdftools pdf_convert
#' @importFrom rlang check_installed
#'
#' @examples
#' library(IDEATools)
#' path <- system.file("example_data/idea_example_1.json", package = "IDEATools")
#' my_data <- read_idea(path)
#' computed_data <- compute_idea(my_data)
#' # Only plotting the radars as a minimal example
#' idea_plots <- plot_idea(computed_data, choices = "radars")
#' # Find your temporary directory
#' tempdir <- tempdir()
#'
#' # Export as raw plots to your tempdir
#' write_idea(idea_plots,
#'   output_directory = tempdir,
#'   type = "local",
#'   prefix = "myFarm",
#'   dpi = 20 # Can be much higher
#' )
write_idea <- function(IDEA_plots, output_directory, type = c("local", "report"), prefix = NULL, dpi = 320, report_format = "docx", append = FALSE, input_file_append = NULL, quiet = FALSE) {
  if (append == TRUE) {
    filetype <- tools::file_ext(input_file_append)
    if (filetype != "xlsx") {
      stop("To append the results to the original file, it should be in xlsx format.")
    }
  }

  # Checks ------------------------------------------------------------------
  if (!any(class(IDEA_plots) %in% c("IDEA_group_plots", "IDEA_plots"))) (stop("The input data is not of class 'IDEA_data'"))


  # Individual analysis --------------------------------------------------------
  if (any(class(IDEA_plots) == "IDEA_plots")) {
    # If prefix is null, assign MTD_01
    if (is.null(prefix)) {
      prefix <- IDEA_plots$data$metadata$MTD_01
    }

    # Creating Global output directory
    output_directory <- file.path(output_directory, Sys.Date(), prefix)

    if (!dir.exists(output_directory)) {
      dir.create(output_directory, recursive = TRUE)
    }


    # If export is "local" ----------------------------------------------------

    if (any(type == "local")) {
      if (!quiet) (message(paste0("Production des ", length(names(IDEA_plots)) - 1, " types de graphiques demand\u00e9s")))

      ### Dimensions

      ## If the input has dimensions plots
      if (any(names(IDEA_plots) == "dimensions")) {
        if (!quiet) (message("Production des graphiques dimensions..."))

        ## Starting duration estimate
        start <- Sys.time()

        ## Creating directory for dimensions
        dimension_plots <- IDEA_plots$dimensions
        dimension_directory <- file.path(output_directory, "Dimensions")

        if (!dir.exists(dimension_directory)) {
          dir.create(dimension_directory, recursive = TRUE)
        }

        ## Creating a table with all paths for ggsave
        tab_res <- tibble::tibble(plotname = names(dimension_plots), plot = dimension_plots) |>
          transform(plotname = ifelse(plotname == "plot_dimensions", "Dimensions",
            ifelse(plotname == "plot_components", "Composantes",
              ifelse(plotname == "plot_components_polarised", "Composantes polaris\u00e9es",
                ifelse(plotname == "plot_indic_st", "Indicateurs Socio-Territoriaux",
                  ifelse(plotname == "plot_indic_ec", "Indicateurs Economiques",
                    ifelse(plotname == "plot_indic_ae", "Indicateurs Agro\u00e9cologiques", plotname)
                  )
                )
              )
            )
          )) |>
          transform(prefix = prefix) |>
          transform(
            widths = c(9.11, 11, 8, 10.69, 10.69, 10.69),
            heights = c(5.6, 11.5, 8, 12, 13.5, 9)
          ) |>
          transform(folder = dimension_directory) |>
          transform(path = file.path(dimension_directory, paste0(prefix, "_", plotname))) |>
          transform(png_path = paste0(path, ".png")) |>
          transform(dpi = dpi)

        # Iterating
        for (i in 1:nrow(tab_res)) {
          tab <- tab_res[i, ]
          ggplot2::ggsave(tab$plot[[1]], filename = tab$png_path, dpi = tab$dpi, width = tab$widths, height = tab$heights)
        }

        ## Duration estimation
        end <- Sys.time()
        duration <- round(difftime(end, start, units = "secs"))

        if (!quiet) (message(paste0("Les graphiques dimensions ont \u00e9t\u00e9 export\u00e9s \u00e0 l'adresse '", dimension_directory, "' (", duration, "s)")))
      }

      ### If the input has radars plots
      if (any(names(IDEA_plots) == "radars")) {
        if (!quiet) (message("Production des graphiques radars..."))

        ## Starting duration estimate
        start <- Sys.time()

        ## Creating directory for radars
        radar_plots <- IDEA_plots$radars
        radar_directory <- file.path(output_directory, "Propri\u00e9t\u00e9s", "Radars")

        if (!dir.exists(radar_directory)) {
          dir.create(radar_directory, recursive = TRUE)
        }

        ## Creating a table with all paths for ggsave
        tab_res <- tibble::tibble(plotname = names(radar_plots), plot = radar_plots) |>
          transform(plotname = ifelse(plotname == "radar_Capacite", "Capacit\u00e9 productive et reproductive de biens et de services",
            ifelse(plotname == "radar_Ancrage", "Ancrage Territorial",
              ifelse(plotname == "radar_Autonomie", "Autonomie",
                ifelse(plotname == "radar_Robustesse", "Robustesse",
                  ifelse(plotname == "radar_Responsabilite", "Responsabilit\u00e9 globale", plotname)
                )
              )
            )
          )) |>
          transform(
            widths = 16.1,
            heights = 7.61
          ) |>
          transform(folder = radar_directory) |>
          transform(path = file.path(radar_directory, paste0(prefix, "_", plotname))) |>
          transform(png_path = paste0(path, ".png")) |>
          transform(dpi = dpi)



        # Iterating
        for (i in 1:nrow(tab_res)) {
          tab <- tab_res[i, ]
          ggplot2::ggsave(tab$plot[[1]], filename = tab$png_path, dpi = tab$dpi, width = tab$widths, height = tab$heights)
        }

        ## Duration estimation
        end <- Sys.time()
        duration <- round(difftime(end, start, units = "secs"))

        if (!quiet) (message(paste0("Les graphiques radars ont \u00e9t\u00e9 export\u00e9s \u00e0 l'adresse '", radar_directory, "' (", duration, "s)")))
      }

      ### Trees

      ## If the input has colored trees
      if (any(names(IDEA_plots) == "trees")) {
        if (!quiet) (message("Production des arbres \u00e9clair\u00e9s"))

        ## Starting duration estimate
        start <- Sys.time()

        ## Creating directory for trees
        tree_plots <- IDEA_plots$trees
        tree_directory <- file.path(output_directory, "Propri\u00e9t\u00e9s", "Arbres \u00e9clair\u00e9s")

        if (!dir.exists(tree_directory)) {
          dir.create(tree_directory, recursive = TRUE)
        }

        ## Creating a table with all paths for ggsave
        tab_res <- tibble::tibble(name = names(tree_plots), itemlist = tree_plots) |>
          transform(folder = tree_directory) |>
          transform(plotname = ifelse(name == "Capacite", "Capacit\u00e9 productive et reproductive de biens et de services",
            ifelse(name == "Ancrage", "Ancrage Territorial",
              ifelse(name == "Autonomie", "Autonomie",
                ifelse(name == "Robustesse", "Robustesse",
                  ifelse(name == "Responsabilite", "Responsabilit\u00e9 globale",
                    ifelse(name == "Global", "Arbre global", name)
                  )
                )
              )
            )
          )) |>
          transform(path = file.path(tree_directory, paste0(prefix, "_", plotname))) |>
          transform(
            png_path = paste0(path, ".png"),
            pdf_path = paste0(path, ".pdf")
          ) |>
          transform(dpi = dpi)

        ## Custom function to iterate (faster than for loop)
        export_heuristic_map <- function(prop, itemlist, folder, png_path, pdf_path) {
          ## List with dimension of trees
          heuristic_res <- list(
            Robustesse = c(40, 26),
            Capacite = c(48, 30),
            Autonomie = c(48, 30),
            Responsabilite = c(49, 37),
            Ancrage = c(33, 20),
            Global = c(45, 28)
          )

          # Dimensions of tree
          dim <- heuristic_res[[prop]]

          # Save to PDF
          ggplot2::ggsave(itemlist, filename = pdf_path, width = dim[1], height = dim[2], device = cairo_pdf)

          # Convert to PNG
          pdftools::pdf_convert(pdf = pdf_path, format = "png", pages = NULL, filenames = basename(png_path), opw = "", upw = "", verbose = FALSE)

          # Move the PNG file to the appropriate folder

          if (prop == "Responsabilite") {
            exported_name <- basename(list.files(".", pattern = "Respons"))
            file.copy(exported_name, png_path, overwrite = TRUE)
            file.remove(exported_name)
          } else if (prop == "Capacite") {
            exported_name <- basename(list.files(".", pattern = "Capacit"))
            file.copy(exported_name, png_path, overwrite = TRUE)
            file.remove(exported_name)
          } else {
            file.copy(basename(png_path), png_path, overwrite = TRUE)
            file.remove(basename(png_path))
          }
        }

        # Iterating
        for (i in 1:nrow(tab_res)) {
          tab <- tab_res[i, ]

          suppressWarnings(
            export_heuristic_map(prop = tab$name, itemlist = tab$itemlist[[1]], tab$folder, tab$png_path, tab$pdf_path)
          )
        }
              ## Duration estimation
      end <- Sys.time()
      duration <- round(difftime(end, start, units = "secs"))

      if (!quiet) (message(paste0("Les arbres \u00e9clair\u00e9s ont \u00e9t\u00e9 export\u00e9s \u00e0 l'adresse '", tree_directory, "' (", duration, "s)")))
      }
    }

    # If export is "report" ------------------------------------------------------

    if (any(type == "report")) {
      rlang::check_installed(c("rmarkdown", "knitr", "openxlsx", "officedown", "gt"), reason = "to produce reports`")

      # Reports requires all 3 types of plots
      if (length(names(IDEA_plots)) < 4) (stop("Reporting functions requires that all three kind of plots are drawn in previous `plots_idea()` call"))

      # Defining a knitting dir in tempdir in case the user doesn't have all permissions in working dir
      knitting_dir <- file.path(tempdir(), "IDEATools_reports")
      if (!dir.exists(knitting_dir)) (dir.create(knitting_dir))
      file.copy(system.file("report/", package = "IDEATools"), knitting_dir, recursive = TRUE)

      if (!quiet) {
        message(paste0("Production des ", length(report_format), " rapports demand\u00e9s"))
      }

      ### PDF reports
      if (any(report_format == "pdf")) {
        if (!quiet) (message("Production du rapport PDF..."))

        start <- Sys.time()

        report_path <- file.path(knitting_dir, "report", "single", "pdf_report.Rmd")

        # Defining params
        params <- list(
          data = IDEA_plots,
          dpi = dpi
        )

        output_file <- paste0("Rapport_individuel_", prefix, ".pdf")

        # Render in new env, in knitting dir to avoid full paths
        suppressWarnings(rmarkdown::render(report_path,
          output_file = output_file,
          params = params,
          envir = new.env(parent = globalenv()), quiet = TRUE
        ))

        file.copy(file.path(dirname(report_path), output_file), file.path(output_directory, output_file))

        end <- Sys.time()
        duration <- round(difftime(end, start, units = "secs"))

        if (!quiet) {
          message(paste0("Le rapport a \u00e9t\u00e9 export\u00e9 \u00e0 l'adresse '", file.path(output_directory, output_file), "' (", duration, "s)"))
        }
      }

      ### DOCX reports
      if (any(report_format == "docx")) {
        if (!quiet) {
          message("Production du rapport Microsoft Word...")
        }



        start <- Sys.time()

        report_path <- file.path(knitting_dir, "report", "single", "docx_report.Rmd")

        # Defining params
        params <- list(
          data = IDEA_plots,
          outdir = "tmp",
          prefix = prefix,
          dpi = dpi
        )

        output_file <- paste0("Rapport_individuel_", prefix, ".docx")

        # Render in new env
        suppressWarnings(rmarkdown::render(report_path,
          output_file = output_file, output_dir = output_directory,
          params = params,
          envir = new.env(parent = globalenv()), quiet = TRUE
        ))

        end <- Sys.time()
        duration <- round(difftime(end, start, units = "secs"))

        if (!quiet) {
          message(paste0("Le rapport a \u00e9t\u00e9 export\u00e9 \u00e0 l'adresse '", file.path(output_directory, output_file), "' (", duration, "s)"))
        }
      }

      ### PPTX reports
      if (any(report_format == "pptx")) {
        if (!quiet) {
          message("Production de la pr\u00e9sentation Microsoft Powerpoint...")
        }

        start <- Sys.time()

        report_path <- file.path(knitting_dir, "report", "single", "pptx_report.Rmd")

        # Defining params
        params <- list(
          data = IDEA_plots,
          outdir = "tmp",
          prefix = prefix,
          dpi = dpi
        )

        output_file <- paste0("Rapport_individuel_", prefix, ".pptx")

        # Render in new env
        suppressWarnings(rmarkdown::render(report_path,
          output_file = output_file, output_dir = output_directory,
          params = params,
          envir = new.env(parent = globalenv()), quiet = TRUE
        ))



        end <- Sys.time()
        duration <- round(difftime(end, start, units = "secs"))

        if (!quiet) {
          message(paste0("Le rapport a \u00e9t\u00e9 export\u00e9 \u00e0 l'adresse '", file.path(output_directory, output_file), "' (", duration, "s)"))
        }
      }

      ### XLSX reports
      if (any(report_format == "xlsx")) {
        if (!quiet) {
          message("Production du rapport Microsoft Excel...")
        }

        start <- Sys.time()

        output_file <- paste0("Rapport_individuel_", prefix, ".xlsx")

        # Using custom function instead of Rmd
        excel_report(
          IDEAdata = IDEA_plots,
          output_dir = output_directory,
          output_file = output_file,
          outdir = file.path(knitting_dir, "tmp"),
          prefix = prefix,
          dpi = dpi,
          append = append,
          input_file_append = input_file_append
        )

        end <- Sys.time()
        duration <- round(difftime(end, start, units = "secs"))

        if (!quiet) {
          message(paste0("Le rapport a \u00e9t\u00e9 export\u00e9 \u00e0 l'adresse '", file.path(output_directory, output_file), "' (", duration, "s)"))
        }
      }
    }
  }


  # Group analysis ----------------------------------------------------------

  if (any(class(IDEA_plots) == "IDEA_group_plots")) {
    ## Number of farms
    n_farm <- nrow(IDEA_plots$data$metadata)

    ## Creating output directory
    output_directory <- file.path(output_directory, Sys.Date(), paste0("Groupe_", n_farm))

    if (!dir.exists(output_directory)) {
      dir.create(output_directory, recursive = TRUE)
    }

    if (any(class(IDEA_plots) == "IDEA_group_plots_ref")) {
      ## Check format
      if (any(type == "report") & any(report_format %in% c("pptx", "docx"))) {
        stop("Reference output can only be a pdf or xlsx report")
      }

      if (any(type == "local")) {
        if (!quiet) {
          message(paste0("Production des graphiques de groupe..."))
        }

        ### Group graphs

        start <- Sys.time()

        ## Creating directory for groups
        group_directory <- file.path(output_directory, "Graphiques")

        if (!dir.exists(group_directory)) {
          dir.create(group_directory, recursive = TRUE)
        }

        ## Creating a table with all paths for ggsave
        tab_res <- tibble::tibble(plotname = names(IDEA_plots), plot = IDEA_plots) |>
          subset(plotname != "data") |>
          subset(!plotname %in% c("heatmap", "dimensions_histogram")) |>
          transform(plotname = ifelse(plotname == "freq_plot", "Fr\u00e9quence_propri\u00e9t\u00e9s",
            ifelse(plotname == "dimensions_boxplot", "Distribution_dimensions",
              ifelse(plotname == "components_boxplot", "Distribution_composantes",
                ifelse(plotname == "indic_ae_boxplot", "Distribution_indicateurs_agroecologiques",
                  ifelse(plotname == "indic_st_boxplot", "Distribution_indicateurs_socio_territoriaux",
                    ifelse(plotname == "indic_ec_boxplot", "Distribution_indicateurs_economiques", plotname)
                  )
                )
              )
            )
          )) |>
          transform(
            widths = c(13, 10, 11.3, 11.9, 11.9, 11.9),
            heights = c(5, 6.91, 8.94, 12.5, 14, 11)
          ) |>
          transform(plotname = gsub(x = plotname, pattern = " ", replacement = "_")) |>
          transform(path = file.path(group_directory, plotname)) |>
          transform(png_path = paste0(path, ".png")) |>
          transform(dpi = dpi)

        ## Custom function to iterate (faster than for loop)
        export_metaplot <- function(plotname, plot, widths, heights, png_path, dpi) {
          ggplot2::ggsave(plot, filename = png_path, width = widths, height = heights, dpi = dpi)
        }

        # Iterating
        for (i in 1:nrow(tab_res)) {
          tab <- tab_res[i, ]
          ggplot2::ggsave(tab$plot[[1]], filename = tab$png_path, width = tab$widths, height = tab$heights, dpi = tab$dpi)
        }
      }


      if (any(type == "report")) {
        rlang::check_installed(c("rmarkdown", "knitr", "openxlsx", "officedown", "knitr", "gt"), reason = "to produce reports`")

        ## Creating output directory
        if (!dir.exists(output_directory)) {
          dir.create(output_directory, recursive = TRUE)
        }

        # Defining a knitting dir in tempdir in case the user doesn't have all permissions in working directory
        knitting_dir <- file.path(tempdir(), "IDEATools_reports")
        if (!dir.exists(knitting_dir)) (dir.create(knitting_dir))
        file.copy(system.file("report/", package = "IDEATools"), knitting_dir, recursive = TRUE)

        if (!quiet) {
          message(paste0("Production des ", length(report_format), " rapports demand\u00e9s"))
        }

        ### PDF reports
        if (any(report_format == "pdf")) {
          if (!quiet) {
            message("Production du rapport PDF...")
          }


          start <- Sys.time()

          # Using the HTML report, converted to PDF
          report_path <- file.path(knitting_dir, "report", "group", "pdf_group_report_ref.Rmd")

          # Defining params
          params <- list(
            data = IDEA_plots,
            dpi = dpi
          )

          output_file <- paste0("Rapport_groupe_ref_", n_farm, ".pdf")

          # Render in new env, in knitting dir to avoid full paths
          suppressWarnings(rmarkdown::render(report_path,
            output_file = output_file,
            params = params,
            envir = new.env(parent = globalenv()), quiet = TRUE
          ))

          file.copy(file.path(dirname(report_path), output_file), file.path(output_directory, output_file))

          end <- Sys.time()
          duration <- round(difftime(end, start, units = "secs"))

          if (!quiet) {
            message(paste0("Le rapport a \u00e9t\u00e9 export\u00e9 \u00e0 l'adresse '", file.path(output_directory, output_file), "' (", duration, "s)"))
          }
        }

        ### XLSX reports
        if (any(report_format == "xlsx")) {
          if (!quiet) {
            message("Production du rapport Microsoft Excel...")
          }

          start <- Sys.time()

          output_file <- paste0("Rapport_groupe_ref_", n_farm, ".xlsx")

          # Using custom function instead of Rmd
          excel_group_report_reference(
            IDEAdata = IDEA_plots,
            output_dir = output_directory,
            output_file = output_file,
            outdir = file.path(knitting_dir, "tmp"),
            dpi = dpi
          )

          end <- Sys.time()
          duration <- round(difftime(end, start, units = "secs"))

          if (!quiet) {
            message(paste0("Le rapport a \u00e9t\u00e9 export\u00e9 \u00e0 l'adresse '", file.path(output_directory, output_file), "' (", duration, "s)"))
          }
        }
      }

      # End of ref pipeline
    } else {
      ## Normal pipeline

      # If type is "local" --------------------------------------------------------

      if (any(type == "local")) {
        if (!quiet) {
          message(paste0("Production des graphiques de groupe..."))
        }

        ### Group graphs

        start <- Sys.time()

        ## Creating directory for groups
        group_directory <- file.path(output_directory, "Graphiques")

        if (!dir.exists(group_directory)) {
          dir.create(group_directory, recursive = TRUE)
        }

        ## Creating a table with all paths for ggsave
        tab_res <- tibble::tibble(plotname = names(IDEA_plots), plot = IDEA_plots) |>
          subset(plotname != "data") |>
          transform(plotname = ifelse(plotname == "heatmap", "Matrice_propri\u00e9t\u00e9s",
            ifelse(plotname == "freq_plot", "Fr\u00e9quence_propri\u00e9t\u00e9s",
              ifelse(plotname == "dimensions_histogram", "Histogramme_dimensions",
                ifelse(plotname == "dimensions_boxplot", "Distribution_dimensions",
                  ifelse(plotname == "components_boxplot", "Distribution_composantes",
                    ifelse(plotname == "indic_ae_boxplot", "Distribution_indicateurs_agroecologiques",
                      ifelse(plotname == "indic_st_boxplot", "Distribution_indicateurs_socio_territoriaux",
                        ifelse(plotname == "indic_ec_boxplot", "Distribution_indicateurs_economiques", plotname)
                      )
                    )
                  )
                )
              )
            )
          )) |>
          transform(
            widths = c(10.4, 10, 14.5, 7.95, 11.3, 11.9, 11.9, 11.9),
            heights = c(6.82, 5, 8.61, 6.91, 8.94, 12.5, 14, 11)
          ) |>
          transform(plotname = gsub(x = plotname, pattern = " ", replacement = "_")) |>
          transform(path = file.path(group_directory, plotname)) |>
          transform(png_path = paste0(path, ".png")) |>
          transform(dpi = dpi)

        ## Custom function to iterate (faster than for loop)
        export_metaplot <- function(plotname, plot, widths, heights, png_path, dpi) {
          ggplot2::ggsave(plot, filename = png_path, width = widths, height = heights, dpi = dpi)
        }

        # Iterating
        for (i in 1:nrow(tab_res)) {
          tab <- tab_res[i, ]
          ggplot2::ggsave(tab$plot[[1]], filename = tab$png_path, width = tab$widths, height = tab$heights, dpi = tab$dpi)
        }


        end <- Sys.time()
        duration <- round(difftime(end, start, units = "secs"))

        if (!quiet) {
          message(paste0("Les figures ont bien \u00e9t\u00e9 export\u00e9es dans le r\u00e9pertoire '", file.path(group_directory), "' (", duration, "s)\n"))
        }
      }


      # If export is "report" -----------------------------------------------------

      if (any(type == "report")) {
        rlang::check_installed(c("rmarkdown", "knitr", "openxlsx", "officedown", "knitr", "gt"), reason = "to produce reports`")

        ## Creating output directory
        if (!dir.exists(output_directory)) {
          dir.create(output_directory, recursive = TRUE)
        }

        # Defining a knitting dir in tempdir in case the user doesn't have all permissions in working directory
        knitting_dir <- file.path(tempdir(), "IDEATools_reports")
        if (!dir.exists(knitting_dir)) (dir.create(knitting_dir))
        file.copy(system.file("report/", package = "IDEATools"), knitting_dir, recursive = TRUE)

        if (!quiet) {
          message(paste0("Production des ", length(report_format), " rapports demand\u00e9s"))
        }


        ### PDF reports
        if (any(report_format == "pdf")) {
          if (!quiet) {
            message("Production du rapport PDF...")
          }


          start <- Sys.time()

          # Using the HTML report, converted to PDF
          report_path <- file.path(knitting_dir, "report", "group", "pdf_group_report.Rmd")

          # Defining params
          params <- list(
            data = IDEA_plots,
            dpi = dpi
          )

          output_file <- paste0("Rapport_groupe_", n_farm, ".pdf")

          # Render in new env, in knitting dir to avoid full paths
          suppressWarnings(rmarkdown::render(report_path,
            output_file = output_file,
            params = params,
            envir = new.env(parent = globalenv()), quiet = TRUE
          ))

          file.copy(file.path(dirname(report_path), output_file), file.path(output_directory, output_file))

          # Actualise for printing
          output_file <- paste0("Rapport_groupe_", n_farm, ".pdf")

          end <- Sys.time()
          duration <- round(difftime(end, start, units = "secs"))

          if (!quiet) {
            message(paste0("Le rapport a \u00e9t\u00e9 export\u00e9 \u00e0 l'adresse '", file.path(output_directory, output_file), "' (", duration, "s)"))
          }
        }


        ### DOCX reports
        if (any(report_format == "docx")) {
          if (!quiet) {
            message("Production du rapport Microsoft Word...")
          }

          start <- Sys.time()

          report_path <- file.path(knitting_dir, "report", "group", "docx_group_report.Rmd")

          # Defining params
          params <- list(
            data = IDEA_plots,
            outdir = "tmp",
            dpi = dpi
          )

          output_file <- paste0("Rapport_groupe_", n_farm, ".docx")

          # Render in new env
          suppressWarnings(rmarkdown::render(report_path,
            output_file = output_file, output_dir = output_directory,
            params = params,
            envir = new.env(parent = globalenv()), quiet = TRUE
          ))

          end <- Sys.time()
          duration <- round(difftime(end, start, units = "secs"))

          if (!quiet) {
            message(paste0("Le rapport a \u00e9t\u00e9 export\u00e9 \u00e0 l'adresse '", file.path(output_directory, output_file), "' (", duration, "s)"))
          }
        }

        ### PPTX reports
        if (any(report_format == "pptx")) {
          if (!quiet) {
            message("Production de la pr\u00e9sentation Microsoft Powerpoint...")
          }

          start <- Sys.time()

          report_path <- file.path(knitting_dir, "report", "group", "pptx_group_report.Rmd")

          # Defining params
          params <- list(
            data = IDEA_plots,
            outdir = "tmp",
            dpi = dpi
          )

          output_file <- paste0("Rapport_groupe_", n_farm, ".pptx")

          # Render in new env
          suppressWarnings(rmarkdown::render(report_path,
            output_file = output_file, output_dir = output_directory,
            params = params,
            envir = new.env(parent = globalenv()), quiet = TRUE
          ))

          end <- Sys.time()
          duration <- round(difftime(end, start, units = "secs"))

          if (!quiet) {
            message(paste0("Le rapport a \u00e9t\u00e9 export\u00e9 \u00e0 l'adresse '", file.path(output_directory, output_file), "' (", duration, "s)"))
          }
        }

        ### XLSX reports
        if (any(report_format == "xlsx")) {
          if (!quiet) {
            message("Production du rapport Microsoft Excel...")
          }

          start <- Sys.time()

          output_file <- paste0("Rapport_groupe_", n_farm, ".xlsx")

          # Using custom function instead of Rmd
          excel_group_report(
            IDEAdata = IDEA_plots,
            output_dir = output_directory,
            output_file = output_file,
            outdir = file.path(knitting_dir, "tmp"),
            dpi = dpi
          )

          end <- Sys.time()
          duration <- round(difftime(end, start, units = "secs"))

          if (!quiet) {
            message(paste0("Le rapport a \u00e9t\u00e9 export\u00e9 \u00e0 l'adresse '", file.path(output_directory, output_file), "' (", duration, "s)"))
          }
        }
      }
    }
  }
}