R/PRISMA_flowdiagram.R

In PRISMA2020: Make Interactive 'PRISMA' Flow Diagrams

# Suppress R CMD check note
#' @importFrom DT addRow
#' @importFrom rio import
#' @importFrom shiny column
#' @importFrom shinyjs alert
#' @importFrom stats median
#' @importFrom utils apropos
#' @importFrom webp read_webp
NULL
#' Plot interactive flow diagrams for systematic reviews
#' @description Produces a PRISMA2020 style flow diagram
#' for systematic reviews, with the option to add
#' interactivity through tooltips (mouseover popups) and
#' hyperlink URLs to each box.
#' Data can be imported from the standard CSV template provided.
#' @param data List of data inputs including numbers of studies,
#' box text, tooltips, and urls for hyperlinks.
#' Data inputted via the [PRISMA_data()] function.
#' If inputting individually, see the necessary parameters
#' listed in the  [PRISMA_data()]) function and
#' combine them in a list using `data <- list()`.
#' @param interactive Logical argument TRUE or FALSE
#' whether to plot interactivity (tooltips and hyperlinked boxes).
#' @param previous Logical argument (TRUE or FALSE) specifying whether previous
#' studies were sought.
#' @param other Logical argument (TRUE or FALSE) specifying whether
#' other studies were sought.
#' @param detail_databases Logical argument (TRUE or FALSE) specifying whether
#' to list specific databases.
#' @param detail_registers Logical argument (TRUE or FALSE) specifying whether
#' to list specific registers.
#' @param font The font for text in each box. The default is 'Helvetica'.
#' @param fontsize The font size for text in each box. The default is '12'.
#' @param title_colour The colour for the upper middle title box (new studies).
#' The default is 'Goldenrod1'. See 'DiagrammeR' colour scheme.
#' <http://rich-iannone.github.io/DiagrammeR/graphviz_and_mermaid.html#colors>.
#' @param greybox_colour The colour for the left and right column boxes. The
#' default is 'Gainsboro'. See 'DiagrammeR' colour scheme
#' <http://rich-iannone.github.io/DiagrammeR/graphviz_and_mermaid.html#colors>.
#' @param main_colour The colour for the main box borders. The default is
#' 'Black'. See 'DiagrammeR' colour scheme
#' <http://rich-iannone.github.io/DiagrammeR/graphviz_and_mermaid.html#colors>.
#' @param arrow_colour The colour for the connecting lines. The default
#' is 'Black'. See 'DiagrammeR' colour scheme
#' <http://rich-iannone.github.io/DiagrammeR/graphviz_and_mermaid.html#colors>.
#' @param arrow_head The head shape for the line connectors. The default is
#' 'normal'. See DiagrammeR arrow shape specification
#' <http://rich-iannone.github.io/DiagrammeR/graphviz_and_mermaid.html#arrow-shapes>. #nolint
#' @param arrow_tail The tail shape for the line connectors. The default is
#' 'none'. See DiagrammeR arrow shape specification
#' <http://rich-iannone.github.io/DiagrammeR/graphviz_and_mermaid.html#arrow-shapes>. #nolint
#' @param side_boxes Whether or not to include the
#' blue label boxes along the side
#' @return A flow diagram plot.
#' @examples
#' csvFile <- system.file("extdata", "PRISMA.csv", package = "PRISMA2020")
#' data <- read.csv(csvFile);
#' data <- PRISMA_data(data);
#' plot <- PRISMA_flowdiagram(data,
#'                 fontsize = 12,
#'                 interactive = TRUE,
#'                 previous = FALSE,
#'                 other = TRUE);
#' plot
#' @export
PRISMA_flowdiagram <- function( #nolint
  data,
  interactive = FALSE,
  previous = TRUE,
  other = TRUE,
  detail_databases = FALSE,
  detail_registers = FALSE,
  fontsize = 7,
  font = "Helvetica",
  title_colour = "Goldenrod1",
  greybox_colour = "Gainsboro",
  main_colour = "Black",
  arrow_colour = "Black",
  arrow_head = "normal",
  arrow_tail = "none",
  side_boxes = TRUE) {
  # removes the need to attach() the data
  # https://stackoverflow.com/a/11505637
  for (var in seq_len(length(data))) {
    assign(names(data)[var], data[[var]])
  }
  # positional attributes, in inches
  diagram_start_x <- 0
  diagram_start_y <- 0
  prev_study_width <- 0
  prev_study_offset <- 0
  prev_study_height <- 0
  total_studies_height <- 0
  other_identified_height <- 0
  other_sought_reports_height <- 0
  other_notretrieved_height <- 0
  other_assessed_height <- 0
  other_excluded_height <- 0
  default_box_width <- 3.5
  min_box_height <- 0.5
  default_box_spacing <- 0.5
  section_label_length <- 0.4
  top_box_width <- default_box_width * 2 + default_box_spacing
  A <- "" #nolint
  Aedge <- "" #nolint
  bottomedge <- ""
  previous_nodes <- ""
  finalnode <- ""
  prev_rank1 <- ""
  prevnode1 <- ""
  prevnode2 <- ""

  #wrap exclusion reasons
  dbr_excluded[, 1] <- stringr::str_wrap(
    dbr_excluded[, 1],
    width = 35
  )
  other_excluded[, 1] <- stringr::str_wrap(
    other_excluded[, 1],
    width = 35
  )
  # wrap specific database registers
  database_specific_results[, 1] <- stringr::str_wrap(
    database_specific_results[, 1],
    width = 35
  )
  register_specific_results[, 1] <- stringr::str_wrap(
    register_specific_results[, 1],
    width = 35
  )
  #remove previous box if both values are zero
  if (is.na(previous_studies) == TRUE && is.na(previous_reports) == TRUE) {
    previous <- FALSE
  }
  if (previous == TRUE) {
    #conditional studies and reports - empty text if blank
    if (is.na(previous_studies) == TRUE) {
      cond_prevstud <- ""
    } else {
      cond_prevstud <- stringr::str_wrap(
        paste0(
            previous_studies_text,
          " (n = ", previous_studies, ")"
        ),
        width = 40)
    }
    if (is.na(previous_reports) == TRUE) {
      cond_prevrep <- ""
    } else {
      cond_prevrep <- paste0(
        stringr::str_wrap(
          previous_reports_text,
          width = 40
        ),
        "\n(n = ", previous_reports, ")"
      )
    }
    if (is.na(previous_studies) == TRUE || is.na(previous_reports) == TRUE) {
      dbl_br <- ""
    } else {
      dbl_br <- "\n"
    }
    prev_study_label <- paste0(cond_prevstud, dbl_br, cond_prevrep)
    total_studies_label <- paste0(
      stringr::str_wrap(
        paste0(
          total_studies_text,
          " (n = ", total_studies, ")"
        ),
        width = 33
      ),
      "\n",
      stringr::str_wrap(
        paste0(
          total_reports_text,
          " (n = ", total_reports, ")"
        ),
        width = 33
      )
    )
    # we multiply by 2 because we need the width
    # from the start, not just the centre
    prev_study_width <- default_box_width * 2
    prev_study_offset <- default_box_spacing
    prev_box_x <- PRISMA_get_pos_(
      diagram_start_x,
      default_box_spacing,
      default_box_width,
      prev_study_offset
    )
    prev_study_height <- PRISMA_get_height_(
      stringr::str_count(prev_study_label, "\n"),
      min_box_height
    )
    total_studies_height <- PRISMA_get_height_(
      stringr::str_count(total_studies_label, "\n"),
      min_box_height
    )
  }
  # conditionals for the node labels
  if (
    is.na(website_results) == TRUE &&
    is.na(organisation_results) == TRUE &&
    is.na(citations_results) == TRUE
  ) {
    other <- FALSE
  }
  if (other == TRUE) {
    # conditionals for the node labels
    if (is.na(website_results) == FALSE) {
      cond_websites <- paste0(
        "\n",
        website_results_text,
        " (n = ", website_results, ")"
      )
    } else {
      cond_websites <- ""
    }
    if (is.na(organisation_results) == FALSE) {
      cond_organisation <- paste0(
        "\n",
        organisation_results_text,
        " (n = ", organisation_results, ")"
      )
    } else {
      cond_organisation <- ""
    }
    if (is.na(citations_results) == FALSE) {
      cond_citation <- paste0(
        "\n",
        citations_results_text,
        " (n = ", citations_results, ")"
      )
    } else {
      cond_citation <- ""
    }
    if (is.data.frame(other_excluded) == TRUE) {
      other_excluded_data <- paste0(
        ":",
        paste(
          paste(
            "\n",
            other_excluded[, 1],
            " (n = ", other_excluded[, 2], ")",
            sep = ""
          ),
        collapse = ""
        )
      )
    } else {
      other_excluded_data <- paste0(
        "\n", "(n = ", other_excluded, ")"
      )
    }
    # labels
    other_identified_label <- paste0(
      "Records identified from:",
      cond_websites,
      cond_organisation,
      cond_citation
    )
    other_sought_reports_label <- paste0(
      other_sought_reports_text,
      "\n(n = ",
        other_sought_reports,
      ")"
    )
    other_notretrieved_label <- paste0(
      other_notretrieved_reports_text,
      "\n(n = ",
        other_notretrieved_reports,
      ")"
    )
    other_assessed_label <- paste0(
      other_assessed_text,
      "\n(n = ",
        other_assessed,
      ")"
    )
    other_excluded_label <- paste0(
       other_excluded_text, other_excluded_data
    )
    # heights
    other_identified_height <- PRISMA_get_height_(
      stringr::str_count(other_identified_label, "\n"),
      min_box_height
    )
    other_sought_reports_height <- PRISMA_get_height_(
      stringr::str_count(other_sought_reports_label, "\n"),
      min_box_height
    )
    other_notretrieved_height <- PRISMA_get_height_(
      stringr::str_count(other_notretrieved_label, "\n"),
      min_box_height
    )
    other_assessed_height <- PRISMA_get_height_(
      stringr::str_count(other_assessed_label, "\n"),
      min_box_height
    )
    other_excluded_height <- PRISMA_get_height_(
      stringr::str_count(other_excluded_label, "\n"),
      min_box_height
    )
  }
  if (is.na(new_studies) == FALSE) {
    cond_newstud <- paste0(
      stringr::str_wrap(new_studies_text, width = 40),
      "\n(n = ", new_studies, ")\n"
    )
  } else {
    cond_newstud <- ""
  }
  if (is.na(new_reports) == FALSE) {
    cond_newreports <- paste0(
      stringr::str_wrap(new_reports_text, width = 40),
      "\n(n = ", new_reports, ")"
    )
  } else {
    cond_newreports <- ""
  }
  if (detail_databases == TRUE) {
    db_specific_data_nr <- paste(
      paste(
        "\n",
        database_specific_results[, 1],
        " (n = ", database_specific_results[, 2], ")",
      sep = ""
      ),
    collapse = ""
    )
    db_specific_data <- paste0(
      ":",
      db_specific_data_nr
    )
  } else {
    db_specific_data <- ""
    db_specific_data_nr <- ""
  }
  if (detail_registers == TRUE) {
    reg_specific_data_nr <- paste(
      paste(
        "\n", register_specific_results[, 1],
        " (n = ", register_specific_results[, 2], ")",
      sep = ""
      ),
    collapse = ""
    )
    reg_specific_data <- paste0(
      ":",
      reg_specific_data_nr
    )
  } else {
    reg_specific_data <- ""
    reg_specific_data_nr <- ""
  }
  if (is.na(database_results) == FALSE) {
    cond_database <- paste0(
      "\n",
      database_results_text,
      " (n = ", database_results, ")", db_specific_data)
  } else {
    cond_database <- paste0("", db_specific_data_nr)
  }
  if (is.na(register_results) == FALSE) {
    cond_register <- paste0(
      "\n",
      register_results_text,
      " (n = ",  register_results, ")", reg_specific_data)
  } else {
    cond_register <- paste0("", reg_specific_data_nr)
  }
  if (any(!grepl("\\D", dbr_excluded)) == FALSE) {
    dbr_excluded_data <- paste0(
      ":",
      paste(
        paste(
          "\n",
          dbr_excluded[, 1],
          " (n = ", dbr_excluded[, 2], ")",
        sep = ""
        ),
      collapse = ""
      )
    )
  } else {
    dbr_excluded_data <- paste0("\n", "(n = ", dbr_excluded, ")")
  }
  if (is.na(duplicates) == FALSE) {
    cond_duplicates <- paste0(
      stringr::str_wrap(
        paste0(
          duplicates_text,
          " (n = ", duplicates, ")"
        ),
        width = 42
      ),
      "\n"
    )
  } else {
    cond_duplicates <- ""
  }
  if (is.na(excluded_automatic) == FALSE) {
    cond_automatic <- paste0(
      stringr::str_wrap(
        paste0(
          excluded_automatic_text,
          " (n = ", excluded_automatic, ")"
        ),
        width = 42
      ),
      "\n"
    )
  } else {
    cond_automatic <- ""
  }
  if (is.na(excluded_other) == FALSE) {
    cond_exclother <- paste0(
      stringr::str_wrap(
        paste0(
          excluded_other_text,
          " (n = ", excluded_other, ")"
        ),
        width = 42
      )
    )
  } else {
    cond_exclother <- ""
  }
  if (
    is.na(duplicates) == TRUE &&
    is.na(excluded_automatic) == TRUE &&
    is.na(excluded_other) == TRUE
  ) {
    cond_duplicates <- "(n = 0)"
  }
  # labels for the nodes
  newstudy_newreports_label <- paste0(cond_newstud, cond_newreports)
  dbr_assessed_label <- paste0(
    dbr_assessed_text,
    "\n(n = ",
      dbr_assessed,
    ")"
  )
  dbr_sought_label <- paste0(
    dbr_sought_reports_text,
    "\n(n = ",
      dbr_sought_reports,
    ")"
  )
  dbr_screened_label <- paste0(
    records_screened_text,
    "\n(n = ",
      records_screened,
    ")"
  )
  dbr_identified_label <- paste0(
    "Records identified from:",
      cond_database,
      cond_register
  )
  dbr_excluded_label <- paste0(
    dbr_excluded_text,
    dbr_excluded_data
  )
  dbr_notretrieved_label <- paste0(
    dbr_notretrieved_reports_text,
    "\n(n = ",
      dbr_notretrieved_reports,
    ")"
  )
  dbr_screened_excluded_label <- paste0(
    records_excluded_text,
    "\n(n = ",
      records_excluded,
    ")"
  )
  dbr_notscreened_label <- paste0(
    "Records removed before screening:\n",
      cond_duplicates,
      cond_automatic,
      cond_exclother
  )
  # we set the height of various nodes here
  newstudy_newreports_height <- PRISMA_get_height_(
    stringr::str_count(newstudy_newreports_label, "\n"),
    min_box_height
  )
  dbr_assessed_height <- PRISMA_get_height_(
    stringr::str_count(dbr_assessed_label, "\n"),
    min_box_height
  )
  dbr_sought_height <- PRISMA_get_height_(
    stringr::str_count(dbr_sought_label, "\n"),
    min_box_height
  )
  dbr_screened_height <- PRISMA_get_height_(
    stringr::str_count(dbr_screened_label, "\n"),
    min_box_height
  )
  dbr_identified_height <- PRISMA_get_height_(
    stringr::str_count(dbr_identified_label, "\n"),
    min_box_height
  )
  dbr_excluded_height <- PRISMA_get_height_(
    stringr::str_count(dbr_excluded_label, "\n"),
    min_box_height
  )
  dbr_notretrieved_height <- PRISMA_get_height_(
    stringr::str_count(dbr_notretrieved_label, "\n"),
    min_box_height
  )
  dbr_screened_excluded_height <- PRISMA_get_height_(
    stringr::str_count(dbr_screened_excluded_label, "\n"),
    min_box_height
  )
  dbr_notscreened_height <- PRISMA_get_height_(
    stringr::str_count(dbr_notscreened_label, "\n"),
    min_box_height
  )
  screening_box_height <- max(
      c(
        dbr_screened_height,
        dbr_screened_excluded_height
      )
    ) + max(
      c(
        dbr_notretrieved_height,
        dbr_sought_height,
        other_sought_reports_height,
        other_notretrieved_height
      )
    ) + max(
      c(
        dbr_assessed_height,
        dbr_excluded_height,
        other_assessed_height,
        other_excluded_height
      )
    ) +
    default_box_spacing * 3
  identification_box_height <- max(
      c(
        dbr_identified_height,
        dbr_notscreened_height,
        prev_study_height
      )
    )
  included_box_height <-
    newstudy_newreports_height +
    total_studies_height +
    default_box_spacing
  assessed_height <- max(
    c(
      dbr_assessed_height,
      other_assessed_height,
      dbr_excluded_height,
      other_excluded_height
    )
  )
  sought_height <- max(
    c(
      dbr_sought_height,
      other_sought_reports_height,
      dbr_notretrieved_height,
      other_notretrieved_height
    )
  )
  screened_height <- max(
    c(
      dbr_screened_height,
      dbr_screened_excluded_height
    )
  )
  identified_height <- max(
    c(
      dbr_identified_height,
      dbr_notscreened_height,
      other_identified_height,
      prev_study_height
    )
  )
  warning(included_box_height)
  # here we set the x and y co-ordinates for new studies
  # (other items depend on this being created)
  dbr_box_x <- PRISMA_get_pos_(
    diagram_start_x,
    prev_study_offset + default_box_spacing,
    prev_study_width,
    default_box_width
  )
  dbr_removed_x <- PRISMA_get_pos_(
    dbr_box_x,
    default_box_spacing,
    default_box_width,
    default_box_width
  )
  newstudy_newreports_y <- PRISMA_get_pos_(
    diagram_start_y,
    default_box_spacing,
    total_studies_height,
    newstudy_newreports_height
  )
  assessed_y <- PRISMA_get_pos_(
    newstudy_newreports_y,
    default_box_spacing * 2,
    newstudy_newreports_height,
    assessed_height
  )
  sought_y <- PRISMA_get_pos_(
    assessed_y,
    default_box_spacing,
    assessed_height,
    sought_height
  )
  screened_y <- PRISMA_get_pos_(
    sought_y,
    default_box_spacing,
    sought_height,
    screened_height
  )
  identified_y <- PRISMA_get_pos_(
    screened_y,
    default_box_spacing * 2,
    screened_height,
    identified_height
  )
  top_box_y <- PRISMA_get_pos_(
    identified_y,
    default_box_spacing,
    identified_height,
    section_label_length
  )
  screening_y <- mean(c(screened_y, sought_y, assessed_y))
  included_y <- if (total_studies_height > 0) {
    mean(c(diagram_start_y, newstudy_newreports_y))
  } else {
    newstudy_newreports_y
  }
  if (side_boxes == TRUE) {
    sidebox <- paste0(
      "node [
        shape = box,
        fontsize = ", fontsize, ",
        fontname = ", font, ",
        color = ", title_colour, "
      ]
      identification [
        color = LightSteelBlue2,
        label = ' ',
        style = 'filled,rounded',
        pos = '", diagram_start_x, ",", identified_y, "!',
        width = ", section_label_length, ",
        height = ", identification_box_height, ",
        tooltip = '", tooltips["identification"], "'
      ];
      screening [
        color = LightSteelBlue2,
        label = ' ',
        style = 'filled,rounded',
        pos = '", diagram_start_x, ",", screening_y, "!',
        width = ", section_label_length, ",
        height = ", screening_box_height, ",
        tooltip = '", tooltips["screening"], "'
      ];
      included [
        color = LightSteelBlue2,
        label = ' ',
        style = 'filled,rounded',
        pos = '", diagram_start_x, ",", included_y, "!',
        width = ", section_label_length, ",
        height = ", included_box_height, ",
        tooltip = '", tooltips["included"], "'
      ];\n"
    )
  } else {
    sidebox <- ""
  }
  if (previous == TRUE) {
        A <- paste0( #nolint
      "A [
        label = '',
        pos = '", prev_box_x, ",", diagram_start_y + 0, "!',
        tooltip = ''
      ]"
    )
    Aedge <- paste0( #nolint
      "subgraph cluster0 {
        edge [
          color = White,
          arrowhead = none,
          arrowtail = none
        ]
        1->2;
        edge [
          color = ", arrow_colour, ",
          arrowhead = none,
          arrowtail = ", arrow_tail, "
        ]
        2->A;
        edge [
          color = ", arrow_colour, ",
          arrowhead = ", arrow_head, ",
          arrowtail = none,
          constraint = FALSE
        ]
        A->19;
      }"
    )
    bottomedge <- paste0(
      "edge [
        color = '", arrow_colour, "',
        arrowhead = '", arrow_head, "',
        arrowtail = '", arrow_tail, "'
      ]
      12->19;\n"
    )
    previous_nodes <- paste0(
      "node [
        shape = box,
        fontsize = ", fontsize, ",
        fontname = ", font, ",
        color = ", greybox_colour, "
      ]
      1 [
        label = '", previous_text, "',
        style = 'rounded,filled',
        width = ", default_box_width, ",
        height = ", section_label_length, ",
        pos = '",
          prev_box_x,
          ",",
          top_box_y,
          "!',
        tooltip = '", tooltips["prevstud"], "'
      ]
      node [
        shape = box,
        fontname = ", font, ",
        color = ", greybox_colour, "
      ]
      2 [
        label = '", prev_study_label, "',
        style = 'filled',
        width = ", default_box_width, ",
        height = ", prev_study_height, ",
        fixed = 'true',
        pos = '", prev_box_x, ",", identified_y, "!',
        tooltip = '", tooltips["previous_studies"], "'
      ]"
    )
    finalnode <- paste0(
      "node [
        shape = box,
        fontname = ", font, ",
        color = ", greybox_colour, "
      ]
      19 [
        label = '", total_studies_label, "',
        style = 'filled',
        width = ", default_box_width, ",
        height = ", total_studies_height, ",
        fixedsize = 'true',
        pos = '",
          PRISMA_get_pos_(
            diagram_start_x,
            prev_study_offset + default_box_spacing,
            prev_study_width,
            default_box_width
          ),
          ",",
          diagram_start_y,
          "!',
        tooltip = '", tooltips["total_studies"], "'
      ]"
    )
    prev_rank1 <- "{rank = same; A; 19}"
    prevnode1 <- "1; "
    prevnode2 <- "2; "
  }
  if (other == TRUE) {
    # positions
    other_box_x <- PRISMA_get_pos_(
      dbr_removed_x,
      default_box_spacing,
      default_box_width,
      default_box_width
    )
    other_removed_x <- PRISMA_get_pos_(
      other_box_x,
      default_box_spacing,
      default_box_width,
      default_box_width
    )
    B <- paste0( #nolint
      "B [
        label = '',
        pos = '", other_box_x, ",", newstudy_newreports_y, "!',
        tooltip = ''
      ]"
    )
    cluster2 <- paste0(
      "subgraph cluster2 {
        edge [
          color = White,
          arrowhead = none,
          arrowtail = none
        ]
        13->14;
        edge [
          color = ", arrow_colour, ",
          arrowhead = ", arrow_head, ",
          arrowtail = ", arrow_tail,
        "]
        14->15;
        15->16;
        15->17;
        17->18;
        edge [
          color = ", arrow_colour, ",
          arrowhead = none,
          arrowtail = ", arrow_tail,
        "]
        17->B;
        edge [
          color = ", arrow_colour, ",
          arrowhead = ", arrow_head, ",
          arrowtail = none,
          constraint = FALSE
        ]
        B->12;
      }"
    )
    othernodes <- paste0(
      "node [
        shape = box,
        fontname = ", font, ",
        color = ", greybox_colour,
      "]
      13 [
        label = '", other_text, "',
        style = 'rounded,filled',
        width = ", top_box_width, ",
        height = ", section_label_length, ",
        pos = '",
          mean(c(other_box_x, other_removed_x)),
          ",",
          top_box_y,
          "!',
        tooltip = '", tooltips["othstud"], "'
      ]
      node [
        shape = box,
        fontname = ", font, ",
        color = ", greybox_colour,
      "]
      14 [
        label = '", other_identified_label, "',
        style = 'filled',
        width = ", default_box_width, ",
        height = ", other_identified_height, ",
        pos = '", other_box_x, ",", identified_y, "!',
        tooltip = '", tooltips["website_results"], "'
      ]
      node [
        shape = box,
        fontname = ", font, ",
        color = ", greybox_colour,
      "]
      15 [
        label = '", other_sought_reports_label, "',
        style = 'filled',
        width = ", default_box_width, ",
        height = ", other_sought_reports_height, ",
        pos = '", other_box_x, ",", sought_y, "!',
        tooltip = '", tooltips["other_sought_reports"], "'
      ]
      node [
        shape = box,
        fontname = ", font, ",
        color = ", greybox_colour,
      "]
      16 [
        label = '", other_notretrieved_label, "',
        style = 'filled',
        width = ", default_box_width, ",
        height = ", other_notretrieved_height, ",
        pos = '", other_removed_x, ",", sought_y, "!',
        tooltip = '", tooltips["other_notretrieved_reports"], "'
      ]
      node [
        shape = box,
        fontname = ", font, ",
        color = ", greybox_colour, "
      ]
      17 [
        label = '", other_assessed_label, "',
        style = 'filled',
        width = ", default_box_width, ",
        height = ", other_assessed_height, ",
        pos = '", other_box_x, ",", assessed_y, "!',
        tooltip = '", tooltips["other_assessed"], "'
      ]
      node [
        shape = box,
        fontname = ", font, ",
        color = ", greybox_colour,
      "]
      18 [
        label = '", other_excluded_label, "',
        style = 'filled',
        width = ", default_box_width, ",
        height = ", other_excluded_height, ",
        pos = '",
          other_removed_x,
          ",",
          assessed_y,
        "!',
        tooltip = '", tooltips["other_excluded"], "'
      ]\n"
    )
    extraedges <- "16->18;"
    othernode13 <- "; 13"
    othernode14 <- "; 14"
    othernode1516 <- "; 15; 16"
    othernode1718 <- "; 17; 18"
    othernodeB <- "; B" #nolint
  } else {
    B <- "" #nolint
    cluster2 <- ""
    othernodes <- ""
    extraedges <- ""
    othernode13 <- ""
    othernode14 <- ""
    othernode1516 <- ""
    othernode1718 <- ""
    othernodeB <- "" #nolint
  }
  x <- DiagrammeR::grViz(
    paste0(
      "digraph TD {
        graph[
          splines = ortho,
          layout = neato,
          tooltip = 'Click the boxes for further information',
          outputorder = edgesfirst,
        ]",
        sidebox,
        previous_nodes,
        "node [
          shape = box,
          fontsize = ", fontsize, ",
          fontname = ", font, ",
          color = ", title_colour,
        "]
        3 [
          label = '", newstud_text, "',
          style = 'rounded,filled',
          width = ", top_box_width, ",
          height = ", section_label_length, ",
          pos = '",
            mean(c(dbr_box_x, dbr_removed_x)),
            ",",
            top_box_y,
            "!',
          tooltip = '", tooltips["newstud"], "'
        ]
        node [
          shape = box,
          fontname = ", font, ",
          color = ", main_colour,
        "]
        4 [
          label = '", dbr_identified_label, "',
          width = ", default_box_width, ",
          height = ", dbr_identified_height, ",
          pos = '", dbr_box_x, ",", identified_y, "!',
          tooltip = '", tooltips["database_results"], "'
        ]
        node [
          shape = box,
          fontname = ", font, ",
          color = ", main_colour,
        "]
        5 [
          label = '", dbr_notscreened_label, "',
          width = ", default_box_width, ",
          height = ", min_box_height, ",
          pos = '", dbr_removed_x, ",", identified_y, "!',
          tooltip = '", tooltips["duplicates"], "'
        ]
        node [
          shape = box,
          fontname = ", font, ",
          color = ", main_colour, "
        ]
        6 [
          label = '", dbr_screened_label, "',
          width = ", default_box_width, ",
          height = ", dbr_screened_height, ",
          pos = '", dbr_box_x, ",", screened_y, "!',
          tooltip = '", tooltips["records_screened"], "'
        ]
        node [
          shape = box,
          fontname = ", font, ",
          color = ", main_colour, "
        ]
        7 [
          label = '", dbr_screened_excluded_label, "',
          width = ", default_box_width, ",
          height = ", min_box_height, ",
          pos = '", dbr_removed_x, ",", screened_y, "!',
          tooltip = '", tooltips["records_excluded"], "'
        ]
        node [
          shape = box,
          fontname = ", font, ",
          color = ", main_colour,
        "]
        8 [
          label = '", dbr_sought_label, "',
          width = ", default_box_width, ",
          height = ", dbr_sought_height, ",
          pos = '", dbr_box_x, ",", sought_y, "!',
          tooltip = '", tooltips["dbr_sought_reports"], "'
        ]
        node [
          shape = box,
          fontname = ", font, ",
          color = ", main_colour,
        "]
        9 [
          label = '", dbr_notretrieved_label, "',
          width = ", default_box_width, ",
          height = ", min_box_height, ",
          pos = '", dbr_removed_x, ",", sought_y, "!',
          tooltip = '", tooltips["dbr_notretrieved_reports"], "'
        ]
        node [
          shape = box,
          fontname = ", font, ",
          color = ", main_colour,
        "]
        10 [
          label = '", dbr_assessed_label, "',
          width = ", default_box_width, ",
          height = ", dbr_assessed_height, ",
          pos = '", dbr_box_x, ",", assessed_y, "!',
          tooltip = '", tooltips["dbr_assessed"], "'
        ]
        node [
          shape = box,
          fontname = ", font, ",
          color = ", main_colour, ",
          fillcolor = White,
          style = filled
        ]
        11 [
          label = '", dbr_excluded_label, "',
          width = ", default_box_width, ",
          height = ", min_box_height, ",
          pos = '",
            dbr_removed_x,
            ",",
            assessed_y,
          "!',
          tooltip = '", tooltips["dbr_excluded"], "'
        ]
        node [
          shape = box,
          fontname = ", font, ",
          color = ", main_colour, ",
          fillcolor = '',
          style = solid
        ]
        12 [
          label = '", newstudy_newreports_label, "',
          width = ", default_box_width, ",
          height = ", newstudy_newreports_height, ",
          pos = '", dbr_box_x, ",", newstudy_newreports_y, "!',
          tooltip = '", tooltips["new_studies"], "'
        ]",
        othernodes,
        finalnode,
        "node [
          shape = square,
          width = 0,
          color=White
        ]\n",
        A,
        "\n",
        B,
        "\n",
        Aedge,
        "node [
          shape = square,
          width = 0,
          style=invis
        ]
        C [
          label = '',
          width = ", default_box_width, ",
          height = ", min_box_height, ",
          pos = '", dbr_removed_x, ",", assessed_y, "!',
          tooltip = ''
        ]
        subgraph cluster1 {
          edge [
            style = invis
          ]
          3->4;
          3->5;
          edge [
            color = ", arrow_colour, ",
            arrowhead = ", arrow_head, ",
            arrowtail = ", arrow_tail, ",
            style = filled
          ]
          4->5;
          4->6;
          6->7;
          6->8;
          8->9;
          8->10;
          10->C;
          10->12;
          edge [
            style = invis
          ]
          5->7;
          7->9;
          9->11;
          ", extraedges, "
        }",
        cluster2,
        "\n",
        bottomedge,
        "\n\n",
        prev_rank1,
        "\n",
        "{
          rank = same; ",
          prevnode1,
          "3",
          othernode13,
        "}
        {
          rank = same; ",
          prevnode2,
          "4; 5",
          othernode14,
        "}
        {
          rank = same; 6; 7
        }
        {
          rank = same; 8; 9",
          othernode1516,
        "}
        {
          rank = same; 10; 11",
          othernode1718,
        "}
        {
          rank = same; 12",
          othernodeB,
        "}
      }"
    )
  )
  if (side_boxes == TRUE) {
    x <- PRISMA_insert_js_(
      x,
      identification_text = identification_text,
      screening_text = screening_text,
      included_text = included_text
    )
  }
  if (interactive == TRUE) {
    x <- PRISMA_interactive_(
      x,
      urls,
      previous = previous,
      other = other
    )
  }
  return(x)
}


#' Read in PRISMA flow diagram data
#'
#' @description Read in a template CSV containing data for the flow diagram
#' @param data File to read in.
#' @return A list of objects needed to plot the flow diagram
#' @examples
#' csvFile <- system.file("extdata", "PRISMA.csv", package = "PRISMA2020")
#' data <- read.csv(csvFile);
#' data <- PRISMA_data(data);
#' @export
PRISMA_data <- function(data) { #nolint
  # Ensure data is a df, not a tibble;
  # tibbles do not return vectors using df[, 1].
  data <- as.data.frame(data)
  #Set parameters
  previous_studies <- scales::comma(
    PRISMA_format_number_( #nolint
      data[
        grep(
          "previous_studies",
          data[, 1]
        ),
      ]$n
    )
  )
  previous_reports <- scales::comma(
    PRISMA_format_number_( #nolint
      data[
        grep(
          "previous_reports",
          data[, 1]
        ),
      ]$n
    )
  )
  register_results <- scales::comma(
    PRISMA_format_number_( #nolint
      data[
        grep(
          "register_results",
          data[, 1]
        ),
      ]$n
    )
  )
  database_results <- scales::comma(
    PRISMA_format_number_( #nolint
      data[
        grep(
          "database_results",
          data[, 1]
        ),
      ]$n
    )
  )
  database_specific_results <- data.frame(
    reason = gsub(
      ",.*$",
      "",
      unlist(
        strsplit(
          as.character(
            data[
              grep(
                "database_specific_results",
                data[, 1]
              ),
            ]$n
          ),
          split = "; "
        )
      )
    ),
    n = scales::comma(
      PRISMA_format_number_( #nolint
        gsub(
          ".*?,(.*)",
          "\\1",
          unlist(
            strsplit(
              as.character(
                data[
                  grep(
                    "database_specific_results",
                    data[, 1]
                  ),
                ]$n
              ),
              split = "; "
            )
          )
        )
      )
    )
  )
  register_specific_results <- data.frame(
    reason = gsub(
      ",.*$",
      "",
      unlist(
        strsplit(
          as.character(
            data[
              grep(
                "register_specific_results",
                data[, 1]
              ),
            ]$n
          ),
          split = "; "
        )
      )
    ),
    n = scales::comma(
      PRISMA_format_number_( #nolint
        gsub(
          ".*?,(.*)",
          "\\1",
          unlist(
            strsplit(
              as.character(
                data[
                  grep(
                    "register_specific_results",
                    data[, 1]
                  ),
                ]$n
              ),
              split = "; "
            )
          )
        )
      )
    )
  )
  website_results <- scales::comma(
    PRISMA_format_number_( #nolint
      data[
        grep(
          "website_results",
          data[, 1]
        ),
      ]$n
    )
  )
  organisation_results <- scales::comma(
    PRISMA_format_number_( #nolint
      data[
        grep(
          "organisation_results",
          data[, 1]
        ),
      ]$n
    )
  )
  citations_results <- scales::comma(
    PRISMA_format_number_( #nolint
      data[
        grep(
          "citations_results",
          data[, 1]
        ),
      ]$n
    )
  )
  duplicates <- scales::comma(
    PRISMA_format_number_( #nolint
      data[
        grep(
          "duplicates",
          data[, 1]
        ),
      ]$n
    )
  )
    excluded_automatic <- scales::comma(
    PRISMA_format_number_( #nolint
      data[
        grep(
          "excluded_automatic",
          data[, 1]
        ),
      ]$n
    )
  )
  excluded_other <- scales::comma(
    PRISMA_format_number_( #nolint
      data[
        grep(
          "excluded_other",
          data[, 1]
        ),
      ]$n
    )
  )
  records_screened <- scales::comma(
    PRISMA_format_number_( #nolint
      data[
        grep(
          "records_screened",
          data[, 1]
        ),
      ]$n
    )
  )
  records_excluded <- scales::comma(
    PRISMA_format_number_( #nolint
      data[
        grep(
          "records_excluded",
          data[, 1]
        ),
      ]$n
    )
  )
  dbr_sought_reports <- scales::comma(
    PRISMA_format_number_( #nolint
      data[
        grep(
          "dbr_sought_reports",
          data[, 1]
        ),
      ]$n
    )
  )
  dbr_notretrieved_reports <- scales::comma(
    PRISMA_format_number_( #nolint
      data[
        grep(
          "dbr_notretrieved_reports",
          data[, 1]
        ),
      ]$n
    )
  )
  other_sought_reports <- scales::comma(
    PRISMA_format_number_( #nolint
      data[
        grep(
          "other_sought_reports",
          data[, 1]
        ),
      ]$n
    )
  )
  other_notretrieved_reports <- scales::comma(
    PRISMA_format_number_( #nolint
      data[
        grep(
          "other_notretrieved_reports",
          data[, 1]
        ),
      ]$n
    )
  )
  dbr_assessed <- scales::comma(
    PRISMA_format_number_( #nolint
      data[
        grep(
          "dbr_assessed",
          data[, 1]
        ),
      ]$n
    )
  )
  dbr_excluded <- data.frame(
    reason = gsub(
      ",.*$",
      "",
      unlist(
        strsplit(
          as.character(
            data[
              grep(
                "dbr_excluded",
                data[, 1]
              ),
            ]$n
          ),
          split = "; "
        )
      )
    ),
    n = scales::comma(
      PRISMA_format_number_( #nolint
        gsub(
          ".*?,(.*)",
          "\\1",
          unlist(
            strsplit(
              as.character(
                data[
                  grep(
                    "dbr_excluded",
                    data[, 1]
                  ),
                ]$n
              ),
              split = "; "
            )
          )
        )
      )
    )
  )
  other_assessed <- scales::comma(
    PRISMA_format_number_( #nolint
      data[
        grep(
          "other_assessed",
          data[, 1]
        ),
      ]$n
    )
  )
  other_excluded <- data.frame(
    reason = gsub(
      ",.*$",
      "",
      unlist(
        strsplit(
          as.character(
            data[
              grep(
                "other_excluded",
                data[, 1]
              ),
            ]$n
          ),
          split = "; "
        )
      )
    ),
    n = scales::comma(
      PRISMA_format_number_( #nolint
        gsub(
          ".*?,(.*)",
          "\\1",
          unlist(
            strsplit(
              as.character(
                data[
                  grep(
                    "other_excluded",
                    data[, 1]
                  ),
                ]$n
              ),
              split = "; "
            )
          )
        )
      )
    )
  )
  new_studies <- scales::comma(
    PRISMA_format_number_( #nolint
      data[
        grep(
          "new_studies",
          data[, 1]
        ),
      ]$n
    )
  )
  new_reports <- scales::comma(
    PRISMA_format_number_( #nolint
      data[
        grep(
          "new_reports",
          data[, 1]
        ),
      ]$n
    )
  )
  total_studies <- scales::comma(
    PRISMA_format_number_( #nolint
      data[
        grep(
          "total_studies",
          data[, 1]
        ),
      ]$n
    )
  )
  total_reports <- scales::comma(
    PRISMA_format_number_( #nolint
      data[
        grep(
          "total_reports",
          data[, 1]
        ),
      ]$n
    )
  )
  tooltips <- list()
  for (i in seq_len(nrow(data))) {
    if (!is.na(data[i, ]$tooltips)) {
      if (is.na(data[i, ]$data)) {
        name <- data[i, ]$box
      } else {
        name <- data[i, ]$data
      }
      tooltips[[name]] <- data[i, ]$tooltips
    }
  }

  urls <- data.frame(
    box = data[!duplicated(data$box), ]$box,
    url = data[!duplicated(data$box), ]$url
  )
  #set text - if text >33 characters,
  previous_text <- data[grep("prevstud", data[, 3]), ]$boxtext
  newstud_text <- data[grep("newstud", data[, 3]), ]$boxtext
  other_text <- data[grep("othstud", data[, 3]), ]$boxtext
  previous_studies_text <- data[grep("previous_studies", data[, 1]), ]$boxtext
  previous_reports_text <- data[grep("previous_reports", data[, 1]), ]$boxtext
  register_results_text <- data[grep("register_results", data[, 1]), ]$boxtext
  database_results_text <- data[grep("database_results", data[, 1]), ]$boxtext
  website_results_text <- data[grep("website_results", data[, 1]), ]$boxtext
  organisation_results_text <- data[
    grep(
      "organisation_results",
      data[, 1]
    ),
  ]$boxtext
  citations_results_text <- data[grep("citations_results", data[, 1]), ]$boxtext
  duplicates_text <- data[grep("duplicates", data[, 1]), ]$boxtext
  excluded_automatic_text <- data[
    grep(
      "excluded_automatic",
      data[, 1]
    ),
  ]$boxtext
  excluded_other_text <- data[grep("excluded_other", data[, 1]), ]$boxtext
  records_screened_text <- data[grep("records_screened", data[, 1]), ]$boxtext
  records_excluded_text <- data[grep("records_excluded", data[, 1]), ]$boxtext
  dbr_sought_reports_text <- data[
    grep(
      "dbr_sought_reports",
      data[, 1]
    ),
  ]$boxtext
  dbr_notretrieved_reports_text <- data[
    grep(
      "dbr_notretrieved_reports",
      data[, 1]
    ),
  ]$boxtext
  other_sought_reports_text <- data[
    grep(
      "other_sought_reports",
      data[, 1]
    ),
  ]$boxtext
  other_notretrieved_reports_text <- data[ #nolint
    grep(
      "other_notretrieved_reports",
      data[, 1]
    ),
  ]$boxtext
  dbr_assessed_text <- data[grep("dbr_assessed", data[, 1]), ]$boxtext
  dbr_excluded_text <- data[grep("dbr_excluded", data[, 1]), ]$boxtext
  other_assessed_text <- data[grep("other_assessed", data[, 1]), ]$boxtext
  other_excluded_text <- data[grep("other_excluded", data[, 1]), ]$boxtext
  new_studies_text <- data[grep("new_studies", data[, 1]), ]$boxtext
  new_reports_text <- data[grep("new_reports", data[, 1]), ]$boxtext
  total_studies_text <- data[grep("total_studies", data[, 1]), ]$boxtext
  total_reports_text <- data[grep("total_reports", data[, 1]), ]$boxtext
  identification_text <- data[grep("identification", data[, 1]), ]$boxtext
  screening_text <- data[grep("screening", data[, 1]), ]$boxtext
  included_text <- data[grep("included", data[, 1]), ]$boxtext
  x <- list(
    previous_studies = previous_studies,
    previous_reports = previous_reports,
    register_results = register_results,
    database_results = database_results,
    database_specific_results = database_specific_results,
    register_specific_results = register_specific_results,
    website_results = website_results,
    organisation_results = organisation_results,
    citations_results = citations_results,
    duplicates = duplicates,
    excluded_automatic = excluded_automatic,
    excluded_other = excluded_other,
    records_screened = records_screened,
    records_excluded = records_excluded,
    dbr_sought_reports = dbr_sought_reports,
    dbr_notretrieved_reports = dbr_notretrieved_reports,
    other_sought_reports = other_sought_reports,
    other_notretrieved_reports = other_notretrieved_reports,
    dbr_assessed = dbr_assessed,
    dbr_excluded = dbr_excluded,
    other_assessed = other_assessed,
    other_excluded = other_excluded,
    new_studies = new_studies,
    new_reports = new_reports,
    total_studies = total_studies,
    total_reports = total_reports,
    previous_text = previous_text,
    newstud_text = newstud_text,
    other_text = other_text,
    previous_studies_text = previous_studies_text,
    previous_reports_text = previous_reports_text,
    register_results_text = register_results_text,
    database_results_text = database_results_text,
    website_results_text = website_results_text,
    organisation_results_text = organisation_results_text,
    citations_results_text = citations_results_text,
    duplicates_text = duplicates_text,
    excluded_automatic_text = excluded_automatic_text,
    excluded_other_text = excluded_other_text,
    records_screened_text = records_screened_text,
    records_excluded_text = records_excluded_text,
    dbr_sought_reports_text = dbr_sought_reports_text,
    dbr_notretrieved_reports_text = dbr_notretrieved_reports_text,
    other_sought_reports_text = other_sought_reports_text,
    other_notretrieved_reports_text = other_notretrieved_reports_text,
    dbr_assessed_text = dbr_assessed_text,
    dbr_excluded_text = dbr_excluded_text,
    other_assessed_text = other_assessed_text,
    other_excluded_text = other_excluded_text,
    new_studies_text = new_studies_text,
    new_reports_text = new_reports_text,
    total_studies_text = total_studies_text,
    total_reports_text = total_reports_text,
    identification_text = identification_text,
    screening_text = screening_text,
    included_text = included_text,
    tooltips = tooltips,
    urls = urls
  )
  return(x)
}

#' Save PRISMA2020 flow diagram
#' @description Save the output from [PRISMA_flowdiagram()] to the
#' working directory.
#' @param plotobj A plot produced using [PRISMA_flowdiagram()].
#' @param filename The filename to save (including extension)
#' @param filetype The filetype to save the plot in, supports:
#' HTML, ZIP, PDF, PNG, SVG, PS and WEBP
#' (if NA, the filetype will be calculated out based on the file extension)
#' HTML files maintain hyperlinks and tooltips
#' The ZIP option creates an archive containing the HTML file,
#' alongside supporting javascript and css files in an adjacent folder,
#' instead of embedded base64 within the HTML file
#' @param overwrite if TRUE, will overwrite an existing file
#' @return the absolute filename of the saved diagram plot.
#' @examples
#' csvFile <- system.file("extdata", "PRISMA.csv", package = "PRISMA2020")
#' data <- read.csv(csvFile);
#' data <- PRISMA_data(data);
#' plot <- PRISMA_flowdiagram(data,
#'                 fontsize = 12,
#'                 interactive = TRUE,
#'                 previous = FALSE,
#'                 other = TRUE);
#' PRISMA_save(plot, filename = tempfile(), filetype="html");
#' @export
PRISMA_save <- function( #nolint
  plotobj,
  filename = "PRISMA2020_flowdiagram.html",
  filetype = NA,
  overwrite = FALSE
) {
  if (!file.exists(filename) || overwrite == TRUE) {
    format_real <- PRISMA_calc_filetype_(filename, filetype) #nolint
    switch(
      format_real,
      "HTML" = {
        tmp_html <- tempfile(
          pattern = "PRISMA2020_",
          tmpdir = tempdir(),
          fileext = ".html"
        )
        htmlwidgets::saveWidget(
          plotobj,
          file = tmp_html,
          title = "PRISMA2020 Flowdiagram"
        )
        if (!(file.copy(tmp_html, filename, overwrite = TRUE))) {
          stop("Error saving HTML")
        }
        file.remove(tmp_html)
      },
      "ZIP" = {
        curr_wd <- getwd()
        tmp_dir <- tempdir()
        setwd(tmp_dir)
        tmp_zipfile <- tempfile(
          pattern = "PRISMA2020_",
          tmpdir = tempdir(),
          fileext = ".zip"
        )
        tmp_html <- paste0(
          tools::file_path_sans_ext(basename(filename)),
          ".html"
        )
        tmp_libdir <- paste0(tmp_html, "_files")
        htmlwidgets::saveWidget(
          plotobj,
          file = tmp_html,
          libdir = tmp_libdir,
          selfcontained = FALSE,
          title = "PRISMA2020 Flowdiagram"
        )
        zip::zip(zipfile = tmp_zipfile, files = c(tmp_html, tmp_libdir))
        setwd(curr_wd)
        if (!(file.copy(paste0(tmp_zipfile), filename, overwrite = TRUE))) {
          stop("Error saving ZIP File")
        }
      },
      "PDF" = {
        tmp_svg <- PRISMA_gen_tmp_svg_(plotobj) #nolint
        rsvg::rsvg_pdf(tmp_svg, filename)
        file.remove(tmp_svg)
      },
      "PNG" = {
        tmp_svg <- PRISMA_gen_tmp_svg_(plotobj) #nolint
        rsvg::rsvg_png(tmp_svg, filename)
        file.remove(tmp_svg)
      },
      "SVG" = {
        tmp_svg <- PRISMA_gen_tmp_svg_(plotobj) #nolint
        if (!(file.copy(tmp_svg, filename, overwrite = TRUE))) {
          stop("Error saving SVG")
        }
        file.remove(tmp_svg)
      },
      "PS" = {
        tmp_svg <- PRISMA_gen_tmp_svg_(plotobj) #nolint
        rsvg::rsvg_ps(tmp_svg, filename)
        file.remove(tmp_svg)
      },
      "WEBP" = {
        tmp_svg <- PRISMA_gen_tmp_svg_(plotobj) #nolint
        rsvg::rsvg_webp(tmp_svg, filename)
        file.remove(tmp_svg)
      },
      stop("Please choose one of the supported file types")
    )
    return(tools::file_path_as_absolute(filename))
  } else {
    stop("File exists, please set overwite = TRUE to overwrite")
  }
}

#' Defunct function - replaced by "PRISMA_interactive_"
#' @description Defunct function - replaced by "PRISMA_interactive_"
#' @seealso [PRISMA_interactive_()]
#' @param plot A plot object from [PRISMA_flowdiagram()].
#' @param urls A dataframe consisting of two columns: nodes and urls. The first
#' column should contain 19 rows for the nodes from node1 to node19. The second
#' column should contain a corresponding URL for each node.
#' @param previous Logical argument (TRUE or FALSE) (supplied through
#' [PRISMA_flowdiagram()]) specifying whether previous studies were sought.
#' @param other Logical argument (TRUE or FALSE) (supplied through
#' [PRISMA_flowdiagram()]) specifying whether other studies were sought.
sr_flow_interactive <- function(plot,
                                urls,
                                previous,
                                other) {
  .Defunct("PRISMA_interactive_")
}

#' Defunct function - replaced by "PRISMA_data"
#' @description Defunct function - replaced by "PRISMA_data"
#' @seealso [PRISMA_data()]
#' @param data File to read in.
read_PRISMAdata <- function(data){ #nolint
  .Defunct("PRISMA_data")
}