#' Create a RevMan-style risk of bias summary chart
#'
#' This function generates summary plots for study quality assessments using the
#' \href{https://bit.ly/2KGQtfG}{Cochrance Risk of Bias Tool}.
#' Summary plots follow the style of \href{https://bit.ly/30eJK29}{RevMan} Risk of Bias (RoB) summary charts.
#'
#' @usage rob.summary(data, name.high="High", name.unclear="Unclear",
#'     name.low="Low", studies, name.missing, table = FALSE)
#'
#' @param data A \code{data.frame} containing a column for each risk of bias criterion, where
#' rows represent each individual studies. The risk of bias assessment for each criterion in each
#' study must be coded as a character string. Up to four codes can be used, referring to low risk of bias,
#' unclear risk of bias, high risk of bias, or missing information. The string used to specify the categories
#' must be specified in \code{name.high}, \code{name.unclear}, \code{name.low} and/or \code{name.missing},
#' unless defaults for those parameters are used.
#' @param name.high Character specifying how the "high risk of bias" category was coded in \code{data}
#' (e.g., \code{name.high = "high"}). Default is \code{"High"}.
#' @param name.unclear Character specifying how the "unclear risk of bias" category was coded in \code{data}
#' (e.g., \code{name.unclear = "unclear"}). Default is \code{"Unclear"}.
#' @param name.low Character specifying how the "low risk of bias" category was coded in \code{data}
#' (e.g., \code{name.low = "low"}). Default is \code{"Low"}.
#' @param name.missing Character specifying how missing information was coded in \code{data}
#' (e.g., \code{name.missing} = \code{"missing"}). Default is \code{"Missing"}. All ratings, including missing
#' information, must be coded as strings, so using \code{NA} in \code{data} to signify missing information
#' is not valid.
#' @param studies A vector of the same length as the number of rows in \code{data} specifying the study
#' labels for the risk of bias ratings. Only has to be specified when \code{table = TRUE}.
#' @param table Should an additional RevMan style risk of bias table be produced? If set to \code{TRUE},
#' \code{studies} must be specified. \code{FALSE} by default.
#'
#' @details The function automatically removes separators like "-" or "." from column names/risk of bias criteria. To produce
#' a "clean" plot, you may therefore separate words in the column names of the \code{data} data frame using these
#' symbols (e.g. \code{"Allocation_Concealment"} to return "Allocation Concealment").
#'
#' @references Harrer, M., Cuijpers, P., Furukawa, T.A, & Ebert, D. D. (2019).
#' \emph{Doing Meta-Analysis in R: A Hands-on Guide}. DOI: 10.5281/zenodo.2551803.
#' \href{https://bookdown.org/MathiasHarrer/Doing_Meta_Analysis_in_R/creating-a-revman-style-risk-of-bias-summary.html}{Chapter 10}
#'
#' @author Mathias Harrer & David Daniel Ebert
#'
#' @import ggplot2
#'
#' @export rob.summary
#'
#' @seealso
#' \code{\link{direct.evidence.plot}}
#'
#' @examples
#' # Example 1: No missing information, only produce summary plot
#' data = data.frame(
#'        "study" = c("Jones et al., 2011", "Smith et al., 2008", "Holm, 1971",
#'                    "Zajonc et al., 2005", "Grenell, 2014"),
#'        "Allocation_concealment" = c("Low", "High", "High", "Unclear", "High"),
#'        "Randomization" = c("Low", "High", "Unclear", "Low", "High"),
#'        "Sequence_generation" = c("Low", "High", "Unclear", "Unclear", "High"),
#'        "ITT.Analyses" = c("Low", "High", "Unclear", "Unclear", "Unclear"),
#'        "Selective_outcome_reporting" = c("Low", "High", "High", "High", "Unclear")
#'        )
#' rob.summary(data)
#'
#' # Example 2: Missing information, produce additional summary table
#' data2 = data.frame(
#'         "study" = c("Higgins et al., 2011", "Borenstein et al., 2008", "Holm, 1971",
#'                     "Zajonc et al., 2005", "Cuijpers, 2014"),
#'         "Allocation_concealment" = c("low", "high", "high", "uc", "high"),
#'         "Randomization" = c("low", "high", "miss", "low", "high"),
#'         "Sequence_generation" = c("low", "high", "uc", "uc", "high"),
#'         "ITT.Analyses" = c("low", "high", "uc", "uc", "uc"),
#'         "Selective_outcome_reporting" = c("low", "high", "high", "high", "uc")
#'        )
#' rob.summary(data2, name.high = "high", name.unclear = "uc", name.low = "low",
#'     name.missing = "miss", studies = data2$study, table = TRUE)


rob.summary = function (data, name.high = "High", name.unclear = "Unclear",
                        name.low = "Low", studies, name.missing, table = FALSE) {


  if (!("data.frame" %in% class(data))) {
    stop("'data' must be of class 'data.frame'.")
  }
  if (missing(name.missing)) {
    colnames.rob = character()
    for (i in 1:ncol(data)) {
      vect = as.character(data[, i])
      for (j in 1:length(data[, i])) {
        if (vect[j] %in% c(name.high, name.unclear, name.low)) {
          colnames.rob[i] = TRUE
        }
        else {
          colnames.rob[i] = FALSE
          message(cat("Column '", colnames(data)[i],
                      "' removed from plot because it did not contain the specified RoB ratings (only). \n",
                      sep = ""))
          break
        }
      }
    }
    rob = data[, as.logical(colnames.rob)]
    for (i in 1:ncol(rob)) {
      rob[, i] = as.character(rob[, i])
      rob[rob[, i] == name.high, i] = "High"
      rob[rob[, i] == name.unclear, i] = "Unclear"
      rob[rob[, i] == name.low, i] = "Low"
    }
    if (table == TRUE) {
      if (missing(studies)) {
        stop("'studies' has to be specified when 'table = TRUE'.")
      }
      if (length(as.vector(studies)) != nrow(data)) {
        stop("'studies' vector is not of equal length as the data.")
      }
      if (length(unique(studies)) != length(studies)) {
        stop("'studies' cannot contain duplicate study labels.")
      }
      robby = rob
      robby = data.frame(study = studies, condition = rep(colnames(robby),
                                                          each = length(studies)), measurement = unlist(robby))
      rownames(robby) = NULL
      robby$condition = gsub("_", " ", robby$condition)
      robby$condition = gsub("-", " ", robby$condition)
      robby$condition = gsub("\\.", " ", robby$condition)
      robby$condition = gsub("  ", " ", robby$condition)
      robby[robby$measurement == "Low", "measurement"] = "+"
      robby[robby$measurement == "Unclear", "measurement"] = "?"
      robby[robby$measurement == "High", "measurement"] = "-"
      robby$study = factor(robby$study, levels = unique(studies)[rev(order(unique(robby$study)))])
      rob.table = ggplot(data = robby, aes(y = study, x = condition)) +
        geom_tile(color = "black", fill = "white", linewidth = 0.8) +
        geom_point(aes(color = as.factor(measurement)),
                   size = 20) + geom_text(aes(label = measurement),
                                          size = 8) + scale_x_discrete(position = "top") +
        scale_color_manual(values = c(`?` = "#E2DF07",
                                      `-` = "#BF0000", `+` = "#02C100")) + theme_minimal() +
        coord_equal() + theme(axis.title.x = element_blank(),
                              axis.title.y = element_blank(), axis.ticks.y = element_blank(),
                              axis.text.y = element_text(size = 15, color = "black"),
                              axis.text.x = element_text(size = 13, color = "black",
                                                         angle = 90, hjust = 0), legend.position = "none",
                              panel.grid.major = element_blank(), panel.grid.minor = element_blank(),
                              panel.background = element_blank())
    }
    rob.long = data.frame(condition = rep(colnames(rob),
                                          each = nrow(rob)), measurement = unlist(rob))
    rownames(rob.long) = NULL
    rob.long$condition = gsub("_", " ", rob.long$condition)
    rob.long$condition = gsub("-", " ", rob.long$condition)
    rob.long$condition = gsub("\\.", " ", rob.long$condition)
    rob.long$condition = gsub("  ", " ", rob.long$condition)
    rob.long$measurement = as.factor(rob.long$measurement)
    rob.long$measurement = factor(rob.long$measurement,
                                  levels(rob.long$measurement)[c(1, 3, 2)])
    rob.long$condition = factor(rob.long$condition,
                                levels = rev(sort(unique(rob.long$condition))))
    rob.plot = ggplot(data = rob.long) +
      geom_bar(mapping = aes(x = condition, fill = measurement),
               width = 0.7, position = "fill", color = "black") +
      coord_flip(ylim = c(0, 1)) +
      guides(fill = guide_legend(reverse = TRUE)) +
      scale_fill_manual("Risk of Bias",
                        labels = c(`High` = "    High risk of bias          ",
                                   `Unclear` = "    Unclear risk of bias       ",
                                   `Low` = "    Low risk of bias  "),
                        values = c(High = "#BF0000",
                                   Unclear = "#E2DF07",
                                   Low = "#02C100")) +
      scale_y_continuous(labels = scales::percent) +
      theme(axis.title.x = element_blank(), axis.title.y = element_blank(),
            axis.ticks.y = element_blank(), axis.text.y = element_text(size = 18,
                                                                       color = "black"), axis.line.x = element_line(colour = "black",
                                                                                                                    linewidth = 0.5, linetype = "solid"), legend.position = "bottom",
            panel.grid.major = element_blank(), panel.grid.minor = element_blank(),
            panel.background = element_blank(), legend.background = element_rect(linetype = "solid",
                                                                                 colour = "black"), legend.title = element_blank(),
            legend.key.size = unit(0.75, "cm"), legend.text = element_text(size = 14))
    plot(rob.plot)
    if (table == TRUE) {
      plot(rob.table)
    }
  }
  else {
    data = as.data.frame(data)
    colnames.rob = character()
    for (i in 1:ncol(data)) {
      vect = as.character(data[, i])
      for (j in 1:length(data[, i])) {
        if (vect[j] %in% c(name.high, name.unclear, name.low,
                           name.missing)) {
          colnames.rob[i] = TRUE
        }
        else {
          colnames.rob[i] = FALSE
          message(cat("Column '", colnames(data)[i],
                      "' removed from plot because it did not contain the specified RoB ratings (only). \n",
                      sep = ""))
          break
        }
      }
    }
    rob = data[, as.logical(colnames.rob)]
    for (i in 1:ncol(rob)) {
      rob[, i] = as.character(rob[, i])
      rob[rob[, i] == name.high, i] = "High"
      rob[rob[, i] == name.unclear, i] = "Unclear"
      rob[rob[, i] == name.low, i] = "Low"
      rob[rob[, i] == name.missing, i] = "Missing"
    }
    if (table == TRUE) {
      if (missing(studies)) {
        stop("'studies' has to be specified when 'table = TRUE'.")
      }
      if (length(as.vector(studies)) != nrow(data)) {
        stop("'studies' vector is not of equal length as the data.")
      }
      robby = rob
      robby = data.frame(study = as.factor(studies), condition = rep(colnames(robby),
                                                                     each = length(studies)), measurement = unlist(robby))
      rownames(robby) = NULL
      robby$condition = gsub("_", " ", robby$condition)
      robby$condition = gsub("-", " ", robby$condition)
      robby$condition = gsub("\\.", " ", robby$condition)
      robby[robby$measurement == "Low", "measurement"] = "+"
      robby[robby$measurement == "Unclear", "measurement"] = "?"
      robby[robby$measurement == "High", "measurement"] = "-"
      robby[robby$measurement == "Missing", "measurement"] = " "
      robby$study = factor(robby$study, levels = unique(studies)[rev(order(unique(robby$study)))])
      rob.table = ggplot(data = robby, aes(y = study, x = condition)) +
        geom_tile(color = "black", fill = "white", linewidth = 0.8) +
        geom_point(aes(color = as.factor(measurement)),
                   size = 20) + geom_text(aes(label = measurement),
                                          size = 8) + scale_x_discrete(position = "top") +
        scale_color_manual(values = c(`?` = "#E2DF07",
                                      `-` = "#BF0000", `+` = "#02C100", ` ` = "white")) +
        theme_minimal() + coord_equal() + theme(axis.title.x = element_blank(),
                                                axis.title.y = element_blank(), axis.ticks.y = element_blank(),
                                                axis.text.y = element_text(size = 15, color = "black"),
                                                axis.text.x = element_text(size = 13, color = "black",
                                                                           angle = 90, hjust = 0), legend.position = "none",
                                                panel.grid.major = element_blank(), panel.grid.minor = element_blank(),
                                                panel.background = element_blank())
    }
    rob.long = data.frame(condition = rep(colnames(rob),
                                          each = nrow(rob)), measurement = unlist(rob))
    rownames(rob.long) = NULL
    rob.long$condition = gsub("_", " ", rob.long$condition)
    rob.long$condition = gsub("-", " ", rob.long$condition)
    rob.long$condition = gsub("\\.", " ", rob.long$condition)
    rob.long$measurement = as.factor(rob.long$measurement)
    rob.long$measurement = factor(rob.long$measurement, levels(rob.long$measurement)[c(3,
                                                                                       1, 4, 2)])
    rob.long$condition = factor(rob.long$condition,
                                levels = rev(sort(unique(rob.long$condition))))
    rob.plot = ggplot(data = rob.long) + geom_bar(mapping = aes(x = condition,
                                                                fill = measurement), width = 0.7, position = "fill",
                                                  color = "black") + coord_flip(ylim = c(0, 1)) + guides(fill = guide_legend(reverse = TRUE)) +
      scale_fill_manual("Risk of Bias", labels = c(`High` = "    High risk of bias          ",
                                                   `Unclear` = "    Unclear risk of bias       ",
                                                   `Low` = "    Low risk of bias  ",
                                                   `Missing` = "    Missing information      "),
                        values = c(Missing = "white",
                                   High = "#BF0000",
                                   Unclear = "#E2DF07",
                                   Low = "#02C100")) +
      scale_y_continuous(labels = scales::percent) + theme(axis.title.x = element_blank(),
                                                           axis.title.y = element_blank(), axis.ticks.y = element_blank(),
                                                           axis.text.y = element_text(size = 18, color = "black"),
                                                           axis.line.x = element_line(colour = "black", linewidth = 0.5,
                                                                                      linetype = "solid"), legend.position = "bottom",
                                                           panel.grid.major = element_blank(), panel.grid.minor = element_blank(),
                                                           panel.background = element_blank(), legend.background = element_rect(linetype = "solid",
                                                                                                                                colour = "black"), legend.title = element_blank(),
                                                           legend.key.size = unit(0.75, "cm"), legend.text = element_text(size = 14))
    plot(rob.plot)
    if (table == TRUE) {
      plot(rob.table)
    }
  }
}