R/set_global_params.R

In adepro: A 'shiny' Application for the (Audio-)Visualization of Adverse Event Profiles

#' set_global_params - sets all global parameters
#'
#' @description
#' Function that sets all global parameters
#'
#' @param ae_data adverse event dataset
#' @param patients patient dataset
#' @param title titles for the treatment groups
#' @param height number of circles on the vertical axis
#'
#' @keywords internal

set_global_params <- function(ae_data, patients, title = NULL, height = NULL) {

  ## Consistency checks
  if(is.null(title)) {
    title <- rep("", length(unique(patients$treat)))
  }
  if (is.null(height)) {
    height <- ceiling(sqrt(850 / 1920 * nrow(patients)))
  }

  check_data(ae_data, patients)

  ## Local variables
  Q <- initQ(ae_data)     # classification matrix of AEs (treatment-emergent, serious etc.)
  AE_options <- 1:ncol(Q) # descriptions of AE classifications
  type_names <- data.frame(short = c("trtem", "ser", "nonser", "studrel", "studrelser", "relprot", "resdisc", "studrelresdisc"),
                           long = c("all treatment-emergent", "serious ", "non-serious ", "study drug-related ",
                                  "study-drug related and serious", "related to procedures required by the protocol",
                                  "resulting in discontinuation of study drug",
                                  "study drug-related and resulting in discontinuation of study drug"))
  names(AE_options) <- sapply(1:ncol(Q), function(x) type_names$long[which(type_names$short == colnames(Q)[x])])

  xylines <- set_group_lines(patients, height)
  xlines  <- xylines[1]
  ylines  <- xylines[2]
  plines  <- xylines[3]

  globals <- list(titles = title,
                  footnote = paste("SAF (N=", nrow(patients), ")", sep = ""),
                  Q = Q,
                  AE_options = AE_options,
                  width = set_width(patients, height),
                  height = height,
                  xlines = xlines,
                  ylines = ylines,
                  plines = plines)
  return(globals)
}