fix s3 method

R/plot.R

@@ -66,42 +66,43 @@ plot_data <- function(data, covariates) {
 
 #' Plot method for "biokinetics_population_trajectories" class
 #'
-#' @param trajectories An object of class "biokinetics_population_trajectories". These are
-#' generated by running biokinetics$simulate_populate_trajectories().
-#' @param data Optional data.table containing raw data as provided to the
-#' biokinetics model.
-#' @seealso
-#' [`bioikinetics$simulate_populate_trajectories`][biokinetics#method-simulate_populate_trajectories]
+#' @param x An object of class "biokinetics_population_trajectories". These are
+#' generated by running biokinetics$simulate_populate_trajectories(). See
+#' \href{../../epikinetics/html/biokinetics.html#method-biokinetics-simulate_population_trajectories}{\code{biokinetics$simulate_population_trajectories()}}
+#' @param \dots Further arguments passed to the method. For now the only extra argument supported is "data", which should be
+#' a data.table containing raw data as provided to the biokinetics model.
 #' @export
-plot.biokinetics_population_trajectories <- function(trajectories, ..., data = NULL) {
-  if (!attr(trajectories, "summarised")) {
-    by <- setdiff(colnames(trajectories), c("t0_pop", "tp_pop", "ts_pop",
+plot.biokinetics_population_trajectories <- function(x, ...) {
+  if (!attr(x, "summarised")) {
+    by <- setdiff(colnames(x), c("t0_pop", "tp_pop", "ts_pop",
                                             "m1_pop", "m2_pop", "m3_pop",
                                             ".draw", "mu"))
-    trajectories <- summarise_draws(
-      trajectories, column_name = "mu", by = by)
+    x <- summarise_draws(
+      x, column_name = "mu", by = by)
   }
+  args <- list(...)
   # Declare variables to suppress notes when compiling package
   # https://github.com/Rdatatable/data.table/issues/850#issuecomment-259466153
   time_since_last_exp <- value <- me <- titre_type <- lo <- hi <- NULL
   day <- last_exp_day <- NULL
 
-  plot <- ggplot(trajectories) +
+  plot <- ggplot(x) +
     geom_line(aes(x = time_since_last_exp, y = me, colour = titre_type)) +
     geom_ribbon(aes(x = time_since_last_exp,
                     ymin = lo,
                     ymax = hi,
                     fill = titre_type), alpha = 0.5)
 
-  if (!is.null(data)) {
+  if (!is.null(args$data)) {
+    data <- args$data
     validate_required_cols(data)
     plot <- plot +
       geom_point(data = data,
                  aes(x = as.integer(day - last_exp_day, units = "days"),
                      y = value), size = 0.5, alpha = 0.5)
   }
   plot + scale_y_continuous(trans = "log2") +
-    facet_wrap(eval(parse(text = facet_formula(attr(trajectories, "covariates"))))) +
+    facet_wrap(eval(parse(text = facet_formula(attr(x, "covariates"))))) +
     guides(fill = guide_legend(title = "Titre type"), colour = "none")
 }