pr suggestions

R/biokinetics.R

@@ -283,7 +283,7 @@ biokinetics <- R6::R6Class(
     #' log or a natural scale.
     #' @return A ggplot2 object.
     plot_model_inputs = function() {
-      plot_data(private$data, private$all_formula_vars)
+      plot_sero_data(private$data, private$all_formula_vars)
     },
     #' @description View the data that is passed to the stan model, for debugging purposes.
     #' @return A list of arguments that will be passed to the stan model.

R/plot.R

@@ -52,7 +52,7 @@ plot.biokinetics_priors <- function(x,
   plot
 }
 
-plot_data <- function(data, covariates) {
+plot_sero_data <- function(data, covariates = character(0)) {
   validate_required_cols(data, c("time_since_last_exp", "value", "titre_type"))
   # Declare variables to suppress notes when compiling package
   # https://github.com/Rdatatable/data.table/issues/850#issuecomment-259466153
@@ -68,7 +68,7 @@ plot_data <- function(data, covariates) {
 #' Plot method for "biokinetics_population_trajectories" class
 #'
 #' @param x An object of class "biokinetics_population_trajectories". These are
-#' generated by running biokinetics$simulate_populate_trajectories(). See
+#' generated by running biokinetics$simulate_population_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.
 #' @param data Optional data.table containing raw data as provided to the biokinetics model.
@@ -90,7 +90,8 @@ plot.biokinetics_population_trajectories <- function(x, ..., data = NULL) {
                       fill = titre_type), alpha = 0.5)
   } else {
     plot <- ggplot(x) +
-      geom_line(aes(x = time_since_last_exp, y = mu, colour = titre_type), alpha = 0.5)
+      geom_line(aes(x = time_since_last_exp, y = mu,
+                    colour = titre_type, group = .draw), alpha = 0.1, linewidth = 0.1)
   }
 
   if (!is.null(data)) {