update docs

NAMESPACE

@@ -23,6 +23,8 @@ importFrom(data.table,data.table)
 importFrom(ggplot2,aes)
 importFrom(ggplot2,annotate)
 importFrom(ggplot2,facet_wrap)
+importFrom(ggplot2,geom_bar)
+importFrom(ggplot2,geom_density_2d)
 importFrom(ggplot2,geom_hline)
 importFrom(ggplot2,geom_line)
 importFrom(ggplot2,geom_path)

R/epikinetics-package.R

@@ -11,7 +11,7 @@
 #' @importFrom data.table .NGRP
 #' @importFrom data.table .SD
 #' @importFrom data.table data.table
-#' @importFrom ggplot2 aes annotate facet_wrap geom_point geom_ribbon geom_line geom_smooth
+#' @importFrom ggplot2 aes annotate facet_wrap geom_point geom_ribbon geom_line geom_smooth geom_bar geom_density_2d
 #' geom_vline geom_hline geom_path labs ggplot guides guide_legend scale_y_continuous
 #' scale_x_continuous scale_x_date sec_axis
 #' @useDynLib epikinetics, .registration = TRUE

R/plot.R

@@ -150,13 +150,15 @@ plot.biokinetics_population_trajectories <- function(x, ...,
 #' generated by running biokinetics$simulate_individual_trajectories(). See
 #' \href{../../epikinetics/html/biokinetics.html#method-biokinetics-simulate_individaul_trajectories}{\code{biokinetics$simulate_individual_trajectories()}}
 #' @param \dots Further arguments passed to the method.
+#' @param data Optional data.table containing raw data as provided to the biokinetics model.
 #' @param min_day Optional minimum date
 #' @param max_day Optional maximum date
-#' @param pid Optional vector of ids to plot simulated trajectories for a subset of individuals. Can only be used
+#' @param pids Optional vector of ids to plot simulated trajectories for a subset of individuals. Can only be used
 #' if x has been generated with summarise=FALSE.
 #' @param titre_types Optional vector of titre types to include.
 #' @export
-plot.biokinetics_individual_trajectories <- function(x, ..., data = NULL,
+plot.biokinetics_individual_trajectories <- function(x, ...,
+                                                     data = NULL,
                                                      min_day = NULL,
                                                      max_day = NULL,
                                                      pids = NULL,
@@ -165,7 +167,7 @@ plot.biokinetics_individual_trajectories <- function(x, ..., data = NULL,
   # Declare variables to suppress notes when compiling package
   # https://github.com/Rdatatable/data.table/issues/850#issuecomment-259466153
   calendar_day <- value <- me <- mu <- titre_type <- day <- pid <- NULL
-  ind_mu_sum <- lo <- hi <- NULL
+  ind_mu_sum <- lo <- hi <- draw <- NULL
 
   if (is.null(min_day)) {
     min_day <- min(x$calendar_day)