Update docs, skip some plot tests if R < 4.1

NAMESPACE

@@ -1,5 +1,7 @@
 # Generated by roxygen2: do not edit by hand
 
+S3method(plot,biokinetics_individual_trajectories)
+S3method(plot,biokinetics_population_stationary_points)
 S3method(plot,biokinetics_population_trajectories)
 S3method(plot,biokinetics_priors)
 export(add_exposure_data)
@@ -18,12 +20,19 @@ importFrom(data.table,.SD)
 importFrom(data.table,data.table)
 importFrom(ggplot2,aes)
 importFrom(ggplot2,facet_wrap)
+importFrom(ggplot2,geom_hline)
 importFrom(ggplot2,geom_line)
+importFrom(ggplot2,geom_path)
 importFrom(ggplot2,geom_point)
 importFrom(ggplot2,geom_ribbon)
 importFrom(ggplot2,geom_smooth)
+importFrom(ggplot2,geom_vline)
 importFrom(ggplot2,ggplot)
 importFrom(ggplot2,guide_legend)
 importFrom(ggplot2,guides)
+importFrom(ggplot2,labs)
+importFrom(ggplot2,scale_x_continuous)
+importFrom(ggplot2,scale_x_date)
 importFrom(ggplot2,scale_y_continuous)
+importFrom(ggplot2,sec_axis)
 useDynLib(epikinetics, .registration = TRUE)

R/epikinetics-package.R

@@ -11,7 +11,9 @@
 #' @importFrom data.table .NGRP
 #' @importFrom data.table .SD
 #' @importFrom data.table data.table
-#' @importFrom ggplot2 aes facet_wrap geom_point geom_ribbon geom_line geom_smooth ggplot guides guide_legend scale_y_continuous
+#' @importFrom ggplot2 aes facet_wrap geom_point geom_ribbon geom_line geom_smooth
+#' 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
 ## usethis namespace: end
 

R/plot.R

@@ -85,7 +85,7 @@ plot.biokinetics_population_trajectories <- function(x, ..., data = NULL) {
 
   # 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
+  time_since_last_exp <- value <- me <- mu <- .draw <- titre_type <- lo <- hi <- NULL
   day <- last_exp_day <- NULL
 
   if (attr(x, "summarised")) {
@@ -124,7 +124,7 @@ plot.biokinetics_population_trajectories <- function(x, ..., data = NULL) {
 #' 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.
-#' @oaram min_day Optional minimum date
+#' @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
 #' if x has been generated with summarise=FALSE.
@@ -138,7 +138,9 @@ 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 <- lo <- hi <- day <- pid <- NULL
+  calendar_day <- value <- me <- mu <- titre_type <- day <- pid <- NULL
+  ind_mu_sum <- lo <- hi <- NULL
+
   if (is.null(min_day)) {
     min_day <- min(x$calendar_day)
   }
@@ -213,7 +215,18 @@ plot.biokinetics_individual_trajectories <- function(x, ..., data = NULL,
            fill = "none")
 }
 
+#' Plot method for "biokinetics_population_stationary_points" class
+#'
+#' @param x An object of class "biokinetics_population_stationary_points". These are
+#' generated by running biokinetics$population_stationary_points(). See
+#' \href{../../epikinetics/html/biokinetics.html#method-biokinetics-population_stationary_points}{\code{biokinetics$population_stationary_points()}}
+#' @param \dots Further arguments passed to the method.
+#' @param upper_detection_limit Numeric. Optional upper detection limit. Will be plotted as a dotted line.
+#' @export
 plot.biokinetics_population_stationary_points <- function(x, ..., upper_detection_limit = NULL) {
+  # Declare variables to suppress notes when compiling package
+  # https://github.com/Rdatatable/data.table/issues/850#issuecomment-259466153
+  mu_p <- mu_s <- mu_p_me <- mu_s_me <- titre_type <- NULL
   covariates <- attr(x, "covariates")
   plot <- ggplot(data = x,
                  aes(x = mu_p, y = mu_s, colour = titre_type)) +

tests/testthat/test-plots.R

@@ -218,6 +218,7 @@ test_that("Can plot individual trajectories for specific pids with data and titr
 })
 
 test_that("Can plot stationary points", {
+  skip_if(getRversion() < 4.1)
   # note that this is using a pre-fitted model with very few iterations, so the
   # fits won't look very good
   local_mocked_bindings(
@@ -231,6 +232,7 @@ test_that("Can plot stationary points", {
 })
 
 test_that("Can plot stationary points with no covariates", {
+  skip_if(getRversion() < 4.1)
   # note that this is using a pre-fitted model with very few iterations, so the
   # fits won't look very good
   local_mocked_bindings(
@@ -244,6 +246,7 @@ test_that("Can plot stationary points with no covariates", {
 
 
 test_that("Can plot stationary points with upper limit", {
+  skip_if(getRversion() < 4.1)
   # note that this is using a pre-fitted model with very few iterations, so the
   # fits won't look very good
   local_mocked_bindings(