fix docs

DESCRIPTION

@@ -18,7 +18,9 @@ Imports:
     logger,
     mosaic,
     pkgload,
+    plotly,
     R6,
+    shiny,
     stats,
     stringr,
     tidybayes

NAMESPACE

@@ -27,4 +27,6 @@ importFrom(ggplot2,ggplot)
 importFrom(ggplot2,guide_legend)
 importFrom(ggplot2,guides)
 importFrom(ggplot2,scale_y_continuous)
+importFrom(ggplot2,theme)
+importFrom(ggplot2,unit)
 useDynLib(epikinetics, .registration = TRUE)

R/epikinetics-package.R

@@ -11,7 +11,7 @@
 #' @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 ggplot guides guide_legend scale_y_continuous theme unit
 #' @useDynLib epikinetics, .registration = TRUE
 ## usethis namespace: end
 

R/inspect-model.R

@@ -150,7 +150,7 @@ inspect_model <- function(mod, private) {
       }
     })
 
-    output$data_plot <- renderUI({
+    output$data_plot <- shiny::renderUI({
       if (nrow(data()) > 0) {
         plotly::plotlyOutput("data")
       } else {

R/plot.R

@@ -86,7 +86,7 @@ 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
-  day <- last_exp_day <- NULL
+  day <- last_exp_day <- mu <- .draw <- NULL
 
   if (attr(x, "summarised")) {
     plot <- ggplot(x) +
@@ -123,6 +123,9 @@ facet_formula <- function(covariates) {
 }
 
 add_censored_indicator <- function(data) {
+  # Declare variables to suppress notes when compiling package
+  # https://github.com/Rdatatable/data.table/issues/850#issuecomment-259466153
+  censored <- NULL
   if (!("censored" %in% colnames(data))) {
     # censored is an optional column in input data
     # if not present, treat all points as uncensored

R/utils.R

@@ -7,13 +7,9 @@
 #' @param vars_to_transform Names of columns to apply the transformation to.
 #' @export
 convert_log2_scale <- function(
-  dt_in, vars_to_transform = "value",
-  simplify_limits = TRUE) {
+  dt_in, vars_to_transform = "value") {
   dt_out <- data.table::copy(dt_in)
   for (var in vars_to_transform) {
-    if (simplify_limits == TRUE) {
-      dt_out[get(var) > 2560, (var) := 2560]
-    }
     dt_out[, (var) := log2(get(var) / 5)]
   }
   return(dt_out)