From 9f0b455b7263971f6111807ac0db734a34735ad2 Mon Sep 17 00:00:00 2001
From: Pavel Demin <paveldemin@me.com>
Date: Fri, 15 Nov 2024 10:58:57 +0000
Subject: [PATCH 01/11] refactor: ability to pass params to run_app

---
 R/run_app.R | 6 ++++--
 1 file changed, 4 insertions(+), 2 deletions(-)

diff --git a/R/run_app.R b/R/run_app.R
index fa17f52..9111a88 100644
--- a/R/run_app.R
+++ b/R/run_app.R
@@ -3,6 +3,8 @@
 #' List of functions imported for the shiny application.
 #' When adding new imports, please keep the alphabetical order, at lest for packages.
 #'
+#' @param ... Arguments passed to `shiny::runApp()`
+#'
 #' @import shiny
 #' @importFrom dplyr mutate filter select group_by summarise pull arrange ungroup
 #' @importFrom dplyr rename_with across case_when left_join rename
@@ -24,6 +26,6 @@
 #' @importFrom utils read.csv write.csv
 #' @importFrom zip zipr
 #' @export
-run_app <- function() {
-  shiny::runApp(system.file("shiny", package = "aNCA"))
+run_app <- function(...) {
+  shiny::runApp(system.file("shiny", package = "aNCA"), ...)
 }

From 668ad7a56749d1e92d614997612eea825176e073 Mon Sep 17 00:00:00 2001
From: Pavel Demin <paveldemin@me.com>
Date: Fri, 15 Nov 2024 11:02:05 +0000
Subject: [PATCH 02/11] docs: add missing importFrom to run_app

---
 R/run_app.R | 1 +
 1 file changed, 1 insertion(+)

diff --git a/R/run_app.R b/R/run_app.R
index 9111a88..97e84fd 100644
--- a/R/run_app.R
+++ b/R/run_app.R
@@ -11,6 +11,7 @@
 #' @importFrom DT DTOutput renderDataTable datatable formatStyle styleEqual
 #' @importFrom ggplot2 ggplot geom_errorbar geom_point geom_line labs aes facet_wrap
 #' @importFrom htmlwidgets JS
+#' @importFrom logger log_trace log_debug log_info log_warn log_error log_fatal
 #' @importFrom PKNCA PKNCAconc PKNCAdose PKNCAdata pk.nca PKNCA.options pknca_units_table
 #' @importFrom plotly plotlyOutput renderPlotly plotly_build event_data
 #' @importFrom reactable reactable reactableOutput renderReactable colDef reactableTheme

From 8606eced84bffee895cb47cec536beb9bfeb665c Mon Sep 17 00:00:00 2001
From: Pavel Demin <paveldemin@me.com>
Date: Fri, 15 Nov 2024 11:02:16 +0000
Subject: [PATCH 03/11] refactor: load libraries inside run_app

---
 R/run_app.R | 17 +++++++++++++++++
 1 file changed, 17 insertions(+)

diff --git a/R/run_app.R b/R/run_app.R
index 97e84fd..790f9ca 100644
--- a/R/run_app.R
+++ b/R/run_app.R
@@ -28,5 +28,22 @@
 #' @importFrom zip zipr
 #' @export
 run_app <- function(...) {
+  require("dplyr")
+  require("DT")
+  require("ggplot2")
+  require("htmlwidgets")
+  require("logger")
+  require("PKNCA")
+  require("plotly")
+  require("reactable")
+  require("rio")
+  require("rmarkdown")
+  require("shinyBS")
+  require("shinyFiles")
+  require("shinyjqui")
+  require("shinyWidgets")
+  require("tools")
+  require("utils")
+  require("zip")
   shiny::runApp(system.file("shiny", package = "aNCA"), ...)
 }

From 3568ffe3226409ce654ba6a079e494330da35704 Mon Sep 17 00:00:00 2001
From: Pavel Demin <paveldemin@me.com>
Date: Fri, 15 Nov 2024 11:14:21 +0000
Subject: [PATCH 04/11] fix: put csv data file in the right place

---
 {www => inst}/data/TLG_order_details.csv | 0
 inst/shiny/modules/tab_tlg.R             | 2 +-
 2 files changed, 1 insertion(+), 1 deletion(-)
 rename {www => inst}/data/TLG_order_details.csv (100%)

diff --git a/www/data/TLG_order_details.csv b/inst/data/TLG_order_details.csv
similarity index 100%
rename from www/data/TLG_order_details.csv
rename to inst/data/TLG_order_details.csv
diff --git a/inst/shiny/modules/tab_tlg.R b/inst/shiny/modules/tab_tlg.R
index bdbf220..fc365f1 100644
--- a/inst/shiny/modules/tab_tlg.R
+++ b/inst/shiny/modules/tab_tlg.R
@@ -88,7 +88,7 @@ tab_tlg_server <- function(id, data) {
 
     # Make available the CSV file with the TLG list and available links to NEST
     tlg_order <- reactiveVal(
-      read.csv(system.file("www/data/TLG_order_details.csv", package = "aNCA")) %>%
+      read.csv(system.file("data/TLG_order_details.csv", package = "aNCA")) %>%
         mutate(PKid = paste0("<a href='", Catalog_Link, "' target='_blank'>", PKid, "</a>"))
     )
 

From 4b2aef9437d39bae337062a3e87583a6c69b7e96 Mon Sep 17 00:00:00 2001
From: Pavel Demin <paveldemin@me.com>
Date: Fri, 15 Nov 2024 11:17:19 +0000
Subject: [PATCH 05/11] fix: require aNCA itself when running the app

---
 R/run_app.R | 2 ++
 1 file changed, 2 insertions(+)

diff --git a/R/run_app.R b/R/run_app.R
index 790f9ca..3f6fddf 100644
--- a/R/run_app.R
+++ b/R/run_app.R
@@ -5,6 +5,7 @@
 #'
 #' @param ... Arguments passed to `shiny::runApp()`
 #'
+#' @import aNCA
 #' @import shiny
 #' @importFrom dplyr mutate filter select group_by summarise pull arrange ungroup
 #' @importFrom dplyr rename_with across case_when left_join rename
@@ -28,6 +29,7 @@
 #' @importFrom zip zipr
 #' @export
 run_app <- function(...) {
+  require("aNCA")
   require("dplyr")
   require("DT")
   require("ggplot2")

From 40cb289f5ed052996cfbaf0296b23f6eb8a1cc1d Mon Sep 17 00:00:00 2001
From: Pavel Demin <paveldemin@me.com>
Date: Fri, 15 Nov 2024 11:28:06 +0000
Subject: [PATCH 06/11] refactor: export functions used in the app

---
 R/utils-slope_selector.R                   | 13 ++++++----
 R/utils.R                                  |  7 ++---
 inst/shiny/modules/slope_selector.R        | 10 ++++----
 tests/testthat/test-utils-slope_selector.R | 30 +++++++++++-----------
 tests/testthat/test-utils.R                | 16 ++++++------
 5 files changed, 40 insertions(+), 36 deletions(-)

diff --git a/R/utils-slope_selector.R b/R/utils-slope_selector.R
index 068cf1f..5e7d57e 100644
--- a/R/utils-slope_selector.R
+++ b/R/utils-slope_selector.R
@@ -12,7 +12,8 @@
 #'          columns modified in accordance to the provided slope filters.
 #' @importFrom dplyr filter group_by mutate
 #'
-.filter_slopes <- function(data, slopes, profiles) {
+#' @export
+filter_slopes <- function(data, slopes, profiles) {
   if (is.null(data) || is.null(data$conc) || is.null(data$conc$data))
     stop("Please provide valid data.")
 
@@ -39,7 +40,7 @@
     # Go over all rules and check if there is no overlap - if there is, edit accordingly
     slopes <- purrr::reduce(
       split(slopes, seq_len(nrow(slopes))),
-      .f = ~ .check_slope_rule_overlap(.x, .y, .keep = TRUE)
+      .f = ~ check_slope_rule_overlap(.x, .y, .keep = TRUE)
     )
   }
 
@@ -84,7 +85,9 @@
 #'                 that the user wants to remove rule if new range already exists in the dataset.
 #'                 If TRUE, in that case full range will be kept.
 #' @returns Data frame with full ruleset, adjusted for new rules.
-.check_slope_rule_overlap <- function(existing, new, .keep = FALSE) {
+#'
+#' @export
+check_slope_rule_overlap <- function(existing, new, .keep = FALSE) {
   # check if any rule already exists for specific patient and profile #
   existing_index <- which(
     existing$TYPE == new$TYPE &
@@ -106,11 +109,11 @@
 
   if (is_diff || .keep) {
     existing$IXrange[existing_index] <- unique(c(existing_range, new_range)) %>%
-      .compress_range()
+      compress_range()
 
   } else if (is_inter) {
     existing$IXrange[existing_index] <- setdiff(existing_range, new_range) %>%
-      .compress_range()
+      compress_range()
   }
 
   dplyr::filter(existing, !is.na(IXrange))
diff --git a/R/utils.R b/R/utils.R
index 4c61203..c831fc3 100644
--- a/R/utils.R
+++ b/R/utils.R
@@ -27,11 +27,12 @@
 #' @examples
 #' \dontrun{
 #' # Basic usage
-#' .compress_range(c(1, 2, 3, 4)) # "1:4"
-#' .compress_range(c(15, 1, 11, 4, 5, 10, 2, 12, 3)) # "1:5,10:12,15"
+#' compress_range(c(1, 2, 3, 4)) # "1:4"
+#' compress_range(c(15, 1, 11, 4, 5, 10, 2, 12, 3)) # "1:5,10:12,15"
 #' }
 #'
-.compress_range <- function(range_vector) {
+#' @export
+compress_range <- function(range_vector) {
   if (!is(range_vector, "numeric")) range_vector <- suppressWarnings(as.numeric(range_vector))
   if (any(is.na(range_vector))) stop("Error: only numeric values allowed")
   if (length(range_vector) == 0) return(NA_integer_)
diff --git a/inst/shiny/modules/slope_selector.R b/inst/shiny/modules/slope_selector.R
index 4d09bff..8c8f9f4 100644
--- a/inst/shiny/modules/slope_selector.R
+++ b/inst/shiny/modules/slope_selector.R
@@ -348,12 +348,12 @@ slope_selector_server <- function(
 
     # Observe input$nca
     observeEvent(profiles_per_patient(), {
-      mydata(.filter_slopes(mydata(), manual_slopes(), profiles_per_patient()))
+      mydata(filter_slopes(mydata(), manual_slopes(), profiles_per_patient()))
     })
 
     #' saves and implements provided ruleset
     observeEvent(input$save_ruleset, {
-      mydata(.filter_slopes(mydata(), manual_slopes(), profiles_per_patient()))
+      mydata(filter_slopes(mydata(), manual_slopes(), profiles_per_patient()))
       rv$trigger <- rv$trigger + 1
     })
 
@@ -362,7 +362,7 @@ slope_selector_server <- function(
     #' and exclusions before applying them to the actual dataset.
     plot_data <- reactive({
       req(mydata(), manual_slopes(), profiles_per_patient())
-      .filter_slopes(mydata(), manual_slopes(), profiles_per_patient())
+      filter_slopes(mydata(), manual_slopes(), profiles_per_patient())
     }) %>%
       shiny::debounce(750)
 
@@ -402,7 +402,7 @@ slope_selector_server <- function(
       )
 
       # Check if there is any overlap with existing rules, adda new or edit accordingly
-      new_manual_slopes <- .check_slope_rule_overlap(manual_slopes(), new_slope_rule)
+      new_manual_slopes <- check_slope_rule_overlap(manual_slopes(), new_slope_rule)
 
       manual_slopes(new_manual_slopes)
 
@@ -429,7 +429,7 @@ slope_selector_server <- function(
         select(TYPE, USUBJID, DOSNO, IX, REASON) %>%
         mutate(PATIENT = as.character(USUBJID), PROFILE = as.character(DOSNO)) %>%
         group_by(TYPE, PATIENT, PROFILE, REASON) %>%
-        summarise(IXrange = .compress_range(IX), .groups = "keep") %>%
+        summarise(IXrange = compress_range(IX), .groups = "keep") %>%
         select(TYPE, PATIENT, PROFILE, IXrange, REASON) %>%
         na.omit()
 
diff --git a/tests/testthat/test-utils-slope_selector.R b/tests/testthat/test-utils-slope_selector.R
index 0b03ccb..afb18a4 100644
--- a/tests/testthat/test-utils-slope_selector.R
+++ b/tests/testthat/test-utils-slope_selector.R
@@ -21,7 +21,7 @@ PROFILES_FIXTURE <- list(
   "4" = list(1)
 )
 
-describe(".filter_slopes", {
+describe("filter_slopes", {
   it("should handle slope selection", {
     selection <- data.frame(
       TYPE = rep("Selection", 2),
@@ -31,7 +31,7 @@ describe(".filter_slopes", {
       REASON = "Test selection"
     )
 
-    res <- .filter_slopes(DATA_FIXTURE, selection, PROFILES_FIXTURE)
+    res <- filter_slopes(DATA_FIXTURE, selection, PROFILES_FIXTURE)
     expect_true(all(res$is.included.hl[c(1:3, 6:8)]))
     expect_true(all(res$REASON[c(1:3, 6:8)] == "Test selection"))
   })
@@ -45,19 +45,19 @@ describe(".filter_slopes", {
       REASON = "Test exclusion"
     )
 
-    res <- .filter_slopes(DATA_FIXTURE, exclusion, PROFILES_FIXTURE)
+    res <- filter_slopes(DATA_FIXTURE, exclusion, PROFILES_FIXTURE)
     expect_true(all(res$is.excluded.hl[c(5, 6, 14, 15)]))
     expect_true(all(res$REASON[c(5, 6, 14, 15)] == "Test exclusion"))
   })
 
   it("should throw an error for invalid data", {
-    expect_error(.filter_slopes(NULL, NULL, PROFILES_FIXTURE), "Please provide valid data.")
-    expect_error(.filter_slopes(list(), NULL, PROFILES_FIXTURE), "Please provide valid data.")
+    expect_error(filter_slopes(NULL, NULL, PROFILES_FIXTURE), "Please provide valid data.")
+    expect_error(filter_slopes(list(), NULL, PROFILES_FIXTURE), "Please provide valid data.")
     expect_error(
-      .filter_slopes(list(conc = list()), NULL, PROFILES_FIXTURE), "Please provide valid data."
+      filter_slopes(list(conc = list()), NULL, PROFILES_FIXTURE), "Please provide valid data."
     )
     expect_error(
-      .filter_slopes(list(conc = list()), NULL, PROFILES_FIXTURE), "Please provide valid data."
+      filter_slopes(list(conc = list()), NULL, PROFILES_FIXTURE), "Please provide valid data."
     )
   })
 })
@@ -69,7 +69,7 @@ EXISTING_FIXTURE <- data.frame(
   IXrange = "3:6"
 )
 
-describe(".check_slope_rule_overlap", {
+describe("check_slope_rule_overlap", {
   it("should add new row if no overlap is detected", {
     # different type #
     NEW <- data.frame(
@@ -78,7 +78,7 @@ describe(".check_slope_rule_overlap", {
       PROFILE = 1,
       IXrange = "1:3"
     )
-    expect_equal(nrow(.check_slope_rule_overlap(EXISTING_FIXTURE, NEW)), 2)
+    expect_equal(nrow(check_slope_rule_overlap(EXISTING_FIXTURE, NEW)), 2)
 
     # different patient #
     NEW <- data.frame(
@@ -87,7 +87,7 @@ describe(".check_slope_rule_overlap", {
       PROFILE = 1,
       IXrange = "1:3"
     )
-    expect_equal(nrow(.check_slope_rule_overlap(EXISTING_FIXTURE, NEW)), 2)
+    expect_equal(nrow(check_slope_rule_overlap(EXISTING_FIXTURE, NEW)), 2)
 
     # different profile #
     NEW <- data.frame(
@@ -96,7 +96,7 @@ describe(".check_slope_rule_overlap", {
       PROFILE = 2,
       IXrange = "1:3"
     )
-    expect_equal(nrow(.check_slope_rule_overlap(EXISTING_FIXTURE, NEW)), 2)
+    expect_equal(nrow(check_slope_rule_overlap(EXISTING_FIXTURE, NEW)), 2)
   })
 
   it("should remove overlapping points if no new points are detected", {
@@ -106,7 +106,7 @@ describe(".check_slope_rule_overlap", {
       PROFILE = 1,
       IXrange = "4:5"
     )
-    expect_equal(.check_slope_rule_overlap(EXISTING_FIXTURE, NEW)$IXrange, "3,6")
+    expect_equal(check_slope_rule_overlap(EXISTING_FIXTURE, NEW)$IXrange, "3,6")
 
     NEW <- data.frame(
       TYPE = "Exclusion",
@@ -114,7 +114,7 @@ describe(".check_slope_rule_overlap", {
       PROFILE = 1,
       IXrange = "3:4"
     )
-    expect_equal(.check_slope_rule_overlap(EXISTING_FIXTURE, NEW)$IXrange, "5:6")
+    expect_equal(check_slope_rule_overlap(EXISTING_FIXTURE, NEW)$IXrange, "5:6")
   })
 
   it("should add new points of partial overlap is detected", {
@@ -124,7 +124,7 @@ describe(".check_slope_rule_overlap", {
       PROFILE = 1,
       IXrange = "4:9"
     )
-    expect_equal(.check_slope_rule_overlap(EXISTING_FIXTURE, NEW)$IXrange, "3:9")
+    expect_equal(check_slope_rule_overlap(EXISTING_FIXTURE, NEW)$IXrange, "3:9")
   })
 
   it("should remove full row if full range of rule is removed", {
@@ -134,6 +134,6 @@ describe(".check_slope_rule_overlap", {
       PROFILE = 1,
       IXrange = "3:6"
     )
-    expect_equal(nrow(.check_slope_rule_overlap(EXISTING_FIXTURE, NEW)), 0)
+    expect_equal(nrow(check_slope_rule_overlap(EXISTING_FIXTURE, NEW)), 0)
   })
 })
diff --git a/tests/testthat/test-utils.R b/tests/testthat/test-utils.R
index 81d2858..5bb8a9b 100644
--- a/tests/testthat/test-utils.R
+++ b/tests/testthat/test-utils.R
@@ -17,29 +17,29 @@ describe(".eval_range", {
   })
 })
 
-describe(".compress_range", {
+describe("compress_range", {
   it("compreses simple range correctly", {
-    expect_equal(.compress_range(c(1, 2, 3, 4)), "1:4")
-    expect_equal(.compress_range(c(1, 5, 10, 15)), "1,5,10,15")
+    expect_equal(compress_range(c(1, 2, 3, 4)), "1:4")
+    expect_equal(compress_range(c(1, 5, 10, 15)), "1,5,10,15")
   })
 
   it("compreses range with breaks correctly", {
-    expect_equal(.compress_range(c(1, 2, 3, 4, 5, 10, 11, 12, 15)), "1:5,10:12,15")
+    expect_equal(compress_range(c(1, 2, 3, 4, 5, 10, 11, 12, 15)), "1:5,10:12,15")
   })
 
   it("handles unsorted vectors correctly", {
-    expect_equal(.compress_range(c(15, 1, 11, 4, 5, 10, 2, 12, 3)), "1:5,10:12,15")
+    expect_equal(compress_range(c(15, 1, 11, 4, 5, 10, 2, 12, 3)), "1:5,10:12,15")
   })
 
   it("coerces character vectors to numeric if possible", {
-    expect_equal(.compress_range(c("1", "2", "03")), "1:3")
+    expect_equal(compress_range(c("1", "2", "03")), "1:3")
   })
 
   it("returns NA when empty vector is provided", {
-    expect_true(is.na(.compress_range(c())))
+    expect_true(is.na(compress_range(c())))
   })
 
   it("throws an error if any values in the vector cannot be coerced to numeric", {
-    expect_error(.compress_range(c(1, 2, "A", 4)), "Error: only numeric values allowed")
+    expect_error(compress_range(c(1, 2, "A", 4)), "Error: only numeric values allowed")
   })
 })

From cac90621485a41128ee9e4438d9241a8dfb58a6f Mon Sep 17 00:00:00 2001
From: Pavel Demin <paveldemin@me.com>
Date: Fri, 15 Nov 2024 11:29:32 +0000
Subject: [PATCH 07/11] docs: devtools::document()

---
 NAMESPACE                                              |  3 +++
 ...ope_rule_overlap.Rd => check_slope_rule_overlap.Rd} |  6 +++---
 man/{dot-compress_range.Rd => compress_range.Rd}       | 10 +++++-----
 man/{dot-filter_slopes.Rd => filter_slopes.Rd}         |  6 +++---
 man/run_app.Rd                                         |  5 ++++-
 5 files changed, 18 insertions(+), 12 deletions(-)
 rename man/{dot-check_slope_rule_overlap.Rd => check_slope_rule_overlap.Rd} (86%)
 rename man/{dot-compress_range.Rd => compress_range.Rd} (76%)
 rename man/{dot-filter_slopes.Rd => filter_slopes.Rd} (91%)

diff --git a/NAMESPACE b/NAMESPACE
index 761a6e3..ce38fcc 100644
--- a/NAMESPACE
+++ b/NAMESPACE
@@ -4,9 +4,12 @@ export(anonymize_pk_data)
 export(apply_filters)
 export(as_factor_preserve_label)
 export(calculate_summary_stats)
+export(check_slope_rule_overlap)
+export(compress_range)
 export(create_conc)
 export(create_dose)
 export(filter_breaks)
+export(filter_slopes)
 export(flexible_violinboxplot)
 export(format_data)
 export(general_lineplot)
diff --git a/man/dot-check_slope_rule_overlap.Rd b/man/check_slope_rule_overlap.Rd
similarity index 86%
rename from man/dot-check_slope_rule_overlap.Rd
rename to man/check_slope_rule_overlap.Rd
index fc724a6..a618807 100644
--- a/man/dot-check_slope_rule_overlap.Rd
+++ b/man/check_slope_rule_overlap.Rd
@@ -1,10 +1,10 @@
 % Generated by roxygen2: do not edit by hand
 % Please edit documentation in R/utils-slope_selector.R
-\name{.check_slope_rule_overlap}
-\alias{.check_slope_rule_overlap}
+\name{check_slope_rule_overlap}
+\alias{check_slope_rule_overlap}
 \title{Check overlap between existing and new slope rulesets}
 \usage{
-.check_slope_rule_overlap(existing, new, .keep = FALSE)
+check_slope_rule_overlap(existing, new, .keep = FALSE)
 }
 \arguments{
 \item{existing}{Data frame with existing selections and exclusions.}
diff --git a/man/dot-compress_range.Rd b/man/compress_range.Rd
similarity index 76%
rename from man/dot-compress_range.Rd
rename to man/compress_range.Rd
index 1ea3c16..c6b9d47 100644
--- a/man/dot-compress_range.Rd
+++ b/man/compress_range.Rd
@@ -1,11 +1,11 @@
 % Generated by roxygen2: do not edit by hand
 % Please edit documentation in R/utils.R
-\name{.compress_range}
-\alias{.compress_range}
+\name{compress_range}
+\alias{compress_range}
 \title{Compresses a numeric vector into the simplest possible character string that, when evaluated,
 will create the same numeric vector.}
 \usage{
-.compress_range(range_vector)
+compress_range(range_vector)
 }
 \arguments{
 \item{range_vector}{numeric vector with numbers to compress into string}
@@ -20,8 +20,8 @@ will create the same numeric vector.
 \examples{
 \dontrun{
 # Basic usage
-.compress_range(c(1, 2, 3, 4)) # "1:4"
-.compress_range(c(15, 1, 11, 4, 5, 10, 2, 12, 3)) # "1:5,10:12,15"
+compress_range(c(1, 2, 3, 4)) # "1:4"
+compress_range(c(15, 1, 11, 4, 5, 10, 2, 12, 3)) # "1:5,10:12,15"
 }
 
 }
diff --git a/man/dot-filter_slopes.Rd b/man/filter_slopes.Rd
similarity index 91%
rename from man/dot-filter_slopes.Rd
rename to man/filter_slopes.Rd
index 536763c..340a8ce 100644
--- a/man/dot-filter_slopes.Rd
+++ b/man/filter_slopes.Rd
@@ -1,10 +1,10 @@
 % Generated by roxygen2: do not edit by hand
 % Please edit documentation in R/utils-slope_selector.R
-\name{.filter_slopes}
-\alias{.filter_slopes}
+\name{filter_slopes}
+\alias{filter_slopes}
 \title{Filter dataset based on slope selections and exclusions}
 \usage{
-.filter_slopes(data, slopes, profiles)
+filter_slopes(data, slopes, profiles)
 }
 \arguments{
 \item{data}{Data to filter. Must be \code{PKNCAdata} list, containing the \code{conc} element with
diff --git a/man/run_app.Rd b/man/run_app.Rd
index ac183c0..3fc491b 100644
--- a/man/run_app.Rd
+++ b/man/run_app.Rd
@@ -4,7 +4,10 @@
 \alias{run_app}
 \title{Run the Shiny app}
 \usage{
-run_app()
+run_app(...)
+}
+\arguments{
+\item{...}{Arguments passed to \code{shiny::runApp()}}
 }
 \description{
 List of functions imported for the shiny application.

From bccd3bf12b6839de853c6eb0eef1635d163efa30 Mon Sep 17 00:00:00 2001
From: Pavel Demin <paveldemin@me.com>
Date: Fri, 15 Nov 2024 11:31:04 +0000
Subject: [PATCH 08/11] fix: import reactable.extras

---
 R/run_app.R | 1 +
 1 file changed, 1 insertion(+)

diff --git a/R/run_app.R b/R/run_app.R
index 3f6fddf..c3b5515 100644
--- a/R/run_app.R
+++ b/R/run_app.R
@@ -38,6 +38,7 @@ run_app <- function(...) {
   require("PKNCA")
   require("plotly")
   require("reactable")
+  require("reactable.extras")
   require("rio")
   require("rmarkdown")
   require("shinyBS")

From eac86681fccf691f8da28bb7b241bef492beaae5 Mon Sep 17 00:00:00 2001
From: Pavel Demin <paveldemin@me.com>
Date: Fri, 15 Nov 2024 11:53:02 +0000
Subject: [PATCH 09/11] chore: require all packages listed in the NAMESPACE

---
 R/run_app.R | 38 +++++++++++++-------------------------
 1 file changed, 13 insertions(+), 25 deletions(-)

diff --git a/R/run_app.R b/R/run_app.R
index c3b5515..40dfff3 100644
--- a/R/run_app.R
+++ b/R/run_app.R
@@ -1,50 +1,38 @@
 #' Run the Shiny app
+#' Please do not add import roxygen comments here. This function
+#' should require every namespace that is documented in the NAMESPACE.
 #'
-#' List of functions imported for the shiny application.
-#' When adding new imports, please keep the alphabetical order, at lest for packages.
+#' Apart from the dependencies, this function should also load the package
+#' itself, in case it is run via `aNCA::run_app()`.
 #'
 #' @param ... Arguments passed to `shiny::runApp()`
 #'
-#' @import aNCA
-#' @import shiny
-#' @importFrom dplyr mutate filter select group_by summarise pull arrange ungroup
-#' @importFrom dplyr rename_with across case_when left_join rename
-#' @importFrom DT DTOutput renderDataTable datatable formatStyle styleEqual
-#' @importFrom ggplot2 ggplot geom_errorbar geom_point geom_line labs aes facet_wrap
-#' @importFrom htmlwidgets JS
-#' @importFrom logger log_trace log_debug log_info log_warn log_error log_fatal
-#' @importFrom PKNCA PKNCAconc PKNCAdose PKNCAdata pk.nca PKNCA.options pknca_units_table
-#' @importFrom plotly plotlyOutput renderPlotly plotly_build event_data
-#' @importFrom reactable reactable reactableOutput renderReactable colDef reactableTheme
-#' @importFrom reactable getReactableState
-#' @importFrom reactable.extras text_extra dropdown_extra
-#' @importFrom rio export_list
-#' @importFrom rmarkdown render
-#' @importFrom shinyBS bsModal
-#' @importFrom shinyFiles shinyDirChoose
-#' @importFrom shinyjqui orderInput updateOrderInput
-#' @importFrom shinyWidgets dropdown pickerInput switchInput updatePickerInput
-#' @importFrom tools file_ext
-#' @importFrom utils read.csv write.csv
-#' @importFrom zip zipr
 #' @export
 run_app <- function(...) {
   require("aNCA")
   require("dplyr")
   require("DT")
+  require("forcats")
   require("ggplot2")
+  require("grid")
+  require("haven")
   require("htmlwidgets")
   require("logger")
+  require("nestcolor")
   require("PKNCA")
   require("plotly")
-  require("reactable")
   require("reactable.extras")
+  require("reactable")
   require("rio")
   require("rmarkdown")
+  require("shiny")
   require("shinyBS")
   require("shinyFiles")
   require("shinyjqui")
   require("shinyWidgets")
+  require("stats")
+  require("tern")
+  require("tidyr")
   require("tools")
   require("utils")
   require("zip")

From f6c101512885a7f0637e09e50eaa2022b8de06e8 Mon Sep 17 00:00:00 2001
From: Pavel Demin <paveldemin@me.com>
Date: Fri, 15 Nov 2024 12:10:38 +0000
Subject: [PATCH 10/11] chore: go back to declaring imports

---
 NAMESPACE      |  1 +
 R/run_app.R    | 28 +++++++++++++++++++++++-----
 man/run_app.Rd |  8 +++++---
 3 files changed, 29 insertions(+), 8 deletions(-)

diff --git a/NAMESPACE b/NAMESPACE
index ce38fcc..64daf20 100644
--- a/NAMESPACE
+++ b/NAMESPACE
@@ -74,6 +74,7 @@ importFrom(logger,log_info)
 importFrom(logger,log_trace)
 importFrom(logger,log_warn)
 importFrom(plotly,event_data)
+importFrom(plotly,ggplotly)
 importFrom(plotly,plotlyOutput)
 importFrom(plotly,plotly_build)
 importFrom(plotly,renderPlotly)
diff --git a/R/run_app.R b/R/run_app.R
index 40dfff3..ebc57c4 100644
--- a/R/run_app.R
+++ b/R/run_app.R
@@ -1,12 +1,30 @@
 #' Run the Shiny app
-#' Please do not add import roxygen comments here. This function
-#' should require every namespace that is documented in the NAMESPACE.
-#'
-#' Apart from the dependencies, this function should also load the package
-#' itself, in case it is run via `aNCA::run_app()`.
 #'
 #' @param ... Arguments passed to `shiny::runApp()`
 #'
+#' List of packages imported for the shiny application.
+#' When adding new imports, please keep the alphabetical order, at lest for packages.
+#' @import shiny
+#' @importFrom dplyr mutate filter select group_by summarise pull arrange ungroup
+#' @importFrom dplyr rename_with across case_when left_join rename
+#' @importFrom DT DTOutput renderDataTable datatable formatStyle styleEqual
+#' @importFrom ggplot2 ggplot geom_errorbar geom_point geom_line labs aes facet_wrap
+#' @importFrom htmlwidgets JS
+#' @importFrom PKNCA PKNCAconc PKNCAdose PKNCAdata pk.nca PKNCA.options pknca_units_table
+#' @importFrom plotly plotlyOutput renderPlotly plotly_build event_data ggplotly
+#' @importFrom reactable reactable reactableOutput renderReactable colDef reactableTheme
+#' @importFrom reactable getReactableState
+#' @importFrom reactable.extras text_extra dropdown_extra
+#' @importFrom rio export_list
+#' @importFrom rmarkdown render
+#' @importFrom shinyBS bsModal
+#' @importFrom shinyFiles shinyDirChoose
+#' @importFrom shinyjqui orderInput updateOrderInput
+#' @importFrom shinyWidgets dropdown pickerInput switchInput updatePickerInput
+#' @importFrom tools file_ext
+#' @importFrom utils read.csv write.csv
+#' @importFrom zip zipr
+#'
 #' @export
 run_app <- function(...) {
   require("aNCA")
diff --git a/man/run_app.Rd b/man/run_app.Rd
index 3fc491b..988721b 100644
--- a/man/run_app.Rd
+++ b/man/run_app.Rd
@@ -7,9 +7,11 @@
 run_app(...)
 }
 \arguments{
-\item{...}{Arguments passed to \code{shiny::runApp()}}
+\item{...}{Arguments passed to \code{shiny::runApp()}
+
+List of packages imported for the shiny application.
+When adding new imports, please keep the alphabetical order, at lest for packages.}
 }
 \description{
-List of functions imported for the shiny application.
-When adding new imports, please keep the alphabetical order, at lest for packages.
+Run the Shiny app
 }

From 4e78b01b9a6bb5dc4465081b0c3f159d30c9b35f Mon Sep 17 00:00:00 2001
From: Pavel Demin <paveldemin@me.com>
Date: Fri, 15 Nov 2024 12:25:58 +0000
Subject: [PATCH 11/11] docs: add a comment before require

---
 R/run_app.R | 1 +
 1 file changed, 1 insertion(+)

diff --git a/R/run_app.R b/R/run_app.R
index ebc57c4..aef005c 100644
--- a/R/run_app.R
+++ b/R/run_app.R
@@ -27,6 +27,7 @@
 #'
 #' @export
 run_app <- function(...) {
+  # Load all packages mentioned in the NAMESPACE
   require("aNCA")
   require("dplyr")
   require("DT")