chore: move required packages to imports

Author: averissimo

DESCRIPTION

@@ -31,15 +31,29 @@ Depends:
     teal.transform (>= 0.5.0)
 Imports:
     checkmate (>= 2.1.0),
+    colourpicker,
     dplyr (>= 1.0.5),
     DT (>= 0.13),
     forcats (>= 1.0.0),
+    generics,
+    ggExtra,
+    ggpmisc (>= 0.4.3),
+    ggpp,
+    ggrepel,
+    goftest,
     grid,
+    gridExtra,
+    htmlwidgets,
+    jsonlite,
+    lattice (>= 0.18-4),
+    MASS,
+    rtables (>= 0.6.8),
     scales,
     shinyjs,
     shinyTree (>= 0.2.8),
     shinyvalidate,
     shinyWidgets (>= 0.5.1),
+    sparkline,
     stats,
     stringr (>= 1.4.1),
     teal.code (>= 0.5.0),
@@ -53,28 +67,14 @@ Imports:
     tools,
     utils
 Suggests:
-    broom (>= 0.7.10),
-    colourpicker,
-    ggExtra,
-    ggpmisc (>= 0.4.3),
-    ggpp,
-    ggrepel,
-    goftest,
-    gridExtra,
-    htmlwidgets,
-    jsonlite,
     knitr (>= 1.42),
-    lattice (>= 0.18-4),
     logger (>= 0.2.0),
-    MASS,
     nestcolor (>= 0.1.0),
     pkgload,
     rlang (>= 1.0.0),
     rmarkdown (>= 2.23),
-    rtables (>= 0.6.8),
     rvest,
     shinytest2,
-    sparkline,
     testthat (>= 3.1.9),
     withr (>= 2.0.0)
 VignetteBuilder:
@@ -88,10 +88,9 @@ Config/Needs/verdepcheck: haleyjeppson/ggmosaic, tidyverse/ggplot2,
     insightsengineering/teal.data, insightsengineering/teal.logger,
     insightsengineering/teal.reporter, insightsengineering/teal.widgets,
     insightsengineering/tern, tidyverse/tibble, tidyverse/tidyr,
-    tidymodels/broom, daattali/colourpicker, daattali/ggExtra,
-    aphalo/ggpmisc, aphalo/ggpp, slowkow/ggrepel, baddstats/goftest,
-    gridExtra, ramnathv/htmlwidgets, jeroen/jsonlite, yihui/knitr,
-    daroczig/logger, deepayan/lattice, MASS,
+    daattali/colourpicker, daattali/ggExtra, aphalo/ggpmisc, aphalo/ggpp,
+    slowkow/ggrepel, baddstats/goftest, gridExtra, ramnathv/htmlwidgets,
+    jeroen/jsonlite, yihui/knitr, daroczig/logger, deepayan/lattice, MASS,
     insightsengineering/nestcolor, r-lib/rlang, rstudio/rmarkdown,
     insightsengineering/rtables, tidyverse/rvest, sparkline,
     rstudio/shinytest2, r-lib/testthat, r-lib/withr

R/tm_g_distribution.R

@@ -121,16 +121,6 @@ tm_g_distribution <- function(label = "Distribution Module",
                               post_output = NULL) {
   message("Initializing tm_g_distribution")
 
-  # Requires Suggested packages
-  extra_packages <- c("ggpmisc", "ggpp", "goftest", "MASS", "broom")
-  missing_packages <- Filter(function(x) !requireNamespace(x, quietly = TRUE), extra_packages)
-  if (length(missing_packages) > 0L) {
-    stop(sprintf(
-      "Cannot load package(s): %s.\nInstall or restart your session.",
-      toString(missing_packages)
-    ))
-  }
-
   # Normalize the parameters
   if (inherits(dist_var, "data_extract_spec")) dist_var <- list(dist_var)
   if (inherits(strata_var, "data_extract_spec")) strata_var <- list(strata_var)
@@ -1176,7 +1166,7 @@ srv_distribution <- function(id,
               expr = {
                 test_stats <- ANL %>%
                   dplyr::select(dist_var) %>%
-                  with(., broom::glance(do.call(test, args))) %>%
+                  with(., generics::glance(do.call(test, args))) %>%
                   dplyr::mutate_if(is.numeric, round, 3)
               },
               env = env
@@ -1190,7 +1180,7 @@ srv_distribution <- function(id,
                 test_stats <- ANL %>%
                   dplyr::select(dist_var, s_var, g_var) %>%
                   dplyr::group_by_at(dplyr::vars(dplyr::any_of(groups))) %>%
-                  dplyr::do(tests = broom::glance(do.call(test, args))) %>%
+                  dplyr::do(tests = generics::glance(do.call(test, args))) %>%
                   tidyr::unnest(tests) %>%
                   dplyr::mutate_if(is.numeric, round, 3)
               },

R/tm_g_scatterplot.R

@@ -229,16 +229,6 @@ tm_g_scatterplot <- function(label = "Scatterplot",
                              ggplot2_args = teal.widgets::ggplot2_args()) {
   message("Initializing tm_g_scatterplot")
 
-  # Requires Suggested packages
-  extra_packages <- c("ggpmisc", "ggExtra", "colourpicker")
-  missing_packages <- Filter(function(x) !requireNamespace(x, quietly = TRUE), extra_packages)
-  if (length(missing_packages) > 0L) {
-    stop(sprintf(
-      "Cannot load package(s): %s.\nInstall or restart your session.",
-      toString(missing_packages)
-    ))
-  }
-
   # Normalize the parameters
   if (inherits(x, "data_extract_spec")) x <- list(x)
   if (inherits(y, "data_extract_spec")) y <- list(y)

R/tm_g_scatterplotmatrix.R

@@ -164,11 +164,6 @@ tm_g_scatterplotmatrix <- function(label = "Scatterplot Matrix",
                                    post_output = NULL) {
   message("Initializing tm_g_scatterplotmatrix")
 
-  # Requires Suggested packages
-  if (!requireNamespace("lattice", quietly = TRUE)) {
-    stop("Cannot load lattice - please install the package or restart your session.")
-  }
-
   # Normalize the parameters
   if (inherits(variables, "data_extract_spec")) variables <- list(variables)
 

R/tm_missing_data.R

@@ -91,14 +91,6 @@ tm_missing_data <- function(label = "Missing data",
                             post_output = NULL) {
   message("Initializing tm_missing_data")
 
-  # Requires Suggested packages
-  if (!requireNamespace("gridExtra", quietly = TRUE)) {
-    stop("Cannot load gridExtra - please install the package or restart your session.")
-  }
-  if (!requireNamespace("rlang", quietly = TRUE)) {
-    stop("Cannot load rlang - please install the package or restart your session.")
-  }
-
   # Normalize the parameters
   if (inherits(ggplot2_args, "ggplot2_args")) ggplot2_args <- list(default = ggplot2_args)
 
@@ -1135,6 +1127,13 @@ srv_missing_data <- function(id, data, reporter, filter_panel_api, dataname, par
         ggtheme = input$ggtheme
       )
 
+      # Unlikely that `rlang` is not available, new hashing may be expensive
+      hashing_function <- if (requireNamespace("rlang", quietly = TRUE)) {
+        quote(rlang::hash)
+      } else {
+        function(x) paste(as.integer(x), collapse = "")
+      }
+
       teal.code::eval_code(
         common_code_q(),
         substitute(
@@ -1149,41 +1148,44 @@ srv_missing_data <- function(id, data, reporter, filter_panel_api, dataname, par
           )
         ) %>%
         teal.code::eval_code(
-          quote({
-            summary_plot_patients <- ANL[, c(parent_keys, analysis_vars)] %>%
-              dplyr::group_by_at(parent_keys) %>%
-              dplyr::mutate(id = dplyr::cur_group_id()) %>%
-              dplyr::ungroup() %>%
-              dplyr::group_by_at(c(parent_keys, "id")) %>%
-              dplyr::summarise_all(anyNA) %>%
-              dplyr::ungroup()
-
-            # order subjects by decreasing number of missing and then by
-            # missingness pattern (defined using sha1)
-            order_subjects <- summary_plot_patients %>%
-              dplyr::select(-"id", -dplyr::all_of(parent_keys)) %>%
-              dplyr::transmute(
-                id = dplyr::row_number(),
-                number_NA = apply(., 1, sum),
-                sha = apply(., 1, rlang::hash)
-              ) %>%
-              dplyr::arrange(dplyr::desc(number_NA), sha) %>%
-              getElement(name = "id")
-
-            # order columns by decreasing percent of missing values
-            ordered_columns <- summary_plot_patients %>%
-              dplyr::select(-"id", -dplyr::all_of(parent_keys)) %>%
-              dplyr::summarise(
-                column = create_cols_labels(colnames(.)),
-                na_count = apply(., MARGIN = 2, FUN = sum),
-                na_percent = na_count / nrow(.) * 100
-              ) %>%
-              dplyr::arrange(na_percent, dplyr::desc(column))
-
-            summary_plot_patients <- summary_plot_patients %>%
-              tidyr::gather("col", "isna", -"id", -dplyr::all_of(parent_keys)) %>%
-              dplyr::mutate(col = create_cols_labels(col))
-          })
+          substitute(
+            expr = {
+              summary_plot_patients <- ANL[, c(parent_keys, analysis_vars)] %>%
+                dplyr::group_by_at(parent_keys) %>%
+                dplyr::mutate(id = dplyr::cur_group_id()) %>%
+                dplyr::ungroup() %>%
+                dplyr::group_by_at(c(parent_keys, "id")) %>%
+                dplyr::summarise_all(anyNA) %>%
+                dplyr::ungroup()
+
+              # order subjects by decreasing number of missing and then by
+              # missingness pattern (defined using sha1)
+              order_subjects <- summary_plot_patients %>%
+                dplyr::select(-"id", -dplyr::all_of(parent_keys)) %>%
+                dplyr::transmute(
+                  id = dplyr::row_number(),
+                  number_NA = apply(., 1, sum),
+                  sha = apply(., 1, hashing_function)
+                ) %>%
+                dplyr::arrange(dplyr::desc(number_NA), sha) %>%
+                getElement(name = "id")
+
+              # order columns by decreasing percent of missing values
+              ordered_columns <- summary_plot_patients %>%
+                dplyr::select(-"id", -dplyr::all_of(parent_keys)) %>%
+                dplyr::summarise(
+                  column = create_cols_labels(colnames(.)),
+                  na_count = apply(., MARGIN = 2, FUN = sum),
+                  na_percent = na_count / nrow(.) * 100
+                ) %>%
+                dplyr::arrange(na_percent, dplyr::desc(column))
+
+              summary_plot_patients <- summary_plot_patients %>%
+                tidyr::gather("col", "isna", -"id", -dplyr::all_of(parent_keys)) %>%
+                dplyr::mutate(col = create_cols_labels(col))
+            },
+            env = list(hashing_function = hashing_function)
+          )
         ) %>%
         teal.code::eval_code(
           substitute(

R/tm_t_crosstable.R

@@ -140,11 +140,6 @@ tm_t_crosstable <- function(label = "Cross Table",
                             basic_table_args = teal.widgets::basic_table_args()) {
   message("Initializing tm_t_crosstable")
 
-  # Requires Suggested packages
-  if (!requireNamespace("rtables", quietly = TRUE)) {
-    stop("Cannot load rtables - please install the package or restart your session.")
-  }
-
   # Normalize the parameters
   if (inherits(x, "data_extract_spec")) x <- list(x)
   if (inherits(y, "data_extract_spec")) y <- list(y)

R/tm_variable_browser.R

@@ -78,17 +78,6 @@ tm_variable_browser <- function(label = "Variable Browser",
                                 ggplot2_args = teal.widgets::ggplot2_args()) {
   message("Initializing tm_variable_browser")
 
-  # Requires Suggested packages
-  if (!requireNamespace("sparkline", quietly = TRUE)) {
-    stop("Cannot load sparkline - please install the package or restart your session.")
-  }
-  if (!requireNamespace("htmlwidgets", quietly = TRUE)) {
-    stop("Cannot load htmlwidgets - please install the package or restart your session.")
-  }
-  if (!requireNamespace("jsonlite", quietly = TRUE)) {
-    stop("Cannot load jsonlite - please install the package or restart your session.")
-  }
-
   # Start of assertions
   checkmate::assert_string(label)
   checkmate::assert_character(datasets_selected)
@@ -1280,7 +1269,6 @@ create_sparklines.default <- function(arr, width = 150, ...) {
   as.character(tags$code("unsupported variable type", class = "text-blue"))
 }
 
-
 custom_sparkline_formatter <- function(labels, counts) {
   htmlwidgets::JS(
     sprintf(