Address styler complaints.

Boehringer-Ingelheim · Jul 21, 2024 · 7e3c45f · 7e3c45f
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Showing 8 changed files with 104 additions and 98 deletions.
diff --git a/R/check_papo_call_manual.R b/R/check_papo_call_manual.R
@@ -1,4 +1,4 @@
-# nolint start object_usage_linter
+# nolint start object_usage_linter # styler: off
 
 # TODO: Generate from mod_patient_profile_API
 # This function has been written manually, but mod_patient_profile_API carries

diff --git a/R/create_plots.R b/R/create_plots.R
@@ -29,57 +29,62 @@ create_ae_cm_plot <- function(data, x_limits, palette, sl_info, vline_vars, vlin
 
   p <- ggplot2::ggplot(data, ggplot2::aes(x = .data[["start_day_z"]], y = .data[["decode"]]))
   p <- p + ggplot2::theme_bw()
-  p <- p + ggplot2::geom_rect(ggplot2::aes(
-    xmin = .data[["start_day_z"]],
-    xmax = .data[["end_day_z"]],
-    ymin = .data[["decode"]],
-    ymax = .data[["decode"]],
-    color = grading
-  ),
-  size = 3
+  p <- p + ggplot2::geom_rect(
+    ggplot2::aes(
+      xmin = .data[["start_day_z"]],
+      xmax = .data[["end_day_z"]],
+      ymin = .data[["decode"]],
+      ymax = .data[["decode"]],
+      color = grading
+    ),
+    size = 3
   )
 
   if ("serious_ae" %in% names(data)) {
     sae_labels <- ifelse(data[["serious_ae"]], "SAE", "")
-    p <- p + ggplot2::geom_text(ggplot2::aes(
-      x = .data[["start_day_z"]],
-      y = .data[["decode"]],
-      label = sae_labels
-    ),
-    colour = "red", nudge_y = 0.25, nudge_x = 1, size = 3
+    p <- p + ggplot2::geom_text(
+      ggplot2::aes(
+        x = .data[["start_day_z"]],
+        y = .data[["decode"]],
+        label = sae_labels
+      ),
+      colour = "red", nudge_y = 0.25, nudge_x = 1, size = 3
     )
   }
 
   # hack to allow hover info at the beginning of the range through transparent dots
-  p <- p + ggplot2::geom_point(ggplot2::aes(
-    x = .data[["start_day_z"]],
-    y = .data[["decode"]],
-    color = grading
-  ),
-  size = 5, alpha = 0, show.legend = FALSE
+  p <- p + ggplot2::geom_point(
+    ggplot2::aes(
+      x = .data[["start_day_z"]],
+      y = .data[["decode"]],
+      color = grading
+    ),
+    size = 5, alpha = 0, show.legend = FALSE
   )
   p <- p + ggplot2::scale_colour_manual(name = "Legend", values = palette)
   p <- p + ggplot2::scale_fill_manual(name = "Legend", values = palette)
 
   if (any(!is.na(data[["arrow_left"]]))) {
-    p <- p + ggplot2::geom_text(ggplot2::aes(
-      x = .data[["arrow_left_z"]] - .5,
-      y = .data[["decode"]],
-      label = sprintf("\u2190"),
-      color = grading
-    ),
-    size = 10, show.legend = FALSE
+    p <- p + ggplot2::geom_text(
+      ggplot2::aes(
+        x = .data[["arrow_left_z"]] - .5,
+        y = .data[["decode"]],
+        label = sprintf("\u2190"),
+        color = grading
+      ),
+      size = 10, show.legend = FALSE
     )
   }
 
   if (any(!is.na(data[["arrow_right"]]))) {
-    p <- p + ggplot2::geom_text(ggplot2::aes(
-      x = .data[["arrow_right_z"]] + .7,
-      y = .data[["decode"]],
-      label = sprintf("\u2192"),
-      color = grading
-    ),
-    size = 10, show.legend = FALSE
+    p <- p + ggplot2::geom_text(
+      ggplot2::aes(
+        x = .data[["arrow_right_z"]] + .7,
+        y = .data[["decode"]],
+        label = sprintf("\u2192"),
+        color = grading
+      ),
+      size = 10, show.legend = FALSE
     )
   }
 
@@ -158,12 +163,13 @@ create_lb_vs_plot <- function(data, date, val, low_limit, high_limit, param, sum
     plot <- plot + ggplot2::geom_line(ggplot2::aes(linetype = .data[[param]]), size = 0.1)
   } else {
     summary_stats_label <- attr(data[[summary_stats]], "label")
-    plot <- plot + ggplot2::geom_line(ggplot2::aes(
-      x = .data[["date_z"]],
-      y = .data[[summary_stats]],
-      linetype = summary_stats_label
-    ),
-    size = 0.1
+    plot <- plot + ggplot2::geom_line(
+      ggplot2::aes(
+        x = .data[["date_z"]],
+        y = .data[[summary_stats]],
+        linetype = summary_stats_label
+      ),
+      size = 0.1
     )
   }
 

diff --git a/R/dressing_room.R b/R/dressing_room.R
@@ -54,7 +54,7 @@ T_is_of_kind <- function(var, type) {
     res <- (is.integer(var) || (is.numeric(var) && all(var[is.finite(var)] %% 1 == 0))) && all(var[is.finite(var)] != 0)
   } else if (type[["kind"]] == "YN") {
     res <- ((is.character(var) && setequal(unique(var), c("Y", "N"))) ||
-              is.factor(var) && setequal(levels(var), c("Y", "N")))
+      is.factor(var) && setequal(levels(var), c("Y", "N")))
   } else {
     browser()
   }
@@ -405,8 +405,10 @@ explorer_ui <- function() {
       shiny::div(
         class = "col-sm-3",
         panel(
-          shiny::h4("DaVinci's Module Dressing Room", align = "center",
-                    style = "margin-top:0; margin-bottom:2rem; font-weight:bold"),
+          shiny::h4("DaVinci's Module Dressing Room",
+            align = "center",
+            style = "margin-top:0; margin-bottom:2rem; font-weight:bold"
+          ),
           inline_shiny_input(
             shiny::selectInput(
               inputId = "spec", label = NULL,

diff --git a/R/mod_patient_info.R b/R/mod_patient_info.R
@@ -26,7 +26,6 @@ patient_info_server <- function(id, record, subjid_var, column_count = 3) {
   shiny::moduleServer(
     id,
     function(input, output, session) {
-
       # parts in ui_out
       output$ui_out <- shiny::renderUI({
         shiny::req(nrow(record()) == 1 && ncol(record()) > 0)

diff --git a/R/prep_safety_data.R b/R/prep_safety_data.R
@@ -18,7 +18,7 @@ prep_safety_data <- function(n = 200) {
   }
 
   adsl_info <- safetyData::adam_adsl[1:n, ]
-  adsl_info[["TRTSDT"]] <- robust_ymd(adsl_info[["TRTSDT"]]) |>  structure(label = "Treatment Start Date")
+  adsl_info[["TRTSDT"]] <- robust_ymd(adsl_info[["TRTSDT"]]) |> structure(label = "Treatment Start Date")
   adsl_info[["TRTEDT"]] <- robust_ymd(adsl_info[["TRTEDT"]], round_up = TRUE) |> structure(label = "Treatment End Date")
   adsl_info[["RFICDT"]] <- robust_ymd(adsl_info[["RFSTDTC"]]) |> structure(label = "Informed Consent Date")
   adsl_info[["TRTDUR"]] <- as.numeric(adsl_info[["TRTDUR"]]) |> structure(label = "Treatment duration (days)")
@@ -44,18 +44,18 @@ prep_safety_data <- function(n = 200) {
   # vs
   vs_info <- safetyData::adam_advs |>
     dplyr::left_join(safetyData::adam_advs |>
-                       dplyr::group_by(.data[["USUBJID"]], .data[["PARAM"]], .data[["VISIT"]]) |>
-                       dplyr::summarise(AVAL_MEAN = mean(as.numeric(.data$AVAL)), .groups = "drop") |>
-                       dplyr::ungroup(), by = c("USUBJID", "PARAM", "VISIT"))
+      dplyr::group_by(.data[["USUBJID"]], .data[["PARAM"]], .data[["VISIT"]]) |>
+      dplyr::summarise(AVAL_MEAN = mean(as.numeric(.data$AVAL)), .groups = "drop") |>
+      dplyr::ungroup(), by = c("USUBJID", "PARAM", "VISIT"))
   attr(vs_info[["AVAL_MEAN"]], "label") <- "Mean Value"
 
 
   # lb
   lb_info <- safetyData::adam_adlbc |>
     dplyr::left_join(safetyData::adam_adlbc |>
-                       dplyr::group_by(.data[["USUBJID"]], .data[["PARAM"]], .data[["VISIT"]]) |>
-                       dplyr::summarise(AVAL_MEAN = mean(as.numeric(.data$AVAL)), .groups = "drop") |>
-                       dplyr::ungroup(), by = c("USUBJID", "PARAM", "VISIT")) |>
+      dplyr::group_by(.data[["USUBJID"]], .data[["PARAM"]], .data[["VISIT"]]) |>
+      dplyr::summarise(AVAL_MEAN = mean(as.numeric(.data$AVAL)), .groups = "drop") |>
+      dplyr::ungroup(), by = c("USUBJID", "PARAM", "VISIT")) |>
     dplyr::filter(
       .data$USUBJID %in% adsl_info$USUBJID
     )

diff --git a/README.Rmd b/README.Rmd
@@ -10,7 +10,7 @@ output:
 knitr::opts_chunk$set(
   collapse = TRUE,
   comment = "#>",
-  out.width = "100%", 
+  out.width = "100%",
   tidy = "styler"
 )
 ```
@@ -42,50 +42,50 @@ To use `dv.papo` inside a DaVinci app, add the module to your module list. The c
 See `vignette("a00-papo")` for further information on how to use `dv.papo` with `dv.manager`.
 
 ```{r example, eval = FALSE}
-  dataset_list <- list(
-    "demo" = dv.papo:::prep_safety_data(5),
-    "demo2" = dv.papo:::prep_safety_data(10)
-  )
+dataset_list <- list(
+  "demo" = dv.papo:::prep_safety_data(5),
+  "demo2" = dv.papo:::prep_safety_data(10)
+)
 
-  module_list <- list(
-    "Patient Profile" = dv.papo::mod_patient_profile(
-       module_id = "papo",
-       subject_level_dataset_name = "adsl",
-       subjid_var = "USUBJID",
-       summary = list(
-         vars = c("SUBJID", "SITEID", "ARM", "TRTSDT", "TRTEDT", "AGE", "RACE", "SEX", "BMIBL"),
-         column_count = 3L
-       ),
-       listings = list(
-         "Concomitant Medication" = list(
-           dataset = "cm"
-         ),
-         "Adverse Events" = list(
-           dataset = "adae",
-           default_vars = c("ASTDT", "ASTDY", "AENDT", "AENDY", "AEDECOD", "AESEV")
-         )
-       ),
-       plots = list(
-         timeline_info = c(trt_start_date = "TRTSDT", trt_end_date = "TRTEDT"),
-         range_plots = list(
-           "Adverse Events" = list(
-             dataset = "adae",
-             vars = c(
-               start_date = "ASTDT", end_date = "AENDT",
-               decode = "AEDECOD", grading = "AESEV", serious_ae = "AESER"
-             ),
-             tooltip = c("AE Start Day: " = "ASTDY", "AE End Day: " = "AENDY")
-           )
-         ),
-         value_plots = list(),
-         vline_vars = c("Informed Consent Date" = "RFICDT")
-       )
+module_list <- list(
+  "Patient Profile" = dv.papo::mod_patient_profile(
+    module_id = "papo",
+    subject_level_dataset_name = "adsl",
+    subjid_var = "USUBJID",
+    summary = list(
+      vars = c("SUBJID", "SITEID", "ARM", "TRTSDT", "TRTEDT", "AGE", "RACE", "SEX", "BMIBL"),
+      column_count = 3L
+    ),
+    listings = list(
+      "Concomitant Medication" = list(
+        dataset = "cm"
+      ),
+      "Adverse Events" = list(
+        dataset = "adae",
+        default_vars = c("ASTDT", "ASTDY", "AENDT", "AENDY", "AEDECOD", "AESEV")
+      )
+    ),
+    plots = list(
+      timeline_info = c(trt_start_date = "TRTSDT", trt_end_date = "TRTEDT"),
+      range_plots = list(
+        "Adverse Events" = list(
+          dataset = "adae",
+          vars = c(
+            start_date = "ASTDT", end_date = "AENDT",
+            decode = "AEDECOD", grading = "AESEV", serious_ae = "AESER"
+          ),
+          tooltip = c("AE Start Day: " = "ASTDY", "AE End Day: " = "AENDY")
+        )
+      ),
+      value_plots = list(),
+      vline_vars = c("Informed Consent Date" = "RFICDT")
     )
   )
-  
-  dv.manager::run_app(
-    data = dataset_list,
-    module_list = module_list,
-    filter_data = "adsl"
-  )
+)
+
+dv.manager::run_app(
+  data = dataset_list,
+  module_list = module_list,
+  filter_data = "adsl"
+)
 ```
diff --git a/tests/testthat/apps/root/app.R b/tests/testthat/apps/root/app.R
@@ -1,4 +1,3 @@
-
 # TODO(miguel): Avoid having to install the package when testing locally by following
 # dv.biomarker.general/browse/tests/testthat/app/app.R?at=dev # nolint (false positive for commented_code_linter)
 # to run the current version of the code

diff --git a/vignettes/a02-communication.Rmd b/vignettes/a02-communication.Rmd
@@ -38,7 +38,7 @@ module_list <- list(
     module_id = "mod2",
     ..., # ommitted for brevity
     receiver_id = "mod1"
-  ) 
+  )
 )
 ```
-Original file line number
+Diff line change
@@ Expand Up / @@ -38,7 +38,7 @@ module_list <- list( @@
         module_id = "mod2",
         ..., # ommitted for brevity
         receiver_id = "mod1"
-      )
+      )
     )
     ```
@@ Expand Down @@