#82 style files

jeffreyad · jeffreyad · commit 0767743604c3 · 2025-08-07T23:06:46.000Z
diff --git a/adam/adae.R b/adam/adae.R
@@ -159,4 +159,3 @@ adae %>%
   xportr_label(metacore) %>% # Assigns variable label from metacore specifications
   xportr_df_label(metacore) %>% # Assigns dataset label from metacore specifications
   xportr_write(file.path(dir, "adae.xpt"), metadata = metacore, domain = "ADAE")
-
diff --git a/adam/adpc.R b/adam/adpc.R
@@ -463,4 +463,3 @@ adpc_xpt <- adpc %>%
   xportr_format(metacore) %>% # Assigns variable format from metacore specifications
   xportr_df_label(metacore) %>% # Assigns dataset label from metacore specifications
   xportr_write(file.path(dir, "adpc.xpt")) # Write xpt v5 transport file
-
diff --git a/adam/adppk.R b/adam/adppk.R
@@ -433,4 +433,3 @@ adppk_xpt <- adppk %>%
   xportr_format(metacore) %>% # Assigns variable format from metacore specifications
   xportr_df_label(metacore) %>% # Assigns dataset label from metacore specifications
   xportr_write(file.path(dir, "adppk.xpt")) # Write xpt v5 transport file
-
diff --git a/adam/adrs.R b/adam/adrs.R
@@ -168,4 +168,3 @@ adrs_xpt <- adrs_checked %>%
   xportr_format(metacore) %>% # Assign variable formats from metadata
   xportr_df_label(metacore) %>% # Assign dataset labels from metadata
   xportr_write(file.path(dir, "adrs.xpt")) # Write the XPT file
-
diff --git a/adam/adsl.R b/adam/adsl.R
@@ -327,4 +327,3 @@ adsl %>%
   xportr_label(metacore) %>% # Assigns variable label from metacore specifications
   xportr_df_label(metacore) %>% # Assigns dataset label from metacore specifications
   xportr_write(file.path(dir, "adsl.xpt"), metadata = metacore, domain = "ADSL")
-
diff --git a/adam/adtte.R b/adam/adtte.R
@@ -145,4 +145,3 @@ adtte_final <- adtte_adsl_checked %>%
 # Write dataset to XPT file (optional)
 dir <- tempdir()
 xportr_write(adtte_final, file.path(dir, "adtte.xpt"))
-
diff --git a/adam/advs.R b/adam/advs.R
@@ -337,4 +337,3 @@ advs_final <- advs_prefinal %>%
   xportr_format(metacore, domain = "ADVS") %>%
   xportr_df_label(metacore, domain = "ADVS") %>%
   xportr_write(file.path(dir, "advs.xpt"), metadata = metacore, domain = "ADVS")
-
diff --git a/functions/print_df.R b/functions/print_df.R
@@ -3,7 +3,7 @@ library(reactablefmtr)
 
 print_df <- function(dataset, n = 10) {
   out <- dataset
-  
+
   reactable(
     head(out, n),
     compact = TRUE,
@@ -20,7 +20,8 @@ print_df <- function(dataset, n = 10) {
       highlightColor = "#dfe6f2",
       cellPadding = "8px"
     )
-  ) %>% 
+  ) %>%
     add_title("Sample of Data",
-              font_size = 16)
+      font_size = 16
+    )
 }
diff --git a/logging/index.qmd b/logging/index.qmd
@@ -1,3 +1,3 @@
 ---
 title: "Logs"
----
+---
diff --git a/logging/logging.qmd b/logging/logging.qmd
@@ -633,8 +633,10 @@ and more details see the
 
 To utilize this feature, begin by creating a list of approved functions:
 ```{r}
-approved_pkgs <- list(base = "mean",
-                      dplyr = "All")
+approved_pkgs <- list(
+  base = "mean",
+  dplyr = "All"
+)
 ```
 
 Next, build the `approved_pkgs` list and save its contents to a file:
diff --git a/logging/script.R b/logging/script.R
@@ -11,4 +11,4 @@ average_mpg <- mtcars %>%
 model <- lm(mpg ~ wt, data = mtcars)
 summary(model)
 
-# log file path: script.log
+# log file path: script.log
diff --git a/sdtm/index.qmd b/sdtm/index.qmd
@@ -1,3 +1,3 @@
 ---
 title: "SDTM"
----
+---
diff --git a/tests/spelling.R b/tests/spelling.R
@@ -1,3 +1,6 @@
-if(requireNamespace('spelling', quietly = TRUE))
-  spelling::spell_check_test(vignettes = TRUE, error = FALSE,
-                             skip_on_cran = TRUE)
+if (requireNamespace("spelling", quietly = TRUE)) {
+  spelling::spell_check_test(
+    vignettes = TRUE, error = FALSE,
+    skip_on_cran = TRUE
+  )
+}
diff --git a/tlg/adverse_events.R b/tlg/adverse_events.R
@@ -57,4 +57,3 @@ lyt <- basic_table(show_colcounts = TRUE) %>%
 result <- build_table(lyt, df = adae, alt_counts_df = adsl)
 
 result
-
diff --git a/tlg/adverse_events.qmd b/tlg/adverse_events.qmd
@@ -5,7 +5,10 @@ order: 2
 
 
 ```{r setup script, include=FALSE, purl=FALSE}
-invisible_hook_purl <- function(before, options, ...) {knitr::hook_purl(before, options, ...); NULL}
+invisible_hook_purl <- function(before, options, ...) {
+  knitr::hook_purl(before, options, ...)
+  NULL
+}
 knitr::knit_hooks$set(purl = invisible_hook_purl)
 ```
 
diff --git a/tlg/demographic.R b/tlg/demographic.R
@@ -12,12 +12,14 @@ adsl <- pharmaverseadam::adsl |>
         between(AGE, 41, 64) ~ "41-64",
         AGE > 64 ~ ">=65"
       ) |>
-      factor(levels = c("18-40", "41-64", ">=65"))
-  ) |> 
-  labelled::set_variable_labels(AGE = "Age (yr)",
-                                AGEGR1 = "Age group",
-                                SEX = "Sex",
-                                RACE = "Race")
+        factor(levels = c("18-40", "41-64", ">=65"))
+  ) |>
+  labelled::set_variable_labels(
+    AGE = "Age (yr)",
+    AGEGR1 = "Age group",
+    SEX = "Sex",
+    RACE = "Race"
+  )
 
 ## ----r gtsummary-table--------------------------------------------------------
 library(cards)
@@ -27,22 +29,22 @@ theme_gtsummary_compact() # reduce default padding and font size for a gt table
 # build the ARD with the needed summary statistics using {cards}
 ard <-
   ard_stack(
-    adsl, 
+    adsl,
     ard_continuous(variables = AGE),
     ard_categorical(variables = c(AGEGR1, SEX, RACE)),
-    .by = ACTARM,      # split results by treatment arm
+    .by = ACTARM, # split results by treatment arm
     .attributes = TRUE # optionally include column labels in the ARD
   )
 
 # use the ARD to create a demographics table using {gtsummary}
 tbl_ard_summary(
-  cards = ard, 
-  by = ACTARM, 
+  cards = ard,
+  by = ACTARM,
   include = c(AGE, AGEGR1, SEX, RACE),
   type = AGE ~ "continuous2",
   statistic = AGE ~ c("{N}", "{mean} ({sd})", "{median} ({p25}, {p75})", "{min}, {max}")
-) |> 
-  bold_labels() |> 
+) |>
+  bold_labels() |>
   modify_header(all_stat_cols() ~ "**{level}**  \nN = {n}") |> # add Ns to header
   modify_footnote(everything() ~ NA) # remove default footnote
 
@@ -56,7 +58,7 @@ gather_ard(tbl)[[1]] |> select(-gts_column) # removing column so ARD fits on pag
 ## ----r rtables-setup, message=FALSE, warning=FALSE, results='hold'------------
 library(tern)
 
-adsl2 <- adsl |> 
+adsl2 <- adsl |>
   df_explicit_na()
 
 ## ----r rtables-table----------------------------------------------------------
@@ -68,9 +70,9 @@ var_labels <- c(
   "Race"
 )
 
-lyt <- basic_table(show_colcounts = TRUE) |> 
-  split_cols_by(var = "ACTARM") |> 
-  add_overall_col("All Patients") |> 
+lyt <- basic_table(show_colcounts = TRUE) |>
+  split_cols_by(var = "ACTARM") |>
+  add_overall_col("All Patients") |>
   analyze_vars(
     vars = vars,
     var_labels = var_labels
@@ -79,4 +81,3 @@ lyt <- basic_table(show_colcounts = TRUE) |>
 result <- build_table(lyt, adsl2)
 
 result
-
diff --git a/tlg/demographic.qmd b/tlg/demographic.qmd
@@ -4,7 +4,10 @@ order: 1
 ---
 
 ```{r setup script, include=FALSE, purl=FALSE}
-invisible_hook_purl <- function(before, options, ...) {knitr::hook_purl(before, options, ...); NULL}
+invisible_hook_purl <- function(before, options, ...) {
+  knitr::hook_purl(before, options, ...)
+  NULL
+}
 knitr::knit_hooks$set(purl = invisible_hook_purl)
 knitr::opts_chunk$set(echo = TRUE)
 ```
@@ -36,12 +39,14 @@ adsl <- pharmaverseadam::adsl |>
         between(AGE, 41, 64) ~ "41-64",
         AGE > 64 ~ ">=65"
       ) |>
-      factor(levels = c("18-40", "41-64", ">=65"))
-  ) |> 
-  labelled::set_variable_labels(AGE = "Age (yr)",
-                                AGEGR1 = "Age group",
-                                SEX = "Sex",
-                                RACE = "Race")
+        factor(levels = c("18-40", "41-64", ">=65"))
+  ) |>
+  labelled::set_variable_labels(
+    AGE = "Age (yr)",
+    AGEGR1 = "Age group",
+    SEX = "Sex",
+    RACE = "Race"
+  )
 ```
 
 ## {gtsummary} & {cards}
@@ -65,22 +70,22 @@ theme_gtsummary_compact() # reduce default padding and font size for a gt table
 # build the ARD with the needed summary statistics using {cards}
 ard <-
   ard_stack(
-    adsl, 
+    adsl,
     ard_continuous(variables = AGE),
     ard_categorical(variables = c(AGEGR1, SEX, RACE)),
-    .by = ACTARM,      # split results by treatment arm
+    .by = ACTARM, # split results by treatment arm
     .attributes = TRUE # optionally include column labels in the ARD
   )
 
 # use the ARD to create a demographics table using {gtsummary}
 tbl_ard_summary(
-  cards = ard, 
-  by = ACTARM, 
+  cards = ard,
+  by = ACTARM,
   include = c(AGE, AGEGR1, SEX, RACE),
   type = AGE ~ "continuous2",
   statistic = AGE ~ c("{N}", "{mean} ({sd})", "{median} ({p25}, {p75})", "{min}, {max}")
-) |> 
-  bold_labels() |> 
+) |>
+  bold_labels() |>
   modify_header(all_stat_cols() ~ "**{level}**  \nN = {n}") |> # add Ns to header
   modify_footnote(everything() ~ NA) # remove default footnote
 ```
@@ -111,7 +116,7 @@ Note that `{tern}` depends on `{rtables}` so the latter is automatically attache
 ```{r rtables-setup, message=FALSE, warning=FALSE, results='hold'}
 library(tern)
 
-adsl2 <- adsl |> 
+adsl2 <- adsl |>
   df_explicit_na()
 ```
 
@@ -126,9 +131,9 @@ var_labels <- c(
   "Race"
 )
 
-lyt <- basic_table(show_colcounts = TRUE) |> 
-  split_cols_by(var = "ACTARM") |> 
-  add_overall_col("All Patients") |> 
+lyt <- basic_table(show_colcounts = TRUE) |>
+  split_cols_by(var = "ACTARM") |>
+  add_overall_col("All Patients") |>
   analyze_vars(
     vars = vars,
     var_labels = var_labels
diff --git a/tlg/index.qmd b/tlg/index.qmd
@@ -1,3 +1,3 @@
 ---
 title: "TLG"
----
+---
diff --git a/tlg/pharmacokinetic.R b/tlg/pharmacokinetic.R
@@ -168,4 +168,3 @@ lsting <- as_listing(
 )
 
 head(lsting, 28)
-
diff --git a/tlg/pharmacokinetic.qmd b/tlg/pharmacokinetic.qmd
@@ -54,7 +54,6 @@ adpc <- adpc %>%
 # Remove DTYPE = COPY records with ANL02FL == "Y"
 adpc <- adpc %>%
   filter(PARAMCD != "DOSE" & TRT01A != "Placebo" & PARCAT1 == "PLASMA" & ANL02FL == "Y")
-
 ```
 
 ## PK Table
@@ -135,7 +134,6 @@ result
 Now we create the PK graph.
 
 ```{r graph}
-
 # Keep only treated subjects for graph
 adsl_f <- adsl %>%
   filter(SAFFL == "Y" & TRT01A != "Placebo")

-Original file line number
+Diff line change
@@ @@ -1,3 +1,3 @@ @@
 ---
 title: "Logs"
 ----
 +---