From e47693688906443d9bd6c924fdec5631bb31ab86 Mon Sep 17 00:00:00 2001
From: Richard Hanna <HANNAR1@EMAIL.CHOP.EDU>
Date: Wed, 6 Mar 2024 10:30:00 -0500
Subject: [PATCH] Styler and lintr

---
 R/clean_redcap_long.R                   | 11 +++++------
 tests/testthat/test-clean_redcap_long.R | 12 ++++++++----
 vignettes/articles/diving_deeper.Rmd    |  5 +++--
 3 files changed, 16 insertions(+), 12 deletions(-)

diff --git a/R/clean_redcap_long.R b/R/clean_redcap_long.R
index c4858761..a2b55f7f 100644
--- a/R/clean_redcap_long.R
+++ b/R/clean_redcap_long.R
@@ -86,7 +86,7 @@ clean_redcap_long <- function(db_data_long,
       mixed_structure_ref <- get_mixed_structure_fields(db_data_long) %>%
         filter(.data$rep_and_nonrep & !str_ends(.data$field_name, "_form_complete")) %>%
         left_join(db_metadata_long %>% select(.data$field_name, .data$form_name),
-                  by = "field_name"
+          by = "field_name"
         )
 
       # Update if project actually has mixed structure
@@ -96,7 +96,6 @@ clean_redcap_long <- function(db_data_long,
       if (has_mixed_structure_forms) {
         db_data_long <- convert_mixed_instrument(db_data_long, mixed_structure_ref)
       }
-
     } else {
       # Throw error if mixed structure detected and not allowed
       check_repeat_and_nonrepeat(db_data_long)
@@ -113,8 +112,10 @@ clean_redcap_long <- function(db_data_long,
           linked_arms
         )
       ),
-      structure = case_when(has_mixed_structure_forms & redcap_form_name %in% mixed_structure_ref$form_name ~ "mixed",
-                            TRUE ~ "repeating")
+      structure = case_when(
+        has_mixed_structure_forms & redcap_form_name %in% mixed_structure_ref$form_name ~ "mixed",
+        TRUE ~ "repeating"
+      )
     )
   }
 
@@ -274,7 +275,6 @@ distill_repeat_table_long <- function(form_name,
                                       db_data_long,
                                       db_metadata_long,
                                       linked_arms) {
-
   has_repeat_forms <- "redcap_repeat_instance" %in% names(db_data_long)
 
   my_record_id <- names(db_data_long)[1]
@@ -391,7 +391,6 @@ distill_repeat_table_long <- function(form_name,
 #' @keywords internal
 
 convert_mixed_instrument <- function(db_data_long, mixed_structure_ref) {
-
   for (i in seq_len(nrow(mixed_structure_ref))) {
     field <- mixed_structure_ref$field_name[i]
     form <- mixed_structure_ref$form_name[i]
diff --git a/tests/testthat/test-clean_redcap_long.R b/tests/testthat/test-clean_redcap_long.R
index 93de218f..04f479f0 100644
--- a/tests/testthat/test-clean_redcap_long.R
+++ b/tests/testthat/test-clean_redcap_long.R
@@ -123,11 +123,15 @@ test_that("clean_redcap_long with mixed structure works", {
     1, "event_2", "Nonrepeat 2", 0
   )
 
-  expect_equal(out$redcap_data[out$redcap_form_name == "mixed_structure_form"][[1]],
-               expected_mixed_data)
+  expect_equal(
+    out$redcap_data[out$redcap_form_name == "mixed_structure_form"][[1]],
+    expected_mixed_data
+  )
 
-  expect_equal(out$redcap_data[out$redcap_form_name == "nonrepeat_form"][[1]],
-               expected_nonrepeat_data)
+  expect_equal(
+    out$redcap_data[out$redcap_form_name == "nonrepeat_form"][[1]],
+    expected_nonrepeat_data
+  )
 })
 
 test_that("distill_nonrepeat_table_long tibble contains expected columns for longitudinal REDCap databases with arms", {
diff --git a/vignettes/articles/diving_deeper.Rmd b/vignettes/articles/diving_deeper.Rmd
index 70812382..8d4d5e48 100644
--- a/vignettes/articles/diving_deeper.Rmd
+++ b/vignettes/articles/diving_deeper.Rmd
@@ -191,8 +191,9 @@ Users are cautioned when enabling this feature, since it changes definitions in
 
 ```{r}
 read_redcap(redcap_uri,
-            mixed_token,
-            allow_mixed_structure = TRUE) |>
+  mixed_token,
+  allow_mixed_structure = TRUE
+) |>
   rmarkdown::paged_table()
 ```