Fix linting

NAMESPACE

@@ -87,6 +87,7 @@ importFrom(readr,parse_integer)
 importFrom(readr,parse_logical)
 importFrom(readr,parse_time)
 importFrom(rlang,"!!!")
+importFrom(rlang,":=")
 importFrom(rlang,.data)
 importFrom(rlang,abort)
 importFrom(rlang,as_closure)

R/REDCapTidieR-package.R

@@ -18,6 +18,7 @@
 #' check_installed cnd_muffle current_call current_env enexpr enquo env_poke
 #' eval_tidy get_env global_env is_atomic is_bare_formula is_bare_list quo_name
 #' is_installed new_environment quo_get_expr try_fetch zap as_label sym syms expr
+#' :=
 #' @importFrom stringi stri_split_fixed
 #' @importFrom stringr str_detect str_replace str_replace_all str_squish str_trunc
 #' str_trim str_ends

R/checks.R

@@ -669,7 +669,6 @@ check_extra_field_values_message <- function(extra_field_values, call = caller_e
 #'
 #' @keywords internal
 check_fields_exist <- function(fields, expr, call = caller_env()) {
-
   expr <- quo_name(expr)
 
   if (length(fields) == 0) {
@@ -694,15 +693,13 @@ check_fields_exist <- function(fields, expr, call = caller_env()) {
 #'
 #' @keywords internal
 
-check_fields_are_checkboxes <- function(metadata_tbl, call = caller_env()){
-
+check_fields_are_checkboxes <- function(metadata_tbl, call = caller_env()) {
   non_checkboxes <- metadata_tbl %>%
-    filter(field_type != "checkbox")
+    filter(.data$field_type != "checkbox")
 
   if (nrow(non_checkboxes) > 0) {
-
     non_checkboxes <- non_checkboxes %>%
-      pull(field_name)
+      pull(.data$field_name)
 
     msg <- c(
       x = "Non-checkbox fields selected for {.code form_name}",
@@ -714,5 +711,4 @@ check_fields_are_checkboxes <- function(metadata_tbl, call = caller_env()){
       class = c("non_checkbox_fields", "REDCapTidieR_cond")
     )
   }
-
 }

R/reduce_multi_to_single_column.R

@@ -46,7 +46,6 @@ combine_checkboxes <- function(supertbl,
                                values_fill = NA,
                                raw_or_label = "label",
                                keep = TRUE) {
-
   # Save user cols to enquosure
   cols_exp <- enquo(cols)
 
@@ -63,42 +62,51 @@ combine_checkboxes <- function(supertbl,
   record_id_field <- supertbl$redcap_metadata[supertbl$redcap_form_name == form_name][[1]]$field_name[1]
 
   # Combine record identifier with remaining possible project identifiers
-  instrument_identifiers <- c(record_id_field,
-                              "redcap_form_instance",
-                              "redcap_form_name",
-                              "redcap_event",
-                              "redcap_event_instance")
+  instrument_identifiers <- c(
+    record_id_field,
+    "redcap_form_instance",
+    "redcap_form_name",
+    "redcap_event",
+    "redcap_event_instance"
+  )
 
   # Define values_to as the count of TRUEs/1s for the given checkbox field
   # Assign TRUE if multiple selections made, and FALSE if one or zero made
   data_tbl_mod <- data_tbl %>%
     select(any_of(instrument_identifiers), !!!eval_select(cols_exp, data_tbl)) %>%
     mutate(
-      !!values_to := case_when(rowSums(select(., eval_tidy(cols_exp))) > 1 ~ TRUE,
-                       TRUE ~ FALSE)
-
+      !!values_to := case_when(
+        rowSums(select(., eval_tidy(cols_exp))) > 1 ~ TRUE,
+        TRUE ~ FALSE
+      )
     )
 
   # Get metadata reference table, check that chosen fields are checkboxes
   metadata <- get_metadata_ref(data_tbl_mod, supertbl, form_name, instrument_identifiers)
 
   # Replace TRUEs/1s with raw/label values from metadata
   data_tbl_mod <- data_tbl_mod %>%
-    mutate(across(-c(any_of(instrument_identifiers), !!values_to), ~ replace_true(.x,
-                                                                    cur_column(),
-                                                                    metadata = metadata,
-                                                                    raw_or_label = raw_or_label)))
-
+    mutate(across(
+      -c(any_of(instrument_identifiers), !!values_to),
+      ~ replace_true(.x,
+        cur_column(),
+        metadata = metadata,
+        raw_or_label = raw_or_label
+      )
+    ))
 
   # Convert values_to from TRUE/FALSE to multi_value_label or identified single val
   data_tbl_mod <- data_tbl_mod %>%
-    mutate(across(field_names, as.character), # enforce to character strings
-           across(!!values_to, ~as.character(.))) %>%
+    mutate(
+      across(field_names, as.character), # enforce to character strings
+      across(!!values_to, ~ as.character(.))
+    ) %>%
     rowwise() %>%
     mutate(
       !!values_to := ifelse(!!sym(values_to) == "TRUE",
-                          multi_value_label,
-                          coalesce(!!!syms(field_names))),
+        multi_value_label,
+        coalesce(!!!syms(field_names))
+      ),
       !!values_to := ifelse(is.na(!!sym(values_to)), values_fill, !!sym(values_to))
     ) %>%
     ungroup() %>%
@@ -139,34 +147,36 @@ get_metadata_ref <- function(data,
                              supertbl,
                              form_name,
                              instrument_identifiers) {
-
   # Create a metadata reference table linking field name to raw and label values
   out <- supertbl$redcap_metadata[supertbl$redcap_form_name == form_name][[1]] %>%
-    filter(field_name %in% names(data)[!names(data) %in% instrument_identifiers])
+    filter(.data$field_name %in% names(data)[!names(data) %in% instrument_identifiers])
 
   # Make sure selection is checkbox metadata field type
   check_fields_are_checkboxes(out)
 
   out <- out %>%
-    select(field_name, select_choices_or_calculations) %>%
+    select(.data$field_name, .data$select_choices_or_calculations) %>%
     mutate(
-      original_field = sub("___.*$", "", field_name)
+      original_field = sub("___.*$", "", .data$field_name)
     ) %>%
-    mutate(pairs = strsplit(select_choices_or_calculations, " \\| "),
-           label_value = NA,
-           label_value = purrr::map2_chr(pairs, row_number(), \(.x, .y) .x[.y]))
+    mutate(
+      pairs = strsplit(.data$select_choices_or_calculations, " \\| "),
+      label_value = NA,
+      label_value = purrr::map2_chr(pairs, row_number(), \(.x, .y) .x[.y])
+    )
 
   out %>%
-    separate_wider_delim(label_value, delim = ", ", names = c("raw", "label")) %>%
-    select(field_name, raw, label)
+    separate_wider_delim(.data$label_value, delim = ", ", names = c("raw", "label")) %>%
+    select(.data$field_name, .data$raw, .data$label)
 }
 
 #' @noRd
 #' @keywords internal
 replace_true <- function(col, col_name, metadata, raw_or_label) {
-
   # Replace TRUEs/1s with the appropriate raw or label value from the metadata
-  replacement <- metadata %>% filter(field_name == col_name) %>% pull(raw_or_label)
+  replacement <- metadata %>%
+    filter(.data$field_name == col_name) %>%
+    pull(raw_or_label)
   col <- ifelse(col == TRUE, replacement, NA) # col == TRUE works for raw or label because TRUE == 1 & 1 == TRUE
   # Convert non-TRUEs to NA, since values can be either "FALSE" or "0" for unchecked values
   return(col)

tests/testthat/test-checks.R

@@ -53,10 +53,10 @@ test_that("check_repeat_and_nonrepeat works", {
   )
 
   expect_error(check_repeat_and_nonrepeat(db_data = test_data_longitudinal),
-               class = "repeat_nonrepeat_instrument"
+    class = "repeat_nonrepeat_instrument"
   )
   expect_error(check_repeat_and_nonrepeat(db_data = test_data_not_longitudinal),
-               class = "repeat_nonrepeat_instrument"
+    class = "repeat_nonrepeat_instrument"
   )
   expect_no_error(check_repeat_and_nonrepeat(db_data = test_repeating_event))
 })
@@ -151,10 +151,10 @@ test_that("checkmate wrappers work", {
 
   # extension
   expect_warning(check_arg_is_valid_extension("temp.docx", valid_extensions = "xlsx"),
-                 class = "invalid_file_extension"
+    class = "invalid_file_extension"
   )
   expect_warning(check_arg_is_valid_extension("xlsx.", valid_extensions = "xlsx"),
-                 class = "invalid_file_extension"
+    class = "invalid_file_extension"
   )
   expect_true(check_arg_is_valid_extension("temp.xlsx", valid_extensions = "xlsx"))
 })
@@ -251,14 +251,14 @@ test_that("check_fields_exist works", {
   check_fields_exist(fields = character(0), expr = expr(starts_with("temp"))) %>%
     expect_error(class = "missing_checkbox_fields")
 
-  check_fields_exist(fields = c(1,2,3), expr = expr(starts_with("temp"))) %>%
+  check_fields_exist(fields = c(1, 2, 3), expr = expr(starts_with("temp"))) %>%
     expect_no_error()
 })
 
 test_that("check_fields_are_checkboxes works", {
   metadata <- tibble::tribble(
     ~field_name, ~field_type,
-    "record_id",  "text",
+    "record_id", "text",
     "text_field", "text",
     "calc_field", "calc",
     "checkbox___1", "checkbox",

tests/testthat/test-reduce_multi_to_single_column.R

@@ -37,10 +37,12 @@ supertbl <- tibble::tribble(
 class(supertbl) <- c("redcap_supertbl", class(supertbl))
 
 test_that("combine_checkboxes returns an expected supertbl", {
-  out <- combine_checkboxes(supertbl = supertbl,
-                            form_name = "nonrepeat_instrument",
-                            cols = starts_with("multi"),
-                            values_to = "new_col") # values_fill declared
+  out <- combine_checkboxes(
+    supertbl = supertbl,
+    form_name = "nonrepeat_instrument",
+    cols = starts_with("multi"),
+    values_to = "new_col"
+  ) # values_fill declared
 
   expect_setequal(class(out), c("redcap_supertbl", "tbl_df", "tbl", "data.frame"))
   expect_equal(nrow(out), 2)
@@ -96,10 +98,12 @@ test_that("combine_checkboxes works for nonrepeat instrument and drop old values
 })
 
 test_that("combine_checkboxes works for repeat instrument", {
-  out <- combine_checkboxes(supertbl = supertbl,
-                            form_name = "repeat_instrument",
-                            cols = starts_with("repeat"),
-                            values_to = "new_col") %>%
+  out <- combine_checkboxes(
+    supertbl = supertbl,
+    form_name = "repeat_instrument",
+    cols = starts_with("repeat"),
+    values_to = "new_col"
+  ) %>%
     pull(redcap_data) %>%
     dplyr::nth(2)
 
@@ -121,7 +125,12 @@ test_that("get_metadata_ref works", {
     select(study_id, contains("multi")) %>%
     mutate(new_data = c(FALSE, TRUE, FALSE))
 
-  out <- get_metadata_ref(data = data, supertbl = supertbl, form_name = "nonrepeat_instrument", instrument_identifiers = "study_id")
+  out <- get_metadata_ref(
+    data = data,
+    supertbl = supertbl,
+    form_name = "nonrepeat_instrument",
+    instrument_identifiers = "study_id"
+  )
 
   expected_out <- tibble::tribble(
     ~"field_name", ~"raw", ~"label",