qualify with .data

to avoid R CMD check warnings ref #420
OuhscBbmc · Oct 2, 2022 · 0075c26 · 0075c26
1 parent db7a393
commit 0075c26
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Showing 2 changed files with 14 additions and 10 deletions.
diff --git a/R/redcap-metadata-coltypes.R b/R/redcap-metadata-coltypes.R
@@ -342,8 +342,8 @@ redcap_metadata_internal <- function(
       field_order_within_form  = seq_len(dplyr::n()),
     ) %>%
     dplyr::ungroup() %>%
-    dplyr::arrange(form_order,  field_order_within_form) %>%
-    dplyr::select(-form_order, -field_order_within_form) %>%
+    dplyr::arrange(.data$form_order,  .data$field_order_within_form) %>%
+    dplyr::select(-.data$form_order, -.data$field_order_within_form) %>%
     tibble::add_row(d_again, .after = 1)
 
   # setdiff(d_meta$field_name_base, d_var$original_field_name)

diff --git a/playgrounds/eav-playground-2.R b/playgrounds/eav-playground-2.R
@@ -11,10 +11,10 @@ requireNamespace("testit")
 # ---- declare-globals ---------------------------------------------------------
 redcap_uri <- "https://bbmc.ouhsc.edu/redcap/api/"
 token <- "9A81268476645C4E5F03428B8AC3AA7B"  # PHI-free demo: simple static
-# token <- "5007DC786DBE39CE77ED8DD0C68069A6"  # PHI-free demo: Checkboxes 1
-# token <- "CCB7E11837D41126D67C744F97389E04"  # PHI-free demo: super-wide --3,000 columns
+token <- "5007DC786DBE39CE77ED8DD0C68069A6"  # PHI-free demo: Checkboxes 1
+token <- "CCB7E11837D41126D67C744F97389E04"  # PHI-free demo: super-wide --3,000 columns
 # token <- "5C1526186C4D04AE0A0630743E69B53C"  # PHI-free demo: super-wide #3--35,000 columns
-# token <- "56F43A10D01D6578A46393394D76D88F"  # PHI-free demo: Repeating Instruments --Sparse
+token <- "56F43A10D01D6578A46393394D76D88F"  # PHI-free demo: Repeating Instruments --Sparse
 
 # fields  <- c("record_id", "dob")
 # forms   <- "health"
@@ -29,7 +29,7 @@ system.time(
 system.time({
   col_types   <- REDCapR::redcap_metadata_coltypes(redcap_uri, token, print_col_types_to_console = FALSE)
 
-  View(REDCapR::redcap_variables(redcap_uri, token)$data)
+  # View(REDCapR::redcap_variables(redcap_uri, token)$data)
 
   ds_metadata <-
     REDCapR:::redcap_metadata_internal(redcap_uri, token)$d_variable %>%
@@ -42,7 +42,7 @@ system.time({
   ds_eav      <- REDCapR:::redcap_read_eav_oneshot(redcap_uri, token, fields = desired_fields)$data
 })
 
-testit::assert(sort(ds_metadata$field_name) == sort(colnames(ds_expected)))
+testit::assert(ds_metadata$field_name == colnames(ds_expected))
 testthat::expect_setequal( ds_metadata$field_name, colnames(ds_expected))
 
 # ---- tweak-data --------------------------------------------------------------
@@ -75,15 +75,19 @@ ds_eav_2 <-
 ds <-
   ds_eav_2 %>%
   dplyr::select(-.data$field_type, -.data$field_name_base) %>%
+  # dplyr::group_by(record, redcap_repeat_instrument, redcap_repeat_instance, event_id, field_name) %>%
+  # dplyr::summarise(n = dplyr::n(), .groups = "drop") %>%
+  # dplyr::filter(n > 1L) %>%
+  # View()
   # dplyr::select(-.data$redcap_repeat_instance) %>%        # TODO: need a good fix for repeats
   # tidyr::drop_na(event_id) %>%                            # TODO: need a good fix for repeats
   tidyr::pivot_wider( # Everything else is considered an ID column
-    names_from  = field_name,
-    values_from = value
+    names_from  = .data$field_name,
+    values_from = .data$value
   ) %>%
   dplyr::select(!!ds_metadata$field_name) %>%
   readr::type_convert(col_types)
   # dplyr::select(.data = ., !!intersect(variables_to_keep, colnames(.)))
 
-testit::assert(sort(colnames(ds)) == sort(colnames(ds_expected)))
+testit::assert(colnames(ds) == colnames(ds_expected))
 testthat::expect_setequal(colnames(ds), colnames(ds_expected))