CHOP-CGTInformatics · rsh52 · Oct 23, 2024 · Oct 16, 2024 · Oct 16, 2024 · Oct 16, 2024
diff --git a/R/checks.R b/R/checks.R
@@ -745,7 +745,7 @@ check_fields_are_checkboxes <- function(metadata_tbl, call = caller_env()) {
 #' @title Check equal distinct values between two columns
 #'
 #' @description
-#' Takes a dataframe and two columns and checks if [n_distinct()] of the second
+#' Takes a dataframe and two columns and checks if `n_distinct` of the second
 #' column is all unique based on grouping of the first column.
 #'
 #' @param data a dataframe
@@ -757,8 +757,8 @@ check_fields_are_checkboxes <- function(metadata_tbl, call = caller_env()) {
 check_equal_col_summaries <- function(data, col1, col2, call = caller_env()) {
   summary <- data %>%
     summarise(
-      .by = {{ col1 }},
-      n = n_distinct({{ col2 }})
+      .by = col1,
+      n = n_distinct(col2)
     )
 
   total_n <- summary %>%

diff --git a/R/combine_checkboxes.R b/R/combine_checkboxes.R
@@ -19,8 +19,7 @@
 #'
 #' @param supertbl A supertibble generated by [read_redcap()]. Required.
 #' @param tbl The `redcap_form_name` of the data tibble to extract. Required.
-#' @param cols <[`tidy-select`][tidyr_tidy_select]> Checkbox columns to combine to
-#' single column. Required.
+#' @param cols Checkbox columns to combine to single column. Required.
 #' @param names_prefix String added to the start of every variable name.
 #' @param names_sep String to separate new column names from `names_prefix`.
 #' @param names_glue Instead of `names_sep` and `names_prefix`, you can supply
@@ -192,23 +191,26 @@ get_metadata_spec <- function(metadata_tbl,
   if (!is.null(names_glue)) {
     # Similar to pivot_*, use of `names_glue` overrides use of names_prefix/sep
     glue_env <- out %>%
-      select(.data$.value) %>%
-      mutate(.new_value = as.character(glue::glue_data(., names_glue))) %>% # nolint: object_usage_linter
+      select(.data$.value)
+
+    glue_env$.new_value <- as.character(glue::glue_data(glue_env, names_glue))
+
+    glue_env <- glue_env %>%
       select(.data$.new_value)
 
     out <- cbind(out, glue_env)
   } else {
     out <- out %>%
       mutate(
-        .new_value = case_when(names_prefix != "" ~ paste(names_prefix, .value, sep = names_sep),
+        .new_value = case_when(names_prefix != "" ~ paste(names_prefix, .data$.value, sep = names_sep),
           .default = paste(names_prefix, .data$.value, sep = "")
         )
       )
   }
 
   # Check that for each unique value of .value there is one unique value of .new_value
   # May be removed in the future
-  check_equal_col_summaries(out, .value, .new_value) # nolint: object_usage_linter
+  check_equal_col_summaries(out, ".value", ".new_value") # nolint: object_usage_linter
 
   # Make sure selection is checkbox metadata field type
   check_fields_are_checkboxes(out)
@@ -257,11 +259,11 @@ replace_true <- function(col, col_name, metadata, raw_or_label) {
 #' based on the overall data tibble cross referenced with a nested section of the
 #' metadata tibble.
 #'
-#' [case_when()] logic helps determine whether the value is a coalesced singular
+#' `case_when` logic helps determine whether the value is a coalesced singular
 #' value or a user-specified one via `multi_value_label` or `values_fill`.
 #'
 #' @details
-#' This function is used in conjunction with [pmap()].
+#' This function is used in conjunction with `pmap()`.
 #'
 #' @keywords internal
 #'

diff --git a/R/read_redcap.R b/R/read_redcap.R
@@ -260,17 +260,24 @@ read_redcap <- function(redcap_uri,
     db_data <- multi_choice_to_labels(db_data, db_metadata, raw_or_label)
   }
 
-  # Longitudinal Arms Check and Cleaning Application ----
-  # Check if database supplied is longitudinal to determine appropriate function
-  # to use
-  is_longitudinal <- if ("redcap_event_name" %in% names(db_data)) {
-    TRUE
+  # Database structure checks and definitions ----
+  is_longitudinal <- "redcap_event_name" %in% names(db_data)
+  has_repeating_structure <- "redcap_repeat_instance" %in% names(db_data)
+  has_repeating_events <- if (is_longitudinal && has_repeating_structure) {
+    any(
+      is.na(db_data$redcap_repeat_instrument) &
+        !is.na(db_data$redcap_repeat_instance)
+    )
   } else {
     FALSE
   }
 
   if (is_longitudinal) {
-    repeat_event_types <- get_repeat_event_types(db_data)
+    repeat_event_types <- if (has_repeating_events) {
+      get_repeat_event_types(db_data)
+    } else {
+      NULL
+    }
 
     linked_arms <- link_arms(
       redcap_uri = redcap_uri,
@@ -453,11 +460,17 @@ add_metadata <- function(supertbl, db_metadata, redcap_uri, token, suppress_redc
 #' @keywords internal
 
 add_event_mapping <- function(supertbl, linked_arms, repeat_event_types) {
-  event_info <- linked_arms %>%
-    left_join(repeat_event_types, by = c("unique_event_name" = "redcap_event_name")) %>%
+  event_info <- linked_arms
+
+  if (!is.null(repeat_event_types)) {
+    event_info <- event_info %>%
+      left_join(repeat_event_types, by = c("unique_event_name" = "redcap_event_name"))
+  }
+
+  event_info <- event_info %>%
     add_partial_keys(.data$unique_event_name) %>%
     select(
-      redcap_form_name = "form", "redcap_event", "event_name", "redcap_arm", "arm_name", "repeat_type"
+      redcap_form_name = "form", "redcap_event", "event_name", "redcap_arm", "arm_name", any_of("repeat_type")
     ) %>%
     nest(redcap_events = !"redcap_form_name")
 

diff --git a/cran-comments.md b/cran-comments.md
@@ -2,41 +2,27 @@
 
 Thank you for taking the time to review this submission and please reach out to either Stephan Kadauke, Richard Hanna, or Ezra Porter for any questions, comments, or concerns.
 
-This submission patches version 1.1.0 to fix a test failure introduced by an upcoming release of `labelled` 2.13.0. We have worked with the developer of `labelled` to ensure this patch resolves their reverse dependency check failures.
+This submission for v1.2.0 adds new functionality, new documentation, and patches several minor bugs.
 
 ## New Features
 
-There are no significant user-facing changes in this release.
-
-`read_redcap(raw_or_label = "haven")` now correctly casts categorical data values to character when their type is not character or numeric. This is a constraint of labels from the `haven` package which `labelled` will be checking for explicitly in their new release.
+The only new feature in this release in is an analytics function that exists in a silo away from the rest of the core package.
 
 ## Test environments
 
-1. Local macOS Ventura 13.6.5, R 4.2.4
+1. Local macOS Sonoma 14.6.1, R 4.4.0
 2. R-hub
-    1. [Ubuntu 22.04.4 LTS, R-next, GCC](https://github.com/CHOP-CGTInformatics/REDCapTidieR/actions/runs/8650642187/job/23719620675)
-    2. [Ubuntu 22.04.4 LTS, R-release, GCC](https://github.com/CHOP-CGTInformatics/REDCapTidieR/actions/runs/8650642187/job/23719621223)
-    3. [Ubuntu 22.04.4 LTS, R-devel, GCC](https://github.com/CHOP-CGTInformatics/REDCapTidieR/actions/runs/8650642187/job/23719620358)
-    4. [Windows Server](https://github.com/CHOP-CGTInformatics/REDCapTidieR/actions/runs/8650642187/job/23719620965)
-3.  [win-builder](https://win-builder.r-project.org/V4B5Ar22pIf5/), development version.
-4.  [GiHub Actions](https://github.com/CHOP-CGTInformatics/REDCapTidieR/actions), Ubuntu 20.04.02 LTS
+    1. [Ubuntu 22.04.5 LTS, R-next, GCC](https://github.com/CHOP-CGTInformatics/REDCapTidieR/actions/runs/11371750216/job/31634537921)
+    2. [Ubuntu 22.04.5 LTS, R-release, GCC](https://github.com/CHOP-CGTInformatics/REDCapTidieR/actions/runs/11371750216/job/31634538851)
+    3. [Ubuntu 22.04.4 LTS, R-devel, GCC](https://github.com/CHOP-CGTInformatics/REDCapTidieR/actions/runs/11371750216/job/31634538452)
+    4. [Microsoft Windows Server 2022, 10.0.20348](https://github.com/CHOP-CGTInformatics/REDCapTidieR/actions/runs/11371750216/job/31634539238)
+3.  [win-builder](https://win-builder.r-project.org/zPkjljy8Z67c/), development version.
+4.  [GiHub Actions](https://github.com/CHOP-CGTInformatics/REDCapTidieR/actions), Ubuntu 20.04.05 LTS
 
 ## R CMD check results:
 
 - 0 ERRORs or WARNINGs on any builds
 
-- A NOTE is generated in win-builder resulting from the package maintainer email address changing relative to the last CRAN release. This is an artifact of a different email address than the package maintainer's being used for the submission to win-builder.
-
-```
-* checking CRAN incoming feasibility ... [14s] NOTE
-Maintainer: 'Richard Hanna <[email protected]>'
-
-New maintainer:
-  Richard Hanna <[email protected]>
-Old maintainer(s):
-  Richard Hanna <[email protected]>
-```
-
 ## Downstream Dependencies:
 
-No downstream packages are affected. No packages depend/import/suggest REDCapTidieR. Results: <https://github.com/CHOP-CGTInformatics/REDCapTidieR/blob/main/revdep/cran.md>
+
diff --git a/inst/WORDLIST b/inst/WORDLIST
@@ -17,8 +17,10 @@ REDCapTidieR's
 RStudio
 Recode
 Recoding
+Stata
 Supertibble
 Supertibbles
+TRUEs
 Tibble
 Tibble's
 Tibbles
@@ -30,6 +32,7 @@ analytics
 api
 appendings
 cli
+de
 dplyr
 dropdown
 edu
@@ -38,6 +41,7 @@ ggplot
 gtsummary
 https
 httptest
+interpretable
 labelled
 multiselection
 nonrepeat
@@ -48,12 +52,15 @@ preprocess
 recode
 recoded
 recodes
+recoding
 skimr
 summarise
 supertbl
 supertibble
 supertibble's
+supertibbles
 tableStyleLight
+tbl
 tibble
 tibble's
 tibbles
@@ -62,7 +69,6 @@ tidyverse
 truefalse
 undirected
 unlabelled
-wb
 xlsx
 yesno
 ︎
diff --git a/man/check_equal_col_summaries.Rd b/man/check_equal_col_summaries.Rd
diff --git a/man/combine_checkboxes.Rd b/man/combine_checkboxes.Rd
diff --git a/man/convert_checkbox_vals.Rd b/man/convert_checkbox_vals.Rd
diff --git a/tests/testthat/test-read_redcap.R b/tests/testthat/test-read_redcap.R
@@ -680,5 +680,4 @@ test_that("get_repeat_event_types() works", {
   )
 
   expect_equal(out, expected_out)
-
 })
diff --git a/utility/cli_message_examples_reprex.md b/utility/cli_message_examples_reprex.md
@@ -34,13 +34,9 @@ read_redcap(letters[1:3], classic_token)
 read_redcap("https://www.google.com", classic_token)
 #> Error in `read_redcap()`:
 #> ✖ The REDCapR export operation was not successful.
-#> ! An unexpected error occured.
-#> ℹ This means that you probably discovered a bug!
-#> ℹ Please consider submitting a bug report here:
-#>   <https://github.com/CHOP-CGTInformatics/REDCapTidieR/issues>.
-#> Caused by error in `redcap_metadata_read()`:
-#> ! The REDCapR metadata export operation was not successful.  The error message was:
-#> <html><body><h1>404 Not Found</h1></body></html>
+#> ! The URL returned the HTTP error code 405 (POST Method not allowed).
+#> ℹ Are you sure the URI points to an active REDCap API endpoint?
+#> ℹ URI: `https://www.google.com`
 
 read_redcap("https://www.google.comm", classic_token)
 #> Error in `read_redcap()`:
@@ -63,13 +59,13 @@ read_redcap(redcap_uri, letters[1:3])
 
 read_redcap(redcap_uri, "")
 #> Error in `read_redcap()`:
-#> ✖ The token is an empty string, not a valid 32-character hexademical
-#>   value.
+#> ✖ The token is an empty string, which is not allowed.
 #> ℹ API token: ``
 
 read_redcap(redcap_uri, "CC0CE44238EF65C5DA26A55DD749AF7") # 31 hex characters
 #> Error in `read_redcap()`:
-#> ✖ The token is not a valid 32-character hexademical value.
+#> ✖ The token does not conform with the regex
+#>   `^([0-9A-Fa-f]{32})(?:\n)?$`.
 #> ℹ API token: `CC0CE44238EF65C5DA26A55DD749AF7`
 
 read_redcap(redcap_uri, "CC0CE44238EF65C5DA26A55DD749AF7A") # will be rejected by server
@@ -259,7 +255,7 @@ withr::with_tempdir({
 })
 #> Error:
 #> ✖ File
-#>   ''/private/var/folders/9c/k1m0bzys7gb1v32g86hfn5sn5k86h1/T/Rtmp1QPC0p/file5c744dd73619/temp.csv''
+#>   ''/private/var/folders/qc/mmjjyjq50530z9r_7mfqcqfhxkkk67/T/Rtmph4LQ3Z/filee5aa7b9bea48/temp.csv''
 #>   already exists.
 #> ℹ Overwriting files is disabled by default. Set `overwrite = TRUE` to overwrite
 #>   existing file.
@@ -300,25 +296,26 @@ withr::with_tempdir({
     write_redcap_xlsx(file = filepath)
 })
 #> Warning in write_redcap_xlsx(., file = filepath): ! No extension provided for `file`:
-#>   '/private/var/folders/9c/k1m0bzys7gb1v32g86hfn5sn5k86h1/T/Rtmp1QPC0p/file5c7456597c2b/temp'
+#>   '/private/var/folders/qc/mmjjyjq50530z9r_7mfqcqfhxkkk67/T/Rtmph4LQ3Z/filee5aa11455c98/temp'
 #> ℹ The extension '.xlsx' will be appended to the file name.
 
 # Printed supertibble
 
 read_redcap(Sys.getenv("REDCAP_URI"), Sys.getenv("REDCAPTIDIER_CLASSIC_API")) %>%
   suppressWarnings()
-#> # A REDCapTidieR Supertibble with 9 instruments
-#>   redcap_form_name       redcap_form_label redcap_data redcap_metadata structure
-#>   <chr>                  <chr>             <list>      <list>          <chr>    
-#> 1 nonrepeated            Nonrepeated       <tibble>    <tibble>        nonrepea…
-#> 2 nonrepeated2           Nonrepeated2      <tibble>    <tibble>        nonrepea…
-#> 3 repeated               Repeated          <tibble>    <tibble>        repeating
-#> 4 data_field_types       Data Field Types  <tibble>    <tibble>        nonrepea…
-#> 5 text_input_validation… Text Input Valid… <tibble>    <tibble>        nonrepea…
-#> 6 api_no_access          API No Access     <tibble>    <tibble>        nonrepea…
-#> 7 api_no_access_2        API No Access 2   <tibble>    <tibble>        nonrepea…
-#> 8 survey                 Survey            <tibble>    <tibble>        nonrepea…
-#> 9 repeat_survey          Repeat Survey     <tibble>    <tibble>        repeating
+#> # A REDCapTidieR Supertibble with 10 instruments
+#>    redcap_form_name      redcap_form_label redcap_data redcap_metadata structure
+#>    <chr>                 <chr>             <list>      <list>          <chr>    
+#>  1 nonrepeated           Nonrepeated       <tibble>    <tibble>        nonrepea…
+#>  2 nonrepeated2          Nonrepeated2      <tibble>    <tibble>        nonrepea…
+#>  3 repeated              Repeated          <tibble>    <tibble>        repeating
+#>  4 data_field_types      Data Field Types  <tibble>    <tibble>        nonrepea…
+#>  5 text_input_validatio… Text Input Valid… <tibble>    <tibble>        nonrepea…
+#>  6 api_no_access         API No Access     <tibble>    <tibble>        nonrepea…
+#>  7 api_no_access_2       API No Access 2   <tibble>    <tibble>        nonrepea…
+#>  8 survey                Survey            <tibble>    <tibble>        nonrepea…
+#>  9 repeat_survey         Repeat Survey     <tibble>    <tibble>        repeating
+#> 10 labelled_vignette     Labelled Vignette <tibble>    <tibble>        nonrepea…
 #> # ℹ 5 more variables: data_rows <int>, data_cols <int>, data_size <lbstr_by>,
 #> #   data_na_pct <formttbl>, form_complete_pct <formttbl>
 
@@ -343,4 +340,4 @@ read_redcap(redcap_uri, Sys.getenv("REDCAPTIDIER_MDC_API"))
 #> #   data_na_pct <formttbl>, form_complete_pct <formttbl>
 ```
 
-<sup>Created on 2024-04-10 with [reprex v2.1.0](https://reprex.tidyverse.org)</sup>
+<sup>Created on 2024-10-16 with [reprex v2.1.0](https://reprex.tidyverse.org)</sup>
Original file line number	Diff line number	Diff line change
Expand Up		@@ -680,5 +680,4 @@ test_that("get_repeat_event_types() works", {
		)

		expect_equal(out, expected_out)

		})