Merge pull request #163 from CHOP-CGTInformatics/minor-updates

Minor Updates & Cleaning 🧹

.github/pull_request_template.md

@@ -19,14 +19,13 @@ Before submitting this PR, please check and verify below that the submission mee
 
 - [ ] New/revised functions have associated tests
 - [ ] New/revised functions that update downstream outputs have associated static testing files (`.RDS`) updated under `inst/testdata/create_test_data.R`
-- [ ] New tests that make API calls use `httptest::with_mock_api` and any new mocks were added to `tests/testthat/fixtures/create_httptest_mocks.R`
 - [ ] New/revised functions use appropriate naming conventions
 - [ ] New/revised functions don't repeat code
 - [ ] Code changes are less than **250** lines total
 - [ ] Issues linked to the PR using [GitHub's list of keywords](https://docs.github.com/en/issues/tracking-your-work-with-issues/linking-a-pull-request-to-an-issue)
 - [ ] The appropriate reviewer is assigned to the PR
 - [ ] The appropriate developers are assigned to the PR
-- [ ] Pre-release package version incremented using `usethis::use_dev_version()`
+- [ ] Pre-release package version incremented using `usethis::use_version()`
 
 # Code Review
 This section to be used by the reviewer and developers during Code Review after PR submission

DESCRIPTION

@@ -1,7 +1,7 @@
 Package: REDCapTidieR
 Type: Package
 Title: Extract 'REDCap' Databases into Tidy 'Tibble's
-Version: 0.4.1.9000
+Version: 0.4.1.9001
 Authors@R: c(
     person("Richard", "Hanna", , "richardshanna91@gmail.com", role = c("aut", "cre")),
     person("Stephan", "Kadauke", , "kadaukes@chop.edu", role = "aut"),

R/REDCapTidieR-package.R

@@ -0,0 +1,30 @@
+#' @keywords internal
+#' @aliases REDCapTidieR-package
+#' @importFrom checkmate assert_character assert_data_frame check_character
+#' check_choice check_environment check_logical expect_character expect_double
+#' expect_factor expect_logical
+#' @importFrom cli cli_abort cli_fmt cli_text cli_vec cli_warn qty
+#' @importFrom dplyr %>% across bind_rows case_when filter group_by if_any if_else
+#' left_join mutate pull recode relocate rename row_number select slice summarise
+#' @importFrom formattable percent
+#' @importFrom lobstr obj_size
+#' @importFrom lubridate is.difftime is.period
+#' @importFrom purrr compose map map2 map_int map_lgl pluck pmap_chr some
+#' @importFrom REDCapR redcap_arm_export redcap_event_instruments redcap_instruments
+#' redcap_metadata_read redcap_read_oneshot sanitize_token
+#' @importFrom rlang .data !!! abort as_closure caller_arg caller_env catch_cnd
+#' 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
+#' is_installed new_environment quo_get_expr try_fetch zap as_label
+#' @importFrom stringi stri_split_fixed
+#' @importFrom stringr str_detect str_replace str_replace_all str_squish str_trunc
+#' str_trim
+#' @importFrom tibble as_tibble is_tibble tibble
+#' @importFrom tidyr complete fill pivot_wider nest unnest unnest_wider
+#' @importFrom tidyselect all_of any_of ends_with eval_select everything
+#' starts_with where
+"_PACKAGE"
+
+## usethis namespace: start
+## usethis namespace: end
+NULL

R/bind_tibbles.R

@@ -17,10 +17,6 @@
 #' @param tbls A vector of the `redcap_form_name`s of the data tibbles to bind to
 #' the environment. Default is `NULL` which binds all data tibbles.
 #'
-#' @importFrom dplyr filter pull %>%
-#' @importFrom rlang env_poke current_env new_environment global_env .data
-#' @importFrom purrr map2 pluck
-#'
 #' @examples
 #' \dontrun{
 #' # Create an empty environment

R/checks.R

@@ -9,12 +9,6 @@
 #' @return
 #' A helpful error message alerting the user to check their API privileges.
 #'
-#' @importFrom rlang .data caller_env
-#' @importFrom dplyr filter select group_by summarise
-#' @importFrom tidyr pivot_wider
-#' @importFrom cli cli_warn cli_text cli_fmt qty cli_abort
-#' @importFrom purrr pmap_chr
-#'
 #' @param db_data The REDCap database output generated by
 #' \code{REDCapR::redcap_read_oneshot()$data}
 #' @param db_metadata The REDCap metadata output generated by \code{REDCapR::redcap_metadata_read()$data}
@@ -103,10 +97,6 @@ check_user_rights <- function(db_data,
 #' \code{REDCapR::redcap_read_oneshot()$data}
 #' @param call the calling environment to use in the error message
 #'
-#' @importFrom dplyr %>% filter
-#' @importFrom cli cli_abort
-#' @importFrom rlang caller_env
-#'
 #' @keywords internal
 
 
@@ -174,9 +164,6 @@ check_repeat_and_nonrepeat <- function(db_data, call = caller_env()) {
 #' \code{REDCapR::redcap_read_oneshot()$data}
 #' @param call the calling environment to use in the error message
 #'
-#' @importFrom cli cli_abort
-#' @importFrom rlang caller_env
-#'
 #' @keywords internal
 
 check_redcap_populated <- function(db_data, call = caller_env()) {
@@ -202,9 +189,6 @@ check_redcap_populated <- function(db_data, call = caller_env()) {
 #' @return
 #' An error message listing the requested instruments that don't exist
 #'
-#' @importFrom cli cli_abort
-#' @importFrom rlang caller_env
-#'
 #' @param db_metadata The metadata file read by
 #' \code{REDCapR::redcap_metadata_read()}
 #' @param forms The character vector of instrument names passed to
@@ -229,11 +213,6 @@ check_forms_exist <- function(db_metadata, forms, call = caller_env()) {
 #' Check that all metadata tibbles within a supertibble contain
 #' \code{field_name} and \code{field_label} columns
 #'
-#' @importFrom purrr map map_int
-#' @importFrom dplyr %>% filter
-#' @importFrom cli cli_abort
-#' @importFrom rlang caller_arg
-#'
 #' @param supertbl a supertibble containing a \code{redcap_metadata} column
 #' @param call the calling environment to use in the error message
 #'
@@ -294,9 +273,6 @@ check_req_labelled_metadata_fields <- function(supertbl, call = caller_env()) {
 #' @title
 #' Check that parsed labels are not duplicated
 #'
-#' @importFrom cli cli_warn qty
-#' @importFrom rlang caller_env
-#'
 #' @param parsed_labels_output a vector of parsed labels produced by `parse_labels()`
 #' @param field_name the name of the field associated with the labels to use in the warning message
 #' @param warn_stripped_text logical for whether to include a note about HTML tag stripping in the message
@@ -367,9 +343,6 @@ check_parsed_labels <- function(parsed_labels_output,
 #' @title
 #' Check an argument with checkmate
 #'
-#' @importFrom cli cli_abort
-#' @importFrom rlang caller_arg
-#'
 #' @param x An object to check
 #' @param arg The name of the argument to include in an error message. Captured
 #' by `rlang::caller_arg()` by default
@@ -386,8 +359,6 @@ check_parsed_labels <- function(parsed_labels_output,
 NULL
 
 # Function factory to wrap checkmate functions
-#' @importFrom rlang caller_arg caller_env
-#' @importFrom cli cli_abort
 #' @noRd
 wrap_checkmate <- function(f) {
   error_class <- caller_arg(f)
@@ -411,9 +382,6 @@ wrap_checkmate <- function(f) {
 }
 
 #' @rdname checkmate
-#' @importFrom cli cli_abort
-#' @importFrom rlang caller_env caller_arg is_bare_list
-#' @importFrom purrr map_lgl
 check_arg_is_supertbl <- function(x,
                                   req_cols = c("redcap_data", "redcap_metadata"),
                                   arg = caller_arg(x),
@@ -471,25 +439,18 @@ check_arg_is_supertbl <- function(x,
 }
 
 #' @rdname checkmate
-#' @importFrom checkmate check_environment
 check_arg_is_env <- wrap_checkmate(check_environment)
 
 #' @rdname checkmate
-#' @importFrom checkmate check_character
 check_arg_is_character <- wrap_checkmate(check_character)
 
 #' @rdname checkmate
-#' @importFrom checkmate check_logical
 check_arg_is_logical <- wrap_checkmate(check_logical)
 
 #' @rdname checkmate
-#' @importFrom checkmate check_choice
 check_arg_choices <- wrap_checkmate(check_choice)
 
 #' @rdname checkmate
-#' @importFrom REDCapR sanitize_token
-#' @importFrom cli cli_abort
-#' @importFrom rlang caller_arg caller_env try_fetch
 check_arg_is_valid_token <- function(x,
                                      arg = caller_arg(x),
                                      call = caller_env()) {
@@ -519,9 +480,6 @@ check_arg_is_valid_token <- function(x,
 #' If x is atomic, x with cli formatting to truncate to 5 values. Otherwise,
 #' a string summarizing x produced by as_label
 #'
-#' @importFrom rlang as_label is_atomic
-#' @importFrom cli cli_vec
-#'
 #' @keywords internal
 format_error_val <- function(x) {
   if (is_atomic(x)) {
@@ -533,8 +491,6 @@ format_error_val <- function(x) {
 }
 
 #' @rdname checkmate
-#' @importFrom cli cli_warn
-#' @importFrom rlang caller_arg caller_env
 check_arg_is_valid_extension <- function(x,
                                          valid_extensions,
                                          arg = caller_arg(x),
@@ -581,9 +537,6 @@ check_arg_is_valid_extension <- function(x,
 #' @return
 #' An error message saying the requested data does not exist
 #'
-#' @importFrom cli cli_abort
-#' @importFrom rlang caller_env
-#'
 #' @param db_data The REDCap database output generated by
 #' \code{REDCapR::redcap_read_oneshot()$data}
 #' @param col The column to check for in `redcap_data`
@@ -626,9 +579,6 @@ check_data_arg_exists <- function(db_data, col, arg, call = caller_env()) {
 #' @return
 #' An error message saying the requested file already exists
 #'
-#' @importFrom cli cli_abort
-#' @importFrom rlang caller_env
-#'
 #' @param file The file that is being checked
 #' @param overwrite Whether the file was declared to be overwritten
 #' @param call The calling environment to use in the error message

R/clean_redcap.R

@@ -16,14 +16,6 @@
 #' can access dataframes under the \code{redcap_data} column with reference to
 #' \code{form_name} and \code{structure} column details.
 #'
-#' @importFrom
-#' checkmate assert_data_frame expect_logical expect_factor expect_character
-#' expect_double
-#' @importFrom dplyr filter pull
-#' @importFrom purrr map
-#' @importFrom tibble tibble
-#' @importFrom rlang .data
-#'
 #' @keywords internal
 
 clean_redcap <- function(db_data,
@@ -108,11 +100,6 @@ clean_redcap <- function(db_data,
 #' @param db_metadata The REDCap metadata output defined by
 #' \code{REDCapR::redcap_metadata_read()$data}
 #'
-#' @importFrom dplyr filter pull select relocate rename
-#' @importFrom tidyselect all_of everything starts_with any_of
-#' @importFrom tibble tibble
-#' @importFrom rlang .data
-#'
 #' @keywords internal
 
 distill_nonrepeat_table <- function(form_name,
@@ -203,11 +190,6 @@ distill_nonrepeat_table <- function(form_name,
 #' @param db_metadata The non-longitudinal REDCap metadata output defined by
 #' \code{REDCapR::redcap_metadata_read()$data}
 #'
-#' @importFrom dplyr filter pull select relocate rename
-#' @importFrom tidyselect all_of everything starts_with any_of
-#' @importFrom tibble tibble
-#' @importFrom rlang .data
-#'
 #' @keywords internal
 
 distill_repeat_table <- function(form_name,

R/clean_redcap_long.R

@@ -18,12 +18,6 @@
 #' can access dataframes under the \code{redcap_data} column with reference to
 #' \code{form_name} and \code{structure} column details.
 #'
-#' @importFrom checkmate assert_data_frame
-#' @importFrom dplyr filter pull
-#' @importFrom purrr map
-#' @importFrom tibble tibble
-#' @importFrom rlang .data
-#'
 #' @keywords internal
 
 clean_redcap_long <- function(db_data_long,
@@ -118,12 +112,6 @@ clean_redcap_long <- function(db_data_long,
 #' @param linked_arms Output of \code{link_arms}, linking instruments to REDCap
 #' events/arms
 #'
-#' @importFrom dplyr filter pull select relocate rename
-#' @importFrom tidyselect all_of everything any_of
-#' @importFrom tibble tibble
-#' @importFrom stringr str_detect
-#' @importFrom rlang .data
-#'
 #' @keywords internal
 
 distill_nonrepeat_table_long <- function(form_name,
@@ -248,11 +236,6 @@ distill_nonrepeat_table_long <- function(form_name,
 #' @param linked_arms Output of \code{link_arms}, linking instruments to REDCap
 #' events/arms
 #'
-#' @importFrom dplyr filter pull select relocate rename
-#' @importFrom tidyselect all_of everything any_of
-#' @importFrom tibble tibble
-#' @importFrom stringr str_detect
-#' @importFrom rlang .data
 #' @keywords internal
 
 distill_repeat_table_long <- function(form_name,

R/dev_utils.R

@@ -1,43 +1,3 @@
-#' Retrieve credentials for creating or using mocks
-#'
-#' @param credentials names of credentials to retrieve. By default all credentials in
-#' `inst/misc/fake_credentials.csv` are retrieved
-#' @param fake logical. Should fake credentials be retrieved? By default `FALSE`
-#'
-#' @return
-#' A named list of credentials from with `Sys.getenv()` if `fake = FALSE`
-#' or from `inst/misc/fake_credentials.csv` if `fake = TRUE`
-#' @keywords internal
-get_credentials <- function(credentials = NULL, fake = FALSE) {
-  creds <- readr::read_csv(
-    system.file("misc/fake_credentials.csv", package = "REDCapTidieR"),
-    col_types = "cc"
-  )
-
-  if (!is.null(credentials)) {
-    if (!all(credentials %in% creds$name)) {
-      missing_creds <- setdiff(credentials, creds$name) # nolint: object_usage_linter
-      cli::cli_abort(c(
-        "x" = "{.code {missing_creds}} {?is/are} missing from {.path inst/misc/fake_credentials.csv}"
-      ))
-    }
-
-    creds <- creds[creds$name %in% credentials, ]
-  }
-
-  res <- rep("", nrow(creds))
-
-  if (fake) {
-    res <- creds$value
-  } else {
-    res <- unname(Sys.getenv(creds$name))
-  }
-
-  res <- as.list(res)
-  names(res) <- creds$name
-  res
-}
-
 #' @title Additional release questions
 #'
 #' @description

R/extract_tibble.R

@@ -14,9 +14,6 @@
 #' @param supertbl A supertibble generated by `read_redcap()`. Required.
 #' @param tbl The `redcap_form_name` of the data tibble to extract. Required.
 #'
-#' @importFrom checkmate assert_character
-#' @importFrom tidyselect all_of
-#'
 #' @examples
 #' superheroes_supertbl
 #'
@@ -55,12 +52,6 @@ extract_tibble <- function(supertbl,
 #' @param tbls A vector of `form_name`s or a tidyselect helper. Default is
 #' `dplyr::everything()`.
 #'
-#' @importFrom rlang enquo
-#' @importFrom dplyr select %>%
-#' @importFrom tidyselect eval_select everything
-#' @importFrom tidyr pivot_wider
-#' @importFrom purrr map pluck
-#'
 #' @examples
 #' superheroes_supertbl
 #'