Closes #434 remove pharmaversesdtm dependency (#439)

* 434 remove pharmaversesdtm dependency * 434 update STYLER * 434 update NEWS file * 434 do not use TIBBLE * 434 remove remaining TIBBLE --------- Co-authored-by: Ben Straub <[email protected]>
pharmaverse · Apr 19, 2024 · f0c7509 · f0c7509
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diff --git a/DESCRIPTION b/DESCRIPTION
@@ -48,7 +48,8 @@ Suggests:
     htmltools,
     knitr,
     methods,
-    pharmaversesdtm,
+    miniUI,
+    pkgdown,
     rmarkdown,
     rstudioapi,
     spelling,

diff --git a/NEWS.md b/NEWS.md
@@ -14,6 +14,7 @@
 
 * No longer exporting `is_named()` function. (#401)
 
+* `pharmaversesdtm` removed as a dependency. (#434)
 * As a part of the error messaging update, the following changes were made.
 
     - The `assert_s3_class(class)` argument has been renamed to `assert_s3_class(cls)`. (#367)

diff --git a/R/assertions.R b/R/assertions.R
@@ -374,11 +374,13 @@ assert_logical_scalar <- function(arg, optional = FALSE,
 #' @keywords assertion
 #' @family assertion
 #' @examples
-#' library(pharmaversesdtm)
 #' library(dplyr, warn.conflicts = FALSE)
 #' library(rlang)
-#' data(dm)
-#'
+#' dm <- dplyr::tribble(
+#'   ~DOMAIN,      ~USUBJID,
+#'   "DM",    "01-701-1015",
+#'   "DM",    "01-701-1016",
+#' )
 #' example_fun <- function(dat, var) {
 #'   var <- assert_symbol(enexpr(var))
 #'   select(dat, !!var)
@@ -486,10 +488,13 @@ assert_expr <- function(arg,
 #' @family assertion
 #'
 #' @examples
-#' library(pharmaversesdtm)
 #' library(dplyr, warn.conflicts = FALSE)
 #' library(rlang)
-#' data(dm)
+#' dm <- dplyr::tribble(
+#'   ~DOMAIN,  ~STUDYID,      ~USUBJID, ~AGE,
+#'   "DM",    "STUDY X", "01-701-1015",   64,
+#'   "DM",    "STUDY X", "01-701-1016",   65,
+#' )
 #'
 #' # typical usage in a function as an argument check
 #' example_fun <- function(dat, x) {

diff --git a/R/tmp_vars.R b/R/tmp_vars.R
@@ -19,8 +19,11 @@
 #'
 #' @examples
 #' library(dplyr, warn.conflicts = FALSE)
-#' library(pharmaversesdtm)
-#' data(dm)
+#' dm <- tribble(
+#'   ~DOMAIN,  ~STUDYID,      ~USUBJID,
+#'   "DM",    "STUDY X", "01-701-1015",
+#'   "DM",    "STUDY X", "01-701-1016",
+#' )
 #'
 #' tmp_var <- get_new_tmp_var(dm)
 #' mutate(dm, !!tmp_var := NA)
@@ -69,8 +72,11 @@ get_new_tmp_var <- function(dataset, prefix = "tmp_var") {
 #'
 #' @examples
 #' library(dplyr, warn.conflicts = FALSE)
-#' library(pharmaversesdtm)
-#' data(dm)
+#' dm <- tribble(
+#'   ~DOMAIN,  ~STUDYID,      ~USUBJID,
+#'   "DM",    "STUDY X", "01-701-1015",
+#'   "DM",    "STUDY X", "01-701-1016",
+#' )
 #' dm <- select(dm, USUBJID)
 #' tmp_var <- get_new_tmp_var(dm)
 #' dm <- mutate(dm, !!tmp_var := NA)

diff --git a/R/warnings.R b/R/warnings.R
@@ -14,8 +14,12 @@
 #' @export
 #'
 #' @examples
-#' library(pharmaversesdtm)
-#' data(dm)
+#' library(dplyr, warn.conflicts = FALSE)
+#' dm <- tribble(
+#'   ~USUBJID,           ~ARM,
+#'   "01-701-1015", "Placebo",
+#'   "01-701-1016", "Placebo",
+#' )
 #'
 #' ## No warning as `AAGE` doesn't exist in `dm`
 #' warn_if_vars_exist(dm, "AAGE")

diff --git a/man/assert_filter_cond.Rd b/man/assert_filter_cond.Rd
diff --git a/man/assert_symbol.Rd b/man/assert_symbol.Rd
diff --git a/man/get_new_tmp_var.Rd b/man/get_new_tmp_var.Rd
diff --git a/man/remove_tmp_vars.Rd b/man/remove_tmp_vars.Rd
diff --git a/man/warn_if_vars_exist.Rd b/man/warn_if_vars_exist.Rd
diff --git a/tests/testthat/_snaps/assertions.md b/tests/testthat/_snaps/assertions.md
@@ -264,7 +264,7 @@
 # assert_one_to_one Test 84: error if there is a one to many mapping
 
     Code
-      assert_one_to_one(pharmaversesdtm::dm, exprs(DOMAIN), exprs(USUBJID))
+      assert_one_to_one(dm, exprs(DOMAIN), exprs(USUBJID))
     Condition
       Error:
       ! For some values of "DOMAIN" there is more than one value of "USUBJID"

diff --git a/tests/testthat/test-assertions.R b/tests/testthat/test-assertions.R
@@ -6,13 +6,21 @@ test_that("assert_has_variables Test 1: error if a required variable is missing
     "1"
   )
 
+  dm <- dplyr::tribble(
+    ~DOMAIN,      ~USUBJID,
+    "DM",    "01-701-1015",
+    "DM",    "01-701-1016",
+    "DM",    "01-701-1023",
+    "DM",    "01-701-1024",
+  )
+
   expect_error(
     assert_has_variables(data, "TRT01P"),
     class = "lifecycle_error_deprecated"
   )
 
   expect_error(
-    assert_has_variables(pharmaversesdtm::dm, c("TRT01P", "AVAL")),
+    assert_has_variables(dm, c("TRT01P", "AVAL")),
     class = "lifecycle_error_deprecated"
   )
 })
@@ -293,7 +301,11 @@ test_that("assert_data_frame Test 15: error if required variables are missing",
     assert_data_frame(dataset, required_vars = exprs(STUDYID, USUBJID))
   }
 
-  admiral_dm <- pharmaversesdtm::dm %>% select(-c(STUDYID, USUBJID))
+  admiral_dm <- dplyr::tribble(
+    ~USUBJID2,
+    "01-701-1015",
+    "01-701-1016",
+  )
 
   expect_error(
     example_fun(admiral_dm)
@@ -306,7 +318,11 @@ test_that("assert_data_frame Test 16: error if required variable is missing", {
     assert_data_frame(dataset, required_vars = exprs(STUDYID, USUBJID))
   }
 
-  admiral_dm <- pharmaversesdtm::dm %>% select(-c(USUBJID))
+  admiral_dm <- dplyr::tribble(
+    ~USUBJID,
+    "01-701-1015",
+    "01-701-1016",
+  )
 
   expect_error(
     example_fun(admiral_dm)
@@ -533,7 +549,11 @@ test_that("assert_symbol Test 28: `assert_symbol` does not throw an error if `ar
     v <- enexpr(var)
   }
 
-  admiral_dm <- pharmaversesdtm::dm
+  admiral_dm <- dplyr::tribble(
+    ~DOMAIN,      ~USUBJID,
+    "DM",    "01-701-1015",
+    "DM",    "01-701-1016",
+  )
 
   example_fun <- function(arg) {
     assert_symbol(arg)
@@ -549,8 +569,14 @@ test_that("assert_symbol Test 28: `assert_symbol` does not throw an error if `ar
 # assert_expr ----
 ## Test 29: `assert_expr` does not throw an error if `arg` is an expression ----
 test_that("assert_expr Test 29: `assert_expr` does not throw an error if `arg` is an expression", {
+  dm <- dplyr::tribble(
+    ~DOMAIN,      ~USUBJID,
+    "DM",    "01-701-1015",
+    "DM",    "01-701-1016",
+  )
+
   expect_invisible(
-    assert_expr(var <- expr(pharmaversesdtm::dm))
+    assert_expr(var <- expr(dm))
   )
 })
 
@@ -873,8 +899,13 @@ test_that("assert_named_exprs Test 54: error if `arg` is not a named list of exp
     example_fun(5),
     class = "lifecycle_error_deprecated"
   )
+  dm <- dplyr::tribble(
+    ~DOMAIN,      ~USUBJID,
+    "DM",    "01-701-1015",
+    "DM",    "01-701-1016",
+  )
   expect_error(
-    example_fun(pharmaversesdtm::dm),
+    example_fun(dm),
     class = "lifecycle_error_deprecated"
   )
   expect_error(
@@ -1267,23 +1298,39 @@ test_that("assert_list_element Test 83: error if the elements do not fulfill the
 # assert_one_to_one ----
 ## Test 84: error if there is a one to many mapping ----
 test_that("assert_one_to_one Test 84: error if there is a one to many mapping", {
+  dm <- dplyr::tribble(
+    ~DOMAIN,      ~USUBJID,
+    "DM",    "01-701-1015",
+    "DM",    "01-701-1016",
+    "DM",    "01-701-1023",
+    "DM",    "01-701-1024",
+  )
+
   expect_error(
-    assert_one_to_one(pharmaversesdtm::dm, exprs(DOMAIN), exprs(USUBJID)),
+    assert_one_to_one(dm, exprs(DOMAIN), exprs(USUBJID)),
     class = "assert_one_to_one"
   )
   admiraldev_environment$one_to_many <- NULL
 
   expect_snapshot(
     error = TRUE,
-    assert_one_to_one(pharmaversesdtm::dm, exprs(DOMAIN), exprs(USUBJID))
+    assert_one_to_one(dm, exprs(DOMAIN), exprs(USUBJID))
   )
   admiraldev_environment$one_to_many <- NULL
 })
 
 ## Test 85: error if there is a many to one mapping ----
 test_that("assert_one_to_one Test 85: error if there is a many to one mapping", {
+  dm <- dplyr::tribble(
+    ~DOMAIN,      ~USUBJID,
+    "DM",    "01-701-1015",
+    "DM",    "01-701-1016",
+    "DM",    "01-701-1023",
+    "DM",    "01-701-1024",
+  )
+
   expect_error(
-    assert_one_to_one(pharmaversesdtm::dm, exprs(USUBJID), exprs(DOMAIN)),
+    assert_one_to_one(dm, exprs(USUBJID), exprs(DOMAIN)),
     class = "assert_one_to_one"
   )
   admiraldev_environment$many_to_one <- NULL

diff --git a/tests/testthat/test-tmp_vars.R b/tests/testthat/test-tmp_vars.R
@@ -1,4 +1,8 @@
-dm <- select(pharmaversesdtm::dm, USUBJID)
+dm <- dplyr::tribble(
+  ~USUBJID,
+  "01-701-1015",
+  "01-701-1016",
+)
 
 # get_new_tmp_var ----
 ## Test 1: creating temporary variables works ----

diff --git a/tests/testthat/test-warnings.R b/tests/testthat/test-warnings.R
@@ -1,7 +1,11 @@
 # warn_if_vars_exist ----
 ## Test 1: warning if a variable already exists in the input dataset ----
 test_that("warn_if_vars_exist Test 1: warning if a variable already exists in the input dataset", {
-  dm <- pharmaversesdtm::dm
+  dm <- dplyr::tribble(
+    ~USUBJID,      ~AGE,   ~AGEU,      ~ARM,
+    "01-701-1015",   25, "YEARS", "Placebo",
+    "01-701-1016",   27, "YEARS", "Placebo",
+  )
 
   expect_snapshot(
     warn_if_vars_exist(dm, "AGE")

diff --git a/vignettes/writing_vignettes.Rmd b/vignettes/writing_vignettes.Rmd
@@ -127,10 +127,16 @@ function so that it is displayed consistently across the vignettes.E.g.
 ```{r, include=FALSE}
 library(lubridate)
 library(dplyr)
-library(pharmaversesdtm)
 library(DT)
 
 data(vs)
+vs <- tribble(
+  ~USUBJID, ~VSTESTCD, ~VISIT, ~VSDTC,
+  "01-701-1015", "WEIGHT", "BASELINE", "2013-12-26",
+  "01-701-1015", "WEIGHT", "WEEK 2", "2014-01-14",
+  "01-701-1016", "WEIGHT", "BASELINE", "2014-01-06",
+  "01-701-1016", "WEIGHT", "WEEK 2", "2014-01-22",
+)
 ```
 
 ```{r, eval=FALSE, echo=TRUE}