87 remove datasets - decrease package size (#228)

In the spirit of package size reduction insightsengineering/nestdevs-tasks#87 I replaced all the calls for tmg datasets with their respective datasets from teal.data. This way we no longer need to have datasets copies in tmg.
insightsengineering · Dec 13, 2024 · f0b28e0 · f0b28e0
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diff --git a/R/choices_labeled.R b/R/choices_labeled.R
@@ -23,8 +23,8 @@
 #' @return Named `character` vector.
 #'
 #' @examples
-#' library(shiny)
 #' library(teal.data)
+#' library(shiny)
 #'
 #' ADSL <- rADSL
 #' ADTTE <- rADTTE
@@ -151,7 +151,6 @@ choices_labeled <- function(choices, labels, subset = NULL, types = NULL) {
 #'
 #' @examples
 #' library(teal.data)
-#'
 #' ADRS <- rADRS
 #' variable_choices(ADRS)
 #' variable_choices(ADRS, subset = c("PARAM", "PARAMCD"))
@@ -267,7 +266,7 @@ variable_choices.data.frame <- function(data, subset = NULL, fill = TRUE, key =
 #' @return named character vector or `delayed_data` object.
 #'
 #' @examples
-#' ADRS <- rADRS
+#' ADRS <- teal.data::rADRS
 #' value_choices(ADRS, "PARAMCD", "PARAM", subset = c("BESRSPI", "INVET"))
 #' value_choices(ADRS, c("PARAMCD", "ARMCD"), c("PARAM", "ARM"))
 #' value_choices(ADRS, c("PARAMCD", "ARMCD"), c("PARAM", "ARM"),

diff --git a/R/choices_selected.R b/R/choices_selected.R
@@ -50,7 +50,7 @@ no_select_keyword <- "-- no selection --"
 #'   selected = "C"
 #' )
 #'
-#' ADSL <- rADSL
+#' ADSL <- teal.data::rADSL
 #' choices_selected(variable_choices(ADSL), "SEX")
 #'
 #' # How to select nothing

diff --git a/R/data.R b/R/data.R
diff --git a/R/resolve_delayed.R b/R/resolve_delayed.R
@@ -12,7 +12,7 @@
 #' @examples
 #' library(shiny)
 #'
-#' ADSL <- rADSL
+#' ADSL <- teal.data::rADSL
 #' isolate({
 #'   data_list <- list(ADSL = reactive(ADSL))
 #'

diff --git a/README.md b/README.md
@@ -47,7 +47,7 @@ Below is a small example usage:
 
 ```r
 library(teal.transform)
-ADSL <- rADSL
+ADSL <- teal.data::rADSL
 
 adsl_extract <- data_extract_spec(
   dataname = "ADSL",

diff --git a/data-raw/data.R b/data-raw/data.R
diff --git a/data/rADAE.rda b/data/rADAE.rda
diff --git a/data/rADLB.rda b/data/rADLB.rda
diff --git a/data/rADRS.rda b/data/rADRS.rda
diff --git a/data/rADSL.rda b/data/rADSL.rda
diff --git a/data/rADTTE.rda b/data/rADTTE.rda
diff --git a/man/choices_labeled.Rd b/man/choices_labeled.Rd
diff --git a/man/choices_selected.Rd b/man/choices_selected.Rd
diff --git a/man/rADAE.Rd b/man/rADAE.Rd
diff --git a/man/rADLB.Rd b/man/rADLB.Rd
diff --git a/man/rADRS.Rd b/man/rADRS.Rd
diff --git a/man/rADSL.Rd b/man/rADSL.Rd
diff --git a/man/rADTTE.Rd b/man/rADTTE.Rd
diff --git a/man/resolve_delayed.Rd b/man/resolve_delayed.Rd
diff --git a/man/value_choices.Rd b/man/value_choices.Rd
diff --git a/man/variable_choices.Rd b/man/variable_choices.Rd
diff --git a/tests/testthat/test-data_extract_module.R b/tests/testthat/test-data_extract_module.R
@@ -1,5 +1,5 @@
-ADLB <- rADLB
-ADTTE <- rADTTE
+ADLB <- teal.data::rADLB
+ADTTE <- teal.data::rADTTE
 
 testthat::test_that("Single filter", {
   data_extract <- data_extract_spec(

diff --git a/tests/testthat/test-data_extract_multiple_srv.R b/tests/testthat/test-data_extract_multiple_srv.R
@@ -1,6 +1,6 @@
-ADSL <- rADSL
-ADLB <- rADLB
-ADTTE <- rADTTE
+ADSL <- teal.data::rADSL
+ADLB <- teal.data::rADLB
+ADTTE <- teal.data::rADTTE
 
 data_list <- list(ADSL = reactive(ADSL), ADTTE = reactive(ADTTE), ADLB = reactive(ADLB))
 join_keys <- teal.data::default_cdisc_join_keys[c("ADSL", "ADTTE", "ADLB")]

diff --git a/tests/testthat/test-data_extract_spec.R b/tests/testthat/test-data_extract_spec.R
@@ -1,5 +1,5 @@
-ADSL <- rADSL
-ADTTE <- rADTTE
+ADSL <- teal.data::rADSL
+ADTTE <- teal.data::rADTTE
 data_list <- list(ADSL = reactive(ADSL), ADTTE = reactive(ADTTE))
 key_list <- list(ADSL = c("STUDYID", "USUBJID"), ADTTE = c("STUDYID", "USUBJID", "PARAMCD"))
 

diff --git a/tests/testthat/test-data_extract_srv.R b/tests/testthat/test-data_extract_srv.R
@@ -1,6 +1,6 @@
-ADSL <- rADSL
-ADLB <- rADLB
-ADTTE <- rADTTE
+ADSL <- teal.data::rADSL
+ADLB <- teal.data::rADLB
+ADTTE <- teal.data::rADTTE
 
 data_list <- list(ADSL = reactive(ADSL), ADTTE = reactive(ADTTE), ADLB = reactive(ADLB))
 join_keys <- teal.data::default_cdisc_join_keys[c("ADSL", "ADTTE", "ADLB")]

diff --git a/tests/testthat/test-delayed_data_extract.R b/tests/testthat/test-delayed_data_extract.R
@@ -1,9 +1,9 @@
 # Contains integration tests between delayed data loading objects and
 # the objects responsible for loading, pulling and filtering the data
-ADSL <- rADSL
-ADTTE <- rADTTE
-ADAE <- rADAE
-ADRS <- rADRS
+ADSL <- teal.data::rADSL
+ADTTE <- teal.data::rADTTE
+ADAE <- teal.data::rADAE
+ADRS <- teal.data::rADRS
 
 data_list <- list(ADSL = reactive(ADSL), ADTTE = reactive(ADTTE), ADAE = reactive(ADAE), ADRS = reactive(ADRS))
 join_keys <- teal.data::default_cdisc_join_keys[c("ADSL", "ADTTE", "ADAE", "ADRS")]

diff --git a/tests/testthat/test-filter_spec.R b/tests/testthat/test-filter_spec.R
@@ -1,5 +1,5 @@
-ADSL <- rADSL
-ADTTE <- rADTTE
+ADSL <- teal.data::rADSL
+ADTTE <- teal.data::rADTTE
 data_list <- list(ADSL = reactive(ADSL), ADTTE = reactive(ADTTE), ADLB = reactive(ADLB))
 join_keys <- teal.data::default_cdisc_join_keys[c("ADSL", "ADTTE", "ADLB")]
 primary_keys_list <- lapply(join_keys, function(x) x[[1]])
@@ -218,7 +218,7 @@ testthat::test_that("filter_spec_internal", {
 })
 
 testthat::test_that("filter_spec_internal contains dataname", {
-  ADSL <- rADSL
+  ADSL <- teal.data::rADSL
 
   x_filter <- filter_spec_internal(
     vars_choices = variable_choices(ADSL)

diff --git a/tests/testthat/test-resolve.R b/tests/testthat/test-resolve.R
@@ -1,5 +1,5 @@
-ADSL <- rADSL
-ADTTE <- rADTTE
+ADSL <- teal.data::rADSL
+ADTTE <- teal.data::rADTTE
 
 arm_ref_comp <- list(
   ARMCD = list(

diff --git a/tests/testthat/test-resolve_delayed.R b/tests/testthat/test-resolve_delayed.R
@@ -1,5 +1,5 @@
-adsl <- rADSL
-adtte <- rADTTE
+adsl <- teal.data::rADSL
+adtte <- teal.data::rADTTE
 
 data_list <- list(ADSL = reactive(adsl), ADTTE = reactive(adtte))
 join_keys <- teal.data::default_cdisc_join_keys[c("ADSL", "ADTTE")]

diff --git a/tests/testthat/test-select_spec.R b/tests/testthat/test-select_spec.R
@@ -1,5 +1,5 @@
-adsl <- rADSL
-adtte <- rADTTE
+adsl <- teal.data::rADSL
+adtte <- teal.data::rADTTE
 data_list <- list(ADSL = reactive(adsl), ADTTE = reactive(adtte))
 primary_keys_list <- list(ADSL = c("STUDYID", "USUBJID"), ADTTE = c("STUDYID", "USUBJID", "PARAMCD"))
 

diff --git a/tests/testthat/test-value_choices.R b/tests/testthat/test-value_choices.R
@@ -1,5 +1,5 @@
-ADSL <- rADSL
-ADTTE <- rADTTE
+ADSL <- teal.data::rADSL
+ADTTE <- teal.data::rADTTE
 data_list <- list(ADSL = reactive(ADSL), ADTTE = reactive(ADTTE))
 primary_keys_list <- list(ADSL = c("STUDYID", "USUBJID"), ADTTE = c("STUDYID", "USUBJID", "PARAMCD"))
 

diff --git a/tests/testthat/test-variable_choices.R b/tests/testthat/test-variable_choices.R
@@ -1,5 +1,5 @@
-ADSL <- rADSL
-ADTTE <- rADTTE
+ADSL <- teal.data::rADSL
+ADTTE <- teal.data::rADTTE
 data_list <- list(ADSL = reactive(ADSL), ADTTE = reactive(ADTTE))
 primary_keys_list <- list(ADSL = c("STUDYID", "USUBJID"), ADTTE = c("STUDYID", "USUBJID", "PARAMCD"))