fix R CMD CHECKS

insightsengineering · Dec 13, 2024 · 20bef3d · 20bef3d
1 parent 38228a9
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diff --git a/R/choices_labeled.R b/R/choices_labeled.R
@@ -23,10 +23,11 @@
 #' @return Named `character` vector.
 #'
 #' @examples
+#' library(teal.data)
 #' library(shiny)
 #'
-#' ADSL <- teal.data::rADSL
-#' ADTTE <- teal.data::rADTTE
+#' ADSL <- rADSL
+#' ADTTE <- rADTTE
 #'
 #' choices1 <- choices_labeled(names(ADSL), col_labels(ADSL, fill = FALSE))
 #' choices2 <- choices_labeled(ADTTE$PARAMCD, ADTTE$PARAM)
@@ -149,7 +150,8 @@ choices_labeled <- function(choices, labels, subset = NULL, types = NULL) {
 #' @return Named `character` vector with additional attributes or `delayed_data` object.
 #'
 #' @examples
-#' ADRS <- teal.data::rADRS
+#' library(teal.data)
+#' ADRS <- rADRS
 #' variable_choices(ADRS)
 #' variable_choices(ADRS, subset = c("PARAM", "PARAMCD"))
 #' variable_choices(ADRS, subset = c("", "PARAM", "PARAMCD"))

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/man/choices_labeled.Rd b/man/choices_labeled.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"))
 

diff --git a/vignettes/data-extract-merge.Rmd b/vignettes/data-extract-merge.Rmd
@@ -40,8 +40,8 @@ library(teal.data)
 library(shiny)
 
 # Define data.frame objects
-ADSL <- rADSL
-ADTTE <- rADTTE
+ADSL <- teal.data::rADSL
+ADTTE <- teal.data::rADTTE
 
 # create a list of reactive data.frame objects
 datasets <- list(

diff --git a/vignettes/data-extract.Rmd b/vignettes/data-extract.Rmd
@@ -37,8 +37,8 @@ library(teal.data)
 library(shiny)
 
 # Define data.frame objects
-ADSL <- rADSL
-ADTTE <- rADTTE
+ADSL <- teal.data::rADSL
+ADTTE <- teal.data::rADTTE
 
 # create a list of reactive data.frame objects
 datasets <- list(

diff --git a/vignettes/data-merge.Rmd b/vignettes/data-merge.Rmd
@@ -41,8 +41,8 @@ library(teal.data)
 library(shiny)
 
 # Define data.frame objects
-ADSL <- rADSL
-ADTTE <- rADTTE
+ADSL <- teal.data::rADSL
+ADTTE <- teal.data::rADTTE
 
 # create a list of reactive data.frame objects
 datasets <- list(