chasing deprecations (#852)

+ changes filer definition in example apps to use `teal_slices`
+ adds namespace prefixes to `get_join_keys` following moving the
function to `teal.data`
+ adds `teal.data` to `Imports`

---------

Co-authored-by: 27856297+dependabot-preview[bot]@users.noreply.github.com <27856297+dependabot-preview[bot]@users.noreply.github.com>

DESCRIPTION

@@ -54,6 +54,7 @@ Imports:
     stats,
     styler,
     teal.code (>= 0.4.0),
+    teal.data (>= 0.3.0.9009),
     teal.logger (>= 0.1.1),
     teal.reporter (>= 0.2.0),
     teal.transform (>= 0.4.0),
@@ -68,7 +69,6 @@ Suggests:
     knitr,
     lubridate,
     nestcolor (>= 0.1.0),
-    teal.data (>= 0.3.0),
     testthat (>= 3.0)
 VignetteBuilder:
     knitr

R/tm_a_gee.R

@@ -444,14 +444,14 @@ srv_gee <- function(id,
       datasets = data,
       selector_list = selector_list,
       merge_function = "dplyr::inner_join",
-      join_keys = get_join_keys(data)
+      join_keys = teal.data::get_join_keys(data)
     )
 
     adsl_inputs <- teal.transform::merge_expression_module(
       datasets = data,
       data_extract = list(arm_var = arm_var),
       anl_name = "ANL_ADSL",
-      join_keys = get_join_keys(data)
+      join_keys = teal.data::get_join_keys(data)
     )
 
     anl_q <- shiny::reactive({

R/tm_a_mmrm.R

@@ -917,14 +917,14 @@ srv_mmrm <- function(id,
     anl_inputs <- teal.transform::merge_expression_srv(
       datasets = data,
       selector_list = selector_list_without_cov,
-      join_keys = get_join_keys(data),
+      join_keys = teal.data::get_join_keys(data),
       merge_function = "dplyr::inner_join"
     )
 
     adsl_merge_inputs <- teal.transform::merge_expression_module(
       datasets = data,
       data_extract = list(arm_var = arm_var),
-      join_keys = get_join_keys(data),
+      join_keys = teal.data::get_join_keys(data),
       anl_name = "ANL_ADSL"
     )
 

R/tm_g_barchart_simple.R

@@ -374,7 +374,7 @@ srv_g_barchart_simple <- function(id,
 
     anl_inputs <- teal.transform::merge_expression_srv(
       datasets = data,
-      join_keys = get_join_keys(data),
+      join_keys = teal.data::get_join_keys(data),
       selector_list = selector_list
     )
 

R/tm_g_ci.R

@@ -399,7 +399,7 @@ srv_g_ci <- function(id, # nolint
 
     anl_inputs <- teal.transform::merge_expression_srv(
       datasets = data,
-      join_keys = get_join_keys(data),
+      join_keys = teal.data::get_join_keys(data),
       selector_list = selector_list
     )
 

R/tm_g_forest_rsp.R

@@ -514,13 +514,13 @@ srv_g_forest_rsp <- function(id,
       datasets = data,
       selector_list = selector_list,
       merge_function = "dplyr::inner_join",
-      join_keys = get_join_keys(data)
+      join_keys = teal.data::get_join_keys(data)
     )
 
     adsl_inputs <- teal.transform::merge_expression_module(
       datasets = data,
       data_extract = list(arm_var = arm_var, subgroup_var = subgroup_var, strata_var = strata_var),
-      join_keys = get_join_keys(data),
+      join_keys = teal.data::get_join_keys(data),
       anl_name = "ANL_ADSL"
     )
 

R/tm_g_forest_tte.R

@@ -517,14 +517,14 @@ srv_g_forest_tte <- function(id,
 
     anl_inputs <- teal.transform::merge_expression_srv(
       datasets = data,
-      join_keys = get_join_keys(data),
+      join_keys = teal.data::get_join_keys(data),
       selector_list = selector_list,
       merge_function = "dplyr::inner_join"
     )
 
     adsl_inputs <- teal.transform::merge_expression_module(
       datasets = data,
-      join_keys = get_join_keys(data),
+      join_keys = teal.data::get_join_keys(data),
       data_extract = list(arm_var = arm_var, subgroup_var = subgroup_var, strata_var = strata_var),
       anl_name = "ANL_ADSL"
     )

R/tm_g_ipp.R

@@ -492,12 +492,12 @@ srv_g_ipp <- function(id,
       datasets = data,
       selector_list = selector_list,
       merge_function = "dplyr::inner_join",
-      join_keys = get_join_keys(data)
+      join_keys = teal.data::get_join_keys(data)
     )
 
     adsl_inputs <- teal.transform::merge_expression_module(
       datasets = data,
-      join_keys = get_join_keys(data),
+      join_keys = teal.data::get_join_keys(data),
       data_extract = list(arm_var = arm_var, id_var = id_var),
       anl_name = "ANL_ADSL"
     )

R/tm_g_km.R

@@ -652,7 +652,7 @@ srv_g_km <- function(id,
 
     anl_inputs <- teal.transform::merge_expression_srv(
       datasets = data,
-      join_keys = get_join_keys(data),
+      join_keys = teal.data::get_join_keys(data),
       selector_list = selector_list,
       merge_function = "dplyr::inner_join"
     )

R/tm_g_lineplot.R

@@ -551,7 +551,7 @@ srv_g_lineplot <- function(id,
 
     anl_inputs <- teal.transform::merge_expression_srv(
       datasets = data,
-      join_keys = get_join_keys(data),
+      join_keys = teal.data::get_join_keys(data),
       selector_list = selector_list,
       merge_function = "dplyr::inner_join"
     )

R/tm_g_pp_adverse_events.R

@@ -492,7 +492,7 @@ srv_g_adverse_events <- function(id,
     anl_inputs <- teal.transform::merge_expression_srv(
       datasets = data,
       selector_list = selector_list,
-      join_keys = get_join_keys(data)
+      join_keys = teal.data::get_join_keys(data)
     )
 
     anl_q <- shiny::reactive(

R/tm_g_pp_patient_timeline.R

@@ -762,7 +762,7 @@ srv_g_patient_timeline <- function(id,
 
     anl_inputs <- teal.transform::merge_expression_srv(
       datasets = data,
-      join_keys = get_join_keys(data),
+      join_keys = teal.data::get_join_keys(data),
       selector_list = selector_list
     )
 

R/tm_g_pp_therapy.R

@@ -602,7 +602,7 @@ srv_g_therapy <- function(id,
 
     anl_inputs <- teal.transform::merge_expression_srv(
       datasets = data,
-      join_keys = get_join_keys(data),
+      join_keys = teal.data::get_join_keys(data),
       selector_list = selector_list,
       merge_function = "dplyr::left_join"
     )

R/tm_g_pp_vitals.R

@@ -425,7 +425,7 @@ srv_g_vitals <- function(id,
 
     anl_inputs <- teal.transform::merge_expression_srv(
       datasets = data,
-      join_keys = get_join_keys(data),
+      join_keys = teal.data::get_join_keys(data),
       selector_list = selector_list,
       merge_function = "dplyr::left_join"
     )

R/tm_t_abnormality.R

@@ -539,14 +539,14 @@ srv_t_abnormality <- function(id,
 
     anl_inputs <- teal.transform::merge_expression_srv(
       datasets = data,
-      join_keys = get_join_keys(data),
+      join_keys = teal.data::get_join_keys(data),
       selector_list = selector_list,
       merge_function = "dplyr::inner_join"
     )
 
     adsl_inputs <- teal.transform::merge_expression_module(
       datasets = data,
-      join_keys = get_join_keys(data),
+      join_keys = teal.data::get_join_keys(data),
       data_extract = list(arm_var = arm_var),
       anl_name = "ANL_ADSL"
     )

R/tm_t_abnormality_by_worst_grade.R

@@ -269,11 +269,9 @@ template_abnormality_by_worst_grade <- function(parentname, # nolint
 #'       add_total = FALSE
 #'     )
 #'   ),
-#'   filter = (
-#'     list(
-#'       ADSL = list(SAFFL = "Y"),
-#'       ADLB = list(ONTRTFL = "Y")
-#'     )
+#'   filter = teal_slices(
+#'     teal_slice("ADSL", "SAFFL", selected = "Y"),
+#'     teal_slice("ADLB", "ONTRTFL", selected = "Y")
 #'   )
 #' )
 #' if (interactive()) {
@@ -529,13 +527,13 @@ srv_t_abnormality_by_worst_grade <- function(id, # nolint
     anl_inputs <- teal.transform::merge_expression_srv(
       selector_list = selector_list,
       datasets = data,
-      join_keys = get_join_keys(data),
+      join_keys = teal.data::get_join_keys(data),
       merge_function = "dplyr::inner_join"
     )
 
     adsl_inputs <- teal.transform::merge_expression_module(
       datasets = data,
-      join_keys = get_join_keys(data),
+      join_keys = teal.data::get_join_keys(data),
       data_extract = list(arm_var = arm_var),
       anl_name = "ANL_ADSL"
     )

R/tm_t_ancova.R

@@ -726,15 +726,15 @@ srv_ancova <- function(id,
     anl_inputs <- teal.transform::merge_expression_srv(
       selector_list = selector_list,
       datasets = data,
-      join_keys = get_join_keys(data),
+      join_keys = teal.data::get_join_keys(data),
       merge_function = "dplyr::inner_join"
     )
 
     adsl_inputs <- teal.transform::merge_expression_module(
       datasets = data,
       data_extract = list(arm_var = arm_var),
       anl_name = "ANL_ADSL",
-      join_keys = get_join_keys(data)
+      join_keys = teal.data::get_join_keys(data)
     )
 
     anl_q <- shiny::reactive({

R/tm_t_binary_outcome.R

@@ -783,13 +783,13 @@ srv_t_binary_outcome <- function(id,
       datasets = data,
       selector_list = selector_list,
       merge_function = "dplyr::inner_join",
-      join_keys = get_join_keys(data)
+      join_keys = teal.data::get_join_keys(data)
     )
 
     adsl_inputs <- teal.transform::merge_expression_module(
       datasets = data,
       data_extract = list(arm_var = arm_var, strata_var = strata_var),
-      join_keys = get_join_keys(data),
+      join_keys = teal.data::get_join_keys(data),
       anl_name = "ANL_ADSL"
     )
 

R/tm_t_coxreg.R

@@ -788,7 +788,7 @@ srv_t_coxreg <- function(id,
 
     anl_inputs <- teal.transform::merge_expression_srv(
       datasets = data,
-      join_keys = get_join_keys(data),
+      join_keys = teal.data::get_join_keys(data),
       selector_list = selector_list,
       merge_function = "dplyr::inner_join"
     )

R/tm_t_events.R

@@ -675,7 +675,7 @@ srv_t_events_byterm <- function(id,
 
     anl_inputs <- teal.transform::merge_expression_srv(
       datasets = data,
-      join_keys = get_join_keys(data),
+      join_keys = teal.data::get_join_keys(data),
       selector_list = selector_list,
       merge_function = "dplyr::inner_join"
     )
@@ -684,7 +684,7 @@ srv_t_events_byterm <- function(id,
       datasets = data,
       data_extract = list(arm_var = arm_var),
       anl_name = "ANL_ADSL",
-      join_keys = get_join_keys(data)
+      join_keys = teal.data::get_join_keys(data)
     )
 
     anl_q <- shiny::reactive({

R/tm_t_events_by_grade.R

@@ -1042,14 +1042,14 @@ srv_t_events_by_grade <- function(id,
     anl_inputs <- teal.transform::merge_expression_srv(
       datasets = data,
       selector_list = selector_list,
-      join_keys = get_join_keys(data),
+      join_keys = teal.data::get_join_keys(data),
       merge_function = "dplyr::inner_join"
     )
 
     adsl_inputs <- teal.transform::merge_expression_module(
       datasets = data,
       data_extract = list(arm_var = arm_var),
-      join_keys = get_join_keys(data),
+      join_keys = teal.data::get_join_keys(data),
       anl_name = "ANL_ADSL"
     )
 

R/tm_t_events_patyear.R

@@ -436,14 +436,14 @@ srv_events_patyear <- function(id,
     anl_inputs <- teal.transform::merge_expression_srv(
       datasets = data,
       selector_list = selector_list,
-      join_keys = get_join_keys(data),
+      join_keys = teal.data::get_join_keys(data),
       merge_function = "dplyr::inner_join"
     )
 
     adsl_inputs <- teal.transform::merge_expression_module(
       datasets = data,
       data_extract = list(arm_var = arm_var),
-      join_keys = get_join_keys(data),
+      join_keys = teal.data::get_join_keys(data),
       anl_name = "ANL_ADSL"
     )
 

R/tm_t_events_summary.R

@@ -820,14 +820,14 @@ srv_t_events_summary <- function(id,
     anl_inputs <- teal.transform::merge_expression_srv(
       datasets = data,
       selector_list = selector_list,
-      join_keys = get_join_keys(data),
+      join_keys = teal.data::get_join_keys(data),
       merge_function = "dplyr::inner_join"
     )
 
     adsl_inputs <- teal.transform::merge_expression_module(
       datasets = data,
       data_extract = Filter(Negate(is.null), list(arm_var = arm_var, dthfl_var = dthfl_var, dcsreas_var = dcsreas_var)),
-      join_keys = get_join_keys(data),
+      join_keys = teal.data::get_join_keys(data),
       anl_name = "ANL_ADSL"
     )
 

R/tm_t_exposure.R

@@ -269,9 +269,7 @@ template_exposure <- function(parentname,
 #'       add_total = FALSE
 #'     )
 #'   ),
-#'   filter = list(
-#'     ADSL = list(SAFFL = "Y")
-#'   )
+#'   filter = teal_slices(teal_slice("ADSL", "SAFFL", selected = "Y"))
 #' )
 #' if (interactive()) {
 #'   shinyApp(app$ui, app$server)
@@ -524,13 +522,13 @@ srv_t_exposure <- function(id,
     anl_inputs <- teal.transform::merge_expression_srv(
       datasets = data,
       selector_list = selector_list,
-      join_keys = get_join_keys(data),
+      join_keys = teal.data::get_join_keys(data),
       merge_function = "dplyr::inner_join"
     )
 
     adsl_inputs <- teal.transform::merge_expression_module(
       datasets = data,
-      join_keys = get_join_keys(data),
+      join_keys = teal.data::get_join_keys(data),
       data_extract = list(col_by_var = col_by_var),
       anl_name = "ANL_ADSL"
     )

R/tm_t_logistic.R

@@ -518,13 +518,13 @@ srv_t_logistic <- function(id,
     anl_inputs <- teal.transform::merge_expression_srv(
       selector_list = selector_list,
       datasets = data,
-      join_keys = get_join_keys(data),
+      join_keys = teal.data::get_join_keys(data),
       merge_function = "dplyr::inner_join"
     )
 
     adsl_inputs <- teal.transform::merge_expression_module(
       datasets = data,
-      join_keys = get_join_keys(data),
+      join_keys = teal.data::get_join_keys(data),
       data_extract = list(arm_var = arm_var),
       anl_name = "ANL_ADSL"
     )

R/tm_t_mult_events.R

@@ -479,15 +479,15 @@ srv_t_mult_events_byterm <- function(id,
     anl_merge_inputs <- teal.transform::merge_expression_srv(
       id = "anl_merge",
       datasets = data,
-      join_keys = get_join_keys(data),
+      join_keys = teal.data::get_join_keys(data),
       selector_list = selector_list,
       merge_function = "dplyr::inner_join"
     )
 
     adsl_merge_inputs <- teal.transform::merge_expression_module(
       id = "adsl_merge",
       datasets = data,
-      join_keys = get_join_keys(data),
+      join_keys = teal.data::get_join_keys(data),
       data_extract = list(arm_var = arm_var),
       anl_name = "ANL_ADSL"
     )

R/tm_t_pp_basic_info.R

@@ -218,7 +218,7 @@ srv_t_basic_info <- function(id,
 
     anl_inputs <- teal.transform::merge_expression_srv(
       datasets = data,
-      join_keys = get_join_keys(data),
+      join_keys = teal.data::get_join_keys(data),
       selector_list = selector_list,
       merge_function = "dplyr::left_join"
     )