adding join_key changes.

insightsengineering · Nov 9, 2023 · 8fb47d5 · 8fb47d5
1 parent b560850
commit 8fb47d5
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Showing 47 changed files with 89 additions and 93 deletions.
diff --git a/R/tm_a_gee.R b/R/tm_a_gee.R
@@ -145,7 +145,7 @@ template_a_gee <- function(output_table,
 #' })
 #' datanames <- c("ADSL", "ADQS")
 #' datanames(data) <- datanames
-#' data@join_keys <- cdisc_join_keys(!!!datanames)
+#' join_keys(data) <- cdisc_join_keys(!!!datanames)
 #'
 #' app <- init(
 #'   data = data,
@@ -447,14 +447,14 @@ srv_gee <- function(id,
       datasets = data,
       selector_list = selector_list,
       merge_function = "dplyr::inner_join",
-      join_keys = teal.data::get_join_keys(data)
+      join_keys = teal.data::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 = teal.data::get_join_keys(data)
+      join_keys = teal.data::join_keys(data)
     )
 
     anl_q <- shiny::reactive({

diff --git a/R/tm_a_mmrm.R b/R/tm_a_mmrm.R
@@ -476,7 +476,7 @@ template_mmrm_plots <- function(fit_name,
 #'
 #' datanames <- c("ADSL", "ADQS")
 #' datanames(data) <- datanames
-#' data@join_keys <- cdisc_join_keys(!!!datanames)
+#' join_keys(data) <- cdisc_join_keys(!!!datanames)
 #' app <- init(
 #'   data = data,
 #'   modules = modules(
@@ -920,14 +920,14 @@ srv_mmrm <- function(id,
     anl_inputs <- teal.transform::merge_expression_srv(
       datasets = data,
       selector_list = selector_list_without_cov,
-      join_keys = teal.data::get_join_keys(data),
+      join_keys = teal.data::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 = teal.data::get_join_keys(data),
+      join_keys = teal.data::join_keys(data),
       anl_name = "ANL_ADSL"
     )
 

diff --git a/R/tm_g_barchart_simple.R b/R/tm_g_barchart_simple.R
@@ -381,7 +381,7 @@ srv_g_barchart_simple <- function(id,
 
     anl_inputs <- teal.transform::merge_expression_srv(
       datasets = data,
-      join_keys = teal.data::get_join_keys(data),
+      join_keys = teal.data::join_keys(data),
       selector_list = selector_list
     )
 

diff --git a/R/tm_g_ci.R b/R/tm_g_ci.R
@@ -403,7 +403,7 @@ srv_g_ci <- function(id, # nolint
 
     anl_inputs <- teal.transform::merge_expression_srv(
       datasets = data,
-      join_keys = teal.data::get_join_keys(data),
+      join_keys = teal.data::join_keys(data),
       selector_list = selector_list
     )
 

diff --git a/R/tm_g_forest_rsp.R b/R/tm_g_forest_rsp.R
@@ -521,13 +521,13 @@ srv_g_forest_rsp <- function(id,
       datasets = data,
       selector_list = selector_list,
       merge_function = "dplyr::inner_join",
-      join_keys = teal.data::get_join_keys(data)
+      join_keys = teal.data::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 = teal.data::get_join_keys(data),
+      join_keys = teal.data::join_keys(data),
       anl_name = "ANL_ADSL"
     )
 

diff --git a/R/tm_g_forest_tte.R b/R/tm_g_forest_tte.R
@@ -522,14 +522,14 @@ srv_g_forest_tte <- function(id,
 
     anl_inputs <- teal.transform::merge_expression_srv(
       datasets = data,
-      join_keys = teal.data::get_join_keys(data),
+      join_keys = teal.data::join_keys(data),
       selector_list = selector_list,
       merge_function = "dplyr::inner_join"
     )
 
     adsl_inputs <- teal.transform::merge_expression_module(
       datasets = data,
-      join_keys = teal.data::get_join_keys(data),
+      join_keys = teal.data::join_keys(data),
       data_extract = list(arm_var = arm_var, subgroup_var = subgroup_var, strata_var = strata_var),
       anl_name = "ANL_ADSL"
     )

diff --git a/R/tm_g_ipp.R b/R/tm_g_ipp.R
@@ -499,12 +499,12 @@ srv_g_ipp <- function(id,
       datasets = data,
       selector_list = selector_list,
       merge_function = "dplyr::inner_join",
-      join_keys = teal.data::get_join_keys(data)
+      join_keys = teal.data::join_keys(data)
     )
 
     adsl_inputs <- teal.transform::merge_expression_module(
       datasets = data,
-      join_keys = teal.data::get_join_keys(data),
+      join_keys = teal.data::join_keys(data),
       data_extract = list(arm_var = arm_var, id_var = id_var),
       anl_name = "ANL_ADSL"
     )

diff --git a/R/tm_g_km.R b/R/tm_g_km.R
@@ -656,7 +656,7 @@ srv_g_km <- function(id,
 
     anl_inputs <- teal.transform::merge_expression_srv(
       datasets = data,
-      join_keys = teal.data::get_join_keys(data),
+      join_keys = teal.data::join_keys(data),
       selector_list = selector_list,
       merge_function = "dplyr::inner_join"
     )

diff --git a/R/tm_g_lineplot.R b/R/tm_g_lineplot.R
@@ -555,7 +555,7 @@ srv_g_lineplot <- function(id,
 
     anl_inputs <- teal.transform::merge_expression_srv(
       datasets = data,
-      join_keys = teal.data::get_join_keys(data),
+      join_keys = teal.data::join_keys(data),
       selector_list = selector_list,
       merge_function = "dplyr::inner_join"
     )

diff --git a/R/tm_g_pp_adverse_events.R b/R/tm_g_pp_adverse_events.R
@@ -496,7 +496,7 @@ srv_g_adverse_events <- function(id,
     anl_inputs <- teal.transform::merge_expression_srv(
       datasets = data,
       selector_list = selector_list,
-      join_keys = teal.data::get_join_keys(data)
+      join_keys = teal.data::join_keys(data)
     )
 
     anl_q <- shiny::reactive(

diff --git a/R/tm_g_pp_patient_timeline.R b/R/tm_g_pp_patient_timeline.R
@@ -375,7 +375,7 @@ template_patient_timeline <- function(dataname = "ANL",
 #' })
 #'
 #' datanames(data) <- c("ADSL", "ADAE", "ADCM")
-#' data@join_keys <- join_keys(
+#' join_keys(data) <- join_keys(
 #'   join_key("ADSL", keys = get_cdisc_keys("ADSL")),
 #'   join_key("ADAE", keys = get_cdisc_keys("ADAE")),
 #'   join_key("ADCM", keys = adcm_keys),
@@ -772,7 +772,7 @@ srv_g_patient_timeline <- function(id,
 
     anl_inputs <- teal.transform::merge_expression_srv(
       datasets = data,
-      join_keys = teal.data::get_join_keys(data),
+      join_keys = teal.data::join_keys(data),
       selector_list = selector_list
     )
 

diff --git a/R/tm_g_pp_therapy.R b/R/tm_g_pp_therapy.R
@@ -613,7 +613,7 @@ srv_g_therapy <- function(id,
 
     anl_inputs <- teal.transform::merge_expression_srv(
       datasets = data,
-      join_keys = teal.data::get_join_keys(data),
+      join_keys = teal.data::join_keys(data),
       selector_list = selector_list,
       merge_function = "dplyr::left_join"
     )

diff --git a/R/tm_g_pp_vitals.R b/R/tm_g_pp_vitals.R
@@ -429,7 +429,7 @@ srv_g_vitals <- function(id,
 
     anl_inputs <- teal.transform::merge_expression_srv(
       datasets = data,
-      join_keys = teal.data::get_join_keys(data),
+      join_keys = teal.data::join_keys(data),
       selector_list = selector_list,
       merge_function = "dplyr::left_join"
     )

diff --git a/R/tm_t_abnormality.R b/R/tm_t_abnormality.R
@@ -251,7 +251,7 @@ template_abnormality <- function(parentname,
 #' })
 #' datanames <- c("ADSL", "ADLB")
 #' datanames(data) <- datanames
-#' data@join_keys <- cdisc_join_keys(!!!datanames)
+#' join_keys(data) <- cdisc_join_keys(!!!datanames)
 #'
 #' app <- init(
 #'   data = data,
@@ -542,14 +542,14 @@ srv_t_abnormality <- function(id,
 
     anl_inputs <- teal.transform::merge_expression_srv(
       datasets = data,
-      join_keys = teal.data::get_join_keys(data),
+      join_keys = teal.data::join_keys(data),
       selector_list = selector_list,
       merge_function = "dplyr::inner_join"
     )
 
     adsl_inputs <- teal.transform::merge_expression_module(
       datasets = data,
-      join_keys = teal.data::get_join_keys(data),
+      join_keys = teal.data::join_keys(data),
       data_extract = list(arm_var = arm_var),
       anl_name = "ANL_ADSL"
     )

diff --git a/R/tm_t_abnormality_by_worst_grade.R b/R/tm_t_abnormality_by_worst_grade.R
@@ -534,13 +534,13 @@ srv_t_abnormality_by_worst_grade <- function(id, # nolint
     anl_inputs <- teal.transform::merge_expression_srv(
       selector_list = selector_list,
       datasets = data,
-      join_keys = teal.data::get_join_keys(data),
+      join_keys = teal.data::join_keys(data),
       merge_function = "dplyr::inner_join"
     )
 
     adsl_inputs <- teal.transform::merge_expression_module(
       datasets = data,
-      join_keys = teal.data::get_join_keys(data),
+      join_keys = teal.data::join_keys(data),
       data_extract = list(arm_var = arm_var),
       anl_name = "ANL_ADSL"
     )

diff --git a/R/tm_t_ancova.R b/R/tm_t_ancova.R
@@ -730,15 +730,15 @@ srv_ancova <- function(id,
     anl_inputs <- teal.transform::merge_expression_srv(
       selector_list = selector_list,
       datasets = data,
-      join_keys = teal.data::get_join_keys(data),
+      join_keys = teal.data::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 = teal.data::get_join_keys(data)
+      join_keys = teal.data::join_keys(data)
     )
 
     anl_q <- shiny::reactive({

diff --git a/R/tm_t_binary_outcome.R b/R/tm_t_binary_outcome.R
@@ -792,13 +792,13 @@ srv_t_binary_outcome <- function(id,
       datasets = data,
       selector_list = selector_list,
       merge_function = "dplyr::inner_join",
-      join_keys = teal.data::get_join_keys(data)
+      join_keys = teal.data::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 = teal.data::get_join_keys(data),
+      join_keys = teal.data::join_keys(data),
       anl_name = "ANL_ADSL"
     )
 

diff --git a/R/tm_t_coxreg.R b/R/tm_t_coxreg.R
@@ -371,7 +371,7 @@ template_coxreg_m <- function(dataname,
 #' })
 #' datanames <- c("ADSL", "ADTTE")
 #' datanames(data) <- datanames
-#' data@join_keys <- cdisc_join_keys(!!!datanames)
+#' join_keys(data) <- cdisc_join_keys(!!!datanames)
 #'
 #' app <- init(
 #'   data = data,
@@ -439,7 +439,7 @@ template_coxreg_m <- function(dataname,
 #'
 #' datanames <- c("ADSL", "ADTTE")
 #' datanames(data) <- datanames
-#' data@join_keys <- cdisc_join_keys(!!!datanames)
+#' join_keys(data) <- cdisc_join_keys(!!!datanames)
 #'
 #' ## Teal application
 #' ## ================
@@ -790,7 +790,7 @@ srv_t_coxreg <- function(id,
 
     anl_inputs <- teal.transform::merge_expression_srv(
       datasets = data,
-      join_keys = teal.data::get_join_keys(data),
+      join_keys = teal.data::join_keys(data),
       selector_list = selector_list,
       merge_function = "dplyr::inner_join"
     )

diff --git a/R/tm_t_events.R b/R/tm_t_events.R
@@ -679,7 +679,7 @@ srv_t_events_byterm <- function(id,
 
     anl_inputs <- teal.transform::merge_expression_srv(
       datasets = data,
-      join_keys = teal.data::get_join_keys(data),
+      join_keys = teal.data::join_keys(data),
       selector_list = selector_list,
       merge_function = "dplyr::inner_join"
     )
@@ -688,7 +688,7 @@ srv_t_events_byterm <- function(id,
       datasets = data,
       data_extract = list(arm_var = arm_var),
       anl_name = "ANL_ADSL",
-      join_keys = teal.data::get_join_keys(data)
+      join_keys = teal.data::join_keys(data)
     )
 
     anl_q <- shiny::reactive({

diff --git a/R/tm_t_events_by_grade.R b/R/tm_t_events_by_grade.R
@@ -794,7 +794,7 @@ template_events_col_by_grade <- function(dataname,
 #'
 #' datanames <- c("ADSL", "ADAE")
 #' datanames(data) <- datanames
-#' data@join_keys <- cdisc_join_keys(!!!datanames)
+#' join_keys(data) <- cdisc_join_keys(!!!datanames)
 #'
 #' app <- init(
 #'   data = data,
@@ -1046,14 +1046,14 @@ srv_t_events_by_grade <- function(id,
     anl_inputs <- teal.transform::merge_expression_srv(
       datasets = data,
       selector_list = selector_list,
-      join_keys = teal.data::get_join_keys(data),
+      join_keys = teal.data::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 = teal.data::get_join_keys(data),
+      join_keys = teal.data::join_keys(data),
       anl_name = "ANL_ADSL"
     )
 

diff --git a/R/tm_t_events_patyear.R b/R/tm_t_events_patyear.R
@@ -443,14 +443,14 @@ srv_events_patyear <- function(id,
     anl_inputs <- teal.transform::merge_expression_srv(
       datasets = data,
       selector_list = selector_list,
-      join_keys = teal.data::get_join_keys(data),
+      join_keys = teal.data::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 = teal.data::get_join_keys(data),
+      join_keys = teal.data::join_keys(data),
       anl_name = "ANL_ADSL"
     )
 

diff --git a/R/tm_t_events_summary.R b/R/tm_t_events_summary.R
@@ -538,7 +538,7 @@ template_events_summary <- function(anl_name,
 #'
 #' datanames <- c("ADSL", "ADAE")
 #' datanames(data) <- datanames
-#' data@join_keys <- cdisc_join_keys(!!!datanames)
+#' join_keys(data) <- cdisc_join_keys(!!!datanames)
 #'
 #' app <- init(
 #'   data = data,
@@ -824,14 +824,14 @@ srv_t_events_summary <- function(id,
     anl_inputs <- teal.transform::merge_expression_srv(
       datasets = data,
       selector_list = selector_list,
-      join_keys = teal.data::get_join_keys(data),
+      join_keys = teal.data::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 = teal.data::get_join_keys(data),
+      join_keys = teal.data::join_keys(data),
       anl_name = "ANL_ADSL"
     )
 

diff --git a/R/tm_t_exposure.R b/R/tm_t_exposure.R
@@ -246,7 +246,7 @@ template_exposure <- function(parentname,
 #'
 #' datanames <- c("ADSL", "ADEX")
 #' datanames(data) <- datanames
-#' data@join_keys <- cdisc_join_keys(!!!datanames)
+#' join_keys(data) <- cdisc_join_keys(!!!datanames)
 #'
 #' app <- init(
 #'   data = data,
@@ -528,13 +528,13 @@ srv_t_exposure <- function(id,
     anl_inputs <- teal.transform::merge_expression_srv(
       datasets = data,
       selector_list = selector_list,
-      join_keys = teal.data::get_join_keys(data),
+      join_keys = teal.data::join_keys(data),
       merge_function = "dplyr::inner_join"
     )
 
     adsl_inputs <- teal.transform::merge_expression_module(
       datasets = data,
-      join_keys = teal.data::get_join_keys(data),
+      join_keys = teal.data::join_keys(data),
       data_extract = list(col_by_var = col_by_var),
       anl_name = "ANL_ADSL"
     )