teal.data::datanames() is deprecated in favor of dot-prefix and `na…

…mes()` (#1239) # Pull Request Part of insightsengineering/teal.data#333 Blocked by: - insightsengineering/teal.code#218 - insightsengineering/teal.data#347 - insightsengineering/teal#1402 --------- Co-authored-by: 27856297+dependabot-preview[bot]@users.noreply.github.com <27856297+dependabot-preview[bot]@users.noreply.github.com>
insightsengineering · Nov 8, 2024 · d2e1408 · d2e1408
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diff --git a/DESCRIPTION b/DESCRIPTION
@@ -32,8 +32,8 @@ BugReports:
     https://github.com/insightsengineering/teal.modules.clinical/issues
 Depends:
     R (>= 4.0),
-    teal (>= 0.15.2.9052),
-    teal.transform (>= 0.5.0),
+    teal (>= 0.15.2.9079),
+    teal.transform (>= 0.5.0.9015),
     tern (>= 0.9.6)
 Imports:
     broom (>= 0.7.10),
@@ -55,8 +55,8 @@ Imports:
     shinyvalidate,
     shinyWidgets (>= 0.5.1),
     stats,
-    teal.code (>= 0.5.0),
-    teal.data (>= 0.4.0),
+    teal.code (>= 0.5.0.9012),
+    teal.data (>= 0.6.0.9015),
     teal.logger (>= 0.2.0.9004),
     teal.reporter (>= 0.2.1),
     teal.widgets (>= 0.4.0),

diff --git a/R/tm_a_gee.R b/R/tm_a_gee.R
@@ -158,8 +158,7 @@ template_a_gee <- function(output_table,
 #'     ) %>%
 #'     droplevels()
 #' })
-#' datanames(data) <- c("ADSL", "ADQS")
-#' join_keys(data) <- default_cdisc_join_keys[datanames(data)]
+#' join_keys(data) <- default_cdisc_join_keys[names(data)]
 #'
 #' app <- init(
 #'   data = data,

diff --git a/R/tm_a_mmrm.R b/R/tm_a_mmrm.R
@@ -491,8 +491,7 @@ template_mmrm_plots <- function(fit_name,
 #'         as.factor() #' making consecutive numeric factor
 #'     )
 #' })
-#' datanames(data) <- c("ADSL", "ADQS")
-#' join_keys(data) <- default_cdisc_join_keys[datanames(data)]
+#' join_keys(data) <- default_cdisc_join_keys[names(data)]
 #'
 #' app <- init(
 #'   data = data,
@@ -1402,7 +1401,7 @@ srv_mmrm <- function(id,
 
     all_q <- reactive({
       if (!is.null(plot_q()) && !is.null(table_q())) {
-        teal.code::join(plot_q(), table_q())
+        c(plot_q(), table_q())
       } else if (!is.null(plot_q())) {
         plot_q()
       } else {

diff --git a/R/tm_g_barchart_simple.R b/R/tm_g_barchart_simple.R
@@ -32,8 +32,7 @@
 #'   ADAE <- tmc_ex_adae %>%
 #'     filter(!((AETOXGR == 1) & (AESEV == "MILD") & (ARM == "A: Drug X")))
 #' })
-#' datanames(data) <- c("ADSL", "ADAE")
-#' join_keys(data) <- default_cdisc_join_keys[datanames(data)]
+#' join_keys(data) <- default_cdisc_join_keys[names(data)]
 #'
 #' ADSL <- data[["ADSL"]]
 #' ADAE <- data[["ADAE"]]
@@ -421,7 +420,9 @@ srv_g_barchart_simple <- function(id,
         count_exprs <- c(count_exprs, count_exprs2, count_str_to_col_exprs)
       }
 
-      data_list <- sapply(teal.data::datanames(data()), function(x) reactive(data()[[x]]),
+      data_list <- sapply(
+        names(data()),
+        function(x) reactive(data()[[x]]),
         simplify = FALSE
       )
 

diff --git a/R/tm_g_ci.R b/R/tm_g_ci.R
@@ -202,8 +202,7 @@ template_g_ci <- function(dataname,
 #'   ADSL <- tmc_ex_adsl
 #'   ADLB <- tmc_ex_adlb
 #' })
-#' datanames(data) <- c("ADSL", "ADLB")
-#' join_keys(data) <- default_cdisc_join_keys[datanames(data)]
+#' join_keys(data) <- default_cdisc_join_keys[names(data)]
 #'
 #' ADSL <- data[["ADSL"]]
 #' ADLB <- data[["ADLB"]]

diff --git a/R/tm_g_forest_rsp.R b/R/tm_g_forest_rsp.R
@@ -260,8 +260,7 @@ template_forest_rsp <- function(dataname = "ANL",
 #'       with_label("Character Result/Finding")) %>%
 #'     filter(PARAMCD != "OVRINV" | AVISIT == "FOLLOW UP")
 #' })
-#' datanames(data) <- c("ADSL", "ADRS")
-#' join_keys(data) <- default_cdisc_join_keys[datanames(data)]
+#' join_keys(data) <- default_cdisc_join_keys[names(data)]
 #'
 #' ADSL <- data[["ADSL"]]
 #' ADRS <- data[["ADRS"]]

diff --git a/R/tm_g_forest_tte.R b/R/tm_g_forest_tte.R
@@ -258,8 +258,7 @@ template_forest_tte <- function(dataname = "ANL",
 #'   ADTTE <- tmc_ex_adtte
 #'   ADSL$RACE <- droplevels(ADSL$RACE) %>% with_label("Race")
 #' })
-#' datanames(data) <- c("ADSL", "ADTTE")
-#' join_keys(data) <- default_cdisc_join_keys[datanames(data)]
+#' join_keys(data) <- default_cdisc_join_keys[names(data)]
 #'
 #' ADSL <- data[["ADSL"]]
 #' ADTTE <- data[["ADTTE"]]

diff --git a/R/tm_g_ipp.R b/R/tm_g_ipp.R
@@ -198,8 +198,7 @@ template_g_ipp <- function(dataname = "ANL",
 #'     df_explicit_na() %>%
 #'     filter(AVISIT != "SCREENING")
 #' })
-#' datanames(data) <- c("ADSL", "ADLB")
-#' join_keys(data) <- default_cdisc_join_keys[datanames(data)]
+#' join_keys(data) <- default_cdisc_join_keys[names(data)]
 #'
 #' ADSL <- data[["ADSL"]]
 #' ADLB <- data[["ADLB"]]

diff --git a/R/tm_g_km.R b/R/tm_g_km.R
@@ -284,8 +284,7 @@ template_g_km <- function(dataname = "ANL",
 #'   ADSL <- tmc_ex_adsl
 #'   ADTTE <- tmc_ex_adtte
 #' })
-#' datanames(data) <- c("ADSL", "ADTTE")
-#' join_keys(data) <- default_cdisc_join_keys[datanames(data)]
+#' join_keys(data) <- default_cdisc_join_keys[names(data)]
 #'
 #' ADSL <- data[["ADSL"]]
 #' ADTTE <- data[["ADTTE"]]

diff --git a/R/tm_g_lineplot.R b/R/tm_g_lineplot.R
@@ -222,8 +222,7 @@ template_g_lineplot <- function(dataname = "ANL",
 #'   ADLB <- tmc_ex_adlb %>%
 #'     mutate(AVISIT == fct_reorder(AVISIT, AVISITN, min))
 #' })
-#' datanames(data) <- c("ADSL", "ADLB")
-#' join_keys(data) <- default_cdisc_join_keys[datanames(data)]
+#' join_keys(data) <- default_cdisc_join_keys[names(data)]
 #'
 #' ADSL <- data[["ADSL"]]
 #' ADLB <- data[["ADLB"]]

diff --git a/R/tm_g_pp_adverse_events.R b/R/tm_g_pp_adverse_events.R
@@ -154,7 +154,7 @@ template_adverse_events <- function(dataname = "ANL",
 
   chart_list <- add_expr(
     expr_ls = chart_list,
-    new_expr = quote(print(plot))
+    new_expr = quote(plot)
   )
 
   y$table <- bracket_expr(table_list)
@@ -201,8 +201,7 @@ template_adverse_events <- function(dataname = "ANL",
 #'   ADSL <- tmc_ex_adsl %>%
 #'     filter(USUBJID %in% ADAE$USUBJID)
 #' })
-#' datanames(data) <- c("ADSL", "ADAE")
-#' join_keys(data) <- default_cdisc_join_keys[datanames(data)]
+#' join_keys(data) <- default_cdisc_join_keys[names(data)]
 #'
 #' ADSL <- data[["ADSL"]]
 #' ADAE <- data[["ADAE"]]

diff --git a/R/tm_g_pp_patient_timeline.R b/R/tm_g_pp_patient_timeline.R
@@ -378,7 +378,6 @@ template_patient_timeline <- function(dataname = "ANL",
 #'     )
 #' })
 #'
-#' datanames(data) <- c("ADSL", "ADAE", "ADCM")
 #' join_keys(data) <- default_cdisc_join_keys[c("ADSL", "ADAE", "ADCM")]
 #' adcm_keys <- c("STUDYID", "USUBJID", "ASTDTM", "CMSEQ", "ATC1", "ATC2", "ATC3", "ATC4")
 #' join_keys(data)["ADCM", "ADCM"] <- adcm_keys

diff --git a/R/tm_g_pp_therapy.R b/R/tm_g_pp_therapy.R
@@ -192,7 +192,7 @@ template_therapy <- function(dataname = "ANL",
         ggtheme +
         theme
 
-      print(therapy_plot)
+      therapy_plot
     }, env = c(
       list(
         dataname = as.name(dataname),
@@ -264,8 +264,6 @@ template_therapy <- function(dataname = "ANL",
 #'   ADCM$CMAENDTM <- ADCM$AENDTM
 #' })
 #'
-#' datanames(data) <- c("ADSL", "ADCM")
-#'
 #' join_keys(data) <- default_cdisc_join_keys[c("ADSL", "ADCM")]
 #' adcm_keys <- c("STUDYID", "USUBJID", "ASTDTM", "CMSEQ", "ATC1", "ATC2", "ATC3", "ATC4")
 #' join_keys(data)["ADCM", "ADCM"] <- adcm_keys

diff --git a/R/tm_g_pp_vitals.R b/R/tm_g_pp_vitals.R
@@ -224,8 +224,7 @@ template_vitals <- function(dataname = "ANL",
 #'   ADSL <- tmc_ex_adsl
 #'   ADVS <- tmc_ex_advs
 #' })
-#' datanames(data) <- c("ADSL", "ADVS")
-#' join_keys(data) <- default_cdisc_join_keys[datanames(data)]
+#' join_keys(data) <- default_cdisc_join_keys[names(data)]
 #'
 #' ADSL <- data[["ADSL"]]
 #' ADVS <- data[["ADVS"]]

diff --git a/R/tm_t_abnormality.R b/R/tm_t_abnormality.R
@@ -259,8 +259,7 @@ template_abnormality <- function(parentname,
 #'       ) %>% with_label("On Treatment Record Flag")
 #'     )
 #' })
-#' datanames(data) <- c("ADSL", "ADLB")
-#' join_keys(data) <- default_cdisc_join_keys[datanames(data)]
+#' join_keys(data) <- default_cdisc_join_keys[names(data)]
 #'
 #' ADSL <- data[["ADSL"]]
 #' ADLB <- data[["ADLB"]]
@@ -544,7 +543,7 @@ srv_t_abnormality <- function(id,
     )
 
     isolate({
-      resolved <- teal.transform::resolve_delayed(treatment_flag, as.list(data()@env))
+      resolved <- teal.transform::resolve_delayed(treatment_flag, as.list(data()))
       teal.widgets::updateOptionalSelectInput(
         session = session,
         inputId = "treatment_flag",

diff --git a/R/tm_t_abnormality_by_worst_grade.R b/R/tm_t_abnormality_by_worst_grade.R
@@ -265,8 +265,7 @@ template_abnormality_by_worst_grade <- function(parentname, # nolint: object_len
 #'   ADLB <- tmc_ex_adlb %>%
 #'     filter(!AVISIT %in% c("SCREENING", "BASELINE"))
 #' })
-#' datanames(data) <- c("ADSL", "ADLB")
-#' join_keys(data) <- default_cdisc_join_keys[datanames(data)]
+#' join_keys(data) <- default_cdisc_join_keys[names(data)]
 #'
 #' ADSL <- data[["ADSL"]]
 #' ADLB <- data[["ADLB"]]
@@ -511,7 +510,7 @@ srv_t_abnormality_by_worst_grade <- function(id, # nolint: object_length.
   moduleServer(id, function(input, output, session) {
     teal.logger::log_shiny_input_changes(input, namespace = "teal.modules.clinical")
     isolate({
-      resolved <- teal.transform::resolve_delayed(worst_flag_indicator, as.list(data()@env))
+      resolved <- teal.transform::resolve_delayed(worst_flag_indicator, as.list(data()))
       teal.widgets::updateOptionalSelectInput(
         session = session,
         inputId = "worst_flag_indicator",

diff --git a/R/tm_t_ancova.R b/R/tm_t_ancova.R
@@ -446,8 +446,7 @@ template_ancova <- function(dataname = "ANL",
 #'   ADSL <- tmc_ex_adsl
 #'   ADQS <- tmc_ex_adqs
 #' })
-#' datanames(data) <- c("ADSL", "ADQS")
-#' join_keys(data) <- default_cdisc_join_keys[datanames(data)]
+#' join_keys(data) <- default_cdisc_join_keys[names(data)]
 #'
 #' ADSL <- data[["ADSL"]]
 #' ADQS <- data[["ADQS"]]

diff --git a/R/tm_t_binary_outcome.R b/R/tm_t_binary_outcome.R
@@ -369,8 +369,7 @@ template_binary_outcome <- function(dataname,
 #'     ) %>%
 #'     filter(PARAMCD != "OVRINV" | AVISIT == "FOLLOW UP")
 #' })
-#' datanames(data) <- c("ADSL", "ADRS")
-#' join_keys(data) <- default_cdisc_join_keys[datanames(data)]
+#' join_keys(data) <- default_cdisc_join_keys[names(data)]
 #'
 #' ADSL <- data[["ADSL"]]
 #' ADRS <- data[["ADRS"]]

diff --git a/R/tm_t_coxreg.R b/R/tm_t_coxreg.R
@@ -388,8 +388,7 @@ template_coxreg_m <- function(dataname,
 #'   ADSL <- tmc_ex_adsl
 #'   ADTTE <- tmc_ex_adtte
 #' })
-#' datanames(data) <- c("ADSL", "ADTTE")
-#' join_keys(data) <- default_cdisc_join_keys[datanames(data)]
+#' join_keys(data) <- default_cdisc_join_keys[names(data)]
 #'
 #' ADSL <- data[["ADSL"]]
 #' ADTTE <- data[["ADTTE"]]
@@ -461,8 +460,7 @@ template_coxreg_m <- function(dataname,
 #'   )
 #' })
 #'
-#' datanames(data) <- c("ADSL", "ADTTE")
-#' join_keys(data) <- default_cdisc_join_keys[datanames(data)]
+#' join_keys(data) <- default_cdisc_join_keys[names(data)]
 #'
 #' ADSL <- data[["ADSL"]]
 #' ADTTE <- data[["ADTTE"]]

diff --git a/R/tm_t_events.R b/R/tm_t_events.R
@@ -472,8 +472,7 @@ template_events <- function(dataname,
 #'   ADSL <- tmc_ex_adsl
 #'   ADAE <- tmc_ex_adae
 #' })
-#' datanames(data) <- c("ADSL", "ADAE")
-#' join_keys(data) <- default_cdisc_join_keys[datanames(data)]
+#' join_keys(data) <- default_cdisc_join_keys[names(data)]
 #'
 #' ADSL <- data[["ADSL"]]
 #' ADAE <- data[["ADAE"]]

diff --git a/R/tm_t_events_by_grade.R b/R/tm_t_events_by_grade.R
@@ -803,13 +803,12 @@ template_events_col_by_grade <- function(dataname,
 #' data <- teal_data()
 #' data <- within(data, {
 #'   ADSL <- tmc_ex_adsl
-#'   lbls_adae <- col_labels(tmc_ex_adae)
+#'   .lbls_adae <- col_labels(tmc_ex_adae)
 #'   ADAE <- tmc_ex_adae %>%
 #'     mutate_if(is.character, as.factor) #' be certain of having factors
-#'   col_labels(ADAE) <- lbls_adae
+#'   col_labels(ADAE) <- .lbls_adae
 #' })
-#' datanames(data) <- c("ADSL", "ADAE")
-#' join_keys(data) <- default_cdisc_join_keys[datanames(data)]
+#' join_keys(data) <- default_cdisc_join_keys[names(data)]
 #'
 #' ADSL <- data[["ADSL"]]
 #' ADAE <- data[["ADAE"]]

diff --git a/R/tm_t_events_patyear.R b/R/tm_t_events_patyear.R
@@ -204,8 +204,7 @@ template_events_patyear <- function(dataname,
 #'     mutate(is_event = CNSR == 0) %>%
 #'     mutate(n_events = as.integer(is_event))
 #' })
-#' datanames(data) <- c("ADSL", "ADAETTE")
-#' join_keys(data) <- default_cdisc_join_keys[datanames(data)]
+#' join_keys(data) <- default_cdisc_join_keys[names(data)]
 #'
 #' ADSL <- data[["ADSL"]]
 #' ADAETTE <- data[["ADAETTE"]]

diff --git a/R/tm_t_events_summary.R b/R/tm_t_events_summary.R
@@ -541,7 +541,7 @@ template_events_summary <- function(anl_name,
 #'     )
 #'   ADAE <- tmc_ex_adae
 #'
-#'   add_event_flags <- function(dat) {
+#'   .add_event_flags <- function(dat) {
 #'     dat <- dat %>%
 #'       mutate(
 #'         TMPFL_SER = AESER == "Y",
@@ -564,13 +564,12 @@ template_events_summary <- function(anl_name,
 #'   }
 #'
 #'   #' Generating user-defined event flags.
-#'   ADAE <- ADAE %>% add_event_flags()
+#'   ADAE <- ADAE %>% .add_event_flags()
 #'
-#'   ae_anl_vars <- names(ADAE)[startsWith(names(ADAE), "TMPFL_")]
-#'   aesi_vars <- names(ADAE)[startsWith(names(ADAE), "TMP_")]
+#'   .ae_anl_vars <- names(ADAE)[startsWith(names(ADAE), "TMPFL_")]
+#'   .aesi_vars <- names(ADAE)[startsWith(names(ADAE), "TMP_")]
 #' })
-#' datanames(data) <- c("ADSL", "ADAE")
-#' join_keys(data) <- default_cdisc_join_keys[datanames(data)]
+#' join_keys(data) <- default_cdisc_join_keys[names(data)]
 #'
 #' app <- init(
 #'   data = data,
@@ -583,14 +582,14 @@ template_events_summary <- function(anl_name,
 #'         selected = "ARM"
 #'       ),
 #'       flag_var_anl = choices_selected(
-#'         choices = variable_choices("ADAE", data[["ae_anl_vars"]]),
-#'         selected = data[["ae_anl_vars"]][1],
+#'         choices = variable_choices("ADAE", data[[".ae_anl_vars"]]),
+#'         selected = data[[".ae_anl_vars"]][1],
 #'         keep_order = TRUE,
 #'         fixed = FALSE
 #'       ),
 #'       flag_var_aesi = choices_selected(
-#'         choices = variable_choices("ADAE", data[["aesi_vars"]]),
-#'         selected = data[["aesi_vars"]][1],
+#'         choices = variable_choices("ADAE", data[[".aesi_vars"]]),
+#'         selected = data[[".aesi_vars"]][1],
 #'         keep_order = TRUE,
 #'         fixed = FALSE
 #'       ),

diff --git a/R/tm_t_exposure.R b/R/tm_t_exposure.R
@@ -241,7 +241,7 @@ template_exposure <- function(parentname,
 #'   ADEX <- tmc_ex_adex
 #'
 #'   set.seed(1, kind = "Mersenne-Twister")
-#'   labels <- col_labels(ADEX, fill = FALSE)
+#'   .labels <- col_labels(ADEX, fill = FALSE)
 #'   ADEX <- ADEX %>%
 #'     distinct(USUBJID, .keep_all = TRUE) %>%
 #'     mutate(
@@ -251,10 +251,9 @@ template_exposure <- function(parentname,
 #'       AVALU = "Days"
 #'     ) %>%
 #'     bind_rows(ADEX)
-#'   col_labels(ADEX) <- labels
+#'   col_labels(ADEX) <- .labels
 #' })
-#' datanames(data) <- c("ADSL", "ADEX")
-#' join_keys(data) <- default_cdisc_join_keys[datanames(data)]
+#' join_keys(data) <- default_cdisc_join_keys[names(data)]
 #'
 #' app <- init(
 #'   data = data,

diff --git a/R/tm_t_logistic.R b/R/tm_t_logistic.R
@@ -236,8 +236,7 @@ template_logistic <- function(dataname,
 #'   ADRS <- tmc_ex_adrs %>%
 #'     filter(PARAMCD %in% c("BESRSPI", "INVET"))
 #' })
-#' datanames(data) <- c("ADSL", "ADRS")
-#' join_keys(data) <- default_cdisc_join_keys[datanames(data)]
+#' join_keys(data) <- default_cdisc_join_keys[names(data)]
 #'
 #' ADSL <- data[["ADSL"]]
 #' ADRS <- data[["ADRS"]]

diff --git a/R/tm_t_mult_events.R b/R/tm_t_mult_events.R
@@ -294,8 +294,7 @@ template_mult_events <- function(dataname,
 #'   ADSL <- tmc_ex_adsl
 #'   ADCM <- tmc_ex_adcm
 #' })
-#' datanames(data) <- c("ADSL", "ADCM")
-#' join_keys(data) <- default_cdisc_join_keys[datanames(data)]
+#' join_keys(data) <- default_cdisc_join_keys[names(data)]
 #' adcm_keys <- c("STUDYID", "USUBJID", "ASTDTM", "CMSEQ", "ATC1", "ATC2", "ATC3", "ATC4")
 #' join_keys(data)["ADCM", "ADCM"] <- adcm_keys
 #'

diff --git a/R/tm_t_pp_basic_info.R b/R/tm_t_pp_basic_info.R
@@ -76,8 +76,7 @@ template_basic_info <- function(dataname = "ANL",
 #' data <- within(data, {
 #'   ADSL <- tmc_ex_adsl
 #' })
-#' datanames(data) <- c("ADSL")
-#' join_keys(data) <- default_cdisc_join_keys[datanames(data)]
+#' join_keys(data) <- default_cdisc_join_keys[names(data)]
 #'
 #' ADSL <- data[["ADSL"]]
 #'