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

…mes()` (#324) # Pull Request Part of insightsengineering/teal.data#333 Blocked by: - insightsengineering/teal.code#218 - insightsengineering/teal.data#347 - insightsengineering/teal#1402
insightsengineering · Nov 8, 2024 · 4063d5a · 4063d5a
1 parent d153e8d
commit 4063d5a
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diff --git a/DESCRIPTION b/DESCRIPTION
@@ -32,8 +32,8 @@ Depends:
     goshawk (>= 0.1.18),
     R (>= 3.6),
     shiny (>= 1.6.0),
-    teal (>= 0.15.2),
-    teal.transform (>= 0.5.0)
+    teal (>= 0.15.2.9079),
+    teal.transform (>= 0.5.0.9015)
 Imports:
     checkmate (>= 2.1.0),
     colourpicker,
@@ -47,7 +47,7 @@ Imports:
     shinyjs,
     shinyvalidate,
     stats,
-    teal.code (>= 0.5.0),
+    teal.code (>= 0.5.0.9012),
     teal.logger (>= 0.2.0.9011),
     teal.reporter (>= 0.2.0),
     teal.widgets (>= 0.4.0)
@@ -58,7 +58,7 @@ Suggests:
     rvest (>= 1.0.0),
     shinytest2,
     stringr (>= 1.4.1),
-    teal.data (>= 0.5.0),
+    teal.data (>= 0.6.0.9015),
     tern (>= 0.7.10),
     testthat (>= 3.0.4),
     utils

diff --git a/R/tm_g_gh_boxplot.R b/R/tm_g_gh_boxplot.R
@@ -54,18 +54,18 @@
 #'   library(stringr)
 #'
 #'   # use non-exported function from goshawk
-#'   h_identify_loq_values <- getFromNamespace("h_identify_loq_values", "goshawk")
+#'   .h_identify_loq_values <- getFromNamespace("h_identify_loq_values", "goshawk")
 #'
 #'   # original ARM value = dose value
-#'   arm_mapping <- list(
+#'   .arm_mapping <- list(
 #'     "A: Drug X" = "150mg QD",
 #'     "B: Placebo" = "Placebo",
 #'     "C: Combination" = "Combination"
 #'   )
 #'   set.seed(1)
 #'   ADSL <- rADSL
 #'   ADLB <- rADLB
-#'   var_labels <- lapply(ADLB, function(x) attributes(x)$label)
+#'   .var_labels <- lapply(ADLB, function(x) attributes(x)$label)
 #'   ADLB <- ADLB %>%
 #'     mutate(
 #'       AVISITCD = case_when(
@@ -86,9 +86,9 @@
 #'         ARMCD == "ARM B" ~ 2,
 #'         ARMCD == "ARM A" ~ 3
 #'       ),
-#'       ARM = as.character(arm_mapping[match(ARM, names(arm_mapping))]),
+#'       ARM = as.character(.arm_mapping[match(ARM, names(.arm_mapping))]),
 #'       ARM = factor(ARM) %>% reorder(TRTORD),
-#'       ACTARM = as.character(arm_mapping[match(ACTARM, names(arm_mapping))]),
+#'       ACTARM = as.character(.arm_mapping[match(ACTARM, names(.arm_mapping))]),
 #'       ACTARM = factor(ACTARM) %>% reorder(TRTORD),
 #'       ANRLO = 50,
 #'       ANRHI = 75
@@ -105,20 +105,17 @@
 #'     )) %>%
 #'     ungroup()
 #'
-#'   attr(ADLB[["ARM"]], "label") <- var_labels[["ARM"]]
-#'   attr(ADLB[["ACTARM"]], "label") <- var_labels[["ACTARM"]]
+#'   attr(ADLB[["ARM"]], "label") <- .var_labels[["ARM"]]
+#'   attr(ADLB[["ACTARM"]], "label") <- .var_labels[["ACTARM"]]
 #'   attr(ADLB[["ANRLO"]], "label") <- "Analysis Normal Range Lower Limit"
 #'   attr(ADLB[["ANRHI"]], "label") <- "Analysis Normal Range Upper Limit"
 #'
 #'   # add LLOQ and ULOQ variables
-#'   ALB_LOQS <- h_identify_loq_values(ADLB, "LOQFL")
+#'   ALB_LOQS <- .h_identify_loq_values(ADLB, "LOQFL")
 #'   ADLB <- left_join(ADLB, ALB_LOQS, by = "PARAM")
 #' })
 #'
-#' datanames <- c("ADSL", "ADLB")
-#' datanames(data) <- datanames
-#'
-#' join_keys(data) <- default_cdisc_join_keys[datanames]
+#' join_keys(data) <- default_cdisc_join_keys[names(data)]
 #'
 #' app <- init(
 #'   data = data,
@@ -308,7 +305,7 @@ srv_g_boxplot <- function(id,
   moduleServer(id, function(input, output, session) {
     teal.logger::log_shiny_input_changes(input, namespace = "teal.goshawk")
     output$axis_selections <- renderUI({
-      env <- shiny::isolate(as.list(data()@env))
+      env <- shiny::isolate(as.list(data()))
       resolved_x <- teal.transform::resolve_delayed(module_args$xaxis_var, env)
       resolved_y <- teal.transform::resolve_delayed(module_args$yaxis_var, env)
       resolved_param <- teal.transform::resolve_delayed(module_args$param, env)
@@ -508,7 +505,7 @@ srv_g_boxplot <- function(id,
 
     joined_qenvs <- reactive({
       req(create_plot(), create_table())
-      teal.code::join(create_plot(), create_table())
+      c(create_plot(), create_table())
     })
 
     code <- reactive(teal.code::get_code(joined_qenvs()))

diff --git a/R/tm_g_gh_correlationplot.R b/R/tm_g_gh_correlationplot.R
@@ -57,22 +57,22 @@
 #'   library(stringr)
 #'
 #'   # use non-exported function from goshawk
-#'   h_identify_loq_values <- getFromNamespace("h_identify_loq_values", "goshawk")
+#'   .h_identify_loq_values <- getFromNamespace("h_identify_loq_values", "goshawk")
 #'
 #'   # original ARM value = dose value
-#'   arm_mapping <- list(
+#'   .arm_mapping <- list(
 #'     "A: Drug X" = "150mg QD",
 #'     "B: Placebo" = "Placebo",
 #'     "C: Combination" = "Combination"
 #'   )
-#'   color_manual <- c("150mg QD" = "#000000", "Placebo" = "#3498DB", "Combination" = "#E74C3C")
+#'   .color_manual <- c("150mg QD" = "#000000", "Placebo" = "#3498DB", "Combination" = "#E74C3C")
 #'   # assign LOQ flag symbols: circles for "N" and triangles for "Y", squares for "NA"
-#'   shape_manual <- c("N" = 1, "Y" = 2, "NA" = 0)
+#'   .shape_manual <- c("N" = 1, "Y" = 2, "NA" = 0)
 #'
 #'   set.seed(1)
 #'   ADSL <- rADSL
 #'   ADLB <- rADLB
-#'   var_labels <- lapply(ADLB, function(x) attributes(x)$label)
+#'   .var_labels <- lapply(ADLB, function(x) attributes(x)$label)
 #'   ADLB <- ADLB %>%
 #'     mutate(AVISITCD = case_when(
 #'       AVISIT == "SCREENING" ~ "SCR",
@@ -102,7 +102,7 @@
 #'         ifelse(grepl("A", ARMCD), 3, NA)
 #'       )
 #'     )) %>%
-#'     mutate(ARM = as.character(arm_mapping[match(ARM, names(arm_mapping))])) %>%
+#'     mutate(ARM = as.character(.arm_mapping[match(ARM, names(.arm_mapping))])) %>%
 #'     mutate(ARM = factor(ARM) %>%
 #'       reorder(TRTORD)) %>%
 #'     mutate(
@@ -130,19 +130,16 @@
 #'       paste(">", round(runif(1, min = 70, max = 75))), LBSTRESC
 #'     )) %>%
 #'     ungroup()
-#'   attr(ADLB[["ARM"]], "label") <- var_labels[["ARM"]]
+#'   attr(ADLB[["ARM"]], "label") <- .var_labels[["ARM"]]
 #'   attr(ADLB[["ANRHI"]], "label") <- "Analysis Normal Range Upper Limit"
 #'   attr(ADLB[["ANRLO"]], "label") <- "Analysis Normal Range Lower Limit"
 #'
 #'   # add LLOQ and ULOQ variables
-#'   ADLB_LOQS <- h_identify_loq_values(ADLB, "LOQFL")
+#'   ADLB_LOQS <- .h_identify_loq_values(ADLB, "LOQFL")
 #'   ADLB <- left_join(ADLB, ADLB_LOQS, by = "PARAM")
 #' })
 #'
-#' datanames <- c("ADSL", "ADLB")
-#' datanames(data) <- datanames
-#'
-#' join_keys(data) <- default_cdisc_join_keys[datanames]
+#' join_keys(data) <- default_cdisc_join_keys[names(data)]
 #'
 #' app <- init(
 #'   data = data,
@@ -374,7 +371,7 @@ srv_g_correlationplot <- function(id,
   moduleServer(id, function(input, output, session) {
     teal.logger::log_shiny_input_changes(input, namespace = "teal.goshawk")
     output$axis_selections <- renderUI({
-      env <- shiny::isolate(as.list(data()@env))
+      env <- shiny::isolate(as.list(data()))
       resolved_x_param <- teal.transform::resolve_delayed(module_args$xaxis_param, env)
       resolved_x_var <- teal.transform::resolve_delayed(module_args$xaxis_var, env)
       resolved_y_param <- teal.transform::resolve_delayed(module_args$yaxis_param, env)

diff --git a/R/tm_g_gh_density_distribution_plot.R b/R/tm_g_gh_density_distribution_plot.R
@@ -40,14 +40,14 @@
 #'   library(stringr)
 #'
 #'   # original ARM value = dose value
-#'   arm_mapping <- list(
+#'   .arm_mapping <- list(
 #'     "A: Drug X" = "150mg QD",
 #'     "B: Placebo" = "Placebo",
 #'     "C: Combination" = "Combination"
 #'   )
 #'   ADSL <- rADSL
 #'   ADLB <- rADLB
-#'   var_labels <- lapply(ADLB, function(x) attributes(x)$label)
+#'   .var_labels <- lapply(ADLB, function(x) attributes(x)$label)
 #'   ADLB <- ADLB %>%
 #'     mutate(
 #'       AVISITCD = case_when(
@@ -68,19 +68,17 @@
 #'         ARMCD == "ARM B" ~ 2,
 #'         ARMCD == "ARM A" ~ 3
 #'       ),
-#'       ARM = as.character(arm_mapping[match(ARM, names(arm_mapping))]),
+#'       ARM = as.character(.arm_mapping[match(ARM, names(.arm_mapping))]),
 #'       ARM = factor(ARM) %>% reorder(TRTORD),
-#'       ACTARM = as.character(arm_mapping[match(ACTARM, names(arm_mapping))]),
+#'       ACTARM = as.character(.arm_mapping[match(ACTARM, names(.arm_mapping))]),
 #'       ACTARM = factor(ACTARM) %>% reorder(TRTORD)
 #'     )
 #'
-#'   attr(ADLB[["ARM"]], "label") <- var_labels[["ARM"]]
-#'   attr(ADLB[["ACTARM"]], "label") <- var_labels[["ACTARM"]]
+#'   attr(ADLB[["ARM"]], "label") <- .var_labels[["ARM"]]
+#'   attr(ADLB[["ACTARM"]], "label") <- .var_labels[["ACTARM"]]
 #' })
 #'
-#' datanames <- c("ADSL", "ADLB")
-#' datanames(data) <- datanames
-#' join_keys(data) <- default_cdisc_join_keys[datanames]
+#' join_keys(data) <- default_cdisc_join_keys[names(data)]
 #'
 #' app <- init(
 #'   data = data,
@@ -256,7 +254,7 @@ srv_g_density_distribution_plot <- function(id, # nolint
   moduleServer(id, function(input, output, session) {
     teal.logger::log_shiny_input_changes(input, namespace = "teal.goshawk")
     output$axis_selections <- renderUI({
-      env <- shiny::isolate(as.list(data()@env))
+      env <- shiny::isolate(as.list(data()))
       resolved_x <- teal.transform::resolve_delayed(module_args$xaxis_var, env)
       resolved_param <- teal.transform::resolve_delayed(module_args$param, env)
       resolved_trt <- teal.transform::resolve_delayed(module_args$trt_group, env)
@@ -416,7 +414,7 @@ srv_g_density_distribution_plot <- function(id, # nolint
 
     joined_qenvs <- reactive({
       req(create_plot(), create_table())
-      teal.code::join(create_plot(), create_table())
+      c(create_plot(), create_table())
     })
 
     code <- reactive(teal.code::get_code(joined_qenvs()))

diff --git a/R/tm_g_gh_lineplot.R b/R/tm_g_gh_lineplot.R
@@ -60,15 +60,15 @@
 #'   library(nestcolor)
 #'
 #'   # original ARM value = dose value
-#'   arm_mapping <- list(
+#'   .arm_mapping <- list(
 #'     "A: Drug X" = "150mg QD",
 #'     "B: Placebo" = "Placebo",
 #'     "C: Combination" = "Combination"
 #'   )
 #'
 #'   ADSL <- rADSL
 #'   ADLB <- rADLB
-#'   var_labels <- lapply(ADLB, function(x) attributes(x)$label)
+#'   .var_labels <- lapply(ADLB, function(x) attributes(x)$label)
 #'   ADLB <- ADLB %>%
 #'     mutate(
 #'       AVISITCD = case_when(
@@ -89,18 +89,16 @@
 #'         ARMCD == "ARM B" ~ 2,
 #'         ARMCD == "ARM A" ~ 3
 #'       ),
-#'       ARM = as.character(arm_mapping[match(ARM, names(arm_mapping))]),
+#'       ARM = as.character(.arm_mapping[match(ARM, names(.arm_mapping))]),
 #'       ARM = factor(ARM) %>% reorder(TRTORD),
-#'       ACTARM = as.character(arm_mapping[match(ACTARM, names(arm_mapping))]),
+#'       ACTARM = as.character(.arm_mapping[match(ACTARM, names(.arm_mapping))]),
 #'       ACTARM = factor(ACTARM) %>% reorder(TRTORD)
 #'     )
-#'   attr(ADLB[["ARM"]], "label") <- var_labels[["ARM"]]
-#'   attr(ADLB[["ACTARM"]], "label") <- var_labels[["ACTARM"]]
+#'   attr(ADLB[["ARM"]], "label") <- .var_labels[["ARM"]]
+#'   attr(ADLB[["ACTARM"]], "label") <- .var_labels[["ACTARM"]]
 #' })
 #'
-#' datanames <- c("ADSL", "ADLB")
-#' datanames(data) <- datanames
-#' join_keys(data) <- default_cdisc_join_keys[datanames]
+#' join_keys(data) <- default_cdisc_join_keys[names(data)]
 #'
 #' app <- init(
 #'   data = data,
@@ -349,7 +347,7 @@ srv_lineplot <- function(id,
     ns <- session$ns
 
     output$axis_selections <- renderUI({
-      env <- shiny::isolate(as.list(data()@env))
+      env <- shiny::isolate(as.list(data()))
       resolved_x <- teal.transform::resolve_delayed(module_args$xaxis_var, env)
       resolved_y <- teal.transform::resolve_delayed(module_args$yaxis_var, env)
       resolved_param <- teal.transform::resolve_delayed(module_args$param, env)

diff --git a/R/tm_g_gh_scatterplot.R b/R/tm_g_gh_scatterplot.R
@@ -45,15 +45,15 @@
 #'   library(stringr)
 #'
 #'   # original ARM value = dose value
-#'   arm_mapping <- list(
+#'   .arm_mapping <- list(
 #'     "A: Drug X" = "150mg QD",
 #'     "B: Placebo" = "Placebo",
 #'     "C: Combination" = "Combination"
 #'   )
 #'
 #'   ADSL <- rADSL
 #'   ADLB <- rADLB
-#'   var_labels <- lapply(ADLB, function(x) attributes(x)$label)
+#'   .var_labels <- lapply(ADLB, function(x) attributes(x)$label)
 #'   ADLB <- ADLB %>%
 #'     mutate(
 #'       AVISITCD = case_when(
@@ -74,18 +74,16 @@
 #'         ARMCD == "ARM B" ~ 2,
 #'         ARMCD == "ARM A" ~ 3
 #'       ),
-#'       ARM = as.character(arm_mapping[match(ARM, names(arm_mapping))]),
+#'       ARM = as.character(.arm_mapping[match(ARM, names(.arm_mapping))]),
 #'       ARM = factor(ARM) %>% reorder(TRTORD),
-#'       ACTARM = as.character(arm_mapping[match(ACTARM, names(arm_mapping))]),
+#'       ACTARM = as.character(.arm_mapping[match(ACTARM, names(.arm_mapping))]),
 #'       ACTARM = factor(ACTARM) %>% reorder(TRTORD)
 #'     )
-#'   attr(ADLB[["ARM"]], "label") <- var_labels[["ARM"]]
-#'   attr(ADLB[["ACTARM"]], "label") <- var_labels[["ACTARM"]]
+#'   attr(ADLB[["ARM"]], "label") <- .var_labels[["ARM"]]
+#'   attr(ADLB[["ACTARM"]], "label") <- .var_labels[["ACTARM"]]
 #' })
 #'
-#' datanames <- c("ADSL", "ADLB")
-#' datanames(data) <- datanames
-#' join_keys(data) <- default_cdisc_join_keys[datanames]
+#' join_keys(data) <- default_cdisc_join_keys[names(data)]
 #'
 #'
 #' app <- init(
@@ -257,7 +255,7 @@ srv_g_scatterplot <- function(id,
   moduleServer(id, function(input, output, session) {
     teal.logger::log_shiny_input_changes(input, namespace = "teal.goshawk")
     output$axis_selections <- renderUI({
-      env <- shiny::isolate(as.list(data()@env))
+      env <- shiny::isolate(as.list(data()))
       resolved_x <- teal.transform::resolve_delayed(module_args$xaxis_var, env)
       resolved_y <- teal.transform::resolve_delayed(module_args$yaxis_var, env)
       resolved_param <- teal.transform::resolve_delayed(module_args$param, env)