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

…mes()` (#794)

# Pull Request

Part of insightsengineering/teal.data#333

Blocked by:

- insightsengineering/teal.code#218
- insightsengineering/teal.data#347
- insightsengineering/teal#1402

DESCRIPTION

@@ -27,8 +27,8 @@ Depends:
     ggplot2 (>= 3.4.0),
     R (>= 3.6),
     shiny (>= 1.6.0),
-    teal (>= 0.15.2.9052),
-    teal.transform (>= 0.5.0)
+    teal (>= 0.15.2.9079),
+    teal.transform (>= 0.5.0.9015)
 Imports:
     checkmate (>= 2.1.0),
     dplyr (>= 1.0.5),
@@ -42,8 +42,8 @@ Imports:
     shinyWidgets (>= 0.5.1),
     stats,
     stringr (>= 1.4.1),
-    teal.code (>= 0.5.0),
-    teal.data (>= 0.5.0),
+    teal.code (>= 0.5.0.9012),
+    teal.data (>= 0.6.0.9015),
     teal.logger (>= 0.2.0.9004),
     teal.reporter (>= 0.3.0),
     teal.widgets (>= 0.4.0),

R/tm_a_pca.R

@@ -30,8 +30,6 @@
 #'   USArrests <- USArrests
 #' })
 #'
-#' datanames(data) <- "USArrests"
-#'
 #' app <- init(
 #'   data = data,
 #'   modules = modules(
@@ -66,8 +64,7 @@
 #'   require(nestcolor)
 #'   ADSL <- rADSL
 #' })
-#' datanames(data) <- "ADSL"
-#' join_keys(data) <- default_cdisc_join_keys[datanames(data)]
+#' join_keys(data) <- default_cdisc_join_keys[names(data)]
 #'
 #' app <- init(
 #'   data = data,

R/tm_a_regression.R

@@ -53,7 +53,6 @@
 #'   require(nestcolor)
 #'   CO2 <- CO2
 #' })
-#' datanames(data) <- c("CO2")
 #'
 #' app <- init(
 #'   data = data,
@@ -98,8 +97,7 @@
 #'   require(nestcolor)
 #'   ADSL <- rADSL
 #' })
-#' datanames(data) <- "ADSL"
-#' join_keys(data) <- default_cdisc_join_keys[datanames(data)]
+#' join_keys(data) <- default_cdisc_join_keys[names(data)]
 #'
 #' app <- init(
 #'   data = data,

R/tm_data_table.R

@@ -40,7 +40,6 @@
 #'   require(nestcolor)
 #'   iris <- iris
 #' })
-#' datanames(data) <- c("iris")
 #'
 #' app <- init(
 #'   data = data,
@@ -68,8 +67,7 @@
 #'   require(nestcolor)
 #'   ADSL <- rADSL
 #' })
-#' datanames(data) <- "ADSL"
-#' join_keys(data) <- default_cdisc_join_keys[datanames(data)]
+#' join_keys(data) <- default_cdisc_join_keys[names(data)]
 #'
 #' app <- init(
 #'   data = data,
@@ -196,7 +194,7 @@ srv_page_data_table <- function(id,
     if_filtered <- reactive(as.logical(input$if_filtered))
     if_distinct <- reactive(as.logical(input$if_distinct))
 
-    datanames <- isolate(teal.data::datanames(data()))
+    datanames <- isolate(names(data()))
     datanames <- Filter(function(name) {
       is.data.frame(isolate(data())[[name]])
     }, datanames)

R/tm_file_viewer.R

@@ -22,7 +22,6 @@
 #' data <- within(data, {
 #'   data <- data.frame(1)
 #' })
-#' datanames(data) <- c("data")
 #'
 #' app <- init(
 #'   data = data,

R/tm_front_page.R

@@ -28,8 +28,7 @@
 #'   ADSL <- rADSL
 #'   attr(ADSL, "metadata") <- list("Author" = "NEST team", "data_source" = "synthetic data")
 #' })
-#' datanames(data) <- "ADSL"
-#' join_keys(data) <- default_cdisc_join_keys[datanames(data)]
+#' join_keys(data) <- default_cdisc_join_keys[names(data)]
 #'
 #' table_1 <- data.frame(Info = c("A", "B"), Text = c("A", "B"))
 #' table_2 <- data.frame(`Column 1` = c("C", "D"), `Column 2` = c(5.5, 6.6), `Column 3` = c("A", "B"))
@@ -169,7 +168,7 @@ srv_front_page <- function(id, data, tables, show_metadata) {
       )
 
       metadata_data_frame <- reactive({
-        datanames <- teal.data::datanames(data())
+        datanames <- names(data())
         convert_metadata_to_dataframe(
           lapply(datanames, function(dataname) attr(data()[[dataname]], "metadata")),
           datanames

R/tm_g_association.R

@@ -38,7 +38,6 @@
 #'   factors <- names(Filter(isTRUE, vapply(CO2, is.factor, logical(1L))))
 #'   CO2[factors] <- lapply(CO2[factors], as.character)
 #' })
-#' datanames(data) <- c("CO2")
 #'
 #' app <- init(
 #'   data = data,
@@ -81,8 +80,7 @@
 #'   require(nestcolor)
 #'   ADSL <- rADSL
 #' })
-#' datanames(data) <- "ADSL"
-#' join_keys(data) <- default_cdisc_join_keys[datanames(data)]
+#' join_keys(data) <- default_cdisc_join_keys[names(data)]
 #'
 #' app <- init(
 #'   data = data,

R/tm_g_bivariate.R

@@ -57,7 +57,6 @@
 #'   require(nestcolor)
 #'   CO2 <- data.frame(CO2)
 #' })
-#' datanames(data) <- c("CO2")
 #'
 #' app <- init(
 #'   data = data,
@@ -116,8 +115,7 @@
 #'   require(nestcolor)
 #'   ADSL <- rADSL
 #' })
-#' datanames(data) <- c("ADSL")
-#' join_keys(data) <- default_cdisc_join_keys[datanames(data)]
+#' join_keys(data) <- default_cdisc_join_keys[names(data)]
 #'
 #' app <- init(
 #'   data = data,

R/tm_g_distribution.R

@@ -39,7 +39,6 @@
 #' data <- within(data, {
 #'   iris <- iris
 #' })
-#' datanames(data) <- "iris"
 #'
 #' app <- init(
 #'   data = data,
@@ -68,8 +67,7 @@
 #' data <- within(data, {
 #'   ADSL <- rADSL
 #' })
-#' datanames(data) <- c("ADSL")
-#' join_keys(data) <- default_cdisc_join_keys[datanames(data)]
+#' join_keys(data) <- default_cdisc_join_keys[names(data)]
 #'
 #' vars1 <- choices_selected(
 #'   variable_choices(data[["ADSL"]], c("ARM", "COUNTRY", "SEX")),
@@ -1216,15 +1214,15 @@ srv_distribution <- function(id,
       # wrapped in if since could lead into validate error - we do want to continue
       test_r_qenv_out <- try(test_q(), silent = TRUE)
       if (!inherits(test_r_qenv_out, c("try-error", "error"))) {
-        qenv_final <- teal.code::join(qenv_final, test_q())
+        qenv_final <- c(qenv_final, test_q())
       }
 
       qenv_final <- if (tab == "Histogram") {
         req(dist_q())
-        teal.code::join(qenv_final, dist_q())
+        c(qenv_final, dist_q())
       } else if (tab == "QQplot") {
         req(qq_q())
-        teal.code::join(qenv_final, qq_q())
+        c(qenv_final, qq_q())
       }
       qenv_final
     })

R/tm_g_response.R

@@ -53,7 +53,6 @@
 #'     mtcars[[v]] <- as.factor(mtcars[[v]])
 #'   }
 #' })
-#' datanames(data) <- "mtcars"
 #'
 #' app <- init(
 #'   data = data,
@@ -98,8 +97,7 @@
 #'   require(nestcolor)
 #'   ADSL <- rADSL
 #' })
-#' datanames(data) <- c("ADSL")
-#' join_keys(data) <- default_cdisc_join_keys[datanames(data)]
+#' join_keys(data) <- default_cdisc_join_keys[names(data)]
 #'
 #' app <- init(
 #'   data = data,

R/tm_g_scatterplot.R

@@ -43,7 +43,6 @@
 #'   require(nestcolor)
 #'   CO2 <- CO2
 #' })
-#' datanames(data) <- "CO2"
 #'
 #' app <- init(
 #'   data = data,
@@ -133,8 +132,7 @@
 #'   require(nestcolor)
 #'   ADSL <- rADSL
 #' })
-#' datanames(data) <- c("ADSL")
-#' join_keys(data) <- default_cdisc_join_keys[datanames(data)]
+#' join_keys(data) <- default_cdisc_join_keys[names(data)]
 #'
 #' app <- init(
 #'   data = data,

R/tm_g_scatterplotmatrix.R

@@ -56,7 +56,6 @@
 #'     profit = rnorm(50, 20, 10)
 #'   )
 #' })
-#' datanames(data) <- c("countries", "sales")
 #' join_keys(data) <- join_keys(
 #'   join_key("countries", "countries", "id"),
 #'   join_key("sales", "sales", "id"),
@@ -117,8 +116,7 @@
 #'   ADSL <- rADSL
 #'   ADRS <- rADRS
 #' })
-#' datanames(data) <- c("ADSL", "ADRS")
-#' join_keys(data) <- default_cdisc_join_keys[datanames(data)]
+#' join_keys(data) <- default_cdisc_join_keys[names(data)]
 #'
 #' app <- init(
 #'   data = data,

R/tm_missing_data.R

@@ -40,7 +40,6 @@
 #'   mtcars[["cyl"]] <- as.factor(mtcars[["cyl"]])
 #'   mtcars[["gear"]] <- as.factor(mtcars[["gear"]])
 #' })
-#' datanames(data) <- c("iris", "mtcars")
 #'
 #' app <- init(
 #'   data = data,
@@ -64,8 +63,7 @@
 #'   ADSL <- rADSL
 #'   ADRS <- rADRS
 #' })
-#' datanames(data) <- c("ADSL", "ADRS")
-#' join_keys(data) <- default_cdisc_join_keys[datanames(data)]
+#' join_keys(data) <- default_cdisc_join_keys[names(data)]
 #'
 #' app <- init(
 #'   data = data,
@@ -173,10 +171,11 @@ srv_page_missing_data <- function(id, data, reporter, filter_panel_api, parent_d
   moduleServer(id, function(input, output, session) {
     teal.logger::log_shiny_input_changes(input, namespace = "teal.modules.general")
 
-    datanames <- isolate(teal.data::datanames(data()))
-    datanames <- Filter(function(name) {
-      is.data.frame(isolate(data())[[name]])
-    }, datanames)
+    datanames <- isolate(names(data()))
+    datanames <- Filter(
+      function(name) is.data.frame(isolate(data())[[name]]),
+      datanames
+    )
     if_subject_plot <- length(parent_dataname) > 0 && parent_dataname %in% datanames
 
     ns <- session$ns
@@ -465,7 +464,7 @@ srv_missing_data <- function(id, data, reporter, filter_panel_api, dataname, par
 
 
     data_parent_keys <- reactive({
-      if (length(parent_dataname) > 0 && parent_dataname %in% teal.data::datanames(data())) {
+      if (length(parent_dataname) > 0 && parent_dataname %in% names(data())) {
         keys <- teal.data::join_keys(data())[[dataname]]
         if (parent_dataname %in% names(keys)) {
           keys[[parent_dataname]]

R/tm_outliers.R

@@ -28,7 +28,6 @@
 #'   CO2 <- CO2
 #'   CO2[["primary_key"]] <- seq_len(nrow(CO2))
 #' })
-#' datanames(data) <- "CO2"
 #' join_keys(data) <- join_keys(join_key("CO2", "CO2", "primary_key"))
 #'
 #' vars <- choices_selected(variable_choices(data[["CO2"]], c("Plant", "Type", "Treatment")))
@@ -77,8 +76,7 @@
 #' data <- within(data, {
 #'   ADSL <- rADSL
 #' })
-#' datanames(data) <- "ADSL"
-#' join_keys(data) <- default_cdisc_join_keys[datanames(data)]
+#' join_keys(data) <- default_cdisc_join_keys[names(data)]
 #'
 #' fact_vars_adsl <- names(Filter(isTRUE, sapply(data[["ADSL"]], is.factor)))
 #' vars <- choices_selected(variable_choices(data[["ADSL"]], fact_vars_adsl))
@@ -396,7 +394,7 @@ srv_outliers <- function(id, data, reporter, filter_panel_api, outlier_var,
     })
 
     # Used to create outlier table and the dropdown with additional columns
-    dataname_first <- isolate(teal.data::datanames(data())[[1]])
+    dataname_first <- isolate(names(data())[[1]])
 
     common_code_q <- reactive({
       req(iv_r()$is_valid())

R/tm_t_crosstable.R

@@ -39,7 +39,6 @@
 #'   }
 #'   mtcars[["primary_key"]] <- seq_len(nrow(mtcars))
 #' })
-#' datanames(data) <- "mtcars"
 #' join_keys(data) <- join_keys(join_key("mtcars", "mtcars", "primary_key"))
 #'
 #' app <- init(
@@ -85,8 +84,7 @@
 #' data <- within(data, {
 #'   ADSL <- rADSL
 #' })
-#' datanames(data) <- "ADSL"
-#' join_keys(data) <- default_cdisc_join_keys[datanames(data)]
+#' join_keys(data) <- default_cdisc_join_keys[names(data)]
 #'
 #' app <- init(
 #'   data = data,

R/tm_variable_browser.R

@@ -37,7 +37,6 @@
 #'   faithful <- faithful
 #'   CO2 <- CO2
 #' })
-#' datanames(data) <- c("iris", "mtcars", "women", "faithful", "CO2")
 #'
 #' app <- init(
 #'   data = data,
@@ -65,8 +64,7 @@
 #'   ADSL <- rADSL
 #'   ADTTE <- rADTTE
 #' })
-#' datanames(data) <- c("ADSL", "ADTTE")
-#' join_keys(data) <- default_cdisc_join_keys[datanames(data)]
+#' join_keys(data) <- default_cdisc_join_keys[names(data)]
 #'
 #' app <- init(
 #'   data = data,
@@ -225,7 +223,7 @@ srv_variable_browser <- function(id,
 
     varname_numeric_as_factor <- reactiveValues()
 
-    datanames <- isolate(teal.data::datanames(data()))
+    datanames <- isolate(names(data()))
     datanames <- Filter(function(name) {
       is.data.frame(isolate(data())[[name]])
     }, datanames)