Merge branch 'main' into spotfire_poc2

Author: gogonzo

DESCRIPTION

@@ -1,8 +1,8 @@
 Type: Package
 Package: teal.modules.general
 Title: General Modules for 'teal' Applications
-Version: 0.3.0.9053
-Date: 2024-11-04
+Version: 0.3.0.9054
+Date: 2024-11-08
 Authors@R: c(
     person("Dawid", "Kaledkowski", , "[email protected]", role = c("aut", "cre")),
     person("Pawel", "Rucki", , "[email protected]", role = "aut"),
@@ -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),

NEWS.md

@@ -1,4 +1,4 @@
-# teal.modules.general 0.3.0.9053
+# teal.modules.general 0.3.0.9054
 
 * Removed `Show Warnings` modals from modules.
 

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,
@@ -197,7 +195,7 @@ 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
     })