rename to qenv

NEWS.md

@@ -2,7 +2,7 @@
 
 ### Breaking changes
 
-* Replaced `chunks` with simpler `Quosure` class.
+* Replaced `chunks` with simpler `qenv` class.
 * Replaced `datasets` argument containing `FilteredData` with the new arguments `data` (list of reactive datasets) and `filter_panel_api` (`FilterPanelAPI`).
 
 ### Enhancements

R/tm_g_gh_boxplot.R

@@ -185,8 +185,8 @@
 #'     )
 #'   )
 #' )
-#' \dontrun{
-#' shinyApp(app$ui, app$server)
+#' if (interactive()) {
+#'   shinyApp(app$ui, app$server)
 #' }
 #'
 tm_g_gh_boxplot <- function(label,
@@ -370,6 +370,7 @@ srv_g_boxplot <- function(id,
                           hline_vars_labels) {
   with_reporter <- !missing(reporter) && inherits(reporter, "Reporter")
   with_filter <- !missing(filter_panel_api) && inherits(filter_panel_api, "FilterPanelAPI")
+  checkmate::assert_class(data, "tdata")
 
   moduleServer(id, function(input, output, session) {
 
@@ -449,7 +450,7 @@ srv_g_boxplot <- function(id,
         sprintf("You can not choose %s as x-axis variable for treatment variable %s.", xaxis, trt_group)
       ))
 
-      anl_q()$quosure %>% teal.code::eval_code(
+      anl_q()$qenv %>% teal.code::eval_code(
         code = bquote({
           p <- goshawk::g_boxplot(
             data = ANL,
@@ -486,7 +487,7 @@ srv_g_boxplot <- function(id,
       font_size <- input$font_size
       trt_group <- input$trt_group
 
-      anl_q()$quosure %>% teal.code::eval_code(
+      anl_q()$qenv %>% teal.code::eval_code(
         code = bquote({
           tbl <- goshawk::t_summarytable(
             data = ANL,

R/tm_g_gh_correlationplot.R

@@ -244,8 +244,8 @@
 #'     )
 #'   )
 #' )
-#' \dontrun{
-#' shinyApp(app$ui, app$server)
+#' if (interactive()) {
+#'   shinyApp(app$ui, app$server)
 #' }
 tm_g_gh_correlationplot <- function(label,
                                     dataname,
@@ -438,6 +438,7 @@ srv_g_correlationplot <- function(id,
                                   vline_vars_labels) {
   with_reporter <- !missing(reporter) && inherits(reporter, "Reporter")
   with_filter <- !missing(filter_panel_api) && inherits(filter_panel_api, "FilterPanelAPI")
+  checkmate::assert_class(data, "tdata")
 
   moduleServer(id, function(input, output, session) {
 
@@ -539,15 +540,15 @@ srv_g_correlationplot <- function(id,
       )
 
       # analysis
-      private_quosure <- teal.code::new_quosure(data) %>%
+      private_qenv <- teal.code::new_qenv(tdata2env(data), code = get_code(data)) %>%
         teal.code::eval_code(
           code = bquote({
             ANL <- .(as.name(dataset_var)) %>% # nolint
               dplyr::filter(.data[[.(param_var)]] %in% union(.(input$xaxis_param), .(input$yaxis_param)))
           })
         )
-      validate_has_data(private_quosure[["ANL"]], 1)
-      return(list(ANL = ANL, quosure = private_quosure))
+      validate_has_data(private_qenv[["ANL"]], 1)
+      return(list(ANL = ANL, qenv = private_qenv))
     })
 
     # constraints
@@ -642,7 +643,7 @@ srv_g_correlationplot <- function(id,
       trt_group <- input$trt_group
       line_vars <- unique(c(input$hline_vars, input$vline_vars))
 
-      private_q <- anl_constraint()$quosure %>% teal.code::eval_code(
+      private_q <- anl_constraint()$qenv %>% teal.code::eval_code(
         code = bquote({
           ANL_TRANSPOSED1 <- ANL %>% # nolint
             dplyr::select(
@@ -721,12 +722,12 @@ srv_g_correlationplot <- function(id,
         code =
           bquote(attr(ANL_TRANSPOSED[[.(trt_group)]], "label") <- attr(ANL[[.(trt_group)]], "label")) # nolint
       )
-      return(list(ANL_TRANSPOSED = private_q[["ANL_TRANSPOSED"]], quosure = private_q))
+      return(list(ANL_TRANSPOSED = private_q[["ANL_TRANSPOSED"]], qenv = private_q))
     })
 
     plot_labels <- reactive({
       req(anl_constraint())
-      ANL <- anl_constraint()$quosure[["ANL"]] # nolint
+      ANL <- anl_constraint()$qenv[["ANL"]] # nolint
 
       xparam <- ANL$PARAM[ANL[[param_var]] == input$xaxis_param][1]
       yparam <- ANL$PARAM[ANL[[param_var]] == input$yaxis_param][1]
@@ -798,7 +799,7 @@ srv_g_correlationplot <- function(id,
       trt_group <- input$trt_group
 
       teal.code::eval_code(
-        object = plot_data_transpose()$quosure,
+        object = plot_data_transpose()$qenv,
         code = bquote({
           # re-establish treatment variable label
           p <- goshawk::g_correlationplot(

R/tm_g_gh_density_distribution_plot.R

@@ -137,8 +137,8 @@
 #'     )
 #'   )
 #' )
-#' \dontrun{
-#' shinyApp(app$ui, app$server)
+#' if (interactive()) {
+#'   shinyApp(app$ui, app$server)
 #' }
 tm_g_gh_density_distribution_plot <- function(label, # nolint
                                               dataname,
@@ -292,6 +292,7 @@ srv_g_density_distribution_plot <- function(id, # nolint
                                             plot_width) {
   with_reporter <- !missing(reporter) && inherits(reporter, "Reporter")
   with_filter <- !missing(filter_panel_api) && inherits(filter_panel_api, "FilterPanelAPI")
+  checkmate::assert_class(data, "tdata")
 
   moduleServer(id, function(input, output, session) {
     anl_q <- constr_anl_q(
@@ -343,7 +344,7 @@ srv_g_density_distribution_plot <- function(id, # nolint
       validate(need(input$trt_group, "Please select a treatment variable"))
 
       teal.code::eval_code(
-        object = anl_q()$quosure,
+        object = anl_q()$qenv,
         code = bquote({
           p <- goshawk::g_density_distribution_plot(
             data = ANL,
@@ -379,7 +380,7 @@ srv_g_density_distribution_plot <- function(id, # nolint
       validate(need(trt_group, "Please select a treatment variable"))
 
       teal.code::eval_code(
-        object = anl_q()$quosure,
+        object = anl_q()$qenv,
         code = bquote(
           tbl <- goshawk::t_summarytable(
             data = ANL,

R/tm_g_gh_lineplot.R

@@ -147,8 +147,8 @@
 #'     )
 #'   )
 #' )
-#' \dontrun{
-#' shinyApp(app$ui, app$server)
+#' if (interactive()) {
+#'   shinyApp(app$ui, app$server)
 #' }
 tm_g_gh_lineplot <- function(label,
                              dataname,
@@ -354,6 +354,7 @@ srv_lineplot <- function(id,
                          plot_width) {
   with_reporter <- !missing(reporter) && inherits(reporter, "Reporter")
   with_filter <- !missing(filter_panel_api) && inherits(filter_panel_api, "FilterPanelAPI")
+  checkmate::assert_class(data, "tdata")
 
   moduleServer(id, function(input, output, session) {
     ns <- session$ns
@@ -706,20 +707,20 @@ srv_lineplot <- function(id,
         )
       )
 
-      private_quosure <- anl_q()$quosure
+      private_qenv <- anl_q()$qenv
 
       if (!methods::is(xtick, "waiver") && !is.null(xtick)) {
-        private_quosure <- teal.code::eval_code(
-          object = private_quosure,
+        private_qenv <- teal.code::eval_code(
+          object = private_qenv,
           code = bquote({
             keep_index <- which(.(xtick) %in% ANL[[.(xaxis)]])
             xtick <- (.(xtick))[keep_index] # extra parentheses needed for edge case, e.g. 1:5[keep_index]
             xlabel <- (.(xlabel))[keep_index]
           })
         )
       } else if (methods::is(xtick, "waiver")) {
-        private_quosure <- teal.code::eval_code(
-          object = private_quosure,
+        private_qenv <- teal.code::eval_code(
+          object = private_qenv,
           code = "
             xtick <- ggplot2::waiver()
             xlabel <- ggplot2::waiver()
@@ -732,7 +733,7 @@ srv_lineplot <- function(id,
       hline_arb_color <- horizontal_line()$line_arb_color
 
       teal.code::eval_code(
-        object = private_quosure,
+        object = private_qenv,
         code = bquote({
           p <- goshawk::g_lineplot(
             data = ANL[complete.cases(ANL[, c(.(yaxis), .(xaxis))]), ],

R/tm_g_gh_scatterplot.R

@@ -135,8 +135,8 @@
 #'     )
 #'   )
 #' )
-#' \dontrun{
-#' shinyApp(app$ui, app$server)
+#' if (interactive()) {
+#'   shinyApp(app$ui, app$server)
 #' }
 #'
 tm_g_gh_scatterplot <- function(label,
@@ -279,6 +279,7 @@ srv_g_scatterplot <- function(id,
                               plot_width) {
   with_reporter <- !missing(reporter) && inherits(reporter, "Reporter")
   with_filter <- !missing(filter_panel_api) && inherits(filter_panel_api, "FilterPanelAPI")
+  checkmate::assert_class(data, "tdata")
 
   moduleServer(id, function(input, output, session) {
 
@@ -326,7 +327,7 @@ srv_g_scatterplot <- function(id,
 
       # nolint end
       teal.code::eval_code(
-        object = anl_q()$quosure,
+        object = anl_q()$qenv,
         code = bquote({
           # re-establish treatment variable label
           p <- goshawk::g_scatterplot(

R/tm_g_gh_spaghettiplot.R

@@ -191,8 +191,8 @@
 #'     )
 #'   )
 #' )
-#' \dontrun{
-#' shinyApp(app$ui, app$server)
+#' if (interactive()) {
+#'   shinyApp(app$ui, app$server)
 #' }
 #'
 tm_g_gh_spaghettiplot <- function(label,
@@ -376,6 +376,7 @@ srv_g_spaghettiplot <- function(id,
                                 hline_vars_labels) {
   with_reporter <- !missing(reporter) && inherits(reporter, "Reporter")
   with_filter <- !missing(filter_panel_api) && inherits(filter_panel_api, "FilterPanelAPI")
+  checkmate::assert_class(data, "tdata")
 
   moduleServer(id, function(input, output, session) {
 
@@ -420,36 +421,36 @@ srv_g_spaghettiplot <- function(id,
       hline_vars <- input$hline_vars
       # nolint end
 
-      private_quosure <- anl_q()$quosure
+      private_qenv <- anl_q()$qenv
 
       # this code is needed to make sure the waiver attribute
       # of ggplot2::waiver is correctly passed to goshawk's spaghettiplot
       if (!methods::is(xtick, "waiver")) {
-        private_quosure <- teal.code::eval_code(
-          object = private_quosure,
+        private_qenv <- teal.code::eval_code(
+          object = private_qenv,
           code = bquote(xtick <- .(xtick))
         )
       } else {
-        private_quosure <- teal.code::eval_code(
-          object = private_quosure,
+        private_qenv <- teal.code::eval_code(
+          object = private_qenv,
           code = quote(xtick <- ggplot2::waiver())
         )
       }
 
       if (!methods::is(xlabel, "waiver")) {
-        private_quosure <- teal.code::eval_code(
-          object = private_quosure,
+        private_qenv <- teal.code::eval_code(
+          object = private_qenv,
           code = bquote(xlabel <- .(xlabel))
         )
       } else {
-        private_quosure <- teal.code::eval_code(
-          object = private_quosure,
+        private_qenv <- teal.code::eval_code(
+          object = private_qenv,
           code = quote(xlabel <- ggplot2::waiver())
         )
       }
 
       teal.code::eval_code(
-        object = private_quosure,
+        object = private_qenv,
         code = bquote({
           p <- goshawk::g_spaghettiplot(
             data = ANL,

R/utils.R

@@ -197,7 +197,7 @@ constr_anl_q <- function(session, input, data, dataname, param_id, param_var, tr
     validate_has_variable(ANL, trt_group)
 
     # analysis
-    private_quosure <- teal.code::new_quosure(data) %>%
+    private_qenv <- teal.code::new_qenv(tdata2env(data), code = get_code(data)) %>%
       teal.code::eval_code(
         substitute(ANL <- dataname, list(dataname = as.name(dataname))) # nolint
       ) %>%
@@ -207,8 +207,8 @@ constr_anl_q <- function(session, input, data, dataname, param_id, param_var, tr
             dplyr::filter(.(as.name(param_var)) == .(param_var_value))
         })
       )
-    validate_has_data(private_quosure[["ANL"]], min_rows)
-    list(ANL = ANL, quosure = private_quosure)
+    validate_has_data(private_qenv[["ANL"]], min_rows)
+    list(ANL = ANL, qenv = private_qenv)
   })
 
   observe({
@@ -293,7 +293,7 @@ constr_anl_q <- function(session, input, data, dataname, param_id, param_var, tr
 # e.g. `ALT.BASE2` (i.e. `PARAMCD = ALT & range_filter_on(BASE2)`)
 create_anl_constraint_reactive <- function(anl_param, input, param_id, min_rows) {
   reactive({
-    private_quosure <- anl_param()$quosure
+    private_qenv <- anl_param()$qenv
 
     # it is assumed that constraint_var is triggering constraint_range which then trigger this clause
     constraint_var <- isolate(input[["constraint_var"]])
@@ -308,8 +308,8 @@ create_anl_constraint_reactive <- function(anl_param, input, param_id, min_rows)
 
     # filter constraint
     if (constraint_var != "NONE") {
-      private_quosure <- teal.code::eval_code(
-        object = private_quosure,
+      private_qenv <- teal.code::eval_code(
+        object = private_qenv,
         code = bquote({
           # the below includes patients who have at least one non-NA BASE value
           # ideally, a patient should either have all NA values or none at all
@@ -334,10 +334,10 @@ create_anl_constraint_reactive <- function(anl_param, input, param_id, min_rows)
           ANL <- ANL %>% dplyr::filter(USUBJID %in% filtered_usubjids) # nolint
         })
       )
-      validate_has_data(private_quosure[["ANL"]], min_rows)
+      validate_has_data(private_qenv[["ANL"]], min_rows)
     }
 
-    return(list(ANL = private_quosure[["ANL"]], quosure = private_quosure))
+    return(list(ANL = private_qenv[["ANL"]], qenv = private_qenv))
   })
 }