prepare for reactive theming - only setting theme on render

R/hosted_version.R

@@ -1 +1 @@
-hosted_version <- function()'v25.5.4-250512'
+hosted_version <- function()'v25.5.4-250513'

R/regression-module.R

@@ -65,16 +65,6 @@ regression_ui <- function(id, ...) {
           #   )
           # ),
           shiny::uiOutput(outputId = ns("regression_type")),
-          shiny::radioButtons(
-            inputId = ns("add_regression_p"),
-            label = "Add p-value",
-            inline = TRUE,
-            selected = "yes",
-            choices = list(
-              "Yes" = "yes",
-              "No" = "no"
-            )
-          ),
           shiny::radioButtons(
             inputId = ns("all"),
             label = "Specify covariables",
@@ -105,6 +95,29 @@ regression_ui <- function(id, ...) {
             auto_reset = TRUE
           ),
           shiny::helpText("Press 'Analyse' to create the regression model and after changing parameters."),
+          shiny::tags$br(),
+          shiny::radioButtons(
+            inputId = ns("add_regression_p"),
+            label = "Show p-value",
+            inline = TRUE,
+            selected = "yes",
+            choices = list(
+              "Yes" = "yes",
+              "No" = "no"
+            )
+          ),
+          # shiny::tags$br(),
+          # shiny::radioButtons(
+          #   inputId = ns("tbl_theme"),
+          #   label = "Show p-value",
+          #   inline = TRUE,
+          #   selected = "jama",
+          #   choices = list(
+          #     "JAMA" = "jama",
+          #     "Lancet" = "lancet",
+          #     "NEJM" = "nejm"
+          #   )
+          # ),
           shiny::tags$br()
         ),
         do.call(
@@ -486,7 +499,7 @@ regression_server <- function(id,
           tryCatch(
             {
               parameters <- list(
-                add_p = input$add_regression_p == "no"
+                p.values = input$add_regression_p == "no"
               )
 
               out <- lapply(rv$list$regression$models, \(.x){
@@ -499,16 +512,6 @@ regression_server <- function(id,
                   )
                 })
 
-              # if (input$add_regression_p == "no") {
-              #   out <- out |>
-              #     lapply(\(.x){
-              #       .x |>
-              #         gtsummary::modify_column_hide(
-              #           column = "p.value"
-              #         )
-              #     })
-              # }
-
               rv$list$regression$models |>
                 purrr::imap(\(.x, .i){
                   rv$list$regression$models[[.i]][["code_table"]] <- paste(
@@ -520,7 +523,6 @@ regression_server <- function(id,
 
               rv$list$regression$tables <- out
               rv$list$input <- input
-
             },
             warning = function(warn) {
               showNotification(paste0(warn), type = "warning")
@@ -532,13 +534,28 @@ regression_server <- function(id,
         }
       )
 
+      ## Consider creating merged table with theming and then passing object
+      ## to render.
+
       output$table2 <- gt::render_gt({
         ## Print checks if a regression table is present
         if (!is.null(rv$list$regression$tables)) {
-          rv$list$regression$tables |>
-            tbl_merge() |>
+          gtsummary::theme_gtsummary_journal(journal = "jama")
+          merged <- rv$list$regression$tables |>
+            tbl_merge()
+
+          if (input$add_regression_p == "no") {
+            merged <- merged |>
+              gtsummary::modify_column_hide(column = dplyr::starts_with("p.value"))
+          }
+
+          out <- merged |>
             gtsummary::as_gt() |>
             gt::tab_header(gt::md(glue::glue("**Table 2: {rv$list$regression$params$descr}**")))
+
+          rv$list$regression$table_merged
+
+          out
         } else {
           return(NULL)
         }
@@ -632,7 +649,7 @@ regression_server <- function(id,
       ##############################################################################
 
       return(shiny::reactive({
-          rv$list
+        rv$list
       }))
     }
   )

R/regression_table.R

@@ -46,6 +46,13 @@
 #'     args.list = list(family = stats::binomial(link = "logit"))
 #'   ) |>
 #'   regression_table()
+#' mtcars|>
+#'  regression_model(
+#'     outcome.str = "mpg",
+#'     args.list = NULL)
+#'   ) |>
+#'   regression_table()
+#'
 #'
 #' list(
 #'   "Univariable" = regression_model_uv,
@@ -133,7 +140,7 @@ regression_table_create <- function(x, ..., args.list = NULL, fun = "gtsummary::
     }
   }
 
-  gtsummary::theme_gtsummary_journal(journal = theme)
+  # gtsummary::theme_gtsummary_journal(journal = theme)
   if (inherits(x, "polr")) {
     # browser()
     out <- do.call(getfun(fun), c(list(x = x), args.list))

inst/apps/FreesearchR/app.R

@@ -3996,7 +3996,7 @@ simple_snake <- function(data){
 #### Current file: /Users/au301842/FreesearchR/R//hosted_version.R 
 ########
 
-hosted_version <- function()'v25.5.4-250512'
+hosted_version <- function()'v25.5.4-250513'
 
 
 ########
@@ -7040,6 +7040,13 @@ symmetrical_scale_x_log10 <- function(plot, breaks = c(1, 2, 3, 5, 10), ...) {
 #'     args.list = list(family = stats::binomial(link = "logit"))
 #'   ) |>
 #'   regression_table()
+#' mtcars|>
+#'  regression_model(
+#'     outcome.str = "mpg",
+#'     args.list = NULL)
+#'   ) |>
+#'   regression_table()
+#'
 #'
 #' list(
 #'   "Univariable" = regression_model_uv,
@@ -7127,7 +7134,7 @@ regression_table_create <- function(x, ..., args.list = NULL, fun = "gtsummary::
     }
   }
 
-  gtsummary::theme_gtsummary_journal(journal = theme)
+  # gtsummary::theme_gtsummary_journal(journal = theme)
   if (inherits(x, "polr")) {
     # browser()
     out <- do.call(getfun(fun), c(list(x = x), args.list))
@@ -7241,16 +7248,6 @@ regression_ui <- function(id, ...) {
           #   )
           # ),
           shiny::uiOutput(outputId = ns("regression_type")),
-          shiny::radioButtons(
-            inputId = ns("add_regression_p"),
-            label = "Add p-value",
-            inline = TRUE,
-            selected = "yes",
-            choices = list(
-              "Yes" = "yes",
-              "No" = "no"
-            )
-          ),
           shiny::radioButtons(
             inputId = ns("all"),
             label = "Specify covariables",
@@ -7281,6 +7278,29 @@ regression_ui <- function(id, ...) {
             auto_reset = TRUE
           ),
           shiny::helpText("Press 'Analyse' to create the regression model and after changing parameters."),
+          shiny::tags$br(),
+          shiny::radioButtons(
+            inputId = ns("add_regression_p"),
+            label = "Show p-value",
+            inline = TRUE,
+            selected = "yes",
+            choices = list(
+              "Yes" = "yes",
+              "No" = "no"
+            )
+          ),
+          # shiny::tags$br(),
+          # shiny::radioButtons(
+          #   inputId = ns("tbl_theme"),
+          #   label = "Show p-value",
+          #   inline = TRUE,
+          #   selected = "jama",
+          #   choices = list(
+          #     "JAMA" = "jama",
+          #     "Lancet" = "lancet",
+          #     "NEJM" = "nejm"
+          #   )
+          # ),
           shiny::tags$br()
         ),
         do.call(
@@ -7662,7 +7682,7 @@ regression_server <- function(id,
           tryCatch(
             {
               parameters <- list(
-                add_p = input$add_regression_p == "no"
+                p.values = input$add_regression_p == "no"
               )
 
               out <- lapply(rv$list$regression$models, \(.x){
@@ -7675,16 +7695,6 @@ regression_server <- function(id,
                   )
                 })
 
-              # if (input$add_regression_p == "no") {
-              #   out <- out |>
-              #     lapply(\(.x){
-              #       .x |>
-              #         gtsummary::modify_column_hide(
-              #           column = "p.value"
-              #         )
-              #     })
-              # }
-
               rv$list$regression$models |>
                 purrr::imap(\(.x, .i){
                   rv$list$regression$models[[.i]][["code_table"]] <- paste(
@@ -7696,7 +7706,6 @@ regression_server <- function(id,
 
               rv$list$regression$tables <- out
               rv$list$input <- input
-
             },
             warning = function(warn) {
               showNotification(paste0(warn), type = "warning")
@@ -7708,13 +7717,28 @@ regression_server <- function(id,
         }
       )
 
+      ## Consider creating merged table with theming and then passing object
+      ## to render.
+
       output$table2 <- gt::render_gt({
         ## Print checks if a regression table is present
         if (!is.null(rv$list$regression$tables)) {
-          rv$list$regression$tables |>
-            tbl_merge() |>
+          gtsummary::theme_gtsummary_journal(journal = "jama")
+          merged <- rv$list$regression$tables |>
+            tbl_merge()
+
+          if (input$add_regression_p == "no") {
+            merged <- merged |>
+              gtsummary::modify_column_hide(column = dplyr::starts_with("p.value"))
+          }
+
+          out <- merged |>
             gtsummary::as_gt() |>
             gt::tab_header(gt::md(glue::glue("**Table 2: {rv$list$regression$params$descr}**")))
+
+          rv$list$regression$table_merged
+
+          out
         } else {
           return(NULL)
         }
@@ -7808,7 +7832,7 @@ regression_server <- function(id,
       ##############################################################################
 
       return(shiny::reactive({
-          rv$list
+        rv$list
       }))
     }
   )

man/regression_table.Rd

@@ -58,6 +58,13 @@ gtsummary::trial |>
     args.list = list(family = stats::binomial(link = "logit"))
   ) |>
   regression_table()
+mtcars|>
+ regression_model(
+    outcome.str = "mpg",
+    args.list = NULL)
+  ) |>
+  regression_table()
+
 
 list(
   "Univariable" = regression_model_uv,