diff --git a/R/hosted_version.R b/R/hosted_version.R index a898784a..32d9fe0f 100644 --- a/R/hosted_version.R +++ b/R/hosted_version.R @@ -1 +1 @@ -hosted_version <- function()'v25.5.4-250513' +hosted_version <- function()'v25.5.4-250512' diff --git a/R/regression-module.R b/R/regression-module.R index f79c0c50..57806bde 100644 --- a/R/regression-module.R +++ b/R/regression-module.R @@ -65,6 +65,16 @@ 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", @@ -95,29 +105,6 @@ 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$br() ), do.call( @@ -499,7 +486,7 @@ regression_server <- function(id, tryCatch( { parameters <- list( - p.values = input$add_regression_p == "no" + add_p = input$add_regression_p == "no" ) out <- lapply(rv$list$regression$models, \(.x){ @@ -512,6 +499,16 @@ 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$models[[.i]][["code_table"]] <- paste( @@ -523,6 +520,7 @@ regression_server <- function(id, rv$list$regression$tables <- out rv$list$input <- input + }, warning = function(warn) { showNotification(paste0(warn), type = "warning") @@ -534,28 +532,13 @@ 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)) { - 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 |> + rv$list$regression$tables |> + tbl_merge() |> gtsummary::as_gt() |> gt::tab_header(gt::md(glue::glue("**Table 2: {rv$list$regression$params$descr}**"))) - - rv$list$regression$table_merged - - out } else { return(NULL) } @@ -649,7 +632,7 @@ regression_server <- function(id, ############################################################################## return(shiny::reactive({ - rv$list + rv$list })) } ) diff --git a/R/regression_table.R b/R/regression_table.R index b0331c72..71e99272 100644 --- a/R/regression_table.R +++ b/R/regression_table.R @@ -46,13 +46,6 @@ #' 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, @@ -140,7 +133,7 @@ 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)) diff --git a/inst/apps/FreesearchR/app.R b/inst/apps/FreesearchR/app.R index 646d4417..7882c2ca 100644 --- a/inst/apps/FreesearchR/app.R +++ b/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()'v25.5.4-250513' +hosted_version <- function()'v25.5.4-250512' ######## @@ -7040,13 +7040,6 @@ 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, @@ -7134,7 +7127,7 @@ 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)) @@ -7248,6 +7241,16 @@ 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", @@ -7278,29 +7281,6 @@ 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$br() ), do.call( @@ -7682,7 +7662,7 @@ regression_server <- function(id, tryCatch( { parameters <- list( - p.values = input$add_regression_p == "no" + add_p = input$add_regression_p == "no" ) out <- lapply(rv$list$regression$models, \(.x){ @@ -7695,6 +7675,16 @@ 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$models[[.i]][["code_table"]] <- paste( @@ -7706,6 +7696,7 @@ regression_server <- function(id, rv$list$regression$tables <- out rv$list$input <- input + }, warning = function(warn) { showNotification(paste0(warn), type = "warning") @@ -7717,28 +7708,13 @@ 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)) { - 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 |> + rv$list$regression$tables |> + tbl_merge() |> gtsummary::as_gt() |> gt::tab_header(gt::md(glue::glue("**Table 2: {rv$list$regression$params$descr}**"))) - - rv$list$regression$table_merged - - out } else { return(NULL) } @@ -7832,7 +7808,7 @@ regression_server <- function(id, ############################################################################## return(shiny::reactive({ - rv$list + rv$list })) } ) diff --git a/man/regression_table.Rd b/man/regression_table.Rd index d319247b..4a47c6f9 100644 --- a/man/regression_table.Rd +++ b/man/regression_table.Rd @@ -58,13 +58,6 @@ 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,