renaming

R/app_version.R

@@ -1 +1 @@
-app_version <- function()'250318_0819'
+app_version <- function()'250318_0827'

R/import-file-ext.R

@@ -254,7 +254,7 @@ import_file_server <- function(id,
         parameters <- parameters[which(names(parameters) %in% rlang::fn_fmls_names(get(read_fns[[extension]])))]
         # parameters <- parameters[which(names(parameters) %in% rlang::fn_fmls_names(read_fns[[extension]]))]
         imported <- try(rlang::exec(read_fns[[extension]], !!!parameters), silent = TRUE)
-        code <- rlang::call2(read_fns[[extension]], !!!modifyList(parameters, list(file = input$file$name)), .ns = "freesearcheR")
+        code <- rlang::call2(read_fns[[extension]], !!!modifyList(parameters, list(file = input$file$name)), .ns = "FreesearchR")
 
         if (inherits(imported, "try-error")) {
           imported <- try(rlang::exec(rio::import, !!!parameters[1]), silent = TRUE)

R/launch_FreesearchR.R

@@ -0,0 +1,24 @@
+#' Easily launch the FreesearchR app
+#'
+#' @description
+#' All data.frames in the global environment will be accessible through the app.
+#'
+#' @param ... passed on to `shiny::runApp()`
+#'
+#' @returns shiny app
+#' @export
+#'
+#' @examples
+#' \dontrun{
+#' data(mtcars)
+#' shiny_FreesearchR(launch.browser = TRUE)
+#' }
+launch_FreesearchR <- function(...){
+  appDir <- system.file("apps", "FreesearchR", package = "FreesearchR")
+  if (appDir == "") {
+    stop("Could not find the app directory. Try re-installing `FreesearchR`.", call. = FALSE)
+  }
+
+  a <- shiny::runApp(appDir = paste0(appDir,"/app.R"), ...)
+  return(invisible(a))
+}

R/regression_plot.R

@@ -15,15 +15,16 @@
 #'
 #' @examples
 #' \dontrun{
-#' mod <- lm(mpg ~ ., mtcars)
+#' mod <- lm(mpg ~ ., default_parsing(mtcars))
 #' p <- mod |>
 #'   gtsummary::tbl_regression() |>
 #'   plot(colour = "variable")
 #' }
 #'
 plot.tbl_regression <- function(x,
-                                # remove_header_rows = TRUE,
-                                # remove_reference_rows = FALSE,
+                                plot_ref = TRUE,
+                                remove_header_rows = TRUE,
+                                remove_reference_rows = FALSE,
                                 ...) {
   # check_dots_empty()
   gtsummary:::check_pkg_installed("ggstats")
@@ -32,18 +33,22 @@ plot.tbl_regression <- function(x,
   # gtsummary:::check_scalar_logical(remove_reference_rows)
 
   df_coefs <- x$table_body
-  # if (isTRUE(remove_header_rows)) {
-  #   df_coefs <- df_coefs |> dplyr::filter(!.data$header_row %in% TRUE)
-  # }
-  # if (isTRUE(remove_reference_rows)) {
-  #   df_coefs <- df_coefs |> dplyr::filter(!.data$reference_row %in% TRUE)
-  # }
-
-  # browser()
+  browser()
+  if (isTRUE(remove_header_rows)) {
+    df_coefs <- df_coefs |> dplyr::filter(!header_row %in% TRUE)
+  }
+  if (isTRUE(remove_reference_rows)) {
+    df_coefs <- df_coefs |> dplyr::filter(!reference_row %in% TRUE)
+  }
 
+  # Removes redundant label
   df_coefs$label[df_coefs$row_type == "label"] <- ""
 
-  df_coefs %>%
+  # Add estimate value to reference level
+  if (plot_ref == TRUE){
+  df_coefs[df_coefs$var_type == "categorical" & is.na(df_coefs$reference_row),"estimate"] <- if (x$inputs$exponentiate) 1 else 0}
+
+  df_coefs |>
     ggstats::ggcoef_plot(exponentiate = x$inputs$exponentiate, ...)
 }
 

R/regression_table.R

@@ -81,7 +81,7 @@
 #' #' @export
 #' regression_table.default <- function(x, ..., args.list = NULL, fun = "gtsummary::tbl_regression") {
 #'   # Stripping custom class
-#'   class(x) <- class(x)[class(x) != "freesearcher_model"]
+#'   class(x) <- class(x)[class(x) != "freesearchr_model"]
 #'
 #'   if (any(c(length(class(x)) != 1, class(x) != "lm"))) {
 #'     if (!"exponentiate" %in% names(args.list)) {
@@ -110,7 +110,7 @@ regression_table <- function(x, ...) {
 
 regression_table_create <- function(x, ..., args.list = NULL, fun = "gtsummary::tbl_regression") {
   # Stripping custom class
-  class(x) <- class(x)[class(x) != "freesearcher_model"]
+  class(x) <- class(x)[class(x) != "freesearchr_model"]
 
   if (any(c(length(class(x)) != 1, class(x) != "lm"))) {
     if (!"exponentiate" %in% names(args.list)) {

R/shiny_freesearcheR.R

@@ -1,37 +0,0 @@
-#' Launch the freesearcheR tool locally
-#'
-#' @description
-#' All data.frames in the global environment will be accessible through the app.
-#'
-#'
-#' @param ... arguments passed on to `shiny::runApp()`
-#'
-#' @return shiny app
-#' @export
-#'
-#' @examples
-#' \dontrun{
-#' data(mtcars)
-#' shiny_freesearcheR(launch.browser = TRUE)
-#' }
-shiny_freesearcheR <- function(...) {
-  appDir <- system.file("apps", "freesearcheR", package = "freesearcheR")
-  if (appDir == "") {
-    stop("Could not find the app directory. Try re-installing `freesearcheR`.", call. = FALSE)
-  }
-
-  a <- shiny::runApp(appDir = paste0(appDir,"/app.R"), ...)
-  return(invisible(a))
-}
-
-
-#' Easily launch the freesearcheR app
-#'
-#' @param ... passed on to `shiny::runApp()`
-#'
-#' @returns shiny app
-#' @export
-#'
-launch_freesearcheR <- function(...){
-  shiny_freesearcheR(...)
-}

R/update-factor-ext.R

@@ -265,7 +265,7 @@ modal_update_factor <- function(id,
 #'
 #' @importFrom shinyWidgets WinBox wbOptions wbControls
 #' @importFrom htmltools tagList
-#' @rdname create-column
+#' @rdname update-factor
 winbox_update_factor <- function(id,
                                  title = i18n("Update levels of a factor"),
                                  options = shinyWidgets::wbOptions(),