renaming

DESCRIPTION

@@ -1,4 +1,4 @@
-Package: freesearcheR
+Package: FreesearchR
 Title: Browser Based Data Analysis
 Version: 25.3.2
 Authors@R: 

FreesearchR.Rproj

@@ -20,4 +20,4 @@ LineEndingConversion: Posix
 BuildType: Package
 PackageUseDevtools: Yes
 PackageInstallArgs: --no-multiarch --with-keep.source
-PackageRoxygenize: rd,collate,namespace
+PackageRoxygenize: rd,collate,namespace,vignette

NAMESPACE

@@ -48,7 +48,7 @@ export(is_consecutive)
 export(is_datetime)
 export(is_valid_redcap_url)
 export(is_valid_token)
-export(launch_freesearcheR)
+export(launch_FreesearchR)
 export(line_break)
 export(m_datafileUI)
 export(m_redcap_readServer)
@@ -81,7 +81,6 @@ export(remove_na_attr)
 export(repeated_instruments)
 export(sankey_ready)
 export(selectInputIcon)
-export(shiny_freesearcheR)
 export(specify_qmd_format)
 export(subset_types)
 export(supported_functions)

NEWS.md

@@ -2,11 +2,11 @@
 
 Focus is on polish and improved ui/ux.
 
-First steps towards an updated name (will be FreesearchR), with renamed repository. Also, the repo will move to an organisation (named FreesearchR).
+First steps towards an updated name (will be FreesearchR), with renamed repository. This may introduce some breaking chances for others calling or installing the package. No future changes are planned. A complete transition is planned before attending and presenting a poster at the European Stroke Organisation COnference 2025 in May.
 
 Testing file upload conducted and improved.
 
-Working on omproving code export.
+Working on improving code export.
 
 # freesearcheR 25.3.1
 

QA.md

@@ -1,6 +1,6 @@
 # Questions and answers
 
-A complete instructions set is not available, but below are a collection of questions and answers about the project and use of the app.
+A complete instructions set [is also available](https://agdamsbo.github.io/FreesearchR/articles/FreesearchR.html), but below are a collection of questions and answers about the project and use of the ***FreesearchR*** app.
 
 ## Are you keeping the uploaded data?
 

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(),

README.md

@@ -1,35 +1,35 @@
-# freesearcheR
+# FreesearchR
 
 <!-- badges: start -->
 [![Lifecycle: experimental](https://img.shields.io/badge/lifecycle-experimental-orange.svg)](https://lifecycle.r-lib.org/articles/stages.html#experimental)
-[![rhub](https://github.com/agdamsbo/freesearcheR/actions/workflows/rhub.yaml/badge.svg)](https://github.com/agdamsbo/freesearcheR/actions/workflows/rhub.yaml)
 [![DOI](https://zenodo.org/badge/DOI/10.5281/zenodo.14527429.svg)](https://doi.org/10.5281/zenodo.14527429) 
-[![freesearcheR](https://img.shields.io/badge/Shiny-shinyapps.io-blue?style=flat&labelColor=white&logo=RStudio&logoColor=blue)](https://agdamsbo.shinyapps.io/freesearcheR/)
+[![rhub](https://github.com/agdamsbo/FreesearchR/actions/workflows/rhub.yaml/badge.svg)](https://github.com/agdamsbo/FreesearchR/actions/workflows/rhub.yaml)
+[![FreesearchR](https://img.shields.io/badge/Shiny-shinyapps.io-blue?style=flat&labelColor=white&logo=RStudio&logoColor=blue)](https://agdamsbo.shinyapps.io/freesearcheR/)
 <!-- badges: end -->
 
-This package is the backbone of the ***freesearcheR***, a free and open-source browser based data exploration and analysis tool for clinicians and researchers with publication ready output.
+This package is the backbone of the ***FreesearchR***, a free and open-source browser based data exploration and analysis tool for clinicians and researchers with publication ready output.
 
-This package and the ***freesearcheR***-tool is part of a larger initiative to democratize health data analysis and remove barriers for clinicians to engage in health research.
+This package and the ***FreesearchR***-tool is part of a larger initiative to democratize health data analysis and remove barriers for clinicians to engage in health research.
 
-the ***freesearcheR***-tool is online and accessible here: [link to the app freely hosted on shinyapps.io](https://agdamsbo.shinyapps.io/freesearcheR/). All feedback is welcome and can be shared as a GitHub issue.
+the ***FreesearchR***-tool is online and accessible here: [link to the app freely hosted on shinyapps.io](https://agdamsbo.shinyapps.io/FreesearchR/). All feedback is welcome and can be shared as a GitHub issue.
 
 Initiatives for funding continued development of the tool and surrounding initiatives is ongoing.
 
 
 ## Install locally
 
-The ***freesearcheR***-tool can also be launched locally. Any data.frame available in the global environment will be accessible from the interface.
+The ***FreesearchR***-tool can also be launched locally. Any data.frame available in the global environment will be accessible from the interface.
 
 ```
 require("devtools")
-devtools::install_github("agdamsbo/freesearcheR")
-library(freesearcheR)
+devtools::install_github("agdamsbo/FreesearchR")
+library(FreesearchR)
 # By loading mtcars to the environment, it will be available 
 # in the interface like any other data.frame
 data(mtcars) 
-shiny_freesearcheR()
+launch_FreesearchR()
 ```
 
 ## Code of Conduct
 
-Please note that the freesearcheR project is released with a [Contributor Code of Conduct](https://contributor-covenant.org/version/2/1/CODE_OF_CONDUCT.html). By contributing to this project, you agree to abide by its terms.
+Please note that the ***FreesearchR*** project is released with a [Contributor Code of Conduct](https://contributor-covenant.org/version/2/1/CODE_OF_CONDUCT.html). By contributing to this project, you agree to abide by its terms.

inst/apps/FreesearchR/app.R

@@ -10,7 +10,7 @@
 #### Current file: R//app_version.R
 ########
 
-app_version <- function()'250318_0819'
+app_version <- function()'250318_0827'
 
 
 ########
@@ -7214,7 +7214,8 @@ ui_elements <- list(
           ),
           shiny::br(),
           shiny::br(),
-          shiny::tags$b("Code snippets:"),
+          shiny::h4("Code snippets"),
+          shiny::tags$p("Below are the code used to create the final data set. This can be saved for reproducibility. The code may not be 100 % correct, but kan be used for learning and example code to get started on coding yourself."),
           shiny::verbatimTextOutput(outputId = "code_import"),
           shiny::verbatimTextOutput(outputId = "code_data"),
           shiny::verbatimTextOutput(outputId = "code_filter"),
@@ -7535,11 +7536,6 @@ server <- function(input, output, session) {
     )
   })
 
-  # shiny::observeEvent(input$reset_confirm, {
-  #   rv$data <- rv$data_original |> default_parsing()
-  # })
-
-
 
   #########
   #########  Modifications
@@ -7612,7 +7608,6 @@ server <- function(input, output, session) {
     }
   )
 
-
   #########  Subset, rename, reclass
 
   updated_data <- update_variables_server(
@@ -7626,8 +7621,6 @@ server <- function(input, output, session) {
     rv$code$modify[[length(rv$code$modify) + 1]] <- attr(rv$data, "code")
   })
 
-
-
   #########  Data filter
   # IDEAFilter has the least cluttered UI, but might have a License issue
   data_filter <- IDEAFilter::IDEAFilter("data_filter",
@@ -7765,7 +7758,6 @@ server <- function(input, output, session) {
   })
 
   output$code_filter <- shiny::renderPrint({
-    shiny::req(rv$code$filter)
     cat(rv$code$filter)
   })
 

inst/apps/FreesearchR/rsconnect/shinyapps.io/agdamsbo/freesearcheR.dcf

@@ -5,6 +5,6 @@ account: agdamsbo
 server: shinyapps.io
 hostUrl: https://api.shinyapps.io/v1
 appId: 13611288
-bundleId: 9958862
+bundleId: 9961770
 url: https://agdamsbo.shinyapps.io/freesearcheR/
 version: 1

man/launch_FreesearchR.Rd

@@ -0,0 +1,23 @@
+% Generated by roxygen2: do not edit by hand
+% Please edit documentation in R/launch_FreesearchR.R
+\name{launch_FreesearchR}
+\alias{launch_FreesearchR}
+\title{Easily launch the FreesearchR app}
+\usage{
+launch_FreesearchR(...)
+}
+\arguments{
+\item{...}{passed on to \code{shiny::runApp()}}
+}
+\value{
+shiny app
+}
+\description{
+All data.frames in the global environment will be accessible through the app.
+}
+\examples{
+\dontrun{
+data(mtcars)
+shiny_FreesearchR(launch.browser = TRUE)
+}
+}

man/launch_freesearcheR.Rd

@@ -1,17 +0,0 @@
-% Generated by roxygen2: do not edit by hand
-% Please edit documentation in R/shiny_freesearcheR.R
-\name{launch_freesearcheR}
-\alias{launch_freesearcheR}
-\title{Easily launch the freesearcheR app}
-\usage{
-launch_freesearcheR(...)
-}
-\arguments{
-\item{...}{passed on to \code{shiny::runApp()}}
-}
-\value{
-shiny app
-}
-\description{
-Easily launch the freesearcheR app
-}

man/plot.tbl_regression.Rd

@@ -4,7 +4,13 @@
 \alias{plot.tbl_regression}
 \title{Regression coef plot from gtsummary. Slightly modified to pass on arguments}
 \usage{
-\method{plot}{tbl_regression}(x, ...)
+\method{plot}{tbl_regression}(
+  x,
+  plot_ref = TRUE,
+  remove_header_rows = TRUE,
+  remove_reference_rows = FALSE,
+  ...
+)
 }
 \arguments{
 \item{x}{(\code{tbl_regression}, \code{tbl_uvregression})\cr
@@ -20,7 +26,7 @@ Regression coef plot from gtsummary. Slightly modified to pass on arguments
 }
 \examples{
 \dontrun{
-mod <- lm(mpg ~ ., mtcars)
+mod <- lm(mpg ~ ., default_parsing(mtcars))
 p <- mod |>
   gtsummary::tbl_regression() |>
   plot(colour = "variable")

man/regression_table.Rd

@@ -93,7 +93,7 @@ regression_table.list <- function(x, ...) {
 #' @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)) {

man/shiny_freesearcheR.Rd

@@ -1,23 +0,0 @@
-% Generated by roxygen2: do not edit by hand
-% Please edit documentation in R/shiny_freesearcheR.R
-\name{shiny_freesearcheR}
-\alias{shiny_freesearcheR}
-\title{Launch the freesearcheR tool locally}
-\usage{
-shiny_freesearcheR(...)
-}
-\arguments{
-\item{...}{arguments passed on to \code{shiny::runApp()}}
-}
-\value{
-shiny app
-}
-\description{
-All data.frames in the global environment will be accessible through the app.
-}
-\examples{
-\dontrun{
-data(mtcars)
-shiny_freesearcheR(launch.browser = TRUE)
-}
-}

man/update-factor.Rd

@@ -5,6 +5,7 @@
 \alias{update_factor_ui}
 \alias{update_factor_server}
 \alias{modal_update_factor}
+\alias{winbox_update_factor}
 \title{Module to Reorder the Levels of a Factor Variable}
 \usage{
 update_factor_ui(id)
@@ -18,6 +19,13 @@ modal_update_factor(
   size = "l",
   footer = NULL
 )
+
+winbox_update_factor(
+  id,
+  title = i18n("Update levels of a factor"),
+  options = shinyWidgets::wbOptions(),
+  controls = shinyWidgets::wbControls()
+)
 }
 \arguments{
 \item{id}{Module ID.}
@@ -39,6 +47,10 @@ pass \code{\link[bslib:bs_theme]{bslib::bs_theme()}} to the \code{theme} argumen
 like \code{\link[shiny:fluidPage]{fluidPage()}}).}
 
 \item{footer}{UI for footer. Use \code{NULL} for no footer.}
+
+\item{options}{List of options, see \code{\link[shinyWidgets:wbOptions]{wbOptions()}}.}
+
+\item{controls}{List of controls, see \code{\link[shinyWidgets:wbControls]{wbControls()}}.}
 }
 \value{
 A \code{\link[shiny:reactive]{shiny::reactive()}} function returning the data.

vignettes/FreesearchR.Rmd

@@ -1,8 +1,8 @@
 ---
-title: "freesearcheR"
+title: "FreesearchR"
 output: rmarkdown::html_vignette
 vignette: >
-  %\VignetteIndexEntry{freesearcheR}
+  %\VignetteIndexEntry{FreesearchR}
   %\VignetteEngine{knitr::rmarkdown}
   %\VignetteEncoding{UTF-8}
 ---
@@ -11,9 +11,9 @@ vignette: >
 knitr::opts_chunk$set(echo = TRUE,eval = FALSE)
 ```
 
-# Getting started with ***freesearcheR***
+# Getting started with ***FreesearchR***
 
-Below is a simple walk-trough and basic instructions for the functions on the freesearcheR app.
+Below is a simple walk-trough and basic instructions for the functions on the FreesearchR app.
 
 ## Launching
 
@@ -21,13 +21,13 @@ The easiest way to get started is to launch [the hosted version of the app on sh
 
 Additionally you have the option to run the app locally with access to any data in your current working environment.
 
-To do this, open *R* (or RStudio or similar), and run the following code to install the latest version of ***freesearcheR*** and launch the app:
+To do this, open *R* (or RStudio or similar), and run the following code to install the latest version of ***FreesearchR*** and launch the app:
 
-``` {r}
+```{r}
 require("pak")
-pak::pak("agdamsbo/freesearcheR")
-library(freesearcheR)
-freesearcheR::launch_freesearcheR()
+pak::pak("agdamsbo/FreesearchR")
+library(FreesearchR)
+FreesearchR::launch_FreesearchR()
 ```
 
 As a small note, a standalone Windows app version is on the drawing board as well, but no time frame is available.