mirror of
https://github.com/agdamsbo/FreesearchR.git
synced 2025-09-12 18:09:39 +02:00
external docs linked and updated
This commit is contained in:
parent
eb93f501ca
commit
83fac94266
9 changed files with 103 additions and 154 deletions
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@ -8,20 +8,21 @@ custom_theme <- function(...,
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version = 5,
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primary = "#1E4A8F",
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secondary = "#FF6F61",
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bootswatch = "united",
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base_font = bslib::font_google("Montserrat"),
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heading_font = bslib::font_google("Public Sans",wght = "700"),
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code_font = bslib::font_google("Open Sans")
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# success = "#1E4A8F",
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# info = ,
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# warning = ,
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# danger = ,
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# fg = "#000",
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# bg="#fff",
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bootswatch = "united",
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base_font = bslib::font_google("Montserrat"),
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# base_font = bslib::font_google("Alice"),
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# heading_font = bslib::font_google("Jost", wght = "800"),
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# heading_font = bslib::font_google("Noto Serif"),
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# heading_font = bslib::font_google("Alice"),
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heading_font = bslib::font_google("Public Sans",wght = "700"),
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code_font = bslib::font_google("Open Sans")){
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){
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bslib::bs_theme(
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...,
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version = version,
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14
README.md
14
README.md
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@ -7,9 +7,9 @@
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[](https://agdamsbo.shinyapps.io/freesearcheR/)
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<!-- badges: end -->
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This package is the backbone of the free and open browser based data exploration and analysis tool with publication ready output.
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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.
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This package and the ***freesearcheR***-tool is part of a large project to democratize health data analysis and removing barriers for clinicians to engage in health research.
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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.
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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.
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@ -17,6 +17,10 @@ Initiatives for funding continued development of the tool and surrounding initia
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## Roadmap
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The current state of the app is considered experimental, and a lot of things are still changing. It is, however, in a usable state, with basic functions available to the user.
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Below are some (the actual list is quite long and growing) of the planned features and improvements:
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- [ ] Stratified analyses
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- Additional study designs:
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@ -33,6 +37,12 @@ Initiatives for funding continued development of the tool and surrounding initia
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- [x] Option to edit labels. 2025-01-16
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- More output controls
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- [ ] Theming output tables
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- [ ] Select analyses to include in report
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- [ ] Plot regression analyses results
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- [x] Export modified data. 2025-01-16
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@ -1,4 +1,11 @@
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url: https://agdamsbo.github.io/freesearcheR/
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template:
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bootstrap: 5
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bslib:
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version: 5
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primary: "#1E4A8F"
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secondary: "#FF6F61"
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bootswatch: "united"
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base_font: bslib::font_google("Montserrat")
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heading_font: bslib::font_google("Public Sans",wght: "700")
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code_font: bslib::font_google("Open Sans")
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@ -123,7 +123,7 @@ library(shiny)
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# structure(match(splitter, names(labs)), levels = labs, class = "factor")
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# }
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#' Title
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#' Extended cutting function
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#'
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#' @param x an object inheriting from class "hms"
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#' @param ... passed on
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@ -808,7 +808,7 @@ add_sparkline <- function(grid, column = "vals", color.main = "#2a8484", color.s
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#'
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#' @param data vector
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#'
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#' @returns
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#' @returns logical
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#' @export
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#'
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#' @examples
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@ -915,6 +915,10 @@ create_overview_datagrid <- function(data) {
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#' @export
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#'
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#' @examples
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#' mtcars |>
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#' overview_vars() |>
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#' toastui::datagrid() |>
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#' add_class_icon()
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add_class_icon <- function(grid, column = "class") {
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out <- toastui::grid_format(
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grid = grid,
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@ -2180,20 +2184,21 @@ custom_theme <- function(...,
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version = 5,
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primary = "#1E4A8F",
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secondary = "#FF6F61",
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bootswatch = "united",
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base_font = bslib::font_google("Montserrat"),
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heading_font = bslib::font_google("Public Sans",wght = "700"),
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code_font = bslib::font_google("Open Sans")
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# success = "#1E4A8F",
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# info = ,
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# warning = ,
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# danger = ,
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# fg = "#000",
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# bg="#fff",
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bootswatch = "united",
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base_font = bslib::font_google("Montserrat"),
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# base_font = bslib::font_google("Alice"),
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# heading_font = bslib::font_google("Jost", wght = "800"),
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# heading_font = bslib::font_google("Noto Serif"),
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# heading_font = bslib::font_google("Alice"),
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heading_font = bslib::font_google("Public Sans",wght = "700"),
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code_font = bslib::font_google("Open Sans")){
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){
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bslib::bs_theme(
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...,
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version = version,
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@ -2599,8 +2604,14 @@ add_var_toset <- function(data, var_name, default = "") {
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data[, datanames]
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}
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#' @importFrom toastui datagrid grid_columns grid_format grid_style_column
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#' grid_style_column grid_editor grid_editor_opts grid_selection_row
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#' Modified from the datamods pacakge
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#'
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#' @param data data
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#'
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#' @param height height
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#' @param selectionId selectionId
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#' @param buttonId buttonId
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#'
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#' @examples
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#' mtcars |>
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#' summary_vars() |>
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@ -3020,7 +3031,8 @@ ui_elements <- list(
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shiny::tags$p(
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"Below is a short summary table of the provided data.
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On the right hand side you have the option to create filters.
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At the bottom you'll find a raw overview of the original vs the modified data.")
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At the bottom you'll find a raw overview of the original vs the modified data."
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)
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)
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),
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fluidRow(
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@ -3306,12 +3318,21 @@ ui_elements <- list(
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######### Documentation panel
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#########
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##############################################################################
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"docs" = bslib::nav_panel(
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title = "Documentation",
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# shiny::tags$iframe("www/docs.html", height=600, width=535),
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shiny::htmlOutput("docs_file"),
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shiny::br()
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"docs" = bslib::nav_item(
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# shiny::img(shiny::icon("book")),
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shiny::tags$a(
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href = "https://agdamsbo.github.io/freesearcheR/",
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"Docs (external)",
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target = "_blank",
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rel = "noopener noreferrer"
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)
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)
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# bslib::nav_panel(
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# title = "Documentation",
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# # shiny::tags$iframe("www/docs.html", height=600, width=535),
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# shiny::htmlOutput("docs_file"),
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# shiny::br()
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# )
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)
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# Initial attempt at creating light and dark versions
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@ -3344,6 +3365,7 @@ ui <- bslib::page_fixed(
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ui_elements$import,
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ui_elements$overview,
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ui_elements$analyze,
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bslib::nav_spacer(),
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ui_elements$docs,
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# bslib::nav_spacer(),
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# bslib::nav_item(shinyWidgets::circleButton(inputId = "mode", icon = icon("moon"),status = "primary")),
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@ -95,7 +95,8 @@ ui_elements <- list(
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shiny::tags$p(
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"Below is a short summary table of the provided data.
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On the right hand side you have the option to create filters.
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At the bottom you'll find a raw overview of the original vs the modified data.")
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At the bottom you'll find a raw overview of the original vs the modified data."
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)
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)
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),
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fluidRow(
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@ -381,12 +382,21 @@ ui_elements <- list(
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######### Documentation panel
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#########
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##############################################################################
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"docs" = bslib::nav_panel(
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title = "Documentation",
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# shiny::tags$iframe("www/docs.html", height=600, width=535),
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shiny::htmlOutput("docs_file"),
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shiny::br()
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"docs" = bslib::nav_item(
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# shiny::img(shiny::icon("book")),
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shiny::tags$a(
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href = "https://agdamsbo.github.io/freesearcheR/",
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"Docs (external)",
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target = "_blank",
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rel = "noopener noreferrer"
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)
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)
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# bslib::nav_panel(
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# title = "Documentation",
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# # shiny::tags$iframe("www/docs.html", height=600, width=535),
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# shiny::htmlOutput("docs_file"),
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# shiny::br()
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# )
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)
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# Initial attempt at creating light and dark versions
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@ -419,6 +429,7 @@ ui <- bslib::page_fixed(
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ui_elements$import,
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ui_elements$overview,
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ui_elements$analyze,
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bslib::nav_spacer(),
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ui_elements$docs,
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# bslib::nav_spacer(),
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# bslib::nav_item(shinyWidgets::circleButton(inputId = "mode", icon = icon("moon"),status = "primary")),
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@ -1,69 +0,0 @@
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<!DOCTYPE html>
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<html xmlns="http://www.w3.org/1999/xhtml" lang="en" xml:lang="en"><head>
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<meta charset="utf-8">
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<meta name="generator" content="quarto-1.5.57">
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<meta name="viewport" content="width=device-width, initial-scale=1.0, user-scalable=yes">
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<title>freesearcheR platform documentation</title>
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<style>
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code{white-space: pre-wrap;}
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span.smallcaps{font-variant: small-caps;}
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div.columns{display: flex; gap: min(4vw, 1.5em);}
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div.column{flex: auto; overflow-x: auto;}
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div.hanging-indent{margin-left: 1.5em; text-indent: -1.5em;}
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ul.task-list{list-style: none;}
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ul.task-list li input[type="checkbox"] {
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width: 0.8em;
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margin: 0 0.8em 0.2em -1em; vertical-align: middle;
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}
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.display.math{display: block; text-align: center; margin: 0.5rem auto;}
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</style>
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</head>
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<body>
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<header id="title-block-header">
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<h1 class="title"><strong><em>freesearcheR</em></strong> platform documentation</h1>
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</header>
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<h1 id="welcome">Welcome!</h1>
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<p>So glad to see you here! Welcome to test this early concept of a platform to easily explore, manipulate and analyse clinical data.</p>
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<p>Below will be a more detailed description of the included features and possibilities, as well as the planned and possible feature additions.</p>
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<h2 id="contribute">Contribute</h2>
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<p>Contributions are very welcome. If you find anything odd, or you think of features to add or remove, please <a href="https://github.com/agdamsbo/freesearcheR/issues">share and report on the project page on GitHub</a>.</p>
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<h2 id="roadmap">Roadmap</h2>
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<ul>
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<li><p><label><input type="checkbox">Stratified analyses</label></p></li>
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<li><p>Additional study designs:</p>
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<ul class="task-list">
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<li><p><label><input type="checkbox" checked>Cross-sectional data analyses</label></p></li>
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<li><p><label><input type="checkbox">Longitudinal data analyses</label></p></li>
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<li><p><label><input type="checkbox">Survival analysis</label></p></li>
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</ul></li>
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<li><p>More detailed variable browser</p>
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<ul class="task-list">
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<li><p><label><input type="checkbox">Add histograms for data distribution</label></p></li>
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<li><p><label><input type="checkbox">Option to edit variable labels for nicer tables</label></p></li>
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</ul></li>
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<li><p><label><input type="checkbox">Plot regression analyses results</label></p></li>
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<li><p><label><input type="checkbox" checked>Export modified data. 2025-01-09</label></p></li>
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<li><p><label><input type="checkbox">Include reproducible code for all steps</label></p></li>
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<li><p><label><input type="checkbox" checked><del>Modify factor levels</del> Factor level modification is possible through converting factors to numeric > cutting numeric with desired fixed values. 2024-12-12</label></p></li>
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<li><p><label><input type="checkbox" checked>More options for date/datetime/time grouping/factoring. Included weekday and month-only options. 2024-12-12</label></p></li>
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</ul>
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</body></html>
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@ -1,45 +0,0 @@
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---
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title: "***freesearcheR*** platform documentation"
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format:
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html:
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self-contained: true
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minimal: true
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---
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# Welcome!
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So glad to see you here! Welcome to test this early concept of a platform to easily explore, manipulate and analyse clinical data.
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Below will be a more detailed description of the included features and possibilities, as well as the planned and possible feature additions.
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## Contribute
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Contributions are very welcome. If you find anything odd, or you think of features to add or remove, please [share and report on the project page on GitHub](https://github.com/agdamsbo/freesearcheR/issues).
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## Roadmap
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- [ ] Stratified analyses
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- Additional study designs:
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- [x] Cross-sectional data analyses
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- [ ] Longitudinal data analyses
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|
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- [ ] Survival analysis
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- More detailed variable browser
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|
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- [ ] Add histograms for data distribution
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|
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- [ ] Option to edit variable labels for nicer tables
|
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|
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- [ ] Plot regression analyses results
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|
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- [x] Export modified data. 2025-01-09
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- [ ] Include reproducible code for all steps
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- [x] ~~Modify factor levels~~ Factor level modification is possible through converting factors to numeric > cutting numeric with desired fixed values. 2024-12-12
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- [x] More options for date/datetime/time grouping/factoring. Included weekday and month-only options. 2024-12-12
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@ -354,18 +354,18 @@ display: none;
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<div id="welcome" class="section level1">
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<h1>Welcome</h1>
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<p>This is the <strong><em>freesearchR</em></strong> web data analysis
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tool. We intend the <strong><em>freesearchR</em></strong> to be a
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<p>This is the <strong><em>freesearcheR</em></strong> web data analysis
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tool. We intend the <strong><em>freesearcheR</em></strong> to be a
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powerful and free tool for easy data evaluation and analysis at the
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hands of the clinician.</p>
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<p>By intention, this tool has been designed to be simple to use with a
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minimum of mandatory options to keep the workflow streamlined, while
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also including a few options to go even further.</p>
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<p>There are four simple steps to go through:</p>
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<p>There are four simple steps to go through (see corresponding tabs in
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the top):</p>
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<ol style="list-style-type: decimal">
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<li><p><a onclick="Shiny.onInputChange('tab', 'widgets');">“Import
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data”</a> (a spreadsheet/file on your machine, direct export from a
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REDCap server, or a local file provided with a package) to get
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<li><p>Import data (a spreadsheet/file on your machine, direct export
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from a REDCap server, or a local file provided with a package) to get
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started.</p></li>
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<li><p>An <em>optional</em> step of data modification (change variable
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classes and creating categorical variables (factors) from numeric or
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@ -379,8 +379,16 @@ compare variables)</p></li>
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depending on specified outcome variable</p></li>
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<li><p>Evaluation of model assumptions</p></li>
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</ul></li>
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<li><p>Export the the analyses results as for MS Word or <a href="https://www.libreoffice.org/">LibreOffice</a>.</p></li>
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<li><p>Export the the analyses results for MS Word or <a href="https://www.libreoffice.org/">LibreOffice</a> as well as the data
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with preserved metadata.</p></li>
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</ol>
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<p>Have a look at the <a href>documentations page</a> for further
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project description. If you’re interested in the source code, then go
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on, <a href="https://github.com/agdamsbo/freesearcheR">have a
|
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look</a>!</p>
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<p>If you encounter anything strange or the app doesn’t act as expected.
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Please <a href="https://github.com/agdamsbo/freesearcheR/issues">report
|
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on Github</a>.</p>
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</div>
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|
|
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@ -19,3 +19,7 @@ There are four simple steps to go through (see corresponding tabs in the top):
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- Evaluation of model assumptions
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4. Export the the analyses results for MS Word or [LibreOffice](https://www.libreoffice.org/) as well as the data with preserved metadata.
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Have a look at the [documentations page]() for further project description. If you're interested in the source code, then go on, [have a look](https://github.com/agdamsbo/freesearcheR)!
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If you encounter anything strange or the app doesn't act as expected. Please [report on Github](https://github.com/agdamsbo/freesearcheR/issues).
|
||||
|
|
|
|||
Loading…
Add table
Reference in a new issue