mirror of
https://github.com/agdamsbo/FreesearchR.git
synced 2025-09-12 09:59:39 +02:00
618 lines
22 KiB
R
618 lines
22 KiB
R
#' FreesearchR UI elements list
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#'
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#' @param selection specify element to output
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#'
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#' @returns Shinu UI elements
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#' @export
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#'
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ui_elements <- function(selection) {
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out <- list(
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##############################################################################
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#########
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######### Home panel
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#########
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##############################################################################
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"home" = bslib::nav_panel(
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title = "FreesearchR",
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# title = shiny::div(htmltools::img(src="FreesearchR-logo-white-nobg-h80.png")),
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icon = shiny::icon("house"),
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shiny::fluidRow(
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# "The browser language is",
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# textOutput("your_lang"),
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# p(i18n$t("Hello")),
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# shiny::uiOutput(outputId = "language_select"),
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## On building the dev-version for shinyapps.io, the dev_banner() is redefined
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## Default just output "NULL"
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## This could probably be achieved more legantly, but this works.
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dev_banner(),
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shiny::column(width = 2),
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shiny::column(
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width = 8,
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shiny::uiOutput(outputId = "language_select"),
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htmlOutput("intro_text")
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# shiny::includeHTML(i18n$t("www/intro.html"))
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# shiny::markdown(readLines(i18n$t("www/intro.md")))
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),
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shiny::column(width = 2)
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)
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),
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##############################################################################
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#########
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######### Import panel
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#########
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##############################################################################
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"import" = bslib::nav_panel(
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title = i18n$t("Get started"),
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icon = shiny::icon("play"),
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value = "nav_import",
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shiny::fluidRow(
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shiny::column(width = 2),
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shiny::column(
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width = 8,
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shiny::h4(i18n$t("Choose your data")),
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# shiny::br(),
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# shiny::uiOutput(outputId = "source"),
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# radioGroupButtons(
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# inputId = "source",
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# selected = "file",
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# choices = c("File" = "file"),
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# size = "lg"
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# ),
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shiny::selectInput(
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inputId = "source",
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label="",
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selected = "file",
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choices = "file",
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width = "100%"
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),
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# shiny::tags$script('document.querySelector("#source div").style.width = "100%"'),
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## Update this to change depending on run locally or hosted
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shiny::helpText(i18n$t("Upload a file, get data directly from REDCap or use local or sample data.")),
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shiny::br(),
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shiny::br(),
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shiny::conditionalPanel(
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condition = "input.source=='file'",
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import_file_ui(
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id = "file_import",
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layout_params = "dropdown",
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# title = "Choose a datafile to upload",
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file_extensions = c(".csv", ".tsv", ".txt", ".xls", ".xlsx", ".rds", ".ods", ".dta")
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)
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),
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shiny::conditionalPanel(
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condition = "input.source=='redcap'",
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shiny::uiOutput(outputId = "redcap_warning"),
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# shinyWidgets::alert(
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# id = "redcap-warning",
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# status = "warning",
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# shiny::tags$h2(i18n$t("Please be mindfull handling sensitive data")),
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# shiny::HTML(i18n$t("<p>The <em><strong>FreesearchR</strong></em> app only stores data for analyses, but please only use with sensitive data when running locally. <a href='https://agdamsbo.github.io/FreesearchR/#run-locally-on-your-own-machine'>Read more here</a></p>")),
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# dismissible = TRUE
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# ),
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m_redcap_readUI(
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id = "redcap_import",
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title = ""
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)
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),
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shiny::conditionalPanel(
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condition = "input.source=='env'",
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import_globalenv_ui(id = "env", title = NULL)
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),
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# shiny::conditionalPanel(
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# condition = "input.source=='redcap'",
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# DT::DTOutput(outputId = "redcap_prev")
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# ),
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shiny::conditionalPanel(
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condition = "output.data_loaded == true",
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shiny::br(),
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shiny::actionButton(
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inputId = "modal_initial_view",
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label = i18n$t("Quick overview"),
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width = "100%",
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icon = shiny::icon("binoculars"),
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disabled = FALSE
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),
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shiny::br(),
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shiny::br(),
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shiny::h5(i18n$t("Select variables for final import")),
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shiny::fluidRow(
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shiny::column(
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width = 6,
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shiny::p(i18n$t("Exclude incomplete variables:")),
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shiny::br(),
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shinyWidgets::noUiSliderInput(
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inputId = "complete_cutoff",
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label = NULL,
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update_on = "end",
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min = 0,
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max = 100,
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step = 5,
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value = 30,
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format = shinyWidgets::wNumbFormat(decimals = 0),
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color = datamods:::get_primary_color()
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),
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shiny::helpText(i18n$t("Only include variables missing less observations than the specified percentage. At 0, only complete variables are included; at 100, all variables are included.")),
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shiny::br()
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),
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shiny::column(
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width = 6,
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shiny::p(i18n$t("Manual selection:")),
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shiny::br(),
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shiny::uiOutput(outputId = "import_var"),
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shiny::br()
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)
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),
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shiny::uiOutput(outputId = "data_info_import", inline = TRUE),
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shiny::br(),
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shiny::br(),
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shiny::actionButton(
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inputId = "act_start",
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label = i18n$t("Let's begin!"),
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width = "100%",
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icon = shiny::icon("play"),
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disabled = TRUE
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),
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shiny::br(),
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shiny::br()
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),
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shiny::column(width = 2)
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),
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shiny::br(),
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shiny::br()
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)
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),
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##############################################################################
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#########
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######### Data overview panel
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#########
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##############################################################################
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"prepare" = bslib::nav_menu(
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title = "Prepare",
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icon = shiny::icon("pen-to-square"),
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value = "nav_prepare",
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bslib::nav_panel(
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title = i18n$t("Overview and filter"),
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icon = shiny::icon("eye"),
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value = "nav_prepare_overview",
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tags$h3(i18n$t("Overview and filtering")),
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fluidRow(
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shiny::column(
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width = 9,
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shiny::uiOutput(outputId = "data_info", inline = TRUE),
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shiny::tags$p(
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i18n$t("Below you find a summary table for quick insigths, and on the right you can visualise data classes, browse data and apply different data filters.")
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)
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),
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shiny::column(
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width = 3,
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shiny::actionButton(
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inputId = "modal_visual_overview",
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label = i18n$t("Visual overview"),
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width = "100%",
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disabled = TRUE
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),
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shiny::br(),
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shiny::br(),
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shiny::actionButton(
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inputId = "modal_browse",
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label = i18n$t("Browse data"),
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width = "100%",
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disabled = TRUE
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),
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shiny::br(),
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shiny::br()
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)
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),
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fluidRow(
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shiny::column(
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width = 9,
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data_summary_ui(id = "data_summary"),
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shiny::br(),
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shiny::br(),
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shiny::br(),
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shiny::br(),
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shiny::br()
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),
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shiny::column(
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width = 3,
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shiny::tags$h6(i18n$t("Filter data types")),
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shiny::uiOutput(
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outputId = "column_filter"
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),
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## This needs to run in server for translation
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shiny::helpText("Read more on how ", tags$a(
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"data types",
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href = "https://agdamsbo.github.io/FreesearchR/articles/data-types.html",
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target = "_blank",
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rel = "noopener noreferrer"
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), " are defined."),
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validation_ui("validation_var"),
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shiny::br(),
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shiny::br(),
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shiny::tags$h6(i18n$t("Filter observations")),
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shiny::tags$p(i18n$t("Apply filter on observation")),
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IDEAFilter::IDEAFilter_ui("data_filter"),
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validation_ui("validation_obs"),
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shiny::br(),
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shiny::br()
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)
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),
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shiny::br(),
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shiny::br(),
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shiny::br()
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),
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bslib::nav_panel(
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title = i18n$t("Edit and create data"),
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icon = shiny::icon("file-pen"),
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tags$h3(i18n$t("Subset, rename and convert variables")),
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fluidRow(
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shiny::column(
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width = 9,
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shiny::tags$p(
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i18n$t("Below, are several options for simple data manipulation like update variables by renaming, creating new labels (for nicer tables in the report) and changing variable classes (numeric, factor/categorical etc.)."),
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i18n$t("There are more advanced options to modify factor/categorical variables as well as create new factor from a continous variable or new variables with R code. At the bottom you can restore the original data."),
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i18n$t("Please note that data modifications are applied before any filtering.")
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)
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)
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),
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update_variables_ui("modal_variables"),
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shiny::tags$br(),
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shiny::tags$br(),
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shiny::tags$h4(i18n$t("Advanced data manipulation")),
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shiny::tags$p(i18n$t("Below options allow more advanced varaible manipulations.")),
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shiny::tags$br(),
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shiny::tags$br(),
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shiny::fluidRow(
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shiny::column(
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width = 4,
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shiny::actionButton(
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inputId = "modal_update",
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label = i18n$t("Reorder factor levels"),
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width = "100%"
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),
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shiny::tags$br(),
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shiny::helpText(i18n$t("Reorder the levels of factor/categorical variables.")),
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shiny::tags$br(),
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shiny::tags$br()
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),
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shiny::column(
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width = 4,
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shiny::actionButton(
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inputId = "modal_cut",
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label = i18n$t("New factor"),
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width = "100%"
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),
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shiny::tags$br(),
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shiny::helpText(i18n$t("Create factor/categorical variable from a continous variable (number/date/time).")),
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shiny::tags$br(),
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shiny::tags$br()
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),
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shiny::column(
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width = 4,
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shiny::actionButton(
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inputId = "modal_column",
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label = i18n$t("New variable"),
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width = "100%"
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),
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shiny::tags$br(),
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shiny::helpText(i18n$t("Create a new variable based on an R-expression.")),
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shiny::tags$br(),
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shiny::tags$br()
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)
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),
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tags$h4(i18n$t("Compare modified data to original")),
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shiny::tags$br(),
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shiny::tags$p(
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i18n$t("Raw print of the original vs the modified data.")
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),
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shiny::tags$br(),
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shiny::fluidRow(
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shiny::column(
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width = 6,
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shiny::tags$b(i18n$t("Original data:")),
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shiny::verbatimTextOutput("original_str")
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),
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shiny::column(
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width = 6,
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shiny::tags$b(i18n$t("Modified data:")),
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shiny::verbatimTextOutput("modified_str")
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)
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),
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shiny::tags$br(),
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shiny::actionButton(
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inputId = "data_reset",
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label = "Restore original data",
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width = "100%"
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),
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shiny::tags$br(),
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shiny::helpText("Reset to original imported dataset. Careful! There is no un-doing."),
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shiny::tags$br()
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)
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# )
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),
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##############################################################################
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#########
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######### Descriptive analyses panel
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#########
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##############################################################################
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"describe" =
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bslib::nav_menu(
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title = "Evaluate",
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icon = shiny::icon("magnifying-glass-chart"),
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value = "nav_describe",
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# id = "navdescribe",
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# bslib::navset_bar(
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# title = "",
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bslib::nav_panel(
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title = "Characteristics",
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icon = bsicons::bs_icon("table"),
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bslib::layout_sidebar(
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sidebar = bslib::sidebar(
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shiny::uiOutput(outputId = "data_info_nochar", inline = TRUE),
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bslib::accordion(
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open = "acc_chars",
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multiple = FALSE,
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bslib::accordion_panel(
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open = TRUE,
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value = "acc_chars",
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title = "Settings",
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icon = bsicons::bs_icon("table"),
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shiny::uiOutput("strat_var"),
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shiny::helpText("Only factor/categorical variables are available for stratification. Go back to the 'Prepare' tab to reclass a variable if it's not on the list."),
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shiny::conditionalPanel(
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condition = "input.strat_var!='none'",
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shiny::radioButtons(
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inputId = "add_p",
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label = "Compare strata?",
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selected = "no",
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inline = TRUE,
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choices = list(
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"No" = "no",
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"Yes" = "yes"
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)
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),
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shiny::helpText("Option to perform statistical comparisons between strata in baseline table.")
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),
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shiny::br(),
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shiny::br(),
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shiny::actionButton(
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inputId = "act_eval",
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label = "Evaluate",
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width = "100%",
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icon = shiny::icon("calculator"),
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disabled = TRUE
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)
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)
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)
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),
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gt::gt_output(outputId = "table1")
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)
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),
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bslib::nav_panel(
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title = "Correlations",
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icon = bsicons::bs_icon("bounding-box"),
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bslib::layout_sidebar(
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sidebar = bslib::sidebar(
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# shiny::uiOutput(outputId = "data_info_nochar", inline = TRUE),
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bslib::accordion(
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open = "acc_chars",
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multiple = FALSE,
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bslib::accordion_panel(
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value = "acc_cor",
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title = "Correlations",
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icon = bsicons::bs_icon("bounding-box"),
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shiny::uiOutput("outcome_var_cor"),
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shiny::helpText("To avoid evaluating the correlation of the outcome variable, this can be excluded from the plot or select 'none'."),
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shiny::br(),
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shinyWidgets::noUiSliderInput(
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inputId = "cor_cutoff",
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label = "Correlation cut-off",
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min = 0,
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max = 1,
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step = .01,
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value = .8,
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format = shinyWidgets::wNumbFormat(decimals = 2),
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color = datamods:::get_primary_color()
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),
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shiny::helpText("Set the cut-off for considered 'highly correlated'.")
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)
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)
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),
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data_correlations_ui(id = "correlations", height = 600)
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)
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),
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bslib::nav_panel(
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title = "Missings",
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icon = bsicons::bs_icon("x-circle"),
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bslib::layout_sidebar(
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sidebar = bslib::sidebar(
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bslib::accordion(
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open = "acc_chars",
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multiple = FALSE,
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bslib::accordion_panel(
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vlaue = "acc_mis",
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title = "Missings",
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icon = bsicons::bs_icon("x-circle"),
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shiny::uiOutput("missings_var"),
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shiny::helpText("To consider if data is missing by random, choose the outcome/dependent variable, if it has any missings to evaluate if there is a significant difference across other variables depending on missing data or not.")
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)
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)
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),
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data_missings_ui(id = "missingness")
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)
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)
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),
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##############################################################################
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#########
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######### Visuals panel
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#########
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##############################################################################
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"visuals" = do.call(
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bslib::nav_panel,
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c(
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list(
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title = "Visuals",
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icon = shiny::icon("chart-line"),
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value = "nav_visuals"
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),
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data_visuals_ui("visuals")
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)
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# do.call(
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# bslib::navset_bar,
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# data_visuals_ui("visuals")#,
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# c(
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# )
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# )
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),
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##############################################################################
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#########
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######### Regression analyses panel
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#########
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##############################################################################
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"analyze" =
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bslib::nav_panel(
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title = "Regression",
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icon = shiny::icon("calculator"),
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value = "nav_analyses",
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do.call(
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bslib::navset_card_tab,
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regression_ui("regression")
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)
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),
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##############################################################################
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#########
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######### Download panel
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#########
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##############################################################################
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"download" =
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bslib::nav_panel(
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title = "Download",
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icon = shiny::icon("download"),
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value = "nav_download",
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shiny::fluidRow(
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shiny::column(width = 2),
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shiny::column(
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width = 8,
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shiny::h4(i18n$t("Analysis validation")),
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validation_ui("validation_all"),
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shiny::fluidRow(
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shiny::column(
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width = 6,
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shiny::h4(i18n$t("Report")),
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shiny::helpText(i18n$t("Choose your favourite output file format for further work, and download, when the analyses are done.")),
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shiny::br(),
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shiny::br(),
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shiny::selectInput(
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inputId = "output_type",
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label = "Output format",
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selected = NULL,
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choices = list(
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"MS Word" = "docx",
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"LibreOffice" = "odt"
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# ,
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# "PDF" = "pdf",
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# "All the above" = "all"
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)
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),
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shiny::br(),
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# Button
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shiny::downloadButton(
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outputId = "report",
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label = "Download report",
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icon = shiny::icon("download")
|
|
)
|
|
# shiny::helpText("If choosing to output to MS Word, please note, that when opening the document, two errors will pop-up. Choose to repair and choose not to update references. The issue is being worked on. You can always choose LibreOffice instead."),
|
|
),
|
|
shiny::column(
|
|
width = 6,
|
|
shiny::h4("Data"),
|
|
shiny::helpText("Choose your favourite output data format to download the modified data."),
|
|
shiny::br(),
|
|
shiny::br(),
|
|
shiny::selectInput(
|
|
inputId = "data_type",
|
|
label = "Data format",
|
|
selected = NULL,
|
|
choices = list(
|
|
"R" = "rds",
|
|
"stata" = "dta",
|
|
"CSV" = "csv"
|
|
)
|
|
),
|
|
shiny::helpText("No metadata is saved when exporting to csv."),
|
|
shiny::br(),
|
|
shiny::br(),
|
|
# Button
|
|
shiny::downloadButton(
|
|
outputId = "data_modified",
|
|
label = "Download data",
|
|
icon = shiny::icon("download")
|
|
)
|
|
)
|
|
),
|
|
shiny::br(),
|
|
shiny::br(),
|
|
shiny::h4("Code snippets"),
|
|
shiny::tags$p("Below are the code bits used to create the final data set and the main analyses."),
|
|
shiny::tags$p("This can be used as a starting point for learning to code and for reproducibility."),
|
|
shiny::tagList(
|
|
lapply(
|
|
paste0("code_", c(
|
|
"import", "format", "data", "variables", "filter", "table1", "univariable", "multivariable"
|
|
)),
|
|
\(.x)shiny::htmlOutput(outputId = .x)
|
|
)
|
|
),
|
|
shiny::tags$br(),
|
|
shiny::br()
|
|
),
|
|
shiny::column(width = 2)
|
|
)
|
|
),
|
|
##############################################################################
|
|
#########
|
|
######### Feedback link
|
|
#########
|
|
##############################################################################
|
|
"feedback" = bslib::nav_item(
|
|
# shiny::img(shiny::icon("book")),
|
|
shiny::tags$a(
|
|
href = "https://redcap.au.dk/surveys/?s=JPCLPTXYDKFA8DA8",
|
|
"Feedback", shiny::icon("arrow-up-right-from-square"),
|
|
target = "_blank",
|
|
rel = "noopener noreferrer"
|
|
)
|
|
),
|
|
##############################################################################
|
|
#########
|
|
######### Documentation link
|
|
#########
|
|
##############################################################################
|
|
"docs" = bslib::nav_item(
|
|
# shiny::img(shiny::icon("book")),
|
|
shiny::tags$a(
|
|
href = "https://agdamsbo.github.io/FreesearchR/",
|
|
"Docs", shiny::icon("arrow-up-right-from-square"),
|
|
target = "_blank",
|
|
rel = "noopener noreferrer"
|
|
)
|
|
)
|
|
# bslib::nav_panel(
|
|
# title = "Documentation",
|
|
# # shiny::tags$iframe("www/docs.html", height=600, width=535),
|
|
# shiny::htmlOutput("docs_file"),
|
|
# shiny::br()
|
|
# )
|
|
)
|
|
if (!is.null(selection)) {
|
|
out[[selection]]
|
|
} else {
|
|
out
|
|
}
|
|
}
|
|
|
|
|
|
# ls <- list("home"=1:4,
|
|
# "test"=1:4)
|
|
#
|