mirror of
https://github.com/agdamsbo/FreesearchR.git
synced 2025-09-12 01:49:39 +02:00
604 lines
21 KiB
R
604 lines
21 KiB
R
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#' 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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## 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::markdown(readLines("www/intro.md")),
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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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#########
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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 = "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("Choose your data source"),
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shiny::br(),
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# shiny::uiOutput(outputId = "source"),
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shinyWidgets::radioGroupButtons(
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inputId = "source",
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selected = "file",
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choices = c(
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"File upload" = "file",
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"REDCap server export" = "redcap",
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"Local or sample data" = "env"
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),
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size = "lg"
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),
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shiny::tags$script('document.querySelector("#source div").style.width = "100%"'),
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shiny::helpText("Upload a file from your device, get data directly from REDCap or select a sample data set for testing from the app."),
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shiny::br(),
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shiny::br(),
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shiny::conditionalPanel(
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condition = "input.source=='file'",
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import_file_ui(
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id = "file_import",
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layout_params = "dropdown",
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# title = "Choose a datafile to upload",
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file_extensions = c(".csv", ".tsv", ".txt", ".xls", ".xlsx", ".rds", ".ods", ".dta")
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)
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),
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shiny::conditionalPanel(
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condition = "input.source=='redcap'",
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shinyWidgets::alert(
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id = "redcap-warning",
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status = "info",
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shiny::tags$h2(shiny::markdown("Careful with sensitive data")),
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shiny::tags$p("The", shiny::tags$i(shiny::tags$b("FreesearchR")), "app only stores data for analyses, but please only use with sensitive data when running locally.", "", shiny::tags$a("Read more here", href = "https://agdamsbo.github.io/FreesearchR/#run-locally-on-your-own-machine"), "."),
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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 = "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("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("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("Only include variables missing less observations than the specified percentage."),
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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("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 = "Start",
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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::helpText('After importing, hit "Start" or navigate to the desired tab.'),
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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 = "Overview",
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icon = shiny::icon("eye"),
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value = "nav_prepare_overview",
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tags$h3("Overview and filtering"),
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fluidRow(
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shiny::column(
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width = 9,
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shiny::uiOutput(outputId = "data_info", inline = TRUE),
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shiny::tags$p(
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"Below is a short summary table, on the right you can click to visualise data classes or browse data and create 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 = "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 = "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$h6("Filter data types"),
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shiny::uiOutput(
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outputId = "column_filter"
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),
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shiny::helpText("Read more on how ", tags$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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shiny::br(),
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shiny::br(),
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shiny::tags$h6("Filter observations"),
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shiny::tags$p("Filter on observation level"),
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IDEAFilter::IDEAFilter_ui("data_filter"),
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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 = "Modify",
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icon = shiny::icon("file-pen"),
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tags$h3("Subset, rename and convert variables"),
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fluidRow(
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shiny::column(
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width = 9,
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shiny::tags$p(
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shiny::markdown("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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shiny::markdown("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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shiny::markdown("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$h4("Advanced data manipulation"),
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shiny::tags$p("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 = "Reorder factor levels",
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width = "100%"
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),
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shiny::tags$br(),
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shiny::helpText("Reorder the levels of factor/categorical variables."),
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shiny::tags$br(),
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shiny::tags$br()
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),
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shiny::column(
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width = 4,
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shiny::actionButton(
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inputId = "modal_cut",
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label = "New factor",
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width = "100%"
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),
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shiny::tags$br(),
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shiny::helpText("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 = "New variable",
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width = "100%"
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),
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shiny::tags$br(),
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shiny::helpText(shiny::markdown("Create a new variable/column based on an *R*-expression.")),
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shiny::tags$br(),
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shiny::tags$br()
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)
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),
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tags$h4("Compare modified data to original"),
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shiny::tags$br(),
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shiny::tags$p(
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"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("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$b("Modified data:"),
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shiny::verbatimTextOutput("modified_str")
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)
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),
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shiny::tags$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),
|
||
|
|
bslib::accordion(
|
||
|
|
open = "acc_chars",
|
||
|
|
multiple = FALSE,
|
||
|
|
bslib::accordion_panel(
|
||
|
|
value = "acc_cor",
|
||
|
|
title = "Correlations",
|
||
|
|
icon = bsicons::bs_icon("bounding-box"),
|
||
|
|
shiny::uiOutput("outcome_var_cor"),
|
||
|
|
shiny::helpText("To avoid evaluating the correlation of the outcome variable, this can be excluded from the plot or select 'none'."),
|
||
|
|
shiny::br(),
|
||
|
|
shinyWidgets::noUiSliderInput(
|
||
|
|
inputId = "cor_cutoff",
|
||
|
|
label = "Correlation cut-off",
|
||
|
|
min = 0,
|
||
|
|
max = 1,
|
||
|
|
step = .01,
|
||
|
|
value = .8,
|
||
|
|
format = shinyWidgets::wNumbFormat(decimals = 2),
|
||
|
|
color = datamods:::get_primary_color()
|
||
|
|
),
|
||
|
|
shiny::helpText("Set the cut-off for considered 'highly correlated'.")
|
||
|
|
)
|
||
|
|
)
|
||
|
|
),
|
||
|
|
data_correlations_ui(id = "correlations", height = 600)
|
||
|
|
)
|
||
|
|
),
|
||
|
|
bslib::nav_panel(
|
||
|
|
title = "Missings",
|
||
|
|
icon = bsicons::bs_icon("x-circle"),
|
||
|
|
bslib::layout_sidebar(
|
||
|
|
sidebar = bslib::sidebar(
|
||
|
|
bslib::accordion(
|
||
|
|
open = "acc_chars",
|
||
|
|
multiple = FALSE,
|
||
|
|
bslib::accordion_panel(
|
||
|
|
vlaue = "acc_mis",
|
||
|
|
title = "Missings",
|
||
|
|
icon = bsicons::bs_icon("x-circle"),
|
||
|
|
shiny::uiOutput("missings_var"),
|
||
|
|
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.")
|
||
|
|
)
|
||
|
|
)
|
||
|
|
),
|
||
|
|
data_missings_ui(id = "missingness")
|
||
|
|
)
|
||
|
|
)
|
||
|
|
),
|
||
|
|
##############################################################################
|
||
|
|
#########
|
||
|
|
######### Download panel
|
||
|
|
#########
|
||
|
|
##############################################################################
|
||
|
|
"visuals" = do.call(
|
||
|
|
bslib::nav_panel,
|
||
|
|
c(
|
||
|
|
list(
|
||
|
|
title = "Visuals",
|
||
|
|
icon = shiny::icon("chart-line"),
|
||
|
|
value = "nav_visuals"
|
||
|
|
),
|
||
|
|
data_visuals_ui("visuals")
|
||
|
|
)
|
||
|
|
# do.call(
|
||
|
|
# bslib::navset_bar,
|
||
|
|
# data_visuals_ui("visuals")#,
|
||
|
|
# c(
|
||
|
|
|
||
|
|
# )
|
||
|
|
# )
|
||
|
|
),
|
||
|
|
##############################################################################
|
||
|
|
#########
|
||
|
|
######### Regression analyses panel
|
||
|
|
#########
|
||
|
|
##############################################################################
|
||
|
|
"analyze" =
|
||
|
|
bslib::nav_panel(
|
||
|
|
title = "Regression",
|
||
|
|
icon = shiny::icon("calculator"),
|
||
|
|
value = "nav_analyses",
|
||
|
|
do.call(
|
||
|
|
bslib::navset_card_tab,
|
||
|
|
regression_ui("regression")
|
||
|
|
)
|
||
|
|
),
|
||
|
|
##############################################################################
|
||
|
|
#########
|
||
|
|
######### Download panel
|
||
|
|
#########
|
||
|
|
##############################################################################
|
||
|
|
"download" =
|
||
|
|
bslib::nav_panel(
|
||
|
|
title = "Download",
|
||
|
|
icon = shiny::icon("download"),
|
||
|
|
value = "nav_download",
|
||
|
|
shiny::fluidRow(
|
||
|
|
shiny::column(width = 2),
|
||
|
|
shiny::column(
|
||
|
|
width = 8,
|
||
|
|
shiny::fluidRow(
|
||
|
|
shiny::column(
|
||
|
|
width = 6,
|
||
|
|
shiny::h4("Report"),
|
||
|
|
shiny::helpText("Choose your favourite output file format for further work, and download, when the analyses are done."),
|
||
|
|
shiny::br(),
|
||
|
|
shiny::br(),
|
||
|
|
shiny::selectInput(
|
||
|
|
inputId = "output_type",
|
||
|
|
label = "Output format",
|
||
|
|
selected = NULL,
|
||
|
|
choices = list(
|
||
|
|
"MS Word" = "docx",
|
||
|
|
"LibreOffice" = "odt"
|
||
|
|
# ,
|
||
|
|
# "PDF" = "pdf",
|
||
|
|
# "All the above" = "all"
|
||
|
|
)
|
||
|
|
),
|
||
|
|
shiny::br(),
|
||
|
|
# Button
|
||
|
|
shiny::downloadButton(
|
||
|
|
outputId = "report",
|
||
|
|
label = "Download report",
|
||
|
|
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)
|
||
|
|
#
|