mirror of
https://github.com/agdamsbo/FreesearchR.git
synced 2025-09-12 09:59:39 +02:00
Andreas Gammelgaard Damsbo
8469a5ca64
Some checks are pending
pkgdown.yaml / pkgdown (push) Waiting to run
528 lines
18 KiB
R
528 lines
18 KiB
R
# ns <- NS(id)
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ui_elements <- 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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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::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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icon = shiny::icon("home")
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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 = "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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shinyWidgets::radioGroupButtons(
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inputId = "source",
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selected = "env",
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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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width = "100%"
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),
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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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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::br(),
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shiny::h5("Specify variables to include"),
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shiny::fluidRow(
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shiny::column(
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width = 6,
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shiny::br(),
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shiny::p("Filter by completeness threshold and manual selection:"),
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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 = 6,
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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 = 70,
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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("Exclude variables with completeness below the specified percentage."),
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shiny::br(),
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shiny::br(),
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shiny::uiOutput(outputId = "import_var"),
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shiny::uiOutput(outputId = "data_info_import", inline = TRUE)
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)
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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::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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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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######### Data overview panel
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#########
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##############################################################################
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"overview" =
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# bslib::nav_panel_hidden(
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bslib::nav_panel(
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# value = "overview",
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title = "Data",
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bslib::navset_bar(
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fillable = TRUE,
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bslib::nav_panel(
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title = "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 create data filters."
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)
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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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),
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shiny::column(
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width = 3,
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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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),
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shiny::tags$br(),
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shiny::tags$br(),
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IDEAFilter::IDEAFilter_ui("data_filter"),
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shiny::tags$br()
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)
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),
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shiny::tags$br(),
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shiny::tags$br(),
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shiny::tags$br(),
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shiny::tags$br(),
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shiny::tags$br()
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),
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bslib::nav_panel(
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title = "Modify",
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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(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::tags$p("There are also more advanced options to modify factor/categorical variables as well as create new factor from a continous variable or new variables with *R* code. At the bottom you can restore the original data."))
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)
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),
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# shiny::tags$br(),
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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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tags$h4("Advanced data manipulation"),
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shiny::tags$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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),
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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$br(),
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shiny::helpText("Create factor/categorical variable from a continous variable (number/date/time).")
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),
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shiny::column(
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width = 4,
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shiny::actionButton(
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inputId = "modal_column",
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label = "New variable",
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width = "100%"
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),
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shiny::tags$br(),
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shiny::helpText(shiny::markdown("Create a new variable/column based on an *R*-expression."))
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)
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),
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shiny::tags$br(),
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shiny::tags$br(),
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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$b("Original data:"),
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# verbatimTextOutput("original"),
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shiny::verbatimTextOutput("original_str")
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),
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shiny::column(
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width = 6,
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shiny::tags$b("Modified data:"),
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# verbatimTextOutput("modified"),
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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_panel(
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title = "Evaluate",
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id = "navdescribe",
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bslib::navset_bar(
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title = "",
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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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value = "acc_chars",
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title = "Characteristics",
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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 'Data' 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 = FALSE
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)
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),
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bslib::accordion_panel(
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vlaue = "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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bslib::nav_panel(
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title = "Characteristics",
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gt::gt_output(outputId = "table1")
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),
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bslib::nav_panel(
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title = "Correlations",
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data_correlations_ui(id = "correlations", height = 600)
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)
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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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"visuals" = bslib::nav_panel(
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title = "Visuals",
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id = "navvisuals",
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do.call(
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bslib::navset_bar,
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c(
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data_visuals_ui("visuals"),
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shiny::tagList(
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bslib::nav_spacer(),
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bslib::nav_panel(
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title = "Notes",
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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::markdown(readLines("www/notes_visuals.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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)
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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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id = "navanalyses",
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do.call(
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bslib::navset_bar,
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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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id = "navdownload",
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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::fluidRow(
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shiny::column(
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width = 6,
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shiny::h4("Report"),
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shiny::helpText("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")
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)
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# 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."),
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),
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shiny::column(
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width = 6,
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shiny::h4("Data"),
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shiny::helpText("Choose your favourite output data format to download the modified data."),
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shiny::br(),
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shiny::br(),
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shiny::selectInput(
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inputId = "data_type",
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label = "Data format",
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selected = NULL,
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choices = list(
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"R" = "rds",
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"stata" = "dta",
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"CSV" = "csv"
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)
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),
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shiny::helpText("No metadata is saved when exporting to csv."),
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shiny::br(),
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shiny::br(),
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# Button
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shiny::downloadButton(
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outputId = "data_modified",
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label = "Download data",
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icon = shiny::icon("download")
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)
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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::h4("Code snippets"),
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shiny::tags$p("Below are the code used to create the final data set. This can be saved for reproducibility. The code may not be 100 % correct, but kan be used for learning and example code to get started on coding yourself."),
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shiny::tagAppendChildren(
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shiny::tagList(
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shiny::verbatimTextOutput(outputId = "code_import"),
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shiny::verbatimTextOutput(outputId = "code_data"),
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shiny::verbatimTextOutput(outputId = "code_filter"),
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shiny::verbatimTextOutput(outputId = "code_table1")
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),
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lapply(paste0("code_",c("univariable","multivariable")),
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\(.x)shiny::verbatimTextOutput(outputId = .x))
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)
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,
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shiny::tags$br(),
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shiny::br()
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),
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shiny::column(width = 2)
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)
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),
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##############################################################################
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#########
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######### Documentation panel
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#########
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##############################################################################
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"docs" = bslib::nav_item(
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# shiny::img(shiny::icon("book")),
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shiny::tags$a(
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href = "https://agdamsbo.github.io/FreesearchR/",
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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$iframe("www/docs.html", height=600, width=535),
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# shiny::htmlOutput("docs_file"),
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# shiny::br()
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# )
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)
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# Initial attempt at creating light and dark versions
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light <- custom_theme()
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dark <- custom_theme(
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bg = "#000",
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fg = "#fff"
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)
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# Fonts to consider:
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# https://webdesignerdepot.com/17-open-source-fonts-youll-actually-love/
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ui <- bslib::page_fixed(
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shiny::tags$head(includeHTML(("www/umami-app.html"))),
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shiny::tags$style(
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type = "text/css",
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# add the name of the tab you want to use as title in data-value
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shiny::HTML(
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".container-fluid > .nav > li >
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a[data-value='FreesearchR'] {font-size: 28px}"
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)
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),
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title = "FreesearchR",
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theme = light,
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shiny::useBusyIndicators(),
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bslib::page_navbar(
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id = "main_panel",
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ui_elements$home,
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ui_elements$import,
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ui_elements$overview,
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ui_elements$describe,
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ui_elements$visuals,
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ui_elements$analyze,
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ui_elements$download,
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bslib::nav_spacer(),
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ui_elements$docs,
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fillable = FALSE,
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footer = shiny::tags$footer(
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style = "background-color: #14131326; padding: 4px; text-align: center; bottom: 0; width: 100%;",
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shiny::p(
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style = "margin: 1",
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"Data is only stored for analyses and deleted immediately afterwards."
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),
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shiny::p(
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style = "margin: 1; color: #888;",
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"AG Damsbo | v", app_version(), " | ", shiny::tags$a("AGPLv3 license", href = "https://github.com/agdamsbo/FreesearchR/blob/main/LICENSE.md", target = "_blank", rel = "noopener noreferrer"), " | ", shiny::tags$a("Source on Github", href = "https://github.com/agdamsbo/FreesearchR/", target = "_blank", rel = "noopener noreferrer")
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),
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)
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)
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)
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