mirror of
https://github.com/agdamsbo/FreesearchR.git
synced 2025-09-12 09:59:39 +02:00
Andreas Gammelgaard Damsbo
268038e49e
Some checks failed
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630 lines
21 KiB
R
630 lines
21 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 = "freesearcheR",
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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", ".sas7bdat", ".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::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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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("Filter variables with completeness above 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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)
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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$h3("Overview and filtering"),
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fluidRow(
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shiny::column(
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width = 9,
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shiny::tags$p(
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"Below is a short summary table of the provided data.
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On the right hand side you have the option to create filters.
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At the bottom you'll find a raw overview of the original vs the modified data."
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)
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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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IDEAFilter::IDEAFilter_ui("data_filter"),
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shiny::tags$br()
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)
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)
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),
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bslib::nav_panel(
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title = "Browse",
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tags$h3("Browse the provided data"),
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shiny::tags$p(
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"Below is a table with all the modified data provided to browse and understand data."
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),
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shinyWidgets::html_dependency_winbox(),
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fluidRow(
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toastui::datagridOutput(outputId = "table_mod")
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),
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shiny::tags$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 to update variables (rename, set new labels (for nicer tables in the report) and change variable classes (numeric, factor/categorical etc.).), modify factor/categorical variables as well as create new factor from a continous variable or new variables with *R* code."))
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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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fluidRow(
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shiny::column(
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width = 2
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),
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shiny::column(
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width = 8,
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fluidRow(
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shiny::column(
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width = 6,
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tags$h4("Update or modify variables"),
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shiny::tags$br(),
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shiny::actionButton(
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inputId = "modal_variables",
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label = "Subset, rename and change class/type",
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width = "100%"
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),
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shiny::tags$br(),
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shiny::helpText("Subset variables, rename variables and labels, and apply new class to variables"),
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shiny::tags$br(),
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shiny::tags$br(),
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shiny::actionButton(
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inputId = "modal_update",
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label = "Reorder factor levels",
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width = "100%"
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),
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shiny::tags$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 = 6,
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tags$h4("Create new variables"),
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shiny::tags$br(),
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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$br(),
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shiny::actionButton(
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inputId = "modal_column",
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label = "New variable",
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width = "100%"
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),
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shiny::tags$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$h4("Restore"),
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shiny::actionButton(
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inputId = "data_reset",
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label = "Restore original data",
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width = "100%"
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),
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shiny::tags$br(),
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shiny::helpText("Reset to original imported dataset. Careful! There is no un-doing.")
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),
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shiny::column(
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width = 2
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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$h4("Restore"),
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shiny::tags$br(),
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shiny::tags$p(
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"Below, you'll find a raw overview of the original vs the modified data."
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),
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shiny::tags$br(),
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shiny::tags$br(),
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fluidRow(
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column(
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width = 6,
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tags$b("Original data:"),
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# verbatimTextOutput("original"),
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verbatimTextOutput("original_str")
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),
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column(
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width = 6,
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tags$b("Modified data:"),
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# verbatimTextOutput("modified"),
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verbatimTextOutput("modified_str")
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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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######### 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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),
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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 = "Baseline 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 = "Variable 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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bslib::navset_bar(
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title = "",
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# bslib::layout_sidebar(
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# fillable = TRUE,
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sidebar = bslib::sidebar(
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bslib::accordion(
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open = "acc_reg",
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multiple = FALSE,
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bslib::accordion_panel(
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value = "acc_reg",
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title = "Regression",
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icon = bsicons::bs_icon("calculator"),
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shiny::uiOutput("outcome_var"),
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# shiny::selectInput(
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# inputId = "design",
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# label = "Study design",
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# selected = "no",
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# inline = TRUE,
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# choices = list(
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# "Cross-sectional" = "cross-sectional"
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# )
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# ),
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shiny::uiOutput("regression_type"),
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shiny::radioButtons(
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inputId = "add_regression_p",
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label = "Add p-value",
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inline = TRUE,
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selected = "yes",
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choices = list(
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"Yes" = "yes",
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"No" = "no"
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)
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),
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bslib::input_task_button(
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id = "load",
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label = "Analyse",
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# icon = shiny::icon("pencil", lib = "glyphicon"),
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icon = bsicons::bs_icon("pencil"),
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label_busy = "Working...",
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icon_busy = fontawesome::fa_i("arrows-rotate",
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class = "fa-spin",
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"aria-hidden" = "true"
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),
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type = "secondary",
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auto_reset = TRUE
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),
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shiny::helpText("Press 'Analyse' again after changing parameters."),
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shiny::tags$br(),
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shiny::uiOutput("plot_model")
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),
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bslib::accordion_panel(
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value = "acc_advanced",
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title = "Advanced",
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icon = bsicons::bs_icon("gear"),
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shiny::radioButtons(
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inputId = "all",
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label = "Specify covariables",
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inline = TRUE, selected = 2,
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choiceNames = c(
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"Yes",
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"No"
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),
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choiceValues = c(1, 2)
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),
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shiny::conditionalPanel(
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condition = "input.all==1",
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shiny::uiOutput("include_vars")
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)
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)
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),
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# shiny::helpText(em("Please specify relevant settings for your data, and press 'Analyse'")),
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# shiny::radioButtons(
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# inputId = "specify_factors",
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# label = "Specify categorical variables?",
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# selected = "no",
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# inline = TRUE,
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# choices = list(
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# "Yes" = "yes",
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# "No" = "no"
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# )
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# ),
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# shiny::conditionalPanel(
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# condition = "input.specify_factors=='yes'",
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# shiny::uiOutput("factor_vars")
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# ),
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# shiny::conditionalPanel(
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# condition = "output.ready=='yes'",
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# shiny::tags$hr(),
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),
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bslib::nav_panel(
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title = "Regression table",
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gt::gt_output(outputId = "table2")
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),
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bslib::nav_panel(
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title = "Coefficient plot",
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shiny::plotOutput(outputId = "regression_plot")
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),
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bslib::nav_panel(
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title = "Model checks",
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shiny::plotOutput(outputId = "check")
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# shiny::uiOutput(outputId = "check_1")
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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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"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::tags$b("Code snippets:"),
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|
shiny::verbatimTextOutput(outputId = "code_import"),
|
|
shiny::verbatimTextOutput(outputId = "code_data"),
|
|
shiny::verbatimTextOutput(outputId = "code_filter"),
|
|
shiny::tags$br(),
|
|
shiny::br(),
|
|
shiny::column(width = 2)
|
|
)
|
|
)
|
|
),
|
|
##############################################################################
|
|
#########
|
|
######### Documentation panel
|
|
#########
|
|
##############################################################################
|
|
"docs" = bslib::nav_item(
|
|
# shiny::img(shiny::icon("book")),
|
|
shiny::tags$a(
|
|
href = "https://agdamsbo.github.io/freesearcheR/",
|
|
"Docs (external)",
|
|
target = "_blank",
|
|
rel = "noopener noreferrer"
|
|
)
|
|
)
|
|
# bslib::nav_panel(
|
|
# title = "Documentation",
|
|
# # shiny::tags$iframe("www/docs.html", height=600, width=535),
|
|
# shiny::htmlOutput("docs_file"),
|
|
# shiny::br()
|
|
# )
|
|
)
|
|
# Initial attempt at creating light and dark versions
|
|
light <- custom_theme()
|
|
dark <- custom_theme(
|
|
bg = "#000",
|
|
fg = "#fff"
|
|
)
|
|
|
|
# Fonts to consider:
|
|
# https://webdesignerdepot.com/17-open-source-fonts-youll-actually-love/
|
|
|
|
ui <- bslib::page_fixed(
|
|
shiny::tags$head(includeHTML(("www/umami-app.html"))),
|
|
shiny::tags$style(
|
|
type = "text/css",
|
|
# add the name of the tab you want to use as title in data-value
|
|
shiny::HTML(
|
|
".container-fluid > .nav > li >
|
|
a[data-value='freesearcheR'] {font-size: 28px}"
|
|
)
|
|
),
|
|
title = "freesearcheR",
|
|
theme = light,
|
|
shiny::useBusyIndicators(),
|
|
bslib::page_navbar(
|
|
id = "main_panel",
|
|
ui_elements$home,
|
|
ui_elements$import,
|
|
ui_elements$overview,
|
|
ui_elements$describe,
|
|
ui_elements$visuals,
|
|
ui_elements$analyze,
|
|
ui_elements$download,
|
|
bslib::nav_spacer(),
|
|
ui_elements$docs,
|
|
fillable = FALSE,
|
|
footer = shiny::tags$footer(
|
|
style = "background-color: #14131326; padding: 4px; text-align: center; bottom: 0; width: 100%;",
|
|
shiny::p(
|
|
style = "margin: 1",
|
|
"Data is only stored for analyses and deleted immediately afterwards."
|
|
),
|
|
shiny::p(
|
|
style = "margin: 1; color: #888;",
|
|
"AG Damsbo | v", app_version(), " | AGPLv3 license | ", shiny::tags$a("Source on Github", href = "https://github.com/agdamsbo/freesearcheR/", target = "_blank", rel = "noopener noreferrer")
|
|
),
|
|
)
|
|
)
|
|
)
|