inst/shiny/ui.r

In boyanangelov/sdmbench: Benchmark Species Distribution Models

library(shinydashboard)

dashboardPage(
    skin = "green",
    dashboardHeader(title = "SDMBench"),
    dashboardSidebar(
        sidebarMenu(
            menuItem("Data", tabName = "get_data"),
            menuItem("General Models", tabName = "gen_methods"),
            menuItem("MaxEnt", tabName = "profile_methods"),
            menuItem("Deep Learning", tabName = "dl_methods")
        ),
        tags$hr(),
        checkboxInput("custom_data", "Use custom data?", FALSE),
        tags$p("* at the moment just for General Models", style  = "margin-left: 15px;"),
        fileInput(
            "file1",
            "Upload custom data",
            multiple = FALSE,
            accept = c("text/csv",
                       "text/comma-separated-values,text/plain",
                       ".csv")
        ),
        actionButton(
            "go_custom",
            "Parse custom data",
            icon = icon("play
"),
            style = "width: 200px;font-weight:bold;border: 2px;"
        ),
        tags$hr(),
        textInput("text", "Species name:"),
        numericInput(
            "limit",
            "Max number of records:",
            1000,
            min = 1,
            max = 200000
        ),
        selectInput(
            "climate_type",
            "Climate type:",
            c("Default" = "default",
              "Future" = "future")
        ),
        textInput("projected_model", "Climate projection*", value = "BC"),
        # TODO edit
        numericInput("rcp", "rcp (26, 45, 60 or 85):", 45),
        numericInput("years", "Years into future (50 or 75):", 50),
        numericInput("climate_resolution", "Climate resolution:", 10),
        checkboxInput("sample", "Undersample?", FALSE),
        tags$p("* check worldclim website for list", style  = "margin-left: 15px;"),
        selectInput(
            "data_partitioning_type",
            "Partitioning:",
            c(
                "Default" = "default",
                "Block" = "block",
                "Checkerboard1" = "checkerboard1",
                "Checkerboard2" = "checkerboard2"
            )
        ),
        actionButton(
            "go",
            "Get Data",
            icon = icon("download"),
            style = "width: 200px;font-weight:bold;border: 2px;"
        ),
        tags$hr(),
        checkboxGroupInput(
            "checkGroup",
            h5("Algorithm selection"),
            choices = list(
                "Random Forest" = "classif.randomForest",
                "Logistic Regression" = "classif.logreg",
                "Decision Tree" = "classif.rpart",
                "Support Vector Machines" = "classif.ksvm",
                "Gradient Boosting Machine" = "classif.gbm",
                "ada Boosting" = "classif.ada",
                "Multinomial Regression" = "classif.multinom",
                "eXtreme Gradient Boosting" = "classif.xgboost",
                "Naive Bayes" = "classif.naiveBayes",
                "K-Nearest Neighbours" = "classif.IBk"
            ),
            selected = "classif.randomForest"
        ),
        actionButton("go_bmr", "General Models", style = "width: 200px;"),
        actionButton("go_maxent", "MaxEnt", style = "width: 200px;"),
        actionButton("go_dl", "Neural Network", style = "width: 200px;")
    ),
    dashboardBody(
        shinyjs::useShinyjs(),
        tags$head(
            tags$link(rel = "stylesheet", type = "text/css", href = "custom.css")
        ),
        tabItems(
            tabItem(tabName = "get_data",
                    fluidRow(
                        box(
                            leaflet::leafletOutput("occ_map"),
                            title = "Occurence Map",
                            collapsible = TRUE,
                            collapsed = TRUE,
                            status = "success",
                            solidHeader = TRUE,
                            width = 12
                        )
                    ),
                    fluidRow(
                        box(
                            div(style = 'overflow-x: scroll', tableOutput('table')),
                            title = "Climate Variables",
                            collapsible = TRUE,
                            collapsed = TRUE,
                            status = "info",
                            solidHeader = TRUE,
                            width = 12
                        )
                    )),
            
            tabItem(
                tabName = "gen_methods",
                fluidRow(
                    box(
                        tableOutput("bmr_results"),
                        title = "Benchmarking Results",
                        solidHeader = TRUE,
                        status = "success"
                    ),
                    box(
                        plotOutput("bmr_plot1"),
                        title = "Benchmarking Results (plot)",
                        solidHeader = TRUE,
                        status = "info"
                    )
                ),
                fluidRow(
                    box(
                        leaflet::leafletOutput("model_map_1"),
                        title = "SDM Map 1",
                        collapsible = TRUE,
                        collapsed = TRUE
                    ),
                    box(
                        leaflet::leafletOutput("model_map_2"),
                        title = "SDM Map 2",
                        collapsible = TRUE,
                        collapsed = TRUE
                    )
                ),
                fluidRow(
                    box(
                        leaflet::leafletOutput("model_map_3"),
                        title = "SDM Map 3",
                        collapsible = TRUE,
                        collapsed = TRUE
                    ),
                    box(
                        leaflet::leafletOutput("model_map_4"),
                        title = "SDM Map 4",
                        collapsible = TRUE,
                        collapsed = TRUE
                    )
                ),
                fluidRow(
                    box(
                        leaflet::leafletOutput("model_map_5"),
                        title = "SDM Map 5",
                        collapsible = TRUE,
                        collapsed = TRUE
                    ),
                    box(
                        leaflet::leafletOutput("model_map_6"),
                        title = "SDM Map 6",
                        collapsible = TRUE,
                        collapsed = TRUE
                    )
                ),
                fluidRow(
                    box(
                        leaflet::leafletOutput("model_map_7"),
                        title = "SDM Map 7",
                        collapsible = TRUE,
                        collapsed = TRUE
                    ),
                    box(
                        leaflet::leafletOutput("model_map_8"),
                        title = "SDM Map 8",
                        collapsible = TRUE,
                        collapsed = TRUE
                    )
                ),
                fluidRow(
                    box(
                        leaflet::leafletOutput("model_map_9"),
                        title = "SDM Map 9",
                        collapsible = TRUE,
                        collapsed = TRUE
                    ),
                    box(
                        leaflet::leafletOutput("model_map_10"),
                        title = "SDM Map 10",
                        collapsible = TRUE,
                        collapsed = TRUE
                    )
                )
                
            ),
            tabItem(tabName = "profile_methods",
                    fluidRow(
                        box(
                            textOutput("maxent_auc"),
                            title = "MaxEnt AUC",
                            status = "success",
                            solidHeader = TRUE
                        ),
                        box(
                            leaflet::leafletOutput("maxent_map"),
                            title = "MaxEnt Map",
                            collapsible = TRUE,
                            collapsed = TRUE
                        )
                    )),
            tabItem(tabName = "dl_methods",
                    fluidRow(
                        box(
                            textOutput("dl_auc"),
                            plotOutput("dl_history"),
                            title = "Deep Learning Performance",
                            status = "success",
                            solidHeader = TRUE
                        ),
                        box(
                            leaflet::leafletOutput("dl_map"),
                            title = "Deep Learning Map",
                            collapsible = TRUE,
                            collapsed = TRUE
                        )
                    ))
        )
        
    )
    
)