shiny/ui.R

In nwfsc-assess/geostatistical_delta-GLMM: Package for conducting spatial estimation of CPUE index standardization (fisheries, ecology, etc)

library(shiny)

# Load stuff
load( file="database/Results-speciesDF.RData" )
RegionTable = read.csv( "Survey_names_and_codes.csv", stringsAsFactors=FALSE )
region_set = unique( RegionTable[which(RegionTable[,'Survey_code']%in%speciesDF[,'Region']),'Region_name'] )

# Page for user interface
fluidPage(

  titlePanel("Visualize fish populations"),

  # Panel for settings
  sidebarPanel(
    # Display useful info
    h1("Background"),
    h4("This page shows indices of abundance and distribution for marine fishes in several regions"),
    h4("For details of computation, please see ", a("www.FishStats.org", href="http://www.FishStats.org")),
    br(),

    # Time series plots
    h1("Plot settings"),
    # Choose region
    selectInput(inputId="region", label="Region to show", choices=region_set, multiple=FALSE, selected="Eastern Bering Sea"),
    h4("General settings"),
    # General settings
    checkboxInput( inputId="plotCI", label="Plot confidence intervals?", value=TRUE),
    checkboxInput( inputId="plotLog", label="Plot log-abundance?", value=TRUE),
    radioButtons( inputId="species_category", label="Which group of species?", choices=list("Top 10 fishes"="top10fish", "All fishes in database"="fish", "All species in database"="all"), selected="top10fish"),
    textInput(inputId="species_match", label="Search group of species", value = ""),
    actionButton(inputId="unselect_all", label="Unselect all species"),
    # Based on region, select species
    uiOutput("speciesSelex"),
    # Only update plot when clicked (to decrease server load)
      #actionButton(inputId="activate", label="Click to plot or refresh selection"),
    br(),
    #br(),

    # Plot animated maps
    uiOutput("speciesMapSelex"),
    uiOutput("sliderSelex"),

    h1("Disclaimer"),
    h4("These results do not reflect all available information for assessing the status of these stocks, and anyone interested should consult stock assessments for a more-complete picture of indivudal stocks"),
    br()
  ),

  # Configuration of plotting tabs
  mainPanel(
    tabsetPanel(
      # Time series tab
      tabPanel("Time series: Index",
        textOutput('debug_text1'),
        textOutput('debug_text2'),
        textOutput('debug_text3'),
        plotOutput('plot1', height="600px")    #
      ),
      tabPanel("Time series: Distribution",
        plotOutput('plot2'),
        plotOutput('plot3')
      ),
      tabPanel("Time series: Effective area occupied",
        plotOutput('plot4')
      ),
      # Mapping tab
      tabPanel("Maps",
        plotOutput('image1')
      ),
      tabPanel("Global coverage",
        plotOutput('image2')
      ),
      tabPanel("Acknowledgements",
        tableOutput('table1')
      )
    )
  )
)