app.R

library(shiny)
library(shinythemes)
library(colorRamps)
library(dplyr)
library(plotly)
library(DT)

library(ggplot2)
library(reshape2)

availableYears<- list("2022", "2021", "2020", "2019","2018", "2017", "2016", "2015")

ui <- fluidPage(
  tags$head(includeScript("google-analytics.js")),
  theme = shinytheme("journal"),
  titlePanel("The Stock Book"),
  # textInput("pdfurl", "PDF URL")
  # htmlOutput('pdfviewer')
  selectInput("year", h3("Select Stock Book Year"),
              choices = availableYears), #this used to be "choices = list("2018", "2017", "2016", "2015"), selected = "2018"),"
  navlistPanel(id="mainpanel", widths=c(2,10), 
               tabPanel("Introduction", 
                        tabsetPanel(type="tabs",
                                    tabPanel("About the Stockbook",
                                             htmlOutput("Introtext"),
                                             HTML("<br><br>")),
                                    tabPanel("Organisation of the Stock Book",htmlOutput("Introtext2"),
                                             HTML("<br><br>")),
                                    tabPanel("Ireland's TAC", 
                                             textOutput("TACsubheading"),
                                             #"Ireland's Share of the EU TAC",
                                             HTML("<br><br>"),
                                             tags$head(tags$style(type="text/css", ".test_type {font-size: 11px;}")),
                                             div(class="test_type", tableOutput("IntroTable")),
                                             textOutput("TACtext1"),
                                             plotOutput("Introplot",height="800px"),
                                             "1 Only TAC areas where Ireland has share of the TAC>0t are included",p(),
                                             textOutput("TACtext2"),
                                             HTML("<br><br>")),
                                    #conditionalPanel(condition = "input.year == '2018'",
                                    tabPanel("Data Quality", htmlOutput("DataQualitytext"),
                                             imageOutput("DataQualityimage", height="50%")),
                                    tabPanel("ICES Rationale",htmlOutput("Rationaletext"),
                                             HTML("<br><br>")))),
               tabPanel("Long Term Management Plans", 
                        htmlOutput("LongTermManagementtext"),
                        p(),
                        imageOutput("MgtPlan", height="100%"), 
                        fluidRow(column(width = 5, imageOutput("MgtPlan2", height="100%")),
                                 column(width = 5, imageOutput("MgtPlan3", height="100%"))),
                        HTML("<br><br>")),
               tabPanel("Advice Summary", textOutput("AdviceSummtext"),p(),
                        imageOutput("AdviceSummtable1", height="100%"),p(),
                        imageOutput("AdviceSummtable2", height="100%"),
                        HTML("<br><br>")),
               #Nov 2022 moved the Sustainability Ass. set-up to a uiOutput() to avoid 'Navigation Containers' warning
               tabPanel("Sustainability Assessment", uiOutput("SustainAss"),
                        HTML("<br><br>")),
               tabPanel("Overviews and Mixed Fisheries", uiOutput("OverviewsAndMF"),
                        HTML("<br><br>")),
               tabPanel("Recent Ecosystem Advice", uiOutput("RecentAdvice"),
                        HTML("<br><br>")),
               tabPanel("Brexit Impacts", htmlOutput("Brexit_Text")),
               tabPanel("Covid Response", uiOutput("CovidResponse"), #p(), HTML("<br>"),
                        HTML("<br><br>")),
                        # imageOutput("AtSea2020_1", height="100%"),
                        # "Figure 1. At sea Self-Sampling Datasheet",HTML("<br><br>")),
               tabPanel("Stock Advice", value="StockAdvice_tab",
                        sidebarLayout(fluidRow(column(3,uiOutput("speciesSelector")),
                                               column(5,uiOutput("DescSelector"))),
                                      mainPanel(uiOutput("tabstest"),width = 12))),
               tabPanel("Definitions", htmlOutput("Defns"), htmlOutput("Defns2"),
                        HTML("<br><br>"))),
  hr(),
  fluidRow(width =12,#style = "margin-top:-4em",
           column(3,img(src="Logos/Irelands_EU_ESIF_2014_2020_en.jpg", width = "300px", height = "90px",style="margin-top: 2em; margin-left: 5px; margin-right: 5px;")),
           column(3,img(src="Logos/dafm_logo.png", width = "300px", height = "100px",style="margin-top: 1.5em;")),
           column(3,img(src="Logos/EU logo with text.jpg", width = "280px", height = "90px",style="margin-top: 32px;")),
           column(3,img(src="Logos/Marine_logo_rgb.jpg", width = "320px", height = "90px",style="margin-left: -0px;margin-top: 2em;"))
           #img(src="Niamh.png", width = "1250px", height = "100px", style="display: block; margin-left: auto; margin-right: auto;margin-top:0em")
  )
)

############################################################################################
############################################################################################
server <- function(input, output, session) {
  
  # This code has been moved here because we need the data for handling URL parameters
  ####################
  # Stock Advice Tab #
  ####################
  #Species Table for mapping different codes
  #setwd("H:/Stockbook/shiny/WIP") #If needing to run it
  ICEStable=read.csv('ICES-New-Old - extra species.csv', header=TRUE)
  ICEStable$Fish=as.character(ICEStable$Fish)
  ICEStable$Fish <- trimws(ICEStable$Fish)
  ICEStable$SpeciesByDiv=as.character(ICEStable$SpeciesByDiv)
  ICEStable$SpeciesByDiv <- trimws(ICEStable$SpeciesByDiv)
  Speciesfilter <- unique(ICEStable$Fish)
  
  
  ## Read parameter strings from the URL and change the selection appropriately
  observe({
    urlParameters <- parseQueryString(session$clientData$url_search)
    
    ## If we have a stock parameter in the URL we will try and use it to
    ## choose our default stock
    if (!is.null(urlParameters[['stock']])) {
      
      stockURLParameter <- urlParameters[['stock']]
      #stockURLParameter <- 'mon.27.78ab'
      
      #print(stockURLParameter)
      
      stockParameterFrame <- ICEStable[as.character(ICEStable$New)==stockURLParameter,]
      stockParameterFish <- stockParameterFrame$Fish
      
      # If we didn't get a match just use the first species in the data frame as the default species
      if (length(stockParameterFish) == 0){
        stockParameterFish <- ICEStable[1,"Fish"]
      }
      
      #print(stockParameterFish)
      
      # create the speciesfilter input
      output$speciesSelector <- renderUI({
        selectInput("speciesfilter", h3("Select Species"), as.list(Speciesfilter), selected = stockParameterFish) 
      })
      
      stockParameterDiv <- stockParameterFrame$SpeciesByDiv
      
      # If we didn't get a match just use the first area for that species in the data frame as the default species
      if (length(stockParameterDiv) == 0){
        stockParameterDiv <- ICEStable[1,"SpeciesByDiv"]
      }
      
      #print(stockParameterDiv)
      
      # create the DescSelector input~~~~~~~~~~
      output$DescSelector <- renderUI({
        SpeciesbyDiv=filter(ICEStable, Fish %in% c(input$speciesfilter))
        Descriptions <- unique(SpeciesbyDiv$SpeciesByDiv)
        selectInput("speciesbydiv", h3("Select Stock Area"), as.list(Descriptions), selected = stockParameterDiv)
      })
      
      #Show the Stock Advice tab using SELECT - this is a bit of hack to make sure the
      # user is taken to the Stock page first if a stock parameter is provided
      showTab("mainpanel","StockAdvice_tab",select= TRUE, session)
      
    } 
    ## If there's no stock parameter we'll just default to Cod, and use the first area as the selected stock
    else 
    {
      # create the speciesfilter input with a default selection
      output$speciesSelector <- renderUI({
        selectInput("speciesfilter", h3("Select Species"), as.list(Speciesfilter), selected = "Cod") 
      }) 
      
      # create the DescSelector input with a default selection
      output$DescSelector <- renderUI({
        SpeciesbyDiv=filter(ICEStable, Fish %in% c(input$speciesfilter))
        Descriptions <- unique(SpeciesbyDiv$SpeciesByDiv)
        selectInput("speciesbydiv", h3("Select Stock Area"), as.list(Descriptions), selected = Descriptions[1])
      })
      
    }
    
    # YEAR 
    # ~~~~
    # If we have a valid year parameter - change the year input selection to the relevent value
    if (!is.null(urlParameters[['year']])) {
      
      yearURLParameter <- urlParameters[['year']]
      
      if(yearURLParameter %in% availableYears){
        updateSelectInput(session, 
                          "year",
                          choices= availableYears,
                          selected= yearURLParameter )
      }
    }
  })
  
  
  #Introduction 
  #~~~~~~~~~~~~
  Introduction=read.csv('Introduction.csv', header=TRUE)
  output$Introtext <- renderText({
    paste0(Introduction[1, which(colnames(Introduction)==paste0("X", input$year))])
  })
  output$Introtext2 <- renderText({
    paste0(Introduction[2, which(colnames(Introduction)==paste0("X", input$year))])
  })
  
  #Introduction Table
  #~~~~~~~~~~~~~~~~~~
  IntroductionTable=read.csv('IntroductionTable.csv', header=TRUE)
  IntroductionTable$Est..Value.of.Irl.Quota=paste("\u20ac", IntroductionTable$Est..Value.of.Irl.Quota)
  IntroductionTable$Est..Value.of.EU.TAC=paste("\u20ac", IntroductionTable$Est..Value.of.EU.TAC)
  IntroductionTable$Stock= paste(IntroductionTable$Species, IntroductionTable$TAC.Area, sep=' ')
  names(IntroductionTable)=c("Year", "Species", "TAC Area", "Irl. Tonnes", 
                             "Est. Value of Irl. Quota", "Est. Value of EU TAC", "Ireland", "Other", "Stock")
  output$IntroTable = renderTable({
    IntroTable1=filter(IntroductionTable, Year==input$year)
    #IntroTable1[,2:6] # now replaced with lines 225 to 229 (SM)
    
    ###SM ADDED 2021--> Due to Brexit, the final two columns are deleted###
    #This also applied to 2022
    if(input$year>=2021){
      IntroTable1[,2:4]
    }else IntroTable1[,2:6]  
  }, colnames = TRUE, bordered = TRUE,height=1600)#,width = '100%')#, height="50%", width = "60%")
  
  output$Introplot= renderPlot({
    FilterbyYear=filter(IntroductionTable, Year==input$year & Species!="Total")
    FilterbyYear$Stock2 <- factor(FilterbyYear$Stock, as.character(FilterbyYear$Stock))
    mdat = melt(FilterbyYear, id.vars=c("Year", "Species", "TAC Area", "Irl. Tonnes", 
                                        "Est. Value of Irl. Quota", "Est. Value of EU TAC", "Stock", "Stock2"), 
                measure.vars=c("Ireland", "Other"))
    
    p4 <- ggplot(aes(y = value, x = Stock2, fill = forcats::fct_rev(variable)), data = mdat) + 
      geom_bar(stat="identity") + 
      scale_fill_manual(values=c('#C6D9F1', '#9EBD5F')) + 
      scale_x_discrete(limits = rev(levels(mdat$Stock2)))+
      coord_flip() +
      geom_text(aes(label = paste(round(mdat$value*100,0),"%",sep=""))) +
      scale_y_continuous(labels = scales::percent, limits = c(0, 1)) +
      theme(axis.title.y=element_blank(),
            axis.title.x=element_blank(),
            legend.title=element_blank())
    p4
    
    ###SM ADDED 2021--> Due to Brexit, the plot is deleted###
    if(input$year==2021){
      p4=FALSE
    }
    
  })
  
  # djc 19/11/2021 Change the TAC sub-heading based on the year selected
  output$TACsubheading=renderText({
    if(input$year==2021){
      paste0(input$year," Irish quota in tonnes and approximate value")
    } else {
      "Ireland's Share of the EU TAC"
    }
  })
  
  output$TACtext1=renderText({
    paste0("% Share of ", input$year, " EU TAC by Ireland and Other EU members and approximate value of Irish Quota")
    ###SM ADDED 2021--> Due to Brexit, the heading of the plot is deleted###
    if(input$year==2021){
      output$TACtext1=NULL
    }
  })
  output$TACtext2=renderText({
    paste0("2 Estimated value per tonne based on ", as.numeric(input$year)-1, " average values of Irish landings in Irish ports")
  })
  
  
  
  #Rationale
  #~~~~~~~~~
  output$Rationaletext <- renderText({
    paste0(Introduction[3, which(colnames(Introduction)==paste0("X", input$year))])
  })
  
  #Data Quality
  #~~~~~~~~~~~~
  output$DataQualitytext <- renderText({
    if(input$year>2017){
      paste0(Introduction[7, which(colnames(Introduction)==paste0("X", input$year))])
    }else{
      paste0("Data Quality Section introduced in 2018 Stockbook")
    }
    
  })
  output$DataQualityimage <- renderImage({
    image_file <- paste0("www/Introduction/DataQuality",input$year,".png")
    return(list(src = image_file, filetype = "image/png", height = 700))
  }, deleteFile = FALSE)
  
  #Management Plan
  #~~~~~~~~~~~~~~~
  output$LongTermManagementtext <- renderText({
    if(input$year>2017){
      paste0(Introduction[8, which(colnames(Introduction)==paste0("X", input$year))])
    }else
      paste0("<p>Long Term Management Strategies (Plans) in Place for Stocks of Irish Interest. </p>
             <p>History of Implementation of Strategies Shown in each case</p>")
  })
  output$MgtPlan <- renderImage({
    image_file <-if(input$year==2018){
      paste0("www/Introduction/ManagementPlan",input$year,".png")
    }else{
      paste0("www/Introduction/ManagementPlan",input$year,".PNG")}
    return(list(src = image_file, filetype = "image/png", height = 850))
  }, deleteFile = FALSE)
  
  output$MgtPlan2 <- renderImage({
    image_file <- paste0("www/Introduction/ManPlanAppIX_Stocks_1_",input$year,".png")
    return(list(src = image_file, filetype = "image/png", height = 950))
  }, deleteFile = FALSE)
  
  output$MgtPlan3 <- renderImage({
    image_file <- paste0("www/Introduction/ManPlanAppIX_Stocks_2_",input$year,".png")
    return(list(src = image_file, filetype = "image/png", height = 950))
  }, deleteFile = FALSE)
  
  
  #Summary of Advice  #original width (too big)--> # width = 1100
  #~~~~~~~~~~~~~~~~~
  output$AdviceSummtable1 <- renderImage({
    image_file <- paste0("www/Introduction/AdviceSumm",input$year,"table1.PNG")
    return(list(src = image_file, filetype = "image/png", width = 750))
  }, deleteFile = FALSE)
  output$AdviceSummtable2 <- renderImage({
    image_file <- paste0("www/Introduction/AdviceSumm",input$year,"table2.PNG")
    return(list(src = image_file, filetype = "image/png", width = 750))
  }, deleteFile = FALSE)
  output$AdviceSummtext<- renderText({
    paste0("Marine Institute Summary on the Status, Scientific Advice for ", as.numeric(input$year)+1,
           " for those Stocks of Interest to Ireland")
  })
  
  #Sustainability #table 3 was width=800 
  #~~~~~~~~~~~~~~
  output$Sustainabilitytext <- renderText({
    paste0(Introduction[4, which(colnames(Introduction)==paste0("X", input$year))])
  })
  output$SustainabilityTabletext <- renderText({
    paste0("Table 4: Stocks with a status change between the ", as.numeric(input$year)-1, 
           " and ", input$year, " assessments.") # SM Nov: changed in 2021 from 'Stock Books'
  })
  # Figure 1 text added in 2022
  output$SustainabilityFigText <- renderText({
    paste0("Figure 1: Number of stocks assessed to be fished below Fmsy and where SSB is above MSY Btrigger in the Stock Book each year, with trends indicated.") 
  })
  # SM Nov: changed in 2021 from 'Stock Books'
  output$Sustainabilitytable1 <- renderImage({
    image_file <- paste0("www/Introduction/Sustain",input$year,"Table1.png")
    return(list(src = image_file, filetype = "image/png", width = 700))
  }, deleteFile = FALSE)
  output$Sustainabilitytable2 <- renderImage({
    image_file <- paste0("www/Introduction/Sustain",input$year,"Table2.png")
    return(list(src = image_file, filetype = "image/png", width = 700))
  }, deleteFile = FALSE)
  output$Sustainabilitytable3 <- renderImage({
    image_file <- paste0("www/Introduction/Sustain",input$year,"Table3.PNG")
    return(list(src = image_file, filetype = "image/png", width = 800))
  }, deleteFile = FALSE)
  output$Sustainabilitytable4 <- renderImage({
    image_file <- paste0("www/Introduction/Sustain",input$year,"Table4.PNG")
    return(list(src = image_file, filetype = "image/png", width = 800))
  }, deleteFile = FALSE)
  #Added in 2022
  output$SustainabilityFig <- renderImage({
    image_file <- paste0("www/Introduction/Sustain",input$year,"Fig1.png")
    return(list(src = image_file, filetype = "image/png", width = 800))
  }, deleteFile = FALSE)
  
  #Definitions
  #~~~~~~~~~~~
  # 2022: SM Oct. The definition list was updated by HG. Additions, Deletions and updates have been applied
  # 2021: Changed the column from '3' to '2' so that the second cell is also displayed ) 
   output$Defns <- renderText({
  #   #print(Introduction[5, 2])
     paste0(Introduction[5, 2])
   })
  output$Defns2 <- renderText({
    #print(Introduction[6, 2])
    paste0(Introduction[6, 2])
  })
  
  #Mixed Fisheries Outputs
  #~~~~~~~~~~~~~~~~~~~~~~~
  #TEXT
  MixedFish=read.csv('MixedFish.csv', header=TRUE)
  output$SummaryText <- renderText({
    paste0(MixedFish[1, which(colnames(MixedFish)==paste0("X", input$year))])
  })
  output$Considerations <- renderText({
    paste0(MixedFish[2, which(colnames(MixedFish)==paste0("X", input$year))])
  })
  output$PressureState<- renderText({
    paste0(MixedFish[3, which(colnames(MixedFish)==paste0("X", input$year))])
  })  
  output$D3summ<- renderText({
    paste0(MixedFish[4, which(colnames(MixedFish)==paste0("X", input$year))])
  }) 
  output$D3text<- renderText({
    paste0(MixedFish[5, which(colnames(MixedFish)==paste0("X", input$year))])
  }) 
  
  ## 2021 'MixedFish' Text: tab in Ecosystem Overview section. Extra cells for control over long text## (SM)
  output$MixedFish_1 <-renderText({
    paste0(MixedFish[6, which(colnames(MixedFish)==paste0("X", input$year))])
  })
  output$MixedFish_2 <-renderText({
    paste0(MixedFish[7, which(colnames(MixedFish)==paste0("X", input$year))])
  })
  output$MixedFish_3 <-renderText({
    paste0(MixedFish[8, which(colnames(MixedFish)==paste0("X", input$year))])
  })
  output$MixedFish_4 <-renderText({
    paste0(MixedFish[9, which(colnames(MixedFish)==paste0("X", input$year))])
  })
  output$MixedFish_5 <-renderText({
    paste0(MixedFish[10, which(colnames(MixedFish)==paste0("X", input$year))])
  })
  output$MixedFish_6 <-renderText({
    paste0(MixedFish[11, which(colnames(MixedFish)==paste0("X", input$year))])
  })
  
  ## 2021 'Fisheries Overview' Text: tab in Ecosystem Overview section. ## SM 
  output$Fisheries_1 <-renderText({
    paste0(MixedFish[12, which(colnames(MixedFish)==paste0("X", input$year))])
  })
  
  #IMAGES
  ##Ecosystem Overview IMAGES ## 
  ## 2021 IMAGES for the new MixedFish tab, in 2021 Ecosystems Section ## Also 2022
  output$MF_Fig1_caption <- renderImage({
    image_file <- paste0("www/MixedFisheries/",input$year,"/MF_Fig1_caption.png")
    return(list(src = image_file, filetype = "image/png", height = 400))
  }, deleteFile = FALSE)
  output$MF_Fig2_caption <- renderImage({
    image_file <- paste0("www/MixedFisheries/",input$year,"/MF_Fig2_caption.png")
    return(list(src = image_file, filetype = "image/png", height = 400))
  }, deleteFile = FALSE)
  output$MF_Fig3_caption <- renderImage({
    image_file <- paste0("www/MixedFisheries/",input$year,"/MF_Fig3_caption.png")
    return(list(src = image_file, filetype = "image/png"))
  }, deleteFile = FALSE)
  output$MF_Fig4_caption <- renderImage({
    image_file <- paste0("www/MixedFisheries/",input$year,"/MF_Fig4_caption.png")
    return(list(src = image_file, filetype = "image/png", height = 400))
  }, deleteFile = FALSE)
  output$MF_Fig5_caption <- renderImage({
    image_file <- paste0("www/MixedFisheries/",input$year,"/MF_Fig5_caption.png")
    return(list(src = image_file, filetype = "image/png", height = 255))
  }, deleteFile = FALSE)
  output$MF_Tbl1 <- renderImage({
    image_file <- paste0("www/MixedFisheries/",input$year,"/MF_Tbl1.png")
    return(list(src = image_file, filetype = "image/png", height = 400))
  }, deleteFile = FALSE)
  output$MF_Tbl2 <- renderImage({
    image_file <- paste0("www/MixedFisheries/",input$year,"/MF_Tbl2.png")
    return(list(src = image_file, filetype = "image/png", height = 175))
  }, deleteFile = FALSE)
  output$MF_Tbl3 <- renderImage({
    image_file <- paste0("www/MixedFisheries/",input$year,"/MF_Tbl3.png")
    return(list(src = image_file, filetype = "image/png", height = 400))
  }, deleteFile = FALSE)
  output$MF_Tbl4 <- renderImage({
    image_file <- paste0("www/MixedFisheries/",input$year,"/MF_Tbl4.png")
    return(list(src = image_file, filetype = "image/png", height = 450)) #2021 height = 400
  }, deleteFile = FALSE)
  output$MF_Tbl5 <- renderImage({
    image_file <- paste0("www/MixedFisheries/",input$year,"/MF_Tbl5.png")
    return(list(src = image_file, filetype = "image/png", height = 350)) #2021 height = 300
  }, deleteFile = FALSE)
  output$MF_Tbl6 <- renderImage({
    image_file <- paste0("www/MixedFisheries/",input$year,"/MF_Tbl6.png")
    return(list(src = image_file, filetype = "image/png", height = 300))
  }, deleteFile = FALSE)
  output$MF_Tbl7 <- renderImage({
    image_file <- paste0("www/MixedFisheries/",input$year,"/MF_Tbl7.png")
    return(list(src = image_file, filetype = "image/png", height = 190))
  }, deleteFile = FALSE)
  output$MF_Tbl8 <- renderImage({
    image_file <- paste0("www/MixedFisheries/",input$year,"/MF_Tbl8.png")
    return(list(src = image_file, filetype = "image/png", height = 200))
  }, deleteFile = FALSE)
  
  ## Specific Images ##
  output$SurfaceArea <- renderImage({
    image_file <- paste0("www/MixedFisheries/",input$year,"/SurfaceArea.png")
    return(list(src = image_file, filetype = "image/png", height = 300))
  }, deleteFile = FALSE)
  output$RelativeF <- renderImage({
    image_file <- paste0("www/MixedFisheries/",input$year,"/RelativeF.png")
    return(list(src = image_file, filetype = "image/png", height = 350))
  }, deleteFile = FALSE)
  output$RelativeSSB <- renderImage({
    image_file <- paste0("www/MixedFisheries/",input$year,"/RelativeSSB.png")
    return(list(src = image_file, filetype = "image/png", height = 350))
  }, deleteFile = FALSE)
  output$Kobe <- renderImage({
    image_file <- paste0("www/MixedFisheries/",input$year,"/Kobe_Plot_Final.png")
    return(list(src = image_file, filetype = "image/png", height = 550))
  }, deleteFile = FALSE)
  output$Bar <- renderImage({
    image_file <- paste0("www/MixedFisheries/",input$year,"/Bar_Plot_Final.png")
    return(list(src = image_file, filetype = "image/png", height = 550))
  }, deleteFile = FALSE)
  
  ## 2018 Specific Images ##
  output$D3table1a <- renderImage({
    image_file <- paste0("www/MixedFisheries/2018/D3Table1a.PNG")
    return(list(src = image_file, filetype = "image/png", width = 550))
  }, deleteFile = FALSE)
  output$D3table1b <- renderImage({
    image_file <- paste0("www/MixedFisheries/2018/D3Table1b.PNG")
    return(list(src = image_file, filetype = "image/png", width = 550))
  }, deleteFile = FALSE)
  output$D3table1c <- renderImage({
    image_file <- paste0("www/MixedFisheries/2018/D3Table1c.PNG")
    return(list(src = image_file, filetype = "image/png", width = 550))
  }, deleteFile = FALSE)
  output$D3table1d <- renderImage({
    image_file <- paste0("www/MixedFisheries/2018/D3Table1d.PNG")
    return(list(src = image_file, filetype = "image/png", width = 550))
  }, deleteFile = FALSE)
  output$D3table1e <- renderImage({
    image_file <- paste0("www/MixedFisheries/2018/D3Table1e.PNG")
    return(list(src = image_file, filetype = "image/png", width = 550))
  }, deleteFile = FALSE)
  output$D3table22018 <- renderImage({
    image_file <- paste0("www/MixedFisheries/2018/D3Table2.PNG")
    return(list(src = image_file, filetype = "image/png", width = 550))
  }, deleteFile = FALSE)
  
  output$MixedFishimage <- renderImage({
    image_file <- paste0("www/MixedFisheries/", input$year, "/MixedFish.PNG")
    return(list(src = image_file, filetype = "image/png", height = 250))
  }, deleteFile = FALSE)
  
  ## 2017 Specific Images ##
  output$guild2017 <- renderImage({
    image_file <- paste0("www/MixedFisheries/2017/cs_guild.png")
    return(list(src = image_file, filetype = "image/png", width = 650))
  }, deleteFile = FALSE)
  output$D3table <- renderImage({
    image_file <- paste0("www/MixedFisheries/2017/D3TablePart1.png")
    return(list(src = image_file, filetype = "image/png", width = 550))
  }, deleteFile = FALSE)
  output$D3table2 <- renderImage({
    image_file <- paste0("www/MixedFisheries/2017/D3TablePart2.png")
    return(list(src = image_file, filetype = "image/png", width = 550))
  }, deleteFile = FALSE)
  output$D3results1 <- renderImage({
    image_file <- paste0("www/MixedFisheries/2017/Results1.png")
    return(list(src = image_file, filetype = "image/png", width = 600))
  }, deleteFile = FALSE)
  output$D3results2 <- renderImage({
    image_file <- paste0("www/MixedFisheries/2017/Results2.png")
    return(list(src = image_file, filetype = "image/png", width = 600))
  }, deleteFile = FALSE)
  output$D3results3 <- renderImage({
    image_file <- paste0("www/MixedFisheries/2017/Results3.png")
    return(list(src = image_file, filetype = "image/png", width = 600))
  }, deleteFile = FALSE)
  
  ## 2016 Specific Images ##
  output$IrishSea <- renderImage({
    image_file <- paste0("www/MixedFisheries/",input$year,"/IrishSea-Pressure-State.png")
    return(list(src = image_file, filetype = "image/png", height = 350))
  }, deleteFile = FALSE)
  output$IrishSeaFSSB <- renderImage({
    image_file <- paste0("www/MixedFisheries/2016/IrishSea-F-SSB.png")
    return(list(src = image_file, filetype = "image/png", height = 350))
  }, deleteFile = FALSE)
  output$CelticSea <- renderImage({
    image_file <- paste0("www/MixedFisheries/2016/CelticSea-Pressure-State.png")
    return(list(src = image_file, filetype = "image/png", height = 350))
  }, deleteFile = FALSE)
  output$CelticSeaFSSB <- renderImage({
    image_file <- paste0("www/MixedFisheries/2016/CelticSea-F-SSB.png")
    return(list(src = image_file, filetype = "image/png", height = 350))
  }, deleteFile = FALSE)
  output$WestScot <- renderImage({
    image_file <- paste0("www/MixedFisheries/2016/WestScot-Pressure-State.png")
    return(list(src = image_file, filetype = "image/png", height = 350))
  }, deleteFile = FALSE)
  output$WestScotFSSB <- renderImage({
    image_file <- paste0("www/MixedFisheries/2016/WestScot-F-SSB.png")
    return(list(src = image_file, filetype = "image/png", height = 350))
  }, deleteFile = FALSE)
  output$DistSpecies <- renderImage({
    image_file <- paste0("www/MixedFisheries/2016/DistSpecies-Pressure-State.png")
    return(list(src = image_file, filetype = "image/png", height = 350))
  }, deleteFile = FALSE)
  output$DistSpeciesFSSB <- renderImage({
    image_file <- paste0("www/MixedFisheries/2016/DistSpecies-F-SSB.png")
    return(list(src = image_file, filetype = "image/png", height = 350))
  }, deleteFile = FALSE)
  
  #2021 Extra Chapters Added: Recent Advice, Brexit Impacts, AtSea2020 Outputs
  #~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
  ExtraChapters=read.csv('ExtraChapters.csv', header=TRUE)
  output$Recent_Beginning <- renderText({
    paste0(ExtraChapters[1, which(colnames(ExtraChapters)==paste0("X", input$year))])
  })
  output$Recent_Middle <- renderText({
    paste0(ExtraChapters[2, which(colnames(ExtraChapters)==paste0("X", input$year))])
  })
  output$Recent_End<- renderText({
    paste0(ExtraChapters[3, which(colnames(ExtraChapters)==paste0("X", input$year))])
  })  
  # output$Brexit_Text<- renderText({
  #   paste0(ExtraChapters[4, which(colnames(ExtraChapters)==paste0("X", input$year))])
  # }) 
  output$AtSea2020<- renderText({
    paste0(ExtraChapters[5, which(colnames(ExtraChapters)==paste0("X", input$year))])
  }) 
  output$AtSeaFootnote<- renderText({
    paste0(ExtraChapters[6, which(colnames(ExtraChapters)==paste0("X", input$year))])
  }) 
  
  #2021 and 2022 Specific - IMAGES added for the three extra chapters
  output$RecentAdvice1 <- renderImage({
    image_file <- paste0("www/MixedFisheries/",input$year,"/RecentAdvice1.png")
    return(list(src = image_file, filetype = "image/png", height = 350))
  }, deleteFile = FALSE)
  output$RecentAdviceColours <- renderImage({
    image_file <- paste0("www/MixedFisheries/",input$year,"/RecentAdviceColours.png")
    return(list(src = image_file, filetype = "image/png", height = 50))
  }, deleteFile = FALSE)
  output$RecentAdvice2 <- renderImage({
    image_file <- paste0("www/MixedFisheries/",input$year,"/RecentAdvice2.png")
    return(list(src = image_file, filetype = "image/png", height = 350))
  }, deleteFile = FALSE)
  output$AtSea2020_1 <- renderImage({
    image_file <- paste0("www/MixedFisheries/",input$year,"/AtSea2020_1.png")
    return(list(src = image_file, filetype = "image/png", height = 700))
  }, deleteFile = FALSE)
  #2022
  output$RecentAdvice3 <- renderImage({
    image_file <- paste0("www/MixedFisheries/",input$year,"/Table_1_cropped.png")
    return(list(src = image_file, filetype = "image/png", height = 450))
  }, deleteFile = FALSE)
  output$RecentAdvice4 <- renderImage({
    image_file <- paste0("www/MixedFisheries/",input$year,"/RecentAdvice3.png")
    return(list(src = image_file, filetype = "image/png", height = 400))
  }, deleteFile = FALSE)
  
  
  # Code moved to the start of the server function because we need it to handle URL parameters
  # ####################
  # # Stock Advice Tab #
  # ####################
  # #Species Table for mapping different codes
  # #setwd("H:/Stockbook/shiny/WIP") #If needing to run it
  # ICEStable=read.csv('ICES-New-Old - extra species.csv', header=TRUE)
  # ICEStable$Fish=as.character(ICEStable$Fish)
  # ICEStable$SpeciesByDiv=as.character(ICEStable$SpeciesByDiv)
  # Speciesfilter <- unique(ICEStable$Fish)
  # output$speciesSelector <- renderUI({
  #   selectInput("speciesfilter", h3("Select Species"), as.list(Speciesfilter), selected = "Cod") 
  # })
  # output$DescSelector <- renderUI({
  #   SpeciesbyDiv=filter(ICEStable, Fish %in% c(input$speciesfilter))
  #   Descriptions <- unique(SpeciesbyDiv$SpeciesByDiv)
  #   selectInput("speciesbydiv", h3("Select Stock Area"), as.list(Descriptions), selected = Descriptions[1])
  # })
  
  ###################
  # Species Summary #
  ###################
  #Biology Text
  #~~~~~~~~~~~~
  output$biology_text <- renderText({
    # djc 10/11/21 - Filtering was previously only done by area description! - Fixed to filter by species and area
    #paste0(ICEStable[which(ICEStable[,"SpeciesByDiv"] %in% input$speciesbydiv),"Description"])
    paste0(ICEStable[ICEStable$Fish == input$speciesfilter & ICEStable$SpeciesByDiv == input$speciesbydiv,"Description" ])
  })
  
  #Fish sketch
  #~~~~~~~~~~~
  output$display.fish <- renderImage({
    # djc 10/11/21 - Filtering was previously only done by area description! - Fixed to filter by species and area
    #image_file <- paste0("www/FishSketches/", 
    #       ICEStable[which(ICEStable[,"SpeciesByDiv"] %in% input$speciesbydiv),"Fish"], ".png")
    image_file <- paste0("www/FishSketches/", 
                         ICEStable[ICEStable$Fish == input$speciesfilter & ICEStable$SpeciesByDiv == input$speciesbydiv,"Fish"], ".png")
    return(list(src = image_file, filetype = "image/png",width = 200))
  }, deleteFile = FALSE)
  
  #International Landings
  #~~~~~~~~~~~~~~~~~~~~~~
  output$display.InternationalLandings <- renderImage({
    # djc 10/11/21 - Filtering was previously only done by area description! - Fixed to filter by species and area
    #image_file <- paste0("www/Internationallandings/", input$year, "/Rect",
    #                    ICEStable[which(ICEStable[,"SpeciesByDiv"] %in% input$speciesbydiv),"FAQCode"], 
    #                    ".png", sep="")
    image_file <- paste0("www/Internationallandings/", input$year, "/Rect",
                         ICEStable[ICEStable$Fish == input$speciesfilter & ICEStable$SpeciesByDiv == input$speciesbydiv,"FAQCode"], 
                         ".png", sep="")
    return(list(src = image_file, width = 350))#
  }, deleteFile = FALSE)
  
  output$text.InternationalLandings <- renderText({
    
    # djc 10/11/21 - Filtering was previously only done by area description! - Fixed to filter by species and area
    
    ## 2022 uses a different year range (SM Sep2022)
    if(input$year==2022){
      if(input$speciesfilter=="Nephrops"){      
        paste0("The distribution of international landings of <em>",
               ICEStable[ICEStable$Fish == input$speciesfilter & ICEStable$SpeciesByDiv == input$speciesbydiv,"Fish"], "</em>  between 2016 - 2020", sep="")
      }
      #Discussed with AC Nov 14th
      else if(input$speciesfilter=="Mackerel" | input$speciesfilter=="Blue Whiting"){      
        paste0("The distribution of international landings of ", 
               ICEStable[ICEStable$Fish == input$speciesfilter & ICEStable$SpeciesByDiv == input$speciesbydiv,"Fish"], 
               " in 2021 (excluding Russia)", sep="")
      }
      #Discussed with AC Nov 14th
      else if(input$speciesfilter=="Horse Mackerel"){      
        paste0("The distribution of international landings of ", 
               ICEStable[ICEStable$Fish == input$speciesfilter & ICEStable$SpeciesByDiv == input$speciesbydiv,"Fish"], 
               " in 2021", sep="")
      }
      #SM added Nov 24th 2021
      else if(input$speciesfilter=="Boarfish"){      
        paste0("The distribution of Irish ", 
               ICEStable[ICEStable$Fish == input$speciesfilter & ICEStable$SpeciesByDiv == input$speciesbydiv,"Fish"], 
               " landings in 2021", sep="")
      }
      # SM added in Nov 2021
      else if(input$speciesfilter=="Anglerfish"){      
        paste0("The distribution of EU landings of ", 
               ICEStable[ICEStable$Fish == input$speciesfilter & ICEStable$SpeciesByDiv == input$speciesbydiv,"Fish"], 
               " between 2016 - 2020 (both species combined)", sep="")
      }
      else{
        paste0("The distribution of international landings of ",
               ICEStable[ICEStable$Fish == input$speciesfilter & ICEStable$SpeciesByDiv == input$speciesbydiv,"Fish"], " between 2016 - 2020 ", sep="")
      }
      
    } 
    ## 2021 uses a different year range (SM Sep2021)
    else if(input$year==2021){
      
      if(input$speciesfilter=="Nephrops"){      
        paste0("The distribution of international landings of <em>",
               ICEStable[ICEStable$Fish == input$speciesfilter & ICEStable$SpeciesByDiv == input$speciesbydiv,"Fish"], "</em>  between 2015 - 2019", sep="")
      }
      else if(input$speciesfilter=="Mackerel" | input$speciesfilter=="Horse Mackerel" | input$speciesfilter=="Blue Whiting"){      
        paste0("The distribution of international landings of ", 
               ICEStable[ICEStable$Fish == input$speciesfilter & ICEStable$SpeciesByDiv == input$speciesbydiv,"Fish"], 
               " in 2020", sep="")
      }
      #SM added Nov 24th 2021
      else if(input$speciesfilter=="Boarfish"){      
        paste0("The distribution of Irish ", 
               ICEStable[ICEStable$Fish == input$speciesfilter & ICEStable$SpeciesByDiv == input$speciesbydiv,"Fish"], 
               " landings in 2020", sep="")
      }
      
      # SM added in Nov 2021
      else if(input$speciesfilter=="Anglerfish"){      
        paste0("The distribution of EU landings of ", 
               ICEStable[ICEStable$Fish == input$speciesfilter & ICEStable$SpeciesByDiv == input$speciesbydiv,"Fish"], 
               " between 2015 - 2019 (black and white Anglerfish combined)", sep="")
      }
      
      else{
        paste0("The distribution of international landings of ",
               ICEStable[ICEStable$Fish == input$speciesfilter & ICEStable$SpeciesByDiv == input$speciesbydiv,"Fish"], " between 2015 - 2019 ", sep="")
      }
      
    } 
    
    
    ## 2020 uses a different year range (SM Nov2020)
    else if(input$year == "2020"){
      
      if(input$speciesfilter=="Nephrops"){      
        paste0("The distribution of international landings of <em>",
               ICEStable[ICEStable$Fish == input$speciesfilter & ICEStable$SpeciesByDiv == input$speciesbydiv,"Fish"], "</em>  between 2015 - 2018", sep="")
      }
      else if(input$speciesfilter=="Mackerel" | input$speciesfilter=="Horse Mackerel"){      
        paste0("The distribution of international landings of ", 
               ICEStable[ICEStable$Fish == input$speciesfilter & ICEStable$SpeciesByDiv == input$speciesbydiv,"Fish"], 
               " during 2019", sep="")
      }
      else{
        paste0("The distribution of international landings of ",
               ICEStable[ICEStable$Fish == input$speciesfilter & ICEStable$SpeciesByDiv == input$speciesbydiv,"Fish"], " between 2015 - 2018 ", sep="")
      }
    } 
    
    
    ## 2019 uses a different text pattern
    else if(input$year == "2019"){
      
      if(input$speciesfilter=="Nephrops"){      
        paste0("The distribution of international landings of <em>",
               ICEStable[ICEStable$Fish == input$speciesfilter & ICEStable$SpeciesByDiv == input$speciesbydiv,"Fish"], "</em>  between 2012 - 2016", sep="")
      }
      else if(input$speciesfilter=="Mackerel" | input$speciesfilter=="Horse Mackerel"){      
        paste0("The distribution of international landings of ", 
               ICEStable[ICEStable$Fish == input$speciesfilter & ICEStable$SpeciesByDiv == input$speciesbydiv,"Fish"], 
               " during 2018", sep="")
      }
      else{
        paste0("The distribution of international landings of ",
               ICEStable[ICEStable$Fish == input$speciesfilter & ICEStable$SpeciesByDiv == input$speciesbydiv,"Fish"], " between 2012 - 2016 ", sep="")
      }
    } 
    
    ## 2018 and earlier
    else {
      
      if(input$speciesfilter=="Nephrops"){      
        paste0("The distribution of international landings of <em>",
               ICEStable[ICEStable$Fish == input$speciesfilter & ICEStable$SpeciesByDiv == input$speciesbydiv,"Fish"], "</em> during ", 
               (as.numeric(as.character(input$year))-1), sep="")
      }else{
        paste0("The distribution of international landings of ",
               ICEStable[ICEStable$Fish == input$speciesfilter & ICEStable$SpeciesByDiv == input$speciesbydiv,"Fish"], " during ", 
               (as.numeric(as.character(input$year))-1), sep="")
      }
    }
  })
  
  
  #Irish Landings
  #~~~~~~~~~~~~~~
  output$display.IrishLandings <- renderImage({
    # djc 10/11/21 - Filtering was previously only done by area description! - Fixed to filter by species and area
    #image_file <- paste0("www/Irishlandings/", input$year, "/Land",
    #                     ICEStable[which(ICEStable[,"SpeciesByDiv"] %in% input$speciesbydiv),"FAQCode"], 
    #                     ".png", sep="")
    
    image_file <- paste0("www/Irishlandings/", input$year, "/Land",
                         ICEStable[ICEStable$Fish == input$speciesfilter & ICEStable$SpeciesByDiv == input$speciesbydiv,"FAQCode"], 
                         ".png", sep="")
    return(list(src = image_file, width = 350))
  }, deleteFile = FALSE)
  
  output$text.IrishLandings <- renderText({
    
    # djc 10/11/21 - Filtering was previously only done by area description! - Fixed to filter by species and area
    
    ## 2022 uses a different year range (SM Sep2022)
    if(input$year == 2022){
      if(input$speciesfilter=="Nephrops"){      
        paste0("The distribution of <em>", 
               ICEStable[ICEStable$Fish == input$speciesfilter & ICEStable$SpeciesByDiv == input$speciesbydiv,"Fish"], 
               "</em> landings by Irish Vessels between 2016 - 2020", sep="")
      } 
      #Discussed with AC Nov 14th
      else if(input$speciesfilter=="Mackerel" | input$speciesfilter=="Horse Mackerel" | input$speciesfilter=="Blue Whiting"){      
        paste0("The distribution of Irish landings of ", 
               ICEStable[ICEStable$Fish == input$speciesfilter & ICEStable$SpeciesByDiv == input$speciesbydiv,"Fish"], 
               " in 2021", sep="")
      }
      
      #SM added Nov 24th 2021 and updated in 2022
      else if(input$speciesfilter=="Boarfish"){      
        paste0("The distribution of Irish ", 
               ICEStable[ICEStable$Fish == input$speciesfilter & ICEStable$SpeciesByDiv == input$speciesbydiv,"Fish"], 
               " landings between 2019-2021", sep="")
      }
      
      
      # SM added in Nov 2021 and updated in 2022
      else if(input$speciesfilter=="Anglerfish"){      
        paste0("The distribution of Irish ", 
               ICEStable[ICEStable$Fish == input$speciesfilter & ICEStable$SpeciesByDiv == input$speciesbydiv,"Fish"], 
               " landings between 2016 - 2020 (both species combined)", sep="")
      }
      
      else{
        paste0("The distribution of ", 
               ICEStable[ICEStable$Fish == input$speciesfilter & ICEStable$SpeciesByDiv == input$speciesbydiv,"Fish"], 
               " landings by Irish Vessels between 2016 - 2020 ", sep="")
      }
    }
    ## 2021 uses a different year range (SM Sep2021)
    else if(input$year==2021){
      
      if(input$speciesfilter=="Nephrops"){      
        paste0("The distribution of <em>", 
               ICEStable[ICEStable$Fish == input$speciesfilter & ICEStable$SpeciesByDiv == input$speciesbydiv,"Fish"], 
               "</em> landings by Irish Vessels between 2015 - 2019", sep="")
      } 
      else if(input$speciesfilter=="Mackerel" | input$speciesfilter=="Horse Mackerel" | input$speciesfilter=="Blue Whiting"){      
        paste0("The distribution of ", 
               ICEStable[ICEStable$Fish == input$speciesfilter & ICEStable$SpeciesByDiv == input$speciesbydiv,"Fish"], 
               " catches from Irish Vessels in 2020", sep="")
      }
      #SM added Nov 24th 2021
      else if(input$speciesfilter=="Boarfish"){      
        paste0("The distribution of Irish ", 
               ICEStable[ICEStable$Fish == input$speciesfilter & ICEStable$SpeciesByDiv == input$speciesbydiv,"Fish"], 
               " landings between 2018-2020", sep="")
      }
      # SM added in Nov 2021
      else if(input$speciesfilter=="Anglerfish"){      
        paste0("The distribution of Irish ", 
               ICEStable[ICEStable$Fish == input$speciesfilter & ICEStable$SpeciesByDiv == input$speciesbydiv,"Fish"], 
               " landings between 2015 - 2019 (black and white Anglerfish combined)", sep="")
      }
      else{
        paste0("The distribution of ", 
               ICEStable[ICEStable$Fish == input$speciesfilter & ICEStable$SpeciesByDiv == input$speciesbydiv,"Fish"], 
               " landings by Irish Vessels between 2015 - 2019 ", sep="")
      }
    }
    ## 2020 uses a different year range (SM Nov2020)
    else if(input$year==2020){
      
      if(input$speciesfilter=="Nephrops"){      
        paste0("The distribution of <em>", 
               ICEStable[ICEStable$Fish == input$speciesfilter & ICEStable$SpeciesByDiv == input$speciesbydiv,"Fish"], 
               "</em> landings by Irish Vessels between 2015 - 2018", sep="")
      } 
      else if(input$speciesfilter=="Mackerel" | input$speciesfilter=="Horse Mackerel"){      
        paste0("The distribution of ", 
               ICEStable[ICEStable$Fish == input$speciesfilter & ICEStable$SpeciesByDiv == input$speciesbydiv,"Fish"], 
               " landings by Irish Vessels during 2019", sep="")
      }
      else{
        paste0("The distribution of ", 
               ICEStable[ICEStable$Fish == input$speciesfilter & ICEStable$SpeciesByDiv == input$speciesbydiv,"Fish"], 
               " landings by Irish Vessels between 2015 - 2018 ", sep="")
      }
    }
    
    
    ## 2019 uses a different text pattern
    else if(input$year==2019){
      
      if(input$speciesfilter=="Nephrops"){      
        paste0("The distribution of <em>", 
               ICEStable[ICEStable$Fish == input$speciesfilter & ICEStable$SpeciesByDiv == input$speciesbydiv,"Fish"], 
               "</em> landings by Irish Vessels between 2014 - 2018", sep="")
      } 
      else if(input$speciesfilter=="Mackerel" | input$speciesfilter=="Horse Mackerel"){      
        paste0("The distribution of ", 
               ICEStable[ICEStable$Fish == input$speciesfilter & ICEStable$SpeciesByDiv == input$speciesbydiv,"Fish"], 
               " landings by Irish Vessels during 2018", sep="")
      }
      else{
        paste0("The distribution of ", 
               ICEStable[ICEStable$Fish == input$speciesfilter & ICEStable$SpeciesByDiv == input$speciesbydiv,"Fish"], 
               " landings by Irish Vessels between 2014 - 2018 ", sep="")
      }
    }
    
    ## 2018 and earlier
    else {
      if(input$speciesfilter=="Nephrops"){      
        paste0("The distribution of <em>", 
               ICEStable[ICEStable$Fish == input$speciesfilter & ICEStable$SpeciesByDiv == input$speciesbydiv,"Fish"], 
               "</em> landings by Irish Vessels during ", (as.numeric(as.character(input$year))-1), sep="")
      }else{
        paste0("The distribution of ", 
               ICEStable[ICEStable$Fish == input$speciesfilter & ICEStable$SpeciesByDiv == input$speciesbydiv,"Fish"], 
               " landings by Irish Vessels during ", (as.numeric(as.character(input$year))-1), sep="")
      }
    }
  })
  
  
  #Landings text
  #~~~~~~~~~~~~~
  output$LandingsText <- renderText({
    # djc 10/11/21 - Filtering was previously only done by area description! - Fixed to filter by species and area
    #paste0(ICEStable[which(ICEStable[,"SpeciesByDiv"] %in% input$speciesbydiv),  
    #                 paste0("TAC", as.numeric(as.character(input$year)), sep="")])
    paste0(ICEStable[ICEStable$Fish == input$speciesfilter & ICEStable$SpeciesByDiv == input$speciesbydiv,  
                     paste0("TAC", as.numeric(as.character(input$year)), sep="")])
  })
  output$DivisionsText <- renderText({
    # djc 10/11/21 - Filtering was previously only done by area description! - Fixed to filter by species and area
    
    if(input$speciesfilter=="Nephrops"){      
      paste0("The distribution of <em>", 
             ICEStable[ICEStable$Fish == input$speciesfilter & ICEStable$SpeciesByDiv == input$speciesbydiv,"Fish"], 
             "</em> landings by Irish vessels by division for the last three years.", sep="")
    }else{
      paste0("The distribution of ", 
             ICEStable[ICEStable$Fish == input$speciesfilter & ICEStable$SpeciesByDiv == input$speciesbydiv,"Fish"], 
             " landings by Irish vessels by division for the last three years.", sep="")
    }
  })
  
  output$ValueText <- renderText({
    # djc 10/11/21 - Filtering was previously only done by area description! - Fixed to filter by species and area
    
    ## 2022 uses landings instead of values (SM Oct2022)
    ##~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
    if(input$year==2022 && input$speciesfilter=="Nephrops"){      
      paste0("A historical view of <em>", 
             ICEStable[ICEStable$Fish == input$speciesfilter & ICEStable$SpeciesByDiv == input$speciesbydiv,"Fish"], 
             "</em> landings", sep="")
      
    }else if(input$speciesfilter=="Nephrops"){      
      paste0("A historical view of the value of <em>", 
             ICEStable[ICEStable$Fish == input$speciesfilter & ICEStable$SpeciesByDiv == input$speciesbydiv,"Fish"], 
             "</em> landings", sep="")
      
    }else if(input$year==2022){
      paste0("A historical view of ", 
             ICEStable[ICEStable$Fish == input$speciesfilter & ICEStable$SpeciesByDiv == input$speciesbydiv,"Fish"], 
             " landings.", sep="")
    }else{paste0("A historical view of the value of ", 
                 ICEStable[ICEStable$Fish == input$speciesfilter & ICEStable$SpeciesByDiv == input$speciesbydiv,"Fish"], 
                 " landings.", sep="")
    }
  })
  
  #Landings by division
  #~~~~~~~~~~~~~~~~~~~~
  output$display.LandingsbyDiv <- renderImage({
    # djc 10/11/21 - Filtering was previously only done by area description! - Fixed to filter by species and area
    #image_file <- paste0("www/LandingsByDivision/", input$year, "/",
    #                    ICEStable[which(ICEStable[,"SpeciesByDiv"] %in% input$speciesbydiv),"Fish"],".png")
    
    
    image_file <- paste0("www/LandingsByDivision/", input$year, "/",
                         ICEStable[ICEStable$Fish == input$speciesfilter & ICEStable$SpeciesByDiv == input$speciesbydiv,"Fish"],".png")
    return(list(src = image_file, filetype = "image/png", height = 300))
  }, deleteFile = FALSE)
  
  #Value of TAC
  output$display.TACValue <- renderImage({
    # djc 10/11/21 - Filtering was previously only done by area description! - Fixed to filter by species and area
    #image_file <- paste0("www/ValueTimeSeries/", input$year, "/", 
    #                    ICEStable[which(ICEStable[,"SpeciesByDiv"] %in% input$speciesbydiv),"Fish"],".png")
    image_file <- paste0("www/ValueTimeSeries/", input$year, "/", 
                         ICEStable[ICEStable$Fish == input$speciesfilter & ICEStable$SpeciesByDiv == input$speciesbydiv,"Fish"],".png")
    return(list(src = image_file, filetype = "image/png", height = 300))
  }, deleteFile = FALSE)
  
  
  #####################
  # Adding MI Summary #  
  #####################
  #SM Oct 2022: In 2022 the layout of the Summary page changed, to allow for a pdf page to be called when a link is clicked (see lines ~1810)
  output$display.SummaryPage <- renderImage({
    #Call the thumbnail png of the Summary page here. (Lines ~1810 calls the pdf)
    req(input$year==2022)
    image_file <- paste0("www/SummaryPage/", input$year, "/",
                         ICEStable[ICEStable$Fish == input$speciesfilter & ICEStable$SpeciesByDiv == input$speciesbydiv,"New"],".png") #, sep=""
    #print(image_file)
    return(list(src = image_file, filetype = "image/png", height = 400))
    
  }, deleteFile = FALSE)
  
  
  # output$display.SummaryPDF <- renderImage({
  #   #Call the pdf of the Summary page here. (Lines ~1810 calls the pdf)
  #   req(input$year == 2022)
  #   image_file <- paste0("www/SummaryPDF/", input$year, "/",
  #                        ICEStable[ICEStable$Fish == input$speciesfilter & ICEStable$SpeciesByDiv == input$speciesbydiv,"New"],".pdf") #, sep=""
  #   #print(image_file)
  #   return(list(src = image_file, filetype = "image/pdf", height = 400))
  #   
  # }, deleteFile = FALSE)
  
  
  output$display.assarea <- renderImage({
    req(input$year < 2022)
    image_file <- paste0("www/maps/",ICEStable[ICEStable$Fish == input$speciesfilter & ICEStable$SpeciesByDiv == input$speciesbydiv,"Old"],
                         ".png", sep="")
    return(list(src = image_file, filetype = "image/png", height = 250))
  }, deleteFile = FALSE)
  
  
  output$display.landingsbygear <- renderImage({
    # djc 10/11/21 - Filtering was previously only done by area description! - Fixed to filter by species and area
    
    if(input$year==2016){
      image_file <- paste0("www/Landingsbygear/", input$year, "/", 
                           ICEStable[ICEStable$Fish == input$speciesfilter & ICEStable$SpeciesByDiv == input$speciesbydiv,"Old"],".png")
      return(list(src = image_file, filetype = "image/png", height = 250))
    }else{
      image_file <- paste0("www/Landingsbygear/", input$year, "/", 
                           ICEStable[ICEStable$Fish == input$speciesfilter & ICEStable$SpeciesByDiv == input$speciesbydiv,"New"],".png")
      return(list(src = image_file, filetype = "image/png", height = 250))}
  }, deleteFile = FALSE)
  
  
  
  #Pie Chart
  #~~~~~~~~~
  output$TACtext <-renderText({
    # djc 10/11/21 - Filtering was previously only done by area description! - Fixed to filter by species and area
    
    #SM Seabass and Sprat have no Quota pie-chart
    #SM Nov 2021: Nephrops has specific Quota titles, so images were snipped from the pdf. The automatic title was therefore hidden.
    if(input$speciesfilter=="Seabass" | input$speciesfilter=="Sprat" | input$speciesfilter=="Nephrops"){
      paste0("")
      
    }else{
      paste0(input$year, " Quota Allocations", sep="")}
  })
  
  
  output$display.TAC <- renderImage({
    image_file <- paste0("www/Quota/",input$year,"/",ICEStable[ICEStable$Fish == input$speciesfilter & ICEStable$SpeciesByDiv == input$speciesbydiv,"New"],
                         ".png", sep="")
    return(list(src = image_file, filetype = "image/png", height = 250))
  }, deleteFile = FALSE)
  
  
  
  #Catch/Discards plot
  #~~~~~~~~~~~~~~~~~~~
  output$display.CatchDiscards <- renderImage({
    # djc 10/11/21 - Filtering was previously only done by area description! - Fixed to filter by species and area
    
    #image_file <- paste0("www/CatchDiscards/", input$year, "/", 
    #                     ICEStable[which(ICEStable[,"SpeciesByDiv"] %in% input$speciesbydiv),"New"],".png", sep="")
    image_file <- paste0("www/CatchDiscards/", input$year, "/", 
                         ICEStable[ICEStable$Fish == input$speciesfilter & ICEStable$SpeciesByDiv == input$speciesbydiv,"New"],".png", sep="")
    return(list(src = image_file, filetype = "image/png", height = 100))
  }, deleteFile = FALSE)
  
  
  
  #Key Points table
  #~~~~~~~~~~~~~~~~
  KeyPoints=read.csv("KeyPoints.csv", header=TRUE)
  output$KPtable = renderTable({
    # djc 10/11/21 - Filtering was previously only done by area description! - Fixed to filter by species and area
    
    if(input$year==2015){
      paste0("There was no Key Points table in the 2015 Stock Book")
    }else{
      KPFilter=filter(KeyPoints, Year==input$year & 
                        Group == "KeyPoints" &
                        FishStock %in% paste0(ICEStable[ICEStable$Fish == input$speciesfilter & ICEStable$SpeciesByDiv == input$speciesbydiv,"New"]))
      KPFilter[,4:5]}
  }, colnames = FALSE, bordered = TRUE) 
  
  output$KPtableFootnote = renderText({
    # djc 10/11/21 - Filtering was previously only done by area description! - Fixed to filter by species and area
    
    KPFilter=filter(KeyPoints, Year==input$year & 
                      Group == "Footnotes" &
                      FishStock %in% paste0(ICEStable[ICEStable$Fish == input$speciesfilter & ICEStable$SpeciesByDiv == input$speciesbydiv,"New"]))
    paste0(KPFilter[,4])
  }) 
  

    
  #Links
  #~~~~~  
  output$Stockbooklink <-renderUI({
    if(input$year==2022){
       #a(href=paste0("The Stock Book 2022.pdf"), #CONNECT TO A PDF UNTIL THE 2022 LINK IS READY
       #  "The Stock Book 2022",target="_blank")
      #The OAR link became live on 23/11/2022 
       a(href=paste0("http://hdl.handle.net/10793/1805"), 
         "The Stock Book 2022",target="_blank")
    }else if(input$year==2021){
      a(href=paste0("http://hdl.handle.net/10793/1726"),
        "The Stock Book 2021",target="_blank")
    }else if(input$year==2020){
      a(href=paste0("http://hdl.handle.net/10793/1660"),
        "The Stock Book 2020",target="_blank")
    }else if(input$year==2019){
      a(href=paste0("https://oar.marine.ie/handle/10793/1433"),
        "The Stock Book 2019",target="_blank")
    }else if(input$year==2018){
      a(href=paste0("https://oar.marine.ie/bitstream/handle/10793/1383/The%20Stock%20Book%202018.pdf"),
        "The Stock Book 2018",target="_blank")
    }else if(input$year==2017){
      a(href=paste0("http://oar.marine.ie/bitstream/10793/1337/1/The%20Stock%20Book%202017.pdf"),
        "The Stock Book 2017",target="_blank")
    }else if(input$year==2016){
      a(href=paste0("http://oar.marine.ie/bitstream/10793/1178/1/The%20Stock%20Book%202016.pdf"),
        "The Stock Book 2016",target="_blank")
    }else if(input$year==2015){
      a(href=paste0("http://oar.marine.ie/bitstream/10793/1121/1/Stock%20Book%202015.pdf"),
        "The Stock Book 2015",target="_blank")
    }else{
      paste0("No Link Available")
    }
  })
  
  output$ICESlink <-renderUI({
    # djc 10/11/21 - Filtering was previously only done by area description! - Fixed to filter by species and area
    
    if(ICEStable[ICEStable$Fish == input$speciesfilter & ICEStable$SpeciesByDiv == input$speciesbydiv,
                 paste0("ICESCode",input$year, sep="")]=="Not Available"){
      paste0("No Link Available")
    }else{
      a(href=paste0(ICEStable[ICEStable$Fish == input$speciesfilter & ICEStable$SpeciesByDiv == input$speciesbydiv,
                              paste0("ICESCode",input$year, sep="")]),
        "ICES Advice ",target="_blank")}
  })
  
  output$ICESlinkpdf <-renderUI({
    # djc 10/11/21 - Filtering was previously only done by area description! - Fixed to filter by species and area
    
    if(ICEStable[ICEStable$Fish == input$speciesfilter & ICEStable$SpeciesByDiv == input$speciesbydiv,
                 paste0("ICESLink",input$year, sep="")]=="Not Available"){
      paste0("No Link Available")
    }else{
      a(href=paste0(ICEStable[ICEStable$Fish == input$speciesfilter & ICEStable$SpeciesByDiv == input$speciesbydiv,
                              paste0("ICESLink",input$year, sep="")]),
        "ICES Advisory Sheet ",target="_blank")}
  })
  
  #Management Advice/Additional Information
  #~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
  output$ManagementAdviceHeader = renderText({
    paste("Management Advice in ", input$year, sep="")
  }) 
  ManagementAdvice=read.csv("ManagementAdvice.csv", header=TRUE)#, encoding = 'ASCII'
  output$ManagementAdvice = renderText({
    # djc 10/11/21 - Filtering was previously only done by area description! - Fixed to filter by species and area
    
    MAFilter=filter(ManagementAdvice, Year==input$year)
    #MAFilter2=filter(MAFilter, FishStock %in% paste0(ICEStable[which(ICEStable[,"SpeciesByDiv"] %in% 
    #                                                                   input$speciesbydiv),"New"]))
    MAFilter2=filter(MAFilter, FishStock %in% paste0(ICEStable[ICEStable$Fish == input$speciesfilter & ICEStable$SpeciesByDiv == input$speciesbydiv,"New"]))
    paste(MAFilter2[,3], sep="")
  }) 
  output$AddInfoHeader = renderText({
    # djc 10/11/21 - Filtering was previously only done by area description! - Fixed to filter by species and area
    if(input$year<2018){
      ("Additional Information")
    }else{
      ("Key Stock Considerations")
    }
  }) 
  output$Addinfo = renderText({
    MAFilter=filter(ManagementAdvice, Year==input$year)
    #MAFilter2=filter(MAFilter, FishStock %in% paste0(ICEStable[which(ICEStable[,"SpeciesByDiv"] %in% 
    #                                                                   input$speciesbydiv),"New"]))
    MAFilter2=filter(MAFilter, FishStock %in% paste0(ICEStable[ICEStable$Fish == input$speciesfilter & ICEStable$SpeciesByDiv == input$speciesbydiv,"New"]))
    paste(MAFilter2[,4], sep="")
  }) 
  
  #Nephrops
  #~~~~~~~~
  output$nephrops <- renderImage({
    image_file <- paste0("www/Nephrops/advicechangeplot",input$year,".png", sep="")
    return(list(src = image_file, filetype = "image/png", height = 500))
  }, deleteFile = FALSE)
  
  ######################
  # Adding ICES output 
  ######################
  #ICCATlist=c("North Atlantic", "East Atlantic and Mediterranean Sea")
  #output$advicelabel <-renderText ({
  #  if(input$speciesbydiv %in% ICCATlist){
  #    paste0("ICCAT Advice")
  #  }else{
  #    paste0("ICES Advice")
  #  }
  #})
  
  output$ICESAdviceTextMI <- renderText({
    paste0("Advice for ", as.numeric(as.character(input$year))+1)
  })
  output$ICESAdviceTextMI2 <- renderText({
    # djc 10/11/21 - Filtering was previously only done by area description! - Fixed to filter by species and area
    
    if(input$year<2018){
      paste0(ICEStable[ICEStable$Fish == input$speciesfilter & ICEStable$SpeciesByDiv == input$speciesbydiv,  
                       paste0("ICESAdvice", as.numeric(as.character(input$year)), sep="")])
    }else{
      paste0(ICEStable[ICEStable$Fish == input$speciesfilter & ICEStable$SpeciesByDiv == input$speciesbydiv,  
                       paste0("FEASAdvice", as.numeric(as.character(input$year)), sep="")])
    }
  })
  output$ICESAdviceText <- renderText({
    # djc 10/11/21 - Filtering was previously only done by area description! - Fixed to filter by species and area
    paste0(ICEStable[ICEStable$Fish == input$speciesfilter & ICEStable$SpeciesByDiv == input$speciesbydiv,  
                     paste0("ICESAdvice", as.numeric(as.character(input$year)), sep="")])
  })
  output$ices_ref <- renderText({
    paste0("Reference: ICES Stock Database, Extraction date: November of STOCK(S)/ASSESSMENT ", 
           input$year,". ICES, Copenhagen" )
  })
  
  output$ICESCategory <- renderText({
    # djc 10/11/21 - Filtering was previously only done by area description! - Fixed to filter by species and area
    paste0(ICEStable[ICEStable$Fish == input$speciesfilter & ICEStable$SpeciesByDiv == input$speciesbydiv,  
                     paste0("Category", as.numeric(as.character(input$year)), sep="")])
  })
  output$ICESFrequency <- renderText({
    # djc 10/11/21 - Filtering was previously only done by area description! - Fixed to filter by species and area
    paste0(ICEStable[ICEStable$Fish == input$speciesfilter & ICEStable$SpeciesByDiv == input$speciesbydiv,  
                     "Frequency"])
  })
  output$ManagementPlan <- renderText({
    # djc 10/11/21 - Filtering was previously only done by area description! - Fixed to filter by species and area
    paste0(ICEStable[ICEStable$Fish == input$speciesfilter & ICEStable$SpeciesByDiv == input$speciesbydiv,  
                     "ManagementPlan"])
  })
  output$ICESAdviceBasis <- renderText({
    # djc 10/11/21 - Filtering was previously only done by area description! - Fixed to filter by species and area
    paste0(ICEStable[ICEStable$Fish == input$speciesfilter & ICEStable$SpeciesByDiv == input$speciesbydiv,  
                     "ICESAdviceBasis"])
  })
  output$Text.Stock <- renderText({
    # djc 10/11/21 - Filtering was previously only done by area description! - Fixed to filter by species and area
    paste0(ICEStable[ICEStable$Fish == input$speciesfilter & ICEStable$SpeciesByDiv == input$speciesbydiv,"SpeciesByDivOrig"])
  })
  
  output$ICESinfo <- renderUI(
    actionButton("click", "Additional ICES Information")
  )
  
  observeEvent(input$click, {
    showModal(modalDialog(
      title = textOutput("Text.Stock"),
      h4("ICES Stock Data Category:"),
      textOutput("ICESCategory"),
      HTML("<hr>"),
      h4("ICES Advice Basis:"),
      textOutput("ICESAdviceBasis"),
      #SM updated on Nov 22nd 2021 with latest document found. 
      #a(href=paste0("https://www.ices.dk/sites/pub/Publication%20Reports/Advice/2021/2021/Advice_on_fishing_opportunities.pdf"),
      #  "Link to description of ICES Advice Basis",target="_blank"),
      #the link is protected so a doi is used but opens on a higher level page
      a(href=paste0("https://doi.org/10.17895/ices.advice.19928060"),
        "Link to description of ICES Advice Basis",target="_blank"),
      #SM updated on Oct 28th 2021 with latest document found. (None for 2020 or 2021)
      #a(href=paste0("http://www.ices.dk/sites/pub/Publication%20Reports/Advice/2019/2019/Introduction_to_advice_2019.pdf"),
      # "Link to description of ICES Advice Basis",target="_blank"),
      #a(href=paste0("http://www.ices.dk/sites/pub/Publication%20Reports/Advice/2016/2016/Introduction_to_advice_2016.pdf"),
      #  "Link to description of ICES Advice Basis",target="_blank"),
      HTML("<hr>"),
      h4("ICES Advice Frequency:"),
      textOutput("ICESFrequency"),
      HTML("<hr>"),
      h4("Management Plan:"),
      textOutput("ManagementPlan"),
      easyClose = TRUE))####fluidRow(column(width=12)))
    
  })
  
  #Stock Development Over Time
  #~~~~~~~~~~~~~~~~~~~~~~~~~~~
  output$display.Stock_Dev <- renderImage({
    # djc 10/11/21 - Filtering was previously only done by area description! - Fixed to filter by species and area
    if(input$year<2017){
      image_file <- paste0("www/ICES/SAG/", input$year, "/", 
                           ICEStable[ICEStable$Fish == input$speciesfilter & ICEStable$SpeciesByDiv == input$speciesbydiv,"Old"],".png")
    }else{
      image_file <- paste0("www/ICES/SAG/", input$year, "/", 
                           ICEStable[ICEStable$Fish == input$speciesfilter & ICEStable$SpeciesByDiv == input$speciesbydiv,"New"],".png")}
    return(list(src = image_file, filetype = "image/png", height = 400))
  }, deleteFile = FALSE)
  
  output$Text.Stock_Dev <- renderText({
    # djc 10/11/21 - Filtering was previously only done by area description! - Fixed to filter by species and area
    
    paste0(ICEStable[ICEStable$Fish == input$speciesfilter & ICEStable$SpeciesByDiv == input$speciesbydiv,
                     paste0("StockDev",input$year, sep="")])
  })
  
  #Stock and Exploitation status
  #~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
  output$display.ICESStatus <- renderImage({
    # djc 10/11/21 - Filtering was previously only done by area description! - Fixed to filter by species and area
    
    if(input$year<2017){
      image_file <- paste0("www/ICES/Status/", input$year, "/", 
                           ICEStable[ICEStable$Fish == input$speciesfilter & ICEStable$SpeciesByDiv == input$speciesbydiv,"Old"],".png")}
    else{
      image_file <- paste0("www/ICES/Status/", input$year, "/",
                           ICEStable[ICEStable$Fish == input$speciesfilter & ICEStable$SpeciesByDiv == input$speciesbydiv,"New"],".png")
    }
    return(list(src = image_file, filetype = "image/png", width = 750))
  }, deleteFile = FALSE)
  
  #SM Nov 2021: Nephrops cannot be italicised 
  output$Text.ICESStatus <- renderText({
    paste0(input$speciesfilter, " in ", input$speciesbydiv,
           ". State of Stock and fishery relative to reference points.")
  })
  
  
  
  #Quality of Assessment
  #~~~~~~~~~~~~~~~~~~~~~
  output$Text.Quality <- renderText({
    paste0(input$speciesfilter, " in ", input$speciesbydiv,
           ". Historical assessment results.")
  })
  
  output$display.SSB_Hist <- renderImage({
    # djc 10/11/21 - Filtering was previously only done by area description! - Fixed to filter by species and area
    
    if(input$year<2017){
      image_file <- paste0("www/ICES/SSB/", input$year, "/", 
                           ICEStable[ICEStable$Fish == input$speciesfilter & ICEStable$SpeciesByDiv == input$speciesbydiv,"Old"],".png")}
    else{
      image_file <- paste0("www/ICES/SSB/", input$year, "/", 
                           ICEStable[ICEStable$Fish == input$speciesfilter & ICEStable$SpeciesByDiv == input$speciesbydiv,"New"],".png")}
    return(list(src = image_file, filetype = "image/png", height = 250))
  }, deleteFile = FALSE)
  
  output$display.Fish_Mort <- renderImage({
    # djc 10/11/21 - Filtering was previously only done by area description! - Fixed to filter by species and area
    
    if(input$year<2017){
      image_file <- paste0("www/ICES/Fishmort/", input$year, "/", 
                           ICEStable[ICEStable$Fish == input$speciesfilter & ICEStable$SpeciesByDiv == input$speciesbydiv,"Old"],".png")
    }else{
      image_file <- paste0("www/ICES/Fishmort/", input$year, "/", 
                           ICEStable[ICEStable$Fish == input$speciesfilter & ICEStable$SpeciesByDiv == input$speciesbydiv,"New"],
                           ".png")}
    return(list(src = image_file, filetype = "image/png", height = 250))
  }, deleteFile = FALSE)
  
  output$display.Recruit_Hist <- renderImage({
    # djc 10/11/21 - Filtering was previously only done by area description! - Fixed to filter by species and area
    
    if(input$year<2017){
      image_file <- paste0("www/ICES/RecruitHist/", input$year, "/", 
                           ICEStable[ICEStable$Fish == input$speciesfilter & ICEStable$SpeciesByDiv == input$speciesbydiv,"Old"],".png")
    }else{
      image_file <- paste0("www/ICES/RecruitHist/", input$year, "/", 
                           ICEStable[ICEStable$Fish == input$speciesfilter & ICEStable$SpeciesByDiv == input$speciesbydiv,"New"],".png")}
    return(list(src = image_file, filetype = "image/png", height = 250))
  }, deleteFile = FALSE)
  
  ###############
  # Forecasting #
  ###############
  #setwd("H:/Stockbook/shiny/WIP")
  Forecasting=read.csv('ForecastingData.csv', header=TRUE, stringsAsFactors=FALSE)
  Forecasting$value <- as.numeric(as.character(Forecasting$value))
  # Djc Basis was brought in as a factor
  Forecasting$Basis <- as.character(Forecasting$Basis)
  # djc Forecasting$value <- as.numeric(Forecasting$value)
  Forecasting$Year <- as.numeric(Forecasting$Year)
  Forecasting = Forecasting[,2:6]
  output$ForecastOptionsSelector <- renderUI({
    # djc 9/11/21 Filtering was previously only done by area description! - Fixed to filter by species and area
    #sbl <- filter(Forecasting, 
    #              FishStock==paste0(ICEStable[which(ICEStable[,"SpeciesByDiv"] %in% input$speciesbydiv),"New"]))
    stockToFilter <- ICEStable[ICEStable$Fish == input$speciesfilter & ICEStable$SpeciesByDiv == input$speciesbydiv,"New" ]
    if (length(stockToFilter) == 0){
      # djc 9/11/21 Leave the function if we can't find a match - stops error messages
      # when you move between species with different valid areas
      return(NULL)
    }
    sbl <- filter(Forecasting, FishStock==stockToFilter)
    #print(input$speciesbydiv)
    #print(paste0(ICEStable[which(ICEStable[,"SpeciesByDiv"] %in% input$speciesbydiv),"New"]))
    #print(unique(Forecasting$FishStock))
    ## djc
    #sbl <- filter(Forecasting, FishStock=='cod.27.6a')
    Options <- unique(sbl$Basis)
    Options <- Options[Options!= "Assessment"]
    Options <- Options[Options!= "ICES Advice"]
    Options <- Options[Options!= "TAC"]
    # djc 23/11/21 Sort the options alphabetically - should match forecast table then
    Options <- sort(Options)
    checkboxGroupInput("forecastoptionselection", h3("Select Forecast Options"), as.list(Options) ,
                       inline = TRUE) #, selected = "F = F2017"
  })
  
  #sbl <-reactive({
  #  filter(Forecasting, FishStock==paste0(ICEStable[which(ICEStable[,"SpeciesByDiv"] %in% input$speciesbydiv),"New"]))
  #})
  
  # djc 23/11/21
  #mypalette<-primary.colors(length(factor(Forecasting$Basis)))
  mypalette<-primary.colors(length(unique(Forecasting$Basis)))
  #print(mypalette)
  
  
  #output$plotforecasting <- renderPlotly({
  output$plotSSB <- renderPlotly({
    # djc 9/11/21 Filtering was previously only done by area description! - Fixed to filter by species and area
    # sbl <- filter(Forecasting, FishStock==paste0(ICEStable[which(ICEStable[,"SpeciesByDiv"] %in% input$speciesbydiv),"New"]))
    stockToFilter <- ICEStable[ICEStable$Fish == input$speciesfilter & ICEStable$SpeciesByDiv == input$speciesbydiv,"New" ]
    if (length(stockToFilter) == 0){
      # djc 9/11/21 Leave the function if we can't find a match - stops error messages
      # when you move between species with different valid areas
      return(NULL)
    }
    sbl <- filter(Forecasting, FishStock==stockToFilter)
    ## djc
    #sbl <- filter(Forecasting, FishStock=='cod.27.6a')
    ssb <- filter(sbl, var=="SSB")
    Blim <- filter(sbl, var=="Blim")[1,5]
    Bpa <- filter(sbl, var=="Bpa")[1,5]
    ssb1 <- filter(ssb, Basis %in% c("Assessment", "ICES Advice"))
    #print(ssb1)
    #ssb2018= data.frame(FishStock=ssb1[1,1], Year=2018, Basis="Assessment", 
    #                    var="SSB", value=ssb1[ssb1$Year==2018 & ssb1$Basis=="ICES Advice",][,5])
    ssb2 <- filter(ssb, Basis %in% c(input$forecastoptionselection))
    ## djc
    #ssb2 <- filter(ssb, Basis %in% c('F=FMSY'))
    ssb3 <- rbind(ssb1, ssb2)#, ssb2018
    
    if (length(ssb3[ssb3$Year==2022 & ssb3$Basis=="Assessment",][,5])>0){
      ssb3[ssb3$Year==2022 & ssb3$Basis=="Assessment",][,5] <- head(ssb3[ssb3$Year==2022 & ssb3$Basis=="ICES Advice",][,5],1)
    }
    # SM Sep2022: Changed 2021 to 2022
    # SM Oct2021: Changed 2020 to 2021
    # SM Nov2020: Changed 2019 to 2020
    # SM this is the 2019 line 
    #ssb3[ssb3$Year==2019 & ssb3$Basis=="Assessment",][,5] <- head(ssb3[ssb3$Year==2019 & ssb3$Basis=="ICES Advice",][,5],1)
    # DJC ssb3[ssb3$Year==2019 & ssb3$Basis=="Assessment",][,5] <- ssb3[ssb3$Year==2019 & ssb3$Basis=="ICES Advice",][,5]
    # DJC ssb3[ssb3$Year==2018 & ssb3$Basis=="Assessment",][,5] <- ssb3[ssb3$Year==2018 & ssb3$Basis=="ICES Advice",][,5]
    
    # djc 23/11/21 Use a defined ordering for the plots to stop the lines changing color
    myCustomOrder <- unlist(lapply(sbl$Basis, FUN = function(x) switch(x, "Assessment" = 1, "ICES Advice" = 2, "TAC" = 3, 4)))
    myPlotFactorOrder <- unique(sbl[order(myCustomOrder,sbl$Basis),"Basis"])
    ssb3$Basis <- factor(ssb3$Basis, levels = myPlotFactorOrder)
    
    p1 <- plot_ly(ssb3, x = ~Year, y = ~value, type = 'scatter', mode = 'lines', showlegend = F, #linetype = ~Basis,
                  color = ~Basis, colors=mypalette, height=375) %>% 
      layout(hovermode="FALSE", #showlegend = FALSE,
             xaxis = list(title = 'Year', range= c(min(ssb3$Year), max(ssb3$Year)+1)),
             yaxis = list (title = 'SSB', range = c(0, max(ssb3$value, na.rm = T)*1.05)),
             shapes = list(
               list(type = "rect", fillcolor = "green", opacity = 0.2, 
                    line = list(color = "green", opacity=0.2), x0 = min(sbl$Year), x1 = max(sbl$Year)+1, 
                    xref = "Year", y0 = Bpa, y1 = max(ssb$value, na.rm=TRUE)*1.05, yref = "value"),
               list(type = "rect", fillcolor = "orange", opacity = 0.2, 
                    line = list(color = "orange", opacity=0.2), x0 = min(sbl$Year), x1 = max(sbl$Year)+1, 
                    xref = "Year", y0 = Blim, y1 = Bpa, yref = "value"),
               list(type = "rect", fillcolor = "red", opacity = 0.2, 
                    line = list(color = "red", opacity=0.2), x0 = min(sbl$Year), x1 = max(sbl$Year)+1, 
                    xref = "Year", y0 = 0, y1 = Blim, yref = "value")))
    p1$elementId <- NULL
    p1
  })
  
  output$plotF <- renderPlotly({
    # djc 9/11/21 Filtering was previously only done by area description! - Fixed to filter by species and area
    #sbl <- filter(Forecasting, FishStock==paste0(ICEStable[which(ICEStable[,"SpeciesByDiv"] %in% input$speciesbydiv),"New"]))
    stockToFilter <- ICEStable[ICEStable$Fish == input$speciesfilter & ICEStable$SpeciesByDiv == input$speciesbydiv,"New" ]
    if (length(stockToFilter) == 0){
      # djc 9/11/21 Leave the function if we can't find a match - stops error messages
      # when you move between species with different valid areas
      return(NULL)
    }
    sbl <- filter(Forecasting, FishStock==stockToFilter)
    f <- filter(sbl, var=="F")
    #if(dim(f[f$Year==2018 & f$Basis=="Assessment",])[1]==0){
    #      f2018= data.frame(FishStock=f[1,1], Year=2018, Basis="Assessment", 
    #                    var="F", value=f[f$Year==2018 & f$Basis=="ICES Advice",][,5])
    #      f=rbind(f, f2018)
    #}else{
    
    if (length(f[f$Year==2022 & f$Basis=="Assessment",][,5])>0){
      f[f$Year==2022 & f$Basis=="Assessment",][,5] <- head(f[f$Year==2022 & f$Basis=="ICES Advice",][,5],1)
    }
    # SM Sep2022: Changed 2021 to 2022
    # SM Oct2021: Changed 2020 to 2021
    # SM Nov2020: Changed 2019 to 2020
    # DJC f[f$Year==2019 & f$Basis=="Assessment",][,5] <- f[f$Year==2019 & f$Basis=="ICES Advice",][,5]
    # DJC f[f$Year==2018 & f$Basis=="Assessment",][,5] <- f[f$Year==2018 & f$Basis=="ICES Advice",][,5]
    #}
    Fmsy <- filter(sbl, var=="Fmsy")[1,5]
    Fpa <- filter(sbl, var=="Fpa")[1,5]
    f1 <- filter(f, Basis %in% c("Assessment", "ICES Advice"))
    f2 <- filter(f, Basis %in% c(input$forecastoptionselection))
    f3 <- rbind(f1,f2) 
    
    # djc 23/11/21 Use a defined ordering for the plots to stop the lines changing color
    myCustomOrder <- unlist(lapply(sbl$Basis, FUN = function(x) switch(x, "Assessment" = 1, "ICES Advice" = 2, "TAC" = 3, 4)))
    myPlotFactorOrder <- unique(sbl[order(myCustomOrder,sbl$Basis),"Basis"])
    f3$Basis <- factor(f3$Basis, levels = myPlotFactorOrder)
    
    p2 <- plot_ly(f3, x = ~Year, y = ~value, type = 'scatter', mode = 'lines', showlegend = F,# linetype = ~Basis,
                  color = ~Basis, colors=mypalette, height=375) %>% 
      layout(hovermode="FALSE", #showlegend = TRUE,
             xaxis = list(title = 'Year', range= c(min(f3$Year), max(f3$Year)+1)),
             yaxis = list (title = 'F', range = c(0, max(f3$value, na.rm = T)*1.05)),
             #margin = list(l = 25, r = 25, b = 25, t = 25, pad = 4),
             shapes = list(
               list(type = "rect", fillcolor = "green", opacity = 0.2, 
                    line = list(color = "green", opacity=0.2), x0 = min(sbl$Year), x1 = max(sbl$Year)+1, 
                    xref = "Year", y0 = 0, y1 = Fmsy, yref = "value"),
               list(type = "rect", fillcolor = "orange", opacity = 0.2, 
                    line = list(color = "orange", opacity=0.2), x0 = min(sbl$Year), x1 = max(sbl$Year)+1, 
                    xref = "Year", y0 = Fmsy, y1 = Fpa, yref = "value"),
               list(type = "rect", fillcolor = "red", opacity = 0.2, 
                    line = list(color = "red", opacity=0.2), x0 = min(sbl$Year), x1 = max(sbl$Year)+1, 
                    xref = "Year", y0 = Fpa, y1 =max(f3$value, na.rm=TRUE)*1.05, yref = "value")))
    p2$elementId <- NULL
    p2
  })
  
  output$plotLandings <- renderPlotly({
    # djc 9/11/21 Filtering was previously only done by area description! - Fixed to filter by species and area
    #sbl <- filter(Forecasting, FishStock==paste0(ICEStable[which(ICEStable[,"SpeciesByDiv"] %in% input$speciesbydiv),"New"]))
    stockToFilter <- ICEStable[ICEStable$Fish == input$speciesfilter & ICEStable$SpeciesByDiv == input$speciesbydiv,"New" ]
    if (length(stockToFilter) == 0){
      # djc 9/11/21 Leave the function if we can't find a match - stops error messages
      # when you move between species with different valid areas
      return(NULL)
    }
    sbl <- filter(Forecasting, FishStock==stockToFilter)
    la <- filter(sbl, var %in% c("Landings", "TAC"))
    #print(la)
    yaxislabel="Landings"
    if(dim(la[la$Year==2022 & la$Basis=="Assessment",])[1]==0){
      # SM Sep2022: Changed 2021 to 2022
      # SM Oct2021: Changed 2020 to 2021
      # SM Nov2020: Changed 2019 to 2020
      # DJC if(dim(la[la$Year==2018 & la$Basis=="Assessment",])[1]==0){
      la2022= data.frame(FishStock=la[1,1], Year=2022, Basis="Assessment", 
                         var="Landings", value=la[la$Year==2022 & la$Basis=="ICES Advice",][,5])
      la=rbind(la, la2022)
      # SM Sep2022: Changed 2021 to 2022
      # SM Oct2021: Changed 2020 to 2021
      # SM Nov2020: Changed 2019 to 2020
      # DJC la2018= data.frame(FishStock=la[1,1], Year=2018, Basis="Assessment", 
      # DJC                   var="Landings", value=la[la$Year==2018 & la$Basis=="ICES Advice",][,5])
      # DJC la=rbind(la, la2018)
    }else{
      la[la$Year==2022 & la$Basis=="Assessment" & la$var =="Landings",][,5] <- la[la$Year==2022 & la$Basis=="F = F2022" & la$var =="Landings",][,5]
      # SM Sep2022: Changed 2021 to 2022
      # SM Oct2021: Changed 2020 to 2021
      # SM Nov2020: Changed 2019 to 2020
      # DJC la[la$Year==2018 & la$Basis=="Assessment" & la$var =="Landings",][,5] <- la[la$Year==2018 & la$Basis=="F = F2018" & la$var =="Landings",][,5]
    }
    if(is.na(la[which(la$Basis=="ICES Advice"),"value"])[1]){
      la <- filter(sbl, var %in% c("Catch", "TAC"))
      yaxislabel="Total Catch"
      la[la$Year==2022 & la$Basis=="Assessment" & la$var =="Catch",][,5] <- la[la$Year==2022 & la$Basis=="F = F2022" & la$var =="Catch",][,5]
      # SM Sep2022: Changed 2021 to 2022
      # SM Oct2021: Changed 2020 to 2021
      # SM Nov2020: Changed 2019 to 2020
      # DJC la[la$Year==2018 & la$Basis=="Assessment" & la$var =="Catch",][,5] <- la[la$Year==2018 & la$Basis=="F = F2018" & la$var =="Catch",][,5]
    }
    la1 <- filter(la, Basis %in% c("Assessment", "ICES Advice", "TAC"))
    la2 <- filter(la, Basis %in% c(input$forecastoptionselection))
    la3 <- rbind(la1, la2)
    
    # djc 23/11/21 Use a defined ordering for the plots to stop the lines changing color
    myCustomOrder <- unlist(lapply(sbl$Basis, FUN = function(x) switch(x, "Assessment" = 1, "ICES Advice" = 2, "TAC" = 3, 4)))
    myPlotFactorOrder <- unique(sbl[order(myCustomOrder,sbl$Basis),"Basis"])
    la3$Basis <- factor(la3$Basis, levels = myPlotFactorOrder)
    
    p3 <- plot_ly(la3, x = ~Year, y = ~value, type = 'scatter', mode = 'lines', showlegend = T, #linetype = ~factor(var), 
                  color = ~Basis, colors=mypalette, height=375) %>% 
      layout(hovermode="FALSE", #showlegend = TRUE,
             xaxis = list(title = 'Year', range= c(min(la3$Year), max(la3$Year)+1)),
             yaxis = list (title = yaxislabel, range = c(0, max(la3$value, na.rm = T)*1.05)))
    p3$elementId <- NULL
    p3
    #subplot(p1, p2, p3)
  })
  
  #Forecasting table
  #~~~~~~~~~~~~~~~~~
  # djc 15/11/21 - don't convert strings to factors
  ForecastingTable=read.csv('ForecastOptionsV2.csv', header=TRUE, stringsAsFactors=FALSE)
  
  # djc 23/11/21 Sort to ensure ICES advice is always first for each stock
  ForecastingTable <- ForecastingTable[order(ForecastingTable$FishStock,ForecastingTable$Options,ForecastingTable$Basis),]
  
  # DJC Get rid of the X column - we don't need it
  ForecastingTable$X <- NULL
  ForecastingTable=ForecastingTable[,c(1,3,4,5,6,7,10,11,13)]#3 missing)]#  was col 12 but that is '%TAC change'. Col 13 '% Advice Change' is needed
  ForecastingTable$Catch...2023=formatC(as.numeric(as.character(ForecastingTable$Catch...2023)), format="d", big.mark=",")
  ForecastingTable$Landings...2023=formatC(as.numeric(as.character(ForecastingTable$Landings...2023)), format="d", big.mark=",")
  ForecastingTable$Discards...2023=formatC(as.numeric(as.character(ForecastingTable$Discards...2023)), format="d", big.mark=",")
  #ForecastingTable$SSB...2024=formatC(as.numeric(as.character(ForecastingTable[,"SSB.2024"])), format="d", big.mark=",") #ForecastingTable$SSB...2024
  ForecastingTable$SSB...2024=formatC(as.numeric(as.character(ForecastingTable$SSB...2024)), format="d", big.mark=",")
  colnames(ForecastingTable)=c("FishStock", "Basis", 
                               "Total Catch (2023)", 
                               "Projected Landings (2023)", "Projected Discards (2023)", 
                               "F total (2023)", "SSB (2024)",
                               "% SSB change*", "% Advice change**")
  # SM Sep2022: Updated year dates by +1
  # SM Nov2021: Changed "% TAC change**" to "% Advice change**", also changed 'Wanted Catch' and 'Unwanted Catch' to 'Projected Landings','Projected Discards'
  # SM Oct2021: Updated year dates by +1
  # SM Nov2020: Updated year dates by +1
  # DJC ForecastingTable$Catch...2019=formatC(as.numeric(as.character(ForecastingTable$Catch...2019)), format="d", big.mark=",")
  # DJC ForecastingTable$Landings...2019=formatC(as.numeric(as.character(ForecastingTable$Landings...2019)), format="d", big.mark=",")
  # DJC ForecastingTable$Discards...2019=formatC(as.numeric(as.character(ForecastingTable$Discards...2019)), format="d", big.mark=",")
  # DJC ForecastingTable$SSB...2020=formatC(as.numeric(as.character(ForecastingTable$SSB...2020)), format="d", big.mark=",")
  # DJC colnames(ForecastingTable)=c("FishStock", "Basis", 
  # DJC                             "Catch (2019)", 
  # DJC                             "Landings (2019)", "Discards (2019)", 
  # DJC                             "F (2019)", "SSB (2020)",
  # DJC                             "% SSB change*", "% TAC change**")
  output$Forecasting_Table <- renderTable({
    #print("test1")
    # djc 9/11/21 Filtering was previously only done by area description! - Fixed to filter by species and area
    # ForecastingFilter=filter(ForecastingTable, FishStock==paste0(ICEStable[which(ICEStable[,"SpeciesByDiv"] %in% input$speciesbydiv),"New"]))
    stockToFilter <- ICEStable[ICEStable$Fish == input$speciesfilter & ICEStable$SpeciesByDiv == input$speciesbydiv,"New" ]
    if (length(stockToFilter) == 0){
      # djc 9/11/21 Leave the function if we can't find a match - stops error messages
      # when you move between species with different valid areas
      return(NULL)
    }
    #print("test2")
    ForecastingFilter <- filter(ForecastingTable, FishStock==stockToFilter)
    #print("test3")
    ForecastingFilter[,c(-1)]
  }, options = list(autoWidth = TRUE,
                    columnDefs = list(list(width = '200px', targets = c(1)))), 
  colnames = TRUE, bordered = TRUE)
  
  # djc 15/11/21 - Fixed some issues with spaces
  ForecastingStocks= c("Seabass Divisions 4.b-c 7.a and 7.d-h (central and southern North Sea Irish Sea English Channel Bristol Channel and Celtic Sea)",
                       #"Cod Subareas 1 and 2 (Northeast Arctic)",
                       "Cod Division 6.a (West of Scotland)",
                       "Cod Division 7.a (Irish Sea)",
                       "Cod Divisions 7.e-k (eastern English Channel and southern Celtic Seas)",
                       "Spurdog Sub-areas 1-14",
                       "Haddock Subarea 4 Division 6.a and Subdivision 20 (North Sea West of Scotland Skagerrak)",
                       
                       "Haddock Division7.a (Irish Sea)",
                       "Haddock Divisions 7.b-k (southern Celtic Seas and English Channel)",
                       "Herring Subareas 1 2 5 and Divisions 4.a and 14.a (the Northeast Atlantic and Arctic Ocean)",
                       "Herring Divisions 7.a South of 52 30N 7.g-h and 7.j-k (Irish Sea Celtic Sea and southwest of Ireland)",
                       "Herring Division 7.a North of 52 30N (Irish Sea)",
                       "Hake Subareas 4 6 and 7 and Divisions 3.a 8.a-b and 8.d Northern stock (Greater North Sea Celtic Seas and the northern Bay of Biscay)",
                       "Horse Mackerel Subarea 8 and Divisions 2.a 4.a 5.b 6.a 7.a-c e-k (the Northeast Atlantic)",
                       "Megrim Divisions 4.a and 6.a (northern North Sea West of Scotland)",
                       "Mackerel Subareas 1-8 and 14 and Division 9.a (the Northeast Atlantic and adjacent waters)",
                       "Megrim Divisions 7.b-k 8.a-b and 8.d (west and southwest of Ireland Bay of Biscay)",
                       "Anglerfish Lophius piscatorius in Divisions 7.b-k, 8.a-b, and 8.d (southern Celtic Seas and Bay of Biscay)",
                       "Anglerfish Lophius budegassa Divisions 7.b-k 8.a-b and 8.d (west and southwest of Ireland and Bay of Biscay)",
                       "Plaice Division 7.a (Irish Sea)",
                       "Saithe Subareas 4 6 and Division 3.a (North Sea Rockall and West of Scotland Skagerrak and Kattegat)",  
                       "Sole Division 7.a (Irish Sea)",
                       "Sole Divisions 7.f and 7.g (Bristol Channel and Celtic Sea)", 
                       "Blue Whiting Subareas 1-9 12 and 14 (Northeast Atlantic and adjacent waters)",
                       
                       "Whiting Divisions 7.b -c and 7.e-k (southern Celtic Seas and eastern English Channel)")
  
  #SM: Oct 2021 Updated list of forecast stocks
  # ForecastingStocks= c("Seabass Divisions 4.b-c  7.a  and 7.d-h (central and southern North Sea  Irish Sea  English Channel  Bristol Channel  and Celtic Sea)",
  #                      "Cod Subareas 1 and 2 (Northeast Arctic)",
  #                      "Cod Division 6.a (West of Scotland)",
  #                      "Cod Divisions 7.e-k (eastern English Channel and southern Celtic Seas)",
  #                      "Spurdog Sub-areas 1-14",
  #                      "Haddock Subarea 4  Division 6.a  and Subdivision 20  (North Sea  West of Scotland  Skagerrak)",
  #                      "Haddock Division 6.b (Rockall)",
  #                      "Haddock Division7.a (Irish Sea)",
  #                      "Haddock Divisions 7.b-k (southern Celtic Seas and English Channel)",
  #                      "Herring Subareas 1  2  5 and Divisions 4.a and 14.a (the Northeast Atlantic and Arctic Ocean)",
  #                      "Herring Divisions 7.a South of 52 30N  7.g-h  and 7.j-k (Irish Sea  Celtic Sea  and southwest of Ireland)",
  #                      "Herring Division 7.a North of 52 30N (Irish Sea)",
  #                      "Hake Subareas 4  6  and 7  and Divisions 3.a  8.a-b  and 8.d  Northern stock (Greater North Sea  Celtic Seas  and the northern Bay of Biscay)",
  #                      "Horse Mackerel Subarea 8 and Divisions 2.a  4.a  5.b  6.a  7.a-c e-k (the Northeast Atlantic)",
  #                      "Megrim Divisions 4.a and 6.a (northern North Sea  West of Scotland)",
  #                      "Mackerel Subareas 1-8 and 14 and Division 9.a (the Northeast Atlantic and adjacent waters)",
  #                      "Megrim Divisions 7.b-k  8.a-b  and 8.d (west and southwest of Ireland  Bay of Biscay)",
  #                      "Anglerfish Lophius piscatorius in Divisions 7.b-k, 8.a-b, and 8.d (southern Celtic Seas and Bay of Biscay)",
  #                      "Plaice Division 7.a (Irish Sea)",
  #                      "Saithe Subareas 4  6 and Division 3.a (North Sea  Rockall and West of Scotland  Skagerrak and Kattegat)",  
  #                      "Sole Division 7.a (Irish Sea)",
  #                      "Sole Divisions 7.f and 7.g (Bristol Channel and Celtic Sea)", 
  #                      "Blue Whiting Subareas 1-9  12  and 14 (Northeast Atlantic and adjacent waters)",
  #                      "Whiting Division 7.a (Irish Sea)",
  #                      "Whiting Divisions 7.b -c and 7.e-k (southern Celtic Seas and eastern English Channel)")
  
  #SM Note Nov 29th 2021: Updated the following list. (Extra spaces removed in 2021)
  NephropsStock=c("Division 7.a Functional Unit 14 (Irish Sea East)",
                  "Division 7.a Functional Unit 15 (Irish Sea West)",
                  "Divisions 7.b-c and 7.j-k Functional Unit 16 (west and southwest of Ireland Porcupine Bank)",
                  "Division 7.b Functional Unit 17 (west of Ireland Aran grounds)",
                  "Divisions 7.a 7.g and 7.j Functional Unit 19 (Irish Sea Celtic Sea eastern part of southwest of Ireland)",
                  "Divisions 7.g and 7.h Functional Units 20 and 21 (Celtic Sea)",
                  "Divisions 7.g and 7.f Functional Unit 22 (Celtic Sea Bristol Channel)",
                  "Subarea 7, outside the Functional Units (southern Celtic Seas, southwest of Ireland)")
  # this used to be:  "Subarea 7 - Functional Unit 18 and rectangles outside the functional units (Southern Celtic Seas, Southwest of Ireland)")
  
  output$tabstest <- renderUI({
    panels= if(is.null(input$speciesfilter) || is.na(input$speciesfilter)){
      list(tabPanel("Stockbook Summary"))
      
      #HERRING 6a7bc was split in 2022 into two new stocks
    } else if (input$year==2022 && input$speciesfilter=="Herring" && input$speciesbydiv=="Divisions 6.a and 7.b-c (West of Scotland West of Ireland)"  ){
      # 17/11/22 - no advice for this stock in 2022 because it has been split into 2 new stocks
      list(tabPanel("Stockbook Summary", value="stockbook_summ",
                    
                    HTML("<br><br><p>From 2015 to 2021 this stock was jointly assessed with herring in 6.a North because it was not possible to segregate 
                    the two stocks in commercial catches or surveys. </p><p>The development of a genetic method to split the Malin shelf herring acoustic survey (MSHAS) 
                    into the component stocks means that separate advice is now possible. </p><p> Following a benchmark in 2022 advice is given for herring in 6a South, 
                    7b,c and herring in 6a North.</p> <br><br><p> Information on the two new stocks has been added to the Stock Area list (above) since 2022. 
                    <li> Herring Division 6.a North (West of Scotland) and </li>
                    <li> Herring in Divisions 6.a and 7.b-c (West of Scotland West of Ireland)</li><br> </p>
                    <p> <h4>Use the year filter above to see historic information on the previous stock Herring in Divisions 6.a and 7.b-c 
                    (west of Scotland West of Ireland) from 2015 to 2021</p><br><br>")))
     
      #ARCTIC COD does not appear in the 2022 stockbook, but historic information needs to be retained
    } else if (input$year==2022 && input$speciesfilter=="Cod" && input$speciesbydiv=="Subareas 1 and 2 (Northeast Arctic)"  ){
      # 18/11/22 - no advice for this stock in 2022 
      list(tabPanel("Stockbook Summary", value="stockbook_summ",
                    
                    HTML("<br><br><p>In 2022 there is no ICES advice for Cod in Subareas 1 and 2 (Northeast Arctic) </p> <br><br>
                    
                    <p> <h4>Use the year filter above to see historic information on Arctic Cod from 2015 to 2021</p><br><br>")))
      
      
    }else if(input$speciesfilter=="Spurdog"){
      list(tabPanel("Stockbook Summary", value="stockbook_summ",
                    h3(textOutput("ICESAdviceTextMI")),
                    htmlOutput("ICESAdviceTextMI2"),p(),
                    HTML("<br><br>"),#Adding white space

                    #SM Oct 2022: In 2022 the layout of the Summary page changed, to allow for a pdf page to be called when a link is clicked (see lines ~1015)
                    #Click here and open the summary page in pdf format
                    if(input$year==2022){
                      
                      list(
                        fluidRow (column(width = 3,
                                         HTML("<br><br>"),
                                         HTML("<br><br>"),
                                         a(h4("To see the stock advice page for 2023 click here"),target="_blank",href=paste0("SummaryPage/", input$year, "/",
                                                                                                                              ICEStable[ICEStable$Fish == input$speciesfilter & ICEStable$SpeciesByDiv == input$speciesbydiv,"New"],".pdf")),
                                         HTML("<br><br>")#Adding white space
                        ),
                        column(width = 6, imageOutput("display.SummaryPage")),  #, height = "50%"
                        )#end of two columns
                      )#end of list
                      
                      
                    }else{ 
                      #SM Oct 2022: Years prior to 2022 need the original page set-up
                      list(                    
                        fluidRow(column(width = 3, imageOutput("display.assarea", height = "50%")),
                                 column(width = 6, imageOutput("display.landingsbygear", height = "50%"))),
                        fluidRow(column(width = 6, 
                                        h3("Key Points"),
                                        tags$head(
                                          tags$style("td:nth-child(1) {font-weight: bold;}
                                                     td:nth-child(1) {background: #f2f2f2;}")),
                                        tableOutput("KPtable"),
                                        if(input$year>2017){
                                          list(tags$head(tags$style(HTML("
                                                                          #KPtableFootnote{
                                                                          font-size: 11px;}"))),
                                               htmlOutput("KPtableFootnote"))
                                        }),
                                 column(width = 6, h3(textOutput("TACtext")),
                                        imageOutput("display.TAC", height = "50%"),
                                        if(input$year>2017){
                                          imageOutput("display.CatchDiscards", height = "25%")})),
                        tabsetPanel(id="MgtAdvice", type="pills",
                                    tabPanel(textOutput("ManagementAdviceHeader"), 
                                             htmlOutput("ManagementAdvice"),p()),
                                    tabPanel(textOutput("AddInfoHeader"), #"Additional Information", 
                                             htmlOutput("Addinfo"),p()))
                      )
                    }
                    
                    ,h3("Links"),
                    h5("Link to the Stock Book PDF:"), 
                    uiOutput("Stockbooklink"),
                    h5("Link to the ICES Species Advice page:"), 
                    uiOutput("ICESlink"), 
                    h5("Link to the ICES Advisory Sheet pdf:"), 
                    uiOutput("ICESlinkpdf"), 
                    HTML("<br><br>")
      ))
    }else{
      list(tabPanel("Species Summary", value="species_summ",
                    h3("Biology"), 
                    fluidRow(column(width = 9, htmlOutput("biology_text")), 
                             column(width = 3, imageOutput("display.fish", height = "50%"))),   
                    h3("Landings Distribution"),
                    if(is.null(input$speciesfilter) || is.na(input$speciesfilter)){
                    }else if(input$speciesfilter=="Seabass"){
                      list("Though distributed around the entire coastline of Ireland, sea bass are 
predominately concentrated along the southwest, south and south-east coasts. During colder periods however, 
the majority of adults are believed to move offshore to feed and spawn where research surveys have found 
a relatively clustered distribution in the eastern Celtic Sea.",
                           fluidRow(column(width= 4, 
                                           imageOutput("display.InternationalLandings",height = "100%")),#
                                    #SM Nov 2022: the year range was added in 2022 but will show for all previous years
                                    column(width= 4,
                                           "The distribution of sea bass sampled during
                                                 research surveys in offshore waters shows
                                                 clustering in the eastern Celtic Sea and Bristol
                                                 Channel region between 2003 and 2021.")),
                           h3("Irish Landings and Value of TAC"),
                           htmlOutput("LandingsText"))
                    }else{
                      list(fluidRow(column(width = 6, htmlOutput("text.InternationalLandings"), HTML("<br>"),
                                           imageOutput("display.InternationalLandings",height = "100%")),#
                                    column(width = 6, htmlOutput("text.IrishLandings"), HTML("<br>"),
                                           imageOutput("display.IrishLandings",height = "100%"))),
                           HTML("<br><br>"),#Adding white space
                           h3("Irish Landings and Value of TAC"),
                           htmlOutput("LandingsText"),HTML("<br>"),
                           fluidRow(column(width = 6, htmlOutput("DivisionsText"), 
                                           imageOutput("display.LandingsbyDiv", height="100%")), 
                                    column(width = 6, htmlOutput("ValueText"),
                                           imageOutput("display.TACValue", height="100%"))))},
                    HTML("<br><br>")) , 
           tabPanel("Stockbook Summary", value="stockbook_summ",
                    h3(textOutput("ICESAdviceTextMI")),
                    htmlOutput("ICESAdviceTextMI2"),p(),
                    HTML("<br><br>"),#Adding white space
                    
                    #SM Oct 2022: In 2022 the layout of the Summary page changed, to allow for a pdf page to be called when a link is clicked (see lines ~1015)
                    #Click here and open the summary page in pdf format
                    if(input$year==2022){
                      
                      list(
                        fluidRow (column(width = 3,
                                         HTML("<br><br>"),
                                         HTML("<br><br>"),
                                         a(h4("To see the stock advice page for 2023 click here"),target="_blank",href=paste0("SummaryPage/", input$year, "/",
                                                                                                                              ICEStable[ICEStable$Fish == input$speciesfilter & ICEStable$SpeciesByDiv == input$speciesbydiv,"New"],".pdf")),
                                         HTML("<br><br>")#Adding white space
                        ),
                        column(width = 6, imageOutput("display.SummaryPage")),  #, height = "50%"
                        )#end of two columns
                      )#end of list
                      
                      
                    }else{ 
                      #SM Oct 2022: Years prior to 2022 need the original page set-up
                      list(
                        fluidRow(column(width = 3, imageOutput("display.assarea", height = "50%")),
                                 column(width = 6, imageOutput("display.landingsbygear", height = "50%"))),
                        fluidRow(column(width = 6, 
                                        h3("Key Points"),
                                        tags$head(
                                          tags$style("td:nth-child(1) {font-weight: bold;}
                                                         td:nth-child(1) {background: #f2f2f2;}")),
                                        tableOutput("KPtable"),
                                        if(input$year>2017){
                                          list(tags$head(tags$style(HTML("
                                                                        #KPtableFootnote{
                                                                        font-size: 11px;}"))),
                                               htmlOutput("KPtableFootnote"))
                                        }),
                                 column(width = 6, h3(textOutput("TACtext")),
                                        imageOutput("display.TAC", height = "50%"),
                                        if(input$year>2017){
                                          imageOutput("display.CatchDiscards", height = "25%")})),
                        
                        tabsetPanel(id="MgtAdvice", type="pills",
                                    tabPanel(textOutput("ManagementAdviceHeader"), 
                                             htmlOutput("ManagementAdvice"),p()),
                                    tabPanel(textOutput("AddInfoHeader"), #"Additional Information", 
                                             htmlOutput("Addinfo"),p()))
                      )
                    }
                    
                    ,h3("Links"),
                    h5("Link to the Stock Book PDF:"), 
                    uiOutput("Stockbooklink"),
                    h5("Link to the ICES Species Advice page:"), 
                    uiOutput("ICESlink"), 
                    h5("Link to the ICES Advisory Sheet pdf:"), 
                    uiOutput("ICESlinkpdf"), 
                    HTML("<br><br>")
           ))}
      
    if(is.null(input$speciesfilter) || is.na(input$speciesfilter)){
     }else if(input$year==2022 && input$speciesfilter=="Herring" && input$speciesbydiv=="Divisions 6.a and 7.b-c (West of Scotland West of Ireland)" ){
      # 17/11/22 - no advice for this stock of herring in 2022 because it has been split into 2 new stocks
     #do nothing!
    } else if(input$year==2022 && input$speciesfilter=="Cod" && input$speciesbydiv=="Subareas 1 and 2 (Northeast Arctic)" ){
      # 18/11/22 - no advice for Arctic Cod in 2022
      #do nothing!
    } else if(!(input$speciesfilter %in% c("Albacore Tuna", "Bluefin Tuna", "Swordfish"))){
      panels[[length(panels)+1]]=tabPanel("ICES Advice", value="ices_summ",
                                          h3("ICES Stock Advice"),
                                          textOutput("ICESAdviceText"),
                                          HTML("<br>"),
                                          uiOutput("ICESinfo"),
                                          HTML("<br>"),
                                          tabsetPanel(id="test", type = "pills",
                                                      tabPanel("Stock Development", 
                                                               h3("Stock Development Over Time"),
                                                               htmlOutput("Text.Stock_Dev"),HTML("<br>"),
                                                               imageOutput("display.Stock_Dev")) ,
                                                      tabPanel("Stock Status", 
                                                               h3("Stock & Exploitation Status"), 
                                                               textOutput("Text.ICESStatus"),HTML("<br>"),
                                                               imageOutput("display.ICESStatus")),
                                                      tabPanel("Quality of Assessment", 
                                                               h3("Quality of Assessment"), 
                                                               textOutput("Text.Quality"), HTML("<br>"),
                                                               fluidRow(column(width = 4, imageOutput("display.SSB_Hist")),
                                                                        column(width = 4, imageOutput("display.Fish_Mort")),
                                                                        column(width = 4, imageOutput("display.Recruit_Hist"))))),
                                          "*Images may be missing due to ICES Stock Data Category or Frequency of Advice.Some tables/graphs may be missing because they are not available for all stocks",p(),
                                          textOutput("ices_ref"),
                                          HTML("<br><br>"))}
    
    
    if(is.null(input$speciesfilter) || is.na(input$speciesfilter)){
    }else 
      #print (paste(input$speciesfilter, input$speciesbydiv, sep=" "))
      if(paste(input$speciesfilter, input$speciesbydiv, sep=" ") %in% ForecastingStocks & input$year == 2022){
        # DJC}else if(paste(input$speciesfilter, input$speciesbydiv, sep=" ") %in% ForecastingStocks){
        # DJC panels[[4]]=tabPanel("Forecasting 2019", value="ForecastingTab",
        # SM Sep2022 Changed input$year from 2021 to 2022 (row 1837) and changed "Forecasting 2022" (row 1843) to "Forecasting 2023"
        # SM Oct2021 Changed input$year from 2020 to 2021 (row 1385) and changed "Forecasting 2021" (row 1390) to "Forecasting 2022"
        # SM Nov2020 Changed input$year from 2019 to 2020 (row 12320) and changed "Forecasting 2020" (row 1236) to "Forecasting 2021"
        
        # In 2022 in Spurdog, a 'ghost' panel appeared between tabs number 2 and 3 when test deployed. (The issue did not show when run locally in the browser.)
        # This was because Spurdog has no biology page, but '4' was hard-coded: panels[[4]] 
        # The number '4' was replaced with 'length(panels)+1' to fix the issue
        panels[[length(panels)+1]]=tabPanel("Forecasting 2023", value="ForecastingTab",
                             uiOutput("ForecastOptionsSelector"),
                             #plotlyOutput("plotforecasting"),
                             fluidRow(column(width = 3 ,plotlyOutput("plotSSB", width = "100%")), 
                                      column(width = 3 ,plotlyOutput("plotF", width = "100%")), 
                                      column(width = 5 ,plotlyOutput("plotLandings", width = "100%"))), HTML("<br><br>"),
                             h3("Annual Catch Options"),
                             "The first row in the table corresponds to the ICES Advice",p(),
                             tags$head(
                               tags$style("td:nth-child(1) {background: #f2f2f2;}")),
                             tableOutput("Forecasting_Table"),
                             "* SSB 2024 relative to SSB 2023",p(),
                             "** Advice value for 2023 relative to Advice value for 2022", HTML("<br><br>") 
                             # SM Sep2022: Updated year dates by +1
                             # SM Nov2021: Changed "** Landings in 2022 relative to TAC in 2021" to the above line 
                             # SM Oct2021: Updated year dates by +1 
                             # SM Nov2020: Updated year dates by +1 
                             # DJC"* SSB 2020 relative to SSB 2019",p(),
                             # DJC"** Landings in 2019 relative to TAC in 2018", HTML("<br><br>")
        )
      }
    
    if(is.null(input$speciesfilter) || is.na(input$speciesfilter)){
    }else if(input$year>2015){
      if(input$speciesbydiv %in% NephropsStock){
        panels[[4]]=tabPanel("% Change in Landings", value="NephropsTab",
                             h5("Figure showing the % change in landings advice for each Functional Unit
                            compared with last year."),
                             fluidRow(column(width = 6 , imageOutput("nephrops")),
                                      column(width = 3 ,
                                             h4("Areas"),
                                             "FU14 Eastern Irish Sea",p(),
                                             "FU15 Western Irish Sea",p(), 
                                             "FU16 Porcupine Bank",p(),
                                             "FU17 Aran Grounds",p(),
                                             "FU18 & 7 Other",p(),
                                             "FU19 SE and SW Coasts of Ireland",p(),
                                             "FU20-21 Labadie, Jones & Cockburn",p(),
                                             "FU22 The Smalls"),
                                      column(width = 3 ,
                                             h4("Links to the UWTV Surveys"),
                                             "No Link Available",p(), #FU14
                                             
                                             #SM/DC In 2021 the code was changed to reflect FU's that have no links in some years, i.e. FU15, FU19, FU2021 and FU22
                                             
                                             if (input$year==2017){a(href="http://hdl.handle.net/10793/1333","Link to UWTV for FU15",target="_blank")}
                                             else if (input$year==2018){a(href="https://oar.marine.ie/handle/10793/1378","Link to UWTV for FU15",target="_blank")}
                                             else if (input$year==2019){a(href="http://hdl.handle.net/10793/1451","Link to UWTV for FU15",target="_blank")}
                                             else{"No Link Available"},p(),
                                             
                                             #FU 16 and FU17 are the only ones to have a report published in 2016
                                             a(href=paste0(
                                               if(input$year==2016){"https://oar.marine.ie/handle/10793/1185"}
                                               else if(input$year==2017){"http://hdl.handle.net/10793/1334"}
                                               else if(input$year==2018){"https://oar.marine.ie/handle/10793/1379"}
                                               else if(input$year==2019){"https://oar.marine.ie/handle/10793/1431"}
                                               else if(input$year==2020){"http://hdl.handle.net/10793/1655"}
                                               else if(input$year==2021){"https://oar.marine.ie/handle/10793/1718"}
                                               else if(input$year==2022){"https://oar.marine.ie/handle/10793/1794"}),"Link to UWTV for FU16",target="_blank"),p(),
                                             a(href=paste0(
                                               if(input$year==2016){"https://oar.marine.ie/handle/10793/1184"}
                                               else if(input$year==2017){"http://hdl.handle.net/10793/1335"}
                                               else if(input$year==2018){"https://oar.marine.ie/handle/10793/1374"}
                                               else if(input$year==2019){"https://oar.marine.ie/handle/10793/1427"}
                                               else if(input$year==2020){"http://hdl.handle.net/10793/1656"}
                                               else if(input$year==2021){"https://oar.marine.ie/handle/10793/1721"}
                                               else if(input$year==2022){"https://oar.marine.ie/handle/10793/1793"}),"Link to UWTV for FU17",target="_blank"),p(),
                                             
                                             "No Link Available",p(), #this lists 'No Link' for outFU
                                             
                                             if (input$year==2017){a(href="http://hdl.handle.net/10793/1332","Link to UWTV for FU19",target="_blank")}
                                             else if (input$year==2018){a(href="https://oar.marine.ie/handle/10793/1375","Link to UWTV for FU19",target="_blank")}
                                             else if (input$year==2019){a(href="https://oar.marine.ie/handle/10793/1429","Link to UWTV for FU19",target="_blank")}
                                             else if (input$year==2020){a(href="http://hdl.handle.net/10793/1654","Link to UWTV for FU19",target="_blank")}
                                             else if (input$year==2021){a(href="https://oar.marine.ie/handle/10793/1722","Link to UWTV for FU19",target="_blank")}
                                             else if (input$year==2022){a(href="https://oar.marine.ie/handle/10793/1795","Link to UWTV for FU19",target="_blank")}
                                             else{"No Link Available"},p(),
                                             
                                             if(input$year==2017){a(href="http://hdl.handle.net/10793/1330","Link to UWTV for FU2021",target="_blank")}
                                             else if(input$year==2018){a(href="https://oar.marine.ie/handle/10793/1377","Link to UWTV for FU2021",target="_blank")}
                                             else if(input$year==2019){a(href="https://oar.marine.ie/handle/10793/1430","Link to UWTV for FU2021",target="_blank")}
                                             else if(input$year==2020){a(href="https://oar.marine.ie/handle/10793/1430","Link to UWTV for FU2021",target="_blank")}
                                             else if(input$year==2021){a(href="https://oar.marine.ie/handle/10793/1724","Link to UWTV for FU2021",target="_blank")}
                                             else if(input$year==2022){a(href="https://oar.marine.ie/handle/10793/1798","Link to UWTV for FU2021",target="_blank")}
                                             else{"No Link Available"},p(),
                                             
                                             if(input$year==2017){a(href="http://oar.marine.ie/handle/10793/1331","Link to UWTV for FU22",target="_blank")}
                                             else if(input$year==2018){a(href="https://oar.marine.ie/handle/10793/1376","Link to UWTV for FU22",target="_blank")}
                                             else if(input$year==2019){a(href="https://oar.marine.ie/handle/10793/1428","Link to UWTV for FU22",target="_blank")}
                                             else if(input$year==2020){a(href="http://hdl.handle.net/10793/1658","Link to UWTV for FU22",target="_blank")}
                                             else if(input$year==2021){a(href="https://oar.marine.ie/handle/10793/1723","Link to UWTV for FU22",target="_blank")}
                                             else if(input$year==2022){a(href="https://oar.marine.ie/handle/10793/1797","Link to UWTV for FU22",target="_blank")}
                                             else{"No Link Available"},p(),
                                      )),
                             HTML("<br><br>"))}}
    do.call(tabsetPanel, panels)
    #tabsetPanel(panels)
  })
  
  #Ecosystem Overview
  #~~~~~~~~~~~~~~~~~~~
  output$OverviewsAndMF <-renderUI({
    #SM added Nov 2021 and Nov 2022
    #  if(input$year==2022){
    #    tagList(h4("A FEAS summary of Ecosystem and Mixed Fisheries advice will be added in late December 2022"))
    # }else if(input$year==2015){
    
    if(input$year==2015){
      tagList(h4("Ecosystem Overview and Mixed Fisheries was introduced in 2016"))
    }
    #}else if(input$year>2016){  #changed this in 2021 to facilitate the changed format for that year - three tabs
    else if(input$year==2017 |input$year==2018 |input$year==2019 |input$year==2020 |input$year==2021 |input$year==2022){  
      panelsEO= list(
        tabPanel("Ecosystem Overview",
                 h2("Ecosystem Overview"),
                 h3("Summary"),
                 fluidRow(column(width = 9, htmlOutput("SummaryText")),
                          column(width = 3, imageOutput("SurfaceArea",height = "50%"),
                                 "Surface swept area ration of otter trawls in 2015 (ICES, 2016)")),
                 h3("FEAS Ecosystem Considerations"),
                 htmlOutput("Considerations"), HTML("<br>"),
                 imageOutput("guild2017"),HTML("<br>"),
                 "Time-series of average of relative fishing mortality (F to Fmsy ratio) and biomass 
                           (SSB to Bmsy trigger ratio) by fish guild. Mean F and mean SSB is by total number of 
                           stocks with reference points."))
      panelsD3MF= list(
        tabPanel("D3 Assessment", 
                 htmlOutput("D3summ"),
                 htmlOutput("D3text"),p(),
                 if(input$year==2017){
                   list("Table 2: MSFD GES assessment for D3 in 2017",
                        fluidRow(column(width = 6, imageOutput("D3table",height = "50%")),
                                 column(width = 6, imageOutput("D3table2",height = "50%"))),
                        HTML("<br>"),
                        h3("Preliminary Results"),
                        "Table 3: MSFD Preliminary GES Results for D3 in 2017",
                        imageOutput("D3results1", height="50%"),
                        imageOutput("D3results2", height="50%"),
                        imageOutput("D3results3", height="50%"),
                        HTML("<br>"),
                        h3("Time Series of Pressure and State Indicators"),
                        htmlOutput("PressureState"), p(), HTML("<br>"),
                        fluidRow(column(width = 4, imageOutput("RelativeF", height="50%")),
                                 column(width = 4, imageOutput("RelativeSSB",height = "50%"))),
                        "Figure 4: Relative F and Relative SSB of all assessed stocks. For stocks 
                            included in each category, see Table 2",
                        HTML("<br><br>"),
                        fluidRow(column(width = 7, imageOutput("Kobe", height="50%"), 
                                        "Figure 5: F/FMSY and SSB/MSYbtrigger for all assessed stocks. 
                                            (Grey lines represent MSY reference values)."),
                                 column(width = 5, imageOutput("Bar",height = "50%"),
                                        "Figure 6: Catch (triangles) and landings (circles) of all 
                                            assessed stocks at GES (green), non GES (red) or unknown (grey).")) )
                 }else if(input$year==2018){
                   list(
                     "Table 1a. MSFD GES assessment for D3 in 2018, demersal stocks.",
                     imageOutput("D3table1a",height = "50%"),
                     "Table 1b. MSFD GES assessment for D3 in 2018, pelagic stocks.",
                     imageOutput("D3table1b",height = "50%"),
                     "Table 1c. MSFD GES assessment for D3 in 2018, Nephrops stocks.",
                     imageOutput("D3table1c",height = "50%"),
                     "Table 1d. MSFD GES assessment for D3 in 2018, elasmobranch stocks.",
                     imageOutput("D3table1d",height = "50%"),
                     "Table 1e. MSFD GES assessment for D3 in 2018, deepwater stocks.",
                     imageOutput("D3table1e",height = "50%"),
                     "Table 2. MSFD Preliminary GES Results for D3 in 2018.",
                     imageOutput("D3table22018",height = "50%"),
                     HTML("<br>"),
                     h3("Time Series of Pressure and State Indicators"),
                     htmlOutput("PressureState"), p(), HTML("<br>"),
                     fluidRow(column(width = 4, imageOutput("RelativeF", height="50%")),
                              column(width = 4, imageOutput("RelativeSSB",height = "50%"))),
                     "Figure 4: Relative F and Relative SSB of all assessed stocks. For stocks 
                               included in each category, see Table 2",
                     HTML("<br><br>"),
                     fluidRow(column(width = 7, imageOutput("Kobe", height="50%"), 
                                     "Figure 5: F/FMSY and SSB/MSYbtrigger for all assessed stocks. 
                                               (Grey lines represent MSY reference values)."),
                              column(width = 5, imageOutput("Bar",height = "50%"),
                                     "Figure 6: Catch (triangles) and landings (circles) of all 
                                               assessed stocks at GES (green), non GES (red) or unknown (grey)."))
                   )},
                 
                 # We don't want these bits for 2019 - very messy :-S. Also don't want them for 2020 SM Dec2020
                 #app.R has been changed in 2020 to stop the Ecosystems Overview tab from appearing. Also stopped the hard-coded headings and graph captions from appearing for those years.                      HTML("<br><br>")),
                 HTML("<br><br>")),###
        tabPanel("Mixed Fisheries", 
                 htmlOutput("MixedFish_1"),
                 htmlOutput("MixedFish_2"),
                 imageOutput("MixedFishimage", height="50%"), HTML("<br><br>")))
      #SM: Inserted for 2021 as the Ecosystems tab above was linked to D3 also
      panelsEO_MF= list(
        
        tabPanel("Fisheries Overview",
                 htmlOutput("Fisheries_1")),        
        
        tabPanel("Mixed Fisheries",
                 if(input$year==2021){ 
                   list( htmlOutput("MixedFish_1"),
                         htmlOutput("MixedFish_2"),
                         fluidRow( column(width = 6, imageOutput("MF_Fig1_caption",height = "50%")),
                                   column(width = 6, imageOutput("MF_Fig2_caption", height="50%"))), 
                         HTML("<br><br>"),
                         htmlOutput("MixedFish_3"),
                         fluidRow( column(width = 6, imageOutput("MF_Tbl1",height = "50%"))), 
                         HTML("<br><br>"),
                         imageOutput("MF_Tbl2", height="50%"),
                         HTML("<br><br>"),
                         fluidRow( column(width = 6, imageOutput("MF_Tbl3",height = "50%")), 
                                   column(width = 6, imageOutput("MF_Tbl4", height="50%"))),
                         HTML("<br><br>"),
                         fluidRow( column(width = 10, imageOutput("MF_Fig3_caption", height="20%"))),
                         #imageOutput("MF_Fig3_caption", height="400px"),
                         HTML("<br><br>"),
                         fluidRow( column(width = 5, imageOutput("MF_Fig4_caption")), 
                                   column(width = 6, imageOutput("MF_Fig5_caption"))),
                         HTML("<br><br>"),
                         fluidRow( column(width = 5, imageOutput("MF_Tbl5",height = "50%")), 
                                   column(width = 7, imageOutput("MF_Tbl6", height="50%"))),
                         HTML("<br><br>"),
                         htmlOutput("MixedFish_4"),         
                         fluidRow( column(width = 6, imageOutput("MF_Tbl7",height = "25%")), 
                                   column(width = 6, imageOutput("MF_Tbl8", height="25%"))),
                         htmlOutput("MixedFish_5"), 
                         htmlOutput("MixedFish_6")
                 )}
                 else if (input$year==2022){
                   list( htmlOutput("MixedFish_1"),
                         htmlOutput("MixedFish_2"),
                         fluidRow( column(width = 5, imageOutput("MF_Fig1_caption",height = "50%")), #,height = "100%"
                                   column(width = 7, imageOutput("MF_Tbl1"))),  #, height="50%"
                         HTML("<br><br>"),
                         htmlOutput("MixedFish_3"),
                         fluidRow( column(width = 6, imageOutput("MF_Tbl2",height = "50%")), 
                                   column(width = 6, imageOutput("MF_Tbl3", height="50%"))), 
                         HTML("<br><br>"),
                         fluidRow( column(width = 6, imageOutput("MF_Tbl4",height = "50%")), 
                                   column(width = 6, imageOutput("MF_Tbl5", height="50%"))), 
                         #In 2022 image names were aligned with 2021 names so that sizes are stable. Therefore there is no Fig2
                         imageOutput("MF_Fig3_caption", height="50%"), #
                         HTML("<br><br>"),
                         fluidRow( column(width = 5, imageOutput("MF_Fig4_caption",height = "50%")), 
                                   column(width = 7, imageOutput("MF_Tbl6", height="50%"))), 
                         #imageOutput("MF_Fig4_caption", height="80%"), #
                         #imageOutput("MF_Tbl6", height="50%"),
                         HTML("<br><br>"),
                         htmlOutput("MixedFish_4"),         
                         fluidRow( column(width = 6, imageOutput("MF_Tbl7",height = "20%")), 
                                   column(width = 6, imageOutput("MF_Tbl8", height="25%"))),
                         HTML("<br><br>"),
                         imageOutput("MF_Fig5_caption", height="50%"),
                         HTML("<br><br>"),
                         htmlOutput("MixedFish_5"), 
                         htmlOutput("MixedFish_6")
                   
                 )}), #end of list and tab panel 'Mixed Fisheries'
        
        tabPanel("Ecosystem Overview",
                 htmlOutput("SummaryText")))  # end of 'panelsEO_MF'
      
      
      #this was the code in 2020. Needed to be changed for 2021
      #panelstest=if(input$year>=2018 ){panelsD3MF}else{c(panelsEO, panelsD3MF)}#changed in 2020 
      #do.call(tabsetPanel, panelstest)
      
      panelstest=if(input$year==2021 |input$year==2022) {c(panelsEO_MF)}
      else if(input$year==2018 |input$year==2019 |input$year==2020 )
      {panelsD3MF}
      else if(input$year==2017) {c(panelsEO, panelsD3MF)}#changed in 2020 
      
      do.call(tabsetPanel, panelstest)
      
    }else if(input$year=="2016"){
      tagList(h2("Ecosystem Overview & Mixed Fisheries"),
              h3("Summary"),
              fluidRow(column(width = 9, htmlOutput("SummaryText")),
                       column(width = 3, imageOutput("SurfaceArea",height = "50%"),
                              "Surface swept area ration of otter trawls in 2015 (ICES, 2016)")),
              h3("FEAS Ecosystem Considerations"),
              htmlOutput("Considerations"),
              fluidRow(column(width = 4, imageOutput("RelativeF", height="50%"),
                              "Relative F (the ratio of F to F_MSY) of all fully assessed stocks with Irish Quota. 
                            (Excludes Haddock in 6a as the ICES advice was not finalised at the time of preparation.)"),
                       column(width = 4, imageOutput("RelativeSSB",height = "50%"),
                              "Relative SSB (the ratio of SSB to BTrigger) of all fully assessed stocks with Irish Quota.
                            (Excludes Haddock in 6a)")),
              h3("Pressure and State Indicators 2016:"), 
              htmlOutput("PressureState"),
              tabsetPanel(id="test", type = "pills",
                          tabPanel("Irish Sea",
                                   fluidRow(column(width = 6, imageOutput("IrishSea",height = "50%")),
                                            column(width = 6, imageOutput("IrishSeaFSSB",height = "50%")))),
                          tabPanel("Celtic Sea",
                                   fluidRow(column(width = 6, imageOutput("CelticSea",height = "50%")),
                                            column(width = 6, imageOutput("CelticSeaFSSB",height = "50%")))),
                          tabPanel("West of Scotland and Rockall",
                                   fluidRow(column(width = 6, imageOutput("WestScot",height = "50%")),
                                            column(width = 6, imageOutput("WestScotFSSB",height = "50%")))),
                          tabPanel("Widely Distributed Species",
                                   fluidRow(column(width = 6, imageOutput("DistSpecies",height = "50%")),
                                            column(width = 6, imageOutput("DistSpeciesFSSB",height = "50%"))))),
              h5("Link to the Celtic Seas Ecoregion - Ecosystem Overview pdf:"),
              a(href=paste0("http://www.ices.dk/sites/pub/Publication%20Reports/Advice/2016/2016/Celtic_Sea_Ecoregion-Ecosystem_overview.pdf"),
                "2016 Ecosystem Overview",target="_blank"),
              h5("Link to the ICES Advice pdf:"), 
              a(href=paste0("http://www.ices.dk/sites/pub/Publication%20Reports/Advice/2016/2016/mix-celt.pdf"),
                "2016 ICES Advice for Mixed Fisheries",target="_blank"))}
    
  })#closing brackets of output$OverviewsAndMF <-renderUI({
  

  #SUSTAINABILITY ASSESSMENT 2022 (output code removed from 'tabpanel' (line ~54) to here)
  # to avoid 'Navigation Containers' warning
  #~~~~~~~~~~~~~~~~~~~~~~~~~~~~
  output$SustainAss <-renderUI({
    
      tagList(
        
        htmlOutput("Sustainabilitytext"),
        "Table 1: Summary of FEAS evaluation of fishing mortality in relation 
                       to FMSY for Stocks of interest to Ireland", 
        imageOutput("Sustainabilitytable1", height="100%"),
        HTML("<br>"),
        "Table 2: Summary of FEAS evaluation of SSB in 
                       relation to biomass reference points for stocks of interest to Ireland.",
        imageOutput("Sustainabilitytable2", height="100%"),
        HTML("<br>"),
        # SM added Fig 1 image and caption in Nov 2022
        imageOutput("SustainabilityFig", height="100%"),
        textOutput("SustainabilityFigText"),
        HTML("<br>"),
        "Table 3: Details of FEAS evaluation of fishing mortality in relation to FMSY and SSB 
                       in relation to biomass reference points for stocks of interest to Ireland.",
        imageOutput("Sustainabilitytable3", height="100%"),HTML("<br>"),
        textOutput("SustainabilityTabletext"),
        imageOutput("Sustainabilitytable4", height="100%"), HTML("<br>"),  
    
        
      )                             # end of taglist
  })                                  # end of output$SustainAss
  
  #~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
  
  #EXTRA CHAPTERS ADDED IN 2021 and continued in 2022
  #~~~~~~~~~~~~~~~~~~~~~~~~~~~~
  output$RecentAdvice <-renderUI({
    if(input$year<2021){
      tagList(h3("Recent Advice on Ecosystem Services and Effects was introduced in 2021"))
    }
    else if(input$year>=2021){
      tagList(
        fluidRow(column(width = 10, htmlOutput("Recent_Beginning")),
                 column(width = 10, imageOutput("RecentAdvice3",height = "50%"),
                 column(width = 10, imageOutput("RecentAdvice4",height = "50%"),
                        if(input$year==2022){"Figure 1. Reported marine mammal bycatch rates in the Celtic Seas ecoregion 2017-2021 by level 4 metier. Here and below: data used for the calculation of bycatch rates was selected based on the following criterion: monitoring coverage within a metier (level 4) was above an arbitrarily set limit of 50 days-at-sea. GNS = set gillnets, GTR = trammelnets, OTB = otter trawls, OTM = midwater otter trawl, OTT = multirig otter trawl, PTB = bottom pair trawl."})),
                 column(width = 10, htmlOutput("Recent_Middle")),
                 column(width = 10, imageOutput("RecentAdvice1",height = "50%"),
                        if(input$year==2021){"Figure 1. Average Swept Area Ratio (SAR) between 2013-2018 for the waters around Ireland"}
                        else if (input$year==2022){"Figure 2. NEAFC Regulatory Area 1 with NEAFC bottom-fishing closures for VME protection (NEAFC closed areas) and NEAFC bottom-fishing areas."})),
        column(width = 10, imageOutput("RecentAdviceColours",height = "50%")),
        HTML("<br><br>"),
        fluidRow(column(width = 10, htmlOutput("Recent_End")),
                 column(width = 10, imageOutput("RecentAdvice2", height="50%"),
                        if(input$year==2021){"Figure 2. New VME habitat and indicator records for the Irish continental slope and Porcupine Bank and Seabight within EU waters. 
                            Note that other existing VME records from the VME database are not displayed for this area. In addition, it is not possible to spatially resolve all records in the map due to their close proximity.
                                 The Belgica Mound Province SAC is shown as the furthest south SAC in the Irish EEZ between the 600-1000 m depth contours."}
                        else if (input$year==2022){"Figure 3. Shellfish and finfish aquaculture sites around the coast of Ireland."})),
      )                             # end of taglist
    }                                  #end of 2021 and 2022 content
  })                                  # end of output$RecentAdvice
  
  #~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
  output$Brexit_Text <- renderText({
        if(input$year<2021){
          "<h4>Brexit Impacts on Fisheries Management, Science and Advice was introduced in 2021</h4>"
        }else if(input$year==2022){
          "<h4>Brexit Impacts on Fisheries Management, Science and Advice is discussed in 2021</h4>"
        }
        else if(input$year==2021){
          paste0(ExtraChapters[4, which(colnames(ExtraChapters)==paste0("X", input$year))])
        }

    })
  #~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 
  output$CovidResponse <-renderUI({
    if(input$year<2021){
      tagList(h4("The Covid Response was introduced in 2021"))
    }
    else if(input$year==2021){
      tagList(
        htmlOutput("AtSea2020"),
        fluidRow(column(width = 10, imageOutput("AtSea2020_1",height = "100%"),
                        "Figure 1. At sea Self-Sampling Datasheet")),
    )}                   
    else if (input$year==2022){
      tagList(
        htmlOutput("AtSea2020")
      )}                            
                                     
  })                                  
  
  #~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~   
  
} #closing bracket of server <- function(input, output, session) {     (line 87)

shinyApp(ui, server)