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2022 Update
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gfmg committed Dec 13, 2023
1 parent e84310e commit 9fb80b9
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2 changes: 2 additions & 0 deletions .gitignore
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.Rhistory
.RData
.Ruserdata
.html
.png
15 changes: 15 additions & 0 deletions server.R
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Expand Up @@ -569,6 +569,21 @@ server <- function(input, output, session) {
}
})

output$C_DataSources<-renderUI({
if(input$SpCIDA == "SELECT SPECIES") {
return(NULL)
} else {
if (input$SpCArea == "SELECT AREA") {
return(NULL)
} else {
includeHTML(file.path("www/Assessment and advice",
input$SpCIDA,
input$SpCArea,
"Data Sources.html"))
}
}
})

output$C_Assessment<-renderUI({
if(input$SpCIDA == "SELECT SPECIES") {
return(NULL)
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116 changes: 85 additions & 31 deletions ui.R
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Expand Up @@ -608,41 +608,61 @@ body<-dashboardBody(
tabPanel("Management Advice",
htmlOutput("C_ManagementAdvice")),
tabPanel("Stock summary",
htmlOutput("C_StockSummary")),
fluidRow(
column(12,
htmlOutput("C_StockSummary")
)
)
),
tabPanel("Data Sources",
fluidRow(
column(12,
htmlOutput("C_DataSources")
)
)
),
tabPanel("Assessment",
htmlOutput("C_Assessment"))
fluidRow(
column(12,
htmlOutput("C_Assessment")
)
)
)
)
),
tabItem(tabName = "GastropodAssessment",
tags$div(h1(paste0("In development")),
style="text-align: center")),
tabItem(tabName = "Oinfo",
br(),
tags$p("This tab provides a series of usefull links to other sources of information relevant to Irish Fisheries"),
br(),
tags$b("Shellfish Stocks and Fisheries Review 2022: an assessment of selected stocks"),
br(),
tags$a(
"https://oar.marine.ie/handle/10793/1814",
target = "_blank",
href = "https://oar.marine.ie/handle/10793/1814#:~:text=The%20intention%20of%20this%20annual,in%20areas%20designated%20under%20European"),
br(),
br(),
tags$b("Shellfish Stocks and Fisheries Review 2021: an assessment of selected stocks"),
br(),
tags$a(
"https://oar.marine.ie/handle/10793/1744",
target = "_blank",
href = "https://oar.marine.ie/handle/10793/1744"),
br(),
br(),
tags$b("Shellfish Stocks and Fisheries Review 2019: an assessment of selected stocks"),
tags$p("This tab provides a series of links to other sources of information relevant to Irish Fisheries"),
br(),
tags$a(
"https://oar.marine.ie/handle/10793/1591",
target = "_blank",
href = "https://oar.marine.ie/handle/10793/1591"),
tags$b("Annual Shellfish Stocks and Fisheries Review: an assessment of selected stocks"),
br(),
tags$p(tags$u("2022:"),
tags$a(
"https://oar.marine.ie/handle/10793/1814",
target = "_blank",
href = "https://oar.marine.ie/handle/10793/1814#:~:text=The%20intention%20of%20this%20annual,in%20areas%20designated%20under%20European")
),
tags$p(tags$u("2021:"),
tags$a(
"https://oar.marine.ie/handle/10793/1744",
target = "_blank",
href = "https://oar.marine.ie/handle/10793/1744")
),
tags$p(tags$u("2020:"),
tags$a(
"https://oar.marine.ie/handle/10793/1688",
target = "_blank",
href = "https://oar.marine.ie/handle/10793/1688")
),
tags$p(tags$u("2019:"),
tags$a(
"https://oar.marine.ie/handle/10793/1591",
target = "_blank",
href = "https://oar.marine.ie/handle/10793/1591")
),
br(),
tags$b("Atlas: Commercial fisheries for shellfish around Ireland"),
br(),
Expand All @@ -660,20 +680,54 @@ body<-dashboardBody(
href = "https://natura2000.eea.europa.eu/"),
br(),
br(),
tags$b("Fisheries Natura Plan for Cockle in Dundalk (2021-2025)"),
tags$b("Fisheries Natura Plan for Cockle in Dundalk"),
br(),
tags$a(
tags$p(tags$u("2021-2025:"),
tags$a(
"http://www.fishingnet.ie/sea-fisheriesinnaturaareas/concludedassessments/dundalkbay-sacspa/",
target = "_blank",
href = "http://www.fishingnet.ie/sea-fisheriesinnaturaareas/concludedassessments/dundalkbay-sacspa/"),
href = "http://www.fishingnet.ie/sea-fisheriesinnaturaareas/concludedassessments/dundalkbay-sacspa/")
),
tags$p(tags$u("2016-2020:"),
tags$a(
"http://www.fishingnet.ie/sea-fisheriesinnaturaareas/concludedassessments/dundalkbay-sacspa/",
target = "_blank",
href = "http://www.fishingnet.ie/sea-fisheriesinnaturaareas/concludedassessments/dundalkbay-sacspa/")
),
br(),
tags$b("Annual Stock Book: Review of Fish Stocks"),
br(),
tags$b("Fisheries Natura Plan for Cockle in Dundalk (2016-2020)"),
tags$p(tags$u("2022:"),
tags$a(
"https://oar.marine.ie/handle/10793/1805",
target = "_blank",
href = "https://oar.marine.ie/handle/10793/1805")
),
tags$p(tags$u("2021:"),
tags$a(
"https://oar.marine.ie/handle/10793/1726",
target = "_blank",
href = "https://oar.marine.ie/handle/10793/1726")
),
tags$p(tags$u("2020:"),
tags$a(
"https://oar.marine.ie/handle/10793/1660",
target = "_blank",
href = "https://oar.marine.ie/handle/10793/1660")
),
tags$p(tags$u("2019:"),
tags$a(
"https://oar.marine.ie/handle/10793/1433",
target = "_blank",
href = "https://oar.marine.ie/handle/10793/1433")
),
br(),
tags$b("Marine Institute Digital Stock Book (Shiny App)"),
br(),
tags$a(
"http://www.fishingnet.ie/sea-fisheriesinnaturaareas/concludedassessments/dundalkbay-sacspa/",
"https://shiny.marine.ie/stockbook/",
target = "_blank",
href = "http://www.fishingnet.ie/sea-fisheriesinnaturaareas/concludedassessments/dundalkbay-sacspa/")
href = "https://shiny.marine.ie/stockbook/"),
)
)
)
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105 changes: 104 additions & 1 deletion www/Assessment and advice/Brown Crab/Malin/Assessment.html
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@@ -1 +1,104 @@
<p>hwreawGEAREYTWef</p>
<!DOCTYPE html>
<html lang="en">

<head>
<meta charset="utf-8">
<meta name="viewport" content="width=device-width">
<title>Assessment</title>

<script src="https://polyfill.io/v3/polyfill.min.js?features=es6"></script>
<script id="MathJax-script" async
src="https://cdn.jsdelivr.net/npm/mathjax@3/es5/tex-mml-chtml.js">
</script>

<style>
table, th, td {
text-align: center;
border: 1px solid black;
border-collapse: collapse;
padding:5px;

}
</style>

</head>

<body>
<div style="display:block; width:100%;">
<div style="width:48%; float: left; display:inline-block; margin-right: 2%" align="justify">
<h3>SPiCT Assessment</h3>

<p>SPiCT (surplus production in continuous time) is a version of a surplus production model which are commonly used in fisheries assessments. The model enables error in the catch process to be reflected in the uncertainty of estimated model parameters and management quantities. Estimates of exploitable biomass and fishing mortality can be obtained at any point in time from data sampled at arbitrary intervals. A number of model scenarios were tested which included varying the time series of landings and catch rate indices included in the assessment and the initial settings for key model parameters (symmetry of the production curve, depletion at the beginning of the time series and intrinsic growth rate for crab).</p>

<p>SPiCT outputs indicate that the stock entered an overfished state around 2016 (Figure 1). Fishing mortality (F) reached its highest point ~2019, and has shown a slight decrease in recent years. Nevertheless, F is still higher than optimum fishing mortality rates (Fmsy) and stock biomass (B) is well below the biomass that, on average, would optimize stock productivity (Bmsy).
</p>

<h3>Catch advice</h3>
<p>The assessment shows that fishing mortality should be reduced in all stocks. The level
to which fishing mortality is reduced depends on the harvest control rule that is adopte
. Two rules are considered below; </p>

<ol>
<li>Fish at Fmsy</li>
<li>Apply the so called 2/3 rule as applied to ICES category 3 stocks for which only trends, rather than a full stock assessment, are available.</li>
</ol>

<p>The Fmsy advice is taken directly from the assessment model presented. The Fmsy rule reduces the F/Fmsy ratio (and corresponding landings) back to 1 or the fishing mortality rate that may lead to recovery of the stock to Bmsy levels. The 2/3 rule takes the average index value (LPUE) in the 2 most recent years in the assessment and for which full data are available (2020, 2021), divides it by the average index value in the 3 years prior to that (2017-2019) and applies it to the most recent year for which landings are available (2021). As the index is declining this rule advises a reduction in landings (Table 1).</p>

<table align="center">
<tr>
<td><b>Stock</b></td>
<td><b>Current landings (2022)</b></td>
<td><b>Landings at Fmsy</b></td>
<td><b>Landings 2/3 rule</b></td>
</tr>
<tr>
<td>Malin Shelf</td>
<td>5,463</td>
<td>3,900</td>
<td>4,500</td>
</tr>

</table>

<h3>Interpretation</h3>
<p>The year on year decline in the observed and standardised LPUE index between 2014 and
2020 has not been previously observed in the time series which extends back to 1990.
Although the LPUE indices can be confounded by changes in grading practice, unrelated to
the minimum landing size, it is unlikely to be the cause of the decline in recent years.
Observed discard rates (DPUE) also declined from 2016-2019 in parallel with the LPUE
index. Decline in LPUE could be linked to growth overfishing whereby the removal of crabs
above the MLS occurs at a higher rate than they can be replaced by growth but
corresponding declines in DPUE and LPUE signal an overall year on year reduction in the
abundance of crab in the fished area. Crabs in the discards are not all recent recruits to
the stock and include a number of age classes. The decline in discards, therefore, may
signal a reduction in recruitment in the past number of years.</p>

<p>The minimum size of 130 mm and more recently 140 mm has been regarded as sufficient to
protect the stock from recruitment overfishing given that the size at maturity is
approximately 120 mm. Spawning escapement is, therefore, significant and above 30 % of
what it would be in an unfished stock. A number of spawning events occur before crabs
are
exposed to fishing mortality. High grading at observed modal size of about 150 mm
provides further protection. Fishing is unlikely to be the sole cause of the recent
declines in stock abundance. However, recruitment decline combined with high fishing
effort will further reduce spawning stock biomass. In such a case, fishing mortality
(landings) should be reduced to avoid further depletion in stock biomass.
</p>

</div>
<br>
<div style="width:50%; float: left; display:inline-block;">
<img class="mb-3 mb-lg-0 me-md-0"
src="Assessment and advice/Brown Crab/Malin/plots/Kb_2022_Assessment.png"
alt="image"
style="max-width: 100%; height: auto; margin-bottom:2px">

<figcaption
style= "margin-bottom:2px"
align="justify">Figure 1: Malin Shelf Stock evolution of relative exploitation and relative stock status from 1990-2020. F/Fmsy > 1 and B/Bmsy < 1 indicate overexploitation and loss in productivity.</figcaption>

</div>
</div>
</body>
</html>
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