First upload

.gitignore

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+.Rproj.user
+.Rhistory
+.RData
+.Ruserdata

App.Rproj

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+EnableCodeIndexing: Yes
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+Encoding: UTF-8
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+RnwWeave: Sweave
+LaTeX: pdfLaTeX

data/Data_prep_Output/Assessment and Advice.csv

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+Specie,Area,ManagementAdvice,Biology,fishery,Assessment,Outputs
+Cockle,Dundalk,"<p>The Dundalk Bay cockle fishery is managed under a Fisheries Natura (management) Plan (FNP) which is a legal mechanism to incorporate environmental protection measures into fisheries management plans when such fisheries occur in Natura 2000 sites. </p>
+
+<p>No fishing occurs at biomass less than 1200 tonnes. The fishery closes when the TAC (17-33 % of biomass over 1200 tonnes) is taken or on November 1st or if the average catch per boat per day declines below 250 kg. The minimum landing size is 22 mm shell width. A quota of 1 tonne per vessel per day for 28 permit holders is in force.</p>
+
+<p>The stock is assessed by annual survey and in season LPUE data. Trends in other ecosystem indicators (benthic habitats, bird populations) are integrated into management advice and the FNP. </p>
+
+<p>Pre-fishery survey estimate of cockle biomass in 2021 was 1,927 tonnes compared to 3,790 and 3,420 tonnes 2019 and 2020 respectively following on from a strong recruitment in 2018. The TAC in 2021 was 642 tonnes of which 638 tonnes were landed.</p>
+
+<p>The harvest control rules in the 2021-2025 FNP should be implemented annually. The FNP will be reviewed in 2025. The estimation of post fishery cockle biomass should be improved.</p>
+
+<p>Maintenance of favourable conservation status of intertidal habitats in which cockle fisheries occur is a primary management objective in order to reduce the risk of future recruitment failure and to ensure that conservation objectives for designated habitats and species are protected. Any cockle fisheries in other SACs or SPAs should be subject to management plans considering their potential effects on designated habitats and birds.</p>
+",,,"<p>A pre-fishery survey was completed between 23-25th May 2022. A total of 373 stations, were sampled, using two different gears: scientific quadrats covering an area of 0.25 m2 and rakes covering an area of 2 m2, resulting in approximately 839 m2 of Dundalk Bay being sampled. GPS locations from each station were recorded using Trimble GPS units. The total area surveyed was 27.8 km2.</p>
+
+<p>Biomass at each station was estimated based on density (number of individuals caught per square metre of sampled area) and a species specific weight-length relationship. Total biomass was then estimated as the sum of mean estimated biomass, using a geostatistical (kriging) model with a zone effect (between the Northern and Southern areas), raised to the surface area.</p> 
+","<p>Total biomass was 1,826 tonnes based on a Geostatistical model, with a significant increase in cockle below 18mm. Biomass of cockles over 22 mm was 912 tonnes. The highest densities (Kg.m-2) of cockles occurred throughout the middle of the surveyed area, with one major hotspot at the northern limits of the southern zone. </p> 
+
+<p>A total of 6,022 cockles were measured from the 2022 survey.  A strong recruitment event is evident based on the size distribution plot for the 2022 survey with a strong cohort at 8mm size. A second cohort is observed at 18mm size, following the growth progression of the small cohort detected in the 2021 survey. The main 2021 mode of large cockle ~27mm has decreased, as also indicated in the interannual biomass reduction for this size range.</p>"
+Razor Clams,North Irish Sea,"<p>All commercially exploited razor clam stocks in Ireland are assessed by survey which provide estimates of biomass by size or grade. Weekly TACs apply to vessels in the north and south Irish Sea. All vessels report iVMS data. </p>
+
+<p>Landings in the North Irish Sea declined between 2015-2021. The number of vessels in the fishery increased from 49 in 2015 to 73 in 2016 and 2017 and declined to 56 in 2019. All indicators (daily landings per vessel, catch per hour) show significant and persistent declines up to 2017 but were stable from 2017-2020. Estimates of biomass, revised following a review of data standardisation protocols in 2020, varied from approximately 9,000 tonnes in 2017 to between 6,000-7,000 tonnes in 2018-2020 and 9,145 in 2021. Exploitation rate was 7.5 % per annum. Large size classes were depleted between 2017 and 2018 but were stable or increased between 2018-2021. Based on average landings 2019-2021 or applying the average exploitation rate for the period 2019-2021 of 7.5% to the average survey estimates for the same period landings in 2022 should not exceed 563 tonnes.</p>
+",,"The North Irish Sea (NIS) fishery began in the early 1980s and quickly developed due to high quality (size) of clams in the Gormanstown bed which attracted premium prices compared to other Ensis species fished in Europe. There may have been 50 vessels in the fishery by 1999. Post 2003 beds at Malahide, Skerries and south Dundalk Bay were being fished in addition to the Gormanstown bed.  The number of vessels in the fishery, total fishing effort and annual landings expanded significantly between 2014 and 2018. The fishery has supported over 70 vessels in recent years and landings peaked at over 1,100 tonnes and a value of approx. 6.5m euros in 2015. The catch is exported mainly to the Far East. Unit prices vary by grade or shell size from 4-10 euros per kg. The fishery, relative to other shellfish, could be classed as medium price and medium volume. 
+The fishery occurs close to the coast in shallow sub-tidal waters along the east coast from Dundalk south to Malahide.","<p>A total of 781 tows were undertaken using five different vessels, with hydraulic dredges ranging from 0.86-1.2m width. GPS data for each tow line was recorded on a Trimble GPS survey unit. Following a standardized protocol applied to the 2017-2021 survey data, GPS tracks were inspected to identify potentially erroneous tracks due to lack of GPS track connectivity, and a Gaussian Kernel regression technique was applied as a way to smooth unrealistic spikes resulting from the position accuracy (1-3m) of the Trimble units. Based on the final track length and the gear width, swept area for each tow was estimated, resulting in a total sampling effort of 22568 m2.</p>
+
+<p>Biomass at each station was estimated as the product of density (number of individuals caught per meter squared towed area) and mean individual weight calculated from the size distribution at the station and a weight-length relationship. Biomass was then interpolated over a 200 m x 200 m grid using ordinary kriging on log(biomass). Total biomass was then estimated as the sum of mean estimated biomass, using a geostatistical (kriging) model, raised to the surface area of the cells. Ninety-five percent confidence intervals were estimated based upon random realisations of the modelled biomass using conditional Gaussian simulations. This method preserves the spatial structure in the biomass, as described by variograms, which modelled the spatial autocorrelation and spatial structure in the survey data.</p>
+","<p>Biomass of all size classes of razors uncorrected for dredge efficiency varied from 0-0.57 kgs.m-2. Distribution of high density patches is similar across size ranges. The estimated biomass was 9,244 tonnes, with 90% of the total biomass above the 130 mm MLS.</p>
+
+<p>The size distribution of razor clams in the North Irish Sea in 2022 shows a rightward move due to growth in the ~120mm cohort observed in the 2021 survey. Densities of razors above the MLS of 130 mm remains similar to the 2021 survey. </p>
+
+"
+Razor Clams,Rosslare,"<p>All commercially exploited razor clam stocks in Ireland are assessed by survey which provide estimates of biomass by size or grade. Weekly TACs apply to vessels in the north and south Irish Sea. All vessels report iVMS data.</p> 
+
+<p>The south Irish Sea fishery opened in 2010 and expanded up to 2013. A strong recruitment event in Rosslare Bay in 2014 (probably) was observed in the 2017 survey and biomass increased significantly between the 2017 and 2020 from 2,000 to 6,300 tonnes. The estimate for 2021 was 5,300 tonnes. A further 1,500 tonnes was estimated in the Curracloe bed in 2021. On the basis that a 7.5 % exploitation rate has led to stable biomass, size distribution and commercial catch rates in the North Irish Sea landings for 2022 in the south Irish Sea should not exceed 535 tonnes.</p>
+",,<p>The fishery in the south Irish Sea opened in 2010. Landings increased from 50 tonnes to 100 tonnes in 2011 and 2012 and peaked at over 200 tonnes in 2016. Landings declined from 2016 to 2019 and were about 30 tonnes in 2021 (Figure 26). The recent declines corresponded with a reduction in fishing effort in the Rosslare Bed in particular as biomass of large grade clams had declined in the period up to 2017 and there was voluntary closure (or part closure) in the period 2018-2019 to enable growth of a strong 2014 year class. The Waterford estuary fishery was closed by court order in 2019.</p>,"<p>The razor bed of Rosslare was surveyed on September 14th 2021.  A total of 45 tows were undertaken, with a single hydraulic dredge of width 1.25m. GPS data for each tow line was recorded on a Trimble GPS survey unit and swept area for each tow was estimated. The survey encompassed a total area of 12.3km2 and a total sampling effort of 1,407m2 (Figure 2).</p>
+
+<p>Biomass at each station was estimated as the product of density (number of individuals caught per meter squared towed area) and mean individual weight calculated from the size distribution at the station and a weight-length relationship. Biomass was then interpolated over a grid using ordinary kriging on log(biomass). Total biomass was then estimated as the sum of mean estimated biomass, using a geostatistical (kriging) model, raised to the surface area of the cells. Ninety-five percent confidence intervals were estimated based upon random realisations of the modelled biomass using conditional Gaussian simulations. This method preserves the spatial structure in the biomass, as described by variograms, which modelled the spatial autocorrelation and spatial structure in the survey data.</p>","<p>Biomass of all size classes of razors, assuming a dredge efficiency of 100%, varied from 0-1.9 kgs.m-2. Higher densities of razor clams <130 mm MLS were found at the centre of the bed, whereas razors >150 mm were more abundant towards the northern part of the surveyed area. </p>
+
+<p>The estimated biomass was 5299 tonnes, almost all of which (85%) was above the 130 mm MLS </p>
+
+<p>The size distribution of razor clams showed a slight increase in modal size indicative of growth compared to the survey carried in 2020(Figure 3). No evidence of any significant recruitment was found as densities of small razor clams were low</p>
+"
+Oyster,,,,,,
+Scallops,,,,,,

data/Data_prep_Output/ICES_LPUE.prj

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+GEOGCS["GCS_unknown",DATUM["D_WGS_1984",SPHEROID["WGS_1984",6378137.0,298.257223563]],PRIMEM["Greenwich",0.0],UNIT["Degree",0.0174532925199433]]

data/Data_prep_Output/Landings_Table_2021Update.csv

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+SpeciesName,2004,2005,2006,2007,2008,2009,2010,2011,2012,2013,2014,2015,2016,2017,2018,2019,2020,2021
+Cockle,207,109,7,629,7,48,4,344,280,349,3,0,269,373,217,374,503,195
+Shrimp,416,153,312,324,180,224,134,111,148,172,289,295,363,281,272,430,343,338
+Edible crab,13119,9413,9248,7158,7029,5525,8093,6825,6115,6227,6953,6900,9332,9086,8167,8095,6406,6644
+Shore crab,266,27,46,91,72,233,129,74,253,30,50,23,165,127,118,288,154,391
+Razor clams,401,404,507,339,456,229,443,523,465,852,903,1265,1127,961,1041,783,672,595
+Lobster,855,644,611,297,498,423,470,250,244,367,445,363,402,415,345,488,437,482
+Velvet crab,291,253,270,138,260,204,342,184,169,366,231,202,277,313,213,253,240,263
+Native oyster,1225,457,399,641,138,2130,4149,3399,3669,2717,335,0,1,0,0,0,0,0
+Periwinkle,1679,1239,1125,609,1172,1103,1280,110,104,218,1135,0,3,1,0,3,0,1
+Queen scallop,110,75,172,28,4,3,0,0,12,134,80,31,201,7,4,3,1,0
+King scallop,2421,1229,644,917,1217,2610,1959,2612,2621,2797,2597,2077,2237,2580,2301,2345,1940,2739
+Spider crab,182,146,151,66,148,443,414,303,402,228,137,193,161,143,119,425,451,477
+Crayfish,80,31,34,16,20,28,30,25,35,34,23,14,10,10,9,30,15,49
+Surf clam,28,0,5,14,34,26,25,36,16,37,67,49,51,45,47,44,12,0
+Whelk,2600,4154,2917,2644,2097,2163,2975,3174,3446,2628,2180,5014,5822,4977,4638,5090,5302,4938

data/Data_prep_Output/NIS_standarized_Razor_Summary_1722.csv

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+Year,Variable,krig_mean,simu_mean,delta%,simu_median,95% HDI inf,95% HDI sup,model,Zone effect,Likelihood
+2017,Weight_Ensis_siliqua,3983.268748,NA,NA,NA,NA,NA,One-step,zone,EV
+2017,Abundance+L-W_Ensis_siliqua,9097.156268,10229.37891,12.45,10225.431,9399.358937,11128.16924,One-step,zone,EV
+2017,Weight_130_Inf_Ensis_siliqua,3987.223883,4404.769209,10.47,4397.609332,4007.529106,4864.254705,One-step,zone,EV
+2017,Abundance+L-W_130_Inf_Ensis_siliqua,7894.952436,9010.37777,14.13,9015.505079,8301.477808,9812.793734,One-step,zone,EV
+2017,Weight_150_Inf_Ensis_siliqua,2910.417357,3473.921946,19.36,3383.234504,2978.030014,4857.161945,One-step,zone,EV
+2017,Abundance+L-W_150_Inf_Ensis_siliqua,5482.77622,6339.842663,15.63,6317.750561,5768.533959,6990.088875,One-step,zone,EV
+2018,Weight_Ensis_siliqua,6010.396826,7043.550676,17.19,7047.451823,6481.754137,7644.122246,Two-steps,~zone,ML
+2018,Abundance+L-W_Ensis_siliqua,5497.894354,6502.82347,18.28,6490.741266,5969.474715,7062.987464,Two-steps,~zone,ML
+2018,Weight_130_Inf_Ensis_siliqua,5473.766191,6510.123099,18.93,6506.114825,5998.905946,7039.005437,Two-steps,~zone,ML
+2018,Abundance+L-W_130_Inf_Ensis_siliqua,5043.459958,5995.63791,18.88,5999.068613,5491.772176,6516.63186,Two-steps,~zone,ML
+2018,Weight_150_Inf_Ensis_siliqua,3780.93196,4428.261571,17.12,4421.833479,4009.154034,4854.529433,Two-steps,~zone,ML
+2018,Abundance+L-W_150_Inf_Ensis_siliqua,3389.781579,4150.53775,22.44,4147.056962,3834.709552,4429.374236,Two-steps,~zone,ML
+2019,Weight_Ensis_siliqua,6920.789287,8248.046559,19.18,8240.726134,7479.478315,9049.398436,Two-steps,~zone,ML
+2019,Abundance+L-W_Ensis_siliqua,6936.293756,8227.594787,18.62,8242.536266,7344.07599,9034.955373,Two-steps,~zone,ML
+2019,Weight_130_Inf_Ensis_siliqua,6602.30333,7961.520942,20.59,7963.546429,7215.492039,8687.438294,Two-steps,~zone,ML
+2019,Abundance+L-W_130_Inf_Ensis_siliqua,6491.266548,7903.339918,21.75,7904.736363,7211.778635,8698.542237,Two-steps,~zone,ML
+2019,Weight_150_Inf_Ensis_siliqua,4846.389717,5866.169251,21.04,5862.037288,5422.050488,6339.032938,Two-steps,~zone,ML
+2019,Abundance+L-W_150_Inf_Ensis_siliqua,4714.210021,5759.110332,22.16,5764.499035,5265.171804,6187.359864,Two-steps,~zone,ML
+2020,Weight_Ensis_siliqua,5954.69704,6866.228817,15.31,6800.423297,5889.389972,8254.613747,Two-steps,~zone,ML
+2020,Abundance+L-W_Ensis_siliqua,6542.046282,7571.498466,15.74,7577.565623,7024.226431,8097.352575,Two-steps,~zone,ML
+2020,Weight_130_Inf_Ensis_siliqua,5548.35815,6503.469986,17.21,6445.44882,5352.573251,7951.177711,Two-steps,~zone,ML
+2020,Abundance+L-W_130_Inf_Ensis_siliqua,6087.408308,7215.862017,18.54,7211.409997,6666.181906,7721.806861,Two-steps,~zone,ML
+2020,Weight_150_Inf_Ensis_siliqua,4728.071549,5523.262336,16.82,5498.698751,4431.868268,6788.12537,Two-steps,~zone,ML
+2020,Abundance+L-W_150_Inf_Ensis_siliqua,5254.795313,6227.232523,18.51,6231.555322,5730.743043,6640.100326,Two-steps,~zone,ML
+2021,Weight_Ensis_siliqua,8367.124472,10146.17978,21.26,10121.41872,9391.386504,10944.5205,Two-steps,~zone,ML
+2021,Abundance+L-W_Ensis_siliqua,9145.358625,11026.83119,20.57,11068.01509,10109.71532,11961.54001,Two-steps,~zone,ML
+2021,Weight_130_Inf_Ensis_siliqua,7606.61322,9234.988746,21.41,9215.751646,8561.623206,9968.747044,Two-steps,~zone,ML
+2021,Abundance+L-W_130_Inf_Ensis_siliqua,7322.969023,9094.883494,24.2,9091.914204,8368.072116,9887.709914,Two-steps,~zone,ML
+2021,Weight_150_Inf_Ensis_siliqua,6764.983475,8264.424916,22.16,8273.768475,7617.990856,8940.473595,Two-steps,~zone,ML
+2021,Abundance+L-W_150_Inf_Ensis_siliqua,5974.474491,7554.79303,26.45,7550.858705,6860.224172,8218.465494,Two-steps,~zone,ML
+2022,Weight_Ensis_siliqua,NA,NA,NA,NA,NA,NA,Two-steps,~zone,LS
+2022,Abundance+L-W_Ensis_siliqua,9244.444692,10197.17537,10.31,10198.33052,8918.499629,11538.00687,Two-steps,~zone,LS
+2022,Weight_130_Inf_Ensis_siliqua,NA,NA,NA,NA,NA,NA,Two-steps,~zone,LS
+2022,Abundance+L-W_130_Inf_Ensis_siliqua,8449.190258,9371.752906,10.92,9364.471475,8026.056276,10665.64651,Two-steps,~zone,LS
+2022,Weight_150_Inf_Ensis_siliqua,NA,NA,NA,NA,NA,NA,Two-steps,~zone,LS
+2022,Abundance+L-W_150_Inf_Ensis_siliqua,6532.751895,7424.557515,13.65,7407.036745,6441.526855,8533.371715,Two-steps,~zone,LS