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Fish farm assessment

Source: vignettes/mpff-compliance.Rmd
mpff-compliance.Rmd

Welcome

This document has been created following the generic assessment guidance.

Description

Basic details about the assessment.

question response
name_short MPFF Compliance
name_long Marine Pen Fish farm Compliance
parameter Marine Benthic Inverts
status prototype
type compliance

Input

A list of questions required to run the assessment.

project_id sample_id question response label parameter
South Cava 44673 12f48793-d3e1-46c9-88cc-d1571b09dfbc Site Name South Cava NA MPFF Compliance
South Cava 44673 12f48793-d3e1-46c9-88cc-d1571b09dfbc Permit CAR/L/1072725 NA MPFF Compliance
South Cava 44673 12f48793-d3e1-46c9-88cc-d1571b09dfbc Responsible person Chris Webb NA MPFF Compliance
South Cava 44673 12f48793-d3e1-46c9-88cc-d1571b09dfbc Operator (if different from above) Cooke Aquaculture Scotland NA MPFF Compliance
South Cava 44673 12f48793-d3e1-46c9-88cc-d1571b09dfbc Maximum licensed biomass (tonnes) 2500 NA MPFF Compliance
South Cava 44673 12f48793-d3e1-46c9-88cc-d1571b09dfbc Date site stocked 44421 NA MPFF Compliance
South Cava 44673 12f48793-d3e1-46c9-88cc-d1571b09dfbc Peak biomass during growing cycle (tonnes) 2344 NA MPFF Compliance
South Cava 44673 12f48793-d3e1-46c9-88cc-d1571b09dfbc Date peak biomass first reached 44602 NA MPFF Compliance
South Cava 44673 12f48793-d3e1-46c9-88cc-d1571b09dfbc Date when biomass reduced to 75% of peak biomass 44658 NA MPFF Compliance
South Cava 44673 12f48793-d3e1-46c9-88cc-d1571b09dfbc Date of survey (start date) 44672 NA MPFF Compliance
South Cava 44673 12f48793-d3e1-46c9-88cc-d1571b09dfbc Date of survey (finish date) 44673 NA MPFF Compliance
South Cava 44673 12f48793-d3e1-46c9-88cc-d1571b09dfbc Biomass on site at time of survey (tonnes) 1485 NA MPFF Compliance
South Cava 44673 12f48793-d3e1-46c9-88cc-d1571b09dfbc If fallow, date fish last on site NA NA MPFF Compliance
South Cava 44673 12f48793-d3e1-46c9-88cc-d1571b09dfbc Site centre Easting 333270 NA MPFF Compliance
South Cava 44673 12f48793-d3e1-46c9-88cc-d1571b09dfbc Site centre Northing 9333270 NA MPFF Compliance
South Cava 44673 12f48793-d3e1-46c9-88cc-d1571b09dfbc Number of pens 16 NA MPFF Compliance
South Cava 44673 12f48793-d3e1-46c9-88cc-d1571b09dfbc Number of pens stocked at time of survey 14 NA MPFF Compliance
South Cava 44673 12f48793-d3e1-46c9-88cc-d1571b09dfbc Pen dimension 120m NA MPFF Compliance
South Cava 44673 12f48793-d3e1-46c9-88cc-d1571b09dfbc Pen configuraton 8 x 2 NA MPFF Compliance
South Cava 44673 12f48793-d3e1-46c9-88cc-d1571b09dfbc Surveyed by Cooke Aquaculture Scotland NA MPFF Compliance
South Cava 44673 12f48793-d3e1-46c9-88cc-d1571b09dfbc Comments (any relevant information) Organic matter results for mps stations are given in “TOC” boxes - NOTE these are %LOI and not TOC figures NA MPFF Compliance
South Cava 44673 12f48793-d3e1-46c9-88cc-d1571b09dfbc Fauna Biotikos NA MPFF Compliance
South Cava 44673 12f48793-d3e1-46c9-88cc-d1571b09dfbc Carbon Peatfield Scientific NA MPFF Compliance
South Cava 44673 12f48793-d3e1-46c9-88cc-d1571b09dfbc Particle Size Peatfield Scientific NA MPFF Compliance
South Cava 44673 12f48793-d3e1-46c9-88cc-d1571b09dfbc Residues NA NA MPFF Compliance
South Cava 44673 12f48793-d3e1-46c9-88cc-d1571b09dfbc Report By Inga Williamson NA MPFF Compliance
South Cava 44673 12f48793-d3e1-46c9-88cc-d1571b09dfbc Report Date 44775 NA MPFF Compliance
South Cava 44673 12f48793-d3e1-46c9-88cc-d1571b09dfbc Authorised By Inga Williamson NA MPFF Compliance
South Cava 44673 12f48793-d3e1-46c9-88cc-d1571b09dfbc Authorised date 44775 NA MPFF Compliance
South Cava 44673 PE-1 Description (unprotected cell - can be edited) SW0 NA MPFF Compliance
South Cava 44673 PE-1 Easting 333031 NA MPFF Compliance
South Cava 44673 PE-1 Northing 998594 NA MPFF Compliance
South Cava 44673 PE-1 Depth (m) 28.3 NA MPFF Compliance
South Cava 44673 PE-1 Date sampled (dd/mm/yy) 44672 NA MPFF Compliance
South Cava 44673 PE-1 Time sampled (hh:mm) 0.4513888888888889 NA MPFF Compliance
South Cava 44673 PE-1 Parmeters sampled: Fauna (Yes/No) Yes NA MPFF Compliance
South Cava 44673 PE-1 Carbon (Yes/No) No NA MPFF Compliance
South Cava 44673 PE-1 Particle Size (Yes/No) Yes NA MPFF Compliance
South Cava 44673 PE-1 Emamectin Benzoate Residues (Yes/No) No NA MPFF Compliance
South Cava 44673 PE-6 Parmeters sampled: Fauna (Yes/No) NA NA MPFF Compliance
South Cava 44673 Add-1 Distance from cages (m) 506 NA MPFF Compliance
South Cava 44673 Add-1 Direction from cages (deg) SW - 222 NA MPFF Compliance
South Cava 44673 PE-1 Description SW0 NA MPFF Compliance
South Cava 44673 PE-1 Depth 28.3 NA MPFF Compliance
South Cava 44673 PE-1 Date sampled 44672 NA MPFF Compliance
South Cava 44673 PE-1 % Grab filled 70 NA MPFF Compliance
South Cava 44673 PE-1 Grab size 4.4999999999999998E-2 NA MPFF Compliance
South Cava 44673 PE-1 Colour Dark brown NA MPFF Compliance
South Cava 44673 PE-1 Consistency/Texture Fine sand, silt NA MPFF Compliance
South Cava 44673 PE-1 Surface smell (Yes/No) No NA MPFF Compliance
South Cava 44673 PE-1 Fungus (Yes/No) No NA MPFF Compliance
South Cava 44673 PE-1 % < 0.063mm 3.2727170993733208 NA MPFF Compliance
South Cava 44673 PE-1 % 0.125-0.063mm 16.226359668755592 NA MPFF Compliance
South Cava 44673 PE-1 % 0.25-0.125mm 51.504168531781552 NA MPFF Compliance
South Cava 44673 PE-1 % 0.5 - 0.25mm 20.387057967770811 NA MPFF Compliance
South Cava 44673 PE-1 % 1 - 0.5mm 3.5312220232766336 NA MPFF Compliance
South Cava 44673 PE-1 % 2 - 1mm 2.2896150402864812 NA MPFF Compliance
South Cava 44673 PE-1 % 4 - 2mm 2.3059814234556848 NA MPFF Compliance
South Cava 44673 PE-1 % 8 - 4mm 0.48287824529991036 NA MPFF Compliance
South Cava 44673 PE-1 % > 8mm 0 NA MPFF Compliance
South Cava 44673 PE-1 Degree of sorting Moderately Sorted NA MPFF Compliance
South Cava 44673 PE-1 Degree of skewness Coarse Skewed NA MPFF Compliance
South Cava 44673 PE-1 Degree of kurtosis Very Leptokurtic NA MPFF Compliance
South Cava 44673 PE-1 Folk Triangle Slightly Gravelly Sand NA MPFF Compliance
South Cava 44673 PE-1 Number of taxa (S) 5 NA MPFF Compliance
South Cava 44673 PE-1 Abundance (N) 1357 NA MPFF Compliance
South Cava 44673 PE-1 Magalef’s Richness (d) 0.55455184291975967 NA MPFF Compliance
South Cava 44673 PE-1 Pielou’s Evenness (J) 0.25807116764664573 NA MPFF Compliance
South Cava 44673 PE-1 S-Wiener Diversity H’log 2 0.59922269463913325 NA MPFF Compliance
South Cava 44673 PE-1 Number of Enrichment Polychaete Species 2 NA MPFF Compliance
South Cava 44673 PE-1 Abundance of Enrichment Polychaetes (m2) 1555.5555555555557 NA MPFF Compliance
South Cava 44673 PE-1 ITI 0.24723655121592003 NA MPFF Compliance
South Cava 44673 PE-1 IQI 0.34918566141370255 NA MPFF Compliance
South Cava 44673 PE-1 Replicate 1 (see note 1 below) NA NA MPFF Compliance
South Cava 44673 PE-1 Replicate 2 (see note 1 below) NA NA MPFF Compliance
South Cava 44673 PE-1 Replicate 3 (see note 1 below) NA NA MPFF Compliance
South Cava 44673 PE-1 Mean (see note 1 below) NA NA MPFF Compliance
South Cava 44673 PE-1 LOD NA NA MPFF Compliance
South Cava 44673 PE-1 Number of replicates 2 NA MPFF Compliance
South Cava 44673 PE-1 MCS Code A Astrorhiza limicola MPFF Compliance
South Cava 44673 PE-1 comment NA Astrorhiza limicola MPFF Compliance
South Cava 44673 PE-1 Taxon abundance 0 Astrorhiza limicola MPFF Compliance
South Cava 44673 PE-2 Transect 2 Species Abundance Matrix A Astrorhiza limicola MPFF Compliance
South Cava 44673 PE-3 Transect 3 Species Abundance Matrix A Astrorhiza limicola MPFF Compliance
South Cava 44673 PE-4 Transect 4 Species Abundance Matrix A Astrorhiza limicola MPFF Compliance
South Cava 44673 PE-5 Transect 5 Species Abundance Matrix MCS Code (optional) Taxon Name (WoRMS compliant) MPFF Compliance
South Cava 44673 PE-6 Transect 6 Species Abundance Matrix MCS Code (optional) Taxon Name (WoRMS compliant) MPFF Compliance
South Cava 44673 Add-1 Additional Stations Species Abundance Matrix A Astrorhiza limicola MPFF Compliance

Assessment

Function code used to run this assessment.

assessment_function <- function(data, ...) {
  args <- list(...)
  if (length(args) > 0) {
    results <- kraken::kraken(data, ...)
  } else {
    results <- kraken::kraken(data, hera_format = TRUE)
  }
  return(results)
}

Outcome

The outcome of your assessment.

question response
stationNumber Compliant: Min. number of stations have been taken (8)
twoConsecutiveStations Compliant: 2 consecutive stations at Good are returned
breachDistanceBestFit 97
breachLongitude -3.16422049312546
breachLatitude 58.8689019637718
area_95_confidence 150767.591036397
package_version 1.0.0
package_date 2025-12-01
IQI 0.349185661413703
Easting 333031
Northing 998594
MCFF_Transect South Cava - 1
Longitude -3.16298523772361
Latitude 58.8694927035989
Bearing -132.717726616201
Distance 0
Number of stations per transect 8
WFD status Poor
ellipse object
polygon object
spotfire_ellipse object
breachPositionEnsemble NA
hex_df object
map object
model_info object
ellipse_warnings NA
sign NA
area_warning NA
geoDf object
Median distance to Good (m) NA

Check

Run checks on the assessment.

#> Test passed with 1 success 🎊.
#> Test passed with 1 success 🎊.
check value
standard_names TRUE
standard_required TRUE
standard_required_values TRUE

Update

Update the catalogue of assessments to make them available.

#> ✔ Setting active project to "/home/runner/work/hera/hera".
#> ✔ Saving "catalogue" to "data/catalogue.rda".
#> ☐ Document your data (see <https://r-pkgs.org/data.html>).

After updating the catalogue, rebuild the package, click on Build > Install and Restart menu or ‘Install and Restart’ button in the Build pane.

Test

This section tests if this assessment is usable using assessment function.

Launch app

Below is an interactive application displaying the results of your assessment.