calcClassScot: Calculate Classification Results for Scotland

In aquaMetrics/fcs2: Fisheries Classification Scheme 2 For SNIFFER

Description

R Script for calculating new EQRs (for latest FCS2 model) for Scotland

Usage

calcClassScot(data, seed = NULL)

Arguments

data

dataframe with columns: DataHeldBy Data owner descriptor Field data SiteCode Unique site code e.g. SEPA location code Field data SiteName Site name Field data SurveyDate Date of survey Field data WBId SEPA Water body ID SEPA GIS system/ SEWeb WBName SEPA Waterbody Name SEPA GIS system/ SEWeb NumberOfRuns Number of separate runs in electrofishing survey Field data SurveyArea Wetted area of survey site in square metres Field data 5-1628 WetWidth Wetted width of survey site in metres Field data 0.3-41 Slope Slope of survey site, in metres per kilometre GIS or paper maps 0.01-153 BarrierType Type of impassable barrier downstream, if present. 3 possible values: Artificial, Manmade or Blank Field data and/or analysis of barrier data on SEWeb ImpassableBarriers Is the site above an impassable barrier? 2 possible values; 1= present, 0= absent Field data and/or analysis of barrier data on SEWeb CatchmentAreaUpstream Total catchment area upstream in square km GIS 0.05-2550 CatchmentDrainageDirection Catchment drainage direction. Where does catchment enter the sea? Seven possible categories: SE= Tweed estuary to Fife Ness E=Fife Ness to Fraserburgh NE= Fraserburgh to Duncansby Head N= Duncansby Head to Cape Wrath NW= Cape Wrath to Mallaig W= Mallaig to Mull of Kintyre SW= Mull of Kintyre to Solway Firth GeologyClass Predominant geology type in catchment. 3 possible categories: S=Siliceous, C=Calcareous, O=Organic Altitude Site altitude (metres above sea level) Field data or GIS 1-499 DistanceFromSource Distance from the site to the furthest upstream source (metres) GIS 115-125066 DistanceToSea Distance downstream from the site to the tidal limit (metres) GIS 2-160267 AnnualMeanFlow Annual mean flow in cubic metres per second Hydrological modelling (Low Flows Enterprise of similar) 0.003-59.9 AlkalinityValue Alkalinity as CaCO3 (mg/L) Chemistry monitoring data 0.54-263.11 TotalPValue Total Phosphorus as P (mg/L) Chemistry monitoring data 0.006-0.505 DOCValue Dissolved organic carbon<0.45μm (mg/L) Chemistry monitoring data 2.023-24.2 SuspendedSolidsValue Suspended solids (mg/L) Chemistry monitoring data 0.63-32.36 HydrometricAreaNo The SEPA-defined hydrometric area which the site lies in SEPA GIS layer LandUse.AgriculturalAreas Defined as the following Corrine codes: Pastures (231), Non-irrigated arable land (211), Complex cultivation patterns (242), Land principally occupied by agriculture with significant areas or natural vegetation (243) GIS analysis of Corrine data 0-99.9 LandUse.ConiferousForests catchment with coniferous forest landuse (Corrine Code 312) GIS analysis of Corrine data 0-92.9 Field Description Source LandUse.Wetlands following Corrine codes: Inland marshes (411), Peat bogs (412), Intertidal flats (423) GIS analysis of Corrine data 0-95.7 Substrate.Small Total Organic", "silt", "sand" and "gravel", from SFCC survey protocol Field data 0-100 Substrate.Large Total "Pebble", "cobble" and "boulder" from SFCC survey protocol Field data 0-100 Substrate.Bedrock Total from SFCC survey protocol Field data 0-90 Salmon_fry.Run1Total Total salmon fry (0+) caught in Run 1 Field data 0-1014 Salmon_fry.Run2Total Total salmon fry (0+) caught in Run 2. Leave blank if no 2nd run fished Field data 0-352 Salmon_fry.Run3Total Total salmon fry (0+) caught in Run 3. Leave blank if no 3rd run fished Field data 0-251 Salmon_fry.Run4Total Total salmon fry (0+) caught in Run 4. Leave blank if no 4th run fished Field data 0-12 Salmon_parr.Run1Total Total salmon parr (1++) caught in Run 1 Field data 0-133 Salmon_parr.Run2Total Total salmon parr (1++) caught in Run 2. Leave blank if no 2nd run fished Field data 0-68 Salmon_parr.Run3Total Total salmon parr (1++) caught in Run 3. Leave blank if no 3rd run fished Field data 0-34 Salmon_parr.Run4Total Total salmon parr (1++) caught in Run 4. Leave blank if no 4th run fished Field data 0-15 Trout_fry.Run1Total Total salmon fry (0+) caught in Run 1 Field data 0-508 Trout_fry.Run2Total Total salmon fry (0+) caught in Run 2. Leave blank if no 2nd run fished Field data 0-225 Trout_fry.Run3Total Total salmon fry (0+) caught in Run 3. Leave blank if no 3rd run fished Field data 0-96 Trout_fry.Run4Total Total salmon fry (0+) caught in Run 4. Leave blank if no 4th run fished Field data 0-59 Trout_parr.Run1Total Total salmon parr (1++) caught in Run 1 Field data 0-120 Trout_parr.Run2Total Total salmon parr (1++) caught in Run 2. Leave blank if no 2nd run fished Field data 0-70 Trout_parr.Run3Total Total salmon parr (1++) caught in Run 3. Leave blank if no 3rd run fished Field data 0-43 Trout_parr.Run4Total Total salmon parr (1++) caught in Run 4. Leave blank if no 4th run fished Field data 0-25

seed

random number seed to alow repeatable results

Details

Calculate Classification Results for Scotland

Value

dataframe

Examples

  ## Not run: 
  results <- calcClassScot(data = fcs2::demo_data)#'

## End(Not run)

aquaMetrics/fcs2 documentation built on Aug. 21, 2021, 12:55 p.m.