diff --git a/R/GB_alternate_balancing.R b/R/GB_alternate_balancing.R index 853fbb3..ea172b2 100644 --- a/R/GB_alternate_balancing.R +++ b/R/GB_alternate_balancing.R @@ -135,6 +135,24 @@ GB.params.adj$model[Group %in% aggEE, EE := 0.8] GB.params.adj$model[Group %in% c('AtlHerring', 'AtlMackerel'), Biomass := Biomass * 10] +# Step 02 - Ocean Quahog ------------------------------------- +GB.new <- rpath(GB.params.adj, eco.name = 'Georges Bank') +check.mort(GB.new, 'OceanQuahog') +# Macrobenthos and Megabenthos. Some AmLobster and OtherDemersals +# Move predation on OceanQuahog to AtlScallop and SurfClam +GB.params.adj$diet[Group == 'OceanQuahog', Macrobenthos := 0.0002] # removed 0.005 +GB.params.adj$diet[Group == 'AtlScallop', Macrobenthos := Macrobenthos + 0.0025] +GB.params.adj$diet[Group == 'SurfClam', Macrobenthos := Macrobenthos + 0.0025] + +GB.params.adj$diet[Group == 'OceanQuahog', Megabenthos := Megabenthos - 0.028] +GB.params.adj$diet[Group == 'SurfClam', Megabenthos := Megabenthos + 0.028] + +GB.params.adj$diet[Group == 'OceanQuahog', AmLobster := AmLobster - 0.02] +GB.params.adj$diet[Group == 'SurfClam', AmLobster := AmLobster + 0.01] +GB.params.adj$diet[Group == 'Detritus', AmLobster := AmLobster + 0.01] + +GB.params.adj$diet[Group == 'OceanQuahog', OtherDemersals := OtherDemersals - 0.06] +GB.params.adj$diet[Group == 'OtherDemersals', OtherDemersals := OtherDemersals + 0.06] #Step 02 - Deal with OceanPout, AmPlaice, and WitchFlounder---- @@ -432,9 +450,12 @@ GB.params.adj$model[Group == 'RedHake', Biomass := Biomass * 2] # Step 18 - EE < 1.5 ----------------- -# Haddock, Microzooplankton, LgCopepods, SmCopepods, Loligo +# OceanQuahog, Haddock, Microzooplankton, LgCopepods, SmCopepods, Loligo # AmPlaice, Scup, AtlHerring, Detritus, WinterFlounder, YTFlounder +# OceanQuahog +GB.params.adj$model[Group == 'OceanQuahog', PB := 0.02] + # Haddock check.mort(GB.new, 'Haddock') # increase B @@ -475,7 +496,7 @@ GB.params.adj$model[Group %in% c('Microzooplankton', 'LgCopepods','SmCopepods'), #Increase unassim to 0.3 for other detritavores GB.params.adj$model[Group %in% c('AmLobster', 'Macrobenthos', 'Megabenthos', - 'AtlScallop', 'OceanQuahog', 'OtherShrimps'), + 'AtlScallop', 'OtherShrimps'), Unassim := 0.3] # Loligo @@ -518,7 +539,7 @@ GB.params.adj$model[Group == 'YTFlounder', Biomass := Biomass * 1.1] GB.params.adj$diet[Group == 'Odontocetes', Sharks := Sharks + 0.025] -# EDITED TO HERE ------------ +# Check EEs and params ------------------------------------- GB.new <- rpath(GB.params.adj, eco.name = 'Georges Bank') check.rpath.params(GB.params.adj) check.ee(GB.new) diff --git a/data-raw/R/GBRpath_bioparams.R b/data-raw/R/GBRpath_bioparams.R index 66d3878..3a291c0 100644 --- a/data-raw/R/GBRpath_bioparams.R +++ b/data-raw/R/GBRpath_bioparams.R @@ -3,9 +3,12 @@ #Required packages-------------------------------------------------------------- #remotes::install_github("ropensci/rfishbase") -library(rfishbase); library(data.table) +library(rfishbase); library(data.table); library(here) load(here('data-raw', 'Species_codes.RData')) +#Load prebal functions +source(here('R', 'PreBal.R')) + #User functions----------------------------------------------------------------- rightcase <- function(x){ out <- c() @@ -116,6 +119,14 @@ surf <- copy(GB.double[RPATH == 'OceanQuahog', ]) surf[, RPATH := 'SurfClam'] GB.double <- rbindlist(list(GB.double, surf)) +# OceanQuahog PB value too high for such a long-lived species +# Frequently reach 200 years old (Butler et al., 2013) +pbcalc(200) + +GB.double[RPATH == 'OceanQuahog', PB := 0.0125] +# Adjust QB so P/Q is 0.1 +GB.double[RPATH == 'OceanQuahog', QB := 0.125] + GB.params <- rbindlist(list(GB.params, GB.double)) #FishBase----------------------------------------------------------------------- diff --git a/data/GB.init.rda b/data/GB.init.rda index 59b9b35..65c853b 100644 Binary files a/data/GB.init.rda and b/data/GB.init.rda differ diff --git a/data/GB.params.rda b/data/GB.params.rda index 1edfe0b..6de979d 100644 Binary files a/data/GB.params.rda and b/data/GB.params.rda differ diff --git a/data/alternate.GB.bal.rda b/data/alternate.GB.bal.rda index 9be3125..bbc1fe2 100644 Binary files a/data/alternate.GB.bal.rda and b/data/alternate.GB.bal.rda differ diff --git a/data/alternate.GB.params.bal.rda b/data/alternate.GB.params.bal.rda index 2505f14..71b8d1f 100644 Binary files a/data/alternate.GB.params.bal.rda and b/data/alternate.GB.params.bal.rda differ diff --git a/data/bio.input.rda b/data/bio.input.rda index dd9e46b..a850ee3 100644 Binary files a/data/bio.input.rda and b/data/bio.input.rda differ diff --git a/data/bioparam.input.rda b/data/bioparam.input.rda index e261781..20af180 100644 Binary files a/data/bioparam.input.rda and b/data/bioparam.input.rda differ diff --git a/data/diet.input.rda b/data/diet.input.rda index 3a3cb39..40c2835 100644 Binary files a/data/diet.input.rda and b/data/diet.input.rda differ