Reduced PB value for OceanQuahog to reflect their long lifespan. Made…

… downstream changes to all impacted files and the resulting balanced model

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)

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-----------------------------------------------------------------------