Upload files for script source

exploration/GR3D_Rdescription/GR3D_NEA_XML_parameters.R

+#read the XML file to upload the set of parameters included in GR3D-US
+fishXML <- xmlToList(xmlParse("../../data/input/northeastamerica/fishRIOBasin_Sapidissima.xml"))
+
+#Upload parameters linked to reproduction
+reproducePar = data.frame(t(unlist(fishXML[[1]][["processes"]][["processesEachStep"]][["species.ReproduceAndSurviveAfterReproductionWithDiagnose"]]))) %>% 
+  select(-c(synchronisationMode, reproductionSeason, proportionOfFemaleAtBirth,
+            sigmaRecruitment, maxNumberOfSuperIndividualPerReproduction, withDiagnose,
+            displayFluxesOnConsole)) %>% 
+  rename("TminRep" = "tempMinRep",
+         "ToptRep" = "tempOptRep",
+         "TmaxRep" = "tempMaxRep",
+         "ratioS95_S50" = "ratioS95__S50",
+         "deltaT" = "delta__t") %>% 
+  mutate_all(~as.numeric(as.character(.))) 
+
+#Upload parameters linked to survival in river 
+survivePar = data.frame(t(unlist(fishXML[[1]][["processes"]][["processesEachStep"]][["species.Survive"]]))) %>% 
+  select(-synchronisationMode) %>% 
+  rename("TminSurv" = "tempMinSurvivalSpawnerInRiv", 
+         "ToptSurv" = "tempOptSurvivalSpawnerInRiv",
+         "TmaxSurv" = "tempMaxSurvivalSpawnerInRiv",
+         "survProbOptRiver" = "survivalProbOptSpawnerInRiv") %>% 
+  mutate_all(~as.numeric(as.character(.))) 
+
+
+#Upload parameters linked to growth at sea
+growPar = data.frame(t(unlist(fishXML[[1]][["processes"]][["processesEachStep"]][["species.Grow"]]))) %>% 
+  select(-synchronisationMode ) %>% 
+  mutate(linfVonBertForMale = fishXML[[1]][["linfVonBertForMale"]], 
+         linfVonBertForFemale = fishXML[[1]][["linfVonBertForFemale"]],
+         lengthAtHatching = fishXML[[1]][["lengthAtHatching"]],
+         lFirstMaturityForMale = fishXML[[1]][["lFirstMaturityForMale"]],
+         lFirstMaturityForFemale = fishXML[[1]][["lFirstMaturityForFemale"]]) %>% 
+  mutate_all(~as.numeric(as.character(.)))
+

exploration/GR3D_Rdescription/GR3D_NEA_env_data.R

+#-------------------------------------
+#Read and upload environmental data 
+#-------------------------------------
+
+#---------Temperature ----------------
+#temperature in river basins
+tempInriver <- read_csv("../../data/input/northeastamerica/observed_river_temperatures.csv")
+#temperature in inshore basins
+tempInInshore <- read_csv("../../data/input/northeastamerica/observed_inshore_temperatures.csv")
+#temperature in offshore basins
+tempInOffshore <- read_csv("../../data/input/northeastamerica/observed_offshore_temperatures.csv")
+#connections between inshore and offshore
+
+#---------Characteristic----------------
+#characteristics of the river basins
+nea_riverbasin_features <- read_csv("../../data/input/northeastamerica/nea_riverbasins.csv")
+#Upload presence and absence in US river basins
+nea_presence <- read_csv("../../data/input/northeastamerica/nea_presence.csv")
+#upload connections between inshore and offshore basins
+connections <- read_csv("../../data/input/northeastamerica/inshore_offshore_connections.csv")
+
+ 
\ No newline at end of file

exploration/GR3D_Rdescription/GR3Dfunction.R

-
+#----------------------------------------------
+# Temperature effect
+#----------------------------------------------
 # temperature effect in GR3D
 # from Rosso
 temperatureEffect = function(tempWater, Tmin, Topt, Tmax){
@@ -18,9 +20,9 @@ thermalRange = function(pct = 0.8, Tmin, Topt, Tmax){
 
 #optimalThermalRange(Tmin = 3, Topt = 17, Tmax =27)
 
-# ----------------------------------------------
-# growth simulation
-#=---------------------------------------------
+#----------------------------------------------
+# Growth simulation
+#---------------------------------------------
 # von Bertalaffy : L = f(age)
 vonBertalanffyGrowth = function(age, L0, Linf, K){
   t0 = log(1 - L0 / Linf) / K
@@ -88,3 +90,113 @@ strayerSurvival = function(distance, m ){
   # m: extra mortality rate for strayers (L-1)
   return(exp(-m * distance))
 }
+
+#-------------------------------------------------------
+# Spwaner survival before reproduction 
+# Dome-shape curve with temperature effect
+#-------------------------------------------------------
+spawnerSurvivalPreReproduction <- function(Triver,Tmin, Topt, Tmax){
+  
+  #River survival
+  survProbOptRiver =  survivePar$survProbOptRiver
+  
+  spRiver = survProbOptRiver * TemperatureEffect(Triver, Tmin, Topt, Tmax)
+  
+  #StockAfterSurv = S * SpRiver
+  
+  return(spRiver)
+  
+}
+
+#----------------------------------------------
+# Stock Recruitement relationship
+#See Rougier et al, 2014; 2015 and Jatteau et al., 2017
+#----------------------------------------------
+#survival of larvae 14dph from Jatteau et al, 2017
+stockRecruitementRelationship <- function(Triver,Tmin, Topt, Tmax, survivalStock) {
+  
+  surfaceWatershed = 84810 #Surface de la Garonne 
+  lambda = reproducePar$lambda
+  deltaT = reproducePar$deltaT
+  survOptRep =  reproducePar$survOptRep
+  n = reproducePar$eta #simule l'effet allee
+  ratioS95_S50 = reproducePar$ratioS95_S50
+  alpha =  reproducePar$a #species fecundity 
+  survProbOptRiver =  survivePar$survProbOptRiver
+  periodAtSea = 5 - deltaT
+  
+  ###--------------------- SR relationship -----------------
+  
+  #parametre c de la RS de BH intgrant un effet du BV considr 
+  cj = lambda/surfaceWatershed
+  
+  #parametre b reprsentant la mortalit densit dpendante de la RS de BH intgrant un effet de la temperature
+  # bj = (-(1/deltaTrecruitement))*
+  #   log(survOptRep * temperatureEffect(temp, 9.8, 20.0, 26.0))
+  
+  bj = -log(survOptRep * temperatureEffect(Triver, Tmin , Topt , Tmax)) / deltaT
+  
+  #parametre a (fcondit de l'espce) de la RS de BH intgrant un effet de la temperature
+  alphaj = (bj * exp(-bj * deltaT)) / (cj * (1 - exp(-bj * deltaT)))
+  alphaj[is.na(alphaj)] <- 0
+  
+  #Bj = paramtre de la relation SR intgrant l'effet de la temprature 
+  betaj = bj/(alpha*cj*(1 - exp(-bj*deltaT)))
+  
+  #p = proportion de gniteurs participant  la reproduction en focntion de la quantit de gniteur total
+  #p = 1/(1+exp(-log(19)*(S-n)/(Ratio*surfaceWatershed)))
+  
+  S95 = n * surfaceWatershed
+  S50 = S95/ratioS95_S50
+  
+  p = 1/(1 + exp(-log(19)*(survivalStock - S50)/(S95 - S50)))
+  
+  #relation Stock Recrutement ie calcul le nombre de recrues en fonction du nombre de gniteurs et de la T en intgrant l'effet Allee 
+  
+  #R0 = aj * S * p 
+  
+  alleeEffect = 1/(1 + exp(-log(19)*(survivalStock - n/ratioS95_S50*surfaceWatershed)/(n*surfaceWatershed - n/ratioS95_S50*surfaceWatershed)))
+  
+  
+  Rj = (alphaj * SurvivalStock * alleeEffect)/(betaj + survivalStock * alleeEffect)
+  
+  #Rj = ((aj * S) * p)/(Bj +S * p)
+  
+  stockRecruitement = as.vector(Rj)
+  
+  return(stockRecruitement)
+}
+
+
+# ----------------------------------------------
+# Spawner survival after reproduction 
+#----------------------------------------------
+#Logit with temperature effect
+spawnerSurvivalPostReproduction <- function(Triver,Tref, coeffa, coeffb){
+  
+  spRiverPostSpawn = (coeffb/ (1 + exp(coeffa*(Triver-Tref))))
+  
+  return(spRiverPostSpawn)
+  
+}
+
+#Dome-shape curve with temperature effect 
+spawnerSurvivalPostReproductionWithBellCurve <- function(Triver, Tmin, Topt, Tmax, coeffa, coeffb){
+  
+  #P1: 
+  #SpRiverPostSpawn = probSurvAfterRepro/(probSurvAfterRepro + (1 - probSurvAfterRepro)*exp(-coeffLogit*(TemperatureEffect(Triver, Tmin, Topt, Tmax))))
+  
+  #P2: 
+  #SpRiverPostSpawn = probSurvAfterRepro/(probSurvAfterRepro + (1 - probSurvAfterRepro)*exp(-coeffLogit))
+  #SpRiverPostSpawnTempEffect = (probSurvAfterRepro/(probSurvAfterRepro + (1 - probSurvAfterRepro)*exp(-coeffLogit))) * TemperatureEffect(Triver, Tmin, Topt, Tmax)
+  
+  #P3: 
+  spRiverPostSpawn = coeffb * temperatureEffect(Triver, Tmin, Topt, Tmax)
+  
+  stockAfterSpawn = S * spRiverPostSpawn 
+  
+  return(spRiverPostSpawn)
+}
+
+
+