G3RD functions corrections for global variables

Coorection to avoid use of global variables in function

exploration/GR3D_Rdescription/GR3Dfunction.R

@@ -96,10 +96,10 @@ strayerSurvival = function(distance, m ){
 # Spwaner survival before reproduction 
 # Dome-shape curve with temperature effect
 #-------------------------------------------------------
-spawnerSurvivalPreReproduction <- function(Triver,Tmin, Topt, Tmax){
+spawnerSurvivalPreReproduction <- function(Triver,Tmin, Topt, Tmax, parSurv){
   
   #River survival
-  survProbOptRiver =  survivePar$survProbOptRiver
+  survProbOptRiver =  parSurv$survProbOptRiver
   
   spRiver = survProbOptRiver * temperatureEffect(Triver, Tmin, Topt, Tmax)
   
@@ -114,16 +114,16 @@ spawnerSurvivalPreReproduction <- function(Triver,Tmin, Topt, Tmax){
 #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$survProbOptRiver
+stockRecruitementRelationship <- function(Triver,Tmin, Topt, Tmax, survivalStock, parRep, parSurv, surfaceWatershed = 84810) {
+  
+  #surfaceWatershed = 84810 Surface de la Garonne 
+  lambda = parRep$lambda
+  deltaT = parRep$deltaT
+  survOptRep =  parRep$survOptRep
+  eta = parRep$eta #simule l'effet allee
+  ratioS95_S50 = parRep$ratioS95_S50
+  alpha =  parRep$a #species fecundity 
+  survProbOptRiver =  parSurv$survProbOptRiver
   periodAtSea = 5 - deltaT
   
   ###--------------------- SR relationship -----------------
@@ -147,7 +147,7 @@ stockRecruitementRelationship <- function(Triver,Tmin, Topt, Tmax, survivalStock
   #p = proportion de g?niteurs participant ? la reproduction en focntion de la quantit? de g?niteur total
   #p = 1/(1+exp(-log(19)*(S-n)/(Ratio*surfaceWatershed)))
   
-  S95 = n * surfaceWatershed
+  S95 = eta * surfaceWatershed
   S50 = S95/ratioS95_S50
   
   p = 1/(1 + exp(-log(19)*(survivalStock - S50)/(S95 - S50)))
@@ -156,7 +156,7 @@ stockRecruitementRelationship <- function(Triver,Tmin, Topt, Tmax, survivalStock
   
   #R0 = aj * S * p 
   
-  alleeEffect = 1/(1 + exp(-log(19)*(survivalStock - n/ratioS95_S50*surfaceWatershed)/(n*surfaceWatershed - n/ratioS95_S50*surfaceWatershed)))
+  alleeEffect = 1/(1 + exp(-log(19)*(survivalStock - eta/ratioS95_S50*surfaceWatershed)/(eta*surfaceWatershed - eta/ratioS95_S50*surfaceWatershed)))
   
   
   Rj = (alphaj * survivalStock * alleeEffect)/(betaj + survivalStock * alleeEffect)
@@ -194,7 +194,7 @@ spawnerSurvivalPostReproductionWithBellCurve <- function(Triver, Tmin, Topt, Tma
   #P3: 
   spRiverPostSpawn = coeffb * temperatureEffect(Triver, Tmin, Topt, Tmax)
   
-  stockAfterSpawn = S * spRiverPostSpawn 
+  #stockAfterSpawn = S * spRiverPostSpawn 
   
   return(spRiverPostSpawn)
 }