Merge branch 'exploration_GR3D_process' of...

Merge branch 'exploration_GR3D_process' of gitlab-ssh.irstea.fr:SimAquaLife/GR3D into SpawnerRunAnalysis

exploration/NEA_calibration_offline/6-Growth_Calibration.Rmd

@@ -184,8 +184,8 @@ Stich2020_sel <- read_csv("../NEA_calibration_offline/Stich_Table 9.csv") %>%
   mutate(L0_theo = vonBertalanffyLengthAtHatch(Linf, K, t0)) 
 #create a data frame and compute L at age with values from Stich
 
-growthInOffshore <- expand_grid(basin_name = nea_riverBasinFeatures$basin_name , age = seq(0,14.75,.25)) %>%
-  mutate(season = case_when(
+growthInOffshore <- expand_grid(basin_name = nea_riverBasinFeatures$basin_name , age = seq(0,9.75,.25)) %>%
+  mutate(season = case_when (
     (age - floor(age)) == 0.00 ~ 'spring',
     (age - floor(age)) == 0.25 ~ 'summer',
     (age - floor(age)) == 0.50 ~ 'fall',
@@ -587,7 +587,7 @@ growParOptim <- data.frame(value = growth_optimal$par) %>%
   rownames_to_column("parameter")
 
 #Rdata
-save(growth_optimal, res, res_B, res_C, file = "growth_optimal.RData")
+#save(growth_optimal, res, res_B, res_C, file = "growth_optimal.RData")
 
 #csv
 write_csv(growParOptim, "growParOptim.csv")
@@ -613,6 +613,7 @@ dataVerif %>% group_by(metapop, age) %>%
   geom_line(aes(y = LStich)) +
   geom_line(aes(y = L)) 
 
+save(dataVerif, growth_optimal,res, res_B, res_C, file = "growth_optimal.RData")
 
 # thermal response curve with average seasonal temperature experienced by fish 
 dataTemperatureMetapop <- dataVerif %>% 
@@ -636,11 +637,10 @@ data.frame(temperature = seq(0,40,0.1)) %>%
 
 ```{r draw growth curves}
 
-load("growth_optimal.RData")
-
+#load("growth_optimal.RData")
 
 growthCurves = computeGrowOpt(growth_optimal$par, growthInOffshore)
-
+save(growthCurves, file = "growthCurves.RData")
 
 #growth curve according to metapopulations 
 growthCurves %>% 
@@ -651,7 +651,8 @@ growthCurves %>%
   #scale_x_continuous(limits = c(0, 10)) +
   geom_hline(yintercept = 45, color = "pink", linetype =1)+ #female
   geom_hline(yintercept = 40, color = "lightblue", linetype = 1)+
-  facet_wrap(.~ metapop, ncol =3)
+  geom_vline(aes(age), xintercept = 8, linetype = 1)+
+  facet_wrap(.~ metapop, ncol =1)
 
 #temperature effect 
 temp <- seq(0,45,0.1)
@@ -680,30 +681,6 @@ df %>%
 ```
 
 
-```{r growth try, echo = FALSE, warning=FALSE}
-
-#k depending on water temperature in ofsshore basins 
-kTempEffect = function(kopt, temp, Tmin, Topt, Tmax){
-  
-  kTemp <- kopt * temperatureEffect(temp, 
-                                    Tmin, 
-                                    Topt, 
-                                    Tmax)
-  
-  return(kTemp)}
-
-#Generic function
-vonBertalanffyGrowthWithTempEffect = function(temp, age, L0, Linf, Kopt, Tmin, Topt, Tmax){
-  
-  
-  koptTemp = kTempEffect(Kopt, temp, Tmin, Topt, Tmax)
-  
-  t0 = log(1 - L0 / Linf) / koptTemp
-  
-  return(Linf * (1 - exp(-koptTemp * (age - t0))))
-}
-
-```