growth exploration R + Rmd

exploration/scriptR/NEAgrowth.R

@@ -19,7 +19,7 @@ inshore %>% filter(basin_name %in% c( 'St. Johns', 'Cape Fear', 'Connecticut', '
 
 inshore %>%  distinct(basin_name)  %>% arrange(basin_name) 
 
-offshore <- read.csv("../../data/input/northeastamerica/observed_offshore_temperatures.csv")
+# ====================
 
 offshore %>%  distinct(basin_name)
 
@@ -123,7 +123,7 @@ growData %>% ggplot(aes(x = age)) + geom_line(aes(y = L))
 
 # -------------------------------------------------------------------------------
 
-# legnth at hatching
+# legth at hatching
 growData$Lincrement[growData$age == 0] = growData$L[growData$age == 0]
 # next increments
 for (i in 2:nrow(growData)) {
@@ -131,12 +131,13 @@ for (i in 2:nrow(growData)) {
   tempEffect <- correctionGrowth  %>%  filter(basin_name == "St Lawrence") %>% select(growData$season_temperature[i])
   growData[i, 'Lincrement'] = unname(vonBertalanffyWithNextIncrement(  growData$Lincrement[i-1], 
                                 growPar$lengthAtHatching, growPar$linfVonBertForMale, growPar$kOptForMale,
-                                deltaT = 0.25, sigma = growPar$sigmaDeltaLVonBert, tempEffect = tempEffect))
+                                timeStepDuration = 0.25, sigma = growPar$sigmaDeltaLVonBert, tempEffect = tempEffect))
 }
+
 growData %>% ggplot(aes(x=age)) + geom_line(aes(y=L)) + geom_line(aes(y=Lincrement)) +
   geom_abline(intercept = growPar$lFirstMaturityForMale, slope= 0, color='red')
 
 vonBertalanffyWithNextIncrement(  growData$Lincrement[i-1], 
                                   growPar$lengthAtHatching, growPar$linfVonBertForMale, growPar$kOptForMale,
-                                  deltaT = 0.25, sigma = growPar$sigmaDeltaLVonBert, tempEffect = tempEffect)
+                                  timeStepDuration = 0.25, sigma = growPar$sigmaDeltaLVonBert, tempEffect = tempEffect)
 

exploration/scriptR/Stich_Table 9.csv

+parameter,cachtment,mean,sd,CRI_2.5%,CRI_97.5%
+Linf,coastwide,477.32,11.67,454.33,499.69
+K,coastwide,0.44,0.3,-0.38,0.51
+t0,coastwide,-0.31,0.04,-0.4,-0.23
+Linf,northern iteroparous,489.4,2.91,483.93,495.27
+Linf,semelparous,454.26,2.44,449.67,459.2
+Linf,southern iteroparous,482.76,1.83,479.36,486.64
+K,northern iteroparous,0.43,0.01,0.41,0.45
+K,semelparous,0.49,0.01,0.47,0.5
+K,southern iteroparous,0.44,0.01,0.42,0.45
+t0,northern iteroparous,-0.31,0.01,-0.34,-0.29
+t0,semelparous,-0.21,0.01,-0.24,-0.18
+t0,southern iteroparous,-0.36,0.01,-0.37,-0.34
+Linf,Albemarle,469.25,3.14,463.27,475.34
+Linf,Cape Fear,480.23,4.22,472.27,488.39
+Linf,Connecticut,531.08,8.81,514.44,549.66
+Linf,Delaware,515.49,1.49,512.63,518.49
+Linf,Merrimack,499.64,2.91,494.18,505.38
+Linf,North (MA),488.91,6.53,476.58,502.22
+Linf,Penobscot,437.98,3.31,431.74,445.01
+Linf,Potomac,463.32,2.49,458.4,468.06
+Linf,St. Johns,428.28,2.29,423.88,432.72
+Linf,Tar-Pamlico,456.94,7.64,443.36,473.36
+Linf,Upper Chesapeake Bay,508.78,2.66,503.64,513.96
+K,Albemarle,0.42,0.01,0.4,0.44
+K,Cape Fear,0.43,0.01,0.41,0.46
+K,Connecticut,0.33,0.02,0.3,0.36
+K,Delaware,0.41,0.01,0.4,0.42
+K,Merrimack,0.35,0.01,0.33,0.36
+K,North (MA),0.38,0.02,0.34,0.43
+K,Penobscot,0.65,0.03,0.59,0.73
+K,Potomac,0.51,0.02,0.48,0.54
+K,St. Johns,0.54,0.01,0.51,0.56
+K,Tar-Pamlico,0.51,0.04,0.44,0.59
+K,Upper Chesapeake Bay,0.33,0.01,0.32,0.34
+t0,Albemarle,-0.32,0.01,-0.34,-0.31
+t0,Cape Fear,-0.23,0.03,-0.28,-0.17
+t0,Connecticut,-0.36,0.01,-0.38,-0.33
+t0,Delaware,-0.29,0.01,-0.3,-0.28
+t0,Merrimack,-0.36,0.03,-0.43,-0.3
+t0,North (MA),-0.33,0.03,-0.4,-0.27
+t0,Penobscot,-0.2,0.01,-0.22,-0.18
+t0,Potomac,-0.26,0.01,-0.28,-0.25
+t0,St. Johns,-0.19,0.01,-0.21,-0.18
+t0,Tar-Pamlico,-0.29,0.03,-0.35,-0.23
+t0,Upper Chesapeake Bay,-0.62,0.01,-0.64,-0.6

exploration/scriptR/temperatureEffects.R

 
-rm(list = ls())
+#rm(list = ls())
 
 Ratkowsky = function(temperature, par){
   # Ratkowsky, D. A., McMEEKIN, T. A. & Chandler, R. E. (1983) Model for Bacterial Culture Growth Rate Throughout the Entire