Made Model 3 (with DD) simulations faster by changing the calibrate_params...

Made Model 3 (with DD) simulations faster by changing the calibrate_params function (based on optim) by an analytical approximation (using match_lam_delta function).

Tests reveals that the approx is largely good enough. Makes no differences in the results.

R/models.R

@@ -125,11 +125,13 @@ M3_WithDD_noDemoStoch <- function(N1, s, f, h, DD_params = NULL){
 
   # Apply density dependence effect
   lam_Nt <- 1 + rMAX*(1-(sum(N1)/K)^theta)
-  lam_Nt
 
   # Calibrate vital rates to match lam_Nt
-  inits <- init_calib(s = s, f = f, lam0 = lam_Nt)
-  vr_Nt <- calibrate_params(inits = inits, f = f, s = s, lam0 = lam_Nt)
+  A <- build_Leslie(s = s, f = f)
+  diff_rel_lam <- (lam_Nt - lambda(A))/lambda(A)
+  d <- match_lam_delta(diff_rel_lam = diff_rel_lam, s=s, f=f)
+  vr_Nt <- c(s,f) + d
+
   s_Nt <- head(vr_Nt, length(s))
   f_Nt <- tail(vr_Nt, length(f))
 

junk.R

@@ -10,32 +10,51 @@ h <- 0.05
 
 
 
-A <- build_Leslie(s = s, f = f)
-lambda(A)
-lam_N
+
+
 
 rMAX = 0.15
 K = sum(N1)*5
 theta = 1
 
 # Apply density dependence effect
+N1 = K
 lam_Nt <- 1 + rMAX*(1-(sum(N1)/K)^theta)
 lam_Nt
 
+
 # Calibrate vital rates to match lam_Nt
-inits <- init_calib(s = s, f = f, lam0 = lam_Nt)
-vr_Nt <- calibrate_params(inits = inits, f = f, s = s, lam0 = lam_Nt)
+A <- build_Leslie(s = s, f = f)
+diff_rel_lam <- (lam_Nt - lambda(A))/lambda(A)
+d <- match_lam_delta(diff_rel_lam = diff_rel_lam, s=s, f=f)
+vr_Nt <- c(s,f) + d
+
 s_Nt <- head(vr_Nt, length(s))
 f_Nt <- tail(vr_Nt, length(f))
 
-s ; s_Nt
-f ; f_Nt
-
 A_Nt <- build_Leslie(s = s_Nt, f = f_Nt)
 lambda(A_Nt)
 
 
 
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+# Calibrate vital rates to match lam_Nt
+inits <- init_calib(s = s, f = f, lam0 = lam_Nt)
+vr_Nt <- calibrate_params(inits = inits, f = f, s = s, lam0 = lam_Nt)
+
+
 s = s_calibrated
 f = f_calibrated
 

run_analysis.R

@@ -51,7 +51,7 @@ run0 <- run_simul(nsim, cumuated_impacts,
                   model_demo, time_horzion, coeff_var_environ, fatal_constant)
 
 
-
+# saved time (ratio): 493/12
 # save(run0, file = "./data/run0.rda")
 names(run0)