diff --git a/R/models.R b/R/models.R index 7fa630dfa3cd8f8587f52cb854978c5b542b4fd2..b0fcf3bfc7313663d1dfe17f784cdb792306003f 100644 --- a/R/models.R +++ b/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)) diff --git a/junk.R b/junk.R index 9541fca6d66ada1b097af8c792e0f5803b612d26..ff3f67df9b0222cbdb22fa8c3112ba7988fb42f0 100644 --- a/junk.R +++ b/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) + + + + + + + + + + + + + +# 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 diff --git a/run_analysis.R b/run_analysis.R index 9e3a0d767a2febd67d67bdce3e315dcdc9e2eb9e..21c6a0048215f8495a4d33c4827e8ffe741fef1b 100644 --- a/run_analysis.R +++ b/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)