From 86bbcde9feb3a7a2a8f31071be0800ec4990a0ed Mon Sep 17 00:00:00 2001
From: thierrychambert <thierry.chambert@gmail.com>
Date: Thu, 24 Jun 2021 09:01:35 +0200
Subject: [PATCH] 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 | 8 +++++---
junk.R | 35 +++++++++++++++++++++++++++--------
run_analysis.R | 2 +-
3 files changed, 33 insertions(+), 12 deletions(-)
diff --git a/R/models.R b/R/models.R
index 7fa630d..b0fcf3b 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 9541fca..ff3f67d 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 9e3a0d7..21c6a00 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)
--
GitLab