From 61c6b31d317aa955db4fbae587469adbebc20caa Mon Sep 17 00:00:00 2001
From: Andreas Gattringer <andreas.gattringer@univie.ac.at>
Date: Sun, 16 Apr 2023 19:36:25 +0200
Subject: [PATCH] made Leslie-matrix consistent with start-of-year conditions +
fixed a bug in juvenile survival rate calculation
---
src/cats/lambda/leslie_matrix.c | 107 +++++++++++++++++++++++++-------
1 file changed, 83 insertions(+), 24 deletions(-)
diff --git a/src/cats/lambda/leslie_matrix.c b/src/cats/lambda/leslie_matrix.c
index fe5c4ea..eade70b 100644
--- a/src/cats/lambda/leslie_matrix.c
+++ b/src/cats/lambda/leslie_matrix.c
@@ -60,7 +60,7 @@ get_rate_for_matrix(enum cats_vital_rate_id rate_type,
cats_dt_rates rate = calculate_rate(info, N, param, l_param->grid, l_param->row, l_param->col, &override);
if (print) {
- log_message(LOG_INFO, "%s: %Lf (maximum %Lf) for population %Lf/%Lf",
+ log_message(LOG_INFO, "%s: %Lf (maximum %Lf) for adult population density %Lf/%Lf",
info->name, rate, info->max_rate, N, K);
}
@@ -68,10 +68,22 @@ get_rate_for_matrix(enum cats_vital_rate_id rate_type,
}
+
+
+
double *
create_leslie_matrix(struct cats_configuration *conf, struct lambda_parameters *l_param, bool silent, int32_t *N_out)
{
+
+#define LM_START
+#ifndef LM_START
+ log_message(LOG_IMPORTANT, "using method LM_MID (old)");
+#else
+ //log_message(LOG_IMPORTANT, "using method LM_START (new)");
+
+#endif
+
assert (N_out != NULL);
const int32_t species_id = l_param->species_id;
const int32_t mat_max = get_vital_age_from_param(&conf->param[species_id], VA_AGE_OF_MATURITY_MAX);
@@ -108,33 +120,35 @@ create_leslie_matrix(struct cats_configuration *conf, struct lambda_parameters *
cats_dt_rates germination_to_adult_survival = get_rate_for_matrix(VR_GERMINATION_TO_ADULT_SURVIVAL,
l_param,
print_rate);
- cats_dt_rates juvenile_survival = get_juvenile_tr_from_germination_to_adult_survival(
+ cats_dt_rates juvenile_transition_rate = get_juvenile_tr_from_germination_to_adult_survival(
germination_to_adult_survival, &conf->param[species_id]);
// printf("%Lf %Lf\n", juvenile_survival, germination_to_adult_survival);
fflush(stdout);
cats_dt_rates hapaxanthy_survival = 1.0;
if (l_param->param->hapaxanthy > 0.0) {
- hapaxanthy_survival = (1.0 - l_param->param->hapaxanthy);
+ hapaxanthy_survival = (1.0 - l_param->param->hapaxanthy) * flowering_frequency;
assert(hapaxanthy_survival >= 0);
assert(hapaxanthy_survival <= 1.0);
- log_message(LOG_INFO, "hapaxanthy survival: %Lf", hapaxanthy_survival);
+ log_message(LOG_INFO, "hapaxanthy survival: %Lf, times flowering frequency %Lf", (1.0 - l_param->param->hapaxanthy), hapaxanthy_survival);
}
if (print_rate) {
- log_message(LOG_INFO, "juvenile transition: %Lf", juvenile_survival);
+ log_message(LOG_INFO, "juvenile transition: %Lf", juvenile_transition_rate);
log_message(LOG_INFO, "local dispersal %Lf", local_dispersal);
}
- double m0 = (double) age_specific_maturation_rate(0, juvenile_survival, mat_min, mat_max);
- double d = (double) (flowering_frequency * seed_yield * local_dispersal);
+
+
+ double m0 = (double) age_specific_maturation_rate(0, juvenile_transition_rate, mat_min, mat_max);
+ double dl = (double) (flowering_frequency * seed_yield * local_dispersal);
if (print_rate) {
for (int32_t i = 0; i < mat_max + 1; i++) {
log_message(LOG_RAW, "m%d = %f\n", i,
- (double) age_specific_maturation_rate(i, juvenile_survival, mat_min, mat_max));
+ (double) age_specific_maturation_rate(i, juvenile_transition_rate, mat_min, mat_max));
}
- log_message(LOG_RAW, "d = %f\n", d);
+ log_message(LOG_RAW, "d = %f\n", dl);
}
// special case:
@@ -154,34 +168,47 @@ create_leslie_matrix(struct cats_configuration *conf, struct lambda_parameters *
//return x;
}
- // FIRST ROW: transition to seeds1
+ // FIRST ROW: transition to seeds0
- // seeds: Si -> S1
+ // seeds: Si -> S0
for (int32_t s = 0; s < seed_persistence; s++) {
assert(s < N);
- matrix[0 * N + s] = (double) (germination_rate * m0 * d * seed_survival);
+ matrix[0 * N + s] = (double) (seed_survival * germination_rate * m0 * dl);
}
- // juveniles: Ji -> S1
+ // juveniles: Ji -> S0
for (int32_t j = 0; j < mat_max; j++) {
+
int32_t col = seed_persistence + j;
assert(col < N);
- cats_dt_rates m = age_specific_maturation_rate(j + 1, juvenile_survival, mat_min, mat_max);
- matrix[0 * N + col] = (double) (m * d * seed_survival);
+ cats_dt_rates m = age_specific_maturation_rate(j + 1, juvenile_transition_rate, mat_min, mat_max);
+#ifndef LM_START
+ matrix[0 * N + col] = (double) (m * dl * seed_survival);
+
+#else
+ cats_dt_rates juvenile_survival_rate = age_modified_juvenile_survival_rate(
+ juvenile_transition_rate, j, mat_min, mat_max);
+ matrix[0 * N + col] = (double) (juvenile_survival_rate * m * dl);
+#endif
}
- // adults: A -> S1
+ // adults: A -> S0
for (int32_t a = seed_persistence + mat_max; a < N; a++) {
assert(a == N - 1);
- matrix[0 * N + a] = (double) (clonal_growth * d * seed_survival);
+#ifndef LM_START
+ matrix[0 * N + a] = (double) (clonal_growth * dl * seed_survival);
+#else
+ matrix[0 * N + a] = (double) (adult_survival * clonal_growth * dl);
+#endif
}
// SEED ROWS: S_i -> S_{i+1}
for (int32_t s = 1; s < seed_persistence; s++) {
- matrix[s * N + (s - 1)] = (double) ((1.0 - germination_rate) * seed_survival);
+ matrix[s * N + (s - 1)] = (double) (seed_survival * (1.0 - germination_rate));
+
}
- // JUVENILE ROW 1:
+ // JUVENILE ROW 1: Si -> J0
for (int32_t s = 0; s < seed_persistence; s++) {
int32_t row = seed_persistence;
if (row * N + s < N * N) {
@@ -192,17 +219,31 @@ create_leslie_matrix(struct cats_configuration *conf, struct lambda_parameters *
log_message(LOG_RAW, "row = %d\n", row);
exit(EXIT_FAILURE);
}
- matrix[row * N + s] = (double) (germination_rate * (1.0 - m0) * juvenile_survival);
+#ifndef LM_START
+ cats_dt_rates juvenile_survival_rate = age_modified_juvenile_survival_rate(
+ juvenile_transition_rate, 0, mat_min, mat_max);
+ matrix[row * N + s] = (double) (germination_rate * (1.0 - m0) * juvenile_survival_rate);
+#else
+ matrix[row * N + s] = (double) ( seed_survival * germination_rate * (1.0 - m0));
+#endif
}
- // JUVENILE ROWS J2 ...: J_i -> J_{i+1}
+ // JUVENILE ROWS J1+ ...: J_i -> J_{i+1}
for (int32_t j = 0; j < mat_max; j++) {
+ cats_dt_rates juvenile_survival_rate = age_modified_juvenile_survival_rate(
+ juvenile_transition_rate, j, mat_min, mat_max);
int32_t row = j + seed_persistence + 1;
int32_t col = j + seed_persistence;
assert(row < N);
- cats_dt_rates m = age_specific_maturation_rate(j + 1, juvenile_survival, mat_min, mat_max);
- matrix[row * N + col] = (double) ((1.0 - m) * juvenile_survival);
+ cats_dt_rates m = age_specific_maturation_rate(j + 1, juvenile_transition_rate, mat_min, mat_max);
+#ifndef LM_START
+
+ matrix[row * N + col] = (double) ((1.0 - m) * juvenile_survival_rate);
+#else
+
+ matrix[row * N + col] = (double) (juvenile_survival_rate * (1.0 - m));
+#endif
}
@@ -210,18 +251,36 @@ create_leslie_matrix(struct cats_configuration *conf, struct lambda_parameters *
int32_t row = seed_persistence + mat_max;
assert(row == N - 1);
for (int32_t s = 0; s < seed_persistence; s++) {
+#ifndef LM_START
matrix[row * N + s] = (double) (germination_rate * m0 * adult_survival);
+#else
+ matrix[row * N + s] = (double) (seed_survival *germination_rate * m0 * hapaxanthy_survival);
+#endif
}
for (int32_t j = 0; j < mat_max; j++) {
+
int32_t col = seed_persistence + j;
- cats_dt_rates m = age_specific_maturation_rate(j + 1, juvenile_survival, mat_min, mat_max);
+ cats_dt_rates m = age_specific_maturation_rate(j + 1, juvenile_transition_rate, mat_min, mat_max);
+#ifndef LM_START
+
assert(col < N - 1);
matrix[row * N + col] = (double) (m * adult_survival);
+#else
+ cats_dt_rates juvenile_survival_rate = age_modified_juvenile_survival_rate(
+ juvenile_transition_rate, j, mat_min, mat_max);
+ assert(col < N - 1);
+ matrix[row * N + col] = (double) (juvenile_survival_rate * m * hapaxanthy_survival);
+#endif
}
// LAST ENTRY
+#ifndef LM_START
matrix[row * N + N - 1] = (double) (clonal_growth * adult_survival * hapaxanthy_survival);
+#else
+ matrix[row * N + N - 1] = (double) (adult_survival * clonal_growth * hapaxanthy_survival);
+#endif
+
return matrix;
}
--
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