From 7b9d9b5fc930b43da9ec0423a9f232d68932835e Mon Sep 17 00:00:00 2001
From: Andreas Gattringer <andreas.gattringer@univie.ac.at>
Date: Fri, 23 Jun 2023 23:30:35 +0200
Subject: [PATCH] butterflies: vital rates changes
---
.../butterflies/butterflies_generations.c | 8 ++++-
src/modules/butterflies/butterflies_main.c | 12 ++++---
src/modules/butterflies/butterflies_main.h | 2 +-
.../butterflies/butterflies_overlays.c | 6 ++++
.../butterflies/butterflies_populations.c | 35 +++++++++----------
.../butterflies/butterflies_populations.h | 2 +-
.../butterflies/butterflies_vital_rates.c | 23 ++++--------
7 files changed, 46 insertions(+), 42 deletions(-)
diff --git a/src/modules/butterflies/butterflies_generations.c b/src/modules/butterflies/butterflies_generations.c
index c2267e7..8252f0c 100644
--- a/src/modules/butterflies/butterflies_generations.c
+++ b/src/modules/butterflies/butterflies_generations.c
@@ -21,12 +21,18 @@ void bf_area_generation_update(struct cats_grid *grid, struct cats_thread_info *
const cats_dt_coord start_col = ts->area.start_col;
const cats_dt_coord end_col = ts->area.end_col;
+ cats_dt_rates ot = grid->param.OT;
+ bool hybrid = grid->param.parametrization == PARAM_HYBRID;
for (cats_dt_coord row = start_row; row < end_row; row++) {
for (cats_dt_coord col = start_col; col < end_col; col++) {
+ bool suitability_to_low = false;
+
+ if (hybrid && get_suitability(grid, row, col) < ot) suitability_to_low = true;
if (cell_excluded_by_overlay(conf, row, col)
- || ! (data->info_layer[row][col] & BF_CELL_VALID_DISPERSAL_TARGET)) {
+ || ! (data->info_layer[row][col] & BF_CELL_VALID_DISPERSAL_TARGET)
+ || suitability_to_low == true) {
data->eggs[row][col] = 0.0f;
data->generations[row][col] = 0.0f;
set_population_ignore_cc(grid, row, col, 0);
diff --git a/src/modules/butterflies/butterflies_main.c b/src/modules/butterflies/butterflies_main.c
index e9650a4..3c6583a 100644
--- a/src/modules/butterflies/butterflies_main.c
+++ b/src/modules/butterflies/butterflies_main.c
@@ -24,17 +24,19 @@ double *butterflies_matrix(struct cats_configuration *conf, struct lambda_parame
struct conf_data_butterflies *module_conf = CATS_MODULE_DATA;
cats_dt_rates eggs_per_female = calculate_rate_for_matrix(&module_conf->eggs_per_female, l_param, print_rate);
- cats_dt_rates adults_per_female = calculate_rate_for_matrix(&module_conf->adults_per_female, l_param, print_rate);
+ cats_dt_rates reproduction_rate = calculate_rate_for_matrix(&module_conf->reproduction_rate, l_param, print_rate);
cats_dt_rates female_fraction = module_conf->female_fraction;
cats_dt_rates stationary = module_conf->probability_to_stay;
cats_dt_rates mobile = 1.0 - stationary;
cats_dt_rates egg_fraction_source = module_conf->egg_fraction_source;
- cats_dt_rates max_eggs = module_conf->eggs_per_female.max_rate;
- cats_dt_rates eggs_to_adults_rate = bf_egg_to_adult_survival_rate(adults_per_female, max_eggs);
cats_dt_rates local_eggs = (stationary + mobile * egg_fraction_source ) * eggs_per_female;
- // female -> female;
+ // female -> female
+ // to achieve the target reproduction rate, the number of eggs per female laid in the cell
+ // that survive and become adult has to be the reproduction rate divided by the female fraction divided by the number of eggs
+ cats_dt_rates eggs_to_adults_rate = bf_egg_to_adult_survival_rate(reproduction_rate, local_eggs, female_fraction);
cats_dt_rates result = local_eggs * eggs_to_adults_rate * female_fraction;
+ log_message(LOG_INFO, "scale factor %Lf: eggs_to_adults_rate %Lf", l_param->grid->param.scale_factor, eggs_to_adults_rate);
double *matrix = calloc_or_die(1, sizeof(double));
@@ -95,7 +97,7 @@ void load_butterflies_species_params(struct cats_configuration *conf, struct cat
load_conf_vital_rate(&data->eggs_per_female, conf, ini, section_name, param);
load_conf_vital_rate(&data->butterfly_generations, conf, ini, section_name, param);
- load_conf_vital_rate(&data->adults_per_female, conf, ini, section_name, param);
+ load_conf_vital_rate(&data->reproduction_rate, conf, ini, section_name, param);
//load_conf_vital_rate(&data->butterfly_egg_to_adult_survival, conf, ini, section_name, param);
diff --git a/src/modules/butterflies/butterflies_main.h b/src/modules/butterflies/butterflies_main.h
index 9da1de6..b122556 100644
--- a/src/modules/butterflies/butterflies_main.h
+++ b/src/modules/butterflies/butterflies_main.h
@@ -47,7 +47,7 @@ struct conf_data_butterflies {
struct cats_vital_rate eggs_per_female;
struct cats_vital_rate butterfly_egg_to_adult_survival;
struct cats_vital_rate butterfly_generations;
- struct cats_vital_rate adults_per_female;
+ struct cats_vital_rate reproduction_rate;
cats_dt_rates female_fraction;
bool actions_added;
diff --git a/src/modules/butterflies/butterflies_overlays.c b/src/modules/butterflies/butterflies_overlays.c
index 9a937c2..4e36332 100644
--- a/src/modules/butterflies/butterflies_overlays.c
+++ b/src/modules/butterflies/butterflies_overlays.c
@@ -6,6 +6,7 @@
#include "butterflies_overlays.h"
#include "butterflies_main.h"
#include "inline_overlays.h"
+#include "inline_population.h"
enum action_status bf_grid_overlay_update(const struct cats_configuration *conf, struct cats_grid *grid)
@@ -32,6 +33,8 @@ enum action_status bf_grid_overlay_update(const struct cats_configuration *conf,
if (cell_excluded_by_overlay(conf, row, col)) {
data->info_layer[row][col] |= BF_CELL_EXCLUDED;
+ data->eggs[row][col] = 0;
+ set_population_ignore_cc(grid, row, col, 0);
cells_excluded += 1;
continue;
}
@@ -54,6 +57,9 @@ enum action_status bf_grid_overlay_update(const struct cats_configuration *conf,
data->info_layer[row][col] |= BF_CELL_VALID_DISPERSAL_TARGET;
cells_habitat_and_resource_ok += 1;
+ } else {
+ data->eggs[row][col] = 0;
+ set_population_ignore_cc(grid, row, col, 0);
}
}
}
diff --git a/src/modules/butterflies/butterflies_populations.c b/src/modules/butterflies/butterflies_populations.c
index a5e9755..5d40f45 100644
--- a/src/modules/butterflies/butterflies_populations.c
+++ b/src/modules/butterflies/butterflies_populations.c
@@ -17,12 +17,9 @@
#include "populations/population.h"
-cats_dt_rates bf_egg_to_adult_survival_rate(cats_dt_rates adults_per_female, cats_dt_rates max_eggs)
+cats_dt_rates bf_egg_to_adult_survival_rate(cats_dt_rates reproduction_rate, cats_dt_rates eggs, cats_dt_rates female_fraction)
{
-
-
- return adults_per_female/max_eggs;
-
+ return (reproduction_rate / female_fraction) / eggs;
}
void bf_cell_maturation(struct cats_grid *grid, struct cats_thread_info *ts, cats_dt_coord row, cats_dt_coord col,
@@ -62,7 +59,7 @@ void bf_cell_maturation(struct cats_grid *grid, struct cats_thread_info *ts, cat
// first the all cells which have 5 (> 4) generations are modelled
// then all the cells with have at least 4 (> 3) generations are modelled
// ...
- // at last all cells with have at least 1 generations are modelled
+ // at last all cells with have at least 1 generation are modelled
float this_generation_fraction = 1.0f;
int32_t local_max_generation = (int32_t) ceilf(data->generations[row][col]);
@@ -89,25 +86,27 @@ void bf_cell_maturation(struct cats_grid *grid, struct cats_thread_info *ts, cat
// not capped, we can have more adults than CC
struct conf_data_butterflies *module_conf = CATS_MODULE_DATA;
- cats_dt_rates adults_per_female = calculate_rate(&module_conf->adults_per_female, NAN, &grid->param,
+ cats_dt_environment suit = get_suitability(grid, row, col);
+ cats_dt_rates reproduction_rate = calculate_rate(&module_conf->reproduction_rate, NAN, &grid->param,
grid, row, col, NULL);
+ if (suit < grid->param.OT && reproduction_rate > 0) {
+ log_message(LOG_ERROR, "Suitability %f under OT %Lf, but adults per female = %Lf", suit, grid->param.OT, reproduction_rate);
+ exit_cats(EXIT_FAILURE);
+ }
- cats_dt_rates max_eggs = module_conf->eggs_per_female.max_rate;
- cats_dt_rates survival = bf_egg_to_adult_survival_rate(adults_per_female, max_eggs);
+ if (reproduction_rate == 0) {
+ data->eggs[row][col] = 0;
+ set_population_ignore_cc(grid, row, col, 0);
+ return;
+ };
+
+ cats_dt_rates survival = bf_egg_to_adult_survival_rate(reproduction_rate, eggs, module_conf->female_fraction);
cats_dt_population adults = poisson(ts->rng, eggs * survival);
assert(adults >= 0);
- //cats_dt_environment suit = get_suitability(grid, row, col);
- //printf("ABCD,%d,%d,%0.3f\n", (int) orig_eggs, adults, suit);
+
set_population(grid, row, col, adults);
-/*
- if (adults > max_cc * 10) {
- log_message(LOG_ERROR, "row %d col %d: number of adults %d exceeds %d time smaximum carrying capacity %d (maturation %Lf, eggs %f, max adults per f %Lf), suit %f, OT %Lf, survival %Lf", row, col, adults, 10, max_cc,
- survival, eggs, module_conf->adults_per_female.max_rate, suit, grid->param.OT, survival);
- exit_cats(EXIT_FAILURE);
- }
- */
}
diff --git a/src/modules/butterflies/butterflies_populations.h b/src/modules/butterflies/butterflies_populations.h
index eed6c10..f8f164b 100644
--- a/src/modules/butterflies/butterflies_populations.h
+++ b/src/modules/butterflies/butterflies_populations.h
@@ -7,6 +7,6 @@
#include "data/cats_grid.h"
void bf_cell_maturation(struct cats_grid *grid, struct cats_thread_info *ts, cats_dt_coord row, cats_dt_coord col, bool check_exclusion);
void bf_area_kill_adults(struct cats_grid *grid, struct cats_thread_info *ts);
-cats_dt_rates bf_egg_to_adult_survival_rate(cats_dt_rates adults_per_female, cats_dt_rates max_eggs);
+cats_dt_rates bf_egg_to_adult_survival_rate(cats_dt_rates reproduction_rate, cats_dt_rates eggs, cats_dt_rates female_ratio);
#endif //CATS_BUTTERFLIES_POPULATIONS_H
diff --git a/src/modules/butterflies/butterflies_vital_rates.c b/src/modules/butterflies/butterflies_vital_rates.c
index 307a7e8..de12309 100644
--- a/src/modules/butterflies/butterflies_vital_rates.c
+++ b/src/modules/butterflies/butterflies_vital_rates.c
@@ -2,7 +2,7 @@
void bf_add_vital_rates(struct cats_configuration *conf, struct conf_data_butterflies *data)
{
- // generations
+ // number of generations
register_module_vital_rate(conf, &data->butterfly_generations,"butterflies generations");
set_vital_rate_name(&data->butterfly_generations, "butterflies generations");
set_vital_rate_suitability_cutoff_hint(&data->butterfly_generations, HYBRID_SUIT_TS_ZT);
@@ -13,21 +13,12 @@ void bf_add_vital_rates(struct cats_configuration *conf, struct conf_data_butter
// adult to eggs
register_module_vital_rate(conf, &data->eggs_per_female, "butterflies eggs per female");
set_vital_rate_name(&data->eggs_per_female, "butterflies eggs per female");
- set_vital_rate_suitability_cutoff_hint(&data->eggs_per_female, HYBRID_SUIT_TS_ZT);
- set_vital_rate_link_hybrid_function(&data->eggs_per_female, conf, LINK_SUITABILITY_SIGMOID);
+ set_vital_rate_suitability_cutoff_hint(&data->eggs_per_female, HYBRID_SUIT_TS_OT);
+ set_vital_rate_link_hybrid_function(&data->eggs_per_female, conf, LINK_CONSTANT);
// eggs to adults
- register_module_vital_rate(conf, &data->adults_per_female, "butterflies adults per female");
- set_vital_rate_name(&data->adults_per_female, "butterflies adults per female");
- set_vital_rate_suitability_cutoff_hint(&data->adults_per_female, HYBRID_SUIT_TS_OT);
- set_vital_rate_link_hybrid_function(&data->adults_per_female, conf, LINK_SUITABILITY_SIGMOID);
-
- // egg to adult survival
- /*
- register_module_vital_rate(conf, &data->butterfly_egg_to_adult_survival,"butterflies egg to adult survival rate");
- set_vital_rate_name(&data->butterfly_egg_to_adult_survival, "butterflies eggs to adult survival rate");
- set_vital_rate_suitability_cutoff_hint(&data->butterfly_egg_to_adult_survival, HYBRID_SUIT_TS_ZT);
- set_vital_rate_link_hybrid_function(&data->butterfly_egg_to_adult_survival, conf, LINK_SUITABILITY_SIGMOID);
- set_vital_density(&data->butterfly_egg_to_adult_survival, NO_DENSITY_DEP);
- */
+ register_module_vital_rate(conf, &data->reproduction_rate, "butterflies reproduction rate");
+ set_vital_rate_name(&data->reproduction_rate, "butterflies reproduction rate");
+ set_vital_rate_link_hybrid_function(&data->reproduction_rate, conf, LINK_SUITABILITY_SIGMOID);
+ set_vital_rate_suitability_cutoff_hint(&data->reproduction_rate, HYBRID_SUIT_TS_OT);
}
--
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