diff --git a/src/cats/hybrid/scalefactor.c b/src/cats/hybrid/scalefactor.c
index defe588b36e578302fc9e6777ba658972cbcb963..10c0869917b01bc83045078f343045e9489b98fc 100644
--- a/src/cats/hybrid/scalefactor.c
+++ b/src/cats/hybrid/scalefactor.c
@@ -42,34 +42,47 @@
#include "lambda/leslie_matrix.h"
#include "lambda/lambda.h"
+struct cats_module *get_demographic_module_for_matrix(struct cats_configuration *conf, int32_t species_id)
+{
+ struct cats_module *module = NULL;
+ struct cats_species_param *param = &conf->param[species_id];
+ if (param->demographic_module == NULL) return module;
+
+ int32_t module_id = param->demographic_module->id;
+
+ if (conf->modules.module[module_id].flags & MODULE_ALTERNATE_DEMOGRAPHIC) return &conf->modules.module[module_id];
+
+ return NULL;
+}
+
+
+bool have_leslie_matrix_function_for_module(struct cats_module *module)
+{
+ if (module == NULL) return true;
+ cats_leslie_matrix_func func = module->create_leslie_matrix;
+ return func != NULL;
+}
cats_dt_rates calculate_scale_factor_from_lambda(struct cats_configuration *conf, int32_t species_id)
{
assert(species_id < conf->param_count);
struct cats_species_param *param = &conf->param[species_id];
- bool ok = false;
- cats_leslie_matrix_func func = NULL;
-
-
- // FIXME LOOKS LIKE A MESS
- if (param->custom_vital_rates == false || param->custom_vital_ages == false) ok = true;
- if (param->custom_vital_rates || param->custom_vital_ages) {
- if (param->demographic_module != NULL) {
- int32_t id = param->demographic_module->id;
- if (conf->modules.module[id].flags & MODULE_ALTERNATE_DEMOGRAPHIC) {
- func = conf->modules.module[id].create_leslie_matrix;
- if (func != NULL) {
- ok = true;
- }
- }
- }
- }
- if (!ok) {
+
+ struct cats_module *module = get_demographic_module_for_matrix(conf, species_id);
+ bool have_func = have_leslie_matrix_function_for_module(module);
+ log_message(LOG_IMPORTANT, "Demographic module %p", module);
+
+ if (module != NULL && have_func == false) {
+
log_message(LOG_WARNING, "unable to calculate scale factor for %s: custom vital rates or vital ages",
param->species_name);
log_message(LOG_WARNING, "Using scale factor 0.5 for %s", param->species_name);
return 0.5;
+
+ } else if (module != NULL) {
+ log_message(LOG_IMPORTANT, "Grid %d uses module %s for demography: %p", species_id,
+ module->canonical_name, module->create_leslie_matrix);
}
@@ -104,8 +117,9 @@ cats_dt_rates calculate_scale_factor_from_lambda(struct cats_configuration *conf
conf->param[species_id].scale_factor = s;
conf->direct_scale_factor = s;
cats_dt_rates old_s = s;
- lambda = calculate_lambda(conf, &l_param, true, func);
- log_message(LOG_INFO, "iteration %d: scale factor %0.25Lf resulted in lambda %0.25Lf", iterations, s, lambda);
+ lambda = calculate_lambda(conf, &l_param, true, module);
+ log_message(LOG_INFO, "iteration %d: scale factor %0.25Lf resulted in lambda %0.25Lf", iterations, s,
+ lambda);
if (fabsl(lambda - 1.0) < threshold) {
conf->lambda_at_OT = lambda;
@@ -164,7 +178,7 @@ cats_dt_rates calculate_scale_factor_from_lambda(struct cats_configuration *conf
iterations);
conf->param[species_id].scale_factor = s;
conf->direct_scale_factor = s;
- calculate_lambda(conf, &l_param, false, func);
+ calculate_lambda(conf, &l_param, false, module);
return s;
diff --git a/src/cats/lambda/lambda-grid.c b/src/cats/lambda/lambda-grid.c
index 4573989fc3e8725345a1fc8960419c4e2bf8cb52..501cc0f6298d62c54685e63c1265fda18c7de0f1 100644
--- a/src/cats/lambda/lambda-grid.c
+++ b/src/cats/lambda/lambda-grid.c
@@ -78,13 +78,15 @@ lookup_lambda(struct cats_configuration *conf, struct cats_grid *grid, cats_dt_p
l_param.suitability = NAN;
break;
}
+ /*
cats_leslie_matrix_func func = NULL;
if (grid->param.demographic_module && grid->param.demographic_module->create_leslie_matrix) {
func = grid->param.demographic_module->create_leslie_matrix;
}
+ */
// we have density dependence
if (N >= 0 || grid->param.parametrization != PARAM_HYBRID) {
- return calculate_lambda(conf, &l_param, true, func);
+ return calculate_lambda(conf, &l_param, true, NULL);
}
assert(grid->param.parametrization == PARAM_HYBRID);
@@ -100,7 +102,7 @@ lookup_lambda(struct cats_configuration *conf, struct cats_grid *grid, cats_dt_p
return param->lambda_cache[index];
} else {
l_param.N = 0;
- cats_dt_rates lambda = calculate_lambda(conf, &l_param, true, func);
+ cats_dt_rates lambda = calculate_lambda(conf, &l_param, true, NULL);
param->lambda_cache[index] = lambda;
return lambda;
}
diff --git a/src/cats/lambda/lambda.c b/src/cats/lambda/lambda.c
index 72f865e9b0323e152534e1b2336fdc7a624d3104..392c95927bcd5fb91b3d8e5e5cc686c8420af55e 100644
--- a/src/cats/lambda/lambda.c
+++ b/src/cats/lambda/lambda.c
@@ -39,18 +39,29 @@ void debug_lambda_problem(struct cats_configuration *conf, gsl_complex largest_e
cats_dt_rates calculate_lambda(struct cats_configuration *conf, struct lambda_parameters *l_param, bool silent,
- cats_leslie_matrix_func leslie_matrix_func)
+ struct cats_module *module)
{
- int32_t N = 0;
- bool debug = conf->command_line_options.debug_flags & DEBUG_LAMBDA;
- const int32_t species_id = l_param->species_id;
+
double *matrix = NULL;
- if (leslie_matrix_func == NULL) {
+ int32_t N = 0;
+
+ if (module == NULL) {
matrix = create_leslie_matrix(conf, l_param, silent, &N);
+ } else if (module->create_leslie_matrix != NULL) {
+ matrix = module->create_leslie_matrix(conf, l_param, silent, &N);
+
} else {
- matrix = leslie_matrix_func(conf, l_param, silent, &N);
+ log_message(LOG_ERROR, "no function to create leslie matrix specified");
+ exit_cats(EXIT_FAILURE);
}
+
+
+ bool debug = conf->command_line_options.debug_flags & DEBUG_LAMBDA;
+ const int32_t species_id = l_param->species_id;
+
+
+
//
double *matrix_copy = NULL;
@@ -76,8 +87,10 @@ cats_dt_rates calculate_lambda(struct cats_configuration *conf, struct lambda_pa
print_matrix(matrix_copy, N, N);
printf("Schur form T:\n");
print_matrix(matrix, N, N);
- debug_lambda_1_found(conf, species_id, largest_eigen_value, matrix_copy, N, l_param);
- printf("============================\n");
+ if (module == NULL) {
+ debug_lambda_1_found(conf, species_id, largest_eigen_value, matrix_copy, N, l_param);
+ printf("============================\n");
+ }
}
if (silent == false && l_param->calculate_scale == true) {
@@ -85,7 +98,9 @@ cats_dt_rates calculate_lambda(struct cats_configuration *conf, struct lambda_pa
if (fabs(GSL_REAL(largest_eigen_value) - 1.0) < LAMBDA_EPS) {
printf("Final matrix\n");
print_matrix(matrix_copy, N, N);
- debug_lambda_1_found(conf, species_id, largest_eigen_value, matrix_copy, N, l_param);
+ if (module == NULL) {
+ debug_lambda_1_found(conf, species_id, largest_eigen_value, matrix_copy, N, l_param);
+ }
}
}
diff --git a/src/cats/lambda/lambda.h b/src/cats/lambda/lambda.h
index a2e0f2dbcef671a2f82443097bdf865f7edcf013..96ec98d68a0b23d34b2f4289f5aac94c960c4248 100644
--- a/src/cats/lambda/lambda.h
+++ b/src/cats/lambda/lambda.h
@@ -28,6 +28,6 @@
#include "leslie_matrix.h"
cats_dt_rates calculate_lambda(struct cats_configuration *conf, struct lambda_parameters *l_param, bool silent,
- cats_leslie_matrix_func leslie_matrix_func);
+ struct cats_module *module);
#endif //CATS_LAMBDA_H
diff --git a/src/cats/lambda/leslie_matrix.c b/src/cats/lambda/leslie_matrix.c
index 5566ece615a77908ae914200056d1193b2ba6a73..9f047a6bda37dd68be333d17290d74492b7c0a73 100644
--- a/src/cats/lambda/leslie_matrix.c
+++ b/src/cats/lambda/leslie_matrix.c
@@ -36,6 +36,37 @@
#include "inline_vital_rates.h"
+cats_dt_rates
+calculate_rate_for_matrix(struct cats_vital_rate *rate,
+ const struct lambda_parameters *l_param,
+ bool print)
+{
+ assert(l_param != NULL);
+ assert(l_param->param != NULL);
+
+ const struct cats_species_param *param = l_param->param; //&conf->param[grid_id];
+
+ const cats_dt_rates N = l_param->N;
+ const cats_dt_rates K = l_param->K;
+ struct link_override_parameters override = {-1};
+
+ if (param->parametrization == PARAM_HYBRID) {
+ override.override_suitability = l_param->suitability;
+ }
+
+ override.override_population = N;
+ override.override_carrying_capacity = l_param->K;
+
+ cats_dt_rates value = calculate_rate(rate, 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",
+ rate->name, value, rate->max_rate, N, K);
+ }
+
+ return value;
+}
+
cats_dt_rates
get_rate_for_matrix(enum cats_vital_rate_id rate_type,
const struct lambda_parameters *l_param,
diff --git a/src/cats/lambda/leslie_matrix.h b/src/cats/lambda/leslie_matrix.h
index 25604c6c9887790293b1212d8b639865a289adca..66cb8590d7b262653ded9737e3df8019585dde36 100644
--- a/src/cats/lambda/leslie_matrix.h
+++ b/src/cats/lambda/leslie_matrix.h
@@ -43,6 +43,10 @@ cats_dt_rates
get_rate_for_matrix(enum cats_vital_rate_id rate_type, const struct lambda_parameters *l_param,
bool print);
+cats_dt_rates
+calculate_rate_for_matrix(struct cats_vital_rate *rate,
+ const struct lambda_parameters *l_param,
+ bool print);
double *
create_leslie_matrix(struct cats_configuration *conf, struct lambda_parameters *l_param, bool silent, int32_t *N_out);
diff --git a/src/cats/modules/load_module.c b/src/cats/modules/load_module.c
index e3494776bd78ff1c09550811ea4918ecf71495e1..67c5862b3770d7ac7c04c6e6c63b2ec556fa547d 100644
--- a/src/cats/modules/load_module.c
+++ b/src/cats/modules/load_module.c
@@ -148,8 +148,8 @@ void register_load_species_param_config_func(struct cats_configuration *conf, ca
void register_create_leslie_matrix_func(struct cats_configuration *conf, cats_leslie_matrix_func func)
{
- conf->param[0].module_data[CATS_MODULE_ID].create_leslie_matrix_function = func;
conf->modules.module[CATS_MODULE_ID].create_leslie_matrix = func;
+ printf("LESLIE MATRIX FUNC: %p\n", conf->modules.module[CATS_MODULE_ID].create_leslie_matrix);
}
diff --git a/src/cats/modules/modules.c b/src/cats/modules/modules.c
index 68dc7f18cf7dbd64d42f19be4a0f416fa3e9cd55..a1949e5c9dfb37eae8bbabc03d76f2b0a4c72300 100644
--- a/src/cats/modules/modules.c
+++ b/src/cats/modules/modules.c
@@ -28,7 +28,6 @@
#include "modules.h"
#include "cats_strings/cats_strings.h"
-
void init_cats_module(struct cats_module *module, int32_t id)
{
module->name = NULL;
@@ -38,6 +37,8 @@ void init_cats_module(struct cats_module *module, int32_t id)
module->id = id;
module->create_leslie_matrix = NULL;
module->stats_header = NULL;
+
+
}
@@ -59,7 +60,6 @@ void init_module_species_data(struct module_species_data *m)
m->grid_init_function = NULL;
m->grid_cleanup_function = NULL;
m->load_species_param_function = NULL;
- m->create_leslie_matrix_function = NULL;
m->grid_stat_function = NULL;
m->module = NULL;
m->vital_rate_count = 0;
diff --git a/src/cats/modules/modules.h b/src/cats/modules/modules.h
index d24d85b36bc14f8282674d73bc8f3a40ddf53b7b..cdae0e9b520950adb93a952318f84d37a1cc632a 100644
--- a/src/cats/modules/modules.h
+++ b/src/cats/modules/modules.h
@@ -23,12 +23,11 @@
#ifndef CATS_MODULES_H
#define CATS_MODULES_H
-
#include <stdint.h>
#include <stdbool.h>
#include "defaults.h"
#include "data/cats_datatypes.h"
-
+#include <gsl/gsl_eigen.h>
struct cats_ini;
struct cats_configuration;
struct lambda_parameters;
@@ -53,13 +52,14 @@ typedef struct string_array *(*cats_grid_stat_function)(struct cats_configuratio
typedef void (*cats_cell_function)(struct cats_configuration *conf, struct cats_grid *grid, cats_dt_coord row,
cats_dt_coord col, cats_dt_population K);
+typedef void (*eigen_system_print_func)(gsl_complex eigen_value, gsl_vector_complex_view *eigen_vector, int32_t N, struct cats_species_param *param);
+
struct module_species_data {
struct cats_module *module;
cats_grid_function grid_init_function;
cats_grid_function grid_cleanup_function;
cats_load_species_param_function load_species_param_function;
- cats_leslie_matrix_func create_leslie_matrix_function;
cats_grid_stat_function grid_stat_function;
cats_cell_function cell_destroyed_action;
cats_cell_function cell_carrying_capacity_action;
@@ -68,7 +68,6 @@ struct module_species_data {
char **vital_rate_name;
bool *vital_rate_required;
int32_t vital_rate_count;
- void *module_data;
};
@@ -79,13 +78,16 @@ enum cats_module_flags {
};
+
+
struct cats_module {
char *name;
char *canonical_name;
char *filename;
void *data;
enum cats_module_flags flags;
- void *create_leslie_matrix;
+ cats_leslie_matrix_func create_leslie_matrix;
+
int32_t id;
struct string_array *stats_header;
};