/*
* Merge the exists and forall variables of constraint i
* - store the variables in solver->all_vars
* - store their values in solver->all_values
*/
static void ef_build_full_map(ef_solver_t *solver, uint32_t i) {
ef_cnstr_t *cnstr;
ivector_t *v;
uint32_t n;
assert(i < ef_prob_num_constraints(solver->prob));
cnstr = solver->prob->cnstr + i;
// collect all variables of cnstr in solver->all_vars
v = &solver->all_vars;
ivector_reset(v);
n = ef_constraint_num_evars(cnstr);
ivector_add(v, cnstr->evars, n);
n = ef_constraint_num_uvars(cnstr);
ivector_add(v, cnstr->uvars, n);
// project the evalues onto the exists variable of constraint i
// store the results in all_values
v = &solver->all_values;
n = ef_constraint_num_evars(cnstr);
resize_ivector(v, n);
v->size = n;
ef_project_exists_model(solver->prob, solver->evalue, cnstr->evars, v->data, n);
// copy the uvalues for constraint i (from uvalue_aux to v)
n = ef_constraint_num_uvars(cnstr);
assert(n == solver->uvalue_aux.size);
ivector_add(v, solver->uvalue_aux.data, n);
#if EF_VERBOSE
printf("Full map\n");
print_full_map(stdout, solver);
fflush(stdout);
#endif
}
///////////////////////////////////////////
// The simulation //
///////////////////////////////////////////
void *sim(void *parameters)
{
const Params P = *((Params*)parameters);
const int k_gen = P.k_gen;
const int kernel = P.kernel;
const int communities = P.communities;
const int j_per_c = P.j_per_c;
const int init_species = P.init_species;
const int init_pop_size = j_per_c / init_species;
const double mu = P.mu;
const double s = P.s;
const double eta = P.eta;
const double width = P.width;
const double width2 = width * width;
const double sigma = P.var;
const double sigma2 = sigma * sigma;
// GSL's Taus generator:
gsl_rng *rng = gsl_rng_alloc(gsl_rng_taus2);
// Initialize the GSL generator with /dev/urandom:
const unsigned int seed = devurandom_get_uint();
gsl_rng_set(rng, seed); // Seed with time
printf(" <seed>%u</seed>\n", seed);
// Used to name the output file:
char *buffer = (char*)malloc(100);
// Nme of the file:
sprintf(buffer, "%s%u.xml", P.ofilename, seed);
// Open the output file:
FILE *restrict out = fopen(buffer, "w");
// Store the total num. of species/1000 generations:
int *restrict total_species = (int*)malloc(k_gen * sizeof(int));
// Number of speciation events/1000 generations:
int *restrict speciation_events = (int*)malloc(k_gen * sizeof(int));
// Number of extinctions/1000 generations:
int *restrict extinction_events = (int*)malloc(k_gen * sizeof(int));
// Number of speciation events/vertex:
int *restrict speciation_per_c = (int*)malloc(communities * sizeof(int));
// Number of local extinction events/vertex:
int *restrict extinction_per_c = (int*)malloc(communities * sizeof(int));
// Store the lifespan of the extinct species:
ivector lifespan;
ivector_init0(&lifespan);
// Store the population size at speciation event:
ivector pop_size;
ivector_init0(&pop_size);
// (x, y) coordinates for the spatial graph:
double *restrict x = (double*)malloc(communities * sizeof(double));
double *restrict y = (double*)malloc(communities * sizeof(double));
for (int i = 0; i < communities; ++i)
{
speciation_per_c[i] = 0;
extinction_per_c[i] = 0;
}
// Initialize an empty list of species:
species_list *restrict list = species_list_init();
// Initialize the metacommunity and fill them with the initial species evenly:
for (int i = 0; i < init_species; ++i)
{
// Intialize the species and add it to the list:
species_list_add(list, species_init(communities, 0, 3));
}
// To iterate the list;
slnode *it = list->head;
// Fill the communities:
while (it != NULL)
{
for (int i = 0; i < communities; ++i)
{
it->sp->n[i] = init_pop_size;
it->sp->genotypes[0][i] = init_pop_size;
}
it = it->next;
}
// To iterate the list;
const int remainder = j_per_c - (init_species * init_pop_size);
for (int i = 0; i < communities; ++i)
{
it = list->head;
for (int j = 0; j < remainder; ++j, it = it->next)
{
++(it->sp->n[i]);
++(it->sp->genotypes[0][i]);
}
}
int sum = 0;
it = list->head;
while (it != NULL)
{
sum += species_total(it->sp);
it = it->next;
}
assert(sum == j_per_c * communities);
#ifdef NOTTOOCLOSE
{
int count_c = 0;
while (count_c < communities)
{
bool within = false;
const double xx = gsl_rng_uniform(rng);
const double yy = gsl_rng_uniform(rng);
for (int i = 0; i < count_c; ++i)
{
if (hypot(x[i] - xx, y[i] - yy) < MINDIST)
{
within = true; // oh nooo, an evil goto!
break;
}
}
if (within == false)
{
x[count_c] = xx;
y[count_c] = yy;
++count_c;
}
}
}
#else
for (int i = 0; i < communities; ++i)
{
x[i] = gsl_rng_uniform(rng);
y[i] = gsl_rng_uniform(rng);
}
#endif
double **m = (double**)malloc(communities * sizeof(double*));
for (int i = 0; i < communities; ++i)
{
m[i] = (double*)malloc(communities * sizeof(double));
}
for (int i = 0; i < communities; ++i)
{
for (int j = 0; j < communities; ++j)
{
const double a = x[i] - x[j];
const double b = y[i] - y[j];
const double x = hypot(a, b);
assert(distance >= 0.0);
if (kernel == gaussian_k)
{
m[i][j] = (1.0 / sqrt(2 * M_PI * sigma2)) * exp((-x * x) / (2 * sigma2));
}
else
{
m[i][j] = -(eta + 2)/(2 * M_PI * width2) * pow(1 + (x * x) / width2, eta / 2);
}
}
}
// Setup the array for migration:
double **cmig = setup_cmig(m, communities);
fprintf(out, "<?xml version=\"1.0\"?>\n");
fprintf(out, "<simulation>\n");
if (kernel == gaussian_k)
{
fprintf(out, " <model>Gaussian</model>\n");
}
else
{
fprintf(out, " <model>Fat-tailed</model>\n");
}
fprintf(out, " <seed>%u</seed>\n", seed);
fprintf(out, " <metacom_size>%d</metacom_size>\n", j_per_c * communities);
fprintf(out, " <k_gen>%d</k_gen>\n", k_gen);
fprintf(out, " <num_comm>%d</num_comm>\n", communities);
fprintf(out, " <individuals_per_comm>%d</individuals_per_comm>\n", j_per_c);
fprintf(out, " <initial_num_species>%d</initial_num_species>\n", init_species);
fprintf(out, " <mutation_rate>%.2e</mutation_rate>\n", mu);
if (kernel == gaussian_k)
{
fprintf(out, " <variance>%.8e</variance>\n", sigma);
}
else
{
fprintf(out, " <width>%.8e</width>\n", width);
fprintf(out, " <eta>%.8e</eta>\n", eta);
}
// To select the species and genotypes to pick and replace:
slnode *s0 = list->head; // species0
slnode *s1 = list->head; // species1
int g0 = 0;
int g1 = 0;
int v1 = 0; // Vertex of the individual 1
/////////////////////////////////////////////
// Groups of 1 000 generations //
/////////////////////////////////////////////
for (int k = 0; k < k_gen; ++k)
{
extinction_events[k] = 0;
speciation_events[k] = 0;
/////////////////////////////////////////////
// 1 000 generations //
/////////////////////////////////////////////
for (int gen = 0; gen < 1000; ++gen)
{
const int current_date = (k * 1000) + gen;
/////////////////////////////////////////////
// A single generation //
/////////////////////////////////////////////
for (int t = 0; t < j_per_c; ++t)
{
/////////////////////////////////////////////
// A single time step (for each community) //
/////////////////////////////////////////////
for (int c = 0; c < communities; ++c)
{
// Select the species and genotype of the individual to be replaced
int position = (int)(gsl_rng_uniform(rng) * j_per_c);
s0 = list->head;
int index = s0->sp->n[c];
while (index <= position)
{
s0 = s0->next;
index += s0->sp->n[c];
}
position = (int)(gsl_rng_uniform(rng) * s0->sp->n[c]);
if (position < s0->sp->genotypes[0][c])
{
g0 = 0;
}
else if (position < (s0->sp->genotypes[0][c] + s0->sp->genotypes[1][c]))
{
g0 = 1;
}
else
{
g0 = 2;
}
// Choose the vertex for the individual
const double r_v1 = gsl_rng_uniform(rng);
v1 = 0;
while (r_v1 > cmig[c][v1])
{
++v1;
}
// species of the new individual
position = (int)(gsl_rng_uniform(rng) * j_per_c);
s1 = list->head;
index = s1->sp->n[v1];
while (index <= position)
{
s1 = s1->next;
index += s1->sp->n[v1];
}
if (v1 == c) // local remplacement
{
const double r = gsl_rng_uniform(rng);
const int aa = s1->sp->genotypes[0][v1];
const int Ab = s1->sp->genotypes[1][v1];
const int AB = s1->sp->genotypes[2][v1];
// The total fitness of the population 'W':
const double w = aa + Ab * (1.0 + s) + AB * (1.0 + s) * (1.0 + s);
if (r < aa / w)
{
g1 = gsl_rng_uniform(rng) < mu ? 1 : 0;
}
else
{
if (AB == 0 || r < (aa + Ab * (1.0 + s)) / w)
{
g1 = gsl_rng_uniform(rng) < mu ? 2 : 1;
}
else
{
g1 = 2;
}
}
}
else
{ // Migration event
g1 = 0;
}
// Apply the changes
s0->sp->n[c]--;
s0->sp->genotypes[g0][c]--;
s1->sp->n[c]++;
s1->sp->genotypes[g1][c]++;
////////////////////////////////////////////
// Check for local extinction //
////////////////////////////////////////////
if (s0->sp->n[c] == 0)
{
extinction_per_c[c]++;
}
////////////////////////////////////////////
// Check for speciation //
////////////////////////////////////////////
else if (s0->sp->genotypes[2][c] > 0 && s0->sp->genotypes[0][c] == 0 && s0->sp->genotypes[1][c] == 0)
{
species_list_add(list, species_init(communities, current_date, 3)); // Add the new species
const int pop = s0->sp->n[c];
list->tail->sp->n[c] = pop;
list->tail->sp->genotypes[0][c] = pop;
s0->sp->n[c] = 0;
s0->sp->genotypes[2][c] = 0;
// To keep info on patterns of speciation...
ivector_add(&pop_size, pop);
++speciation_events[k];
++speciation_per_c[c];
}
} // End 'c'
} // End 't'
// Remove extinct species from the list and store the number of extinctions.
extinction_events[k] += species_list_rmv_extinct2(list, &lifespan, current_date);
} // End 'g'
total_species[k] = list->size;
} // End 'k'
//////////////////////////////////////////////////
// PRINT THE FINAL RESULTS //
//////////////////////////////////////////////////
fprintf(out, " <global>\n");
fprintf(out, " <avr_lifespan>%.4f</avr_lifespan>\n", imean(lifespan.array, lifespan.size));
fprintf(out, " <median_lifespan>%.4f</median_lifespan>\n", imedian(lifespan.array, lifespan.size));
fprintf(out, " <avr_pop_size_speciation>%.4f</avr_pop_size_speciation>\n", imean(pop_size.array, pop_size.size));
fprintf(out, " <median_pop_size_speciation>%.4f</median_pop_size_speciation>\n", imedian(pop_size.array, pop_size.size));
fprintf(out, " <speciation_per_k_gen>");
int i = 0;
for (; i < k_gen - 1; ++i)
{
fprintf(out, "%d ", speciation_events[i]);
}
fprintf(out, "%d</speciation_per_k_gen>\n", speciation_events[i]);
fprintf(out, " <extinctions_per_k_gen>");
for (i = 0; i < k_gen - 1; ++i)
{
fprintf(out, "%d ", extinction_events[i]);
}
fprintf(out, "%d</extinctions_per_k_gen>\n", extinction_events[i]);
fprintf(out, " <extant_species_per_k_gen>");
for (i = 0; i < k_gen - 1; ++i)
{
fprintf(out, "%d ", total_species[i]);
}
fprintf(out, "%d</extant_species_per_k_gen>\n", total_species[i]);
// Print global distribution
fprintf(out, " <species_distribution>");
ivector species_distribution;
ivector_init1(&species_distribution, 128);
it = list->head;
while (it != NULL)
{
ivector_add(&species_distribution, species_total(it->sp));
it = it->next;
}
ivector_sort_asc(&species_distribution);
ivector_print(&species_distribution, out);
fprintf(out, "</species_distribution>\n");
double *octaves;
int oct_num = biodiversity_octaves(species_distribution.array, species_distribution.size, &octaves);
fprintf(out, " <octaves>");
for (i = 0; i < oct_num; ++i)
{
fprintf(out, "%.2f ", octaves[i]);
}
fprintf(out, "%.2f</octaves>\n", octaves[i]);
fprintf(out, " </global>\n");
// Print info on all vertices
double *restrict ric_per_c = (double*)malloc(communities * sizeof(double));
for (int c = 0; c < communities; ++c)
{
fprintf(out, " <vertex>\n");
fprintf(out, " <id>%d</id>\n", c);
fprintf(out, " <xcoor>%.4f</xcoor>\n", x[c]);
fprintf(out, " <ycoor>%.4f</ycoor>\n", y[c]);
fprintf(out, " <total_mig_rate>%.8f</total_mig_rate>\n", 1.0 - ((c==0)?cmig[0][0]:cmig[c][c]-cmig[c][c-1]));
fprintf(out, " <speciation_events>%d</speciation_events>\n", speciation_per_c[c]);
fprintf(out, " <extinction_events>%d</extinction_events>\n", extinction_per_c[c]);
int vertex_richess = 0;
ivector_rmvall(&species_distribution);
it = list->head;
while (it != NULL)
{
ivector_add(&species_distribution, it->sp->n[c]);
it = it->next;
}
// Sort the species distribution and remove the 0s
ivector_sort_asc(&species_distribution);
ivector_trim_small(&species_distribution, 1);
ric_per_c[c] = (double)species_distribution.size;
fprintf(out, " <species_richess>%d</species_richess>\n", species_distribution.size);
fprintf(out, " <species_distribution>");
ivector_print(&species_distribution, out);
fprintf(out, "</species_distribution>\n");
// Print octaves
free(octaves);
oct_num = biodiversity_octaves(species_distribution.array, species_distribution.size, &octaves);
fprintf(out, " <octaves>");
for (i = 0; i < oct_num - 1; ++i)
{
fprintf(out, "%.2f ", octaves[i]);
}
fprintf(out, "%.2f</octaves>\n", octaves[i]);
fprintf(out, " </vertex>\n");
}
fprintf(out, "</simulation>\n");
sprintf(buffer, "%s%u-bc.xml", P.ofilename, seed);
FILE *restrict obc = fopen(buffer, "w");
fprintf(obc, "<dissimilarity>\n");
for (int i = 0; i < communities; ++i)
{
for (int j = 0; j < communities - i; ++j)
{
const double a = x[i] - x[j];
const double b = y[i] - y[j];
int sum = 0;
s0 = list->head;
while (s0 != NULL)
{
const int n_a = s0->sp->n[i];
const int n_b = s0->sp->n[j];
if (n_a > 0 && n_b > 0)
{
sum += MIN(n_a, n_b);
}
s0 = s0->next;
}
const double bray_curtis = ((double)sum) / j_per_c;
fprintf(obc, " <pair><distance>%.8f</distance><bc>%.8f</bc></pair>\n", hypot(a, b), bray_curtis);
}
}
fprintf(obc, "</dissimilarity>\n");
//////////////////////////////////////////////////
// EPILOGUE... //
//////////////////////////////////////////////////
// Close files;
fclose(out);
fclose(obc);
// Free arrays;
free(x);
free(y);
free(ric_per_c);
//free(spe_per_c);
free(buffer);
free(total_species);
free(octaves);
free(speciation_per_c);
free(extinction_per_c);
free(speciation_events);
free(extinction_events);
// Free structs;
species_list_free(list);
ivector_free(&species_distribution);
ivector_free(&lifespan);
ivector_free(&pop_size);
gsl_rng_free(rng);
return NULL;
}
///////////////////////////////////////////
// The simulation //
///////////////////////////////////////////
void *sim(void *parameters)
{
const Params P = *((Params*)parameters);
char *shape = P.shape;
const int k_gen = P.k_gen;
const int communities = P.communities;
const int j_per_c = P.j_per_c;
const int init_species = P.init_species;
const int init_pop_size = j_per_c / init_species;
const double omega = P.omega;
const double mu = P.mu;
const double s = P.s;
const double radius = P.r;
const double width = P.w;
// GSL's Taus generator:
gsl_rng *rng = gsl_rng_alloc(gsl_rng_taus2);
// Initialize the GSL generator with /dev/urandom:
const unsigned int seed = devurandom_get_uint();
gsl_rng_set(rng, seed); // Seed with time
printf(" <seed>%u</seed>\n", seed);
// Used to name the output file:
char *buffer = (char*)malloc(100);
// Nme of the file:
sprintf(buffer, "%s%u.xml", P.ofilename, seed);
// Open the output file:
FILE *restrict out = fopen(buffer, "w");
// Store the total num. of species/1000 generations:
int *restrict total_species = (int*)malloc(k_gen * sizeof(int));
// Number of speciation events/1000 generations:
int *restrict speciation_events = (int*)malloc(k_gen * sizeof(int));
// Number of extinctions/1000 generations:
int *restrict extinction_events = (int*)malloc(k_gen * sizeof(int));
// Number of speciation events/vertex:
int *restrict speciation_per_c = (int*)malloc(communities * sizeof(int));
// Number of local extinction events/vertex:
int *restrict extinction_per_c = (int*)malloc(communities * sizeof(int));
// Store the lifespan of the extinct species:
ivector lifespan;
ivector_init0(&lifespan);
// Store the population size at speciation event:
ivector pop_size;
ivector_init0(&pop_size);
// (x, y) coordinates for the spatial graph:
double *restrict x = (double*)malloc(communities * sizeof(double));
double *restrict y = (double*)malloc(communities * sizeof(double));
for (int i = 0; i < communities; ++i)
{
speciation_per_c[i] = 0;
extinction_per_c[i] = 0;
}
// Initialize an empty list of species:
species_list *restrict list = species_list_init();
// Initialize the metacommunity and fill them with the initial species evenly:
for (int i = 0; i < init_species; ++i)
{
// Intialize the species and add it to the list:
species_list_add(list, species_init(communities, 0, 3));
}
// To iterate the list;
slnode *it = list->head;
// Fill the communities:
while (it != NULL)
{
for (int i = 0; i < communities; ++i)
{
it->sp->n[i] = init_pop_size;
it->sp->genotypes[0][i] = init_pop_size;
}
it = it->next;
}
// To iterate the list;
const int remainder = j_per_c - (init_species * init_pop_size);
for (int i = 0; i < communities; ++i)
{
it = list->head;
for (int j = 0; j < remainder; ++j, it = it->next)
{
++(it->sp->n[i]);
++(it->sp->genotypes[0][i]);
}
}
// Test (will be removed for v2.0):
int sum = 0;
it = list->head;
while (it != NULL)
{
sum += species_total(it->sp);
it = it->next;
}
assert(sum == j_per_c * communities);
// Create the metacommunity;
graph g;
switch(shape[0])
{
case 's':
shape = "star";
graph_get_star(&g, communities);
break;
case 'c':
if (shape[1] == 'o')
{
shape = "complete";
graph_get_complete(&g, communities);
break;
}
else
{
shape = "circle";
graph_get_circle(&g, communities);
break;
}
case 'r':
if (shape[1] == 'e')
{
shape = "rectangle";
graph_get_rec_crgg(&g, communities, width, radius, x, y, rng);
break;
}
else
{
shape = "random";
graph_get_crgg(&g, communities, radius, x, y, rng);
break;
}
default:
shape = "random";
graph_get_crgg(&g, communities, radius, x, y, rng);
}
// Setup the cumulative jagged array for migration:
double **cumul = setup_cumulative_list(&g, omega);
fprintf(out, "<?xml version=\"1.0\"?>\n");
fprintf(out, "<simulation>\n");
fprintf(out, " <model>");
if (P.m == MODEL_BDM_NEUTRAL)
{
fprintf(out, "Neutral BDM speciation</model>\n");
}
else if (P.m == MODEL_BDM_SELECTION)
{
fprintf(out, "BDM speciation with selection</model>\n");
}
fprintf(out, " <seed>%u</seed>\n", seed);
fprintf(out, " <shape_metacom>%s</shape_metacom>\n", shape);
fprintf(out, " <metacom_size>%d</metacom_size>\n", j_per_c * communities);
fprintf(out, " <k_gen>%d</k_gen>\n", k_gen);
fprintf(out, " <num_comm>%d</num_comm>\n", communities);
fprintf(out, " <individuals_per_comm>%d</individuals_per_comm>\n", j_per_c);
fprintf(out, " <initial_num_species>%d</initial_num_species>\n", init_species);
fprintf(out, " <mutation_rate>%.2e</mutation_rate>\n", mu);
fprintf(out, " <omega>%.2e</omega>\n", omega);
if (P.m == MODEL_BDM_SELECTION)
{
fprintf(out, " <selection>%.2e</selection>\n", s);
}
if (shape[0] == 'r')
{
fprintf(out, " <radius>%.4f</radius>\n", radius);
}
if (shape[0] == 'r' && shape[1] == 'e')
{
fprintf(out, " <width>%.4f</width>\n", width);
}
// To select the species and genotypes to pick and replace:
slnode *s0 = list->head; // species0
slnode *s1 = list->head; // species1
int g0 = 0;
int g1 = 0;
int v1 = 0; // Vertex of the individual 1
/////////////////////////////////////////////
// Groups of 1 000 generations //
/////////////////////////////////////////////
for (int k = 0; k < k_gen; ++k)
{
extinction_events[k] = 0;
speciation_events[k] = 0;
/////////////////////////////////////////////
// 1 000 generations //
/////////////////////////////////////////////
for (int gen = 0; gen < 1000; ++gen)
{
const int current_date = (k * 1000) + gen;
/////////////////////////////////////////////
// A single generation //
/////////////////////////////////////////////
for (int t = 0; t < j_per_c; ++t)
{
/////////////////////////////////////////////
// A single time step (for each community) //
/////////////////////////////////////////////
for (int c = 0; c < communities; ++c)
{
// Select the species and genotype of the individual to be replaced
int position = (int)(gsl_rng_uniform(rng) * j_per_c);
s0 = list->head;
int index = s0->sp->n[c];
while (index <= position)
{
s0 = s0->next;
index += s0->sp->n[c];
}
position = (int)(gsl_rng_uniform(rng) * s0->sp->n[c]);
if (position < s0->sp->genotypes[0][c])
{
g0 = 0;
}
else if (position < (s0->sp->genotypes[0][c] + s0->sp->genotypes[1][c]))
{
g0 = 1;
}
else
{
g0 = 2;
}
// Choose the vertex for the individual
const double r_v1 = gsl_rng_uniform(rng);
v1 = 0;
while (r_v1 > cumul[c][v1])
{
++v1;
}
v1 = g.adj_list[c][v1];
// species of the new individual
position = (int)(gsl_rng_uniform(rng) * j_per_c);
s1 = list->head;
index = s1->sp->n[v1];
while (index <= position)
{
s1 = s1->next;
index += s1->sp->n[v1];
}
if (v1 == c) // local remplacement
{
const double r = gsl_rng_uniform(rng);
const int aa = s1->sp->genotypes[0][v1];
const int Ab = s1->sp->genotypes[1][v1];
const int AB = s1->sp->genotypes[2][v1];
// The total fitness of the population 'W':
const double w = aa + Ab * (1.0 + s) + AB * (1.0 + s) * (1.0 + s);
if (r < aa / w)
{
g1 = gsl_rng_uniform(rng) < mu ? 1 : 0;
}
else
{
if (AB == 0 || r < (aa + Ab * (1.0 + s)) / w)
{
g1 = gsl_rng_uniform(rng) < mu ? 2 : 1;
}
else
{
g1 = 2;
}
}
}
else
{ // Migration event
g1 = 0;
}
// Apply the changes
s0->sp->n[c]--;
s0->sp->genotypes[g0][c]--;
s1->sp->n[c]++;
s1->sp->genotypes[g1][c]++;
////////////////////////////////////////////
// Check for local extinction //
////////////////////////////////////////////
if (s0->sp->n[c] == 0)
{
extinction_per_c[c]++;
}
////////////////////////////////////////////
// Check for speciation //
////////////////////////////////////////////
else if (s0->sp->genotypes[2][c] > 0 && s0->sp->genotypes[0][c] == 0 && s0->sp->genotypes[1][c] == 0)
{
species_list_add(list, species_init(communities, current_date, 3)); // Add the new species
const int pop = s0->sp->n[c];
list->tail->sp->n[c] = pop;
list->tail->sp->genotypes[0][c] = pop;
s0->sp->n[c] = 0;
s0->sp->genotypes[2][c] = 0;
// To keep info on patterns of speciation...
ivector_add(&pop_size, pop);
++speciation_events[k];
++speciation_per_c[c];
}
} // End 'c'
} // End 't'
// Remove extinct species from the list and store the number of extinctions.
extinction_events[k] += species_list_rmv_extinct2(list, &lifespan, current_date);
} // End 'g'
total_species[k] = list->size;
} // End 'k'
//////////////////////////////////////////////////
// PRINT THE FINAL RESULTS //
//////////////////////////////////////////////////
fprintf(out, " <global>\n");
fprintf(out, " <proper_edges>%d</proper_edges>\n", graph_edges(&g));
fprintf(out, " <links_per_c>%.4f</links_per_c>\n", (double)graph_edges(&g) / communities);
fprintf(out, " <avr_lifespan>%.4f</avr_lifespan>\n", imean(lifespan.array, lifespan.size));
fprintf(out, " <median_lifespan>%.4f</median_lifespan>\n", imedian(lifespan.array, lifespan.size));
fprintf(out, " <avr_pop_size_speciation>%.4f</avr_pop_size_speciation>\n", imean(pop_size.array, pop_size.size));
fprintf(out, " <median_pop_size_speciation>%.4f</median_pop_size_speciation>\n", imedian(pop_size.array, pop_size.size));
fprintf(out, " <speciation_per_k_gen>");
int i = 0;
for (; i < k_gen - 1; ++i)
{
fprintf(out, "%d ", speciation_events[i]);
}
fprintf(out, "%d</speciation_per_k_gen>\n", speciation_events[i]);
fprintf(out, " <extinctions_per_k_gen>");
for (i = 0; i < k_gen - 1; ++i)
{
fprintf(out, "%d ", extinction_events[i]);
}
fprintf(out, "%d</extinctions_per_k_gen>\n", extinction_events[i]);
fprintf(out, " <extant_species_per_k_gen>");
for (i = 0; i < k_gen - 1; ++i)
{
fprintf(out, "%d ", total_species[i]);
}
fprintf(out, "%d</extant_species_per_k_gen>\n", total_species[i]);
// Print global distribution
fprintf(out, " <species_distribution>");
ivector species_distribution;
ivector_init1(&species_distribution, 128);
it = list->head;
while (it != NULL)
{
ivector_add(&species_distribution, species_total(it->sp));
it = it->next;
}
ivector_sort_asc(&species_distribution);
ivector_print(&species_distribution, out);
fprintf(out, "</species_distribution>\n");
double *octaves;
int oct_num = biodiversity_octaves(species_distribution.array, species_distribution.size, &octaves);
fprintf(out, " <octaves>");
for (i = 0; i < oct_num; ++i)
{
fprintf(out, "%.2f ", octaves[i]);
}
fprintf(out, "%.2f</octaves>\n", octaves[i]);
fprintf(out, " </global>\n");
// Print info on all vertices
double *restrict ric_per_c = (double*)malloc(communities * sizeof(double));
for (int c = 0; c < communities; ++c)
{
fprintf(out, " <vertex>\n");
fprintf(out, " <id>%d</id>\n", c);
if (shape[0] == 'r')
{
fprintf(out, " <xcoor>%.4f</xcoor>\n", x[c]);
fprintf(out, " <ycoor>%.4f</ycoor>\n", y[c]);
}
fprintf(out, " <degree>%d</degree>\n", g.num_e[c] + 1);
fprintf(out, " <speciation_events>%d</speciation_events>\n", speciation_per_c[c]);
fprintf(out, " <extinction_events>%d</extinction_events>\n", extinction_per_c[c]);
int vertex_richess = 0;
ivector_rmvall(&species_distribution);
it = list->head;
while (it != NULL)
{
ivector_add(&species_distribution, it->sp->n[c]);
it = it->next;
}
// Sort the species distribution and remove the 0s
ivector_sort_asc(&species_distribution);
ivector_trim_small(&species_distribution, 1);
ric_per_c[c] = (double)species_distribution.size;
fprintf(out, " <species_richess>%d</species_richess>\n", species_distribution.size);
fprintf(out, " <species_distribution>");
ivector_print(&species_distribution, out);
fprintf(out, "</species_distribution>\n");
// Print octaves
free(octaves);
oct_num = biodiversity_octaves(species_distribution.array, species_distribution.size, &octaves);
fprintf(out, " <octaves>");
for (i = 0; i < oct_num - 1; ++i)
{
fprintf(out, "%.2f ", octaves[i]);
}
fprintf(out, "%.2f</octaves>\n", octaves[i]);
fprintf(out, " </vertex>\n");
}
fprintf(out, "</simulation>\n");
// GraphML output:
sprintf(buffer, "%s%u.graphml", P.ofilename, seed);
FILE *outgml = fopen(buffer, "w");
graph_graphml(&g, outgml, seed);
// Print to SVG files.
sprintf(buffer, "%s%u.svg", P.ofilename, seed);
FILE *outsvg = fopen(buffer, "w");
graph_svg(&g, x, y, 400.0, 20.0, outsvg);
sprintf(buffer, "%s%u-speciation.svg", P.ofilename, seed);
FILE *outsvgspe = fopen(buffer, "w");
double *spe_per_c = (double*)malloc(communities * sizeof(double));
for (int c = 0; c < communities; ++c)
{
spe_per_c[c] = (double)speciation_per_c[c];
}
scale_0_1(spe_per_c, communities);
graph_svg_abun(&g, x, y, 400.0, 20.0, spe_per_c, 2, outsvgspe);
sprintf(buffer, "%s%u-richness.svg", P.ofilename, seed);
FILE *outsvgric = fopen(buffer, "w");
scale_0_1(ric_per_c, communities);
graph_svg_abun(&g, x, y, 400.0, 20.0, ric_per_c, 1, outsvgric);
//////////////////////////////////////////////////
// EPILOGUE... //
//////////////////////////////////////////////////
// Close files;
fclose(out);
fclose(outgml);
fclose(outsvg);
fclose(outsvgspe);
fclose(outsvgric);
// Free arrays;
free(x);
free(y);
free(ric_per_c);
free(spe_per_c);
free(buffer);
free(total_species);
free(octaves);
free(speciation_per_c);
free(extinction_per_c);
free(speciation_events);
free(extinction_events);
// Free structs;
species_list_free(list);
ivector_free(&species_distribution);
ivector_free(&lifespan);
ivector_free(&pop_size);
graph_free(&g);
gsl_rng_free(rng);
return NULL;
}
