// Destroy the pdf
void pf_pdf_discrete_free(pf_pdf_discrete_t *pdf)
{
gsl_ran_discrete_free(pdf->ran);
gsl_rng_free(pdf->rng);
free(pdf->probs);
free(pdf);
return;
}
void rdist_free(t_rdist *x){
if(x->r_rng){
gsl_rng_free(x->r_rng);
}
if(x->r_g){
gsl_ran_discrete_free(x->r_g);
}
if(x->r_arIn){
free(x->r_arIn);
}
if(x->r_output_buffer){
free(x->r_output_buffer);
}
}
void rdist_nonparametric(t_rdist *x, t_symbol *msg, short argc, t_atom *argv){
double f[argc];
int i;
x->r_dist = msg;
for(i = 0; i < argc; i++){
f[i] = librdist_atom_getfloat(argv + i);
//post("%d, %f", i, f[i]);
}
if(x->r_g){
gsl_ran_discrete_free(x->r_g);
}
x->r_g = gsl_ran_discrete_preproc(argc, f);
x->r_function = librdist_nonparametric;
}
GenomicElementType::~GenomicElementType(void)
{
//EIDOS_ERRSTREAM << "GenomicElementType::~GenomicElementType" << std::endl;
if (lookup_mutation_type_)
{
gsl_ran_discrete_free(lookup_mutation_type_);
lookup_mutation_type_ = nullptr;
}
if (mm_thresholds)
{
free(mm_thresholds);
mm_thresholds = nullptr;
}
}
std::vector<intType> ran_mult_multinomial(const std::vector<uint64_t>& pop, intType sample_size, const gsl_rng* r, intType min_coverage = 0)
{
std::vector<intType> sample;
sample.resize(bins);
// 1.) first generate N_reads samples, not all of which will satisfy >= min_coverage
std::vector<double> p_PCR(pop.begin(), pop.end());
gsl_ran_multinomial(r, bins, sample_size, p_PCR.data(), sample.data());
uint64_t valid_samples = 0;
for (const auto& i : sample) {
if (i >= min_coverage) {
valid_samples += i;
}
}
// 2.) proceed to add remaining samples
if (valid_samples < sample_size) {
gsl_ran_discrete_t* categorical_distrib = gsl_ran_discrete_preproc(bins, p_PCR.data());
intType ind;
while (valid_samples < sample_size) {
ind = gsl_ran_discrete(r, categorical_distrib);
++sample[ind];
if (sample[ind] > min_coverage) {
++valid_samples;
}
else {
if (sample[ind] == min_coverage)
valid_samples += min_coverage;
}
}
gsl_ran_discrete_free(categorical_distrib);
}
return sample;
}
void GenomicElementType::InitializeDraws(void)
{
size_t mutation_type_count = mutation_type_ptrs_.size();
if (mutation_type_count != mutation_fractions_.size())
EIDOS_TERMINATION << "ERROR (GenomicElementType::InitializeDraws): mutation types and fractions have different sizes." << EidosTerminate();
if (lookup_mutation_type_)
{
gsl_ran_discrete_free(lookup_mutation_type_);
lookup_mutation_type_ = nullptr;
}
// We allow an empty mutation type vector initially, because people might want to add mutation types in script.
// However, if DrawMutationType() is called and our vector is still empty, that will be an error.
if (mutation_type_count)
{
// Prepare to randomly draw mutation types
std::vector<double> A(mutation_type_count);
bool nonzero_seen = false;
for (unsigned int i = 0; i < mutation_type_count; i++)
{
double fraction = mutation_fractions_[i];
if (fraction > 0.0)
nonzero_seen = true;
A[i] = fraction;
}
// A mutation type vector with all zero proportions is treated the same as an empty vector: we allow it
// on the assumption that it will be fixed later, but if it isn't, that will be an error.
if (nonzero_seen)
lookup_mutation_type_ = gsl_ran_discrete_preproc(mutation_type_count, A.data());
}
}
// Resample
void pmap_resample(pmap_t *self, int scan_count)
{
int i, n;
double e, p, norm=0.0;
gsl_ran_discrete_t *dist=NULL;
pmap_sample_t *oldset=NULL, *newset=NULL;
pmap_sample_t *old=NULL, *newsample=NULL;
double *sample_probs;
sample_probs = new double[self->samples_len];
// Work out old and new sample sets
oldset = self->samples + self->sample_set * self->samples_len;
newset = self->samples + ((self->sample_set + 1) % 2) * self->samples_len;
// Convert to probability
for (i = 0; i < self->samples_len; i++)
{
old = oldset + i;
e = old->w / self->num_ranges / scan_count;
p = exp(-e / (self->resample_s * self->resample_s));
norm += p;
sample_probs[i] = p;
}
// Normalize probabiities
for (i = 0; i < self->samples_len; i++)
{
sample_probs[i] /= norm;
#ifdef __QNXNTO__
assert(std::finite(sample_probs[i]));
#else
assert(finite(sample_probs[i]));
#endif
}
dist = gsl_ran_discrete_preproc(self->samples_len, sample_probs);
assert(dist);
// Create discrete distribution
for (i = 0; i < self->samples_len; i++)
{
assert(self);
assert(self->rng);
n = gsl_ran_discrete(self->rng, dist);
old = oldset + n;
newsample = newset + i;
newsample->w = 0.0;
newsample->err = old->err;
newsample->pose = old->pose;
memcpy(newsample->cells, old->cells, self->grid_size);
memcpy(newsample->poses, old->poses, self->traj_size);
}
gsl_ran_discrete_free(dist);
delete [] sample_probs;
self->sample_set = (self->sample_set + 1) % 2;
return;
}
virtual ~DiscreteSelection() {
gsl_ran_discrete_free( m_lookup );
}
int
main (void)
{
gsl_ieee_env_setup ();
gsl_rng_env_setup ();
r_global = gsl_rng_alloc (gsl_rng_default);
#define FUNC(x) test_ ## x, "test gsl_ran_" #x
#define FUNC2(x) test_ ## x, test_ ## x ## _pdf, "test gsl_ran_" #x
test_shuffle ();
test_choose ();
testMoments (FUNC (ugaussian), 0.0, 100.0, 0.5);
testMoments (FUNC (ugaussian), -1.0, 1.0, 0.6826895);
testMoments (FUNC (ugaussian), 3.0, 3.5, 0.0011172689);
testMoments (FUNC (ugaussian_tail), 3.0, 3.5, 0.0011172689 / 0.0013498981);
testMoments (FUNC (exponential), 0.0, 1.0, 1 - exp (-0.5));
testMoments (FUNC (cauchy), 0.0, 10000.0, 0.5);
testMoments (FUNC (discrete1), -0.5, 0.5, 0.59);
testMoments (FUNC (discrete1), 0.5, 1.5, 0.40);
testMoments (FUNC (discrete1), 1.5, 3.5, 0.01);
testMoments (FUNC (discrete2), -0.5, 0.5, 1.0/45.0 );
testMoments (FUNC (discrete2), 8.5, 9.5, 0 );
testMoments (FUNC (discrete3), -0.5, 0.5, 0.05 );
testMoments (FUNC (discrete3), 0.5, 1.5, 0.05 );
testMoments (FUNC (discrete3), -0.5, 9.5, 0.5 );
test_dirichlet_moments ();
test_multinomial_moments ();
testPDF (FUNC2 (beta));
testPDF (FUNC2 (cauchy));
testPDF (FUNC2 (chisq));
testPDF (FUNC2 (dirichlet));
testPDF (FUNC2 (erlang));
testPDF (FUNC2 (exponential));
testPDF (FUNC2 (exppow0));
testPDF (FUNC2 (exppow1));
testPDF (FUNC2 (exppow1a));
testPDF (FUNC2 (exppow2));
testPDF (FUNC2 (exppow2a));
testPDF (FUNC2 (exppow2b));
testPDF (FUNC2 (fdist));
testPDF (FUNC2 (flat));
testPDF (FUNC2 (gamma));
testPDF (FUNC2 (gamma1));
testPDF (FUNC2 (gamma_int));
testPDF (FUNC2 (gamma_large));
testPDF (FUNC2 (gamma_small));
testPDF (FUNC2 (gamma_mt));
testPDF (FUNC2 (gamma_mt1));
testPDF (FUNC2 (gamma_mt_int));
testPDF (FUNC2 (gamma_mt_large));
testPDF (FUNC2 (gamma_mt_small));
testPDF (FUNC2 (gaussian));
testPDF (FUNC2 (gaussian_ratio_method));
testPDF (FUNC2 (gaussian_ziggurat));
testPDF (FUNC2 (ugaussian));
testPDF (FUNC2 (ugaussian_ratio_method));
testPDF (FUNC2 (gaussian_tail));
testPDF (FUNC2 (gaussian_tail1));
testPDF (FUNC2 (gaussian_tail2));
testPDF (FUNC2 (ugaussian_tail));
testPDF (FUNC2 (bivariate_gaussian1));
testPDF (FUNC2 (bivariate_gaussian2));
testPDF (FUNC2 (bivariate_gaussian3));
testPDF (FUNC2 (bivariate_gaussian4));
testPDF (FUNC2 (gumbel1));
testPDF (FUNC2 (gumbel2));
testPDF (FUNC2 (landau));
testPDF (FUNC2 (levy1));
testPDF (FUNC2 (levy2));
testPDF (FUNC2 (levy1a));
testPDF (FUNC2 (levy2a));
testPDF (FUNC2 (levy_skew1));
testPDF (FUNC2 (levy_skew2));
testPDF (FUNC2 (levy_skew1a));
testPDF (FUNC2 (levy_skew2a));
testPDF (FUNC2 (levy_skew1b));
testPDF (FUNC2 (levy_skew2b));
testPDF (FUNC2 (logistic));
testPDF (FUNC2 (lognormal));
testPDF (FUNC2 (pareto));
testPDF (FUNC2 (rayleigh));
testPDF (FUNC2 (rayleigh_tail));
testPDF (FUNC2 (tdist1));
testPDF (FUNC2 (tdist2));
testPDF (FUNC2 (laplace));
testPDF (FUNC2 (weibull));
testPDF (FUNC2 (weibull1));
testPDF (FUNC2 (dir2d));
testPDF (FUNC2 (dir2d_trig_method));
testPDF (FUNC2 (dir3dxy));
testPDF (FUNC2 (dir3dyz));
testPDF (FUNC2 (dir3dzx));
testDiscretePDF (FUNC2 (discrete1));
testDiscretePDF (FUNC2 (discrete2));
testDiscretePDF (FUNC2 (discrete3));
testDiscretePDF (FUNC2 (poisson));
testDiscretePDF (FUNC2 (poisson_large));
testDiscretePDF (FUNC2 (bernoulli));
testDiscretePDF (FUNC2 (binomial));
testDiscretePDF (FUNC2 (binomial0));
testDiscretePDF (FUNC2 (binomial1));
testDiscretePDF (FUNC2 (binomial_knuth));
testDiscretePDF (FUNC2 (binomial_large));
testDiscretePDF (FUNC2 (binomial_large_knuth));
testDiscretePDF (FUNC2 (binomial_huge));
testDiscretePDF (FUNC2 (binomial_huge_knuth));
testDiscretePDF (FUNC2 (geometric));
testDiscretePDF (FUNC2 (geometric1));
testDiscretePDF (FUNC2 (hypergeometric1));
testDiscretePDF (FUNC2 (hypergeometric2));
testDiscretePDF (FUNC2 (hypergeometric3));
testDiscretePDF (FUNC2 (hypergeometric4));
testDiscretePDF (FUNC2 (hypergeometric5));
testDiscretePDF (FUNC2 (hypergeometric6));
testDiscretePDF (FUNC2 (logarithmic));
testDiscretePDF (FUNC2 (multinomial));
testDiscretePDF (FUNC2 (multinomial_large));
testDiscretePDF (FUNC2 (negative_binomial));
testDiscretePDF (FUNC2 (pascal));
gsl_rng_free (r_global);
gsl_ran_discrete_free (g1);
gsl_ran_discrete_free (g2);
gsl_ran_discrete_free (g3);
exit (gsl_test_summary ());
}
