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sitemodel.c
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sitemodel.c
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/*
* sitemodel.c
* PhyC
*
* Created by Mathieu Fourment on 12/13/10.
* Copyright (C) 2016 Mathieu Fourment. All rights reserved.
*
* This program is free software; you can redistribute it and/or modify it under the terms of the GNU General Public License
* as published by the Free Software Foundation; either version 2 of the License, or (at your option) any later version.
*
* This program is distributed in the hope that it will be useful, but WITHOUT ANY WARRANTY; without even the implied warranty
* of MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the GNU General Public License for more details.
*
* You should have received a copy of the GNU General Public License along with this program; if not,
* write to the Free Software Foundation, Inc., 59 Temple Place, Suite 330, Boston, MA 02111-1307 USA
*/
#include "sitemodel.h"
#include <assert.h>
#include <strings.h>
#include <math.h>
#include "parameters.h"
#include "gamma.h"
#include "gausslaguerre.h"
#include "mstring.h"
#include "matrix.h"
#include "mathconstant.h"
#include "gaussian.h"
#include "distkumaraswamy.h"
#ifndef GSL_DISABLED
#include <gsl/gsl_cdf.h>
#endif
static bool _gamma_approx_quantile( SiteModel *sm );
static void _calculate_rates_discrete( SiteModel *sm );
static double _get_rate( SiteModel *sm, const int index );
static double _get_proportion( SiteModel *sm, const int index );
static double *_get_proportions( SiteModel *sm );
static double _get_rate_gamma( SiteModel *sm, const int index );
static double _get_proportion_gamma( SiteModel *sm, const int index );
static double *_get_proportions_gamma( SiteModel *sm );
static double _get_rate_laguerre( SiteModel *sm, const int index );
static double _get_proportion_laguerre( SiteModel *sm, const int index );
static double * _get_proportions_laguerre( SiteModel *sm );
static double _get_rate_discrete( SiteModel *sm, const int index );
static double _get_proportion_discrete( SiteModel *sm, const int index );
static double *_get_proportions_discrete( SiteModel *sm );
static double icdf_weibull_1(double p, double k);
static void _site_model_handle_change( Model *self, Model *model, int index ){
SiteModel *sm = (SiteModel*)self->obj;
sm->need_update = true;// one of the sitemodel parameters
self->listeners->fire( self->listeners, self, index );
}
static void _site_model_store(Model* self){
Model *mprop = (Model*)self->data;
if(mprop != NULL) mprop->store(mprop); // simplex proportion model
SiteModel* sm = self->obj;
if (Parameters_count(sm->rates) > 0) {
Parameters_store(sm->rates);
}
if (sm->mu != NULL) {
Parameter_store(sm->mu);
}
}
static void _site_model_restore(Model* self){
Model *mprop = (Model*)self->data;
if(mprop != NULL) mprop->restore(mprop); // simplex proportion model
SiteModel* sm = self->obj;
if (Parameters_count(sm->rates) > 0) {
bool changed = false;
Parameter*p = NULL;
for (int i = 0; i < Parameters_count(sm->rates); i++) {
p = Parameters_at(sm->rates, i);
if (Parameter_changed(p)) {
changed = true;
Parameter_restore_quietly(p);
}
}
if (changed) {
p->listeners->fire_restore(p->listeners, NULL, p->id);
}
}
if (sm->mu != NULL) {
Parameter_restore(sm->mu);
}
}
static void _site_model_handle_restore( Model *self, Model *model, int index ){
SiteModel *sm = (SiteModel*)self->obj;
sm->need_update = true;// one of the sitemodel parameters
self->listeners->fire_restore( self->listeners, self, index );
}
static void _site_model_free( Model *self ){
#ifdef DEBUG_REF_COUNTING
printf("Free site model: %d\n", self->ref_count);
#endif
if(self->ref_count == 1){
//printf("Free site model %s\n", self->name);
SiteModel *sm = (SiteModel*)self->obj;
if(self->data != NULL){
Model* model = (Model*)self->data;
model->free(model);
}
if(sm->rates != NULL) free_Parameters(sm->rates);
//TODO: deal with this
if(sm->mu!=NULL)free_Parameter(sm->mu);
if ( sm->cat_proportions != NULL ) free(sm->cat_proportions);
free(sm->cat_rates);
free(sm);
free_Model(self);
}
else{
self->ref_count--;
}
}
static Model* _site_model_clone( Model *self, Hashtable* hash ){
if (Hashtable_exists(hash, self->name)) {
return Hashtable_get(hash, self->name);
}
Model* mprop = (Model*)self->data;
Model* mpropclone = NULL;
Simplex* propclone = NULL;
if(mprop != NULL){
if (Hashtable_exists(hash, mprop->name)) {
mpropclone = Hashtable_get(hash, mprop->name);
mpropclone->ref_count++; // it is decremented at the end using free
}
else{
mpropclone = mprop->clone(mprop, hash);
Hashtable_add(hash, mpropclone->name, mpropclone);
}
propclone = mpropclone->obj;
}
SiteModel* sm = (SiteModel*)self->obj;
Parameters* ps = new_Parameters(1);
for (int i = 0; i < Parameters_count(sm->rates); i++) {
char* name = Parameters_name(sm->rates, i);
if (Hashtable_exists(hash, name)) {
Parameters_add(ps, Hashtable_get(hash, name));
}
else{
Parameter* p = clone_Parameter(Parameters_at(sm->rates, i));
Parameters_move(ps, p);
Hashtable_add(hash, name, p);
}
}
Parameter* mu = NULL;
if (sm->mu != NULL) {
char* name = Parameter_name(sm->mu);
if (Hashtable_exists(hash, name)) {
mu = Hashtable_get(hash, name);
mu->refCount++;
}
else{
mu = clone_Parameter(sm->mu);
Hashtable_add(hash, name, mu);
}
}
SiteModel* smclone = clone_SiteModel_with_parameters(sm, propclone, ps, mu);
free_Parameters(ps);
free_Parameter(mu);
Model* clone = new_SiteModel2(self->name, smclone, mpropclone);
Hashtable_add(hash, clone->name, clone);
if(mpropclone != NULL)mpropclone->free(mpropclone);
clone->print = self->print;
return clone;
}
// SubstitutionModel2 listen to the rate and freq parameters
Model * new_SiteModel2( const char* name, SiteModel *sm, Model* proportions ){
Model *model = new_Model(MODEL_SITEMODEL, name, sm);
if ( sm->rates != NULL ) {
for ( int i = 0; i < Parameters_count(sm->rates); i++ ) {
Parameters_at(sm->rates, i)->listeners->add( Parameters_at(sm->rates, i)->listeners, model );
}
}
if ( sm->mu != NULL ) {
sm->mu->listeners->add( sm->mu->listeners, model );
}
if (proportions != NULL) {
model->data = proportions;
proportions->ref_count++;
proportions->listeners->add( proportions->listeners, model );
}
model->update = _site_model_handle_change;
model->handle_restore = _site_model_handle_restore;
model->store = _site_model_store;
model->restore = _site_model_restore;
model->free = _site_model_free;
model->clone = _site_model_clone;
return model;
}
static void _SiteModel_print(Model* model, FILE* out){
SiteModel* sm = model->obj;
sm->get_proportions(sm); // make sure it is updated
if (Parameters_count(sm->rates)) {
for (int i = 0; i < Parameters_count(sm->rates); i++) {
fprintf(out, "%s %f\n", Parameters_name(sm->rates, i),Parameters_value(sm->rates, i));
}
double sum = 0;
fprintf(out, "proportion rate\n");
for (int i = 0; i < sm->cat_count; i++){
fprintf(out, "%f %f\n",sm->cat_proportions[i], sm->cat_rates[i]);
sum += sm->cat_proportions[i]*sm->cat_rates[i];
}
fprintf(out, "sum %f\n", sum);
}
else if(sm->proportions != NULL){
fprintf(out, "proportion rate %lu\n", sm->proportions->K);
for (int i = 0; i < sm->proportions->K; i++){
fprintf(out, "%f %f\n",sm->cat_proportions[i], sm->cat_rates[i]);
}
}
else if(sm->cat_count > 1){
fprintf(out, "proportion rate %d\n", sm->cat_count);
for (int i = 0; i < sm->cat_count; i++){
fprintf(out, "%f %f\n",sm->cat_proportions[i], sm->cat_rates[i]);
}
}
}
void set_rate(SiteModel* sm, const int index, const double value){
Parameters_set_value(sm->rates, index, value);
sm->need_update = true;
}
int _get_site_category(SiteModel* sm, const int pattern){
return 0;
}
void _no_gradient( SiteModel *sm, const double* ingrad, double* grad ){
}
double _no_derivative( SiteModel *sm, const double* ingrad, Parameter* p ){
return 0;
}
double _gamma_shape_derivative( SiteModel *sm, const double* ingrad ){
double derivsum = 0;
double sum = 0;
size_t catCount = sm->cat_count;
size_t variableCat = sm->proportions != NULL ? catCount - 1 : catCount;
double* proportions = sm->get_proportions(sm);
double shape = Parameters_value(sm->rates, 0);
size_t j = (variableCat == catCount ? 0 : 1); // ignore category 0 with r_0=0
double* temp = dvector(variableCat*2);
const double eps = pow(DBL_EPSILON, 1.0/3.0);
#ifndef GSL_DISABLED
gsl_error_handler_t* handler = gsl_set_error_handler_off();
#endif
size_t i = 0;
for ( ; i < variableCat; i++, j++) {
double prob = (2.0*i + 1.0)/(2.0*variableCat);
double xp = shape*(1.0 + eps);
double xm = shape*(1.0 - eps);
#ifndef GSL_DISABLED
double plus = gsl_cdf_gamma_Qinv( prob, xp, 1.0/xp );
double minus = gsl_cdf_gamma_Qinv( prob, xm, 1.0/xm );
temp[i+variableCat] = gsl_cdf_gamma_Qinv( prob, shape, 1.0/shape);
#else
double plus = qgamma( prob, xp, xp );
double minus = qgamma( prob, xm, xm );
temp[i+variableCat] = qgamma( prob, shape, shape);
#endif
temp[i] = (plus - minus)/(xp-xm);
if(isnan(plus) || isnan(minus) || isnan(temp[i+variableCat])){
break;
}
derivsum += temp[i] * proportions[j];
sum += temp[i+variableCat] * proportions[j];
}
#ifndef GSL_DISABLED
gsl_set_error_handler(handler);
#endif
double shape_gradient = NAN;
if(i == variableCat){
shape_gradient = 0.0;
j = (variableCat == catCount ? 0 : 1); // ignore category 0 with r_0=0
for (size_t i = 0; i < variableCat; i++, j++) {
double prob = (2.0*i + 1.0)/(2.0*variableCat);
double deriv_rate = temp[i]/sum - (temp[i+variableCat]*derivsum)/sum/sum;
shape_gradient += ingrad[j] * deriv_rate * proportions[j];
}
}
free(temp);
return shape_gradient;
}
double _gamma_inv_derivative( SiteModel *sm, const double* ingrad ){
double* proportions = sm->get_proportions(sm);
assert(proportions[0] == Parameters_value(sm->proportions->parameters, 0));
// with Gamma
if(Parameters_count(sm->rates) > 0){
size_t variableCatCount = sm->cat_count - 1;
double shape = Parameters_value(sm->rates, 0);
double sum_rate = 0;
for (size_t i = 0; i < variableCatCount; i++) {
double prob = (2.0*i + 1.0)/(2.0*variableCatCount);
#ifndef GSL_DISABLED
sum_rate += gsl_cdf_gamma_Qinv( prob, shape, 1.0/shape );
#else
sum_rate += qgamma( prob, shape, shape );
#endif
}
double pinv_gradient = 0;
for (size_t i = 0; i < variableCatCount; i++) {
double prob = (2.0*i + 1.0)/(2.0*variableCatCount);
#ifndef GSL_DISABLED
pinv_gradient += ingrad[i+1] * gsl_cdf_gamma_Qinv( prob, shape, 1.0/shape );
#else
pinv_gradient += ingrad[i+1] * qgamma( prob, shape, shape );
#endif
}
return ingrad[0] + pinv_gradient/(sum_rate*(1.0 - proportions[0]));
}
// +I only
else{
return ingrad[0] + ingrad[1]/proportions[1];
}
}
double _gamma_derivative( SiteModel *sm, const double* ingrad, Parameter* p ){
// pinv
if(sm->proportions != NULL && Parameters_at(sm->proportions->parameters, 0) == p){
return _gamma_inv_derivative(sm, ingrad);
}
else{
return _gamma_shape_derivative(sm, ingrad);
}
return 0;
}
void _gamma_gradient( SiteModel *sm, const double* ingrad, double* grad ){
size_t offset = 0;
if(Parameters_count(sm->rates) > 0){
grad[offset++] = _gamma_shape_derivative(sm, ingrad);
}
if(sm->proportions != NULL){
grad[offset] = _gamma_inv_derivative(sm, ingrad);
}
}
double _weibull_shape_derivative( SiteModel *sm, const double* ingrad ){
double derivsum = 0;
double sum = 0;
size_t catCount = sm->cat_count;
size_t variableCat = sm->proportions != NULL ? catCount - 1 : catCount;
double* proportions = sm->get_proportions(sm);
double shape = Parameters_value(sm->rates, 0);
double shape2 = shape*shape;
size_t j = (variableCat == catCount ? 0 : 1); // ignore category 0 with r_0=0
for (size_t i = 0; i < variableCat; i++, j++) {
double prob = (2.0*i + 1.0)/(2.0*variableCat);
derivsum += -pow(-log(1.0 - prob), 1.0/shape) * log(-log(1.0 - prob))/shape2*proportions[j];
sum += pow(-log(1.0 - prob), 1.0/shape)*proportions[j];
}
double shape_gradient = 0;
j = (variableCat == catCount ? 0 : 1); // ignore category 0 with r_0=0
for (size_t i = 0; i < variableCat; i++, j++) {
double prob = (2.0*i + 1.0)/(2.0*variableCat);
double deriv = -pow(-log(1.0 - prob), 1.0/shape) * log(-log(1.0 - prob))/shape2;
double deriv_rate = deriv/sum - (pow(-log(1.0 - prob), 1.0/shape)*derivsum)/sum/sum;
shape_gradient += ingrad[j] * deriv_rate * proportions[j];
}
return shape_gradient;
}
double _weibull_inv_derivative( SiteModel *sm, const double* ingrad ){
double* proportions = sm->get_proportions(sm);
assert(proportions[0] == Parameters_value(sm->proportions->parameters, 0));
// with Weibull
if(Parameters_count(sm->rates) > 0){
size_t variableCatCount = sm->cat_count - 1;
double shape = Parameters_value(sm->rates, 0);
double sum_rate = 0;
for (size_t i = 0; i < variableCatCount; i++) {
double prob = (2.0*i + 1.0)/(2.0*variableCatCount);
sum_rate += icdf_weibull_1(prob, shape);
}
double pinv_gradient = 0;
for (size_t i = 0; i < variableCatCount; i++) {
double prob = (2.0*i + 1.0)/(2.0*variableCatCount);
pinv_gradient += ingrad[i+1] * icdf_weibull_1(prob, shape);
}
return ingrad[0] + pinv_gradient/(sum_rate*(1.0 - proportions[0]));
}
// +I only
else{
return ingrad[0] + ingrad[1]/proportions[1];
}
}
double _weibull_derivative( SiteModel *sm, const double* ingrad, Parameter* p ){
// pinv
if(sm->proportions != NULL && Parameters_at(sm->proportions->parameters, 0) == p){
return _weibull_inv_derivative(sm, ingrad);
}
else{
return _weibull_shape_derivative(sm, ingrad);
}
return 0;
}
void _weibull_gradient( SiteModel *sm, const double* ingrad, double* grad ){
size_t offset = 0;
if(Parameters_count(sm->rates) > 0){
grad[offset++] = _weibull_shape_derivative(sm, ingrad);
}
if(sm->proportions != NULL){
grad[offset] = _weibull_inv_derivative(sm, ingrad);
}
}
bool _update_gamma_approx_quantile(SiteModel *sm){
if ( sm->need_update ) {
return _gamma_approx_quantile(sm);
}
return true;
}
bool _update_nothing(SiteModel *sm){
return true;
}
// (Gamma or/and Invariant) or one rate
// should not be used directly
SiteModel * new_SiteModel_with_parameters( const Parameters *params, Simplex* proportions, const size_t cat_count, distribution_t distribution, bool invariant, quadrature_t quad){
SiteModel *sm = (SiteModel *)malloc(sizeof(SiteModel));
assert(sm);
sm->site_category = NULL;
sm->sp = NULL;
sm->get_site_category = _get_site_category;
sm->distribution = distribution;
sm->invariant = invariant;
sm->quadrature = quad;
sm->cat_count = cat_count;
if (invariant) sm->cat_count++;
sm->cat_rates = NULL;
sm->cat_proportions = NULL;
sm->proportions = proportions;
sm->epsilon = 1.e-6;
sm->rates = NULL;
if(Parameters_count(params) > 0){
sm->rates = new_Parameters(Parameters_count(params));
Parameters_add_parameters(sm->rates, params);
if (Parameters_name2(params) != NULL) {
Parameters_set_name2(sm->rates, Parameters_name2(params));
}
}
for(size_t i = 0; i < Parameters_count(params); i++){
Parameters_at(sm->rates, i)->model = MODEL_SITEMODEL;
}
sm->mu = NULL;
sm->set_rate = set_rate;
sm->cat_rates = dvector(sm->cat_count);
sm->cat_proportions = dvector(sm->cat_count);
sm->gradient = _no_gradient;
sm->derivative = _no_derivative;
sm->update = _update_nothing;
if (distribution == DISTRIBUTION_UNIFORM) {
sm->get_rate = _get_rate;
sm->get_proportion = _get_proportion;
sm->get_proportions = _get_proportions;
sm->cat_rates[0] = sm->cat_proportions[0] = 1;
}
else if (distribution == DISTRIBUTION_DISCRETE && Parameters_count(sm->rates) != 0) {
sm->get_rate = _get_rate_discrete;
sm->get_proportion = _get_proportion_discrete;
sm->get_proportions = _get_proportions_discrete;
}
else if (quad == QUADRATURE_GAUSS_LAGUERRE){
sm->get_rate = _get_rate_laguerre;
sm->get_proportion = _get_proportion_laguerre;
sm->get_proportions = _get_proportions_laguerre;
}
else{
sm->get_rate = _get_rate_gamma;
sm->get_proportion = _get_proportion_gamma;
sm->get_proportions = _get_proportions_gamma;
sm->update = _update_gamma_approx_quantile;
}
// Discrete gamma or prop of invariant or both
if (distribution == DISTRIBUTION_WEIBULL ||
(distribution == DISTRIBUTION_DISCRETE && Parameters_count(sm->proportions->parameters) == 1)) {
sm->gradient = _weibull_gradient;
sm->derivative = _weibull_derivative;
}
else if (distribution == DISTRIBUTION_GAMMA){
sm->gradient = _gamma_gradient;
sm->derivative = _gamma_derivative;
}
sm->integrate = true;
sm->need_update = true;
return sm;
}
double _get_rate( SiteModel *sm, const int index ){
return (sm->mu == NULL ? 1.0 : Parameter_value(sm->mu));
}
double _get_proportion( SiteModel *sm, const int index ){
return 1.0;
}
double *_get_proportions( SiteModel *sm ){
return sm->cat_proportions;
}
double _get_rate_gamma( SiteModel *sm, const int index ){
if ( sm->need_update ) {
_gamma_approx_quantile(sm);
}
return sm->cat_rates[index] * (sm->mu == NULL ? 1.0 : Parameter_value(sm->mu));
}
double _get_proportion_gamma( SiteModel *sm, const int index ){
if ( sm->need_update ) {
_gamma_approx_quantile(sm);
}
return sm->cat_proportions[index];
}
double *_get_proportions_gamma( SiteModel *sm ){
if ( sm->need_update ) {
_gamma_approx_quantile(sm);
}
return sm->cat_proportions;
}
double icdf_weibull(double p, double lambda, double k){
return lambda*pow(-log(1.0 - p), 1.0/k);
}
double icdf_weibull_1(double p, double k){
return pow(-log(1.0 - p), 1.0/k);
}
bool _gamma_approx_quantile( SiteModel *sm ) {
double propVariable = 1.0;
int cat = (sm->invariant ? 1 : 0);
const int nCat = sm->cat_count - cat;
double* quantiles = dvector(sm->cat_count); // cat_count includes invariant sites if specified
#ifndef GSL_DISABLED
// proportions are estimated from beta distribution
if (sm->quadrature == QUADRATURE_BETA || sm->quadrature == QUADRATURE_KUMARASWAMY){
double shape_alpha = Parameters_value(sm->rates, Parameters_count(sm->rates)-2);
double shape_beta = Parameters_value(sm->rates, Parameters_count(sm->rates)-1);
// proportion of invariant is estimated from beta
// cat can be equal to 0 or 1
if(sm->proportions == NULL){
if(sm->quadrature == QUADRATURE_BETA){
for (int i = 0; i < sm->cat_count; i++) {
quantiles[i] = gsl_cdf_beta_Pinv((double)i/sm->cat_count, shape_alpha, shape_beta);
}
}
else{
for (int i = 0; i < sm->cat_count; i++) {
quantiles[i] = DistributionModel_kumaraswamy_inverse_CDF((double)i/sm->cat_count, shape_alpha, shape_beta);
}
}
for (int i = 0; i < sm->cat_count-1; i++) {
// calculate cat proportions
sm->cat_proportions[i] = quantiles[i + 1] - quantiles[i];
// calculate quantiles for gamma distribution
quantiles[i] = quantiles[i] + (quantiles[i+1] - quantiles[i])/2.0;
}
sm->cat_proportions[sm->cat_count-1] = 1.0 - quantiles[sm->cat_count-1];
quantiles[sm->cat_count-1] = quantiles[sm->cat_count-1] + (1.0 - quantiles[sm->cat_count-1])/2.0;
}
// proportion of invariant come from a simplex
// cat should be equal to 1
else{
for (int i = 0; i < sm->cat_count-cat; i++) {
quantiles[i+cat] = gsl_cdf_beta_Pinv((double)i/(sm->cat_count-cat), shape_alpha, shape_beta);
}
propVariable = sm->proportions->get_value(sm->proportions, 1);
sm->cat_proportions[0] = sm->proportions->get_value(sm->proportions, 0);
for (int i = 0; i < sm->cat_count-1-cat; i++) {
// calculate cat proportions
sm->cat_proportions[i+cat] = (quantiles[i + 1 + cat] - quantiles[i+cat])*propVariable;
// calculate quantiles for gamma distribution
quantiles[i+cat] = quantiles[i+cat] + (quantiles[i+1+cat] - quantiles[i+cat])/2.0;
}
sm->cat_proportions[sm->cat_count-1] = (1.0 - quantiles[sm->cat_count-1])*propVariable;
quantiles[sm->cat_count-1] = quantiles[sm->cat_count-1] + (1.0 - quantiles[sm->cat_count-1])/2.0;
}
}
// That's +G+D or +G+I+D
else if(sm->quadrature == QUADRATURE_DISCRETE){
#else
if(sm->quadrature == QUADRATURE_DISCRETE){
#endif
const double* values = sm->proportions->get_values(sm->proportions);
double sum = 0;
for (int i = 0; i < sm->cat_count-cat; i++) {
quantiles[i+cat] = sum + values[i+cat]/2.0; // pick midpoint
sum += values[i];
}
memcpy(sm->cat_proportions, values, sizeof(double)*sm->proportions->K);
}
// if the dimension of the simplex is then only pinv is estimated
// and the remaining categories split 1.0-pinv equally
// That's the traditional +G+I or +I
else if (sm->proportions != NULL && sm->proportions->K == 2) {
const double* values = sm->proportions->get_values(sm->proportions);
// +I
if(sm->distribution == DISTRIBUTION_DISCRETE){
memcpy(sm->cat_proportions, values, sizeof(double)*2);
sm->cat_rates[0] = 0;
sm->cat_rates[1] = 1.0 / sm->cat_proportions[1];
sm->need_update = false;
free(quantiles);
return true;
}
// +G+I
else{
cat = 1;
sm->cat_proportions[0] = values[0];
propVariable = values[1];
int gammaCat = sm->cat_count - 1;
for (int i = 0; i < gammaCat; i++) {
quantiles[i+cat] = (2.0 * i + 1.0) / (2.0 * gammaCat);
sm->cat_proportions[i+cat] = propVariable/gammaCat;
}
}
}
// distribution without invariant and proportions not estimated
// cat_proportions corresponds to quantiles not proportions
// That's the traditional +G
else if(sm->proportions == NULL){
for (int i = 0; i < nCat; i++) {
quantiles[i] = (2.0 * i + 1.0) / (2.0 * nCat);
sm->cat_proportions[i] = 1.0/nCat;
}
}
double mean = 0.0;
const double alpha = Parameters_value(sm->rates, 0);
// median
if(sm->quadrature == QUADRATURE_QUANTILE_MEDIAN || sm->quadrature == QUADRATURE_DISCRETE ||
sm->quadrature == QUADRATURE_BETA || sm->quadrature == QUADRATURE_KUMARASWAMY){
sm->cat_rates[0] = 0;
size_t i = 0;
if(sm->distribution == DISTRIBUTION_GAMMA){
#ifndef GSL_DISABLED
gsl_error_handler_t* handler = gsl_set_error_handler_off();
for ( ; i < sm->cat_count - cat; i++) {
sm->cat_rates[i + cat] = gsl_cdf_gamma_Qinv( quantiles[i+cat], alpha, 1.0/alpha );
if(isnan(sm->cat_rates[i + cat])){
break;
}
}
gsl_set_error_handler(handler);
#else
for ( ; i < sm->cat_count - cat; i++) {
sm->cat_rates[i + cat] = qgamma( quantiles[i+cat], alpha, alpha );
if(isnan(sm->cat_rates[j + cat])){
break;
}
}
#endif
}
else if(sm->distribution == DISTRIBUTION_WEIBULL){
for ( ; i < sm->cat_count - cat; i++) {
// Unit mean Weibull
// sm->cat_rates[i + cat] = gsl_cdf_weibull_Qinv( sm->cat_proportions[i + cat], alpha, 1.0/exp(gammln(1.0 + 1.0/alpha)) );
// Fix lambda:=1
sm->cat_rates[i + cat] = icdf_weibull_1( quantiles[i+cat], alpha);
if(isnan(sm->cat_rates[i + cat])){
break;
}
}
}
#ifndef GSL_DISABLED
else if(sm->distribution == DISTRIBUTION_LOGNORMAL){
for ( ; i < sm->cat_count - cat; i++) {
sm->cat_rates[i + cat] = gsl_cdf_lognormal_Qinv( quantiles[i+cat], -alpha*alpha/2, alpha );
}
}
else if(sm->distribution == DISTRIBUTION_BETA){
for ( ; i < sm->cat_count - cat; i++) {
sm->cat_rates[i + cat] = gsl_cdf_beta_Qinv( quantiles[i+cat], alpha, Parameters_value(sm->rates, 1) );
}
}
#endif
if(i != sm->cat_count - cat){
free(quantiles);
sm->need_update = false;
return false;
}
if (sm->quadrature == QUADRATURE_BETA || sm->quadrature == QUADRATURE_KUMARASWAMY) {
for (int i = 0; i < sm->cat_count - cat; i++) {
mean += sm->cat_rates[i + cat]*sm->cat_proportions[i + cat];
}
}
// QUADRATURE_DISCRETE
else if ( (sm->proportions != NULL && sm->proportions->K == sm->cat_count)){
for (int i = 0; i < nCat; i++) {
mean += sm->cat_rates[i + cat]*sm->cat_proportions[i + cat];
}
}
// +G or +G+I
else if(sm->proportions == NULL || (sm->proportions != NULL && sm->proportions->K != sm->cat_count)){
for (int i = 0; i < sm->cat_count - cat; i++) {
mean += sm->cat_rates[i + cat];
}
mean = (propVariable * mean) / nCat;
}
for (int i = 0; i < sm->cat_count - cat; i++) {
sm->cat_rates[i + cat] /= mean;
}
}
// mean
else{
for (int i = 0; i < nCat - 1; i++){
sm->cat_proportions[i+cat] = qgamma((i + 1.0) / nCat, alpha, alpha);
sm->cat_proportions[i+cat] = gammp(alpha + 1, sm->cat_proportions[i+cat] * alpha);
}
sm->cat_rates[cat] = sm->cat_proportions[cat]*nCat;
for (int i = cat+1; i < nCat - 1; i++){
sm->cat_rates[i] = (sm->cat_proportions[i] - sm->cat_proportions[i - 1])*nCat;
}
sm->cat_rates[nCat - 1] = (1 - sm->cat_proportions[nCat - 2])*nCat;
for (int i = 0; i < nCat; i++){
sm->cat_proportions[i + cat] = propVariable/nCat;
}
}
free(quantiles);
sm->need_update = false;
return true;
}
// Gamma distribution approximated using Laguerre quadrature
void _gamma_approx_laguerre( SiteModel *sm ){
const double alpha = Parameters_value(sm->rates, 0);
// calculate using alpha -1
gaulag(sm->cat_rates, sm->cat_proportions, sm->cat_count, alpha-1);
double gamalpha = gamm(alpha);
for ( int i = 0; i < sm->cat_count; i++ ) {
sm->cat_rates[i] /= alpha;
sm->cat_proportions[i] /= gamalpha;
}
sm->need_update = false;
}
double _get_rate_laguerre( SiteModel *sm, const int index ){
if ( sm->need_update ) {
_gamma_approx_laguerre(sm);
}
return sm->cat_rates[index];
}
double _get_proportion_laguerre( SiteModel *sm, const int index ){
if ( sm->need_update ) {
_gamma_approx_laguerre(sm);
}
return sm->cat_proportions[index];
}
double *_get_proportions_laguerre( SiteModel *sm ){
if ( sm->need_update ) {
_gamma_approx_laguerre(sm);
}
return sm->cat_proportions;
}
int _get_site_category_CAT(SiteModel* sm, const int pattern){
return sm->site_category[pattern];
}
void SiteModel_set_mu(SiteModel *sm, Parameter* mu){
sm->mu = mu;
sm->mu->model = MODEL_SITEMODEL;
mu->refCount++;
}
#pragma mark -
// MARK: Discrete SiteModel
double _get_rate_discrete( SiteModel *sm, const int index ){
if ( sm->need_update ) {
_calculate_rates_discrete(sm);
}
return sm->cat_rates[index];
}
double _get_proportion_discrete( SiteModel *sm, const int index ){
if ( sm->need_update ) {
_calculate_rates_discrete(sm);
}
return sm->cat_proportions[index];
}
double *_get_proportions_discrete( SiteModel *sm ){
if ( sm->need_update ) {
_calculate_rates_discrete(sm);
}
return sm->cat_proportions;
}
void _calculate_rates_discrete( SiteModel *sm ) {
int j = 0;
int cat = (sm->invariant ? 1 : 0);
int cat_count = sm->proportions->K;
memset(sm->cat_rates, 0, sizeof(double)*cat_count);
const double* cat_proportions = sm->proportions->get_values(sm->proportions);
memcpy(sm->cat_proportions, cat_proportions, sizeof(double)*cat_count);
if(Parameters_count(sm->rates) == 0){
sm->cat_rates[1] = 1.0/sm->cat_proportions[1];
sm->need_update = false;
return;
}
sm->cat_rates[cat] = Parameters_value(sm->rates, j++);
sm->cat_rates[cat+1] = 1;
double sum = sm->cat_rates[cat]*sm->cat_proportions[cat] + sm->cat_proportions[cat+1];
if(sm->invariant) sum += sm->cat_proportions[0];
double prod = 1;
for (int i = cat+2; i < cat_count; i++, j++ ) {
prod *= Parameters_value(sm->rates, j);
sm->cat_rates[i] = prod;
sum += prod*sm->cat_proportions[i];
}
for (int i = 0; i < cat_count; i++ ) {
sm->cat_rates[i] /= sum;
}
sm->need_update = false;
}
#pragma mark -
#pragma mark CAT
void _cat_update(SiteModel* sm){
double avg = 0;
for (int i = 0; i < sm->sp->count; i++ ) {
avg += Parameters_value(sm->rates, sm->get_site_category(sm, i)) * sm->sp->weights[i];
}
avg /= sm->sp->nsites;
for (int i = 0; i < sm->cat_count; i++ ) {
sm->cat_rates[i] = Parameters_value(sm->rates, i)/avg;
}
sm->need_update = false;
}
double _get_rate_cat( SiteModel *sm, const int index ){
if ( sm->need_update ) {
_cat_update(sm);
}
return sm->cat_rates[index] * (sm->mu == NULL ? 1.0 : Parameter_value(sm->mu));
}
SiteModel * new_CATSiteModel_with_parameters( const Parameters *params, const size_t cat_count, SitePattern* sp){
SiteModel *sm = (SiteModel *)malloc(sizeof(SiteModel));
assert(sm);
sm->sp = sp;
sm->site_category = ivector(sp->count);
sm->get_site_category = _get_site_category_CAT;
sm->distribution = -1;
sm->invariant = false;
sm->quadrature = -1;
sm->cat_count = cat_count;
sm->cat_rates = dvector(sm->cat_count);
sm->cat_proportions = NULL;
sm->proportions = NULL;
sm->rates = NULL;
if(Parameters_count(params) > 0){
sm->rates = new_Parameters(Parameters_count(params));
Parameters_add_parameters(sm->rates, params);
if (Parameters_name2(params) != NULL) {
Parameters_set_name2(sm->rates, Parameters_name2(params));
}
}
sm->mu = NULL;
sm->set_rate = set_rate;
sm->get_rate = _get_rate_cat;
sm->get_proportion = _get_proportion;
sm->get_proportions = _get_proportions;
sm->update = _update_nothing;
sm->integrate = false;
sm->need_update = true;
return sm;
}
#pragma mark -
SiteModel * clone_SiteModel( const SiteModel *sm ){
return clone_SiteModel_with(sm);
}
SiteModel * clone_SiteModel_with( const SiteModel *sm ){
SiteModel *newsm = (SiteModel *)malloc(sizeof(SiteModel));
assert(newsm);
newsm->rates = NULL;
newsm->cat_count = sm->cat_count;
if ( sm->rates != NULL ){
newsm->rates = clone_Parameters(sm->rates);
}
newsm->mu = NULL;
if ( sm->mu != NULL ){
newsm->mu = clone_Parameter(sm->mu);
}
newsm->cat_rates = clone_dvector(sm->cat_rates, sm->cat_count);
newsm->cat_proportions = NULL;
if ( sm->cat_proportions != NULL ){
newsm->cat_proportions = clone_dvector(sm->cat_proportions, sm->cat_count);
}
newsm->integrate = sm->integrate;
newsm->need_update = false;
newsm->set_rate = sm->set_rate;
newsm->get_rate = sm->get_rate;
newsm->get_proportion = sm->get_proportion;
newsm->get_proportions = sm->get_proportions;
newsm->get_site_category = sm->get_site_category;
newsm->update = sm->update;
newsm->distribution = sm->distribution;
newsm->invariant = sm->invariant;
newsm->quadrature = sm->quadrature;
newsm->gradient = sm->gradient;
newsm->derivative = sm->derivative;
newsm->epsilon = sm->epsilon;
return newsm;
}
SiteModel * clone_SiteModel_with_parameters( const SiteModel *sm, Simplex* props, const Parameters* params, Parameter* mu ){
SiteModel *newsm = (SiteModel *)malloc(sizeof(SiteModel));
assert(newsm);
newsm->proportions = props;