Searched refs:gamma_rr_unscaled (Results 1 – 9 of 9) sorted by relevance
726 …0;i<mod->ras->n_catg;i++) sum += mod->ras->gamma_r_proba->v[i] * mod->ras->gamma_rr_unscaled->v[i]; in Update_RAS()727 … for(i=0;i<mod->ras->n_catg;i++) mod->ras->gamma_rr->v[i] = mod->ras->gamma_rr_unscaled->v[i]/sum; in Update_RAS()731 …for(i=0;i<mod->ras->n_catg;i++) mod->ras->gamma_rr->v[i] = mod->ras->gamma_rr_unscaled->v[i] * mod… in Update_RAS()808 if(mod->ras->gamma_rr_unscaled->v[i] < GAMMA_RR_UNSCALED_MIN) in Update_Boundaries()809 mod->ras->gamma_rr_unscaled->v[i] = GAMMA_RR_UNSCALED_MIN; in Update_Boundaries()811 if(mod->ras->gamma_rr_unscaled->v[i] > GAMMA_RR_UNSCALED_MAX) in Update_Boundaries()812 mod->ras->gamma_rr_unscaled->v[i] = GAMMA_RR_UNSCALED_MAX; in Update_Boundaries()
3138 a = tree->mod->ras->gamma_rr_unscaled->v[permut[i]] / 2.; in Optimize_Free_Rate()3213 wm = Weighted_Mean(tree->mod->ras->gamma_rr_unscaled->v, in Optimize_Free_Rate_Rr()3228 a = tree->mod->ras->gamma_rr_unscaled->v[i] * .1; in Optimize_Free_Rate_Rr()3229 c = tree->mod->ras->gamma_rr_unscaled->v[i] * 10.+1; in Optimize_Free_Rate_Rr()3231 Generic_Brent_Lk(&(tree->mod->ras->gamma_rr_unscaled->v[i]), in Optimize_Free_Rate_Rr()3255 wm = Weighted_Mean(tree->mod->ras->gamma_rr_unscaled->v, in Optimize_Free_Rate_Rr()3272 a = tree->mod->ras->gamma_rr_unscaled->v[i] * .1; in Optimize_Free_Rate_Rr()3273 c = tree->mod->ras->gamma_rr_unscaled->v[i] * 10.+1.; in Optimize_Free_Rate_Rr()3275 Generic_Brent_Lk(&(tree->mod->ras->gamma_rr_unscaled->v[i]), in Optimize_Free_Rate_Rr()3336 wm = Weighted_Mean(tree->mod->ras->gamma_rr_unscaled->v, in Optimize_Free_Rate_Weights()[all …]
924 ras->gamma_rr_unscaled = (vect_dbl *)mCalloc(1,sizeof(vect_dbl)); in Make_RAS_Basic()925 Init_Vect_Dbl(0,ras->gamma_rr_unscaled); in Make_RAS_Basic()926 ras->gamma_rr_unscaled->v = NULL; in Make_RAS_Basic()951 ras->gamma_rr_unscaled->v = (phydbl *)mCalloc(ras->n_catg,sizeof(phydbl)); in Make_RAS_Complete()
860 Free(ras->gamma_rr_unscaled->v); in Free_RAS()868 Free(ras->gamma_rr_unscaled); in Free_RAS()
1064 for(i=0;i<mod->ras->n_catg;i++) mod->ras->gamma_rr_unscaled->v[i] = (phydbl)i; in Init_Model()1069 mod->ras->gamma_rr_unscaled->v[0] = 1.0; in Init_Model()1074 …for(i=0;i<mod->ras->n_catg;i++) mod->ras->gamma_rr_unscaled->v[i] = mod->ras->gamma_rr->v[i]; in Init_Model()
1050 …vect_dbl *gamma_rr_unscaled; /*! substitution rates defined by the RAS distribution (unscaled… member
2923 …for(i=0;i<tree->mod->ras->n_catg-1;i++) tree->mod->ras->gamma_rr_unscaled->v[i] = (phydbl)i+0.1; /… in MCMC_Randomize_Rate_Across_Sites()2924 … tree->mod->ras->gamma_rr_unscaled->v[tree->mod->ras->n_catg-1] = (phydbl)tree->mod->ras->n_catg; in MCMC_Randomize_Rate_Across_Sites()3832 v = tree->mod->ras->gamma_rr_unscaled->v; in MCMC_Free_Mixt_Rate()
2158 for(i=0;i<mod->ras->n_catg;i++) PhyML_Printf(" %f ",mod->ras->gamma_rr_unscaled->v[i]); in Print_Model()
3792 cpy->ras->gamma_rr_unscaled->v[i] = ori->ras->gamma_rr_unscaled->v[i]; in Record_Model()