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Searched refs:cov_l (Results 1 – 8 of 8) sorted by relevance

/dports/biology/phyml/phyml-3.3.20200621/src/
H A Drates.c598 For(i,(2*n_otu-2)*(2*n_otu-2)) to->cov_l[i] = from->cov_l[i]; in RATES_Copy_Rate_Struct()
2595 for(i=0;i<dim+1;++i) tree->rates->cov_l[i*(dim+1)+tree->n_root->v[2]->num] /= 2.; in RATES_Get_Cov_Matrix_Rooted()
2596 for(i=0;i<dim+1;++i) tree->rates->cov_l[i*(dim+1)+tree->n_root->v[1]->num] /= 2.; in RATES_Get_Cov_Matrix_Rooted()
2597 for(i=0;i<dim+1;++i) tree->rates->cov_l[tree->n_root->v[2]->num*(dim+1)+i] /= 2.; in RATES_Get_Cov_Matrix_Rooted()
2598 for(i=0;i<dim+1;++i) tree->rates->cov_l[tree->n_root->v[1]->num*(dim+1)+i] /= 2.; in RATES_Get_Cov_Matrix_Rooted()
2625 tree->rates->cov_l[d->num*(dim+1) + n->num] = cov[b->num*dim + i]; in RATES_Get_Cov_Matrix_Rooted_Pre()
2636 tree->rates->cov_l[d->num*(dim+1) + n->num] = cov[b->num*dim + i]; in RATES_Get_Cov_Matrix_Rooted_Pre()
2638 tree->rates->cov_l[d->num*(dim+1) + n->num] = cov[tree->e_root->num*dim + i]; in RATES_Get_Cov_Matrix_Rooted_Pre()
2642 tree->rates->cov_l[d->num*(dim+1) + n->num] = cov[b->num*dim + i]; in RATES_Get_Cov_Matrix_Rooted_Pre()
2644 tree->rates->cov_l[d->num*(dim+1) + n->num] = cov[tree->e_root->num*dim + i]; in RATES_Get_Cov_Matrix_Rooted_Pre()
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H A Dinvitee.c630 Free(tree -> rates -> cov_l); in PhyTime_XML()
631 tree -> rates -> cov_l = Hessian_Seo(tree); in PhyTime_XML()
634 For(i, (2 * tree -> n_otu - 3) * (2 * tree -> n_otu - 3)) tree -> rates -> cov_l[i] *= -1.0; in PhyTime_XML()
635 …if(!Iter_Matinv(tree -> rates -> cov_l, 2 * tree -> n_otu - 3, 2 * tree -> n_otu - 3, YES)) Exit("… in PhyTime_XML()
636 … tree -> rates -> covdet = Matrix_Det(tree -> rates -> cov_l, 2 * tree -> n_otu - 3, YES); in PhyTime_XML()
637 … -> n_otu - 3) * (2 * tree -> n_otu - 3)) tree -> rates -> invcov[i] = tree -> rates -> cov_l[i]; in PhyTime_XML()
H A Dfree.c1312 Free(rates->cov_l); in RATES_Free_Rates()
H A Dutilities.h1575 phydbl *cov_l; member
H A Dmake.c1306 rates->cov_l = (phydbl *)mCalloc((2*n_otu-2)*(2*n_otu-2),sizeof(phydbl)); in RATES_Make_Rate_Struct()
H A Dinit.c872 for(i=0;i<(2*n_otu-2)*(2*n_otu-2);++i) rates->cov_l[i] = 0.0; in RATES_Init_Rate_Struct()
H A Dutilities.c9595 tree->rates->cov_l[b->num*dim+b->num],&err); in Diff_Lk_Norm_At_Given_Edge()
9631 tree->rates->cov_l[i*(2*tree->n_otu-3)+i] = 0.1; in Adjust_Variances()
9656 Generic_Brent_Lk(&(tree->rates->cov_l[i*(2*tree->n_otu-3)+i]), in Adjust_Variances()
H A Dstats.c4061 cov = tree->rates->cov_l; in VarCov_Approx_Likelihood()