phyml-3.3.20200621/src/rates.h

37 void RATES_Monte_Carlo_Mean_Rates_Pre(t_node *a, t_node *d, t_edge *b, phydbl curr_rate, t_tree *tr…
48 …S_Monte_Carlo_Mean_Rates_Core(phydbl t_lim_sup, phydbl t_lim_inf, phydbl *curr_rate, phydbl *mean_…
49 phydbl RATES_Lk_Rates(t_tree *tree);
51 void RATES_Fill_Node_Rates_Pre(t_node *a, t_node *d, t_edge *b, phydbl *node_r, t_tree *tree);
52 void RATES_Fill_Node_Rates(phydbl *node_r, t_tree *tree);
58 phydbl RATES_Dmu(phydbl mu, int n_jumps, phydbl dt, phydbl a, phydbl b, phydbl lexp, int min_n, int…
59 phydbl RATES_Dr_X_Dx(phydbl r, phydbl mu, phydbl y, phydbl dt, phydbl a, phydbl b, phydbl lexp);
60 phydbl RATES_Dmu_Given_Y_Trpzd(phydbl mu, phydbl y, phydbl dt, phydbl a, phydbl b, phydbl lexp,
61 			       int nsteps, phydbl beg, phydbl end, phydbl prevs);
62 phydbl RATES_Dmu_Given_Y_Std(phydbl mu, phydbl y, phydbl dt, phydbl a, phydbl b, phydbl lexp);
63 phydbl RATES_Dmu_Given_Y_Romb(phydbl mu, phydbl y, phydbl dt, phydbl a, phydbl b, phydbl lexp);
64 phydbl RATES_Dmu_Given_Y(phydbl mu, phydbl y, phydbl dt, phydbl a, phydbl b, phydbl lexp);
65 phydbl RATES_Dy_Given_Mu(phydbl mu, phydbl y, phydbl dt, phydbl a, phydbl b, phydbl lexp);
66 phydbl RATES_Dmu2_Given_Y_X_Dy_Given_Mu1(phydbl mu1, phydbl mu2, phydbl y, phydbl dt1, phydbl dt2, …
67 phydbl RATES_Dmu2_Given_Mu1_Trpz(phydbl mu1, phydbl mu2, phydbl dt1, phydbl dt2, phydbl a, phydbl b…
68 				 int nsteps, phydbl beg, phydbl end, phydbl prevs);
69 phydbl RATES_Dmu2_And_Mu1(phydbl mu1, phydbl mu2, phydbl dt1, phydbl dt2, phydbl a, phydbl b, phydb…
70 phydbl RATES_Dmu2_Given_Mu1(phydbl mu1, phydbl mu2, phydbl dt1, phydbl dt2, phydbl a, phydbl b, phy…
71 phydbl RATES_Dmu2_Given_Mu1_Romb(phydbl mu1, phydbl mu2, phydbl dt1, phydbl dt2, phydbl a, phydbl b…
73 void RATES_Bracket_N_Jumps(int *up, int *down, phydbl param);
77 phydbl RATES_Exp_Y(phydbl mu1, phydbl mu2, phydbl dt1, phydbl lexp);
78 phydbl RATES_Dmu2_Given_Mu1_Bis(phydbl mu1, phydbl mu2, phydbl dt1, phydbl dt2, phydbl alpha, phydb…
83 void RATES_Get_Mean_Rates_Pre(t_node *a, t_node *d, t_edge *b, phydbl r_a, t_tree *tree);
84 void RATES_Expect_Number_Subst(phydbl t_beg, phydbl t_end, phydbl r_beg,  int *n_jumps, phydbl *mea…
86 phydbl RATES_Dmu1_Given_Lbda_And_Mu2(phydbl lbda, phydbl mu1, phydbl mu2, phydbl alpha, phydbl beta…
87 phydbl RATES_Dmu1_And_Mu2_One_Jump_Trpz(phydbl mu1, phydbl mu2, phydbl a, phydbl b,
88 					  int nsteps, phydbl beg, phydbl end, phydbl prevs);
89 phydbl RATES_Dmu1_And_Mu2_One_Jump_One_Interval(phydbl mu1, phydbl mu2, phydbl a, phydbl b);
90 phydbl RATES_Dmu1_And_Mu2_One_Jump_Two_Intervals(phydbl dt1, phydbl dt2, phydbl mu1, phydbl mu2, ph…
92 phydbl RATES_Dmu1_And_Mu2_One_Jump_Old(phydbl mu1, phydbl mu2, phydbl a, phydbl b);
94 phydbl RATES_Dmu2_And_Min_N_Given_Mu1(phydbl mu1, phydbl mu2, phydbl dt1, phydbl dt2, int n_min, ph…
95 phydbl RATES_Dmu2_And_Mu1_Given_N(phydbl mu1, phydbl mu2, phydbl dt1, phydbl dt2, int n, phydbl a, …
96 phydbl RATES_Lk_Rates_Core(phydbl br_r_a, phydbl br_r_d, phydbl nd_r_a, phydbl nd_r_d, int n_a, int…
98 phydbl RATES_Lk_Change_One_Time(t_node *n, phydbl new_t, t_tree *tree);
101 phydbl RATES_Lk_Change_One_Rate(t_node *d, phydbl new_rate, t_tree *tree);
102 phydbl RATES_Dmu2_And_Mu1_Given_Min_N(phydbl mu1, phydbl mu2, phydbl dt1, phydbl dt2, int n_min, ph…
103 phydbl RATES_Dmu2_And_Mu1_Given_N_Normal(phydbl mu1, phydbl mu2, phydbl dt1, phydbl dt2, int n, phy…
104 phydbl RATES_Coeff_Corr(phydbl alpha, phydbl beta, int n1, int n2);
105 phydbl RATES_Dmu2_And_Mu1_Given_N_Full(phydbl mu1, phydbl mu2, phydbl dt1, phydbl dt2, int n, phydb…
106 phydbl RATES_Dmu1_Given_V_And_N(phydbl mu1, phydbl v, int n, phydbl dt1, phydbl a, phydbl b);
107 phydbl RATES_Yule(t_tree *tree);
108 phydbl RATES_Check_Mean_Rates(t_tree *tree);
109 void RATES_Check_Mean_Rates_Pre(t_node *a, t_node *d, t_edge *b, phydbl *sum, t_tree *tree);
112 phydbl RATES_Dmu_Given_V_And_MinN(phydbl mu, phydbl dt, phydbl v, int minn, phydbl a, phydbl b, phy…
113 phydbl RATES_Dmu_One(phydbl mu, phydbl dt, phydbl a, phydbl b, phydbl lexp);
114 phydbl RATES_Compound_Core(phydbl mu1, phydbl mu2, int n1, int n2, phydbl dt1, phydbl dt2, phydbl a…
122 phydbl RATES_Compound_Core_Joint(phydbl mu1, phydbl mu2, int n1, int n2, phydbl dt1, phydbl dt2,
123 				 phydbl alpha, phydbl beta, phydbl lexp, phydbl eps, int approx);
124 phydbl RATES_Dmu_Joint(phydbl mu, int n, phydbl dt, phydbl a, phydbl b, phydbl lexp, int min_n);
125 phydbl RATES_Compound_Core_Marginal(phydbl mu1, phydbl mu2, phydbl dt1, phydbl dt2, phydbl alpha,
126 				    phydbl beta, phydbl lexp, phydbl eps, int approx);
127 phydbl RATES_Lk_Jumps(t_tree *tree);
136 void RATES_Get_Cov_Matrix_Rooted(phydbl *unroot_cov, t_tree *tree);
137 void RATES_Get_Cov_Matrix_Rooted_Pre(t_node *a, t_node *d, t_edge *b, phydbl *cov, t_tree *tree);
152 phydbl RATES_Expected_Tree_Length(t_tree *tree);
153 void RATES_Expected_Tree_Length_Pre(t_node *a, t_node *d, phydbl eranc, phydbl *mean, int *n, t_tre…
155 phydbl RATES_Check_Mean_Rates_True(t_tree *tree);
156 phydbl RATES_Find_Min_Dt_Bisec(phydbl r0, phydbl r1, phydbl t0, phydbl t1, phydbl nu, phydbl thresh…
157 phydbl RATES_Find_Max_Dt_Bisec(phydbl r0, phydbl r1, phydbl t0, phydbl t1, phydbl nu, phydbl thresh…
158 void RATES_Min_Max_Interval(phydbl u0, phydbl u1, phydbl u2, phydbl u3, phydbl t0, phydbl t2, phydb…
159 			    phydbl *t_min, phydbl *t_max, phydbl nu, phydbl p_thresh, t_tree *tree);
162 phydbl RATES_Get_Correction_Factor(phydbl mode, phydbl sd, int *err, t_tree *tree);
163 phydbl RATES_Average_Substitution_Rate(t_tree *tree);
171 phydbl RATES_Average_Rate(t_tree *tree);
173 phydbl RATES_Lk_Linreg(t_tree *tree);
174 phydbl RATES_Get_Mean_Rate_In_Subtree(t_node *root, t_tree *tree);
175 void RATES_Get_Mean_Rate_In_Subtree_Pre(t_node *a, t_node *d, phydbl *sum, int *n, t_tree *tree);
184 phydbl RATES_Realized_Substitution_Rate(t_tree *tree);