compatible | Returns whether two clades are compatible |
get_clade_elements | Get elements of a clade |
get_clade_size | Returns the size of a clade. |
Gn | Auxiliary function for computing joint probabilities. |
joint_prob_clades | Computes the joint probability for two clades for a given... |
log_diff_exp | Logarithm of the difference between two logarithms |
make_all_clades | Create all (non-trivial) clades on 'n' taxa. |
make_clade_corr_grid | Construct a grid of 'all vs all' correlations for a list of K... |
make_clade_corr_mat | Build the correlation matrix for a list of K clades on 'n'... |
make_clade_cov_mat | Build the variance-covariance matrix for a list of K clades... |
make_clade_joint_mat | Build the matrix of joint probabilities for a list of K... |
max_corr | Maximum possible correlation between clades on 'n' taxa. |
min_corr | Minimum possible correlation between clades on 'n' taxa. |
pclade | Probability of a clade of size 'k' on 'n' taxa. |
pclades | Joint probability of two clades |
prob_clade | Probability of a clade under a PDA model on 'n' taxa. |
prop_compat | Proportion of clades which are pairwise compatible. |
rho_clades | Computes the correlation between two clades. |
Rn | Auxiliary function for computing joint clade probability. |
rrn | Auxiliary function for computing joint probabilities |
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