Man pages for maxbiostat/cladeCorrelation
Clade probabilities and correlations under uniform-on-topologies tree probability distributions;
| 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 |
