Man pages for nodeSub
Simulate DNA Alignments Using Node Substitutions
| calc_expected_hidden_nodes | Calculate the number of expected hidden nodes in a... |
| calc_fraction | Calculate the expected fraction of substitutions at the... |
| calc_required_node_time | Calculate the required node time to obtain a desired fraction... |
| calc_sum_stats | calculate summary statistics of a phylogenetic tree, compared... |
| count_hidden | Function to calculate the number of hidden speciation events,... |
| create_balanced_tree | create a balanced tree out of branching times |
| create_equal_alignment | function create an alignment with identical information... |
| create_equal_alignment_explicit | function create an alignment with identical information... |
| create_unbalanced_tree | create an unbalanced tree out of branching times |
| estimate_marginal_models | estimate the marginal likelihood of the relaxed and strict... |
| get_p_matrix | calculate p matrix |
| infer_phylogeny | infer the time calibrated phylogeny associated with the... |
| nodeSub-package | Package providing functions to simulate sequences under... |
| reduce_tree | Function to remove speciation events occuring after an... |
| sim_linked | simulate a sequence assuming conditional substitutions on the... |
| sim_normal | Simulate sequences for a given evolutionary tree, using a... |
| sim_normal_explicit | simulate a sequence assuming substitutions are only... |
| sim_unlinked | Simulate a sequence assuming node substitutions are not... |
| sim_unlinked_explicit | Simulate a sequence assuming node substitutions are not... |
| slow_matrix | this function calculates the p matrix within R this is slower... |
