Man pages for nodeSub
Simulate DNA Alignments Using Node Substitutions

calc_expected_hidden_nodesCalculate the number of expected hidden nodes in a...
calc_fractionCalculate the expected fraction of substitutions at the...
calc_required_node_timeCalculate the required node time to obtain a desired fraction...
calc_sum_statscalculate summary statistics of a phylogenetic tree, compared...
count_hiddenFunction to calculate the number of hidden speciation events,...
create_balanced_treecreate a balanced tree out of branching times
create_equal_alignmentfunction create an alignment with identical information...
create_equal_alignment_explicitfunction create an alignment with identical information...
create_unbalanced_treecreate an unbalanced tree out of branching times
estimate_marginal_modelsestimate the marginal likelihood of the relaxed and strict...
get_p_matrixcalculate p matrix
infer_phylogenyinfer the time calibrated phylogeny associated with the...
nodeSub-packagePackage providing functions to simulate sequences under...
reduce_treeFunction to remove speciation events occuring after an...
sim_linkedsimulate a sequence assuming conditional substitutions on the...
sim_normalSimulate sequences for a given evolutionary tree, using a...
sim_normal_explicitsimulate a sequence assuming substitutions are only...
sim_unlinkedSimulate a sequence assuming node substitutions are not...
sim_unlinked_explicitSimulate a sequence assuming node substitutions are not...
slow_matrixthis function calculates the p matrix within R this is slower...
nodeSub documentation built on Aug. 19, 2022, 5:23 p.m.