Man pages for JanEngelstaedter/cophy
Constructing random cophylogenetic trees and analysing their statistics
| cophylogeny | Creates a cophylogeny object |
| get_branchNThroughTime | Branch (species) numbers through time. |
| get_GDist | Calculating the distance matrix between host branches alive... |
| get_hostShifts | Counting parasite host-jumps. |
| get_infectionFrequencies | Distribution of parasite numbers on the tips of a... |
| get_infectionFrequenciesSubtrees | Parasite infection frequency per host subtree. |
| get_infectionStatistics | Basic statistics describing a cophylogeny. |
| get_PEventsThroughTime | Numbers of different events in parasite evolution. |
| get_PextinctionTime | Parasite lineage extinction time |
| get_PHDistCorrelation | Correlation between pairwise distances of associated hosts... |
| get_PHDistSubtreeCorrelation | Correlation between pairwise distances of associated hosts... |
| plot.cophylogeny | Cophylogeny plot |
| print.cophylogeny | Printing a cophylogeny |
| prune_Cophylo | Pruning a cophylogeny |
| rcophylo | Simulate cophylogenies |
| rcophylo_HP | Cophylogeny simulation |
| rcophylo_HresP | Cophylogeny simulation |
| rcophylo_PonH | Cophylogeny simulation on an existing host tree. |
| rphylo_H | Phylogenetic (host) tree simulation |
