Simulate Discrete Character Data along Phylogenetic Trees
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Documentation for package ‘MorphSim’ version 1.2.0
Help Pages
| as.morpho | Morpho object |
| combine.morpho | Combine Two Morpho Objects |
| convergent_evol | Determines the number of convergently evolved traits |
| find_path_to_tip | Determines the route (nodes and branches) for a tip in a phylogenetic tree |
| get.convergent | Identify convergent traits |
| get.matrix | Get Specific Morphological Matrix |
| get.reconstructed | Add reconstructed tree and matrix to morpho object |
| get.transitions | Get Tranisition History |
| get_gamma_rates | Get discrete gamma rates |
| get_lognormal_rates | Get discrete log-normal rates |
| is.morpho | Morpho object |
| morpho | Morpho object |
| morpho_data | Example morpho dataset |
| morphsim_fossilsim | Match sampled ancestor labels |
| plot.morpho | Plot full evolutionary history |
| plotMorphoGrid | Plots morphological matrix |
| reconstruct.matrix | Get reconstructed matrix |
| reconstruct.tree | Color branches for plotting a reconstructed tree |
| sim.missing.data | Remove morphological character data |
| sim.morpho | Simulate characters along branches in a tree |
| stats.morpho | Calculates statistics for a morpho object |
| symmetric.Q.matrix | Generate a symmetric Q matrix |
| write.morpho | Write morpho data to file |
| write.recon.matrix | Write reconstructed character matrix to file |
| write.recon.tree | Write reconstructed tree to file |
| write.recon.tsv | Write the taxa ages of reconstructed tree |
| write.tsv | Write the taxa ages |