R: Simulate Discrete Character Data along Phylogenetic Trees

# Simulate Discrete Character Data along Phylogenetic Trees

## Documentation for package ‘MorphSim’ version 1.2.0

- DESCRIPTION file.
- User guides, package vignettes and other documentation.

## 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