Simulate Discrete Character Data along Phylogenetic Trees

Documentation for package ‘MorphSim’ version 0.1.0

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.reconstructed	Add reconstructed tree and matrix to morpho object
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.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