bm_path_sim | brownian motion path simulator |
bootstrap | bootstrap: a function to compute bootstrap replicates |
bootstrap.multiOU | function to bootstrap a multiOU object |
brownie_path_sim | Release of constraint path simulator |
convert | toggles between ouch and ape format trees |
custom.llik.closure | returns a custom-built likelihood function |
custom_multiType | get the likelihood of a custom model custom_multiType allows... |
evaluate_likelihood | get the likelihood of the specified model using the specified... |
format_data | format data in ape format into ouch format |
get_clade | A function that returns the edge numbers of all branches... |
get_indices | Helper function to work with llik.closure indexing |
getParameters | get parameters of a fitted object |
getParameters.multiOU | get parameters for the multiOU model |
getParameters.wrighttree | An internal S3 method to get the parameters from the... |
labrids | labrids data |
lca_calc | Wrappers for the C functions that actually calculate the... |
llik.closure | returns the likelihood function for the chosen submodel |
loglik.multiOU | get the log likelihood |
loglik.wrighttree | An internal S3 method to get the likelihood of a wrightscape... |
mrcaOUCH | Finds the most recent common ancestor on an OUCH formatted... |
multiOU_lik_lca | compute the likelihood by passing data to the C level... |
multiTypeOU | Fits the generic multitype OU. |
ou_path_sim | OU path simulator |
paintBranches | Paints branches with regimes changing at nodes specified |
paint_phy | returns a phylogenetic tree painted for ouwie and data |
parrotfish | parrotfish data |
release_path_sim | Release of constraint path simulator |
setup_pars | Helper function to work with llik.closure indexing |
simulate.multiOU | simulate the multiOU model |
simulate.wrighttree | An internal S3 method, simulates the data of a wrightscape... |
summary.multiOU | Summarize a multiOU fit's outputs, including bootstraps, if... |
tip_plot | creates a color-coded plot of how well each tip fits it's... |
wrightscape | fit the full model entirely in C code, for speed. |
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