Man pages for cboettig/wrightscape
wrightscape
| 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. |
