Man pages for cboettig/wrightscape

bm_path_simbrownian motion path simulator
bootstrapbootstrap: a function to compute bootstrap replicates
bootstrap.multiOUfunction to bootstrap a multiOU object
brownie_path_simRelease of constraint path simulator
converttoggles between ouch and ape format trees
custom.llik.closurereturns a custom-built likelihood function
custom_multiTypeget the likelihood of a custom model custom_multiType allows...
evaluate_likelihoodget the likelihood of the specified model using the specified...
format_dataformat data in ape format into ouch format
get_cladeA function that returns the edge numbers of all branches...
get_indicesHelper function to work with llik.closure indexing
getParametersget parameters of a fitted object
getParameters.multiOUget parameters for the multiOU model
getParameters.wrighttreeAn internal S3 method to get the parameters from the...
labridslabrids data
lca_calcWrappers for the C functions that actually calculate the...
llik.closurereturns the likelihood function for the chosen submodel
loglik.multiOUget the log likelihood
loglik.wrighttreeAn internal S3 method to get the likelihood of a wrightscape...
mrcaOUCHFinds the most recent common ancestor on an OUCH formatted...
multiOU_lik_lcacompute the likelihood by passing data to the C level...
multiTypeOUFits the generic multitype OU.
ou_path_simOU path simulator
paintBranchesPaints branches with regimes changing at nodes specified
paint_phyreturns a phylogenetic tree painted for ouwie and data
parrotfishparrotfish data
release_path_simRelease of constraint path simulator
setup_parsHelper function to work with llik.closure indexing
simulate.multiOUsimulate the multiOU model
simulate.wrighttreeAn internal S3 method, simulates the data of a wrightscape...
summary.multiOUSummarize a multiOU fit's outputs, including bootstraps, if...
tip_plotcreates a color-coded plot of how well each tip fits it's...
update.multiOUupdate the model fit
wrightscapefit the full model entirely in C code, for speed.
cboettig/wrightscape documentation built on Oct. 19, 2017, 7:45 a.m.