Reference

All functions

tree trait

An example dataset

OUwie()

Generalized Hansen models

OUwie.anc()

Estimate ancestral states given a fitted OUwie model

OUwie.boot()

Parametric bootstrap function

OUwie.contour()

Generates data for contour plot of likelihood surface

OUwie.dredge()

Generalized Detection of shifts in OU process

OUwie.fixed()

Generalized Hansen model likelihood calculator

OUwie.sim()

Generalized Hansen model simulator

check.identify()

A test of regime identifiability

dent_propose()

Propose new values This proposes new values using a normal distribution centered on the original parameter values, with desired standard deviation. If any proposed values are outside the bounds, it will propose again.

dent_walk()

Sample points from along a ridge

fix.kappa()

Adjust tree for matrix condition

getModelAvgParams()

Model average the parameter estimates over severl hOUwie fits.

getModelTable()

Generate a table from a set of hOUwie models describing their relative fit to data.

getOUParamStructure()

Generate a continuous model parameter structure

hOUwie()

Fit a joint model of discrete and continuous characters via maximum-likelihood.

hOUwie.fixed()

Fit a joint model of discrete and continuous characters via maximum-likelihood with fixed regimes.

hOUwie.recon()

Reconstruct the marginal probability of discrete node states under the hOUwie model.

hOUwie.sim()

Simulate a discrete and continuous character following a Markov and Ornstein-Uhlenbeck model.

hOUwie.thorough()

Rerun a set of hOUwie models with the best mappings of the set.

hOUwie.walk()

Sample points from along a ridge for a hOUwie model

plot(<OUwie.contour>)

Contour plot

plot(<dentist>)

Plot the dented samples This will show the univariate plots of the parameter values versus the likelihood as well as bivariate plots of pairs of parameters to look for ridges.

print(<dentist>)

Print dentist print summary of output from dent_walk

summary(<dentist>)

Summarize dentist Display summary of output from dent_walk