evaluate_likelihood: get the likelihood of the specified model using the specified...
In cboettig/wrightscape: wrightscape

Description Usage Arguments Details Value

get the likelihood of the specified model using the specified parameters

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  evaluate_likelihood(data, tree, regimes,
    model_spec = list(alpha = "indep", sigma = "indep", theta = "indep"),
    Xo, alpha, sigma, theta)

`data`	the trait data
`tree`	the phylogenetic tree in ouch format
`regimes`	the regimes in ouch format
`model_spec`	a list that specifies the model, see details
`Xo`	root state
`alpha`	a vector of length n_regimes if indep in model, or a scalar
`sigma`	a vector of length n_regimes if indep in model, or a scalar
`theta`	a vector of length n_regimes if indep in model, or a scalar

the general model form is specified by model_spec list. This specifies which parameters out of alpha, theta, and sigma are independently estimated on each regime, kept global across regimes, or, in the case of alpha, fixed to zero (to give purely Brownian behavior). i.e. ouch model is equivalent to: list(alpha="global", sigma="global", theta="indep"), while the brownie model is equivalent to list(alpha="fixed", sigma="indep", theta="global")

log likelihood

cboettig/wrightscape documentation built on May 13, 2019, 2:12 p.m.