custom.llik.closure: returns a custom-built likelihood function
In cboettig/wrightscape: wrightscape

Description Usage Arguments Details Value

returns a custom-built likelihood function

1 2	custom.llik.closure(data, tree, regimes, indices, make_bm)

`data`	the trait data
`tree`	the phylogenetic tree in ouch format
`regimes`	the regimes in ouch format
`indices`	a list with vectors alpha_i, sigma_i, and theta_i. Each vector contains the index number of the parameter to be used for that regime – repeated index numbers indicate a parameter that is the same for both regimes. The entries in the vector are in order of the regimes and must be of length n_regimes.
`make_bm`	the regimes which should have their alpha value set to BM.

Consider this example: Regimes are numbered 1 to 7. 1-6 follow modelspec global alpha/sigma, indep theta and regime 7 follows modelspec alpha=0, theta, shares global sigma imagine a parameter list: (alpha, sigma, theta1,2,3,4,5,6,7) indices = list(alpha_i = rep(1,7), sigma_i = rep(2,7), theta_i = 3:(7+2)) make_bm <- c(7) # makes the 7th alpha value set to zero always

the negative log likelihood of the parameters given the data.

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