multiOU_lik_lca: compute the likelihood by passing data to the C level...
In cboettig/wrightscape: wrightscape

Description Usage Arguments Details Value

compute the likelihood by passing data to the C level function, wrightscape

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  multiOU_lik_lca(data, tree, regimes, alpha = NULL,
    sigma = NULL, theta = NULL, Xo = NULL, lca,
    scale = max(tree@times))

`data`	- ouch-style data – a numeric, in the same order as nodes given in "tree"
`tree`	- ouch-tree
`regimes`	- painting of selective regimes, as in ouch
`alpha`	- (vector length n_regimes) gives strength of selection in each regime
`sigma`	- (vector length n_regimes) gives diversification rate in each regime
`theta`	- (vector length n_regimes) gives optimum trait in each regime
`Xo`	- root value
`lca`	- least common ancestor matrix, from lca_calc fun
`scale`	normalize branch lengths by this amount

A version of the multitype OU likelihood function that accepts the least common ancestor matrix as a parameter. This may increase computational speed, since the calculation needs to be done only once and is rather slow as implemented .C calls should do some error checking on the length of inputs maybe, to avoid crashes when given inappropriate calls

the log likelihood at the given parameter values

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