Description Usage Arguments Value Author(s)
Calculates the negative log-likelihood of a chromosome or ploidy model
1 | chromploid_nllike(log.par, phy, tip.values, pi.0, Q.FUN, Q.ARGS)
|
log.par |
A vector of parameter values in ln scale. Length of the vector depends on model defined by Q.FUN |
phy |
Binary rooted phylogenetic tree |
tip.values |
A data frame with at least two columns first column has tip labels in the same order than phylogenetic tree, second column ploidy or chromosome numbers depending on Q.FUN |
pi.0 |
Probability distribution to be used at the root of phylogeny |
Q.FUN |
A function that calculates the Q-matrix of the parameters of interest |
Q.ARGS |
A list of arguments to be passed to Q.FUN |
Result is the negative log-likelihood of parameters log.par given the model in Q.FUN
Rosana Zenil-Ferguson
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