LogLike function

Likelihood of an observed annotated phylogenetic tree

This function computes the log-likelihood of the chosen parameters given a particular dataset. The arguments annotations, and offspring

should be as those returned by new_aphylo(). For complete parameter estimation see aphylo_estimates .

LogLike(tree, psi, mu_d, mu_s, eta, Pi, verb_ans = TRUE, check_dims = TRUE)

Arguments

• tree: A phylogenetic tree of class aphylo .
• psi: Numeric vector of length 2. Misclasification probabilities. (see LogLike).
• mu_d, mu_s: Numeric vector of length 2. Gain/loss probabilities (see LogLike).
• eta: Numeric vector of length 2. Annotation bias probabilities (see LogLike).
• Pi: Numeric scalar. Root node probability of having the function (see LogLike).
• verb_ans: Logical scalar. When FALSE (default) the function returns a list with a single scalar (the log-likelihood).
• check_dims: Logical scalar. When TRUE (default) the function checks the dimmension of the passed parameters.

Returns

A list of class phylo_LogLik with the following elements: - S: An integer matrix of size $2^p * p$ as returned by states.

• Pr: A numeric matrix of size $G * 2^p$ with node/state probabilities.

• ll: A numeric scalar with the log-likelihood value given the chosen parameters.

Details

The parameters to estimate are described as follows:

1. psi: A vector of length 2 with $psi[0]$ and $psi[1]$, which are the misclassification probabilities fo $s[p]=0$ and $s[p]=1$

   respectively.

2. mu_d, mu_s: A vector of length 2 with $mu[0]$ and $mu[1]$ which are the gain and loss probabilities respectively. The subscript d denotes duplication nodes and s speciation node.

3. eta: A vector of length 2 with $eta[0]$ and $eta[1]$ which are the annotation bias probabilities.

4. Pi: A numeric scalar which for which equals the probability of the root node having the function.