Calculate likelihood of each sequence based on gamma distribution of pairwise distances.
sequenceLikelihoods(
x,
model = "N",
pairwise.deletion = FALSE,
n = NULL,
plot = TRUE,
simplify = TRUE,
...
)a DNAbin object.
a character string specifying the evolutionary model to be
used. Passed to dist.dna.
a logical indicating whether to delete the
sites with missing data in a pairwise way. Passed to
dist.dna.
number of sequences with lowest delta(log-likelihoods) to plot. Defaults to all sequences Set to 0 to supress plotting.
generate a plot of top n most unlikely sequences.
if there is a single locus, return result in a simplified
form? If FALSE a list will be returned wth one element per locus.
arguments passed from other functions (ignored).
vector of delta(log-Likelihoods) for each sequence, sorted from smallest to largest, and a plot of their distributions.
Fits a Gamma distribution to the pairwise distances of sequences and calculates the log-likelihood for each (sum of all pairwise log-likelihoods for that sequence). Sequences that are extremely different from all others will have low log-likelihoods. Values returned as delta(log-likelhoods) = difference of log-likelihoods from maximum observed values.
# NOT RUN {
data(dolph.haps)
sequenceLikelihoods(dolph.haps)
# }
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