A list with class phyclust
will be returned containing
several elements as the following:
'N.X.org'number of sequences in the X
matrix.
'N.X.unique'number of unique sequences in the X
matrix.
'L'number of sites, length of sequences, number of column of the X
matrix.
'K'number of clusters.
'Eta'proportion of subpopulations, \(\eta_k\), length = K
, sum to 1.
'Z.normalized'posterior probabilities, \(Z_{nk}\), each row sums to 1.
'Mu'centers of subpopulations, dim = \(K\times L\), each row is a center.
'QA'Q matrix array, information for the evolution model, a list contains:
'pi' |
equilibrium probabilities, each row sums to 1. |
'kappa' |
transition and transversion bias. |
'Tt' |
total evolution time, \(t\). |
'identifier' |
identifier for QA. |
'logL'log likelihood values.
'p'number of parameters.
'bic'BIC, \(-2\log L + p \log N\).
'aic'AIC, \(-2\log L + 2p\).
'N.seq.site'number of segregating sites.
'class.id'class id for each sequences based on the maximum posterior.
'n.class'number of sequences in each cluster.
'conv'convergence information, a list contains:
'eps' |
relative error. |
'error' |
error if the likelihood decreased. |
'flag' |
convergence state. |
'iter' |
convergence iterations. |
'inner.iter' |
convergence of inner iterations other than EM. |
'cm.iter' |
convergence of CM iterations. |
'check.param' |
parameter states. |
'init.procedure'initialization procedure.
'init.method'initialization method.
'substitution.model'substitution model.
'edist.model'evolution distance model.
'code.type'code type.
'em.method'EM algorithm.
'boundary.method'boundary method.
'label.method'label method.