- '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.