PhylogeneticEM (version 1.2.1)

extract.variance_covariance: Extract sub-matrices of variance.

Description

extract.variance_covariance return the adequate sub-matrix.

Usage

# S3 method for variance_covariance
extract(struct, what = c("YY", "YZ", "ZZ"),
  masque_data = c(rep(TRUE, attr(struct, "ntaxa") * attr(struct,
  "p_dim")), rep(FALSE, (dim(struct)[1] - attr(struct, "ntaxa")) *
  attr(struct, "p_dim"))))

Arguments

struct

structural matrix of size (ntaxa+nNode)*p, result of function compute_variance_covariance

what:

sub-matrix to be extracted: "YY" : sub-matrix of tips (p*ntaxa first lines and columns) "YZ" : sub matrix tips x nodes (p*nNodes last rows and p*ntaxa first columns) "ZZ" : sub matrix of nodes (p*nNodes last rows and columns)

miss;

missing values of Y_data

Value

sub-matrix of variance covariance.