Expected covariance of two tips at given root-tip time and phylogenetic distance

Source: R/paramsPOUMM.R

Expected covariance of two tips at given root-tip time and phylogenetic distance

covPOUMM(
  alpha,
  sigma,
  sigmae,
  t,
  tau,
  tanc = t - tau/2,
  corr = FALSE,
  as.matrix = FALSE
)

Arguments

alpha, sigma, sigmae

POUMM parameters
t

A non-negative number or vector time from the beginning of the POUMM process (root-tip distance). If a vector, the evaluation is done on each couple (row) from cbind(t, tau).
tau

A non-negative number or vector indicating the phylogenetic distance between two tips, each of them located at time t from the root. If a vector, the evaluation is done on each couple (row) from cbind(t, tau).
tanc

A non-negative number or vector indication the root-mrca distance for a couple of tips. Defaults to t-tau/2 corresponding to an ultrametric tree.
corr

Logical indicating whether correlation should be returned instead of covariance.
as.matrix

Logical indicating if a variance-covariance matrix should be returned.

Value

If as.matrix == FALSE, a number. Otherwise a two by two symmetric matrix. If t or tau is a vector of length bigger than 1, then a vector of numbers or a list of matrices.

Details

The function assumes that the two tips are at equal distance t from the root. This implies that the root-tip distance of their mrca is t - tau/2.