countprop (version 1.1.1)

logitNormalVariation: Logit Normal Variation

Description

Estimates the variation matrix of count-compositional data based on a multinomial logit-Normal distribution. Estimation is performed using only the parameters of the distribution.

Usage

logitNormalVariation(
  mu,
  Sigma,
  type = c("standard", "phi", "phis", "rho"),
  lr = c("alr", "clr"),
  order = c("second", "first")
)

Value

An estimate of the requested metric of proportionality.

Arguments

mu

The mle estimate of the mu matrix

Sigma

The mle estimate of the Sigma matrix (input Sigma on the ALR scale, even if requesting metrics on the CLR scale)

type

Type of variation metric to be calculated: standard, phi, phis (a symmetrical version of phi), or rho

lr

Which scale to calculate the proportionality metric on, either alr or clr.

order

Deprecated: The order of the Taylor-series approximation to be used in the estimation

Examples

data(singlecell)
mle <- mleLR(singlecell)
mu.hat <- mle$mu
Sigma.hat <- mle$Sigma

logitNormalVariation(mu.hat, Sigma.hat)
logitNormalVariation(mu.hat, Sigma.hat, type="phi")
logitNormalVariation(mu.hat, Sigma.hat, type="rho")