estDisp: Estimate the overdispersion

Description Usage Arguments Details Value

View source: R/F_estDisp.R

Description

Estimate the overdispersion

Usage

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estDisp(
  X,
  cMat = NULL,
  rMat = NULL,
  muMarg,
  psis,
  trended.dispersion = NULL,
  prior.df = 10,
  dispWeights = NULL,
  rowMat = NULL,
  allowMissingness = FALSE,
  naId
)

Arguments

X

the data matrix of dimensions nxp

cMat

a 1xp colum scores matrix

rMat

a nx1 rowscores matrix, if unconstrained

muMarg

an nxp offset matrix

psis

a scalar, the current psi estimate

trended.dispersion

a vector of length p with pre-calculated trended.dispersion estimates. They do not vary in function of the offset anyway

prior.df

an integer, number of degrees of freedom of the prior for the Bayesian shrinkage

dispWeights

Weights for estimating the dispersion in a zero-inflated model

rowMat

matrix of row scores in case of constrained ordination

allowMissingness

A boolean, are missing values present

naId

The numeric index of the missing values in X

Details

Information between taxa is shared with empirical Bayes using the edgeR pacakage, where the time-limiting steps are programmed in C.

Value

A vector of length p with dispersion estimates


RCM documentation built on Nov. 8, 2020, 5:22 p.m.

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