getDevianceRes: A function to calculate the matrix of deviance residuals.

In RCM: Fit row-column association models with the negative binomial distribution for the microbiome

Description

A function to calculate the matrix of deviance residuals.

Usage

getDevianceRes(RCM, Dim = RCM$k)

Arguments

RCM	an RCM object
Dim	The dimensions to use For the deviance residuals we use the overdispersions from the reduced model. Standard dimensions used are only first and second, since these are also plotted

Value

A matrix with deviance residuals of the same size as the original data matrix

Examples

data(Zeller)
require(phyloseq)
tmpPhy = prune_taxa(taxa_names(Zeller)[1:120],
prune_samples(sample_names(Zeller)[1:75], Zeller))
#Subset for a quick fit
zellerRCM = RCM(tmpPhy, k = 2, round = TRUE, prevCutOff = 0.03)
devRes = getDevianceRes(zellerRCM)

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