mxtrmodLRT: A function to run likelihood ratio tests on full vs. reduced...

In metabomxtr: A package to run mixture models for truncated metabolomics data with normal or lognormal distributions

Description

This function runs likelihood ratio tests on full vs. reduced mixture models. Input arguments are data frame outputs from the mxtrmod function.

Usage

mxtrmodLRT(fullmod, redmod, adj = NULL)

Arguments

fullmod	The output data frame from the mxtrmod function on the full mixture model.
redmod	The output data frame from the mxtrmod function on the reduced mixture model.
adj	The adjustment method for multiple comparisons. The default is set to NULL. Options for adjustment methods are described in the documentation for the function mt.rawp2adjp in the multtest package.

Value

A data frame containing the response variables (i.e. metabolites), negative log likelihoods of full and reduced models, chi square statistics, degrees of freedom, p-values, and, if requested, adjusted p-values.

Author(s)

Michael Nodzenski, Anna Reisetter, Denise Scholtens

References

Moulton LH, Halsey NA. A mixture model with detection limits for regression analyses of antibody response to vaccine. Biometrics. 1995 Dec;51(4):1570-8.

Examples

#Create sample data
set.seed(123)
yvar<-rlnorm(200)
these<-sample(1:100,20)
yvar[these]<-NA
logyvar<-log(yvar)
y2var<-rlnorm(200)
those<-sample(1:200,25)
y2var[those]<-NA
logy2var<-log(y2var)
pred1<-sample(0:1,200,replace=TRUE)
pred2<-sample(1:10,200,replace=TRUE)
pred3<-sample(0:1,200,replace=TRUE)
pred3miss<-sample(1:200,50)
pred3[pred3miss]<-NA
testdata<-data.frame(cbind(yvar,y2var,logyvar,logy2var,pred1,pred2,pred3))

#Get the names of the response variables 
ynames<-names(testdata)[3:4]

#Run a full mixture model on each response variable 
fullMod<-~pred1+pred2+pred3|pred1+pred2+pred3
fullModRes<-mxtrmod(ynames=ynames,mxtrModel=fullMod,data=testdata)
fullModRes

#Run a reduced mixture model on each response variable
redMod<-~pred2|pred2
redModRes<-mxtrmod(ynames=ynames,mxtrModel=redMod,data=testdata,fullModel=fullMod)
redModRes

#Compare models using likelihood ratio test
mxtrmodLRT(fullModRes,redModRes)

metabomxtr documentation built on Nov. 8, 2020, 6:50 p.m.