## ----include = FALSE----------------------------------------------------------
knitr::opts_chunk$set(
  collapse = TRUE,
  comment = "#>"
)

## ----setup--------------------------------------------------------------------
library(NPLStoolbox)

## ----process the data---------------------------------------------------------
processedTongue = parafac4microbiome::processDataCube(Cornejo2025$Tongue_microbiome, sparsityThreshold=0.5, considerGroups=TRUE, groupVariable="GenderID", centerMode=1, scaleMode=2)

processedSaliva = parafac4microbiome::processDataCube(Cornejo2025$Salivary_microbiome, sparsityThreshold=0.5, considerGroups=TRUE, groupVariable="GenderID", centerMode=1, scaleMode=2)

processedCytokine = Cornejo2025$Salivary_cytokines

## ----make CP models-----------------------------------------------------------
modelTongue = parafac4microbiome::parafac(processedTongue$data, nfac=2, nstart=100)
modelSaliva = parafac4microbiome::parafac(processedSaliva$data, nfac=2, nstart=100)
modelCytokine = parafac4microbiome::parafac(processedCytokine$data, nfac=2, nstart=100)

## ----make NPLS models---------------------------------------------------------
Y = as.numeric(as.factor(Cornejo2025$Tongue_microbiome$mode1$GenderID))
Ycnt = Y - mean(Y)
tongue_NPLS = triPLS1(processedTongue$data, Ycnt, 1)

Y = as.numeric(as.factor(Cornejo2025$Salivary_microbiome$mode1$GenderID))
Ycnt = Y - mean(Y)
saliva_NPLS = triPLS1(processedSaliva$data, Ycnt, 1)

Y = as.numeric(as.factor(Cornejo2025$Salivary_cytokines$mode1$GenderID))
Ycnt = Y - mean(Y)
cytokine_NPLS = triPLS1(processedCytokine$data, Ycnt, 1)