SCRIPT for NIR "DEMO" Tutorial - 001

########### RAW NIR Demo Data##################################

demo<-read.table("demo.txt",header=TRUE)

VIS<-demo[,6:355]

VIS<-as.matrix(VIS)

NIR<-demo[,356:1055]

NIR<-as.matrix(NIR)

ALL<-demo[,6:1055]

ALL<-as.matrix(ALL)

Protein<-demo[,1]

Fat<-demo[,2]

Ash<-demo[,3]

DM<-demo[,4]

Moisture<-demo[,5]

demo_raw<-data.frame(Protein=I(Protein),Fat=I(Fat),Ash=I(Ash),DM=I(DM),

+ Moisture=I(Moisture),VIS=I(VIS),NIR=I(NIR),ALL=I(ALL))

wave_vis<-seq(400,1098,by=2)

wave_nir<-seq(1100,2498,by=2)

wave_all<-seq(400,2498,by=2)

matplot(wave_vis,t(demo_raw$VIS),lty=1,pch=".",xlab="nm",ylab="log(1/R)")

matplot(wave_nir,t(demo_raw$NIR),lty=1,pch=".",xlab="nm",ylab="log(1/R)")

matplot(wave_all,t(demo_raw$ALL),lty=1,pch=".",xlab="nm",ylab="log(1/R)")

########### MSC (Multiple Scatter Correction) ##########################

library(ChemometricsWithR)

VIS_msc<-msc(NIR)

VIS_msc<-as.matrix(VIS_msc)

NIR_msc<-msc(NIR)

NIR_msc<-as.matrix(NIR_msc)

ALL_msc<-msc(ALL)

ALL_msc<-as.matrix(ALL_msc)

demo_msc<-data.frame(Protein=I(Protein),Fat=I(Fat),Ash=I(Ash),DM=I(DM),

+ Moisture=I(Moisture),VIS=I(VIS_msc),NIR=I(NIR_msc),ALL=I(ALL_msc))

matplot(wave_vis,t(demo_msc$VIS),lty=1,pch=".",xlab="nm",ylab="log(1/R)")
matplot(wave_nir,t(demo_msc$NIR),lty=1,pch=".",xlab="nm",ylab="log(1/R)")
matplot(wave_all,t(demo_msc$ALL),lty=1,pch=".",xlab="nm",ylab="log(1/R)")

########### SNV (Standard Normal Variate )####################################

tVIS<-t(VIS)

tNIR<-t(NIR)

tVISsnv<-scale(tVIS,center=TRUE,scale=TRUE)

tNIRsnv<-scale(tNIR,center=TRUE,scale=TRUE)

VIS_snv<-t(tVISsnv)

VIS_snv<-as.matrix(VIS_snv)

NIR_snv<-t(tNIRsnv)

NIR_snv<-as.matrix(NIR_snv)

tALL<-t(ALL)

tALLsnv<-scale(tALL,center=TRUE,scale=TRUE)

ALL_snv<-t(tALLsnv)

ALL_snv<-as.matrix(ALL_snv)

demo_snv<-data.frame(Protein=I(Protein),Fat=I(Fat),Ash=I(Ash),DM=I(DM),
+ Moisture=I(Moisture),VIS=I(VIS_snv),NIR=I(NIR_snv),ALL=I(ALL_snv))

matplot(wave_nir,t(demo_snv$NIR),lty=1,pch=".",xlab="nm",ylab="log(1/R)")

matplot(wave_vis,t(demo_snv$VIS),lty=1,pch=".",xlab="nm",ylab="log(1/R)")

matplot(wave_all,t(demo_snv$ALL),lty=1,pch=".",xlab="nm",ylab="log(1/R)")