First approach to ANN calibrations

This is a first approach to develop ANN calibrations with the soymeal data from Infratec and it is really promising.
I follow this code and plot the results:

#We build a dataframe with the constituent values
#and with the spectra math treated with MSC
Sample<-sm_ift[,1]
Y<-as.matrix(sm_ift[,2])        # La matriz Y son los datos de proteina.
which(is.na(Y), arr.ind=TRUE)   # La 462 tiene por valor NA y la quitamos
Y<-Y[-462,]
X<-as.matrix(sm_ift[,6:105]) # La matriz X son los datos NIR
X<-X[-462,]
library(ChemometricsWithR)
library(pls)
X<-msc(X)
##====================================================================
##PRINCIPAL COMPONENTS ANALYSIS using package "Chemometrics" NIPALS)
##====================================================================
library(chemometrics)
X_nipals<-nipals(X,a=4)
T<-X_nipals$T
T<-round(T,4)
T1<-T[,1]
T2<-T[,2]
T3<-T[,3]
T4<-T[,4]
P<-X_nipals$P
P<-round(P,4)
###################################################################
soymeal=data.frame(T1=T1,T2=T2,T3=T3,T4=T4,Y=Y)
#' Split the data into 65% training and 35% test
rndIndices=sample(nrow(soymeal))
sepPnt=round(.65*nrow(soymeal))
train=soymeal[rndIndices[1:sepPnt],]
test=soymeal[rndIndices[(sepPnt+1):length(rndIndices)],]
#' Create an neural network model with 3 hidden
#' nodes of Y~. using the training data.
#' Store this model as 'model'
library(datasets)
library(nnet)
library(graphics)
model=nnet(Y~.,train,size=4,linout=T)
#' Use this model to estimate the Y values of the test data
pre=(predict(model,test))
pre=round(pre,2)
#' Calculate the MSE of the model on the test data and output
#' it using the print or cat functions
mse=mean((test$Y-pre)^2)
cat("The MSE of the model on the test data is: ",mse,"\n")
#The MSE of the model on the test data is:  0.9314747
plot(pre,test$Y)
abline(0,1)

The loss function in this case is MSE (Mean Square Error).
More practice these coming days