This time I´m going to use my own data to develop a model to predict some fatty acid in the solid fat (pork).Samples had been analyzed in a NIT (Near Infrared Transmittance) instrument. The range of the wavelengths is from 850 to 1048 nm (100 data poi...
Outliers have an important influence over the PCs, for this reason they must be detected and examinee.We have just the spectra without lab data, and we have to check if any of the sample spectra is an outlier ( a noisy spectrum, a sample which belongs ...
We saw how to plot the raw spectra (X), how to calculate the mean spectrum, how to center the sprectra (subtracting the mean spectrum from every spectra of the original matrix X). After that we have developed the PCAs with the NIPALS algorithm, getting...
This plot in 2D, help us to decide the number of PCs, it is easy to create in R, once we have discompose the X matrix into a P matrix (loadings) and a T matrix (scores).For this plot, we just need the T matrix.> CPs<-seq(1,10,by=1)> matp...
> X<-yarn$NIR> X_nipals<-nipals(X,a=10,it=100)Two matrices are generated (P and T)As in other posts, we are going to look to the loadings & scores, for firsts three principal components:> wavelengths<-seq(1,268,by=1)> matplot(w...
The idea of this post is to compare the score plots for the first 3 principal components obtained with the algorithm “svd” with the scores plot of other chemometric software (Win ISI in this case). Previously I had exported the yarn spectra t...
There are different algorithms to calculate the Principal Components (PCs). Kurt Varmuza & Peter Filzmozer explain them in their book: “Introduction to Multivariate Statistical Analysis in Chemometrics”.I´m going to apply one of them, to...
(This article was first published on NIR-Quimiometría, and kindly contributed to R-bloggers) This is another pretreatment used quite often in Near Infrared to remove the scatter. It is applied to every spectrum individually. The average and standard deviation of all the data points for that spectra is calculated. Every data point of the spectra is substracted from the mean and...
(This article was first published on NIR-Quimiometría, and kindly contributed to R-bloggers) Mean spectrum calculation is important: To center a matrix of spectra, we subtract the mean spectrum, from every spectrum in the matrix. There are also many options to use the mean spectrum, like average subsamples. Let´s calculate and plot the mean spectra for the Yarn NIR Data:...
We have to check different options before to decide for one model:Configure different cross validations.Configure different math treatments.Configure number of terms.With the Yarn NIR data, I have develop 4 models, for a simple exercise.Of course...
Zero Inflated Models and Generalized Linear Mixed Models with R.
Zuur, Saveliev, Ieno (2012).
