Identifying gypsum peaks

 Identify the peaks in the gypsum spectrum, using the function "peaks" from the package "IDPmisc".

You can obtain the gypsum spectra from the data(mineralRef) in the package "soilspec". Th spectrum is in reflectance and I converted it to absorbance using the log 1/R transformation.

wavelength <- seq(350, 2500, by = 1)
matplot(wavelength, mineralRef$gypsum, 

        type = "l", col = "blue", 

        xlab = "wavelength", 

        ylab = "Absorbance", 

        main = "Gypsum" )

With this code we get the spectrum, and see (visually) the peaks, so we can decide the value for the arguments of the function.

Now let´s get the peaks:

ppeaks_gypsum <- peaks(wavelength, 

                 mineralRef$gypsum , 

                 minPH = 0.03)

> ppeaks_gypsum

      x         y   w

1   350 0.1364889 114

3   994 0.1623408  39

4  1204 0.2884482  67

5  1445 1.0510481 127

8  1489 0.8744469  11

7  1537 0.7541421  14

6  1748 0.7571059  54

9  1944 2.1366552  83

10 2215 1.3251868  43

11 2266 1.2514346  15

2  2488 2.1942896 191

In the X column we have the peak wavelength, in the "y" the absorbance values, and in the "w" the width at half maximum of the peaks.

Now we add the vertical lines to see the marked peaks:

abline(v = ppeaks_gypsum$x, col = "red")

Just change the minPH value or the or the other arguments in the peaks function to get more or less peaks.

We can exclude the vertical lines at the extreme wavelengths.

We can use this spectrum to compare it to our soil samples checking for any trace of gypsum on them.