diffractogram: Complete analysis of diffractograms as described in Davies et...

In thmild/diffractometry: Baseline Identification and Peak Decomposition for x-Ray Diffractograms

Description

Performs a complete analysis of x-ray diffractogram, i.e. calculation of the baseline and the peak intervals as well as decomposition of the peaks.

Usage

diffractogram(data, tau=2.5,gam=1, scl.factor=1.2, maxwdth=5, intnum=0, 
alpha=0.1, maxiter1=500, maxiter=10000, hmax=5, maxsolutions=3,
heterosk=TRUE, baselim=c(0.05,5), dispers=1)

Arguments

data	A diffractogram given as a matrix, where the first column gives the angles of diffraction in 2θ and the second column gives the corresponding photon counts. Angles of diffraction are taken to be equidistant.
tau	Value of Parameter tau used in the residual criterion.
gam	Factor which is used in the separation between peaks and baseline.
scl.factor	Factor which is used in the heteroscedastic residual criterion.
maxwdth	Maximum width of the peaks. By default set to 5 degrees.
intnum	Vector of numbers of intervals. If intnum = 0, all intervals are used
alpha	Test level for residual criterion
maxiter1	Number of attempts to fit a model with 1 component
maxiter	Number of attempts to fit a model with k > 1 components
hmax	Maximum number of components
maxsolutions	Number of solutions with k components
heterosk	If TRUE, the estimate of noise level given in baslfit is used (default); otherwise noise level is taken to be proportional to signal height
baselim	Limits for changes in the baseline estimate; first component is given in percent of the baseline height, second in counts per 2θ
dispers	Additional dispersion factor; not used if heterosk==T

Details

diffractogram first calls baselinefit with the specified parameters and then pkdecomp for the output of baselinefit. For further details, see the corresponding help pages.

Value

Returns a LIST with components

basl	Output of baselinefit
pks	Output of pkdecomp

Author(s)

P.L. Davies, M. Meise, T.Mildenberger

References

P.L. Davies, U. Gather, M. Meise, D. Mergel, T. Mildenberger (2008): "Residual based localization and quantification of peaks in x-ray diffractograms", Annals of Applied Statistics, Vol. 2, No. 3, 861-886.. http://www.statistik.tu-dortmund.de/fileadmin/user_upload/Lehrstuehle/MSind/Publikationen/2008/2008_-_Davies_Gather_Meise_Mergel_Mildenberger_-_Residual_based_localization_and_quantification_of_peaks_in_x-ray_diffractograms.pdf

See Also

baselinefit, pkdecomp

Examples

## Complete Analysis of a segment from indiumoxide data:
## Identification of baseline and peak as well as decomposition of the peaks  
## Plot shows baseline and decomposition of first found peak into two components 

set.seed(0)

par(mfrow=c(3,1))

data(indiumoxide)
indox<-indiumoxide[1901:2400,]

sol<-diffractogram(indox,maxsolutions=1,maxiter1=50,maxiter=250)

ind<-c(sol$bas$indlsep[1],sol$bas$indrsep[1])

plot(indox,xlab="",ylab="")
lines(indox[,1],sol$bas$baseline$basisl,col="red")
points(indox[ind[1]:ind[2],],col="blue")


plot(indox[ind[1]:ind[2],1], sol$bas$baseline$peaks[ind[1]:ind[2]],xlab="",ylab="")

lines(indox[ind[1]:ind[2],1],sol$pks[[2]]$fit,col="red")
plot(indox[ind[1]:ind[2],1],sol$pks[[2]]$fitpk[1,],ylim=c(0,1800),type="l",xlab="",ylab="")
lines(indox[ind[1]:ind[2],1],sol$pks[[2]]$fitpk[2,])

thmild/diffractometry documentation built on May 31, 2019, 10:45 a.m.