diffractogram {diffractometry} | R Documentation |
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.
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)
data |
A diffractogram given as a matrix, where the first column gives the angles of diffraction in 2theta 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 2theta |
dispers |
Additional dispersion factor; not used if heterosk==T |
diffractogram
first calls baselinefit
with the specified parameters and then pkdecomp
for the output of baselinefit
. For further details, see the corresponding help pages.
Returns a LIST with components
basl |
Output of baselinefit |
pks |
Output of pkdecomp |
P.L. Davies, M. Meise, T.Mildenberger
P.L. Davies, U. Gather, M. Meise, D. Mergel, T. Mildenberger (2008): "Residual based localization and quantification of peaks in x-ray diffractograms", to appear in the Annals of Applied Statistics. http://arxiv.org/abs/0711.3687
## 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 par(mfrow=c(3,1)) data(indiumoxide) indox<-indiumoxide[1901:2400,] sol<-diffractogram(indox,maxsolutions=1) 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,])