AFMImageVariogramAnalysis-evaluateVariogramModels-method: evaluateVariogramModels method to evaluate the basic...

In AFM: Atomic Force Microscope Image Analysis

Description

evaluateVariogramModels method to evaluate the basic variogram models available in the gstat package A AFMImageVariogramAnalysis method to handle the variogram analysis of an AFMImage. The variogram models used can be seen with the show.vgms() function from the gstat package.

Usage

evaluateVariogramModels(AFMImageVariogramAnalysis, AFMImage)

## S4 method for signature 'AFMImageVariogramAnalysis'
evaluateVariogramModels(AFMImageVariogramAnalysis, AFMImage)

Arguments

AFMImageVariogramAnalysis	an object
AFMImage	an AFMImage

Examples

## Not run: 
library(AFM)

data("AFMImageOfRegularPeaks")
# take an extract of the image to fasten the calculation      
AFMImage<-extractAFMImage(AFMImageOfRegularPeaks, 40, 40, 32)
# e.g. AFMImage@fullfilename<-"/users/ubuntu/AFMImageOfRegularPeaks-extract.txt"
AFMImage@fullfilename<-paste(tempdir(), "AFMImageOfRegularPeaks-extract.txt", sep="/")
 
AFMImageAnalyser<-AFMImageAnalyser(AFMImage)
 
 # Variogram analysis 
sampleFitPercentage<-3.43/100
variogramAnalysis<-AFMImageVariogramAnalysis(sampleFitPercentage)
variogramAnalysis@omnidirectionalVariogram<- 
              AFM::calculateOmnidirectionalVariogram(AFMImage=AFMImage,
                                                     AFMImageVariogramAnalysis=variogramAnalysis)
variogramAnalysis@directionalVariograms<- 
              AFM::calculateDirectionalVariograms(AFMImage=AFMImage,
                                                 AFMImageVariogramAnalysis=variogramAnalysis)
 
# manage model evaluations
AFMImageVariogram<-variogramAnalysis@omnidirectionalVariogram
class(AFMImageVariogram)=c("gstatVariogram","data.frame")
variogramAnalysis<-evaluateVariogramModels(variogramAnalysis, AFMImage)

mergedDT<-getDTModelEvaluation(variogramAnalysis)
mergedDT
sillRangeDT<-getDTModelSillRange(variogramAnalysis)
sillRangeDT

## End(Not run)

AFM documentation built on Oct. 23, 2020, 5:23 p.m.