AFM (version 2.0)

calculateOmnidirectionalVariogram: Calculate experimental omnidirectional semi-variogram

Description

calculateOmnidirectionalVariogram returns the semivariance calculated for all the directions calculate the experimental omnidirectional variogram of an AFMImage with the variogram function of the gstat package. The experimental semi-variogram is used to fit (find the best sill and range) the theoretical variogram models. With 512*512 images, it takes several minutes to calculate.

Usage

calculateOmnidirectionalVariogram(AFMImageVariogramAnalysis, AFMImage)

Arguments

AFMImageVariogramAnalysis

an AFMImageVariogramAnalysis to manage and store the result of variogram analysis

AFMImage

an AFMImage from Atomic Force Microscopy

Value

the semivariance calculated in all the directions

Examples

# NOT RUN {
library(AFM)
library(ggplot2)

data(AFMImageOfRegularPeaks)
variogramAnalysis<-AFMImageVariogramAnalysis(sampleFitPercentage=3.43/100)
avario<-AFM::calculateOmnidirectionalVariogram(AFMImageVariogramAnalysis= variogramAnalysis, 
                                               AFMImage= AFMImageOfRegularPeaks)
dist<-gamma<-NULL
p <- ggplot(avario, aes(x=dist, y=gamma))
p <- p + geom_point()
p <- p + geom_line()
p <- p + ylab("semivariance")
p <- p + xlab("distance (nm)")
p <- p + ggtitle("Experimental semivariogram")
p
# }