[R] geoR, plot of variog4 lines incomplete

From: Michael Fuller <mmfuller_at_tiem.utk.edu>
Date: Sat 03 Jun 2006 - 04:54:46 EST


I'm using R for Mac OSX version 1.14 (2129) and the geoR package version 1.6-5 (the current version in the R repository). I'm running R in OS 10.4.6 on a Mac G4 iBook (933MHz, 640 MB DDR SDRAM). I searched the R archive and did not find a posting on this issue.

I want to use the variog and variog4 functions of geoR to characterize the pattern of spatial autocorrelation of tree density on a forest plot. But I get incomplete line plots when I plot the output of variog4, compared to the plot for the output of variog. I'm using the same geodata for each plot.

I've attached 2 graphs to illustrate. The first is a plot of a 90- degree directional variogram created using variog:
> trees90.vgm<-variog(trees.geo,max.dist=100,direction=pi/2)
> plot(trees90.vgm)

The second is a plot of a multidirectional variogram created using variog4:
> trees.vgm4<-variog4(trees.geo,max.dist=100)
> plot(trees.vgm4)

The graphs are also available at:
www.tiem.utk.edu/~mmfuller/R_plots.pdf

You can see that the 90 degree line in the multi-line plot from variog4 (dotted green line) does not include all the data shown in the single 90 degree variogram (circles) plotted using variog. The lines for other directions in the variog4 plot are also incompletely drawn.

Any suggestions as to what's causing this plotting problem?

The raw data is a file containing 3 columns x,y,z. The x,y values are the coordinates of quadrats placed end to end in a grid on a forest plot. The z values are the density of trees in each quadrat. Each quadrat is 15m square and the plot dimensions are 220x780m. The data are arranged in columns (coordinates 20 to 240) and rows (coordiantes 765 to 150) representing the data posting of each quadrat.

I create geodata objects using:
trees.geo<-read.geodata("tree.dat",header=TRUE)

Here is a data sample:

x	y	z
20	765	0.1556
35	765	0.1556
50	765	0.0356
65	765	0.0622
80	765	0.0933
95	765	0.0400
110	765	0.1111
125	765	0.1244
140	765	0.0800
155	765	0.0667
170	765	0.0711
185	765	0.0889
200	765	0.0667
215	765	0.0844
20	750	0.1067
35	750	0.0800
50	750	0.0578
65	750	0.0622
80	750	0.0578
95	750	0.0933
110	750	0.0844
125	750	0.1200
140	750	0.0711
155	750	0.0711
170	750	0.0711
185	750	0.0578
200	750	0.0489
215	750	0.0933

etc

I have repeated the analysis using different quadrat sizes and the problem of incomplete drawing of lines is unaffected.

Any suggestions are appreciated!
Mike



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Received on Sat Jun 03 05:02:06 2006

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