A rather strange situation here and I've not found the source of the
problem.
The point is to print a ternary plot matrix of compositional data with
ellipses enclosing 95% of the variance in each plot. The ellipses
display on
the monitor, dev = x11cairo (see attached winters-x11cairo.pdf), but not
when
sent directly to a file, dev = pdf (see attached winters-pdf.pdf).
Here's winters.acomp:
structure(c(0.0666666666666667, 0.0612244897959184, 0.0434782608695652,
0.043956043956044, 0.05, 0.0161290322580645, 0.6, 0.571428571428571,
0.623188405797101, 0.593406593406593, 0.433333333333333,
0.629032258064516, 0.0666666666666667, 0.0612244897959184,
0.101449275362319, 0.0659340659340659, 0.0666666666666667,
0.032258064516129, 0.244444444444444, 0.26530612244898,
0.217391304347826, 0.263736263736264, 0.366666666666667,
0.290322580645161, 0.0222222222222222, 0.0408163265306122,
0.0144927536231884, 0.032967032967033, 0.0833333333333333,
0.032258064516129), .Dim = c(6L, 5L), .Dimnames = list(
NULL, c("filter", "gather", "graze", "predate", "shred")), class =
"acomp")
And this is the command sequence:
library(compositions)
plot(winters.acomp, main="Winters Creek", cex=0.5)
r <- sqrt(qchisq(p=0.95, df=4))
mn <- mean(winters.acomp)
vr <- var(winters.acomp)
plot(winters.acomp, main="Winters Creek", cex=0.5)
ellipses(mean=mn, var=vr, r=r, steps=72, thinRatio=NULL, aspanel=FALSE,
col='red', lwd=2)
# monitor plot window is manually closed.
pdf("winters-pdf.pdf")
plot(winters.acomp, main="Winters Creek", cex=0.5)
ellipses(mean=mn, var=vr, r=r, steps=72, thinRatio=NULL, aspanel=FALSE,
col='red', lwd=2)
dev.off()
What am I not seeing here that causes the different outputs?
Rich
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