getPCtol: determine the minimum ratio for two subsequent eigenvalues to...

In Morpho: Calculations and Visualisations Related to Geometric Morphometrics

determine the minimum ratio for two subsequent eigenvalues to be considered different

Description

determine the minimum ratio for two subsequent eigenvalues to be considered different

Usage

getPCtol(n, expect = 2)

Arguments

n	sample size
expect	expectation value for chi-square distribution of df=2

Value

returns the minimum ratio between two subsequent subsequent eigenvalues to be considered different.

References

Bookstein, F. L. Measuring and reasoning: numerical inference in the sciences. Cambridge University Press, 2014

See Also

getMeaningfulPCs

Examples

## reproduce the graph from Bookstein (2014, p. 324)
## and then compare it to ratios for values to be considered
## statistically significant
myseq <- seq(from=10,to = 50, by = 2)
myseq <- c(myseq,seq(from=50,to=1000, by =20))
ratios <- getPCtol(myseq)
plot(log(myseq),ratios,cex=0,xaxt = "n",ylim=c(1,5.2))
ticks <- c(10,20,50,100,200,300,400,500,600,700,800,900,1000)
axis(1,at=log(ticks),labels=ticks)
lines(log(myseq),ratios)
abline(v=log(ticks), col="lightgray", lty="dotted")
abline(h=seq(from=1.2,to=5, by = 0.2), col="lightgray", lty="dotted")

## now we raise the bar and compute the ratios for values
## to be beyond the 95th percentile of
## the corresponding chi-square distribution:
ratiosSig <- getPCtol(myseq,expect=qchisq(0.95,df=2))
lines(log(myseq),ratiosSig,col=2)

Morpho documentation built on June 22, 2024, 7:19 p.m.