pboot is the proportion of the sample to select, and so if it's
greater than or equal to 1 you're using the entire sample rather than
a subsample, so of course the limits are equal.
If you look at the usage line in the help for mantel, where defaults
are given, the default for pboot = 0.9.
The details are discussed in the associated JSS paper that is given by
citation("ecodist")
Sarah
On Thu, Jun 28, 2012 at 9:28 PM, nevil amos <nevil.amos at gmail.com> wrote:
Thanks Sarah, It is not clear to me exactly how I set this value. if I enter a value for pboot then the ulim==llim
X<-dist(1:100) Y<-dist(1:100+50*rnorm(100)) length(X)
[1] 4950
print(mantel(X~Y,nperm=1000,nboot=1000,pboot=10))
mantelr pval1 pval2 pval3 llim.2.5% ulim.97.5% 0.1396906 0.0010000 1.0000000 0.0010000 0.1396906 0.1396906 if I do not set a value for pboot then as expected ulim>llim
print(mantel(X~Y,nperm=1000,nboot=1000))
mantelr pval1 pval2 pval3 llim.2.5% ulim.97.5% 0.1396906 0.0010000 1.0000000 0.0010000 0.1005011 0.1805416 What is the default for pboot? this does not appear to be dealt with in help for mantel On Thu, Jun 28, 2012 at 8:35 PM, Sarah Goslee <sarah.goslee at gmail.com> wrote:
You can set it using the pboot argument. Sarah On Thursday, June 28, 2012, nevil amos wrote:
What is the size of the boostrapped subsample in ecodist mantel() thanks
Sarah Goslee http://www.functionaldiversity.org