Re: [R] Size of subsample in ecodist mantel()
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.a...@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 0.001 1.000 0.001 0.1396906 0.1396906 if I do not set a value for pboot then as expected ulimllim print(mantel(X~Y,nperm=1000,nboot=1000)) mantelr pval1 pval2 pval3 llim.2.5% ulim.97.5% 0.1396906 0.001 1.000 0.001 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.gos...@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 __ R-help@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide http://www.R-project.org/posting-guide.html and provide commented, minimal, self-contained, reproducible code.
Re: [R] Size of subsample in ecodist mantel()
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 0.001 1.000 0.001 0.1396906 0.1396906 if I do not set a value for pboot then as expected ulimllim print(mantel(X~Y,nperm=1000,nboot=1000)) mantelr pval1 pval2 pval3 llim.2.5% ulim.97.5% 0.1396906 0.001 1.000 0.001 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.gos...@gmail.comwrote: 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 [[alternative HTML version deleted]] __ R-help@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide http://www.R-project.org/posting-guide.html and provide commented, minimal, self-contained, reproducible code. -- Sarah Goslee http://www.stringpage.com http://www.sarahgoslee.com http://www.functionaldiversity.org [[alternative HTML version deleted]] __ R-help@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide http://www.R-project.org/posting-guide.html and provide commented, minimal, self-contained, reproducible code.
[R] Size of subsample in ecodist mantel()
What is the size of the boostrapped subsample in ecodist mantel() thanks [[alternative HTML version deleted]] __ R-help@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide http://www.R-project.org/posting-guide.html and provide commented, minimal, self-contained, reproducible code.
Re: [R] Size of subsample in ecodist mantel()
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 [[alternative HTML version deleted]] __ R-help@r-project.org javascript:; mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide http://www.R-project.org/posting-guide.html and provide commented, minimal, self-contained, reproducible code. -- Sarah Goslee http://www.stringpage.com http://www.sarahgoslee.com http://www.functionaldiversity.org [[alternative HTML version deleted]] __ R-help@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide http://www.R-project.org/posting-guide.html and provide commented, minimal, self-contained, reproducible code.
