[R] Size of subsample in ecodist mantel()

[Sarah Goslee]

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