It is not possible in ecodist, and I'd be wary of doing it in other
packages. Instead, I would consider the model matrix approach described in
Legendre and Fortin 1989.

Sarah

On Saturday, December 3, 2011, Nevil Amos <nevil.amos@gmail.com> wrote:
> I would like to perform partial mantel tests  on only within group
values, with "between group" values assigned to NA.
> This is possible in package ncf partial.mantel.test, however this sues a
different permutation to that used in ecodist.ecodist will not accept data
with NA values, returning a "matrix is not square error.
>
> is it possible to perform this test in ecodist?
>
> many thanks
>
> Nevil Amos
>
>> library(ecodist)
>> library(ncf)
>> x<-sample(1:1000,20)
>> y<-sample(1:1000,20)
>> z<-sample(1:1000,20)
>> M1<-as.matrix( distance(x))
>> M2 <-as.matrix( distance(y ))
>> M3<-as.matrix( distance(z ))
>> D1<-(lower(M1))
>> D2<-(lower(M2))
>> D3<-(lower(M3))
>> mantel(D1 ~ D2+D3, nperm=1000)
>   mantelr      pval1      pval2      pval3  llim.2.5% ulim.97.5%
> 0.09014696 0.10300000 0.89800000 0.18400000 0.01857311 0.18468621
>> partial.mantel.test(M1,M2,M3,quiet=T)
> $MantelR
>        r12         r13         r23       r12.3       r13.2
>  0.08977575  0.02170997 -0.01561346  0.09014696  0.02320821
>
> $p
> [1] 0.09590410 0.30769231 0.47552448 0.09490509 0.30169830
>
> $call
> [1] "partial.mantel.test(M1 = M1, M2 = M2, M3 = M3, quiet = T)"
>
> attr(,"class")
> [1] "partial.Mantel"
>> M1[1:10,11:20]<-NA
>> M1[11:20,1:10]<-NA
>> D1<-(lower(M1))
>> mantel(D1 ~ D2+D3, nperm=1000)
> Error in mantel(D1 ~ D2 + D3, nperm = 1000) : Matrix not square.
>> partial.mantel.test(M1,M2,M3,quiet=T)
> $MantelR
>         r12          r13          r23        r12.3        r13.2
>  0.054906562  0.003446670 -0.015613460  0.054967403  0.004310979
>
> $p
> [1] 0.2837163 0.4275724 0.4555445 0.2857143 0.4235764
>
> $call
> [1] "partial.mantel.test(M1 = M1, M2 = M2, M3 = M3, quiet = T)"
>
> attr(,"class")
> [1] "partial.Mantel"
> Warning message:
> In partial.mantel.test(M1, M2, M3, quiet = T) :
>  Missing values exist; Pairwise deletion will be used
> ______________________________________________
> 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

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