R help - Dec 2009 - mantel test and NAs

Dear R users,

I am having a problem performing the mantel test (both with functions mantel
{vegan} and mantel.test {ape}) due to I believe the presence of NAs on my
distance matrices, which look like e.g.:

NA
1    2
1    2   3
NA  4   5  6

and 

1
1   2
2   3   4
5   6   7  8

Would any of you have a solution for that?

Thank you for much for your help!

Marcia Rocha


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Could you please supply with a reproducible self sufficient script ?


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On Thu, Dec 17, 2009 at 7:33 PM, marciarocha <marcia.rocha@gmail.com>
wrote:
>
> Dear R users,
>
> I am having a problem performing the mantel test (both with functions
> mantel
> {vegan} and mantel.test {ape}) due to I believe the presence of NAs on my
> distance matrices, which look like e.g.:
>
> NA
> 1    2
> 1    2   3
> NA  4   5  6
>
> and
>
> 1
> 1   2
> 2   3   4
> 5   6   7  8
>
> Would any of you have a solution for that?
>
> Thank you for much for your help!
>
> Marcia Rocha
>
>
> --
> View this message in context:
> http://n4.nabble.com/mantel-test-and-NAs-tp966682p966682.html
> Sent from the R help mailing list archive at Nabble.com.
>
> ______________________________________________
> 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.
>
	[[alternative HTML version deleted]]

You will most likely need to drop the samples that are causing the NA
values from both of your datasets. The function won't work with NA values.

Sarah

On Thu, Dec 17, 2009 at 12:33 PM, marciarocha <marcia.rocha at gmail.com>
wrote:
>
> Dear R users,
>
> I am having a problem performing the mantel test (both with functions
mantel
> {vegan} and mantel.test {ape}) due to I believe the presence of NAs on my
> distance matrices, which look like e.g.:
>
> NA
> 1 ? ?2
> 1 ? ?2 ? 3
> NA ?4 ? 5 ?6
>
> and
>
> 1
> 1 ? 2
> 2 ? 3 ? 4
> 5 ? 6 ? 7 ?8
>
> Would any of you have a solution for that?
>
> Thank you for much for your help!
>
> Marcia Rocha
>
>
-- 
Sarah Goslee
http://www.functionaldiversity.org