Re: [R-sig-phylo] Infinite Recursion Error with write, tree() on an stree()
Ah, the answer was there before my eyes! Thank you very much!
-Dave
On Thu, Sep 16, 2010 at 1:42 AM, Klaus Schliep wrote:
> Hi David,
>
> increase as the error message indicates the number of nested expressions:
> options("expressions"=2)
> This should work for trees with 1700 taxa.
>
> Cheers,
> Klaus
>
>
> On 9/15/10, David Bapst wrote:
>> Hello all,
>>
>> I am having trouble with write.tree() in ape, when used on a tree
>> produced with stree() with type="left", at a certain number of tip
>> taxa.
>>
>> You can reproduce the error with:
>>
>> x<-stree(1000,type="left")
>> write.tree(x,file.choose())
>>
>> produces the following:
>>
>> Error: evaluation nested too deeply: infinite recursion /
>> options(expressions=)?
>>
>> Any idea what produces this error and if there is any way around it? I
>> have no difficulty with rtree(), "star" type trees produced with
>> stree(), nor when I reduce the number of tips to 100 (which doesn't
>> work for my purposes: I need to produce "left" type trees with over
>> 1700 tip taxa). I have also had problems with plot() on such trees,
>> but most functions seem to work fine on such trees.
>>
>> Thanks for the help,
>> -Dave Bapst, UChicago
>>
>> ___
>> R-sig-phylo mailing list
>> [email protected]
>> https://stat.ethz.ch/mailman/listinfo/r-sig-phylo
>>
>
>
> --
> Klaus Schliep
> Université Paris 6 (Pierre et Marie Curie)
> 9, Quai Saint-Bernard, 75005 Paris
>
> ___
> R-sig-phylo mailing list
> [email protected]
> https://stat.ethz.ch/mailman/listinfo/r-sig-phylo
>
___
R-sig-phylo mailing list
[email protected]
https://stat.ethz.ch/mailman/listinfo/r-sig-phylo
Re: [R-sig-phylo] Infinite Recursion Error with write, tree() on an stree()
Hi David,
increase as the error message indicates the number of nested expressions:
options("expressions"=2)
This should work for trees with 1700 taxa.
Cheers,
Klaus
On 9/15/10, David Bapst wrote:
> Hello all,
>
> I am having trouble with write.tree() in ape, when used on a tree
> produced with stree() with type="left", at a certain number of tip
> taxa.
>
> You can reproduce the error with:
>
> x<-stree(1000,type="left")
> write.tree(x,file.choose())
>
> produces the following:
>
> Error: evaluation nested too deeply: infinite recursion /
> options(expressions=)?
>
> Any idea what produces this error and if there is any way around it? I
> have no difficulty with rtree(), "star" type trees produced with
> stree(), nor when I reduce the number of tips to 100 (which doesn't
> work for my purposes: I need to produce "left" type trees with over
> 1700 tip taxa). I have also had problems with plot() on such trees,
> but most functions seem to work fine on such trees.
>
> Thanks for the help,
> -Dave Bapst, UChicago
>
> ___
> R-sig-phylo mailing list
> [email protected]
> https://stat.ethz.ch/mailman/listinfo/r-sig-phylo
>
--
Klaus Schliep
Université Paris 6 (Pierre et Marie Curie)
9, Quai Saint-Bernard, 75005 Paris
___
R-sig-phylo mailing list
[email protected]
https://stat.ethz.ch/mailman/listinfo/r-sig-phylo
Re: [R-sig-phylo] Infinite Recursion Error with write, tree() on an stree()
Hi David,
increase as the error message indicates the number of nested expressions:
options("expressions"=2)
This should work for trees with 1700 taxa.
Cheers,
Klaus
On 9/15/10, David Bapst wrote:
> Hello all,
>
> I am having trouble with write.tree() in ape, when used on a tree
> produced with stree() with type="left", at a certain number of tip
> taxa.
>
> You can reproduce the error with:
>
> x<-stree(1000,type="left")
> write.tree(x,file.choose())
>
> produces the following:
>
> Error: evaluation nested too deeply: infinite recursion /
> options(expressions=)?
>
> Any idea what produces this error and if there is any way around it? I
> have no difficulty with rtree(), "star" type trees produced with
> stree(), nor when I reduce the number of tips to 100 (which doesn't
> work for my purposes: I need to produce "left" type trees with over
> 1700 tip taxa). I have also had problems with plot() on such trees,
> but most functions seem to work fine on such trees.
>
> Thanks for the help,
> -Dave Bapst, UChicago
>
> ___
> R-sig-phylo mailing list
> [email protected]
> https://stat.ethz.ch/mailman/listinfo/r-sig-phylo
>
--
Klaus Schliep
Université Paris 6 (Pierre et Marie Curie)
9, Quai Saint-Bernard, 75005 Paris
___
R-sig-phylo mailing list
[email protected]
https://stat.ethz.ch/mailman/listinfo/r-sig-phylo
