Re: [R-sig-phylo] Testing tree disagreement: SH-test disappeared in ape-package

[Sebastian Y . Müller]

Dear Klaus,

Thanks for pointing this out, that's exactly what I was looking for!
I have a question concerning the bootstrapping method and wheater it 
makes sense to add the block bootstrap to better model adjacent that are 
autocorrelated (presumably breaking the iid assumption).
But since it's on github I best add an issue there I suppose?

Best wishes,
Seb

On 08/06/18 13:59, Klaus Schliep wrote:
> Hi Sebastian,
> there is an implementation of the SH-test and SOWH-test in phangorn. 
> Send me an mail off list if you have problems using them.
> Regards,
> Klaus
>
> On Jun 8, 2018 8:50 AM, "Sebastian Y. Müller"  > wrote:
>
> Dear all,
>
> I'd was wondering how to best perform a test to determine test
> disagreement (congruence test) in R?
> Additional information can be found in Planet et al (DOI:
> 10.1016/j.jbi.2005.08.008).
>
> A common test seems the Shimodaira-Hasegawa Test (SH-test) which
> used to
> be implemented in APE:
> https://www.rdocumentation.org/packages/ape/versions/2.3-3/topics/sh.test
>
> However, it seem to have disappeared in recent versions (e.g. ape
> 5.0).
> Did this happen for a reason? Or maybe it has been replaced by a more
> appropriate test?
>
> Failing this, is anyone aware of other software to perform SH-,
> KH- or
> SOWH-tests?
>
> Thanks for any help!
>
>
> -- 
> Dr. Sebastian Müller
> Department of Plant Sciences
> University of Cambridge
> Downing Street, Cambridge, CB2 3EA, UK
> http://www.plantsci.cam.ac.uk/directory/mueller-sebastian
> Phone: 0044 1223 748976
>
> ___
> R-sig-phylo mailing list - R-sig-phylo@r-project.org
> 
> https://stat.ethz.ch/mailman/listinfo/r-sig-phylo
> Searchable archive at
> http://www.mail-archive.com/r-sig-phylo@r-project.org/
>
>


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Re: [R-sig-phylo] Testing tree disagreement: SH-test disappeared in ape-package

[Emmanuel Paradis]

Hi Sebastian,

All the likelihood-based phylogenetic inference functions have been 
removed from ape since version 2.4 (released in Oct 2009) because of the 
(incomparably better) implementation in phangorn:


library(phangorn)
?SH.test

Best,

Emmanuel

Le 08/06/2018 à 14:50, Sebastian Y. Müller a écrit :

Dear all,

I'd was wondering how to best perform a test to determine test 
disagreement (congruence test) in R?
Additional information can be found in Planet et al (DOI: 
10.1016/j.jbi.2005.08.008).


A common test seems the Shimodaira-Hasegawa Test (SH-test) which used to 
be implemented in APE:

https://www.rdocumentation.org/packages/ape/versions/2.3-3/topics/sh.test

However, it seem to have disappeared in recent versions (e.g. ape 5.0).
Did this happen for a reason? Or maybe it has been replaced by a more 
appropriate test?


Failing this, is anyone aware of other software to perform SH-, KH- or 
SOWH-tests?


Thanks for any help!



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Re: [R-sig-phylo] Testing tree disagreement: SH-test disappeared in ape-package

[Klaus Schliep]

Hi Sebastian,
there is an implementation of the SH-test and SOWH-test in phangorn. Send
me an mail off list if you have problems using them.
Regards,
Klaus

On Jun 8, 2018 8:50 AM, "Sebastian Y. Müller"  wrote:

Dear all,

I'd was wondering how to best perform a test to determine test
disagreement (congruence test) in R?
Additional information can be found in Planet et al (DOI:
10.1016/j.jbi.2005.08.008).

A common test seems the Shimodaira-Hasegawa Test (SH-test) which used to
be implemented in APE:
https://www.rdocumentation.org/packages/ape/versions/2.3-3/topics/sh.test

However, it seem to have disappeared in recent versions (e.g. ape 5.0).
Did this happen for a reason? Or maybe it has been replaced by a more
appropriate test?

Failing this, is anyone aware of other software to perform SH-, KH- or
SOWH-tests?

Thanks for any help!


-- 
Dr. Sebastian Müller
Department of Plant Sciences
University of Cambridge
Downing Street, Cambridge, CB2 3EA, UK
http://www.plantsci.cam.ac.uk/directory/mueller-sebastian
Phone: 0044 1223 748976

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