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

[Sebastian Y. Müller]

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 Or maybe it has been replaced by a more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: [phone]

_______________________________________________
R-sig-phylo mailing list - R-sig-***@r-project.org
https://stat.ethz.ch/mailman/listinfo/r-sig-phylo
Searchable archive at http://www.mail-archive.com/r-sig-***@r-project.org/

[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" <***@cam.ac.uk> 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 Or maybe it has been replaced by a more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: [phone]

_______________________________________________
R-sig-phylo mailing list - R-sig-***@r-project.org
https://stat.ethz.ch/mailman/listinfo/r-sig-phylo
Searchable archive at http://www.mail-archive.com/r-sig-***@r-project.org/

[[alternative HTML version deleted]]

_______________________________________________
R-sig-phylo mailing list - R-sig-***@r-project.org
https://stat.ethz.ch/mailman/listinfo/r-sig-phylo
Searchable archive at http://www.mail-archive.com/r-sig-***@r-project.org/

[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

Post by 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
Dear all,
I'd was wondering how to best perform a test to determine test
disagreement (congruence test) in R?
10.1016/j.jbi.2005.08.008).
A common test seems the Shimodaira-Hasegawa Test (SH-test) which used to
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: [phone]
_______________________________________________
https://stat.ethz.ch/mailman/listinfo/r-sig-phylo
Searchable archive at

[[alternative HTML version deleted]]

_______________________________________________
R-sig-phylo mailing list - R-sig-***@r-project.org
https://stat.ethz.ch/mailman/listinfo/r-sig-phylo
Searchable archive at http://www.mail-archive.com/r-sig-***@r-project.org/

[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

Post by Sebastian Y. Müller
Dear all,
I'd was wondering how to best perform a test to determine test
disagreement (congruence test) in R?
10.1016/j.jbi.2005.08.008).
A common test seems the Shimodaira-Hasegawa Test (SH-test) which used to
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!

_______________________________________________
R-sig-phylo mailing list - R-sig-***@r-project.org
https://stat.ethz.ch/mailman/listinfo/r-sig-phylo
Searchable archive at http://www.mail-archive.com/r-sig-***@r-project.org/