Re: [R-sig-phylo] Error in plotBS when number of taxa is small

[Klaus Schliep]

HI Kamilla,
can you send me your code and data and what phangorn version are you using?
Cheers,
Klaus

On Tue, Jun 14, 2016 at 6:42 PM, Kamila Naxerova 
wrote:

> Hi all,
>
> I am trying to attach bootstrap values to a small tree (just 4 taxa).
> plotBS() in the phangorn package gives me the following error:
>
> tree <- plotBS(phylotree,bstrees,type="phylogram",p=90)
>
> Error in if (drop[j]) next : missing value where TRUE/FALSE needed
>
>
> This error disappears and everything work great as soon as I have 5 taxa.
> But removing one always leads to this error, for multiple independent trees.
>
> Am I missing something obvious? Unfortunately I don’t understand the error
> message.
>
> Many thanks!
> Kamila
>
>
>
> The information in this e-mail is intended only for th...{{dropped:28}}

___
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/

[R-sig-phylo] Error in plotBS when number of taxa is small

[Kamila Naxerova]

Hi all,

I am trying to attach bootstrap values to a small tree (just 4 taxa). plotBS() 
in the phangorn package gives me the following error: 

tree <- plotBS(phylotree,bstrees,type="phylogram",p=90)

Error in if (drop[j]) next : missing value where TRUE/FALSE needed


This error disappears and everything work great as soon as I have 5 taxa. But 
removing one always leads to this error, for multiple independent trees.

Am I missing something obvious? Unfortunately I don’t understand the error 
message.

Many thanks!
Kamila



The information in this e-mail is intended only for the person to whom it is
addressed. If you believe this e-mail was sent to you in error and the e-mail
contains patient information, please contact the Partners Compliance HelpLine at
http://www.partners.org/complianceline . If the e-mail was sent to you in error
but does not contain patient information, please contact the sender and properly
dispose of the e-mail.
___
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/

Re: [R-sig-phylo] Pagel 94 Baysian Version 3 states?

[mailbox Franz]

Hi Manabu,

thanks for that! 
I can see the discrete model allows 2 binaries. There is no implementation of a 
3 binaries model as a pendant to corDISC, I guess?!

Cheers,
Franz


> Am 14.06.2016 um 11:17 schrieb Manabu Sakamoto :
> 
> Hi Franz,
> 
> It is implemented in BayesTraits 
> (http://www.evolution.rdg.ac.uk/BayesTraits.html 
> ).
> I know it's not R, and it's a command line based program, so might take a 
> while to get used to, but BayesTraits is really powerful (and it's Bayesian!)
> 
> thanks,
> Manabu
> 
> On 14 June 2016 at 09:58, mailbox Franz  > wrote:
> Hi everybody,
> 
> does anyone know if the bayesian version of Pagels 94 Method of correlated 
> binary traits is implemented in R somewhere?
> There is the corHMM package which implements a 3-state ML version of it, but 
> I couldn’t find a Baysian version anywhere.
> 
> So I search for a Bayesian version of a 2 or 3 binary state correlated 
> evolution method (preferably in R).
> 
> The Paper I refer to is:
> 
> http://www.ncbi.nlm.nih.gov/pubmed/16685633 
> 
> 
> All the best,
> Franz
> 
> ___
> 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/ 
> 
> 
> 
> -- 
> Manabu Sakamoto, PhD
> manabu.sakam...@gmail.com 

[[alternative HTML version deleted]]

___
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/

Re: [R-sig-phylo] Pagel 94 Baysian Version 3 states?

[Manabu Sakamoto]

Hi Franz,

It is implemented in BayesTraits (
http://www.evolution.rdg.ac.uk/BayesTraits.html).
I know it's not R, and it's a command line based program, so might take a
while to get used to, but BayesTraits is really powerful (and it's
Bayesian!)

thanks,
Manabu

On 14 June 2016 at 09:58, mailbox Franz  wrote:

> Hi everybody,
>
> does anyone know if the bayesian version of Pagels 94 Method of correlated
> binary traits is implemented in R somewhere?
> There is the corHMM package which implements a 3-state ML version of it,
> but I couldn’t find a Baysian version anywhere.
>
> So I search for a Bayesian version of a 2 or 3 binary state correlated
> evolution method (preferably in R).
>
> The Paper I refer to is:
>
> http://www.ncbi.nlm.nih.gov/pubmed/16685633
>
> All the best,
> Franz
>
> ___
> 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/




-- 
Manabu Sakamoto, PhD
manabu.sakam...@gmail.com

[[alternative HTML version deleted]]

___
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/

[R-sig-phylo] Pagel 94 Baysian Version 3 states?

[mailbox Franz]

Hi everybody,

does anyone know if the bayesian version of Pagels 94 Method of correlated 
binary traits is implemented in R somewhere?
There is the corHMM package which implements a 3-state ML version of it, but I 
couldn’t find a Baysian version anywhere.

So I search for a Bayesian version of a 2 or 3 binary state correlated 
evolution method (preferably in R).

The Paper I refer to is:

http://www.ncbi.nlm.nih.gov/pubmed/16685633

All the best,
Franz

___
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/