[R-sig-phylo] abundance-weighted Faith phylogenetic diversity index

2019-11-25 Thread Saleh Rahimlouye Barabi 
Dear list members,

In order to calculate the abundance-weighted Faith phylogenetic diversity 
index, I ran the function "weighted.faith()" from the lefse package (link 
below) using a community data matrix and a phylogeny. But I got the following 
error. I would be appreciated if you could help me to solve it.

AED <- weighted.faith(phy, comm)
Error in integer(max(oldnodes)) : vector size cannot be infinite
In addition: Warning message:
In max(oldnodes) : no non-missing arguments to max; returning -Inf

https://rdrr.io/github/NGSwenson/lefse_0.5/man/weighted.faith.html

Saleh Rahimlou
Ph.D. Candidate
Department of Botany and Ecology
University of Tartu
14A Ravila, 50411 Tartu
Estonia
Email: saleh.rahim...@ut.ee


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[R-sig-phylo] Phylogenetic D-statistics

2019-10-25 Thread Saleh Rahimlouye Barabi 
Hello everybody,

I have calculated phylogenetic D-value for a binary trait (nitrogen-fixation) 
using a phylogenetic supertree. I have got D-value = 0.127 and the probability 
resulting from Brownian motion phylogenetic structure is P= 0.30. My question 
is what does it mean when you receive D-value close to zero with a low 
probability?

Best regards,
Saleh Rahimlou
Ph.D. Candidate
Department of Botany and Ecology
University of Tartu
14A Ravila, 50411 Tartu
Estonia
Email: saleh.rahim...@ut.ee


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Re: [R-sig-phylo] plotting time-calibrated trees

2019-09-30 Thread Saleh Rahimlouye Barabi 
Thnaks Liam. The problem is solved.

-Original Message-
From: Saleh Rahimlouye Barabi 
Sent: 30. september 2019. a. 16:32
To: Liam Revell; R-sig-phylo@r-project.org
Subject: RE: [R-sig-phylo] plotting time-calibrated trees

Dear Liam,

Yes, It is the best solution. But I'm getting an error with the negative sign 
of the "by" argument in the following code. Would you please explain it to me?

obj<-axis(1,pos=0,at=seq(T,min.tick,by=-tick.spacing),cex.axis=0.5,labels=FALSE)
error : wrong sign in 'by' argument

Best Regards,
Saleh

-Original Message-
From: Liam Revell [mailto:liam.rev...@umb.edu]
Sent: 30. september 2019. a. 15:03
To: Saleh Rahimlouye Barabi; R-sig-phylo@r-project.org
Subject: Re: [R-sig-phylo] plotting time-calibrated trees

Dear Saleh.

You can do this using my package phytools or using ape::axisPhylo. I have an 
example using both options on my blog: 
http://blog.phytools.org/2018/02/another-technique-for-including-time.html.

All the best, Liam

Liam J. Revell
Associate Professor, University of Massachusetts Boston Profesor Asistente, 
Universidad Católica de la Ssma Concepción
web: http://faculty.umb.edu/liam.revell/, http://www.phytools.org

Academic Director UMass Boston Chile Abroad (starting 2019):
https://www.umb.edu/academics/caps/international/biology_chile

On 9/30/2019 8:46 AM, Saleh Rahimlouye Barabi wrote:
> [EXTERNAL SENDER]
> 
> Hello,
> 
> I have constructed a big time-calibrated tree (683 tip labels) using the  
> ape::chronopl function. What is a good way of visualizing this tree in a 
> circular way with time scale axis?
> 
> Best,
> Saleh Rahimlou
> Ph.D. Candidate
> Department of Botany and Ecology
> University of Tartu
> 14A Ravila, 50411 Tartu
> Estonia
> Email: saleh.rahim...@ut.ee<mailto:saleh.rahim...@ut.ee>
> 
> 
>  [[alternative HTML version deleted]]
> 
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Re: [R-sig-phylo] plotting time-calibrated trees

2019-09-30 Thread Saleh Rahimlouye Barabi 
Dear Liam,

Yes, It is the best solution. But I'm getting an error with the negative sign 
of the "by" argument in the following code. Would you please explain it to me?

obj<-axis(1,pos=0,at=seq(T,min.tick,by=-tick.spacing),cex.axis=0.5,labels=FALSE)
error : wrong sign in 'by' argument

Best Regards,
Saleh

-Original Message-
From: Liam Revell [mailto:liam.rev...@umb.edu] 
Sent: 30. september 2019. a. 15:03
To: Saleh Rahimlouye Barabi; R-sig-phylo@r-project.org
Subject: Re: [R-sig-phylo] plotting time-calibrated trees

Dear Saleh.

You can do this using my package phytools or using ape::axisPhylo. I have an 
example using both options on my blog: 
http://blog.phytools.org/2018/02/another-technique-for-including-time.html.

All the best, Liam

Liam J. Revell
Associate Professor, University of Massachusetts Boston Profesor Asistente, 
Universidad Católica de la Ssma Concepción
web: http://faculty.umb.edu/liam.revell/, http://www.phytools.org

Academic Director UMass Boston Chile Abroad (starting 2019):
https://www.umb.edu/academics/caps/international/biology_chile

On 9/30/2019 8:46 AM, Saleh Rahimlouye Barabi wrote:
> [EXTERNAL SENDER]
> 
> Hello,
> 
> I have constructed a big time-calibrated tree (683 tip labels) using the  
> ape::chronopl function. What is a good way of visualizing this tree in a 
> circular way with time scale axis?
> 
> Best,
> Saleh Rahimlou
> Ph.D. Candidate
> Department of Botany and Ecology
> University of Tartu
> 14A Ravila, 50411 Tartu
> Estonia
> Email: saleh.rahim...@ut.ee<mailto:saleh.rahim...@ut.ee>
> 
> 
>  [[alternative HTML version deleted]]
> 
> ___
> R-sig-phylo mailing list - R-sig-phylo@r-project.org
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> vell%40umb.edu%7Cceb0491244b3475a361d08d7459bf638%7Cb97188711ee9442595
> 3c1ace1373eb38%7C0%7C1%7C637054408469241957sdata=KjF9wmmInmu%2FtI
> LKWt5Yda65fvPRtKiVGjGkYuLsuA0%3Dreserved=0
> Searchable archive at 
> https://nam01.safelinks.protection.outlook.com/?url=http%3A%2F%2Fwww.m
> ail-archive.com%2Fr-sig-phylo%40r-project.org%2Fdata=02%7C01%7Cli
> am.revell%40umb.edu%7Cceb0491244b3475a361d08d7459bf638%7Cb97188711ee94
> 425953c1ace1373eb38%7C0%7C1%7C637054408469251946sdata=Sb1DvrI6ECA
> EaMf8rUX56db5NVz7j0be003l31fY9nw%3Dreserved=0
> 
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[R-sig-phylo] molecular dating of a phylogenetic tree

2019-09-30 Thread Saleh Rahimlouye Barabi 
Hello,

Do you have any suggestion about any function in R for dating a phylogenetic 
tree based on a single node age (fixed node)? The calculation of the confidence 
intervals for each node would be beneficial.

Best regards,
Saleh Rahimlou
Ph.D. Candidate
Department of Botany and Ecology
University of Tartu
14A Ravila, 50411 Tartu
Estonia
Email: saleh.rahim...@ut.ee


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[R-sig-phylo] plotting time-calibrated trees

2019-09-30 Thread Saleh Rahimlouye Barabi 
Hello,

I have constructed a big time-calibrated tree (683 tip labels) using the  
ape::chronopl function. What is a good way of visualizing this tree in a 
circular way with time scale axis?

Best,
Saleh Rahimlou
Ph.D. Candidate
Department of Botany and Ecology
University of Tartu
14A Ravila, 50411 Tartu
Estonia
Email: saleh.rahim...@ut.ee


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[R-sig-phylo] cophylo

2019-06-17 Thread Saleh Rahimlouye Barabi 
Hello,

I want to plot two phylogenetic trees face-to-face using phytools::cophylo 
function. I see there is no possibility to connect 2 or 3 same taxa in a tree 
to one taxon in the other tree (attached). Is there anyway doing this in R?

Best
Saleh Rahimlou
Ph.D. Candidate
Department of Botany and Ecology
University of Tartu
14A Ravila, 50411 Tartu
Estonia
Email: saleh.rahim...@ut.ee



Rplot03.pdf
Description: Rplot03.pdf
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[R-sig-phylo] comparePhylo

2019-06-13 Thread Saleh Rahimlouye Barabi 
Hello,

I'm using comparePhylo() function from APE package in R. I want to know is 
there anyway to change the tip labels size when plotting it? Arguments like 
'cex' does not work in this case.

Best
Saleh Rahimlou
Ph.D. Candidate
Department of Botany and Ecology
University of Tartu
14A Ravila, 50411 Tartu
Estonia
Email: saleh.rahim...@ut.ee


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