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
> 
> 
>  [[alternative HTML version deleted]]
> 
> ___
> R-sig-phylo mailing list - R-sig-phylo@r-project.org
> https://nam01.safelinks.protection.outlook.com/?url=https%3A%2F%2Fstat
> .ethz.ch%2Fmailman%2Flistinfo%2Fr-sig-phylodata=02%7C01%7Cliam.re
> 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
> 
___
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] 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
> 
> 
>  [[alternative HTML version deleted]]
> 
> ___
> R-sig-phylo mailing list - R-sig-phylo@r-project.org 
> https://nam01.safelinks.protection.outlook.com/?url=https%3A%2F%2Fstat
> .ethz.ch%2Fmailman%2Flistinfo%2Fr-sig-phylodata=02%7C01%7Cliam.re
> 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
> 
___
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] 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


[[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] plotting time-calibrated trees

2019-09-30 Thread Liam Revell 
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
> 
> 
>  [[alternative HTML version deleted]]
> 
> ___
> R-sig-phylo mailing list - R-sig-phylo@r-project.org
> https://nam01.safelinks.protection.outlook.com/?url=https%3A%2F%2Fstat.ethz.ch%2Fmailman%2Flistinfo%2Fr-sig-phylodata=02%7C01%7Cliam.revell%40umb.edu%7Cceb0491244b3475a361d08d7459bf638%7Cb97188711ee94425953c1ace1373eb38%7C0%7C1%7C637054408469241957sdata=KjF9wmmInmu%2FtILKWt5Yda65fvPRtKiVGjGkYuLsuA0%3Dreserved=0
> Searchable archive at 
> https://nam01.safelinks.protection.outlook.com/?url=http%3A%2F%2Fwww.mail-archive.com%2Fr-sig-phylo%40r-project.org%2Fdata=02%7C01%7Cliam.revell%40umb.edu%7Cceb0491244b3475a361d08d7459bf638%7Cb97188711ee94425953c1ace1373eb38%7C0%7C1%7C637054408469251946sdata=Sb1DvrI6ECAEaMf8rUX56db5NVz7j0be003l31fY9nw%3Dreserved=0
> 
___
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] 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


[[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/