[R-sig-phylo] simulate tree by specifying taxa distance
Dear all, I want to simulate tree with restricted taxa distances (e.g. all taxa distance should be less than 0.1). Is there any R package can do this? Best wishes, Guangchuang -- --~--~-~--~~~---~--~~ Guangchuang Yu, PhD Candidate State Key Laboratory of Emerging Infectious Diseases School of Public Health The University of Hong Kong Hong Kong SAR, China www: https://guangchuangyu.github.io -~--~~~~--~~--~--~--- [[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] simulate tree by specifying taxa distance
Dear Guangchuang, Wouldn't that require that the distance between root and current time is, at most, 0.05 (= 0.1 /2) ? In that case, I believe you just need to rescale the tree you simulated. That can be done in a number of way according to which package you use, e.g., in phytool: pbtree(n=1000,scale=0.05) Best, Giulio Valentino Dalla Riva Beaty Biodiversity Research Centre University of British Columbia Vancouver, Canada From: R-sig-phylo on behalf of Yu, Guangchuang Sent: November 3, 2016 5:02:25 AM To: r-sig-phylo@r-project.org Subject: [R-sig-phylo] simulate tree by specifying taxa distance Dear all, I want to simulate tree with restricted taxa distances (e.g. all taxa distance should be less than 0.1). Is there any R package can do this? Best wishes, Guangchuang -- --~--~-~--~~~---~--~~ Guangchuang Yu, PhD Candidate State Key Laboratory of Emerging Infectious Diseases School of Public Health The University of Hong Kong Hong Kong SAR, China www: https://guangchuangyu.github.io -~--~~~~--~~--~--~--- [[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/ [[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] simulate tree by specifying taxa distance
Dear Guilio, Thank you! I will try phytools. Best wishes, Guangchuang On Thu, Nov 3, 2016 at 11:57 PM, Giulio V. Dalla Riva wrote: > Dear Guangchuang, > > > Wouldn't that require that the distance between root and current time is, > at most, 0.05 (= 0.1 /2) ? > > In that case, I believe you just need to rescale the tree you simulated. > That can be done in a number of way according to which package you use, > e.g., in phytool: > > pbtree(n=1000,scale=0.05) > > > Best, > Giulio Valentino Dalla Riva > > Beaty Biodiversity Research Centre > University of British Columbia > Vancouver, Canada > -- > *From:* R-sig-phylo on behalf of Yu, > Guangchuang > *Sent:* November 3, 2016 5:02:25 AM > *To:* r-sig-phylo@r-project.org > *Subject:* [R-sig-phylo] simulate tree by specifying taxa distance > > Dear all, > > I want to simulate tree with restricted taxa distances (e.g. all taxa > distance should be less than 0.1). Is there any R package can do this? > > Best wishes, > Guangchuang > -- > --~--~-~--~~~---~--~~ > Guangchuang Yu, PhD Candidate > State Key Laboratory of Emerging Infectious Diseases > School of Public Health > The University of Hong Kong > Hong Kong SAR, China > www: https://guangchuangyu.github.io > -~--~~~~--~~--~--~--- > > [[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-ph...@r-project.org/ > -- --~--~-~--~~~---~--~~ Guangchuang Yu, PhD Candidate State Key Laboratory of Emerging Infectious Diseases School of Public Health The University of Hong Kong Hong Kong SAR, China www: https://guangchuangyu.github.io -~--~~~~--~~--~--~--- [[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/