Awesome, thanks Joseph!

On Wed, Jul 26, 2017 at 9:10 AM, Joseph W. Brown <josep...@umich.edu> wrote:

> I think this'll work, depending on how you store your data.
>
> # assumes a tree 'phy' and a dataframe, 'df', with first column of tip
> names, and second column of values
> for (i in 1:dim(df)[1]) {
> # find index of edge length
> idx <- which(phy$edge[,2] == which(phy$tip.label == df[1,i]));
> # apply it. this assume you want to extend it, not just set it
> phy$edge.length[idx] <- phy$edge.length[idx] + as.numeric(df[i,2]);
> }
>
> Probably a nicer way to do it without a loop...
>
> JWB
> ________________________________________
> Joseph W. Brown
> Post-doctoral Researcher, Smith Laboratory
> University of Michigan
> Department of Ecology & Evolutionary Biology
> Room 2071, Kraus Natural Sciences Building
> Ann Arbor MI 48109-1079
> josep...@umich.edu
>
>
>
> On 26 Jul, 2017, at 11:57, William Gearty <wgea...@stanford.edu> wrote:
>
> That's definitely helpful, Joseph, but I'll need to extend the tips to
> varying amounts.
>
> Basically, I performed a tip-dating analysis using constraints based on
> the FADs of a bunch of fossils.
> However, now some of the analyses I want to perform require that the tips
> extend to the species' extinctions, so I need to extend them to the LADs
> (or farther, I suppose).
> How would I, given a vector of LAD ages for the tips, extend the tips to
> those ages?
>
> On Wed, Jul 26, 2017 at 8:50 AM, Joseph W. Brown <josep...@umich.edu>
> wrote:
>
>> If you want to just extend all tips by a constant amount you can do this:
>>
>> # extend terminal edges by arbitrary amount (here: 13)
>> idx <- which(phy$edge[,2] < (phy$Nnode + 1));
>> phy$edge.length[idx] <- phy$edge.length[idx] + 13;
>>
>> HTH.
>> Joseph.
>> ________________________________________
>> Joseph W. Brown
>> Post-doctoral Researcher, Smith Laboratory
>> University of Michigan
>> Department of Ecology & Evolutionary Biology
>> Room 2071, Kraus Natural Sciences Building
>> Ann Arbor MI 48109-1079
>> josep...@umich.edu
>>
>>
>>
>> On 26 Jul, 2017, at 11:39, David Bapst <dwba...@gmail.com> wrote:
>>
>> Not sure what you mean by extending tips, Will. Could you describe a
>> small example?
>> -Dave
>>
>> On Fri, Jul 21, 2017 at 5:15 PM, William Gearty <wgea...@stanford.edu>
>> wrote:
>>
>> Hi all,
>>
>> Before I go ahead and wrote a whole script, I was wondering if there is a
>> function or script out there for extending tips (or setting the ages of
>> tips) given a list of taxa and ages?
>> I haven't found anything, but perhaps I'm searching the wrong phrase(s).
>>
>> Thanks,
>> Will
>>
>> --
>> William Gearty
>> PhD Candidate, Paleobiology
>> Department of Geological Sciences
>> Stanford School of Earth, Energy & Environmental Sciences
>> williamgearty.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-ph...@r-project.org/
>>
>>
>>
>>
>> --
>> David W. Bapst, PhD
>> https://github.com/dwbapst/paleotree
>>
>> _______________________________________________
>> 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/
>>
>>
>>
>
>
> --
> William Gearty
> PhD Candidate, Paleobiology
> Department of Geological Sciences
> Stanford School of Earth, Energy & Environmental Sciences
> williamgearty.com
>
>
>


-- 
William Gearty
PhD Candidate, Paleobiology
Department of Geological Sciences
Stanford School of Earth, Energy & Environmental Sciences
williamgearty.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/

Reply via email to