Dear Mario.
From your drawing it looks like each node & tip has a value, and then
you update these values by reassigning each node a value equal to the
sum of its value and that of all its descendants. Is this correct?
If so, then assuming you have ordered your quantities in x such that
they are in the order of their node indices in the "phylo" tree object,
you should be able to just compute:
library(phytools)
desc<-sapply(1:(Ntip(tree)+tree$Nnode),function(n,tree)
if(n<=Ntip(tree)) n else c(n,getDescendants(tree,n)),
tree=tree)
y<-sapply(desc,function(n,x) sum(x[n]),x=x)
Does that help?
Here is a complete example using a small random tree & randomly chosen
integer values for the tips & nodes. In the illustrative plot, the
values being summed are shown in round parentheses, while the sums are
given in square brackets:
library(phytools)
## random tree
tree<-rtree(n=6,tip.label=LETTERS[1:6],br=NULL)
## random starting values at nodes
x<-setNames(sample(0:5,Ntip(tree)+tree$Nnode,replace=TRUE),
c(tree$tip.label,1:tree$Nnode+Ntip(tree)))
x
x<-x[c(tree$tip.label,1:tree$Nnode+Ntip(tree))]
plotTree(tree,type="cladogram",nodes="centered")
tiplabels(paste("(",x[1:Ntip(tree)],")",sep=""),
tip=1:Ntip(tree),frame="none",adj=c(-1,-1))
nodelabels(paste("(",x[1:tree$Nnode+Ntip(tree)],")",sep=""),
node=1:tree$Nnode+Ntip(tree),frame="none",
adj=c(0.5,-1))
desc<-sapply(1:(Ntip(tree)+tree$Nnode),function(n,tree)
if(n<=Ntip(tree)) n else c(n,getDescendants(tree,n)),
tree=tree)
y<-sapply(desc,function(n,x) sum(x[n]),x=x)
tiplabels(paste("[",y[1:Ntip(tree)],"]",sep=""),
tip=1:Ntip(tree),frame="none",adj=c(-1,1))
nodelabels(paste("[",y[1:tree$Nnode+Ntip(tree)],"]",sep=""),
node=1:tree$Nnode+Ntip(tree),frame="none",
adj=c(0.5,1.5))
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 8/3/2019 9:32 PM, Mario Schädel wrote:
> Dear people on this list,
>
> I am a German PhD student in the field of arthropod palaeontology. I
> want to develop a new approach for comparing abundance data in a
> phylogenetic context. Unlike following the standard techniques of
> community ecology, I want to include the abundance data not only for the
> tips of a tree but also for its nodes. The background for this is, that
> in palaeontology it is often not possible to identify specimens to
> species level and also some fossils are better preserved as others,
> hence the level of identification within samples can vary a lot.
>
> So, I want to link a vector, or at best a data frame, that holds
> abundance data for tips and nodes, to a tree (even this proved to be
> problematic as all functions that I found make distinctions between tip
> and node data). In the next step, I would like to recursively sum-up the
> abundances along the tree, from the leaves to the root. When the data is
> properly linked, this should not be too complicated, once the tree is
> reordered into the “postorder” format. Afterwards, the computed data
> should be converted in a format, that can be included into plots.
> Alternatively, I also came up with the idea, that the abundance data
> could be visualised by the branch lengths of the tree.
>
> I would be more than grateful, if someone could offer me some help with
> this project. I have been wrecking my head around this since months now.
>
> I attached a graphical representation of my idea in case my explanations
> are a bit confusing (orange color, abundances before computation; green,
> summed up aundances).
>
>
> Best wishes to all of you!
>
> Mario
>
>
>
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