Dear Liam, dear Emmanuel,
thank you so much for your answers! This helped me a lot. Liam's script
does exactly what I wanted to do. Thanks to both of you, I feel
confident that I will be able to implement this in my research projects.
All the best!
Mario
Am 05.08.19 um 11:31 schrieb Emmanuel Paradis:
Hi Mario,
In the class "phylo", nodes and tips are numbered sequentially so it
is no problem to have data associated with both. This is done in many
functions in ape and in phangorn. I think the solution to your
headaches is in this document (§ 4.4):
http://ape-package.ird.fr/misc/FormatTreeR_24Oct2012.pdf
HTH
Best,
Emmanuel
Sun, 4 Aug 2019 03:32:16 +0200 Mario Schädel <mario.schae...@gmail.com>:
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
Pour nous remonter une erreur de filtrage, veuillez vous rendre ici :
https://www.security-mail.net/ndc/reporter/mid/2641.5d4635bf.476a1.0/r/emmanuel.para...@ird.fr/c/402709068db61d2ee7dfb2c7aaff9a71ffa8b19c
--
PhD Student
Haug Lab
LMU Munich
Großhaderner Str. 2
82152 Planegg
Germany
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