Hi Julien,

Many thanks for your suggestion! It is a nice compromise between using all
three characters separately or combined in a single multistate character.
But I do see some caveats:

First, given the nature of your suggested multistate character, I would
assume it should be ordered, where 0>B>BC. Is that possible?

Second, if I understand correctly the ARD model would significantly
increase the number of rate parameters so I am not sure if that would be a
good idea (given that I have few observations which quickly results
in overparameterization). I think a SYM model would be good enough for my
purposes.

Third, as I mentioned before, I have more dependent characters. I ignored
those in my original query to keep things simple but here we go: There is a
substructure within the developmental tissue that can also comprise cells
originating from the different layers (A, B, AB, or BC). But obviously if a
layer does not contribute to the main structure it can also not contribute
to the substructure.
You can see that this additional level of dependency complicates things a
lot and I am not sure if there would be a way to atomize this similarly to
your solution for the original three states.

Therefore, I still think the best solution would be if I can keep the
characters separate and specify which character state combinations are
possible and which are not. Unless this is impossible? Or, alternatively,
perhaps I can achieve the same thing by combining characters while setting
some rates to be zero?

Thanks again & with best wishes,

Robin

PS the solution does not necessarily have to be in R. I just figured this
would be the best place to ask for advice.


> Date: Wed, 23 Aug 2017 16:52:16 +0200
> From: Julien CLAUDE <julien.cla...@univ-montp2.fr>
> To: r-sig-phylo@r-project.org
> Subject: Re: [R-sig-phylo] Mapping complex characters
> Message-ID: <58d4d9b746f44b308189fac26f72a...@univ-montp2.fr>
> Content-Type: text/plain; charset=UTF-8; format=flowed
>
> Hi Robin, if I understand  C depends on B.
>
> to atomize your developmental set and possibly avoid
> overparametrisation, look at A and the combination of BC independently
> (with 0, B and BC as states), then use the model ARD in ape, it will
> return actual the rates for these two characters.
>
> julien
>
> Le 23/08/2017 14:16, Robin van Velzen a ?crit?:
> > Dear all,
> >
> > I want to reconstruct ancestral states of morphological characters on a
> > phylogenetic tree. However, these are 'complex' and I am not sure how
> > best
> > to appropriately code these characters and do the mapping.
> >
> > Specifically, I have developmental data where three adjacent cell
> > layers
> > (A,B,C) can contribute to a particular developing tissue, either singly
> > or
> > in combination. However, layer C can in principle not contribute
> > singly,
> > and combinations can only comprise adjacent layers (so AB, BC, and ABC
> > are
> > possible but AC is not).
> >
> > A solution would be to code everything as a single character with a
> > total
> > of 5 states (A,B,AB,BC,ABC). But this would require a matrix that would
> > appropriately set the rates of change between all these states. Given
> > that
> > I do not have many observations I fear that this would result in
> > overparameterization (also I have many more than three dependent
> > characters
> > that I ignored for the sake of clarity). Moreover, reconstruction as a
> > single character would not give much insight in the underlying
> > processes at
> > the level of cell layers.
> >
> > Ideally, therefore, I would code the three layers separately so that
> > all
> > three ancestral states can be reconstructed. But that would require
> > specifying character combinations that are not allowed. But I am not
> > sure
> > if that is possible and if there are packages that would be able to do
> > such
> > reconstructions?
> >
> > Any advice would be greatly appreciated!
> >
> > Robin van Velzen
> >
> >       [[alternative HTML version deleted]]
> >
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