Dear Carolina.
After running make.simmap with nsim=100 or more, just run summary( ) on
your "multiSimmap" object and then plot the result. For instance:
map.trees<-make.simmap(tree,x,model="SYM",nsim=200)
map.summary<-summary(map.trees)
print(map.summary)
plot(map.summary,ftype="off",lwd=1,cex=c(0.7,0.4))
map.summary$ace ## probabilities at nodes
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:
https://www.umb.edu/academics/caps/international/biology_chile
On 2/24/2020 2:33 PM, Carolina Santos Vieira wrote:
**[EXTERNAL SENDER]
Hi Liam,
Thank you very much for clearing that up!
I was able to run the make.simmap script, but in the first plot instead
of getting one symbol of the corresponding state at the tips, they are
displayed in proportional sizes (I've attached the plot).
I have also looked into how to get the likelihoods from each ancestral
state from this analysis (like we get from "lik.anc" in ace function),
but didn't find it. Is it possible to get it?
Thank you again for the help!
Best regards,
Carolina Vieira
Bióloga - Mestre em Ecologia e Conservação
Doutoranda em Biologia Animal (PPGBAN - UFRGS)
Em sex., 21 de fev. de 2020 às 22:53, Liam J. Revell
<liam.rev...@umb.edu <mailto:liam.rev...@umb.edu>> escreveu:
Dear Carolina.
I don't know how rayDISC works (but the authors of corHMM are on this
list, so they will probably respond); however, for
phytools::make.simmap
& phytools::rerootingMethod, which can also handle missing data,
missingness is coded by supplying the input data in the form of an N
x k
matrix for N species & k character states. In this case, we would
put 0s
and 1s in any row in which the character state was known; and a series
of values of 1/k for any completely unknown state.
For instance:
0 1 2
sp A 0 0 1
sp B 1 0 0
sp C 1/3 1/3 1/3
sp D 0 1/2 1/2
corresponds to species A in state '2', species B in state '0', and
species C unknown or missing. Species D is in either state '1' or '2',
but not in state '0'. (Instead of 1/k you can also set them all to
be 1.
The likelihood changes, but ancestral states are the same.)
I hope this is helpful. 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
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Academic Director UMass Boston Chile Abroad:
https://www.umb.edu/academics/caps/international/biology_chile
On 2/21/2020 8:22 PM, Carolina Santos Vieira wrote:
> [EXTERNAL SENDER]
>
> Dear all,
>
> I am working with a morphological matrix which contains multistate
> characters (including polymorphism) and some missing data entries
(coded as
> NA in data file for input). There are no unvariable characters in
coding.
> For the reconstruction of ancestral characters, I came across
with rayDISC
> function from corHMM package (since fitDiscrete doesn't seem to
account for
> it).
>
> However, when running the script two kinds of errors are displayed:
>
> - Calling the full data file with the rayDISC function, no matter
which
> character is selected for the analysis, it returns with this error:
>
> rayDISC(phy,data, ntraits=1, charnum=1, rate.mat=NULL, model=c("ER"),
> node.states=c("marginal"), state.recon=c("subsequently"),
> lewis.asc.bias=FALSE, p=NULL, root.p=NULL, ip=NULL, lb=0, ub=100,
verbose=TRUE,
> diagn=FALSE)
>
> $diagnostic
> [1] "Character 1 is invariant. Analysis stopped."
>
>
> - I have tried clipping the data creating a new object with just one
> of the characters, but a new error appears:
>
> Error in data[, 1] : incorrect number of dimensions
>
> I also looked into running make.simmap in parallel
>
(https://nam01.safelinks.protection.outlook.com/?url=http%3A%2F%2Fblog.phytools.org%2F2017%2F11%2Frunning-makesimmap-in-parallel.html&data=02%7C01%7Cliam.revell%40umb.edu%7Ce210401fdd8c483d2bde08d7b735d3f4%7Cb97188711ee94425953c1ace1373eb38%7C0%7C1%7C637179314141242835&sdata=%2FHwtbpjRxREIS7T2PPIQZ%2B5iyRpVbGaHMKWX6e8%2Fb5U%3D&reserved=0
<https://nam01.safelinks.protection.outlook.com/?url=http%3A%2F%2Fblog.phytools.org%2F2017%2F11%2Frunning-makesimmap-in-parallel.html&data=02%7C01%7Cliam.revell%40umb.edu%7Cbeaccbb894534e0785d708d7b9607ccd%7Cb97188711ee94425953c1ace1373eb38%7C0%7C0%7C637181696380988260&sdata=Xbyv%2F2R6lsf7ArCi%2F5SmiV2r2nE57ZMsAsYrsL5uhhI%3D&reserved=0>),
> and this happens: " Error in if (any(x < 0)) x <- x - min(x) :
> missing Value when TRUE/FALSE needed ". Trying to replace NA as
> 'unknown' to be considered in the analysis by changing its
"status" to
> FALSE, it returns in the matrix coded as "0", which is not properly
> valid since this implies coding it as a known state (and not missing
> data, as it truly is).
>
>
> I appreciate if anyone could shine a light on this matter.
> With regards,
> Carolina Vieira
> Bióloga - Mestre em Ecologia e Conservação
> Doutoranda em Biologia Animal (PPGBAN - UFRGS)
>
> [[alternative HTML version deleted]]
>
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