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
(http://blog.phytools.org/2017/11/running-makesimmap-in-parallel.html),
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)
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