We corresponded with Carolina offline, but here I'm including a generalized
solution of the quick solution we just sent her in case it's useful for
others (avoiding the issue lampooned in https://xkcd.com/979/).
The data was a delimited file with a species column and columns for each
character,
Hi Liam and everyone
The numbers from this message "1000 trees with a mapped discrete character
with states: 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43,
44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55" are the same numbers from
the nodes on my tree. As I replied to Brian, I assumed
Hi Carolina.
I agree with Brian that a Q matrix in which the elements of a row are
all zeros is not likely to be you problem. It just means that the ML
estimated transition rate from 1->0, in your case, is zero.
I agree with Brian that the message "1000 trees with a mapped discrete
With raydisc, you need one column with the species name and a column with
the data; so something like data[,c(1,2)] might be needed. If you want, you
could email the files (tree, data, script to run) to Jeremy (
jmbea...@uark.edu) and me to check out.
For the simmap results, a rate of zero can be
Hi Liam and all users
My morphological data varies from binary and multisate characters,
including polymorphism and non-applicable coding for many of those
characters. I've made a lot of progress after Liam's advices, but lately I
have been getting an error from make.simmap.
By trying to run a
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)
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
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
