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
