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 the estimate if it seems that
there are no transitions from state 0 to 1. But the number of discrete
states at the end ("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") seems unexpected to me.
Best,
Brian
_______________________________________________________________________
Brian O'Meara
Professor, Dept. of Ecology & Evolutionary Biology, UT Knoxville
Associate Head, Dept. of Ecology & Evolutionary Biology, UT Knoxville
He/Him/His
On Mon, Apr 13, 2020 at 2:32 PM Carolina Santos Vieira <
carolsantosvie...@gmail.com> wrote:
> 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 simulation with make.simmap under ARD model on
> characters with states that the probability is zero on occuring in a given
> terminal, after calling summary(), this error is displayed:
>
> Error in colMeans(x$count) : 'x' must be an array of at least two
> dimensions
>
> When changing the input of the same data in a two column array, the error
> still persists. The same data was analyzed with make.simmap under "ER" and
> "SYM" models, and they run just fine. I am also comparing the results using
> fitDiscrete (geiger) and ace (ape) functions and they display results for
> "ARD" model without a glitch. According to output from fitDiscrete
> function, ARD model is indicated as the "best" model comparing AIC
> likelihoods.
> I've noticed that in this particular character, the "Q" matrix extracted
> from make.simmap simmulation under "ARD" is the following:
>
> Q =
> 0 1
> 0 -1.916782 1.916782
> 1 0.000000 0.000000
>
> Are those "zero" probabilities the cause of the error? And by that I mean,
> should I take from this evidence that "ARD" is not an appropriate model to
> this character?
>
> Also, results from characters with "non-applicable" coding (NA in matrix)
> for some terminal are coming out very different from what I would expect.
> Is this coding allowed for ancestral reconstruction?
> I am sorry for the many questions, and I would be very glad if any
> suggestions come to mind.
>
> Best wishes,
> Carolina Vieira.
>
> ---------------------------------------------
> This is the error rundown:
>
> > anc.tree_ard<-make.simmap(tree,ch434,model="ARD")
> make.simmap is sampling character histories conditioned on the transition
> matrix
>
> Q =
> 0 1
> 0 -1.916782 1.916782
> 1 0.000000 0.000000
> (estimated using likelihood);
> and (mean) root node prior probabilities
> pi =
> 0 1
> 0.5 0.5
> Done.
> > plot(anc.tree_ard,node.numbers=T,cores,fsize=0.5,ftype="i")
> > add.simmap.legend(colors=cores,prompt=FALSE,x=0.5*par()$usr[1],
> + y=-30*par()$usr[3],fsize=0.8)
> > title(main="ACSR \"ARD\" model (make.simmap)")
> > anc.tree_ard<-make.simmap(tree,ch434,model="ARD",nsim=1000)
> make.simmap is sampling character histories conditioned on the transition
> matrix
>
> Q =
> 0 1
> 0 -1.916782 1.916782
> 1 0.000000 0.000000
> (estimated using likelihood);
> and (mean) root node prior probabilities
> pi =
> 0 1
> 0.5 0.5
> Done.
> > anc.tree_ard
> 1000 phylogenetic trees with mapped discrete characters
> > simmap_ard<-summary(anc.tree_ard)
> > simmap_ard
> 1000 trees with a mapped discrete character with states:
> 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46,
> 47, 48, 49, 50, 51, 52, 53, 54, 55
>
> Error in colMeans(x$count) : 'x' must be an array of at least two
> dimensions
>
>
>
> Carolina Vieira
> Bióloga - Mestre em Ecologia e Conservação
> Doutoranda em Biologia Animal (PPGBAN - UFRGS)
>
>
> <
> https://www.avast.com/sig-email?utm_medium=email&utm_source=link&utm_campaign=sig-email&utm_content=webmail
> >
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> de vírus. www.avast.com
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> >.
> <#DAB4FAD8-2DD7-40BB-A1B8-4E2AA1F9FDF2>
>
> Em qua., 26 de fev. de 2020 às 23:54, Liam J. Revell <liam.rev...@umb.edu>
> escreveu:
>
> > 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
> > > <
> >
> https://nam01.safelinks.protection.outlook.com/?url=http%3A%2F%2Fwww.phytools.org%2F&data=02%7C01%7Cliam.revell%40umb.edu%7Cbeaccbb894534e0785d708d7b9607ccd%7Cb97188711ee94425953c1ace1373eb38%7C0%7C0%7C637181696380978269&sdata=%2Fialzss4jrVm8Rpt6jDUXwkdGqQZMMFA4N84HgVhWps%3D&reserved=0
> > >
> > >
> > > 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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> > >
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