Question: Stochastic mapping & discrete characters
0
gravatar for NK
5.6 years ago by
NK0
European Union
NK0 wrote:

Hi all,

 I am trying to examine a correlation between two discrete traits, using stochastic mapping.

 

I tried two options and ran into problems with both:

 

1. Using stochastic mapping of Phytools –

make.simmap - The problem is that I need to use constraints - for one character

I need to set the state of the root to 0 (I figured how to do that), while for the second

character I need to set the reverse rate to 0. Couldn’t figure out this second constraints.

Tried this

mtrees<-make.simmap(tree,mtree$states,nsim=10, model=matrix(c(0,1,0,0),2))

But model=matrix(c(0,1,0,0)) leads to the following error:

 BLAS/LAPACK routine 'DGEBAL' gave error code -3

In addition: Warning message:

In matrix(XX$rates[II], m, m, dimnames = list(lvls, lvls)) :

  data length [3] is not a sub-multiple or multiple of the number of rows [2]

 The same command works if I use , model=matrix(c(0,1,0,0),2))

In addition, I wonder if anyone has examined the distribution of two characters -
i.e. how can I calculate the percentage of time spent in (0,0), (0,1), etc. for the

classes generated by phytools.

  

2. Using Diversitree -

I used asr.stoch with a likelihood function and parameters. I managed to make constraints in the

two needed ways (i.e. on the root, and on the rates)

pars <- c(.1, .1, .03, .03, .03, .06)

set.seed(1)

phy <- trees(pars, "bisse", max.taxa=4, max.t=Inf, x0=0)[[1]]

h <- history.from.sim.discrete(phy, 0:1)

plot(h, phy, main="True history")

lik <- make.mk2(phy, phy$tip.state)

#lik<-constrain(q13~q12,q21~q12,q23~q12,q31~q12,q32~q12)

argnames(lik)

lik2<-constrain(lik, q10~0)

argnames(lik2)

fit = find.mle(lik2,c(.1))

st.s1 <- asr.stoch(lik2, fit$par)

plot(st.s1, phy)

st.s2 <- asr.stoch(lik2, fit$par)

 

What I do not understand is how to simulate stochastic mappings on my trees randomly – I want to

use the same rate parameters, but with no constraints on the tips. These simulations will help me

Determine whether the statistic I am examining is significantly large for my data.

 

In addition, I wonder if anyone has examined the distribution of two characters -

i.e. how can I calculate the percentage of time spent in (0,0), (0,1), etc. for the

classes generated by Diversitree.

 

Thanks a lot for your help!

 

software error genome • 1.8k views
ADD COMMENTlink modified 5.4 years ago • written 5.6 years ago by NK0
1
gravatar for Asaf
5.6 years ago by
Asaf6.6k
Israel
Asaf6.6k wrote:

I used the tool discrete of BayesTraits with good success for this kind of problem.

ADD COMMENTlink written 5.6 years ago by Asaf6.6k
0
gravatar for NK
5.4 years ago by
NK0
European Union
NK0 wrote:

Thanks Asaf, I am also using Bayestraits, but I would like to compare its results to another tool/method. 

ADD COMMENTlink written 5.4 years ago by NK0
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