Closed richelbilderbeek closed 4 years ago
As the man that eats branching times for breakfast, I assign @Giappo to this one :+1:
@richelbilderbeek I do not understand this issue. For two reasons:
1) If you want a yule process you need to set the parameters in such a way that lambda > 0 and mu = 0. In the example you proposed lambda = 0 and mu > 0. I do not see how this can be working.
2) Why would you expect a yule process and a bd process to have the same branching times? Different processes are expected to return different branching times.
My take on this is: this test is not correct. If you want me to do something else write a test and I will work on it.
If you want a yule process you need to set the parameters in such a way that lambda > 0 and mu = 0. In the example you proposed lambda = 0 and mu > 0. I do not see how this can be working.
You are indeed right: I switched lambda
and mu
! I will create another Issue to rename these to speciation_rate
and extinction_rate
.
Closing this Issue, sorry for the noise :+1:
pirouette
provides for the creation of Yule twin trees, thus it should be possible to create a set of branching times for a Yule tree. A Yule tree has, by definition, an extinction rate of zero.Whenever I use that knowledge to call
create_twin_branching_times
I get an error:Here is the test to reproduce the error with:
There are many ways to solve this.
create_twin_branching_times
to provide for an extinction rate of zerocreate_twin_yule_branching_times
andcreate_twin_bd_branching_times
Good luck :+1: