Post date: Aug 20, 2020 7:0:28 PM
Rates to be set:
Alpha: shape parameter for the gamma prior on population sizes.
Beta: rate parameter for the gamma prior on population sizes.
Kappa: parameter used when selecting the CIR rate prior (below).
Lambda: Birth rate for the Yule model prior on the species tree.
Rateprior: prior on rates can be Gamma, InverseGamma, CIR, or Uniform.
- λ -
SNAPP uses the Yule model for branching. It is a birth process in which each branch has associated with it a birth rate = λ = instantaneous rate at which the branch gives birth to a new branch.
λ can be used to estimate the tree height.
I use the following script from (https://github.com/joaks1/pyule/blob/master/README.md) to estimate λ.
git clone https://github.com/joaks1/pyule.git
se the fI have a hard time to understand what lambda is and how to estimate it from my data. I left the default value of 2.
[u6028866@kp019 run4]$ sbatch RunBeast.sh
Submitted batch job 8545050
It still did not work. Try other commands to see if there are missing dependencies:
cpan upgrade Test::More