-SP needed even when size is informed for every population

[Érico Polo]

Hello,

I'm running SimPhy while informing population sizes for both ancestral and current populations (with the "#" after each one in the extended newick) and nevertheless SimPhy gives me the following error:

"Improper value sampling the parameter -SP, Haploid effective population size. Please, check your sampling settings and try again"

When I add the -SP flag everything works fine, but I wonder if the value I inform changes any parameter on the simulations.

Cheers,

Érico.

[Diego M.]

Dear Érico,

I am glad you are using SimPhy, and I am sorry for this bug you just found. 

SimPhy considers the haploid effective population size as a required parameter and thus generates an error if the user does not provide it. You are correct that this parameter is not needed if all population sizes are given by the user in a tree (species or locus) input. However, SimPhy does not check for this to generate the error message.

I will try to fix this in the next version of SimPhy. In the meantime, you can just run it with any valid general effective population size specified with the -SP parameter. That value will not be used if all effective population sizes are provided in a tree.

Thanks, and please, do not hesitate to contact me if you have any other questions!

Diego M.