Rename 'lambda' and 'mu' to 'speciation_rate' and 'extinction_rate'
richelbilderbeek opened this issue · comments
In Issue 342 I expected a Yule tree to be generated from a BD process with lambda/mu equals to zero. I swapped the interpretation of these symbols.
Instead of using lambda and mu, use speciation_rate and extinction_rate, as these are directly expressing what they are.
I think @Giappo would enjoy this (very simple) one 👍
@richelbilderbeek speciation and extinction rates are universally named, respectively, lambda and mu in pretty much the entire field. I think we can live with that.
Nah, I would enjoy to change it. Will assign myself then.
I agree with @Giappo , across CRAN, universally lambda and mu are used for speciation and extinction rate.
Consider the packages:
TreeSim (sim.bd.taxa and related functions)
TESS (tess.sim.taxa and related functions)
DDD (dd_sim and related functions)
RPANDA (the function fit_bd)
However, ape, apTreeshape and geiger use 'b' and 'd'
I am personally more interested in readability: if '[any symbol]' denotes an extinction rate, call it 'extinction_rate'.
For reference, this video from Kevlin Henney at 31:16: 'Name things what they are':
Well let pass, for now.