For which parameter settings are less than 1000 taxons expected?

[richelbilderbeek]

AFAIK, there is no equation of the expected number of extant species for the PBD model [*], i.e.:

pbd_expected_n_extant <- function(crown_age, scr, sirg, siri, erg, eri) { }

I suggest to write this function for the PBD package (hence the pbd_ prefix) by simulating PBD trees and averaging. Clumsy, but AFAIK, the best we can do.

[*] To be precise, [1] claims it is too hard, and I could not find it in later papers.

References

• [1] Etienne, Rampal S., and James Rosindell. "Prolonging the past counteracts the pull of the present: protracted speciation can explain observed slowdowns in diversification." Systematic Biology 61.2 (2012): 204-213.

See also the cer_raket issue

[richelbilderbeek]

Let's first put it in raket :+1:

[richelbilderbeek]

Added it on the develop branch, emailed @J-Damhuis and @Tomdkkr that they may complete the function. Would be a good exercise for them :angel:

[richelbilderbeek]

In practice, this already works by using a small difference between speciation-initiation and extinction rate, instead of using pbd_expected_n_extant.