Coalescent rate trajectory ignores a population's activation time #2289
Description
A population can have an activation time that is greater than zero -- for example, to sample ancient individuals. When using the demography debugger's coalescence_rate_trajectory() function, specifying lineages from that population has the unwanted behavior of allowing coalescence prior to the population's activation time. This means that the reported proportion of coalesced lineages can be less than 1 before the sampling time of that population.
For a demography built from demes, the population size is set to zero prior to activation, which leads to unreasonable outputs. There also seems to be some strange behavior with cross-population coalescences that I haven't gotten to the bottom of yet.
A short example:
import msprime, demes, numpy as np
b = demes.Builder()
b.add_deme("A", epochs=[dict(start_size=10000)])
b.add_deme("B", ancestors=["A"], start_time=2000, epochs=[dict(start_size=1000, end_time=100)])
g = b.resolve()
demog = msprime.Demography.from_demes(g)
db = demog.debug()
steps = np.linspace(100, 2100, 201)
coalrates, puncoal = db.coalescence_rate_trajectory(steps, lineages={"B": 2})
print(puncoal[0]) ## should be 1
print(np.exp(-0.5 * 100)) ## the actual value, which is the prob of no coal with min population size of 1This also shows some strange outputs when asking for cross-coalescence rates:
db.coalescence_rate_trajectory(np.linspace(0, 200, 201), {"A": 1, "B": 1})