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Description
For a species that is a result of local speciation this call is broken:
meta_abund = self.region._get_abundance(cname)
This is setting abundance for the sister species in the metacommunity, but it doesn't work at all for local speciation, this should get the abundance of the parent species at time of divergence. Some relevant debug info:
[####################] 100% 0.2460 ming Simulations | 0:00:00 | > /home/isaac/Continuosity/MESS/MESS/LocalCommunity.py(969)_simulate_seqs()
-> pop_cfgs.append(pop_meta)
(Pdb) l
964 meta_abund = self.region._get_abundance(cname)
965 try:
966 pop_meta = msprime.PopulationConfiguration(sample_size = 10, initial_size = meta_abund)
967 except ValueError:
968 import pdb; pdb.set_trace()
969 -> pop_cfgs.append(pop_meta)
970 species_dict = {}
971 for sp, idx in sp_idxs.items():
972 if not sp:
973 continue
974 try:
(Pdb) species_list
['t8.Loc1-191']
(Pdb) cname
't8.Loc1-191'
(Pdb) self.local_info[species_list]
t8.Loc1-191
colonization_times 2809
post_colonization_migrants 0
abundances_through_time {}
ancestor t8
ancestral_abundance []
speciation_completion 0
meta_abund 0
local_abund 3
(Pdb) self.region._get_abundance("t8")
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