Fix sim.arg crash at high rho - #183
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…inguish individuals; recombination parent lineages inherit source pathogen id, coalescent inherits a child's id. do.infection counts unique carrier.id for rhyper().
… to distinguish individuals; recombination parent lineages inherit source pathogen id, coalescent inherits a child's id. do.infection counts unique carrier.id for rhyper()." This reverts commit 3a33bed.
…d earlier carrier.id because I don't think it was modelled in a biologically accurate way.
…a fixed pool of p.size lineages (a proportion of which are currently active), only activating a previously-inactive one when chosen. Total pool size never changes.
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If one or more active lineages are transferred out of the Host by a superinfection event, they need to be instantaneously replaced by inactive lineages to the set effective population size, as we continue to follow that host backwards in time. Otherwise superinfections will deplete the pool |
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Explicitly storing a list of Pathogen objects to the effective population size for every Host object results in too many objects, I think. Pathogen objects were meant to be used for active (sampled) lineages only. It should be possible to store the same kind of information without creating so many objects. |
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issue #182