July 1 meeting

[isaacovercast]

• Record fluctuating population sizes Done
• Investigate weird negative growth rate pattern
• Retain the 'abundance' model but consider this as 'carrying capacity', which is instantaneously saturated. Done

[isaacovercast]

I think the predominant negative growth rates in some of the simulations that we saw are an expected result, given the growth rate mean and sigma. Here we're looking at 2 sets of simulations (tests 6 & 7 in the current rmarkdown). Test 6 (bllue) uses the 'rate' process and growth rate mean and sigma both equal 1e-4. Test 7 (orange) uses the 'abundance' process (thereby ignoring growth rate, yet still simulating it) and growth rate mean/sigma both equal 1e-3. If we look at a histogram of the total number of negative growth rate lineages per test we see this: The small starting mean and small sigma allow growth rates to wander negative, even for a large fraction of the species on occasion, yet the negative growth rates remain quite small, so populatin decilnes happen very slowly. Also notice that for test 6 the entire tree never goes negative, but for test 7 this happens with appreciable frequency.

Now if we look at the turnover rate:

Average turnover rate per simulation is much higher in test 6 than test 7, which is expected if the negative growth rates are truly driving species to extinction.