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[stem-ebola] Operon Labs Ebola Models Versions C3 Released

New Fixed 'C3' STEM Ebola Models are up for West Africa and USA.

First, thanks to Dr. Christian Althaus for his insights, which were necessary to get these parameters working properly. There may be a few minor bugs in these new models, but they are much better than before.

The main results was that the STEM Ebola C3 model shows the West African incidence peaks in late-March 2015 (with I+R+D in millions) assuming no changes in parameters like R0, and no effective control interventions. In reality, however, the Confidence Interval here is so wide you could drive a truck through it.

Too many unknowns to predict that far out, but I suppose this could be a worst-case scenario assuming R0 doesn't increase..

Christian: I ended up using pretty much all your recommendations, including deriving Gamma from the published serial interval. Your formulas for derivation of the infectious mortality rate also worked great. Thank you.

The latest Operon 'C3' Ebola Outbreak Model SEIR parameters are as follows (derived from the NEJM/WHO data):

1/σ (Incubation Period) : 9.4 days (Single-day Exposures, All Countries, Observed) 1/γ (Infectivity Period): 8.2 days (Derived from Observed Serial Interval (All Countries) - Incubation Period) (17.6 Days - 9.4 Days)=8.2 days
σ (Incubation Rate, STEM)  : 1 / 9.4 days = 0.1063830
γ (Infectivity Rate)  : 1 / 8.2 days = 0.12195120
f (Case Fatality Rate): 0.708 (NEJM/WHO)
γ_STEM:	Recovery Rate (STEM): (1-f)*γ = 0.292*γ = 0.03560976
δ_STEM	Mortality Rate (STEM):	f*γ = 0.708γ = 0.0863414496
R0 (Reproduction Num#) : 1.84 ( Weighted Avg, All Countries)
βstem(Transmission Rate) = R0 * γ
βstem(Transmission Rate) = 1.84 * 0.12195120
βstem(Transmission Rate): = 0.224390208

Td_model (Model Doubling Time) = ~16.3 days (Simple calc.. from two points in output..Td=(t2-t1)*(log 2 / log(q2/q1)) Td_actual (Actual Doubling Time) = 15.74 days (Weighted Average, Liberia+SL+Guinea)
Serial Interval (Model Serial Interval) = Not Calculated
Serial Interval (Actual Serial Interval) = 17.6 days (NEJM/WHO. Used to derive the infectious period)

The models for the USA and West Africa can be downloaded here:

Feedback is appreciated -- in case I missed anything. Feel free to use these as a base to build other models.


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