Approach to select appropriate priors for generation and sampling time distributions about transphylo HOT 6 CLOSED

Yes this sounds like a good approach. Bear in mind that these are Gamma distributions, and therefore the mean is shape*scale and the variance is shape*scale^2. Unless you have a good reason to suspect that is not the case, I would keep the sampling time distribution the same as the generation time distribution, which is what happens by default if you do not specify the parameters of the sampling time distribution.

from transphylo.

The mean of the gamma distribution presenting in your paper (TB experiment) comes to 0.39 (1.3 * 0.3). Does this equate to saying that the average generation time of TB is 0.39 years?

from transphylo.

The paper states that we "used a Gamma distribution with shape parameter 1.3 and rate parameter 0.3"
In other words this has shape 1.3 and scale 1/0.3=3.333
The mean is shape * scale=1.3*3.333=4.33 years
The 95% range is from 0.23 to 14.31 years

from transphylo.

If I am working with a pathogen with a smaller generation time (say 2 months), should I select the parameters of the gamma distribution such that the mean is ~0.16 (2/12)?

from transphylo.

Yes that's right, and if you also consider the variance you want around this mean then you can deduce both scale and shape parameters as explained previously in this thread.

from transphylo.

Understood. I appreciate your help!

from transphylo.