swifco_rs.mortality module

swifco_rs.mortality.default_mortality(max_age_years=12.0, piglet_mortality_limits=(0.1, 0.9), yearling_mortality_limits=(0.1, 0.6), adult_mortality_limits=(0.1, 0.6), share_hunted=0.8)

Default, age class specific mortality

Iterating over the entire population, each individual either stochastically dies with age-class-dependent mortality rates or after reaching a certain maximum age max_age_years. Stochastic age-class-dependent mortality rates are adjusted to annual survival estimates from the literature. Survival estimates and reported variability determine a Gaussian distribution which is used in the model to draw the random annual survival \(surv\_prob_{year}\). This stochastic effect resembles ‘good’ or ‘bad’ years for the host species, i.e. environmental noise. In the application, the Gaussian distributions are truncated symmetrically around the mean.

Per time step, the adjusted age-dependent mortality \(mort_{week}\) was applied to the individual:

\[mort_{week} = 1 - \left( surv\_prob_{year} \right)^{1 / 52}\]

Mortality due to infection is independently treated by the disease course sub-model.

Parameters:

max_age_years - maximum age of boars that can’t be exceeded (default value based on [Jezierski_1977])

piglet_mortality_limits - limits of piglet mortality, 95% interval of normal distribution (default value based on [Focardi_1996])

yearling_mortality_limits - limits of yearling mortality, 95% interval of normal distribution (default value based on [Gaillard_1987])

adult_mortality_limits - limits of piglet mortality, 95% interval of normal distribution (default value based on [Focardi_1996])

share_hunted - proportion of mortality attributed to hunting (default value based on [Focardi_1996], [To_go_2010] and [Keuling_2013])