swifco_rs.asf.infection module

swifco_rs.asf.infection.default_infection(p_inf_within=0.05, p_inf_between=0.0, p_inf_carcass=0.1, carcass_contact_delay=3)

Default, neighborhood infection including carcasses

Transmission of infection with the ASF virus is modelled directly and carcass-mediated.

Direct transmission within groups: The mode refers to transmission between animals in direct animal-to-animal contact, i.e., members of the same female group and males associated with the group. Direct transmission within groups is modelled stochastically. Parameter p_inf_within determines the probability of contracting the infection from an infectious group mate for one week. For each susceptible animal, the probability of becoming infected accumulates over all infectious animals within the group:

\[\Pi^{(w)}_i= 1 − \left( 1 − p\_inf\_within \right)^{\lambda^{(w)}_i}\]

where \(\lambda^{(w)}_i\) is the number of infectious individuals in the same direct contact group as the receiving individual.

Direct transmission between neighbouring groups: The mode refers to transmission between animals of different female groups and males associated with those. Between groups direct transmission is modelled stochastically. Parameter p_inf_between determines the probability of contracting the infection from an infectious member of a neighbouring group for one week. For each susceptible animal, the probability of between group infections accumulates over infectious animals of all neighbouring groups:

\[\Pi^{(b)}_i= 1 − \left( 1 − p\_inf\_between \right)^{\lambda^{(b)}_i}\]

where \(\lambda^{(b)}_i\) is the number of infectious individuals in the neighbouring groups of the one containing the receiving individual. Default neighbourhood addresses all groups with a common edge point of their grid cells (i.e., eight neighbours).

Carcass transmission: The mode refers to wild boar carcasses of infected animals, lying in the habitat area. Possible transmission is assumed to be associated with physical contact to the carcass, i.e., no airborne or mechanical mechanisms are considered relevant. Transmission through carcasses is modelled stochastically. Parameter p_inf_carcass determines the probability of contracting the infection from an infectious carcass during one week. For each susceptible animal in age group a, the probability of becoming infected accumulates over accessible carcasses

\[\Pi^{(c)}_i = 1 − \left( 1 − p\_inf\_carcass \right)^{\omega^{(c)}_i} \cdot \left( 1 − p\_inf\_carcass \right)^{\sum_j \omega^{(c)}_{ij}}\]

where \(\omega^{(c)}_i\) is the number of carcasses in the respective core home range \(i\), \(\omega^{(c)}_{ij}\) is the number of carcasses in the connecting edges to neighbouring cells \(j\).

Effective transmission: For every habitat cell and per time step, the transmission probability is accumulated from direct, within and between, and carcass transmission probabilities

\[\Pi^{(t)}_i = 1 − \left( 1 − \Pi^{(w)}_i \right) \cdot \left( 1 − \Pi^{(b)}_i \right) \cdot \left( 1 − \Pi^{(c)}_i \right)\]

The model iterates over all individuals and stochastically sets each susceptible individual to infected with the probability \(\Pi^{(t)}_i\) associated with its home cell \(i\).

Alternative defaults based on previous calibrations of SwiFCoIBM in [Lange_2018] are:

• p_inf_within=0.05

• p_inf_between=0.0003

• p_inf_carcass=0.05

• carcass_contact_delay=2

Parameters:

p_inf_within - per-tick and per-capita infection probability within herds (default value based on [Blome_2012] and [Guinat_2014])

p_inf_between - per-tick and per-capita infection probability between herds (default value based on [Lange_2018])

p_inf_carcass - per-tick and per-capita infection probability for carcasses (default value based on [Lange_2017])

carcass_contact_delay - number of ticks carcasses are not contacted by living hosts (default value based on [Probst_2017])

swifco_rs.asf.infection.store_infection_location()

Stores the current location of newly infected animals