Transform individual events to node events for a model

In many countries, individual-based livestock data are collected to enable contact tracing during disease outbreaks. However, the livestock databases are not always structured in such a way that relevant information for disease spread simulations is easily retrieved. The aim of this function is to facilitate cleaning livestock event data and prepare it for usage in SimInf.

Usage

node_events(x, time = NULL, target = NULL, age = NULL)

# S4 method for class 'SimInf_indiv_events'
node_events(x, time = NULL, target = NULL, age = NULL)

Arguments

x

an individual events object of class SimInf_indiv_events.

time

All events that occur after ‘time’ are included. Default is NULL which means to extract the events after the minimum time-point in the SimInf_indiv_events object.

target

The SimInf model ('SEIR', 'SIR', 'SIS', 'SISe3', 'SISe3_sp', 'SISe', or 'SISe_sp') to target the events and u0 for. The default, NULL, creates events but they might have to be post-processed to fit the specific use case.

age

Integer vector with break points in days for the ageing events.

Value

a data.frame with the columns event, time, node, dest, n, proportion, select, and shift.

Details

The individual-based events will be aggregated on node-level. The select value is determined by the event type and age category. If there is only one age category, i.e., age=NULL, then select=1 for the enter events, and select=2 for all other events. If there are two age categories, then select=1 for the enter events in the first age category, and select=2 for the enter events in the second age category. Similarly, select=3 for all other events in the first age category, and select=4 for all other events in the first second category. With three age categories, it works similarly with select=1,2,3 for the enter events in each age category, respectively. And select=4,5,6 for all other events.

See also

individual_events.