getTableHosts: Extracts 'table.hosts' from a 'nosoiSim' object

In nosoi: A Forward Agent-Based Transmission Chain Simulator

Extracts table.hosts from a nosoiSim object

Description

This function extracts the table.hosts for the request host-type from a nosoiSim object.

Usage

getTableHosts(nosoi.output, pop = "A")

Arguments

nosoi.output	an object of class nosoiSim
pop	the host-type to be extracted (either "A" or "B", if not dual-host, then "A")

Value

Returns a data.table with the requested data. The table.hosts (class data.table) contains informations about each host that has been simulated (one row is one host). The structure of the table is the following:

hosts.ID

Unique identifier for the host, based on user-defined prefix and an integer.

inf.by

Unique identifier for the host that infected the current one.

inf.in

(only if structure is present) State or coordinates (in that case inf.in.x and inf.in.y) in which the host was infected.

current.in

(only if structure is present) State or coordinates (in that case current.in.x and current.in.y) in which the host is at the end of the simulation.

current.env.value

(only if continuous structure is present) Environmental value (raster cell value) in which the host is at the end of the simulation.

current.cell.raster

(only if continuous structure is present) Raster cell numeric ID in which the host is at the end of the simulation.

host.count

(only if structure is present) Host count in the current state or raster cell (beware, updated only if used).

inf.time

When did the host enter the simulation (infection time).

out.time

When did the host exit the simulation (NA if still active).

active

Is the host still active at the end of the simulation (TRUE for YES, FALSE for NO)?

parameters

The remaining columns are the sampled values for the individual-based parameters (if any) specified by the user.

nosoi documentation built on May 29, 2024, 9 a.m.