color_tea: Create a TEA Variable for Infection Status for 'ndtv'...

In EpiModel: Mathematical Modeling of Infectious Disease Dynamics

Create a TEA Variable for Infection Status for ndtv Animations

Description

Creates a new color-named temporally-extended attribute (TEA) variable in a networkDynamic object containing a disease status TEA in numeric format.

Usage

color_tea(
  nd,
  old.var = "testatus",
  old.sus = "s",
  old.inf = "i",
  old.rec = "r",
  new.var = "ndtvcol",
  new.sus,
  new.inf,
  new.rec,
  verbose = TRUE
)

Arguments

nd	An object of class networkDynamic.
old.var	Old TEA variable name.
old.sus	Status value for susceptible in old TEA variable.
old.inf	Status value for infected in old TEA variable.
old.rec	Status value for recovered in old TEA variable.
new.var	New TEA variable name to be stored in networkDynamic object.
new.sus	Status value for susceptible in new TEA variable.
new.inf	Status value for infected in new TEA variable.
new.rec	Status value for recovered in new TEA variable.
verbose	If TRUE, print progress to console.

Details

The ndtv package (https://cran.r-project.org/package=ndtv) produces animated visuals for dynamic networks with evolving edge structures and nodal attributes. Nodal attribute dynamics in ndtv movies require a temporally extended attribute (TEA) containing a standard R color for each node at each time step. By default, the EpiModel package uses TEAs to store disease status history in network model simulations run in netsim. But that status TEA is in numeric format (0, 1, 2). The color_tea function transforms those numeric values of that disease status TEA into a TEA with color values in order to visualize status changes in ndtv.

The convention in plot.netsim is to color the susceptible nodes as blue, infected nodes as red, and recovered nodes as green. Alternate colors may be specified using the new.sus, new.inf, and new.rec parameters, respectively.

Using the color_tea function with a netsim object requires that TEAs for disease status be used and that the networkDynamic object be saved in the output: tergmListe must be set to FALSE in control.net.

Value

The updated object of class networkDynamic.

See Also

netsim and the ndtv package documentation.

EpiModel documentation built on Oct. 12, 2024, 1:06 a.m.