as.data.frame.dcm: Extract Model Data for Deterministic Compartmental Models

In EpiModel: Mathematical Modeling of Infectious Disease Dynamics

Extract Model Data for Deterministic Compartmental Models

Description

This function extracts a model run from an object of class dcm into a data frame using the generic as.data.frame function.

Usage

## S3 method for class 'dcm'
as.data.frame(x, row.names = NULL, optional = FALSE, run, ...)

Arguments

x	An EpiModel object of class dcm.
row.names	See as.data.frame.default.
optional	See as.data.frame.default.
run	Run number for model; used for multiple-run sensitivity models. If not specified, will output data from all runs in a stacked data frame.
...	See as.data.frame.default.

Details

Model output from dcm simulations are available as a data frame with this helper function. The output data frame will include columns for time, the size of each compartment, the overall population size (the sum of compartment sizes), and the size of each flow.

For models with multiple runs (i.e., varying parameters - see example below), the default with the run parameter not specified will output all runs in a single stacked data frame.

Value

A data frame containing the data from x.

Examples

## Example 1: One-group SIS model with varying act.rate
param <- param.dcm(inf.prob = 0.2, act.rate = seq(0.05, 0.5, 0.05),
                   rec.rate = 1/50)
init <- init.dcm(s.num = 500, i.num = 1)
control <- control.dcm(type = "SIS", nsteps = 10)
mod1 <- dcm(param, init, control)
as.data.frame(mod1)
as.data.frame(mod1, run = 1)
as.data.frame(mod1, run = 10)

## Example 2: Two-group SIR model with vital dynamics
param <- param.dcm(inf.prob = 0.2, inf.prob.g2 = 0.1,
                   act.rate = 3, balance = "g1",
                   rec.rate = 1/50, rec.rate.g2 = 1/50,
                   a.rate = 1/100, a.rate.g2 = NA,
                   ds.rate = 1/100, ds.rate.g2 = 1/100,
                   di.rate = 1/90, di.rate.g2 = 1/90,
                   dr.rate = 1/100, dr.rate.g2 = 1/100)
init <- init.dcm(s.num = 500, i.num = 1, r.num = 0,
                 s.num.g2 = 500, i.num.g2 = 1, r.num.g2 = 0)
control <- control.dcm(type = "SIR", nsteps = 10)
mod2 <- dcm(param, init, control)
as.data.frame(mod2)

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