fortify_aggregate.netsim: Take external aggregate data and put it in a format used in...

In skgallagher/EpiCompare: A Pipeline to Analyze and Compare Infectious Disease Epidemics

Description

Take external aggregate data and put it in a format used in this package

Usage

## S3 method for class 'netsim'
fortify_aggregate(data, states = NULL, package_source = NULL)

Arguments

data	output from external source package. See details
states	names of states we want aggregate totals of at each time
package_source	optional argument to include the package from which the output is derived from, which helps with the fortify function when outputs are of generic classes such as list or data.frame

Details

This function converts external data sources (we currently support output from the EpiModel and pomp R packages), which is already aggregated and puts it in a format that can be used by our exploring functions.

Value

a data frame with the following columns

t

time

Xk

columns X0, ..., X_K. which are numeric

Examples

## For netsim  NOT RUN
## From http://statnet.org/tut/BasicNet.html
## est1 <- netest(nw, formation, target.stats, coef.diss, edapprox = TRUE)

## nw <- network.initialize(n = 1000, directed = FALSE)
## nw <- set.vertex.attribute(nw, "race", rep(0:1, each = 50))
## formation <- ~edges + nodefactor("race") + nodematch("race") + concurrent
## target.stats <- c(250, 375, 225, 100)
## coef.diss <- dissolution_coefs(dissolution = ~offset(edges),
## duration = 25)

## param <- param.net(inf.prob = 0.1, act.rate = 5, rec.rate = 0.02)
## status.vector <- c(rbinom(500, 1, 0.1), rep(0, 500))
## status.vector <- ifelse(status.vector == 1, "i", "s")
## init <- init.net(status.vector = status.vector)
## control <- control.net(type = "SIS", nsteps = 50,
##nsims = 10, epi.by = "race")
## sim1 <- netsim(est1, param, init, control)

## out <- fortify_aggregate(sim1)
## head(out)

skgallagher/EpiCompare documentation built on Sept. 14, 2021, 5:45 a.m.