as.phylo.transmat: Convert transmat Infection Tree into a phylo Object

In EpiModel: Mathematical Modeling of Infectious Disease Dynamics

Convert transmat Infection Tree into a phylo Object

Description

Converts a transmission matrix from the get_transmat function into a phylo class object.

Usage

## S3 method for class 'transmat'
as.phylo(x, vertex.exit.times, ...)

Arguments

x	An object of class transmat, the output from get_transmat.
vertex.exit.times	Optional numeric vector providing the time of departure of vertices, to be used to scale the lengths of branches reaching to the tips. Index position on vector corresponds to network id. NA indicates no departure, so branch will extend to the end of the tree.
...	Further arguments (unused).

Details

Converts a transmat object containing information about the history of a simulated infection into a ape::phylo object representation suitable for plotting as a tree with plot.phylo. Each infection event becomes a 'node' (horizontal branch) in the resulting phylo tree, and each network vertex becomes a 'tip' of the tree. The infection events are labeled with the vertex ID of the infector to make it possible to trace the path of infection.

The infection timing information is included to position the phylo-nodes, with the lines to the tips drawn to the max time value +1 (unless vertex.exit.times are passed in it effectively assumes all vertices are active until the end of the simulation).

If the transmat contains multiple infection seeds (there are multiple trees with separate root nodes), this function will return a list of class multiPhylo, each element of which is a phylo object. See read.tree.

Value

A phylo class object.

Examples

set.seed(13)

# Fit a random mixing TERGM with mean degree of 1 and mean edge
# duration of 20 time steps
nw <- network_initialize(n = 100)
formation <- ~edges
target.stats <- 50
coef.diss <- dissolution_coefs(dissolution = ~offset(edges), duration = 20)
est <- netest(nw, formation, target.stats, coef.diss, verbose = FALSE)

# Parameterize the epidemic model as SI with one infected seed
param <- param.net(inf.prob = 0.5)
init <- init.net(i.num = 1)
control <- control.net(type = "SI", nsteps = 40, nsims = 1, verbose = FALSE)

# Simulate the model
mod1 <- netsim(est, param, init, control)

# Extract the transmission matrix
tm <- get_transmat(mod1)
head(tm, 15)

# Convert to phylo object and plot
tmPhylo <- as.phylo.transmat(tm)
par(mar = c(1,1,1,1))
plot(tmPhylo, show.node.label = TRUE,
              root.edge = TRUE,
              cex = 0.75)

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