In Huimin-stat/simTransmission: Simulate Transmission Tree

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simTransmission

The goal of simTransmission is to provides functions to simulate, summarize and plot transmission network and its corresponding phylogenetic tree.

Installation

You can install simTransmission in R using the following command:

devtools::install_github('Huimin-stat/simTransmission')

Example

This is a basic example which shows you how to simulate a transmission and plot the transmission network:

library(simTransmission)
set.seed(23)
transmission <- simTransmission(inf_rate = c(0.423,0.3), inf_rate_time = c(0,50), diag_rate = 0.143, rec_rate_asy = 0.052, rec_rate_sym = 0.0476, death_prop = 0.05, death_rate = 0.0357, inf_rate_diag = 0.02, asy_prop = 0.179, ngeneration = 8)
transmission1 <- simTransmission(inf_rate = c(0.423,0.3), inf_rate_time = c(0,50), diag_rate = 0.143, rec_rate_asy = 0.052, rec_rate_sym = 0.0476, death_prop = 0.05, death_rate = 0.0357, inf_rate_diag = 0.02, asy_prop = 0, ngeneration = 8)
times <- c(15, 30, 45, 60, 75)
cases.plot(transmatrix = transmission, times)
cases.plot(transmatrix = transmission1, times)

trunc <- timeTruncate(transmission1, 7)

set.seed(23)
(modeltree <- modelTreefromTransmission(trunc$truncTM))
(coaltree <- simCoalModeltree(1, modeltree, 0.8))
plotTree(modeltree)
plotTree(coaltree)

trunc1 <- timeTruncate(transmission, 15)
plotTransNet(trunc1$truncTM, trunc1$index_sym_latent, trunc1$index_sym_diagnosed, trunc1$index_sym_recovered, trunc1$index_asy_infectious, trunc1$index_asy_recovered, trunc1$index_dead)

trunc2 <- timeTruncate(transmission1, 15)
plotTransNet(trunc2$truncTM, trunc2$index_sym_latent, trunc2$index_sym_diagnosed, trunc2$index_sym_recovered, trunc2$index_asy_infectious, trunc2$index_asy_recovered, trunc1$index_dead)