plotLLE: plotLLE

In tsiR: An Implementation of the TSIR Model

Description

Function to plot the Local Lyapunov Exponents. The output is of class ggplot2 so you can add standard ggplot2 options to it if desired.

Usage

plotLLE(LLE)

Arguments

LLE	The output from TSIR_LLE

Examples

## Not run: 
require(kernlab)
require(ggplot2)
require(kernlab)
London <- twentymeas$London
## just analyze the biennial portion of the data
London <- subset(London, time > 1950)

## define the interval to be 2 weeks
IP <- 2

## first estimate paramters from the London data
parms <- estpars(data=London, IP=2, regtype='gaussian',family='poisson',link='log')

## look at beta and alpha estimate
plotbeta(parms)

## simulate the fitted parameters
sim <- simulatetsir(data=London,parms=parms,IP=2,method='deterministic',nsim=2)

## now lets predict forward 200 years using the mean birth rate,
## starting from rough initial conditions
times <- seq(1965,2165, by = 1/ (52/IP))
births <- rep(mean(London$births),length(times))
S0 <- parms$sbar
I0 <- 1e-5*mean(London$pop)

pred <- predicttsir(times=times,births=births,
                   beta=parms$contact$beta,alpha=parms$alpha,
                  S0=S0,I0=I0,
                  nsim=50,stochastic=T)

## take the last 10 years
pred <- lapply(pred, function(x)  tail(x, 52/IP * 20) )

## now compute the Lyapunov Exponent for the simulate and predicted model

simLE <- TSIR_LE(
time=sim$res$time,
S=sim$simS$mean,
I=sim$res$mean,
alpha=sim$alpha,
  beta=sim$contact$beta,
IP=IP
)

predLE <- TSIR_LE(
time=pred$I$time,
S=pred$S$X3,
I=pred$I$X3,
alpha=parms$alpha,
beta=parms$contact$beta,
IP=IP
)

simLE$LE
predLE$LE

simLLE <- TSIR_LLE(simLE)
predLLE <- TSIR_LLE(predLE)

plotLLE(simLLE)
plotLLE(predLLE)

## End(Not run)

tsiR documentation built on Jan. 21, 2021, 1:06 a.m.