inst/doc/DSAIDE.R

In DSAIDE: Dynamical Systems Approach to Infectious Disease Epidemiology (Ecology/Evolution)

## ---- include = FALSE---------------------------------------------------------
packagename = 'DSAIDE'

## ---- eval=FALSE, echo=TRUE---------------------------------------------------
#  library('DSAIDE')

## ---- eval=FALSE, echo=TRUE---------------------------------------------------
#  dsaidemenu()

## ----dsaidemenu,  fig.cap='Main menu of the DSAIDE package.', echo=FALSE------
knitr::include_graphics("mainmenu.png")

## ----appexample,  fig.cap='Screenshot of the input-output elements of one of the apps.', echo=FALSE----
knitr::include_graphics("appexample.png")

## ----modelexample,  fig.cap='Screenshot of the _Model_ section of one of the apps.', echo=FALSE----
knitr::include_graphics("modelexample.png")

## ----whattodoexample,  fig.cap='Screenshot of the _What to do_ section of one of the apps.', echo=FALSE----
knitr::include_graphics("whattodoexample.png")

## ----eval=TRUE, echo=TRUE-----------------------------------------------------
library('DSAIDE') 

## ----eval=FALSE, echo=TRUE----------------------------------------------------
#  help('simulate_SIR_model_ode')

## ---- eval=TRUE, echo=TRUE----------------------------------------------------
result <- simulate_SIR_model_ode()

## ---- eval=TRUE, echo=TRUE----------------------------------------------------
plot(result$ts[ , "time"],result$ts[ , "S"],xlab='Time',ylab='Number Susceptible',type='l')

## ---- eval=TRUE, echo=TRUE----------------------------------------------------
result <- simulate_SIR_model_ode(S = 2000, b = 0.001, g = 0.5, tfinal = 200)
plot(result$ts[ , "time"],result$ts[ , "S"],xlab='Time',ylab='Number Susceptible',type='l')

## ---- eval=TRUE, echo=TRUE----------------------------------------------------
gvec = seq(0.01,0.3,by=0.01) #values of recovery rate, g, for which to run the simulation 
peak = rep(0,length(gvec)) #this will record the peak values for each g
for (n in 1:length(gvec))
{
  #call the simulator function with different values of g each time
  result <- simulate_SIR_model_ode(S = 500, b = 1/2500, g = gvec[n],  tfinal = 200)
  peak[n] <- max(result$ts[,"I"]) #record max number of infected for each value of g
}
#plot final result
plot(gvec,peak,type='p',xlab='Rate of recovery',ylab='Max number of infected')

## ----eval=FALSE, echo=TRUE----------------------------------------------------
#  simulate_SIR_model_ode <- function(S = 1000, I = 1, R = 0, b = 0.002, g = 1, tstart = 0, tfinal = 100, dt = 0.1)

## ----eval=FALSE, echo=TRUE, color='red'---------------------------------------
#  mysimulator <- function( S = 1000, I = 1, R = 0, b = 0.002, g = 1, w = 0, tstart = 0, tfinal = 100, dt = 0.1 )

## ----eval=FALSE, echo=TRUE----------------------------------------------------
#  parvec_mb = c(b = b, g = g)

## ----eval=FALSE, echo=TRUE, color='red'---------------------------------------
#  parvec_mb = c(b = b, g = g, w = w)

## ----eval=FALSE, echo=TRUE----------------------------------------------------
#  dS_mb = -b*S*I
#  dI_mb = b*S*I -g*I
#  dR_mb = g*I

## ----eval=FALSE, echo=TRUE, color='red'---------------------------------------
#  dS_mb = -b*S*I +w*R
#  dI_mb = b*S*I -g*I
#  dR_mb = g*I -w*R

## ----eval=TRUE, echo=TRUE-----------------------------------------------------
source('mysimulator.R') #to initialize the new function - it needs to be in same directory as this code
wvec = seq(0,1,by=0.02) #values of immunity loss rate, w, for which to run the simulation 
peak = rep(0,length(wvec)) #this will record the peak values for each g
for (n in 1:length(wvec))
{
  result <- mysimulator( S = 1000, I = 1, R = 0, b = 1e-3, g = 0.5, w = wvec[n], tstart = 0, tfinal = 300, dt = 0.1)
  peak[n] <- max(result$ts[,"I"])
}
plot(wvec,peak,type='p',xlab='Rate of waning immunity',ylab='Max number of infected')