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############################################################
##a simple model for an acute virus infection
##written by Andreas Handel (ahandel@uga.edu), last change 5/29/10
##this short program is a companion to the YaRI tutorial,
##available at http://ahandel.myweb.uga.edu/resources.htm
############################################################
rm(list=ls()) #this clears the workspace to make sure no leftover variables are floating around. Not strictly needed but often a good idea
graphics.off(); #close all graphics windows, in case there are still some open from previous stuff we did
library(deSolve) #loads ODE solver package. You need to have the package installed, for instance by going to "Packages" -> "Install Packages"
###################################################################
#first, we specify the function that describes the differential equation model for the simulated virus infection
#this function is called by lsoda (the ode solver) in the main program
###################################################################
odeequations=function(t,y,parameters) #the function needs to have a certain form, dictated by lsoda
{
Utc=y[1]; Itc=y[2]; Vir=y[3]; #uninfected target cells, infected target cells, virus
b=parameters[1]; delta=parameters[2]; p=parameters[3]; clear=parameters[4]; #four model parameters, passed into function by main program
#these are the 3 differential equations which describe an acute viral infection
#see for instance: Perelson (2002) Nature Reviews Immunology for a brief, easy introduction to such models
dUtcdt=-b*Vir*Utc;
dItcdt=b*Vir*Utc-delta*Itc;
dVirdt=p*Itc-clear*Vir;
return(list(c(dUtcdt,dItcdt,dVirdt))); #this command returns the result, which is the right side of the ODEs as a list, back to the solver (i.e. lsoda).
} #end function specifying the ODEs
###################################################################
#main program
###################################################################
timevec=seq(0,10,by=0.1); #this creates a vector of times for which integration is evaluated (from 0 to 10 days in steps of 0.1)
#assign numerical values to the parameters and initial conditions of the model
#initial conditions
Utc0=1e8; #initial number of uninfected cells
Itc0=0; #initial number of infected cells
Vir0=10; #initial condition for free virus V
Y0=c(Utc0, Itc0, Vir0); #combine initial conditions into a vector
#values for model parameters, units are assumed to be 1/days
b=1e-8; #rate at which virus infects uninfected cells
delta=2; #rate at which infected cells die
p=1e2; #rate at which infected cells produce new virus
clear=10; #rate at which free virus is cleared
#Note: we don't call the parameter "c" since c is a reserved function in R that creates vectors (see next line for a use of it)
#always make sure that your variable names do not clash with built-in definitions, or you might get unpredictable results
parvec=c(b,delta,p,clear); #this combines all parameters into a vector called parvec which is sent to the ODE function
#call ode-solver to integrate ODEs. this solver is part of the deSolve package.
#It starts the simulation with initial conditions Y0, integrates and returns values for the time and the different variables (here: uninfected cells, infected cells, virus)
#the function odeequations specifies the actual set of differential equations describing our model - see below.
#parvec is the vector of parameters we created above. It is sent into the function odeequations and used there - see below
odeoutput=lsoda(Y0,timevec,odeequations,parvec);
#plot results
#odeoutput, which is returned from calling lsoda, contains a matrix with rows that contain values for a given time, and columns with the 1st column being the time and the remaining columns the variables
#here, column 2 is uninfected cells, column 3 contains infected cell counts, and column 4 contains the virus load
plot(odeoutput[,1],odeoutput[,2],type="l",xlab="time (days)",ylab="",col="green",lwd=2,log="y",xlim=c(0,10),ylim=c(100,1e9))
lines(odeoutput[,1],odeoutput[,3],type="l",col="red",lwd=2)
lines(odeoutput[,1],odeoutput[,4],type="l",col="blue",lwd=2)
legend(7,1e8, c("Uninfected cells","Infected cells","Virus"),col = c("green","red","blue"),lwd=2)
###################################################################
#end main program
###################################################################
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