deSolve (version 1.7)

events: Implementing events in differential equation models.

Description

An event occurs when the value of a state variable is suddenly changed, e.g. because a value is added, subtracted, or multiplied. The integration routines cannot deal easily with such state variable changes. Typically these events occur only at specific times. In deSolve, events can be imposed by means of an input data.frame, that specifies at which time a certain state variable is altered, or via an event function.

code

events$time

link

lsodar

R

-function, must be defined as: function(t, y, parms,...). t is the current time point in the integration, y is the current estimate of the variables in the ODE system. If the initial values y has a names attribute, the names will be available inside events$func. parms is a vector or list of parameters; ... (optional) are any other arguments passed to the function. The function should return the modified y-values, as a vector. If events$func is a string, this indicates that the events are specified by a function in compiled code. This function has as arguments, the number of state variables, the time, and the state variable vector. See package vignette "compiledCode" for more details.

In addition, either the time at which the events take place should be specified as a vector (event$time). When the model is solved with lsodar, or with lsode, an event can also be triggered by a root function, as specified with argument rootfunc. In this case, the integrator is informed that the simulation it to be continued after a root is found by setting events$root equal to TRUE. See two last examples; also see example of ccl4model. If specified by a data.frame (argument events$data), this should contain the following columns (and in that order):

1. var

{the state variable name or number that is affected by the event} time{the time at which the event is to take place; the solvers will check if the time is embraced by the simulation time} value{the value, magnitude of the event} method{which event is to take place; should be one of ("replace", "add", "multiply"); also allowed is to specify the number (1=replace, 2=add, 3=multiply) }

Details

The events are specified by means of argument events passed to the integration routines. events should be a list that contains one of the following:

1. func:

{an R-function or the name of a function in compiled code that specifies the event,} data:{a data.frame that specifies the variables, times, values and types of the events,} time:{when events are specified by a function: the times at which the events take place,} root:{when events are specified by a function and triggered by a root, this logical should be set equal to TRUE,} ties:{if events, as specified by a data.frame are "ordered", set to "ordered", the default is "notordered". This will save some computational time.}

See Also

forcings, for how to implement forcing functions.

Examples

## =============================================================================
## EVENTS in a data.frame
## =============================================================================

# model: rate of change set to 0
eventmod <- function(t,var,parms) {
  list(dvar = rep(0,2))
}

yini <- c(v1 = 1, v2 = 2)
times <- seq(0,10, by=0.1)

#
eventdat <- data.frame(var = c("v1", "v2", "v2", "v1"), time = c(1,1,5,9) ,
  value = c(1,2,3,4), method =c("add", "mult","rep","add"))

eventdat
  
out <- vode(func=eventmod, y=yini, times=times, parms=NULL, 
  events=list(data=eventdat))
plot(out,type="l")

#
eventdat <- data.frame(var = c(rep("v1",10),rep( "v2", 10)), 
  time = c(1:10,1:10), value = runif(20), method =rep("add", 20))

eventdat
out <- ode(func=eventmod, y=yini, times=times, parms=NULL, 
  events=list(data=eventdat))

plot(out,type="l")

## =============================================================================
## EVENTS in a function
## =============================================================================

# model: rate of change v1 = 0, v2 consumed at first-order rate
eventmod <- function(t,var,parms) {
   list(c(0,-0.5*var[2]))
}


# events: add 1 to v1,multiply v2 with 0.8
eventfun <- function(t,y,parms){
  with (as.list(y),{
    v1 <- v1+1
    v2 <- 5*runif(1)
    return(c(v1,v2))
  })
}

yini <- c(v1 = 1, v2 = 2)
times <- seq(0,10, by=0.1)

out <- ode(func=eventmod, y=yini, times=times, parms=NULL, 
  events=list(func=eventfun, time=1:9) )
plot(out,type="l")

## =============================================================================
## EVENTS triggered by a root function
## =============================================================================

# derivative: simple first-order decay
func <- function(t, y, pars) {
  return(list(-0.1*y))
}

# event triggered if state variable =0.5
rootfun <- function (t, y, pars) {
  return(y-0.5)
}

# sets state vaiable = 1                                                  
eventfun <- function(t, y, pars) {
  return(y=1)
}

yini <- 2

times <- seq(0,100,0.1)

# uses lsodar to solve; root =TRUE specifies that the event is triggered by 
# a root.
out <- lsodar(times=times, y=yini, func = func, parms=NULL,
  events=list(func = eventfun, root = TRUE),  
  rootfun = rootfun)

plot(out,type="l")