[R-sig-dyn-mod] Initial value for additive events

[Daniel Kaschek]

Hi John,

you could plot log(x + offset) instead of log(x). In ggplot2 you can 
even define your own transform, e.g. based on log(x + offset) and then 
use it in analogy to the predifined scales scale_y_log10() or 
scale_y_sqrt().

Cheers,
Daniel

---------------------------------
Daniel Kaschek
Institute of Physics
Freiburg University

Room:  210
Phone: +49 761 2038531


On Sa, Apr 18, 2015 at 1:24 , John Harrold <john.m.harrold at gmail.com> 
wrote:
> Hello,
> 
> When I have an additive event that occurs at the initial sample time 
> the
> state receiving the value has a value of the specified initial 
> condition.
> For example see the code below. I understand that the initial 
> condition is
> set to zero, but I guess from my perspective adding a value at time 
> zero
> should change that initial condition. This is important for me because
> bolus injections (impulse functions) into states with a value of zero 
> is
> pretty common for my work. It makes plotting things on a log scale
> difficult when a zero value always exists. It also looks kind of 
> silly to
> have the system start at zero when the injection was supposed to 
> occur.
> 
> So my question is more about how to deal with this if my goal is to 
> remove
> this point? One option is to automatically sample at a really small 
> value
> (SV = 250*.Machine$double.eps) then set the value of the state 
> receiving
> the event at time zero to the value at time SV. It's messy but doable.
> Anyway I was wondering if there were any thoughts?
> 
> Thanks
> John
> 
> <CODE>
> rm(list=ls())
> library("deSolve")
> library("ggplot2")
> yini <- c(v1=0)
> times <-seq(0,10, by=.01)
> f1 <- function  (t, y, parms) {
>    ydot <- vector(len = 1)
>    ydot[1] <- - 0.1*y[1]
>  return(list(ydot))
> }
> eventdat <- data.frame(var    = c("v1", "v1", "v1", "v1"),
>                        time   = c(0, 1, 2, 3),
>                        value  = c(1, 1, 1, 1),
>                        method = c("add", "add", "add", "add"))
> out <- ode(func=f1,
>            y=yini,
>            times = times,
>           parms = NULL,
>           events = list(data = eventdat))
> plot(out, type="l", lwd=2)
> </CODE>
> 
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