# NOT RUN {
## =======================================================================
## Example 1:
## A simple resource limited Lotka-Volterra-Model
##
## Note:
## 1. parameter and state variable names made
## accessible via "with" function
## 2. function sigimp accessible through lexical scoping
## (see also ode and rk examples)
## =======================================================================
SPCmod <- function(t, x, parms) {
with(as.list(c(parms, x)), {
import <- sigimp(t)
dS <- import - b*S*P + g*C #substrate
dP <- c*S*P - d*C*P #producer
dC <- e*P*C - f*C #consumer
res <- c(dS, dP, dC)
list(res)
})
}
## Parameters
parms <- c(b = 0.0, c = 0.1, d = 0.1, e = 0.1, f = 0.1, g = 0.0)
## vector of timesteps
times <- seq(0, 100, length = 101)
## external signal with rectangle impulse
signal <- as.data.frame(list(times = times,
import = rep(0,length(times))))
signal$import[signal$times >= 10 & signal$times <= 11] <- 0.2
sigimp <- approxfun(signal$times, signal$import, rule = 2)
## Start values for steady state
y <- xstart <- c(S = 1, P = 1, C = 1)
## Solving
out <- lsoda(xstart, times, SPCmod, parms)
## Plotting
mf <- par("mfrow")
plot(out, main = c("substrate", "producer", "consumer"))
plot(out[,"P"], out[,"C"], type = "l", xlab = "producer", ylab = "consumer")
par(mfrow = mf)
## =======================================================================
## Example 2:
## from lsoda source code
## =======================================================================
## names makes this easier to read, but may slow down execution.
parms <- c(k1 = 0.04, k2 = 1e4, k3 = 3e7)
my.atol <- c(1e-6, 1e-10, 1e-6)
times <- c(0,4 * 10^(-1:10))
lsexamp <- function(t, y, p) {
yd1 <- -p["k1"] * y[1] + p["k2"] * y[2]*y[3]
yd3 <- p["k3"] * y[2]^2
list(c(yd1, -yd1-yd3, yd3), c(massbalance = sum(y)))
}
exampjac <- function(t, y, p) {
matrix(c(-p["k1"], p["k1"], 0,
p["k2"]*y[3],
- p["k2"]*y[3] - 2*p["k3"]*y[2],
2*p["k3"]*y[2],
p["k2"]*y[2], -p["k2"]*y[2], 0
), 3, 3)
}
## measure speed (here and below)
system.time(
out <- lsoda(c(1, 0, 0), times, lsexamp, parms, rtol = 1e-4,
atol = my.atol, hmax = Inf)
)
out
## This is what the authors of lsoda got for the example:
## the output of this program (on a cdc-7600 in single precision)
## is as follows..
##
## at t = 4.0000e-01 y = 9.851712e-01 3.386380e-05 1.479493e-02
## at t = 4.0000e+00 y = 9.055333e-01 2.240655e-05 9.444430e-02
## at t = 4.0000e+01 y = 7.158403e-01 9.186334e-06 2.841505e-01
## at t = 4.0000e+02 y = 4.505250e-01 3.222964e-06 5.494717e-01
## at t = 4.0000e+03 y = 1.831975e-01 8.941774e-07 8.168016e-01
## at t = 4.0000e+04 y = 3.898730e-02 1.621940e-07 9.610125e-01
## at t = 4.0000e+05 y = 4.936363e-03 1.984221e-08 9.950636e-01
## at t = 4.0000e+06 y = 5.161831e-04 2.065786e-09 9.994838e-01
## at t = 4.0000e+07 y = 5.179817e-05 2.072032e-10 9.999482e-01
## at t = 4.0000e+08 y = 5.283401e-06 2.113371e-11 9.999947e-01
## at t = 4.0000e+09 y = 4.659031e-07 1.863613e-12 9.999995e-01
## at t = 4.0000e+10 y = 1.404280e-08 5.617126e-14 1.000000e+00
## Using the analytic Jacobian speeds up execution a little :
system.time(
outJ <- lsoda(c(1, 0, 0), times, lsexamp, parms, rtol = 1e-4,
atol = my.atol, jacfunc = exampjac, jactype = "fullusr", hmax = Inf)
)
all.equal(as.data.frame(out), as.data.frame(outJ)) # TRUE
diagnostics(out)
diagnostics(outJ) # shows what lsoda did internally
# }
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