# NOT RUN {
## =============================================================================
## FORCING FUNCTION: The sediment oxygen consumption example - R-code:
## =============================================================================
## Forcing function data
Flux <- matrix(ncol=2,byrow=TRUE,data=c(
1, 0.654, 11, 0.167, 21, 0.060, 41, 0.070, 73,0.277, 83,0.186,
93,0.140,103, 0.255, 113, 0.231,123, 0.309,133,1.127,143,1.923,
153,1.091,163,1.001, 173, 1.691,183, 1.404,194,1.226,204,0.767,
214, 0.893,224,0.737, 234,0.772,244, 0.726,254,0.624,264,0.439,
274,0.168,284 ,0.280, 294,0.202,304, 0.193,315,0.286,325,0.599,
335, 1.889,345, 0.996,355,0.681,365,1.135))
parms <- c(k=0.01)
times <- 1:365
## the model
sediment <- function( t, O2, k)
list (c(Depo(t) - k * O2), depo = Depo(t))
# the forcing functions; rule = 2 avoids NaNs in interpolation
Depo <- approxfun(x = Flux[,1], y = Flux[,2], method = "linear", rule = 2)
Out <- ode(times = times, func = sediment, y = c(O2 = 63), parms = parms)
## same forcing functions, now constant interpolation
Depo <- approxfun(x = Flux[,1], y = Flux[,2], method = "constant",
f = 0.5, rule = 2)
Out2 <- ode(times = times, func = sediment, y = c(O2 = 63), parms = parms)
mf <- par(mfrow = c(2, 1))
plot (Out, which = "depo", type = "l", lwd = 2, mfrow = NULL)
lines(Out2[,"time"], Out2[,"depo"], col = "red", lwd = 2)
plot (Out, which = "O2", type = "l", lwd = 2, mfrow = NULL)
lines(Out2[,"time"], Out2[,"O2"], col = "red", lwd = 2)
## =============================================================================
## SCOC is the same model, as implemented in FORTRAN
## =============================================================================
out<- SCOC(times, parms = parms, Flux = Flux)
plot(out[,"time"], out[,"Depo"], type = "l", col = "red")
lines(out[,"time"], out[,"Mineralisation"], col = "blue")
## Constant interpolation of forcing function - left side of interval
fcontrol <- list(method = "constant")
out2 <- SCOC(times, parms = parms, Flux = Flux, fcontrol = fcontrol)
plot(out2[,"time"], out2[,"Depo"], type = "l", col = "red")
lines(out2[,"time"], out2[,"Mineralisation"], col = "blue")
# }
# NOT RUN {
## =============================================================================
## show examples (see respective help pages for details)
## =============================================================================
example(aquaphy)
## show package vignette with tutorial about how to use compiled models
## + source code of the vignette
## + directory with C and FORTRAN sources
vignette("compiledCode")
edit(vignette("compiledCode"))
browseURL(paste(system.file(package = "deSolve"), "/doc", sep = ""))
# }
# NOT RUN {
# }
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