Description Details Note Author(s) See Also Examples

A `forcing function`

is an external variable that is essential to the
model, but not explicitly modeled. Rather, it is imposed as a time-series.
Thus, if a model uses forcing variables, their value at each time point
needs to be estimated by interpolation of a data series.

The `forcing functions`

are imposed as a data series, that contains
the values of the forcings at specified times.

Models may be defined in compiled C or FORTRAN code, as well as in R.

If the model is defined in *R code*, it is most efficient to:

1. define a function that performs the linear interpolation,
using **R**'s `approxfun`

. It is generally recommended to use
`rule = 2`

, such as to allow extrapolation outside of the time interval,
especially when using the Livermore solvers, as these may exceed the last
time point.

2. call this function within the model's derivative function, to interpolate at the current timestep.

See first example.

If the models are defined in *compiled C or FORTRAN code*, it is possible to
use `deSolve`

s forcing function update algorithm. This is the
compiled-code equivalent of `approxfun`

or `approx`

.

In this case:

1. the forcing function data series is provided by means
of argument `forcings`

,

2. `initforc`

is the name of the forcing function initialisation function,
as provided in ‘dllname’, while

3. `fcontrol`

is a list used to finetune how the forcing update should
be performed.

The **fcontrol** argument is a list that can supply any of the following
components (conform the definitions in the approxfun function):

- method
specifies the interpolation method to be used. Choices are

`"linear"`

or`"constant"`

,- rule
an integer describing how interpolation is to take place outside the interval [min(times), max(times)]. If

`rule`

is`1`

then an error will be triggered and the calculation will stop if`times`

extends the interval of the forcing function data set. If it is`2`

, the**default**, the value at the closest data extreme is used, a warning will be printed if`verbose`

is`TRUE`

,Note that the default differs from the

`approx`

default.- f
For

`method = "constant"`

a number between`0`

and`1`

inclusive, indicating a compromise between left- and right-continuous step functions. If`y0`

and`y1`

are the values to the left and right of the point then the value is`y0 * (1 - f) + y1 * f`

so that`f = 0`

is right-continuous and`f = 1`

is left-continuous,- ties
Handling of tied

`times`

values. Either a function with a single vector argument returning a single number result or the string`"ordered"`

.Note that the default is

`"ordered"`

, hence the existence of ties will NOT be investigated; in the`C`

code this will mean that -if ties exist, the first value will be used; if the dataset is not ordered, then nonsense will be produced.Alternative values for

`ties`

are`mean`

,`min`

etc

The defaults are:

`fcontrol = list(method = "linear", rule = 2, f = 0, ties = "ordered")`

Note that only ONE specification is allowed, even if there is more than one forcing function data set.

More information about models defined in compiled code is in the package vignette ("compiledCode").

How to write compiled code is described in package vignette
`"compiledCode"`

, which should be referred to for details.

This vignette also contains examples on how to pass forcing functions.

Karline Soetaert,

Thomas Petzoldt,

R. Woodrow Setzer

`approx`

or `approxfun`

, the **R** function,

`events`

for how to implement events.

1 2 3 4 5 6 7 8 9 10 11 12 13 14 15 16 17 18 19 20 21 22 23 24 25 26 27 28 29 30 31 32 33 34 35 36 37 38 39 40 41 42 43 44 45 46 47 48 49 50 51 52 53 54 55 56 57 58 59 60 61 62 63 64 65 66 67 68 69 70 71 72 | ```
## =============================================================================
## 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 = ""))
## End(Not run)
``` |

deSolve documentation built on May 10, 2018, 3 p.m.

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