run.streambugs: Run the streambugs ODE model

In streambugs: Parametric Ordinary Differential Equations Model of Growth, Death, and Respiration of Macroinvertebrate and Algae Taxa

Run the streambugs ODE model

Description

Numerically solve streambugs ODE model (in either R or C version) for given parameters, inputs and time points, using the ode routine.

Usage

run.streambugs(
  y.names,
  times,
  par,
  inp = NA,
  C = FALSE,
  file.def = NA,
  file.res = NA,
  file.add = NA,
  return.res.add = FALSE,
  tout.add = NA,
  verbose = TRUE,
  method = "lsoda",
  rtol = 1e-04,
  atol = 1e-04,
  ...
)

Arguments

y.names	state variables names, either as a vector encoded in the form "Reach_Habitat_Taxon" or "Reach_Habitat_Taxon_Group", or a list as returned by decode.statevarnames function
times	vector with time points for which output is wanted; the first
par	vector with constant parameters and model inputs
inp	list with time-dependent parameters or model inputs with one list element for each parameter or input that includes a matrix where first column is the time and second the corresponding parameter or input value
C	identifier for C- or R-Version
file.def	file name for writing system definition
file.res	file name for results
file.add	file name for additional output (e.g. process rates)
return.res.add	returns res.add output additionally to res
tout.add	optional identifier for specific output times for the additional output, if NA all res.add is calculated for all times
verbose	prints some outputs to console
method	method used by ode
rtol	argument of ode function defining relative error tolerance, either a scalar or an array of the same size as y.names
atol	argument of ode function defining absolute error, either a scalar or an array of the same size as y.names
...	further arguments passed to ode

Value

A list with:

$res

matrix of class streambugs with up to as many rows aselements in times and as many columns as elements in y.names, plus an additional column for the time value. There will be a row for each element in times unless the FORTRAN routine "lsoda" returns with an unrecoverable error.

$res.add

optional additional output matrix with process rates and taxon specific factors, present only if return.res.add input parameter is set to TRUE.

Model syntax

See "docs/Streambugs_syntax.pdf" file in the package installation folder: system.file("docs", "Streambugs_syntax.pdf", package="streambugs").

Examples

m <- streambugs.example.model.toy()
# Display inputs: list of perturbed variables with time points and new values
m$inp
# Simluate
res.C.default <- run.streambugs(y.names = m$y.names, times = m$times,
   par = m$par, inp = m$inp, C = TRUE)
# Modify input (halve second perturbation size) and re-simulate
m$inp$Reach3_w[2,2] <- m$inp$Reach3_w[2,2] / 2
m$inp
res.C.modified <- run.streambugs(y.names = m$y.names, times = m$times,
   par = m$par, inp = m$inp, C = TRUE)
# Compare examplary trajectory of organic matter in one of the habitats
var.name <- "Reach3_Hab1_POM1_POM"
plot(m$times,res.C.default$res[, var.name], type="l", col="red")
lines(m$times, res.C.modified$res[, var.name], col="green")

streambugs documentation built on Feb. 16, 2023, 9:48 p.m.