Description Usage Format Note Author(s) References See Also Examples
Model describing Iron (Fe) in St. Kevin Gulch, a 1904 m long headwater stream in the Rocky Mountains. In a certain stretch, this stream receives metal-rich waters from a large mine dump, and at a constant rate.
Originally implemented in the OTIS modelling framework (Runkel, 1989) (application 6)
The model describes Fe in a free-flowing zone and in a stagnant zone.
The stream is subdivided into seven segments with different cross-sectional areas, storage zone areas and exchange parameters.
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An S4 object according to the odeModel
specification.
The object contains the following slots:
main
Model specifications.
parms
Vector with the named parameters of the model -
see code
times
Simulation time and integration interval.
init
Vector with start values for the
state variables.
The model is solved using steady-state solver steady.1D
from package rootSolve
.
The original parameter settings from the OTIS application are used, except for lambda, which has been fitted to the data.
Karline Soetaert
Runkel, R.L., 1998. One-dimensional transport with inflow and storage (OTIS): a solute transport model for streams and rivers. US geological Survey. Water-Resources Investigations Report 98-4018. Denver, Colorado.
R-package simecol
for a description of the
simObj
class
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#----------------------#
# Create Instance #
#----------------------#
# Note: lower case letter of the instance and capital letter of the constructor
streamIron <- StreamIron()
# show model code, parameter settings,...
print(streamIron)
#----------------------#
# RUNNING the model: #
#----------------------#
# run simulation
outp <- out(sim(streamIron))
#------------------------#
# PLOTTING model output: #
#------------------------#
Data <- data.frame(Dist = c(
26 ,363 ,413 ,421 ,439 ,455 ,464 ,484 ,526 ,586 ,641 ,701 ,754 ,781 ,881 ,
948 ,1068,1265,1308,1421,1497,1557,1677,1767,1776,1804 ),
Fe = c(
0.64, 0.63, 1.5 , 2.5 , 5.6 , 12 , 12 , 13 , 5.0 , 4.4 , 4.2 , 3.9 , 3.8 ,
3.4 , 2.9 , 1.4 , 2.5 , 1.7 , 1.8 , 1.7 , 1.6 , 1.3 , 1.3 , 1.2 , 1.4 , 1.4 )
)
# Plot Fe concentration
Dist <- inputs(streamIron)$boxes$x
plot(Dist,outp[,"Fe"],xlab="Distance, m", ylab="Fe conc",type="l",
ylim=c(0,13),main="St. Kevin Gulch")
points(Data,pch=15,cex=1.5)
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