chemostat {simecol} | R Documentation |
simecol example: Model of continuos culture of microorganisms (chemostat).
data(chemostat)
An S4 object according to the odeModel
specification.
The object contains the following slots:
main
the differential equations for substrate (S
)
and cells (X
).
parms
a vector with the named parameters of the model:
vm
maximum growth rate of the cells,
km
half saturation constant,
Y
yield coefficient (conversion factor of substrate into cells).
D
dilution rate,
S0
substrate concentration in the inflow.
times
simulation time and integration interval.
init
vector with start values for substrate (S
)
and cells (X
).
To see all details, please have a look into the implementation below.
simecol-package
,
sim
,
parms
,
init
,
times
.
##============================================ ## Basic Usage: ## work with the example ##============================================ data(chemostat) plot(sim(chemostat)) parms(chemostat)["D"] <- 0.9 plot(sim(chemostat)) ##============================================ ## Implementation: ## The code of the chemostat model ##============================================ chemostat <- new("odeModel", main = function(time, init, parms, inputs = NULL) { with(as.list(c(init, parms)), { mu <- vm * S/(km + S) # Monod equation dx1 <- mu * X - D * X # cells, e.g. algae dx2 <- D *(S0 - S) - 1/Y * mu * X # substrate, e.g. phosphorus list(c(dx1, dx2)) }) }, parms = c( vm = 1.0, # max growth rate, 1/d km = 2.0, # half saturation constant, mumol / L Y = 100, # cells /mumol Substrate D = 0.5, # dilution rate, 1/d S0 = 10 # substrate in inflow, mumol / L ), times = c(from=0, to=40, by=.5), init = c(X=10, S=10), # cells / L; Substrate umol / L solver = "lsoda" )