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
S
)
and cells (X
).
parms
vm
km
Y
D
S0
times
init
S
)
and cells (X
).
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) { vm <- parms["vm"] # max growth rate km <- parms["km"] # half saturation constant D <- parms["D"] # dilution rate S0 <- parms["S0"] # substrate in inflow Y <- parms["Y"] # yield coefficient for substrate X <- init[1] # cells (e.g. algae) S <- init[2] # substrate (e.g. phosphorus) mu <- vm * S/(km + S) # Monod equation dx1 <- mu * X - D * X # cells dx2 <- D *(S0 - S) - 1/Y * mu * X # substrate list(c(dx1, dx2)) }, parms = c( vm = 1.0, # 1/d km = 2.0, # mumol Substrate/l Y = 100, # cells /mumol Substrate D = 0.5, # 1/d S0 = 10 # mumol Substrate/l ), times = c(from=0, to=40, by=.5), init = c(X=10, S=10), # cells/l; umol Substrate/l solver = "lsoda" )