| ThreepairMMmodel {SoilR} | R Documentation |
This function implements a 6-pool Michaelis-Meneten model with pairs of microbial biomass and substrate pools.
ThreepairMMmodel(t, ks, kb, Km, r, Af = 1, ADD, ival)
t |
vector of times to calculate a solution. |
ks |
a vector of length 3 representing SOM decomposition rate (m3 d-1 (gCB)-1) |
kb |
a vector of length 3 representing microbial decay rate (d-1) |
Km |
a vector of length 3 representing the Michaelis constant (g m-3) |
r |
a vector of length 3 representing the respired carbon fraction (unitless) |
Af |
a scalar representing the Activity factor; i.e. a temperature and moisture modifier (unitless) |
ADD |
a vector of length 3 representing the annual C input to the soil (g m-3 d-1) |
ival |
a vector of length 6 with the initial values of the SOM pools and the microbial biomass pools (g m-3) |
An object of class NlModel that can be further queried.
There are other predefinedModels and also more
general functions like Model.
days=seq(0,1000)
#Run the model with default parameter values
MMmodel=ThreepairMMmodel(t=days,ival=rep(c(100,10),3),ks=c(0.1,0.05,0.01),
kb=c(0.005,0.001,0.0005),Km=c(100,150,200),r=c(0.9,0.9,0.9),
ADD=c(3,1,0.5))
Cpools=getC(MMmodel)
#Time solution
matplot(days,Cpools,type="l",ylab="Concentrations",xlab="Days",lty=rep(1:2,3),
ylim=c(0,max(Cpools)*1.2),col=rep(1:3,each=2),
main="Multi-substrate microbial model")
legend("topright",c("Substrate 1", "Microbial biomass 1",
"Substrate 2", "Microbial biomass 2",
"Substrate 3", "Microbial biomass 3"),
lty=rep(1:2,3),col=rep(1:3,each=2),
bty="n")
#State-space diagram
plot(Cpools[,2],Cpools[,1],type="l",ylab="Substrate",xlab="Microbial biomass")
lines(Cpools[,4],Cpools[,3],col=2)
lines(Cpools[,6],Cpools[,5],col=3)
legend("topright",c("Substrate-Enzyme pair 1","Substrate-Enzyme pair 2",
"Substrate-Enzyme pair 3"),col=1:3,lty=1,bty="n")
#Microbial biomass over time
plot(days,Cpools[,2],type="l",col=2,xlab="Days",ylab="Microbial biomass")