mattfidler
commented
5 years ago Hi Arindam
Thank you for the reproducible example.
You need to change the following:
initsneed to be specified by naming the argument- You are missing the gPro differential equation in your model
Here is my R information when trying your model:
library(RxODE)
##################################################################
# model
ode <- "
Gc(0) = Gss*Vg;
Ge(0) = Gss;
Gp(0) = Gss*Vp;
Gpro(0) = Gss*(Clg + Clgi*Iss);
Gcm = (Ge/Gss)^IPRG;
Iabsg = 1 + (Emax*absg)/(absg+absg50)
Ie(0) = Iss;
I(0) = Iss*Vi;
Isec = Iss*Cli*Gcm*Iabsg;
ktr = (n+1)/mtt
d/dt(depot) = transit(n,mtt,bio)-ka*depot;
d/dt(Gc) = ka*depot + Gpro + (Q/Vp)*Gp - (Clg + Clgi*Ie + Q)*Gc/Vg;
d/dt(Gp) = Q*(Gc/Vg - Gp/Vp);
d/dt(Ge) = keog*Gc/Vg - keog*Ge;
d/dt(I) = Isec - Cli/Vi*I;
d/dt(Ie) = keoi*I/Vi - keoi*Ie
"
mod <- RxODE(model=ode, modName = "mod")
# initial conditions for ODEs
inits <- c(0,0,0,0,0,0,0)
# thetas
Params <- c(Gss=0.891, Vg=9.33, Vp=8.56, Q=0.442,
Clg=0.0287, Clgi=0.0059, Iss=0.93, Cli=1.22,
Vi=6.09, Sinc=0.001, IPRG=1.42, keog=0.0289, keoi=0.0213,
ka=0.5, mtt=34.9 , bio=0.811, n=1.27, absg50=14.8, Emax=1.47)
ev <- eventTable(amount.units = "g", time.units = "min")
ev$add.dosing(dose=75, nbr.doses=1, start.time = 0, dosing.to = 1)
ev$add.sampling(seq(0,24,1))
igi <- as.data.frame(rxSolve(mod, inits, Params, ev))
#> Events:
#> Parameters:
#> Error in rxSolve_(object, rxControl(..., events = events, params = params), : Need some event information (observation/dosing times) to solve.
#> You can use either 'eventTable' or an RxODE compatible data.frame/matrix.
###########################################################
## The issue here is the order of parameters
## You can fix it by specifying inits=inits
igi <- rxSolve(mod, inits=inits, Params, ev)
#> Error in rxSolve_(object, rxControl(..., events = events, params = params), : Length mismatch
#> req: c(depot, Gc, Gp, Ge, I, Ie)
#> vec: c(0.000000, 0.000000, 0.000000, 0.000000, 0.000000, 0.000000, 0.000000)
## But in this case you need to match the number of initial conditions
## specified by your ODE. You seem to be missing gPro
## OR you can drop the inits argument since they are all equal to zero
## Note you can solve this
igi <- rxSolve(mod, Params, ev)
#> Warning in rxSolve_(object, rxControl(..., events = events, params =
#> params), : Assumed transit compartment model since 'podo' is in the model.
#> Model:
#>
#> Gc(0)=Gss*Vg;
#> Ge(0)=Gss;
#> Gp(0)=Gss*Vp;
#> Gpro(0)=Gss*(Clg+Clgi*Iss);
#> Gcm=(Ge/Gss)^IPRG;
#> Iabsg=1+(Emax*absg)/(absg+absg50);
#> Ie(0)=Iss;
#> I(0)=Iss*Vi;
#> Isec=Iss*Cli*Gcm*Iabsg;
#> ktr=(n+1)/mtt;
#> d/dt(depot)=transit(n,mtt,bio)-ka*depot;
#> d/dt(Gc)=ka*depot+Gpro+(Q/Vp)*Gp-(Clg+Clgi*Ie+Q)*Gc/Vg;
#> d/dt(Gp)=Q*(Gc/Vg-Gp/Vp);
#> d/dt(Ge)=keog*Gc/Vg-keog*Ge;
#> d/dt(I)=Isec-Cli/Vi*I;
#> d/dt(Ie)=keoi*I/Vi-keoi*Ie;
#> Error in rxSolve_(object, rxControl(..., events = events, params = params), : The following parameter(s) are required for solving: absg, Gpro
## This shows you are missing gProCreated on 2019-03-29 by the reprex package (v0.2.1)
palar359
Hi Matt, I have started using RxODE and faced an error message, which I don't know how to turn around:
"Events: Parameters: Error in rxSolve.default(mod, inits, Params, ev) : Need some event information (observation/dosing times) to solve. You can use either 'eventTable' or an RxODE compatible data.frame/matrix."
Any help is appreciated.
Regards Arindam