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Simulate with modified parameter values

Source: vignettes/NMsim-varyPars.Rmd
NMsim-varyPars.Rmd

Built 2024-05-19 using NMsim 0.1.0.911.

Objectives

This vignettes aims at enabling you to use NMsim for the following purposes

  • Simulation with parameters modified from the estimated values

Vary parameter values

Sometimes we want to simulate with some modification to the estimated model. NMsim can make such user-specified modifications to the model before simulating through the list.sections argument.

The SAD study was run with a fast solution formulation. We want to see how a slower absorption rate would affect the PK prediction for the multiple dose regimen. In the model estimate, TVKA=2.17. We now try with a four times slower absorption:

simres <- NMsim(file.mod=file.mod
               ,data=dat.sim
               ,dir.sims="~/NMsim_vignette" ## where to store simulation files
               ,seed=12345
                )

simres.slowabs <- NMsim(file.mod=file.mod,
                        data=dat.sim
                       ,dir.sims="~/NMsim_vignette" ## where to store simulation files
                       ,name.sim="slower_abs"
                       ,seed=12345
                       ,list.sections=list(PK=function(x)c(x,"TVKA=TVKA/4","KA=KA/4"))
                        )
rbind(simres,simres.slowabs) |>
    ggplot(aes(TIME,PRED,colour=model))+
    geom_line()

We used list.sections to modify the $PK section. We used it to append two lines. We could use it to modify any section in the model, and we could essentially do any modification. However, appending to $PK or $PRED is simple and often both robust and flexible enough.

That was a very spcific analysis of one specific KA value. It is often more convenient to control the numeric changes to the model using the simulation input data set rather than hard-coding numerical values into list.sections. The following tries a number of fold changes to KA.

NMdataConf(as.fun="data.table")
dat.sim.varka <- egdt(dat.sim,data.table(KASCALE=c(1,4,10)))
dat.sim.varka[,ID:=.GRP,by=.(KASCALE,ID)]
setorder(dat.sim.varka,ID,TIME,EVID)

simres.varka <- NMsim(file.mod=file.mod,
                      data=dat.sim.varka
                     ,dir.sims="~/NMsim_vignette" ## where to store simulation files
                     ,name.sim="varka"
                     ,seed=12345
                     ,list.sections=list(PK=function(x)c(x,"TVKA=TVKA/KASCALE","KA=KA/KASCALE"))
                      )
ggplot(simres.varka[simres.varka$EVID==2,],aes(TIME,PRED,colour=factor(KASCALE)))+
geom_line()+
labs(colour="Fold absorption prolongation")