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Built 2024-11-22 using NMsim 0.1.5.902.

A basic simulation data set

As long as a simulation data set is in a data.frame structure with columns and values compatible with the Nonmem model(s) to be simulated, it does not matter to NMsim how it was created. However, NMsim and NMdata do provide powerful methods to easily create such data sets.

As an example we create a regimen with a loading dose of 300 mg followed by 150 QD for 6 days. We dose into compartment 1, and we want to simulate samples in the second compartment. These numbers depend on the model which the data set is intended to be used with.

NMcreateDoses() is a flexible function that creates dosing records based on a concise syntax. We add a label to the regimen right away.

### multiple dose regimens with loading are easily created with NMcreateDoses too
## We use ADDL+II (either method easy)
doses <- NMcreateDoses(TIME=c(0,24),AMT=c(300,150),addl=data.frame(ADDL=c(0,5),II=c(0,24)),CMT=1)
doses <- transform(doses,trt="300 mg then 150 mg QD")
## Notice, the ID and MDV columns are included
doses
#>       ID  TIME  EVID   CMT   AMT    II  ADDL   MDV                   trt
#>    <int> <num> <num> <num> <num> <num> <num> <num>                <char>
#> 1:     1     0     1     1   300     0     0     1 300 mg then 150 mg QD
#> 2:     1    24     1     1   150    24     5     1 300 mg then 150 mg QD

Now we add the sample records using addEVID2().

## Add simulation records - longer for QD regimens
dat.sim <- addEVID2(doses,time.sim=0:(24*7),CMT=2)
#> Argument time.sim is deprecated. Use TIME instead.

dat.sim is now a valid simulation data set with one subject. However, even though addEVID2() does try to order the data in a meaningful way, it is recommended to always manually order the data set. We use data.table’s setorder(). dplyr::arrange can just as well be used. A row identifier (counter) can make post-processing easier, so we add that too.

## sort data set 
setorder(dat.sim,ID,TIME,EVID)
## Adding a row identifier (generally not necessary but recommended)
dat.sim$ROW <- 1:nrow(dat.sim)

NMsim does not include any plotting functionality, but here is a simple way to show dosing amounts and sample times. NMdata::NMexpandDoses() is used to expand the doses coded with ADDL/II in order to get a data row to plot for each dose. We also take the sum of the amounts by time point in case doses are simultaneous.

dtplot <- NMdata::NMexpandDoses(dat.sim,as.fun="data.table")
dtplot <- dtplot[,.(AMT=sum(AMT)),by=.(ID,CMT,TIME,EVID)]

ggplot(dtplot,aes(TIME,factor(CMT),colour=factor(EVID)))+
    geom_point(data=function(x)x[EVID==1],aes(size=AMT))+
    geom_point(data=function(x)x[EVID==2],shape="|")+
    labs(x="Time (hours)",y="Compartment")+
    theme(legend.position="bottom")
After using `NMexpandDoses()` the simulation data set is plottet.

After using NMexpandDoses() the simulation data set is plottet.

A brief overview of the number of events broken down by event type EVID and dose amount AMT:

trt CMT EVID AMT Nrows
300 mg then 150 mg QD 1 1 150 6
300 mg then 150 mg QD 1 1 300 1
300 mg then 150 mg QD 2 2 NA 169

Showing the top five rows for understanding what the data now looks like. Notice that the following are not issues:

  • Data contains a mix of numeric and non-numeric columns
  • Columns are not sorted in Nonmem-friendly style with non-numeric columns to the right
#>       ID  TIME  EVID   CMT   AMT    II  ADDL   MDV                   trt   ROW
#>    <int> <num> <num> <num> <num> <num> <num> <num>                <char> <int>
#> 1:     1     0     1     1   300     0     0     1 300 mg then 150 mg QD     1
#> 2:     1     0     2     2    NA    NA    NA     1 300 mg then 150 mg QD     2
#> 3:     1     1     2     2    NA    NA    NA     1 300 mg then 150 mg QD     3
#> 4:     1     2     2     2    NA    NA    NA     1 300 mg then 150 mg QD     4
#> 5:     1     3     2     2    NA    NA    NA     1 300 mg then 150 mg QD     5

Finally, We check the simulation data set for various potential issues in Nonmem data sets using NMdata::NMcheckData and summarize the number of doses and observations:

## until NMdata 0.1.7 NMcheckData requires a DV column
dat.sim[,DV:=NA_real_]
NMdata::NMcheckData(dat.sim,type.data="sim")
#> No findings. Great!

Just like for preparation of data set with observed data, time after previous dose may be the relevant time to analyze the simulation results against. We use NMdata::addTAPD() to add this automatically.

dat.sim2 <- addTAPD(dat.sim)
head(dat.sim2)
#>       ID  TIME  EVID   CMT   AMT    II  ADDL   MDV                   trt   ROW
#>    <int> <num> <num> <num> <num> <num> <num> <num>                <char> <int>
#> 1:     1     0     1     1   300     0     0     1 300 mg then 150 mg QD     1
#> 2:     1     0     2     2    NA    NA    NA     1 300 mg then 150 mg QD     2
#> 3:     1     1     2     2    NA    NA    NA     1 300 mg then 150 mg QD     3
#> 4:     1     2     2     2    NA    NA    NA     1 300 mg then 150 mg QD     4
#> 5:     1     3     2     2    NA    NA    NA     1 300 mg then 150 mg QD     5
#> 6:     1     4     2     2    NA    NA    NA     1 300 mg then 150 mg QD     6
#>       DV DOSCUMN TPDOS  TAPD PDOSAMT DOSCUMA
#>    <num>   <int> <num> <num>   <num>   <num>
#> 1:    NA       1     0     0     300     300
#> 2:    NA       0    NA    NA      NA       0
#> 3:    NA       1     0     1     300     300
#> 4:    NA       1     0     2     300     300
#> 5:    NA       1     0     3     300     300
#> 6:    NA       1     0     4     300     300

Here is something important to decide for simulations. Notice TAPD for the sample at TIME==0. addTAPD does not use the order of the data set to determine the time-order or the records. The default behavior of addTAPD is to treat a sample taken at the exact same time as a dose as a pre-dose. If instead we want them to be considered post-dose, we have to specify how to order EVID numbers.

## order.evid=c(1,2) means doses are ordered before EVID=2 records
dat.sim2 <- addTAPD(dat.sim,order.evid=c(1,2))
## now the TIME=0 sample has TAPD=0
head(dat.sim2)
#>       ID  TIME  EVID   CMT   AMT    II  ADDL   MDV                   trt   ROW
#>    <int> <num> <num> <num> <num> <num> <num> <num>                <char> <int>
#> 1:     1     0     1     1   300     0     0     1 300 mg then 150 mg QD     1
#> 2:     1     0     2     2    NA    NA    NA     1 300 mg then 150 mg QD     2
#> 3:     1     1     2     2    NA    NA    NA     1 300 mg then 150 mg QD     3
#> 4:     1     2     2     2    NA    NA    NA     1 300 mg then 150 mg QD     4
#> 5:     1     3     2     2    NA    NA    NA     1 300 mg then 150 mg QD     5
#> 6:     1     4     2     2    NA    NA    NA     1 300 mg then 150 mg QD     6
#>       DV DOSCUMN TPDOS  TAPD PDOSAMT DOSCUMA
#>    <num>   <int> <num> <num>   <num>   <num>
#> 1:    NA       1     0     0     300     300
#> 2:    NA       1     0     0     300     300
#> 3:    NA       1     0     1     300     300
#> 4:    NA       1     0     2     300     300
#> 5:    NA       1     0     3     300     300
#> 6:    NA       1     0     4     300     300

addTAPD uses NMdata::NMexpandDoses to make sure all dosing times are considered. See ?NMdata::addTAPD for what the other created columns mean and for many useful features.

Multiple endpoints (e.g. parent and metabolite)

Pass a data.frame to addEVID2’s CMT argument to include multiple endpoints.

addEVID2(doses,CMT=data.frame(CMT=c(2,3),DVID=c("Parent","Metabolite")),time.sim=1:2)
#> Argument time.sim is deprecated. Use TIME instead.
#>       ID  TIME  EVID   CMT   AMT    II  ADDL   MDV                   trt
#>    <int> <num> <num> <num> <num> <num> <num> <num>                <char>
#> 1:     1     0     1     1   300     0     0     1 300 mg then 150 mg QD
#> 2:     1     1     2     2    NA    NA    NA     1 300 mg then 150 mg QD
#> 3:     1     1     2     3    NA    NA    NA     1 300 mg then 150 mg QD
#> 4:     1     2     2     2    NA    NA    NA     1 300 mg then 150 mg QD
#> 5:     1     2     2     3    NA    NA    NA     1 300 mg then 150 mg QD
#> 6:     1    24     1     1   150    24     5     1 300 mg then 150 mg QD
#>          DVID
#>        <char>
#> 1:       <NA>
#> 2:     Parent
#> 3: Metabolite
#> 4:     Parent
#> 5: Metabolite
#> 6:       <NA>

Cohort-dependent or individual sampling schemes

Same way as for the CMT argument, time.sim can also be a data.frame. If it contains a covariate found in the doses data, the added simulation times will be merged on accordingly. You can use say a cohort identifier, or it could be ID which allows you to reuse (all or parts of) the observed sample times.

Other features

As the name implies the default of function is to use EVID=2 (which means they are neither doses, samples, nor resetting events) for these records. Should you want to change that (maybe to EVID=0), use the EVID argument.