```
$PROB
# Final PK model
- Author: Pmetrics Scientist
- Client: Pharmaco, Inc.
- Date: `r Sys.Date()`
- NONMEM Run: 12345
- Structure: one compartment, first order absorption
- Implementation: closed form solutions
- Error model: Additive + proportional
- Covariates:
- WT on clearance
- SEX on volume
- Random effects on: `CL`, `V`, `KA`
```

# 11 Topics

## 11.1 Annotated model specification

Here is a complete annotated `mrgsolve`

model. The goal was to get in several of the most common blocks that you might want to annotate. The different code blocks are rendered here separately for clarity in presentation; but users should include all relevant blocks in a single file (or R string).

```
@annotated
[PARAM] : 1.1 : Clearance (L/hr)
TVCL : 35.6 : Volume of distribution (L)
TVV : 1.35 : Absorption rate constant (1/hr)
TVKA : 70 : Weight (kg)
WT : 1 : Male = 0, Female 1
SEX : 0.75 : Exponent weight on CL
WTCL : 0.878 : Volume female/Volume male SEXV
```

```
[MAIN]= TVCL*pow(WT/70,WTCL)*exp(ECL);
double CL = TVV *pow(SEXVC,SEX)*exp(EV);
double V = TVKA*exp(EKA); double KA
```

```
@name OMGA @correlation @block @annotated
[OMEGA] : 1.23 : Random effect on CL
ECL : 0.67 0.4 : Random effect on V
EV : 0.25 0.87 0.2 : Random effect on KA EKA
```

```
@name SGMA @annotated
[SIGMA] : 0.25 : Proportional residual error
PROP: 25 : Additive residual error ADD
```

```
@annotated
[CMT] : Dosing compartment (mg)
GUT : Central compartment (mg) CENT
```

`= 1, depot=TRUE [PKMODEL] ncmt `

```
[TABLE]= CENT/V;
capture IPRED = IPRED*(1+PROP) + ADD; double DV
```

```
@annotated
[CAPTURE] : Concentration (mg/L)
DV : Random effect on CL
ECL : Individual clearance (L/hr) CL
```

## 11.2 Set initial conditions

```
library(mrgsolve)
library(dplyr)
```

### 11.2.1 Summary

`mrgsolve`

keeps a base list of compartments and initial conditions that you can update**either**from`R`

or from inside the model specification- When you use
`$CMT`

, the value in that base list is assumed to be 0 for every compartment `mrgsolve`

will by default use the values in that base list when starting the problem- When only the base list is available, every individual will get the same initial condition
- You can
**override**this base list by including code in`$MAIN`

to set the initial condition - Most often, you do this so that the initial is calculated as a function of a parameter
- For example,
`$MAIN RESP_0 = KIN/KOUT;`

when`KIN`

and`KOUT`

have some value in`$PARAM`

- This code in
`$MAIN`

overwrites the value in the base list for the current`ID`

- For typical PK/PD type models, we most frequently initialize in
`$MAIN`

- This is equivalent to what you might do in your NONMEM model
- For larger systems models, we often just set the initial value via the base list

### 11.2.2 Make a model only to examine `init`

behavior

Note: `IFLAG`

is my invention only for this demo. The demo is always responsible for setting and interpreting the value (it is not reserved in any way and `mrgsolve`

does not control the value).

For this demo

- Compartment
`A`

initial condition defaults to 0 - Compartment
`A`

initial condition will get set to`BASE`

**only**if`IFLAG > 0`

- Compartment
`A`

always stays at the initial condition

```
<- '
code $PARAM BASE=100, IFLAG = 0
$CMT A
$MAIN
if(IFLAG > 0) A_0 = BASE;
$ODE dxdt_A = 0;
'
```

`<- mcode("init",code) mod `

**Check the initial condition**

`init(mod)`

```
.
. Model initial conditions (N=1):
. name value . name value
. A (1) 0 | . ... .
```

Note:

- We used
`$CMT`

in the model spec; that implies that the base initial condition for`A`

is set to 0 - In this chunk, the code in
`$MAIN`

doesn’t get run because`IFLAG`

is 0 - So, if we don’t update something in
`$MAIN`

the initial condition is as we set it in the base list

`%>% mrgsim() %>% plot() mod `

**Next, we update the base initial condition for A to 50**

Note:

- The code in
`$MAIN`

still doesn’t get run because`IFLAG`

is 0

`%>% init(A = 50) %>% mrgsim() %>% plot() mod `

**Now, turn on IFLAG**

Note:

- Now, that code in
`$MAIN`

gets run `A_0`

is set to the value of`BASE`

`%>% param(IFLAG=1) %>% mrgsim() %>% plot() mod `

`%>% param(IFLAG=1, BASE=300) %>% mrgsim() %>% plot() mod `

### 11.2.3 Example PK/PD model with initial condition

Just to be clear, there is no need to set any sort of flag to set the initial condition as seen here:

```
<- '
code $PARAM AUC=0, AUC50 = 75, KIN=200, KOUT=5
$CMT RESP
$MAIN
RESP_0 = KIN/KOUT;
$ODE
dxdt_RESP = KIN*(1-AUC/(AUC50+AUC)) - KOUT*RESP;
'
```

`<- mcode("init2", code) mod `

The initial condition is set to 40 per the values of `KIN`

and `KOUT`

`%>% mrgsim() %>% plot() mod `

Even when we change `RESP_0`

in `R`

, the calculation in `$MAIN`

gets the final say

`%>% init(RESP=1E9) %>% mrgsim() mod `

```
. Model: init2
. Dim: 25 x 3
. Time: 0 to 24
. ID: 1
. ID time RESP
. 1: 1 0 40
. 2: 1 1 40
. 3: 1 2 40
. 4: 1 3 40
. 5: 1 4 40
. 6: 1 5 40
. 7: 1 6 40
. 8: 1 7 40
```

### 11.2.4 Remember: calling `init`

will let you check to see what is going on

- It’s a good idea to get in the habit of doing this when things aren’t clear
`init`

first takes the base initial condition list, then calls`$MAIN`

and does any calculation you have in there; so the result is the calculated initials

`init(mod)`

```
.
. Model initial conditions (N=1):
. name value . name value
. RESP (1) 40 | . ... .
```

`%>% param(KIN=100) %>% init() mod `

```
.
. Model initial conditions (N=1):
. name value . name value
. RESP (1) 20 | . ... .
```

### 11.2.5 Set initial conditions via `idata`

Go back to house model

`<- house() mod `

`init(mod)`

```
.
. Model initial conditions (N=3):
. name value . name value
. CENT (2) 0 | RESP (3) 50
. GUT (1) 0 | . ... .
```

Notes

- In
`idata`

(only), include a column with`CMT_0`

(like you’d do in`$MAIN`

). - When each ID is simulated, the
`idata`

value will override the base initial list for that subject. - But note that if
`CMT_0`

is set in`$MAIN`

, that will override the`idata`

update.

`<- expand.idata(CENT_0 = seq(0,25,1)) idata `

`%>% head() idata `

```
. ID CENT_0
. 1 1 0
. 2 2 1
. 3 3 2
. 4 4 3
. 5 5 4
. 6 6 5
```

```
<-
out %>%
mod idata_set(idata) %>%
mrgsim(end=40)
```

`plot(out, CENT~.)`

## 11.3 Updating parameters

The parameter list was introduced in Section 1.1 and the `$PARAM`

code block was shown in Section 2.2.4. Once a model is compiled, the names and number of parameters in a model is fixed. However, the values of parameters can be changed: parameters may be updated either by the user (in `R`

) or by `mrgsolve`

(in the `C++`

simulation engine, as the simulation proceeds).

- To update in
`R`

, use the`param()`

function (see examples below) - To have
`mrgsolve`

update the parameters, attach columns to your data set (either`data_set`

or`idata_set`

) with the same name as items in the parameter list

Both of these methods are discussed and illustrated in the following sections.

### 11.3.1 Parameter update hierarchy

As we noted above, new parameter values can come from three potential sources:

- Modification of the (base) parameter list
- A column in an
`idata_set`

that has the same name as a model parameter - A column in a
`data_set`

that has the same name as a model parameter

These sources for new parameter values are discussed below. We note here that the sources listed above are listed in the order of the parameter update *hierarchy*. So, the base parameter list provides the value by default. A parameter value coming from an `idata_set`

will override the value in the base list. And a parameter value coming from a `data_set`

will override the value coming from the base list or an `idata_set`

(in case a parameter is listed in both the `idata_set`

and the `data_set`

). In other words, the hierarchy is:

- base parameter list is the default
- the
`idata_set`

overrides the base list - the
`data_set`

overrides the`idata_set`

and the base list

The parameter update hierarchy is discussed in the following sections.

**Base parameter set**

- Every model has a base set of “parameters”
- These are named and set in
`$PARAM`

- Parameters can only get into the parameter list in
`$PARAM`

(or`$THETA`

) - No changing the names or numbers of parameters once the model is compiled
- But, several ways to change the values

```
<- '
code $VCMT KYLE
$PARAM CL = 1.1, VC=23.1, KA=1.7, KM=10
$CAPTURE CL VC KA KM
'
<- mcode("tmp", code, warn=FALSE) mod
```

`param(mod)`

```
.
. Model parameters (N=4):
. name value . name value
. CL 1.1 | KM 10
. KA 1.7 | VC 23.1
```

**The base parameter set is the default**

The base parameter set allows you to run the model without entering any other data; there are some default values in place.

**The parameters in the base list can be changed or updated in R**

Use the `param()`

function to both set and get:

`<- param(mod, CL=2.1) mod `

`param(mod)`

```
.
. Model parameters (N=4):
. name value . name value
. CL 2.1 | KM 10
. KA 1.7 | VC 23.1
```

But whatever you’ve done in `R`

, there is a base set (with values) to use. See Section 11.3.2 for a more detailed discussion of using `param()`

to updated the base list.

**Parameters can also be updated during the simulation run**

Parameters can be updated by putting columns in `idata`

set or `data_set`

that have the same name as one of the parameters in the parameter list. But there is no changing values in the base parameter set once the simulation starts.

That is, the following model specification will not compile:

```
= 2
$PARAM CL
= 3; // ERROR $MAIN CL
```

You cannot over-write the value of a parameter in the model specification.

Let `mrgsolve`

do the updating.

`mrgsolve`

always reverts to the base parameter set when starting work on a new individual.

**Parameters updated from idata_set**

When `mrgsolve`

finds parameters in `idata`

, it will update the base parameter list with those parameters prior to starting that individual.

```
data(exidata)
head(exidata)
```

```
. ID CL VC KA KOUT IC50 FOO
. 1 1 1.050 47.80 0.8390 2.45 1.280 4
. 2 2 0.730 30.10 0.0684 2.51 1.840 6
. 3 3 2.820 23.80 0.1180 3.88 2.480 5
. 4 4 0.552 26.30 0.4950 1.18 0.977 2
. 5 5 0.483 4.36 0.1220 2.35 0.483 10
. 6 6 3.620 39.80 0.1260 1.89 4.240 1
```

Notice that there are several columns in `exidata`

that match up with the names in the parameter list

`names(exidata)`

`. [1] "ID" "CL" "VC" "KA" "KOUT" "IC50" "FOO"`

`names(param(mod))`

`. [1] "CL" "VC" "KA" "KM"`

The matching names tell `mrgsolve`

to update, assigning each individual their individual parameter.

```
<-
out %>%
mod idata_set(exidata) %>%
mrgsim(end=-1 , add=c(0,2))
```

` out`

```
. Model: tmp
. Dim: 20 x 7
. Time: 0 to 2
. ID: 10
. ID time KYLE CL VC KA KM
. 1: 1 0 0 1.050 47.8 0.8390 10
. 2: 1 2 0 1.050 47.8 0.8390 10
. 3: 2 0 0 0.730 30.1 0.0684 10
. 4: 2 2 0 0.730 30.1 0.0684 10
. 5: 3 0 0 2.820 23.8 0.1180 10
. 6: 3 2 0 2.820 23.8 0.1180 10
. 7: 4 0 0 0.552 26.3 0.4950 10
. 8: 4 2 0 0.552 26.3 0.4950 10
```

**Parameters updated from data_set**

Like an `idata`

set, we can put parameters on a `data`

set

`<- expand.ev(amt=0, CL=c(1,2,3), VC=30) data `

```
<-
out %>%
mod data_set(data) %>%
%>%
obsonly mrgsim(end=-1, add=c(0,2))
```

` out`

```
. Model: tmp
. Dim: 6 x 7
. Time: 0 to 2
. ID: 3
. ID time KYLE CL VC KA KM
. 1: 1 0 0 1 30 1.7 10
. 2: 1 2 0 1 30 1.7 10
. 3: 2 0 0 2 30 1.7 10
. 4: 2 2 0 2 30 1.7 10
. 5: 3 0 0 3 30 1.7 10
. 6: 3 2 0 3 30 1.7 10
```

This is how we do time-varying parameters:

```
<-
data data_frame(CL=seq(1,5)) %>%
mutate(evid=0,ID=1,cmt=1,time=CL-1,amt=0)
```

```
. Warning: `data_frame()` was deprecated in tibble 1.1.0.
. ℹ Please use `tibble()` instead.
```

```
%>%
mod data_set(data) %>%
mrgsim(end=-1)
```

```
. Model: tmp
. Dim: 5 x 7
. Time: 0 to 4
. ID: 1
. ID time KYLE CL VC KA KM
. 1: 1 0 0 1 23.1 1.7 10
. 2: 1 1 0 2 23.1 1.7 10
. 3: 1 2 0 3 23.1 1.7 10
. 4: 1 3 0 4 23.1 1.7 10
. 5: 1 4 0 5 23.1 1.7 10
```

For more information on time-varying covariates (parameters), see Section 11.8 and Chapter 7.

**Parameters are carried back when first record isn’t at time == 0**

What about this?

```
<- expand.ev(amt=100,time=24,CL=5,VC=32)
data data
```

```
. ID time amt cmt evid CL VC
. 1 1 24 100 1 1 5 32
```

The first `data`

record happens at `time==24`

```
%>%
mod data_set(data) %>%
mrgsim(end=-1, add=c(0,2))
```

```
. Model: tmp
. Dim: 3 x 7
. Time: 0 to 24
. ID: 1
. ID time KYLE CL VC KA KM
. 1: 1 0 0 5 32 1.7 10
. 2: 1 2 0 5 32 1.7 10
. 3: 1 24 100 5 32 1.7 10
```

Since the data set doesn’t start until `time==5`

, we might think that `CL`

doesn’t change from the base parameter set until then.

But by default, `mrgsolve`

carries those parameter values back to the start of the simulation. This is by design … by far the more useful configuration.

If you wanted the base parameter set in play until that first data set record, do this:

```
%>%
mod data_set(data) %>%
mrgsim(end=-1,add=c(0,2), filbak=FALSE)
```

```
. Model: tmp
. Dim: 3 x 7
. Time: 0 to 24
. ID: 1
. ID time KYLE CL VC KA KM
. 1: 1 0 0 5 32 1.7 10
. 2: 1 2 0 5 32 1.7 10
. 3: 1 24 100 5 32 1.7 10
```

Will this work?

```
<- do.call("expand.idata", as.list(param(mod)))
idata
idata
```

```
. ID CL VC KA KM
. 1 1 2.1 23.1 1.7 10
```

Here, we’ll pass in **both** `data_set`

and `idata_set`

and they have conflicting values for the parameters.

```
%>%
mod data_set(data) %>%
idata_set(idata) %>%
mrgsim(end=-1,add=c(0,2))
```

```
. Model: tmp
. Dim: 3 x 7
. Time: 0 to 24
. ID: 1
. ID time KYLE CL VC KA KM
. 1: 1 0 0 5 32 1.7 10
. 2: 1 2 0 5 32 1.7 10
. 3: 1 24 100 5 32 1.7 10
```

The data set always gets the last word.

### 11.3.2 Updating the base parameter list

From the previous section

`param(mod)`

```
.
. Model parameters (N=4):
. name value . name value
. CL 2.1 | KM 10
. KA 1.7 | VC 23.1
```

**Update with name-value pairs**

We can call `param()`

to update the model object, directly naming the parameter to update and the new value to take

`%>% param(CL = 777, KM = 999) %>% param mod `

```
.
. Model parameters (N=4):
. name value . name value
. CL 777 | KM 999
. KA 1.7 | VC 23.1
```

The parameter list can also be updated by scanning the names in a list

```
<- list(CL = 555, VC = 888, KYLE = 123, MN = 100)
what
%>% param(what) %>% param mod
```

```
.
. Model parameters (N=4):
. name value . name value
. CL 555 | KM 10
. KA 1.7 | VC 888
```

`mrgsolve`

looks at the names to drive the update. `KYLE`

(a compartment name) and `MN`

(not in the model anywhere) are ignored.

Alternatively, we can pick a row from a data frame to provide the input for the update

```
<- data_frame(CL=c(9,10), VC=c(11,12), KTB=c(13,14))
d
%>% param(d[2,]) %>% param mod
```

```
.
. Model parameters (N=4):
. name value . name value
. CL 10 | KM 10
. KA 1.7 | VC 12
```

Here the second row in the data frame drives the update. Other names are ignored.

A warning will be issued if an update is attempted, but no matching names are found

`%>% param(ZIP = 1, CODE = 2) %>% param mod `

```
Warning message:
Found nothing to update: param
```

## 11.4 Time grid objects

**Simulation times in mrgsolve**

`<- mrgsolve:::house() %>% Req(CP) %>% ev(amt = 1000, ii = 24, addl = 1000) mod `

`mrgsolve`

keeps track of a simulation `start`

and `end`

time and a fixed size step between `start`

and `end`

(called `delta`

). `mrgsolve`

also keeps an arbitrary vector of simulation times called `add`

.

```
%>%
mod mrgsim(end = 4, delta = 2, add = c(7,9,50)) %>%
as.data.frame()
```

```
. ID time CP
. 1 1 0 0.00000
. 2 1 0 0.00000
. 3 1 2 42.47580
. 4 1 4 42.28701
. 5 1 7 36.75460
. 6 1 9 33.26649
. 7 1 50 60.97754
```

`tgrid`

objects

The `tgrid`

object abstracts this setup and allows us to make complicated sampling designs from elementary building blocks.

**Make a day 1 sampling with intensive sampling around the peak and sparser otherwise**

```
<- tgrid(1, 4, 0.1)
peak1 <- tgrid(0, 24, 4) sparse1
```

**Use the c operator to combine simpler designs into more complicated designs**

`<- c(peak1, sparse1) day1 `

Check this by calling `stime`

`stime(day1)`

```
. [1] 0.0 1.0 1.1 1.2 1.3 1.4 1.5 1.6 1.7 1.8 1.9 2.0 2.1 2.2 2.3
. [16] 2.4 2.5 2.6 2.7 2.8 2.9 3.0 3.1 3.2 3.3 3.4 3.5 3.6 3.7 3.8
. [31] 3.9 4.0 8.0 12.0 16.0 20.0 24.0
```

Pass this object in to `mrgsim`

as `tgrid`

. It will override the default `start/end/delta/add`

sequence.

```
%>%
mod mrgsim(tgrid = day1) %>%
plot(type = 'b')
```

**Now, look at both day 1 and day 10**:

Adding a number to a `tgrid`

object will offset those times by that amount.

```
<- c(day1, day1 + 10*24)
des
%>%
mod mrgsim(tgrid = des) %>%
plot(type = 'b')
```

Pick up day 5 as well

```
<- c(des, day1 + 5*24)
des
%>%
mod mrgsim(tgrid = des) %>%
plot(type = 'b')
```

## 11.5 Individualized sampling designs

Here is a PopPK model and a full `data_set`

.

```
<- house()
mod
data(exTheoph)
<- exTheoph
df
head(df)
```

```
. ID WT Dose time conc cmt amt evid
. 1 1 79.6 4.02 0.00 0.00 1 4.02 1
. 2 1 79.6 4.02 0.25 2.84 0 0.00 0
. 3 1 79.6 4.02 0.57 6.57 0 0.00 0
. 4 1 79.6 4.02 1.12 10.50 0 0.00 0
. 5 1 79.6 4.02 2.02 9.66 0 0.00 0
. 6 1 79.6 4.02 3.82 8.58 0 0.00 0
```

```
%>%
mod Req(CP) %>%
carry.out(a.u.g) %>%
data_set(df) %>%
obsaug() %>%
mrgsim()
```

```
. Model: housemodel
. Dim: 5904 x 4
. Time: 0 to 120
. ID: 12
. ID time a.u.g CP
. 1: 1 0.00 1 0.00000
. 2: 1 0.00 0 0.00000
. 3: 1 0.25 1 0.04552
. 4: 1 0.25 0 0.04552
. 5: 1 0.50 1 0.07870
. 6: 1 0.57 0 0.08624
. 7: 1 0.75 1 0.10274
. 8: 1 1.00 1 0.12001
```

Now, define two time grid objects: `des1`

runs from 0 to 24 and `des2`

runs from 0 to 96, both every hour.

```
<- tgrid(0, 24, 1)
des1 <- tgrid(0, 96, 1)
des2
range(stime(des1))
```

`. [1] 0 24`

`range(stime(des2))`

`. [1] 0 96`

Now, derive an `idata_set`

after adding a grouping column (`GRP`

) that splits the data set into two groups

```
<- mutate(df, GRP = as.integer(ID > 5))
df
<- distinct(df, ID, GRP)
id
id
```

```
. ID GRP
. 1 1 0
. 2 2 0
. 3 3 0
. 4 4 0
. 5 5 0
. 6 6 1
. 7 7 1
. 8 8 1
. 9 9 1
. 10 10 1
. 11 11 1
. 12 12 1
```

Now, we have two groups in `GRP`

in `idata_set`

and we have two `tgrid`

objects.

- Pass in both the
`idata_set`

and the`data_set`

- Call
`design`

- Identify
`GRP`

as`descol`

; the column**must**be in`idata_set`

- Pass in a list of designs; it
**must**be at least two because there are two levels in`GRP`

When we simulate, the individuals in `GRP 1`

will get `des1`

and those in `GRP 2`

will get `des2`

```
<-
out %>%
mod Req(CP) %>%
carry.out(a.u.g,GRP) %>%
idata_set(id) %>%
data_set(df) %>%
design(descol = "GRP", deslist = list(des1, des2)) %>%
obsaug() %>%
mrgsim()
plot(out, CP~time|GRP)
```

## 11.6 Some helpful `C++`

Recall that the following blocks require valid `C++`

code:

`$PREAMBLE`

`$MAIN`

`$ODE`

`$TABLE`

`$GLOBAL`

`$PRED`

We don’t want users to have to be proficient in `C++`

to be able to use mrgsolve. and we’ve created several macros to help simplify things as much as possible.

However, it is required to become familiar with some of the basics and certainly additional knowledge of how to do more than just the basics will help you code more and more complicated models in mrgsolve.

There are an unending stream of tutorials, references and help pages on `C++`

to be found on the interweb. As a general source, I like to use https://en.cppreference.com/. But, again, there many other good resources out there that can suit your needs.

The rest of this section provides a very general reference of the types of `C++`

code and functions that you might be using in your model.

### 11.6.1 Semi-colons

Every statement in `C++`

must end with a semi-colon. For example;

```
[ MAIN ]
double CL = exp(log_TVCL + ETA(1));
```

or

```
[ ODE ]
= -KA * DEPOT; dxdt_DEPOT
```

### 11.6.2 if-else

`if(a == 2) b = 2;`

```
if(a==2) {
= 2;
b }
```

```
if(a == 2) {
=2;
b} else {
=3;
b}
```

This is the equivalent of `x <- ifelse(c == 4, 8, 10)`

in R

`double x = c == 4 ? 8 : 10;`

### 11.6.3 Functions

The following functions are hopefully understandable based on the function name. Consult https://cppreference.com for further details.

```
# base^exponent
double d = pow(base,exponent);
double e = exp(3);
# absolute value
double f = fabs(-4);
double g = sqrt(5);
double h = log(6);
double i = log10(7);
double j = floor(4.2);
double k = ceil(4.2);
double l = std::max(0.0, -3.0);
double m = std::min(0.0, -3.0);
```

### 11.6.4 Integer division

The user is warned about division with two integers. In `R`

, the following statement evaluates to `0.75`

:

`3/4`

`. [1] 0.75`

But in `C++`

it evaluates to 0:

`double x = 3/4;`

This is because both the `3`

and the `4`

are taken as integer literals. This produces the same result as

```
int a = 3;
int b = 4;
double x = a/b;
```

When one integer is divided by another integer, the remainder is discarded (the result is rounded down). This is the way `C++`

works. The user is warned.

Note that parameters in mrgsolve are `doubles`

so this will evaluate to `0.75`

```
[ PARAM ] a = 3
[ MAIN ]
double x = a/4;
```

Since `a`

is a parameter the operation of `a/4`

is not integer division and the result is `0.75`

.

Unless you are already very comfortable with this concept, users are encouraged to add `.0`

suffix to any literal number **written as C++ code**. For example:

`double x = 3.0 / 4.0;`

I think it’s fair to say that the vast majority of time you want this to evaluate to `0.75`

and writing `3.0/4.0`

rather than `3/4`

will ensure you will not discard any remainder here.

If you would like to experiment with these concepts, try running this code

```
library(mrgsolve)
<- '
code [ param ] a = 3
[ main ]
capture x = 3/4;
capture y = 3.0/4.0;
capture z = a/4;
'
<- mcode("foo", code)
mod
mrgsim(mod)
```

```
. Model: foo
. Dim: 25 x 5
. Time: 0 to 24
. ID: 1
. ID time x y z
. 1: 1 0 0 0.75 0.75
. 2: 1 1 0 0.75 0.75
. 3: 1 2 0 0.75 0.75
. 4: 1 3 0 0.75 0.75
. 5: 1 4 0 0.75 0.75
. 6: 1 5 0 0.75 0.75
. 7: 1 6 0 0.75 0.75
. 8: 1 7 0 0.75 0.75
```

### 11.6.5 Pre-processor directives

Pre-processor directives are global substitutions that are made in your model code at the time the model is compiled. For example

```
$GLOBAL
#define CP (CENT/VC)
```

When you write this into your model, the pre-processor will find every instance of `CP`

and **replace** it with `(CENT/VC)`

. This substitution happens right as the model is compiled; you won’t see this substitution happen anywhere, but think of it as literal replacement of `CP`

with `(CENT/VC)`

.

**Note**:

- Put all pre-processor directives in
`$GLOBAL`

. - It is usually a good idea to enclose the substituted coded in parentheses; this ensures that, for example,
`CENT/VC`

is evaluated as is, regardless of the surrounding code where it is evaluated. - Under the hood, mrgsolve uses lots of pre-processor directives to define parameter names, compartment names and other variables; you will see a compiler error if you try to re-define an existing pre-processor directive. If so, just choose another name for your directive.

## 11.7 Resimulate `ETA`

and `EPS`

**Call simeps(n) to resimulate ETA**

- No
`$PLUGIN`

is required `simeta(n)`

takes a single argument (`n`

), the ETA number to resimulate

For example, we can simulate individual-level covariates within a certain range:

```
<- '
code $PARAM TVCL = 1, TVWT = 70
$MAIN
capture WT = TVWT*exp(EWT);
int i = 0;
while((WT < 60) || (WT > 80)) {
if(++i > 100) break;
simeta(1);
WT = TVWT*exp(EWT);
}
$OMEGA @labels EWT
4
$CAPTURE EWT WT
'
<- mcode("simeta", code) mod
```

```
. Warning in check_sim_eta_eps_n(x, spec): simeta(n) was requested; resimulating
. single ETA values is now discouraged and will soon be deprecated; use simeta()
. to resimulate all ETA; silence this warning by setting MRGSOLVE_RESIM_N_WARN to
. FALSE in $ENV.
```

```
<- mod %>% mrgsim(nid=100, end=-1)
out
<- summary(out)
sum
sum
```

```
. ID time EWT WT
. Min. : 1.00 Min. :0 Min. :-0.1524084 Min. :60.10
. 1st Qu.: 25.75 1st Qu.:0 1st Qu.:-0.0682351 1st Qu.:65.38
. Median : 50.50 Median :0 Median :-0.0090525 Median :69.37
. Mean : 50.50 Mean :0 Mean : 0.0009205 Mean :70.31
. 3rd Qu.: 75.25 3rd Qu.:0 3rd Qu.: 0.0847712 3rd Qu.:76.19
. Max. :100.00 Max. :0 Max. : 0.1318273 Max. :79.86
```

**Call simeps(n) to resimulate EPS**

- No
`$PLUGIN`

is required `simeps()`

takes a single argument (`n`

), the EPS number to resimulate

For example, we can resimulate until all concentrations are greater than zero:

```
<- '
code $PARAM CL = 1, V = 20,
$CMT CENT
$SIGMA 50
$PKMODEL ncmt=1
$TABLE
capture CP = CENT/V + EPS(1);
int i = 0;
while(CP < 0 && i < 100) {
simeps(1);
CP = CENT/V + EPS(1);
++i;
}
'
<- mcode("simeps", code) mod
```

```
. Warning in check_sim_eta_eps_n(x, spec): simeps(n) was requested; resimulating
. single EPS values is now discouraged and will soon be deprecated; use simeps()
. to resimulate all EPS; silence this warning by setting MRGSOLVE_RESIM_N_WARN to
. FALSE in $ENV.
```

```
<- mod %>% ev(amt=100) %>% mrgsim(end=48)
out <- summary(out)
sum
sum
```

```
. ID time CENT CP
. Min. :1 Min. : 0.00 Min. : 0.00 Min. : 0.1533
. 1st Qu.:1 1st Qu.:11.25 1st Qu.: 15.93 1st Qu.: 2.4251
. Median :1 Median :23.50 Median : 29.38 Median : 4.3800
. Mean :1 Mean :23.52 Mean : 37.47 Mean : 6.2113
. 3rd Qu.:1 3rd Qu.:35.75 3rd Qu.: 54.21 3rd Qu.: 9.7018
. Max. :1 Max. :48.00 Max. :100.00 Max. :17.5997
```

**A safety check is recommended** Note that in both examples, we implement a safety check: an integer counter is incremented every time we resimulated. The resimulation process stops if we don’t reach the desired condition within 100 replicates. You might also consider issuing a message or a flag in the simulated data if you are not able to reach the desired condition.

## 11.8 Time varying covariates

A note in a previous section showed how to implement time-varying covariates or other time-varying parameters by including those parameters as column in the data set.

By default, `mrgsolve`

performs next observation carried backward (`nocb`

) when processing time-varying covariates. That is, when the system advances from `TIME1`

to `TIME2`

, and the advance is a function of a covariate found in the data set, the system advances using the covariate value `COV2`

rather than the covariate `COV1`

.

The user can change the behavior to last observation carried forward (`locf`

), so that the system uses the value of `COV1`

to advance from `TIME1`

to `TIME2`

. To use `locf`

advance, set `nocb`

to `FALSE`

when calling `mrgsim`

. For example,

`%>% mrgsim(nocb = FALSE) mod `

There is additional information about the sequence of events that takes place during system advance in Chapter 7.