NONMEM input data
CautionUnder construction
Data review
Important
Do a thorough exploratory data analysis before starting to model.
- Tab-separated (less likely to be present in the actual data)
- Start every dataset with a âCommentâ column, the
IGNORE=@
will then ignore a row if there is a text comment- The second column should be a
REF
column with each line number
- The second column should be a
Sparse vs Rich data
The ârichnessâ of data has different meanings.
It can relate to ETAs and RSE/RUV. It can also relate to where on the PK-curve samples are taken. If samples are taken on in the absorption-phase (pre-Cmax), around Cmax, and in the elimination phase, and Ctrough (pre-dose), then it can be considered ârichâ sampling.
- PK Studies:
- âIntensive studiesâ (Phase 1/2)
- Few subjects (homogeneous)
- Single dose
- Frequent (rich) sampling
- âPopulation studiesâ (Phase 3/4)
- Many subjects (heterogeneous)
- Multiple dose
- Sparse sampling
- âIntensive studiesâ (Phase 1/2)
ADDL and II
- Additional Dose (ADDL): Describes how many additional doses
- Interdose interval (II): Time between the additional doses
TIME | AMT | ADDL | II | DV |
---|---|---|---|---|
10 | 15 | 0 | 0 | . |
15 | . | . | . | 25.7 |
20 | 10 | 0 | 0 | . |
22 | 15 | 0 | 0 | . |
34 | 15 | 0 | 0 | . |
36 | . | . | . | 30.2 |
same as:
TIME | AMT | ADDL | II | DV |
---|---|---|---|---|
10 | 15 | 2 | 12 | . |
15 | . | . | . | 25.7 |
20 | 10 | 0 | 0 | . |
36 | . | . | . | 30.2 |
ID | TIME=DAY | DOSE | ADDL | II | CYCLE |
---|---|---|---|---|---|
1 | 1 | 90 | 0 | 0 | 1 |
1 | 8 | 90 | 0 | 0 | 1 |
1 | 15 | 90 | 0 | 0 | 1 |
1 | 22 | . | 0 | 0 | 1 |
1 | 29 | 90 | 0 | 0 | 2 |
1 | 36 | 90 | 0 | 0 | 2 |
1 | 43 | 90 | 0 | 0 | 2 |
1 | 50 | . | 0 | 0 | 2 |
1 | 57 | 90 | 0 | 0 | 3 |
1 | 64 | 90 | 0 | 0 | 3 |
1 | 71 | 90 | 0 | 0 | 3 |
1 | 78 | . | 0 | 0 | 3 |
1 | 85 | 90 | 0 | 0 | 4 |
1 | 92 | 90 | 0 | 0 | 4 |
1 | 99 | 90 | 0 | 0 | 4 |
1 | 106 | . | 0 | 0 | 4 |
same as:
ID | TIME=DAY | DOSE | ADDL | II | CYCLE |
---|---|---|---|---|---|
1 | 1 | 90 | 4 | 28 | 1 |
1 | 8 | 90 | 4 | 28 | 1 |
1 | 15 | 90 | 4 | 28 | 1 |
1 | 22 | . | 0 | 0 | 1 |
Modify the NONMEM-dataset, inside a model file
Letâs say TIME
is all -99, and we want to modify it.
$INPUT ID TIME NTIME TAFD DV TYPE MDV EVID
AMT CMT DOSE AGE SEX HT WT BMI BSA
BLOQ COMMENT=DROP
$DATA data.csv IGNORE=@
$SUBROUTINE ADVAN=13 TOL=6
$MODEL
COMP=(CENTRAL,DEFDOSE,DEFOBS)
COMP=PERIPHERAL
$INFN
1 IF (ICALL == 1) THEN
2 DOWHILE(DATA)
3 IF (NEWIND < 2) START_TIME = TAFD
TIME = TAFD - START_TIME
ENDDO
ENDIF
$PK
...
- 1
-
ICALL==1
, the routine has been called for initialization at the beginning of a NONMEM problem, one such call per problem - 2
-
DOWHILE
loop over entire dataset - 3
- Modifying statements here. They will be considered as âoriginal datasetâ by NONMEM.