Description Usage Arguments Details Value Functions Setting up the NONMEM model file Author(s) References See Also Examples
View source: R/compute.cwres.R
This function computes the conditional weighted residuals (CWRES) from a NONMEM run. CWRES are an extension of the weighted residuals (WRES), but are calculated based on the firstorder with conditional estimation (FOCE) method of linearizing a pharmacometric model (WRES are calculated based on the firstorder (FO) method). The function requires a NONMEM table file and an extra output file that must be explicitly asked for when running NONMEM, see details below.
1 2 3 4 5 6 7 8 9  compute.cwres(run.number, tab.prefix = "cwtab", sim.suffix = "",
est.tab.suffix = ".est", deriv.tab.suffix = ".deriv",
old.file.convention = FALSE, id = "ALL", printToOutfile = TRUE,
onlyNonZero = TRUE, ...)
xpose.calculate.cwres(object, cwres.table.prefix = "cwtab", tab.suffix = "",
sim.suffix = "sim", est.tab.suffix = ".est",
deriv.tab.suffix = ".deriv", old.file.convention = FALSE, id = "ALL",
printToOutfile = TRUE, onlyNonZero = FALSE, classic = FALSE, ...)

run.number 
The run number of the NONMEM from which the CWRES are to be calculated. 
tab.prefix 
The prefix to two NONMEM file containing the needed values for the computation of the CWRES, described in the details section. 
sim.suffix 
The suffix ,before the ".", of the NONMEM file containing
the needed values for the computation of the CWRES, described in the details
section. For example, the table files might be named 
est.tab.suffix 
The suffix, after the ".", of the NONMEM file containing the estimated parameter values needed for the CWRES calculation. 
deriv.tab.suffix 
The suffix, after the ".", of the NONMEM file containing the derivatives of the model with respect to the random parameters needed for the CWRES calculation. 
old.file.convention 
For backwards compatibility. Use this if you are using the previous file convention for CWRES (table files named cwtab1, cwtab1.50, cwtab1.51, ... , cwtab.58 for example). 
id 
Can be either "ALL" or a number matching an ID label in the

printToOutfile 
Logical (TRUE/FALSE) indicating whether the CWRES
values calculated should be appended to a copy of the 
onlyNonZero 
Logical (TRUE/FALSE) indicating if the return value (the
CWRES values) of 
... 
Other arguments passed to basic functions in code. 
object 
An xpose.data object. 
cwres.table.prefix 
The prefix to the NONMEM table file containing the derivative of the model with respect to the etas and epsilons, described in the details section. 
tab.suffix 
The suffix to the NONMEM table file containing the derivative of the model with respect to the etas and epsilons, described in the details section. 
classic 
Indicates if the function is to be used in the classic menu system. 
The function reads in the following two files:
paste(tab.prefix,run.number,sim.suffix,est.tab.suffix,sep="")
paste(tab.prefix,run.number,sim.suffix,deriv.tab.suffix,sep="")
Which might be for example:
1  cwtab1.est cwtab1.deriv

and (depending on the input values to the function) returns the CWRES in vector form as well as creating a new table file named:
paste(tab.prefix,run.number,sim.suffix,sep="")
Which might be for example:
1  cwtab1

Returns a vector containing the values of the CWRES.
Returns an Xpose data object that contains the CWRES. If simulated data is present, then the CWRES will also be calculated for that data.
xpose.calculate.cwres
: This function is a wrapper around
the function compute.cwres
. It computes the CWRES for the model file
associated with the Xpose data object input to the function. If possible it
also computes the CWRES for any simulated data associated with the current
Xpose data object. If you have problems with this function try using
compute.cwres
and then rereading your dataset into Xpose.
In order for this function to calculate the CWRES, NONMEM must be run while requesting certain tables and files to be created. How these files are created differs depending on if you are using $PRED or ADVAN as well as the version of NONMEM you are using. These procedures are known to work for NONMEM VI but may be different for NONMEM V and NONMEM VII. We have attempted to indicate where NONMEM V may be different, but this has not been extensively tested! For NONMEM VII the CWRES are calculated internally so this function is rarely needed.
This procedure can be done automatically using Perl Speaks NONMEM (PsN) and
we highly recommend using PsN for this purpose. After installing PsN just
type 'execute [modelname] cwres
'. See
http://psn.sourceforge.net for more details.
There are five main insertions needed in your NONMEM control file:
$ABB COMRES=X.
Insert this line directly after your $DATA line. The value of X is the number of ETA() terms plus the number of EPS() terms in your model. For example for a model with three ETA() terms and two EPS() terms the code would look like this:
$DATA temp.csv [email protected] $ABB COMRES=5 $INPUT ID TIME DV MDV AMT EVID $SUB ADVAN2 TRANS2
Verbatim code.
Using ADVAN.
If you are using ADVAN routines in your model, then Verbatim code should be inserted directly after the $ERROR section of your model file. The length of the code depends again on the number of ETA() terms and EPS() terms in your model. For each ETA(y) in your model there is a corresponding term G(y,1) that you must assign to a COM() variable. For each EPS(y) in your model, there is a corresponding HH(y,1) term that you must assign to a COM() variable.
For example for a model using ADVAN routines with three ETA() terms and two EPS() terms the code would look like this:
"LAST " COM(1)=G(1,1) " COM(2)=G(2,1) " COM(3)=G(3,1) " COM(4)=HH(1,1) " COM(5)=HH(2,1)
Using PRED.
If you are using $PRED, the verbatim code should be inserted directly after the $PRED section of your model file. For each ETA(y) in your model there is a corresponding term G(y,1) that you must assign to a COM() variable. For each EPS(y) in your model, there is a corresponding H(y,1) term that you must assign to a COM() variable. The code would look like this for three ETA() terms and two EPS() terms:
"LAST " COM(1)=G(1,1) " COM(2)=G(2,1) " COM(3)=G(3,1) " COM(4)=H(1,1) " COM(5)=H(2,1)
INFN routine.
Using ADVAN with NONMEM VI and higher.
If you are using ADVAN routines in your model, then an $INFN section should be placed directly after the $PK section using the following code. In this example we are assuming that the model file is named something like 'run1.mod', thus the prefix to these file names 'cwtab' has the same run number attached to it (i.e. 'cwtab1'). This should be changed for each new run number.
$INFN IF (ICALL.EQ.3) THEN OPEN(50,FILE='cwtab1.est') WRITE(50,*) 'ETAS' DO WHILE(DATA) IF (NEWIND.LE.1) WRITE (50,*) ETA ENDDO WRITE(50,*) 'THETAS' WRITE(50,*) THETA WRITE(50,*) 'OMEGAS' WRITE(50,*) OMEGA(BLOCK) WRITE(50,*) 'SIGMAS' WRITE(50,*) SIGMA(BLOCK) ENDIF
Using ADVAN with NONMEM V.
If you are using ADVAN routines in your model, then you need to use an INFN subroutine. If we call the INFN subroutine 'myinfn.for' then the $SUBS line of your model file should include the INFN option. That is, if we are using ADVAN2 and TRANS2 in our model file then the $SUBS line would look like:
$SUB ADVAN2 TRANS2 INFN=myinfn.for
The 'myinfn.for' routine for 4 thetas, 3 etas and 1 epsilon is shown below. If your model has different numbers of thetas, etas and epsilons then the values of NTH, NETA, and NEPS, should be changed respectively. These vales are found in the DATA statement of the subroutine. additionally, in this example we are assuming that the model file is named something like 'run1.mod', thus the prefix to the output file names ('cwtab') in this subroutine has the same run number attached to it (i.e. 'cwtab1'). This number should be changed for each new run number (see the line beginning with 'OPEN').
SUBROUTINE INFN(ICALL,THETA,DATREC,INDXS,NEWIND) DIMENSION THETA(*),DATREC(*),INDXS(*) DOUBLE PRECISION THETA COMMON /ROCM6/ THETAF(40),OMEGAF(30,30),SIGMAF(30,30) COMMON /ROCM7/ SETH(40),SEOM(30,30),SESIG(30,30) COMMON /ROCM8/ OBJECT COMMON /ROCM9/ IERE,IERC DOUBLE PRECISION THETAF, OMEGAF, SIGMAF DOUBLE PRECISION OBJECT REAL SETH,SEOM,SESIG DOUBLE PRECISION ETA(10) INTEGER J,I INTEGER IERE,IERC INTEGER MODE INTEGER NTH,NETA,NEPS DATA NTH,NETA,NEPS/4,3,1/ IF (ICALL.EQ.0) THEN C open files here, if necessary OPEN(50,FILE='cwtab1.est') ENDIF IF (ICALL.EQ.3) THEN MODE=0 CALL PASS(MODE) MODE=1 WRITE(50,*) 'ETAS' 20 CALL PASS(MODE) IF (MODE.EQ.0) GO TO 30 IF (NEWIND.NE.2) THEN CALL GETETA(ETA) WRITE (50,97) (ETA(I),I=1,NETA) ENDIF GO TO 20 30 CONTINUE WRITE (50,*) 'THETAS' WRITE (50,99) (THETAF(J),J=1,NTH) WRITE(50,*) 'OMEGAS' DO 7000 I=1,NETA 7000 WRITE (50,99) (OMEGAF(I,J),J=1,NETA) WRITE(50,*) 'SIGMAS' DO 7999 I=1,NEPS 7999 WRITE (50,99) (SIGMAF(I,J),J=1,NEPS) ENDIF 99 FORMAT (20E15.7) 98 FORMAT (2I8) 97 FORMAT (10E15.7) RETURN END
Using $PRED with NONMEM VI and higher.
If you are using $PRED, then an the following code should be placed at the end of the $PRED section of the model file (together with the verbatim code). In this example we are assuming that the model file is named something like 'run1.mod', thus the prefix to these file names 'cwtab' has the same run number attached to it (i.e. 'cwtab1'). This should be changed for each new run number.
IF (ICALL.EQ.3) THEN OPEN(50,FILE='cwtab1.est') WRITE(50,*) 'ETAS' DO WHILE(DATA) IF (NEWIND.LE.1) WRITE (50,*) ETA ENDDO WRITE(50,*) 'THETAS' WRITE(50,*) THETA WRITE(50,*) 'OMEGAS' WRITE(50,*) OMEGA(BLOCK) WRITE(50,*) 'SIGMAS' WRITE(50,*) SIGMA(BLOCK) ENDIF
Using $PRED with NONMEM V.
If you are using $PRED with NONMEM V, then you need to add verbatim code immediately after the $PRED command. In this example we assume 4 thetas, 3 etas and 1 epsilon. If your model has different numbers of thetas, etas and epsilons then the values of NTH, NETA, and NEPS, should be changed respectively. These vales are found in the DATA statement below.
$PRED "FIRST " COMMON /ROCM6/ THETAF(40),OMEGAF(30,30),SIGMAF(30,30) " COMMON /ROCM7/ SETH(40),SEOM(30,30),SESIG(30,30) " COMMON /ROCM8/ OBJECT " DOUBLE PRECISION THETAF, OMEGAF, SIGMAF " DOUBLE PRECISION OBJECT " REAL SETH,SEOM,SESIG " INTEGER J,I " INTEGER MODE " INTEGER NTH,NETA,NEPS " DATA NTH,NETA,NEPS/4,3,1/
After this verbatim code you add all of the abbreviated code needed for the $PRED routine in your model file. After the abbreviated code more verbatim code is needed. This verbatim code should be added before the verbatim code discussed above under point 2. In the example below we are assuming that the model file is named something like 'run1.mod', thus the prefix to the output file names ('cwtab') has the same run number attached to it (i.e. 'cwtab1'). This number should be changed for each new run number (see the line beginning with 'OPEN').
" IF (ICALL.EQ.0) THEN "C open files here, if necessary " OPEN(50,FILE='cwtab1.est') " ENDIF " IF (ICALL.EQ.3) THEN " MODE=0 " CALL PASS(MODE) " MODE=1 " WRITE(50,*) 'ETAS' "20 CALL PASS(MODE) " IF (MODE.EQ.0) GO TO 30 " IF (NEWIND.NE.2) THEN " CALL GETETA(ETA) " WRITE (50,97) (ETA(I),I=1,NETA) " ENDIF " GO TO 20 "30 CONTINUE " WRITE (50,*) 'THETAS' " WRITE (50,99) (THETAF(J),J=1,NTH) " WRITE (50,*) 'OMEGAS' " DO 7000 I=1,NETA "7000 WRITE (50,99) (OMEGAF(I,J),J=1,NETA) " WRITE (50,*) 'SIGMAS' " DO 7999 I=1,NEPS "7999 WRITE (50,99) (SIGMAF(I,J),J=1,NEPS) " ENDIF "99 FORMAT (20E15.7) "98 FORMAT (2I8) "97 FORMAT (10E15.7)
cwtab*.deriv table file.
A special table file needs to be created to print out the values contained
in the COMRES
variables. In addition the ID, IPRED, MDV, DV,
PRED and RES
data items are needed for the computation of the CWRES. The
following code should be added to the NONMEM model file. In this example we
continue to assume that we are using a model with three ETA() terms and two
EPS() terms, extra terms should be added for new ETA() and EPS() terms in
the model file. We also assume the model file is named something like
'run1.mod', thus the prefix to these file names 'cwtab' has the same run
number attached to it (i.e. 'cwtab1'). This should be changed for each new
run number.
$TABLE ID COM(1)=G11 COM(2)=G21 COM(3)=G31 COM(4)=H11 COM(5)=H21 IPRED MDV NOPRINT ONEHEADER FILE=cwtab1.deriv
$ESTIMATION.
To compute the CWRES, the NONMEM model file must use (at least) the FO
method with the POSTHOC
step. If the FO method is used and the
POSTHOC
step is not included then the CWRES values will be equivalent
to the WRES. The CWRES calculations are based on the FOCE approximation,
and consequently give an idea of the ability of the FOCE method to fit the
model to the data. If you are using another method of parameter estimation
(e.g. FOCE with interaction), the CWRES will not be calculated based on the
same model linearization procedure.
Andrew Hooker
Hooker AC, Staatz CE, Karlsson MO. Conditional weighted residuals, an improved model diagnostic for the FO/FOCE methods. PAGE 15 (2006) Abstr 1001 [http://www.pagemeeting.org/?abstract=1001].
Hooker AC, Staatz CE and Karlsson MO, Conditional weighted residuals (CWRES): a model diagnostic for the FOCE method, Pharm Res, 24(12): p. 218797, 2007, [http://link.springer.com/article/10.1007%2Fs110950079361x].
Other data functions: add_transformed_columns
,
change_graphical_parameters
,
change_misc_parameters
,
data.checkout
,
data_extract_or_assign
,
db.names
, export.graph.par
,
export.variable.definitions
,
import.graph.par
,
import.variable.definitions
,
make.sb.data
, nsim
,
par_cov_summary
,
read.TTE.sim.data
,
read.nm.tables
,
read_NM_output
,
read_nm_table
,
simprazExample
,
tabulate.parameters
, xlabel
,
xpose.data
, xpose.print
,
xpose4package
, xsubset
1 2 3 4 5 6 7 8 9 10 11 12 13 14 15 16 17 18 19 20 21 22 23 24  ## Not run:
## Capture CWRES from cwtab5.est and cwtab5.deriv
cwres < compute.cwres(5)
mean(cwres)
var(cwres)
## Capture CWRES from cwtab1.est and cwtab1.deriv, do not print out, allow zeroes
cwres < compute.cwres("1", printToOutFile = FALSE,
onlyNonZero = FALSE)
## Capture CWRES for ID==1
cwres.1 < compute.cwres("1", id=1)
## xpdb5 is an Xpose data object
## We expect to find the required NONMEM run and table files for run
## 5 in the current working directory
xpdb5 < xpose.data(5)
## Compare WRES, CWRES
xpdb5 < xpose.calculate.cwres(xpdb5)
cwres.wres.vs.idv(xpdb5)
## End(Not run)

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