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Re: Analyzing bootstrap output in R

From: saik.urien.svp <saik.urien>
Date: Wed, 26 Nov 2008 11:07:45 +0100

Kellie

As far as I can see from your input, the problem arises because some rows
must have NA or blank or no values. I suspect this can be due to the
theta.se. A simple way to fix the problem could be to delete the $COVARIANCE
statement.

Saik


----- Original Message -----
From: Kellie Turner <kellie.turner
To: <nmusers
Sent: Wednesday, November 26, 2008 9:45 AM
Subject: [NMusers] Analyzing bootstrap output in R


> From: Kellie Turner
> Sent: 25 November 2008 15:38
> To: nmusers
> Subject: Analyzing bootstrap output in R
>
> Dear NONMEM users,
> I am trying to analyze in R the results of a bootstrap run of a model. The
bootsrap runs fine with NONMEM VI level 1.0, implemented in PDxPOP 3.0.
> However, when I try to view the output in R, I get this error message:
> Error in data.frame (est=c(unlist(theta)), se= c(unlinst(theta.se))):
arguments imply differing number of rows:7, 0.
>
> The data is from 2 courses,and the problem seems to be with including both
courses, as I have no problems when I include only 1 course. I have tried
going back to the base model (no covariates, no IOV, no correlation between
CL and V), and I get the same error message when data from both courses are
included.
> Does anyone know how I can fix this problem so that I can view the
bootstrap results in R?
> Thanks in advance for your assistance,
> Kellie
>
>
> Here is the control file
> $INPUT C ID TIME DV AMT RATE EVID GFR GT1 GT2 WT OCC
> $DATA bootstrap.csv IGNORE=C
> $SUBROUTINES ADVAN3 TRANS4
> $PK
> HET=0
> HOM=0
> UNK=0
> IF(GT1.EQ.2) HET=1
> IF(GT1.EQ.3) HOM=1
> IF(GT1.EQ.0) UNK=1
>
> OCC1=0
> OCC2=0
> IF(OCC.EQ.0) OCC1=1
> IF(OCC.EQ.1) OCC2=1
>
> IF (AMT.GT.0) THEN
> TDOS=TIME
> TAD= 0.0
> ENDIF
> IF (AMT.EQ.0) TAD=TIME-TDOS
>
> TVCL=THETA(1)*(1-(THETA(5)*HET + 2*THETA(5)*HOM))*(1-THETA(6)*UNK)
> CL=TVCL*EXP(ETA(1)+OCC1*ETA(5)+OCC2*ETA(6))
> TVV1=THETA(2) + THETA(7)*(WT/70)
> TVQ=THETA(3)
> TVV2=THETA(4)
> V1=TVV1*EXP(ETA(2)+OCC1*ETA(7)+OCC2*ETA(8))
> Q=TVQ*EXP(ETA(3))
> V2=TVV2*EXP(ETA(4))
> S1=V1
> AUC=AMT/CL
> SID=ID
>
> $ERROR
> DEL=0
> IF (F.EQ.0) DEL=1
> W=F+DEL
> Y=F+W*EPS(1)
> IPRED=F
> IRES=DV-IPRED
> IWRES=IRES/W
> $THETA (0,.05,2) ; [CL]
> $THETA (5,10,20) ; [V1]
> $THETA (0,.2,2) ; [Q]
> $THETA (3,9,30) ; [V2]
> $THETA (0,.05,.5) ; [GT1]
> $THETA (0,.05,.5) ; [UNK GT1]
> $THETA (0,5,20) ; [WT]
> $OMEGA BLOCK (2)
> 0.5 ;[P] (1,1)
> 0.1 ;[F] (1,2)
> 0.5 ;[P] (2,2)
> $OMEGA 0 FIXED ;[P] INTER IND VAR IN Q
> $OMEGA 0.1 ;[P] INTERIND VAR IN V2
> $OMEGA BLOCK (1).2 ;[F]
> $OMEGA BLOCK (1) SAME ;[F]
> $OMEGA BLOCK (1).2 ;[F]
> $OMEGA BLOCK (1) SAME ;[F]
> $SIGMA 0.05 ;[P] PROPORTIONAL COMPONENT
>
> ;$MSFI
> $EST METHOD=0 SIGDIGITS=4 POSTHOC NOABORT MSF=boot-275.msf
> $COVARIANCE
> $TABLE FILE=boot-275.TAB ID TIME CL DV V1 V2 Q GT1 WT IPRED PRED ETA1 ETA2
ETA3 ETA4 ETA5 ETA6 ETA7 ETA8 NOPRINT ONEHEADER
> $TABLE ID NOPRINT ONEHEADER FILE=patabboot-275
> $TABLE ID NOPRINT ONEHEADER FILE=cotabboot-275
> $TABLE ID NOPRINT ONEHEADER FILE=catabboot-275
> $TABLE ID TIME IPRED IWRES NOPRINT ONEHEADER FILE=sdtabboot-275
>
Received on Wed Nov 26 2008 - 05:07:45 EST

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