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Analyzing bootstrap output in R

From: Kellie Turner <kellie.turner>
Date: Wed, 26 Nov 2008 08:45:50 +0000

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))): a=
rguments 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 g=
oing 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 bootstra=
p 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 ETA=
2 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 - 03:45:50 EST

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