Analyzing bootstrap output in R
From: Kellie Turner
Sent: 25 November 2008 15:38
To: [email protected]
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