From:"Bachman, William"
Subject:[NMusers] "Tip of the Week #3 - February 25, 2002" - Coding Time After Dose
Date:Tue, February 26, 2002 4:42 pm
Topic for Tip of the "Random Time Interval" #3 was suggested by Nick
Holford.
Having the time of an observation after a dose (TAD) is useful in generating
diagnostic plots, particulary in multiple dose studies. (TAD is also used
in diagnostic plots that are automatically generated with the PDx-Pop
interface and must be found in the table file for the run.)
Several ways of generating TAD are given below in order of increasing
complexity:
1. in this version, I keyed off of AMT:
$PK
IF (AMT.GT.0) THEN
TDOS=TIME
TAD=0.0
ENDIF
IF (AMT.EQ.0) TAD=TIME-TDOS
Caution: will not work for SS infustion (AMT is 0).
2. you could also use EVID:
$PK
IF (EVID.EQ.1.OR.EVID.EQ.4) THEN
TDOS=TIME
TAD=0.0
ENDIF
IF (EVID.NE.1.AND.EVID.NE.4) TAD=TIME-TDOS
Caution: will not work for observations before the first dose as may be
found in PK-PD data.
3. this version uses EVID and NEWIND. The code below sets TAD=0.0 for all
nondose records prior to the first dose.
$PK
IF(NEWIND.LT.2) THEN
IFL=0
TAD=0.0
ENDIF
IF(EVID.EQ.1.OR.EVID.EQ.4) THEN
TDOS=TIME
TAD=0.0
IFL=1
ENDIF
IF(IFL.EQ.1.AND.EVID.NE.1.AND.EVID.NE.4)TAD=TIME-TDOS
Caution: will not calculate correct TAD for observations after an ADDL dose
[Note: Remember to ask for TAD in the $TABLE record of your control stream.]
and now ... (drum roll please) ... the NONMEM Coding Challenge #1
CHALLENGE: how would you code to get the correct TAD after ADDL doses?
(control stream and data below)
[To be honest, I haven't figured this one out yet myself! This tip is
already late enough, so, for those of you who like a challenge or who just
have a lot of time on your hands, give it a shot! The solution that I like
the best will be published in a subsequent "Tip" {- NO, THIS IS NOT A
DEMOCRACY -}.] Hint: may require an INFN subroutine
CONTROL STREAM:
$PROB RUN# 705 nonmem coding challenge #1
$INPUT C ID TIME DV AMT WT AGE CRCL SMK ADDL II EVID
$DATA 704.csv IGNORE=C
$SUBROUTINE ADVAN2 TRANS2
$PK
;replace this TAD code with yours for ADDL TAD's
IF(NEWIND.LT.2) THEN
IFL=0
TAD=0.0
ENDIF
IF(EVID.EQ.1.OR.EVID.EQ.4) THEN
TDOS=TIME
TAD=0.0
IFL=1
ENDIF
IF(IFL.EQ.1.AND.EVID.NE.1.AND.EVID.NE.4)TAD=TIME-TDOS
CL=THETA(1)*EXP(ETA(1))
TVV=THETA(2)
V=TVV*EXP(ETA(2))
TVKA=THETA(3)
KA=TVKA*EXP(ETA(3))
S2=V
$THETA
(0, 10)
(0, 100)
(0, 0.5)
$ERROR
Y=F+ERR(1)
IPRED=F
$OMEGA
0.04 ;[P] INTERIND VAR IN CL
0.04 ;[P] INTERIND VAR IN V
0.04 ;[P] INTERIND VAR IN KA
$SIGMA
0.2 ;[A] ADDITIVE COMPONENT
$EST MAXEVAL=0 PRINT=2 NOABORT ;POSTHOC
$TABLE ID TIME IPRED TAD NOPRINT ONEHEADER FILE=705.tab
DATA FILE (704.CSV):
C,Data Desc: test of TAD for ADDL,,,,,,,,,,
C,ID,TIME,DV,AMT,WT,AGE,CRCL,SMK,ADDL,II,EVID
,1,0,0,0,58.4,51,4.49,1,0,0,2
,1,0.1,0,500,58.4,51,4.49,1,1,24,1
,1,1.1,1.67538,0,58.4,51,4.49,1,0,0,0
,1,4.1,2.79283,0,58.4,51,4.49,1,0,0,0
,1,10.1,0.583263,0,58.4,51,4.49,1,0,0,0
,1,24.1,0.146255,0,58.4,51,4.49,1,0,0,0
,1,25.1,1.67538,0,58.4,51,4.49,1,0,0,0
,2,0,0,0,79.3,53,5.05,0,0,0,2
,2,0.1,0,500,79.3,53,5.05,0,1,24,1
,2,1.1,1.32864,0,79.3,53,5.05,0,0,0,0
,2,4.1,3.89134,0,79.3,53,5.05,0,0,0,0
,2,10.1,3.27451,0,79.3,53,5.05,0,0,0,0
,2,24.1,1.1749,0,79.3,53,5.05,0,0,0,0
,2,25.1,1.32864,0,79.3,53,5.05,0,0,0,0
,3,0,0,0,88.3,53,6.55,1,0,0,2
,3,0.1,0,500,88.3,53,6.55,1,1,24,1
,3,1.1,0.803595,0,88.3,53,6.55,1,0,0,0
,3,4.1,1.62364,0,88.3,53,6.55,1,0,0,0
,3,10.1,0.508614,0,88.3,53,6.55,1,0,0,0
,3,24.1,0.13739,0,88.3,53,6.55,1,0,0,0
,3,25.1,0.803595,0,88.3,53,6.55,1,0,0,0
,4,0,0,0,69.9,25,5.96,1,0,0,2
,4,0.1,0,500,69.9,25,5.96,1,1,24,1
,4,1.1,2.45726,0,69.9,25,5.96,1,0,0,0
,4,4.1,5.92102,0,69.9,25,5.96,1,0,0,0
,4,10.1,3.18875,0,69.9,25,5.96,1,0,0,0
,4,24.1,0.564405,0,69.9,25,5.96,1,0,0,0
,4,25.1,2.45726,0,69.9,25,5.96,1,0,0,0
,5,0,0,0,76.7,51,7.92,0,0,0,2
,5,0.1,0,500,76.7,51,7.92,0,1,24,1
,5,1.1,1.55213,0,76.7,51,7.92,0,0,0,0
,5,4.1,4.31103,0,76.7,51,7.92,0,0,0,0
,5,10.1,3.8874,0,76.7,51,7.92,0,0,0,0
,5,24.1,1.3813,0,76.7,51,7.92,0,0,0,0
,5,25.1,1.55213,0,76.7,51,7.92,0,0,0,0
,6,0,0,0,84.8,58,5.57,0,0,0,2
,6,0.1,0,500,84.8,58,5.57,0,1,24,1
,6,1.1,1.39749,0,84.8,58,5.57,0,0,0,0
,6,4.1,3.14751,0,84.8,58,5.57,0,0,0,0
,6,10.1,2.4798,0,84.8,58,5.57,0,0,0,0
,6,24.1,0.870149,0,84.8,58,5.57,0,0,0,0
,6,25.1,1.39749,0,84.8,58,5.57,0,0,0,0
,7,0,0,0,79.3,59,3.31,1,0,0,2
,7,0.1,0,500,79.3,59,3.31,1,1,24,1
,7,1.1,2.27435,0,79.3,59,3.31,1,0,0,0
,7,4.1,3.17944,0,79.3,59,3.31,1,0,0,0
,7,10.1,1.04811,0,79.3,59,3.31,1,0,0,0
,7,24.1,0.006388,0,79.3,59,3.31,1,0,0,0
,7,25.1,2.27435,0,79.3,59,3.31,1,0,0,0
,8,0,0,0,76.8,60,7.05,1,0,0,2
,8,0.1,0,500,76.8,60,7.05,1,1,24,1
,8,1.1,1.10077,0,76.8,60,7.05,1,0,0,0
,8,4.1,2.27792,0,76.8,60,7.05,1,0,0,0
,8,10.1,1.10827,0,76.8,60,7.05,1,0,0,0
,8,24.1,0.069864,0,76.8,60,7.05,1,0,0,0
,8,25.1,1.10077,0,76.8,60,7.05,1,0,0,0
,9,0,0,0,92.2,56,6.8,1,0,0,2
,9,0.1,0,500,92.2,56,6.8,1,1,24,1
,9,1.1,1.11266,0,92.2,56,6.8,1,0,0,0
,9,4.1,2.35879,0,92.2,56,6.8,1,0,0,0
,9,10.1,1.39264,0,92.2,56,6.8,1,0,0,0
,9,24.1,0.115128,0,92.2,56,6.8,1,0,0,0
,9,25.1,1.11266,0,92.2,56,6.8,1,0,0,0
,10,0,0,0,79.6,65,6.59,1,0,0,2
,10,0.1,0,500,79.6,65,6.59,1,1,24,1
,10,1.1,1.47965,0,79.6,65,6.59,1,0,0,0
,10,4.1,2.87565,0,79.6,65,6.59,1,0,0,0
,10,10.1,1.47107,0,79.6,65,6.59,1,0,0,0
,10,24.1,0.189881,0,79.6,65,6.59,1,0,0,0
,10,25.1,1.47965,0,79.6,65,6.59,1,0,0,0
,11,0,0,0,72.6,57,7.26,1,0,0,2
,11,0.1,0,500,72.6,57,7.26,1,1,24,1
,11,1.1,2.78516,0,72.6,57,7.26,1,0,0,0
,11,4.1,5.9958,0,72.6,57,7.26,1,0,0,0
,11,10.1,2.74331,0,72.6,57,7.26,1,0,0,0
,11,24.1,0.272643,0,72.6,57,7.26,1,0,0,0
,11,25.1,2.78516,0,72.6,57,7.26,1,0,0,0
,12,0,0,0,83.3,63,4.41,1,0,0,2
,12,0.1,0,500,83.3,63,4.41,1,1,24,1
,12,1.1,2.36294,0,83.3,63,4.41,1,0,0,0
,12,4.1,4.37676,0,83.3,63,4.41,1,0,0,0
,12,10.1,2.21826,0,83.3,63,4.41,1,0,0,0
,12,24.1,0.127228,0,83.3,63,4.41,1,0,0,0
,12,25.1,2.36294,0,83.3,63,4.41,1,0,0,0
,13,0,0,0,76.2,28,5.91,0,0,0,2
,13,0.1,0,500,76.2,28,5.91,0,1,24,1
,13,1.1,2.05905,0,76.2,28,5.91,0,0,0,0
,13,4.1,5.18627,0,76.2,28,5.91,0,0,0,0
,13,10.1,3.31315,0,76.2,28,5.91,0,0,0,0
,13,24.1,0.690486,0,76.2,28,5.91,0,0,0,0
,13,25.1,2.05905,0,76.2,28,5.91,0,0,0,0
,14,0,0,0,58.4,27,5.16,0,0,0,2
,14,0.1,0,500,58.4,27,5.16,0,1,24,1
,14,1.1,1.78423,0,58.4,27,5.16,0,0,0,0
,14,4.1,5.60111,0,58.4,27,5.16,0,0,0,0
,14,10.1,4.88792,0,58.4,27,5.16,0,0,0,0
,14,24.1,1.71557,0,58.4,27,5.16,0,0,0,0
,14,25.1,1.78423,0,58.4,27,5.16,0,0,0,0
,15,0,0,0,53.4,33,6.2,0,0,0,2
,15,0.1,0,500,53.4,33,6.2,0,1,24,1
,15,1.1,2.31405,0,53.4,33,6.2,0,0,0,0
,15,4.1,4.82135,0,53.4,33,6.2,0,0,0,0
,15,10.1,2.78629,0,53.4,33,6.2,0,0,0,0
,15,24.1,0.44581,0,53.4,33,6.2,0,0,0,0
,15,25.1,2.31405,0,53.4,33,6.2,0,0,0,0
,16,0,0,0,80.9,63,2.32,1,0,0,2
,16,0.1,0,500,80.9,63,2.32,1,1,24,1
,16,1.1,1.63497,0,80.9,63,2.32,1,0,0,0
,16,4.1,3.31025,0,80.9,63,2.32,1,0,0,0
,16,10.1,1.3666,0,80.9,63,2.32,1,0,0,0
,16,24.1,0.105905,0,80.9,63,2.32,1,0,0,0
,16,25.1,1.63497,0,80.9,63,2.32,1,0,0,0
,17,0,0,0,91.1,62,7.45,0,0,0,2
,17,0.1,0,500,91.1,62,7.45,0,1,24,1
,17,1.1,1.69697,0,91.1,62,7.45,0,0,0,0
,17,4.1,2.56591,0,91.1,62,7.45,0,0,0,0
,17,10.1,1.07543,0,91.1,62,7.45,0,0,0,0
,17,24.1,0.173012,0,91.1,62,7.45,0,0,0,0
,17,25.1,1.69697,0,91.1,62,7.45,0,0,0,0
,18,0,0,0,60.7,48,4.5,1,0,0,2
,18,0.1,0,500,60.7,48,4.5,1,1,24,1
,18,1.1,1.34805,0,60.7,48,4.5,1,0,0,0
,18,4.1,2.82872,0,60.7,48,4.5,1,0,0,0
,18,10.1,1.17772,0,60.7,48,4.5,1,0,0,0
,18,24.1,0.166779,0,60.7,48,4.5,1,0,0,0
,18,25.1,1.34805,0,60.7,48,4.5,1,0,0,0
,19,0,0,0,69.6,39,4.78,0,0,0,2
,19,0.1,0,500,69.6,39,4.78,0,1,24,1
,19,1.1,1.41609,0,69.6,39,4.78,0,0,0,0
,19,4.1,3.64124,0,69.6,39,4.78,0,0,0,0
,19,10.1,2.85268,0,69.6,39,4.78,0,0,0,0
,19,24.1,0.443417,0,69.6,39,4.78,0,0,0,0
,19,25.1,1.41609,0,69.6,39,4.78,0,0,0,0
,20,0,0,0,71.5,46,7.47,0,0,0,2
,20,0.1,0,500,71.5,46,7.47,0,1,24,1
,20,1.1,1.45283,0,71.5,46,7.47,0,0,0,0
,20,4.1,3.70842,0,71.5,46,7.47,0,0,0,0
,20,10.1,2.52282,0,71.5,46,7.47,0,0,0,0
,20,24.1,0.633448,0,71.5,46,7.47,0,0,0,0
,20,25.1,1.45283,0,71.5,46,7.47,0,0,0,0
,21,0,0,0,71.1,45,3.19,0,0,0,2
,21,0.1,0,500,71.1,45,3.19,0,1,24,1
,21,1.1,1.3647,0,71.1,45,3.19,0,0,0,0
,21,4.1,4.23997,0,71.1,45,3.19,0,0,0,0
,21,10.1,4.22604,0,71.1,45,3.19,0,0,0,0
,21,24.1,2.19366,0,71.1,45,3.19,0,0,0,0
,21,25.1,1.3647,0,71.1,45,3.19,0,0,0,0
,22,0,0,0,56.2,72,3.9,0,0,0,2
,22,0.1,0,500,56.2,72,3.9,0,1,24,1
,22,1.1,1.25251,0,56.2,72,3.9,0,0,0,0
,22,4.1,3.15997,0,56.2,72,3.9,0,0,0,0
,22,10.1,2.08904,0,56.2,72,3.9,0,0,0,0
,22,24.1,0.516536,0,56.2,72,3.9,0,0,0,0
,22,25.1,1.25251,0,56.2,72,3.9,0,0,0,0
,23,0,0,0,60.9,49,2.89,0,0,0,2
,23,0.1,0,500,60.9,49,2.89,0,1,24,1
,23,1.1,3.87079,0,60.9,49,2.89,0,0,0,0
,23,4.1,6.33528,0,60.9,49,2.89,0,0,0,0
,23,10.1,4.26429,0,60.9,49,2.89,0,0,0,0
,23,24.1,1.26654,0,60.9,49,2.89,0,0,0,0
,23,25.1,3.87079,0,60.9,49,2.89,0,0,0,0
,24,0,0,0,85.9,41,5.43,0,0,0,2
,24,0.1,0,500,85.9,41,5.43,0,1,24,1
,24,1.1,1.25722,0,85.9,41,5.43,0,0,0,0
,24,4.1,3.19174,0,85.9,41,5.43,0,0,0,0
,24,10.1,2.61531,0,85.9,41,5.43,0,0,0,0
,24,24.1,0.995998,0,85.9,41,5.43,0,0,0,0
,24,25.1,1.25722,0,85.9,41,5.43,0,0,0,0
,25,0,0,0,75.5,38,4.16,0,0,0,2
,25,0.1,0,500,75.5,38,4.16,0,1,24,1
,25,1.1,2.57073,0,75.5,38,4.16,0,0,0,0
,25,4.1,5.01613,0,75.5,38,4.16,0,0,0,0
,25,10.1,2.99356,0,75.5,38,4.16,0,0,0,0
,25,24.1,0.653015,0,75.5,38,4.16,0,0,0,0
,25,25.1,2.57073,0,75.5,38,4.16,0,0,0,0
,26,0,0,0,51.5,51,3.79,0,0,0,2
,26,0.1,0,500,51.5,51,3.79,0,1,24,1
,26,1.1,3.64646,0,51.5,51,3.79,0,0,0,0
,26,4.1,8.05537,0,51.5,51,3.79,0,0,0,0
,26,10.1,5.38704,0,51.5,51,3.79,0,0,0,0
,26,24.1,1.19447,0,51.5,51,3.79,0,0,0,0
,26,25.1,3.64646,0,51.5,51,3.79,0,0,0,0
,27,0,0,0,60.6,60,3.99,0,0,0,2
,27,0.1,0,500,60.6,60,3.99,0,1,24,1
,27,1.1,2.32245,0,60.6,60,3.99,0,0,0,0
,27,4.1,4.62563,0,60.6,60,3.99,0,0,0,0
,27,10.1,2.86928,0,60.6,60,3.99,0,0,0,0
,27,24.1,0.830628,0,60.6,60,3.99,0,0,0,0
,27,25.1,2.32245,0,60.6,60,3.99,0,0,0,0
,28,0,0,0,81.6,39,5.44,1,0,0,2
,28,0.1,0,500,81.6,39,5.44,1,1,24,1
,28,1.1,1.6357,0,81.6,39,5.44,1,0,0,0
,28,4.1,3.02622,0,81.6,39,5.44,1,0,0,0
,28,10.1,1.19906,0,81.6,39,5.44,1,0,0,0
,28,24.1,0.039839,0,81.6,39,5.44,1,0,0,0
,28,25.1,1.6357,0,81.6,39,5.44,1,0,0,0
,29,0,0,0,86.5,47,7.5,0,0,0,2
,29,0.1,0,500,86.5,47,7.5,0,1,24,1
,29,1.1,0.645889,0,86.5,47,7.5,0,0,0,0
,29,4.1,1.76215,0,86.5,47,7.5,0,0,0,0
,29,10.1,1.07923,0,86.5,47,7.5,0,0,0,0
,29,24.1,0.209841,0,86.5,47,7.5,0,0,0,0
,29,25.1,0.645889,0,86.5,47,7.5,0,0,0,0
,30,0,0,0,67.3,55,7.18,1,0,0,2
,30,0.1,0,500,67.3,55,7.18,1,1,24,1
,30,1.1,1.52906,0,67.3,55,7.18,1,0,0,0
,30,4.1,3.7605,0,67.3,55,7.18,1,0,0,0
,30,10.1,2.03334,0,67.3,55,7.18,1,0,0,0
,30,24.1,0.244644,0,67.3,55,7.18,1,0,0,0
,30,25.1,1.52906,0,67.3,55,7.18,1,0,0,0
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"Tip of the Week #3 - February 25, 2002" - Coding Time After Dose
From:Mats Karlsson [mailto:Mats.Karlsson@farmbio.uu.se]
Subject:Re: [NMusers] "Tip of the Week #3 - February 25, 2002" - Coding
Time After Dose(TAD) and ... the NONMEM Coding Challenge #1
Date:Wed, February 27, 2002 10:20 am
Hi,
Rather than trying to answer the difficult ADDL problem, I'd just like to
say
that Nick and Bill kindly made this oppotunity to point out (and warn) that
Xpose allows an even simpler way to calculate TAD. In Xpose, TAD is
calculated
(use "managing databases option 24.2") from the table files assuming that
any
non-observation record (i.e. WRES=0) is a dosing record. Thus, the
generation of
TAD in Xpose won't appropriately handle ADDL records, SS infusions or EVID=2
(observations before the first dose will be assumed to be zero though).
Mats
Mats Karlsson, PhD
Professor of Pharmacometrics
Div. of Pharmacokinetics and Drug Therapy
Dept. of Pharmaceutical Biosciences
Faculty of Pharmacy
Uppsala University
Box 591
SE-751 24 Uppsala
Sweden
phone +46 18 471 4105
fax +46 18 471 4003
mats.karlsson@farmbio.uu.se