NONMEM Analysis for Future Bayesian Estimation
I'm trying to work through the cycle of analyzing clinical data (as for an
aminoglycoside) using a one compartment model with elimination rate
described by:
kel = a * CR-CL + b and V
with the intent of being able to use the results for Bayesian analysis of
future data. My understanding is that I would like to calculate population
mean and standard deviation values for 'a', 'b', and V. Thus I simulated
256 data sets (one dose and two data points per set) and analyzed the
combined data using NONMEM.
Model: One compartment model with a one hour infusion. 256 data set generated
One time point between 1.25 and 2.5 and one time point between 6 and 12 hours.
Model parameters used for the simulation
CR-Cl = 65 +/- 20 (std.dev.) between 5 - 125
kel = a*CR-Cl + b
a = 0.005 +/- 10 % (c.v.) between 0.0001 - 0.1
b = 0.01 +/- 20 % (c.v.) between 0.0001 - 1.0
V = 15 +/- 5 % (c.v) between 1 - 200
Data for first 5 subjects...
1 90 90 0.0 0.0 69.16
1 0.0 0.0 1.75 3.44664 69.16
1 0.0 0.0 9.00 0.27351 69.16
2 60 60 0.0 0.0 67.25
2 0.0 0.0 2.00 2.64588 67.25
2 0.0 0.0 8.00 0.35496 67.25
3 60 60 0.0 0.0 113.72
3 0.0 0.0 2.50 1.34226 113.72
3 0.0 0.0 8.00 0.06132 113.72
4 50 50 0.0 0.0 74.7
4 0.0 0.0 1.75 1.78155 74.7
4 0.0 0.0 9.00 0.05505 74.7
5 60 60 0.0 0.0 22.85
5 0.0 0.0 2.00 3.2508 22.85
5 0.0 0.0 6.00 2.38014 22.85
......
My first attempt was to include ETA's for both the 'a' and 'b' values. Thus
after analysis I could include these in the Bayesian analysis. The control
file and the (some) output are below:
NONMEM control file > nmtran > nonmem
$PROBLEM Aminoglycoside example
$INPUT ID AMT RATE TIME DV CRCL
$DATA TEST
$SUBROUTINES ADVAN1
$PK
TA = THETA(1)*(1.+ETA(1))
TB = THETA(2)*(1.+ETA(2))
K = TA*CRCL + TB
V = THETA(3)*(1.+ETA(3))
S1 = V
$ERROR
Y = F*(1. + ERR(1))
$THETA (0.,.005,0.1) (0.,.01,1.0) (1,15,100)
$OMEGA .2 .2 .2
$SIGMA .2
$ESTIMATION PRINT=5 MAXEVALS=900
$COVARIANCE
$TABLE ID TIME AMT DV
$SCAT PRED VS DV UNIT
$SCAT WRES VS DV TIME CRCL
Partial output from NONMEM
*** MINIMUM VALUE OF OBJECTIVE FUNCTION
*** -1266.431
*** FINAL PARAMETER ESTIMATE
THETA - VECTOR OF FIXED EFFECTS *********************
TH 1 TH 2 TH 3
4.93E-03 8.75E-03 1.50E+01
OMEGA - COV MATRIX FOR RANDOM EFFECTS - ETAS ********
ETA1 ETA2 ETA3
ETA1 9.29E-03
ETA2 0.00E+00 1.54E-08
ETA3 0.00E+00 0.00E+00 3.02E-03
SIGMA - COV MATRIX FOR RANDOM EFFECTS - EPSILONS ****
EPS1
EPS1 5.06E-03
This gives:
Theta(1) = a = 4.93E-03 +/- 9.64 % sqrt(9.29E-03) * 100
Theta(2) = b = 8.75E-03 +/- 0.0124 % sqrt(1.54E-08) * 100
Theta(3) = V = 15.0 +/- 5.50 % sqrt(3.02E-03) * 100
Data = +/- 7.11 % sqrt(5.06E-03) * 100
These are all similar to the input parameters (except the c.v. for 'b').
Modeling these data as apparently suggested in the manual etc., I used the
control file below:
$PROBLEM Aminoglycoside example
$INPUT ID AMT RATE TIME DV CRCL
$DATA TEST
$SUBROUTINES ADVAN1
$PK
TA = THETA(1)
TB = THETA(2)
TK = TA*CRCL + TB
K = TK*(1.+ETA(1))
V = THETA(3)*(1.+ETA(2))
S1 = V
$ERROR
Y = F*(1. + ERR(1))
$THETA (0.,.005,0.1) (0.,.01,1.0) (1,15,100)
$OMEGA .2 .2
$SIGMA .2
$ESTIMATION PRINT=5 MAXEVALS=900
$COVARIANCE
$TABLE ID TIME AMT DV
$SCAT PRED VS DV UNIT
$SCAT WRES VS DV TIME CRCL
This produced the results:
*** MINIMUM VALUE OF OBJECTIVE FUNCTION
*** -1265.415
*** FINAL PARAMETER ESTIMATE
THETA - VECTOR OF FIXED EFFECTS *********************
TH 1 TH 2 TH 3
4.94E-03 8.04E-03 1.50E+01
OMEGA - COV MATRIX FOR RANDOM EFFECTS - ETAS ********
ETA1 ETA2
ETA1 8.82E-03
ETA2 0.00E+00 3.02E-03
SIGMA - COV MATRIX FOR RANDOM EFFECTS - EPSILONS ****
EPS1
EPS1 5.05E-03
This gives:
Theta(1) = a = 4.94E-03
Theta(2) = b = 8.04E-03
kel = a * CR-CL + b +/- 9.39 % sqrt(8.82E-03) * 100
Theta(3) = V = 1.50E+01 +/- 5.50 % sqrt(3.02E-03) * 100
Data = +/- 7.11 % sqrt(5.06E-03) * 100
These are all similar to the input parameters (except for the meaning of the
kel c.v.). This seemed to be a satisfactory approach except for the input
into the subsequent Bayesian analysis.
Any comments or suggestions. Thanks.