ADAPT II Release 4 Instructions
Red Text Lines are Instructions
Blue Characters are user entries
A) Log on to BINGER (binger.ouhsc.edu) and create a new class directory
BINGER$ create/dir [.class]
B) Move to the new directory The new directory is home.CLASS
where home (here and later) is the name of your home directory
BINGER$ cd [.class]
U1:[home.CLASS]
C) Copy the file db-copy.com to this directory
BINGER$ COPY U1:[DAVID.MAC.PUB]DB-COPY.COM DB-COPY.COM
D) Use this file, twice
BINGER$ @db-copy
U1:[home.CLASS]
%COPY-S-COPIED, U1:[DAVID.MAC.PUB]DB-COPY.COM;23 copied to U1:[home.CLASS]DB-COP
Y.COM;13 (2 blocks)
%COPY-S-COPIED, U1:[DAVID.MAC.PUB]TUT5.BAT;1 copied to U1:[home.CLASS]TUT5.BAT;1
1 (8 blocks)
%COPY-S-COPIED, U1:[DAVID.MAC.PUB]TUTORIAL_5.DAT;1 copied to
...
BINGER$ @db-copy
U1:[home.CLASS]
%COPY-S-COPIED, U1:[DAVID.MAC.PUB]DB-COPY.COM;23 copied to U1:[home.CLASS]DB-COP
Y.COM;14 (2 blocks)
%COPY-S-COPIED, U1:[DAVID.MAC.PUB]TUT5.BAT;1 copied to ...
E) Run ADAPT II Release 4
BINGER$ adapt
ADAPT II
Release 4
Biomedical Simulations Resource
University of Southern California
Installed at: OUHSC COLLEGE OF PHARMACY
Initialize Session
Terminal Options:
1. VT/TEK Terminal
2. X Windows (not available)
Enter option number: 1
Editor Options:
1. EDT
2. EMACS
Enter option number: 1
Program Menu:
1. SIM
2. ID
3. SAMPLE
4. Previous executeable image
5. Exit ADAPT
Enter option number: 2
Model File Menu:
1. Define a new model 4. Return to Program Menu
2. Use an existing model 5. Exit ADAPT
3. Modify an existing model
Enter option number: 3
Enter name of existing model file (e.g., 1compk): oneciv
Enter name for new model file (e.g., newname): firsteg
F) Edit S/R if necessary - not necessary here
C**********************************************************************
C ADAPT II *
C Release 4 *
C**********************************************************************
C *
C MODEL *
C *
C This file contains the Fortran subroutines listed below in *
C which the user must enter the relevant equations and constants. *
C Consult the user's manual for details concerning the format for *
C entered equations and definition of symbols. *
C *
C 1. DiffEq- System Differential Equations. *
C 2. Amat - System State Matrix. *
C 3. Output- System Output Equations. *
C 4. Symbol- Parameter Symbols,Constants. *
C 5. Varmod- Variance Model Equations used *
C 6. Prior - Prior Mean and Covariance values *
C 7. Sparam- Secondary parameters *
C *
C**********************************************************************
Subroutine DIFFEQ(T,X,XP)
Implicit None
c Include 'globals.inc'
c Include 'model.inc'
include 'u1:[david.adapt4]globals.inc'
include 'u1:[david.adapt4]model.inc'
Real*8 T,X(MaxNDE),XP(MaxNDE)
CC
C----------------------------------------------------------------------C
C 1. Enter Differential Equations Below {e.g. XP(1) = -P(1)*X(1) } C
C----c-----------------------------------------------------------------C
xp(1) = -p(1)*x(1)
C----------------------------------------------------------------------C
C----------------------------------------------------------------------C
C
Return
End
C######################################################################C
Subroutine AMAT(A)
Implicit None
c Include 'globals.inc'
c Include 'model.inc'
include 'u1:[david.adapt4]globals.inc'
include 'u1:[david.adapt4]model.inc'
Integer I,J
Real*8 A(MaxNDE,MaxNDE)
DO I=1,Ndeqs
Do J=1,Ndeqs
A(I,J)=0.0D0
End Do
End Do
CC
C----------------------------------------------------------------------C
C 2. Enter non zero elements of state matrix {e.g. A(1,1) = -P(1) } C
C----c-----------------------------------------------------------------C
C----------------------------------------------------------------------C
C----------------------------------------------------------------------C
C
Return
End
C######################################################################C
Subroutine OUTPUT(Y,T,X)
Implicit None
c Include 'globals.inc'
c Include 'model.inc'
include 'u1:[david.adapt4]globals.inc'
include 'u1:[david.adapt4]model.inc'
Real*8 Y(MaxNOE),T,X(MaxNDE)
CC
C----------------------------------------------------------------------C
C 3. Enter Output Equations Below {e.g. Y(1) = X(1)/P(2) } C
C----c-----------------------------------------------------------------C
Y(1) = x(1)/p(2)
C----------------------------------------------------------------------C
C----------------------------------------------------------------------C
C
Return
End
C######################################################################C
Subroutine SYMBOL
Implicit None
c Include 'globals.inc'
c Include 'model.inc'
include 'u1:[david.adapt4]globals.inc'
include 'u1:[david.adapt4]model.inc'
CC
C----------------------------------------------------------------------C
C 4. Enter as Indicated C
C----c-----------------------------------------------------------------C
NDEqs = 1 ! Enter # of Diff. Eqs.
NSParam = 2 ! Enter # of System Parameters.
NVparam = 1 ! Enter # of Variance Model Parameters.
NSecPar = 0 ! Enter # of Secondary Parameters.
NSecOut = 0 ! Enter # of Secondary Outputs (not used).
Ieqsol = 1 ! Model type: 1 - DIFFEQ, 2 - AMAT, 3 - OUTPUT only.
Descr = 'One Compartment IV Bolus Example'
C----------------------------------------------------------------------C
C----------------------------------------------------------------------C
C
CC
C----------------------------------------------------------------------C
C 4. Enter Symbol for Each System Parameter (eg. Psym(1)='Kel') C
C----c-----------------------------------------------------------------C
PSym(1) = 'kel'
PSym(2) = 'V'
C----------------------------------------------------------------------C
C----------------------------------------------------------------------C
CC
C----------------------------------------------------------------------C
C 4. Enter Symbol for Each Variance Parameter {eg: PVsym(1)='Sigma'} C
C----c-----------------------------------------------------------------C
PVsym(1) = 'Sigma'
C----------------------------------------------------------------------C
C----------------------------------------------------------------------C
CC
C----------------------------------------------------------------------C
C 4. Enter Symbol for Each Secondary Parameter {eg: PSsym(1)='CLt'} C
C----c-----------------------------------------------------------------C
C----------------------------------------------------------------------C
C----------------------------------------------------------------------C
C
Return
End
C######################################################################C
Subroutine VARMOD(V,T,X,Y)
Implicit None
c Include 'globals.inc'
c Include 'model.inc'
include 'u1:[david.adapt4]globals.inc'
include 'u1:[david.adapt4]model.inc'
Real*8 V(MaxNOE),T,X(MaxNDE),Y(MaxNOE)
CC
C----------------------------------------------------------------------C
C 5. Enter Variance Model Equations Below C
C {e.g. V(1) = PV(1)**2 * Y(1)**PV(2) } C
C----c-----------------------------------------------------------------C
V(1) = Y(1)**pv(1)
C----------------------------------------------------------------------C
C----------------------------------------------------------------------C
C
Return
End
C######################################################################C
Subroutine PRIOR(Pmean,Pcov,ICmean,ICcov)
Implicit None
c Include 'globals.inc'
c Include 'model.inc'
include 'u1:[david.adapt4]globals.inc'
include 'u1:[david.adapt4]model.inc'
Integer I,J
Real*8 Pmean(MaxNSP+MaxNDE), ICmean(MaxNDE)
Real*8 Pcov(MaxNSP+MaxNDE,MaxNSP+MaxNDE), ICcov(MaxNDE,MaxNDE)
CC
C----------------------------------------------------------------------C
C 6. Enter Nonzero Elements of Prior Mean Vector C
C { e.g. Pmean(2) = 10.0 } C
C----c-----------------------------------------------------------------C
C----------------------------------------------------------------------C
C----------------------------------------------------------------------C
CC
C----------------------------------------------------------------------C
C 6. Enter Nonzero Elements of Covariance Matrix (Lower Triang.) C
C { e.g. Pcov(2,1) = 0.25 } C
C----c-----------------------------------------------------------------C
C----------------------------------------------------------------------C
C----------------------------------------------------------------------C
C
Return
End
C######################################################################C
Subroutine SPARAM(PS,P,IC)
Implicit None
c Include 'globals.inc'
include 'u1:[david.adapt4]globals.inc'
Real*8 PS(MaxNSECP), P(MaxNSP+MaxNDE), IC(MaxNDE)
CC
C----------------------------------------------------------------------C
C 7. Enter Equations Defining Secondary Parameters C
C { e.g. PS(1) = P(1)*P(2) } C
C----c-----------------------------------------------------------------C
C----------------------------------------------------------------------C
C----------------------------------------------------------------------C
C
Return
End
G) Exit edit mode with control-Z and exit (to save changes)
or quit (to make no changes - i.e. keep the file the same)
control-Z
*exit
U1:[home.CLASS]FIRSTEG.FOR;11 258 lines
ADAPT II
Release 4
Biomedical Simulations Resource
University of Southern California
Installed at: OUHSC COLLEGE OF PHARMACY
compiling... FIRSTEG
linking..... FIRSTEG & $ADAPT:ID
Enter file name to save executable program (e.g., 1compk) else : firsteg
ADAPT II ID -- PARAMETER ESTIMATION Date: 3/07/1999 Time: 20:35
Read data from a file (Y/N)? n
Do you want to save these data in an output file (Y/N)? n
----- SUPPLY MODEL INPUT INFORMATION -----
Enter the number of model inputs: 0
Enter the number of bolus inputs: 1
Enter the compartment number for each bolus input (e.g. 1,3,...): 1
Enter the number of input event times: 1
For each input event enter as required:
Time Value for all Inputs
Event Units, B(1)
1. 0,250
----- SUPPLY MODEL OUTPUT INFORMATION -----
Enter the number of model output equations: 1
Enter the number of observation times: 5
For each observation enter as required:
Time Measured Value For Each Output
Observation Units , Y(1)
1. 1,8
2. 2,5
3. 3,2.6
4. 5,0.9
5. 6,0.56
----- ESTIMATOR SELECTION -----
The following estimation procedures are available:
1. Weighted least squares (WLS)
2. Maximum likelihood (ML)
3. Generalized least squares (GLS)
4. Maximum a posteriori probability (MAP)
Enter option number: 1
--- Supply Weighting Information For WLS Estimator ---
The following weighting options are available:
1. General
2. Inverse variance of the output error (linear)
3. Inverse variance of the output error (nonlinear)
For Y( 1):
Enter the number of the desired weighting procedure: 2
Define the Linear Std. Dev. vs Output Curve:
Y( 1) Value, Std. Dev.
Low Measurement .5,.05
High Measurement 10,1
Enter the number of 0 weight observations: 0
----- INITIALIZE ESTIMATION PROCEDURE -----
Read parameter values from a file (Y/N)? n
Enter initial values for parameters & specify those to be estimated:
Value Estimate (Y/N)?
kel .5,y
V 20,y
IC( 1) 0,n
Do you want to store the parameter values in a file (Y/N)? n
Enter maximum number of iterations: 300
Do you want the iterations printed (Y/N)? n
----- RESULTS -----
--- A. Iterations ---
Number of iterations = 0
Number of function calls = 1
Fitted Parameters
kel = 0.5000
V = 20.00
Estimator criterion value = 4.64870
Working...
---B. Iteration Summary---
Convergence has been achieved.
Number of iterations = 16
Number of function calls = 67
Fitted Parameters
kel = 0.5407
V = 18.06
Estimator criterion value= 0.863689
--- C. WLS Estimation Summary---
Do you want an estimation summary table(Y/N)? y
Do you want the estimation summary table stored in a file (Y/N)? n
Date: 3/07/1999 Time: 20:37
Model: One Compartment IV Bolus Example
Weighting Information
Option for Y( 1): 2 with (.5000 ,.5000E-01) and (10.00 ,1.000 )
Convergence achieved
Number of iterations: 16
Number of function calls: 67
Estimator criterion value: 0.863689
Weighted
Output R-squared Sum of Squares Sum of Squares
Y( 1) 0.997 0.863689 0.116391
Model Selection Criteria
AIC: 3.2673
SCHWARZ: 2.4862
Press Enter to continue: [cr]
Initial Final
Parameter Value Estimate CV(%) Confidence interval (95%)
kel 0.5000 0.5407 4.528 [ 0.4628 , 0.6186 ]
V 20.00 18.06 9.453 [ 12.63 , 23.50 ]
IC( 1) 0.0000E+00 Fixed
Do you want a correlation (1) or covariance (2) matrix, or neither (N)? 1
kel V
kel 1.00
V -0.88 1.00
Do you want a correlation (1) or covariance (2) matrix, or neither (N)? 2
kel V
kel 0.599E-03
V -.368E-01 2.92
Do you want a correlation (1) or covariance (2) matrix, or neither (N)? n
--- D. WLS Estimation Model Prediction and Data Summary ---
Do you want a prediction and data summary table (Y/N)? y
Do you want the prediction and data summary stored in a file (Y/N)? n
Date: 3/07/1999 Time: 20:37
Model: One Compartment IV Bolus Example
Y( 1)
Obs.Num. Time Data Model Est. Residual Weight
1 1.000 8.000 8.059 -0.5939E-01 1.563
2 2.000 5.000 4.693 0.3065 4.000
3 3.000 2.600 2.733 -0.1333 14.79
4 5.000 0.9000 0.9270 -0.2696E-01 123.5
5 6.000 0.5600 0.5398 0.2018E-01 318.9
Press Enter to continue: [cr]
Y( 1) (Continued) Std. Dev. Standardized
Obs.Num. Model Est. Model Est. Residual
1 8.059 0.5948 -0.7424E-01
2 4.693 0.2644 0.6131
3 2.733 0.1252 -0.5126
4 0.9270 0.5509E-01 -0.2996
5 0.5398 0.4194E-01 0.3603
Plotting options:
1. Default plots
2. Plotting with options
3. Store plot data to a file
4. No plots
Enter option number: 4
________________________________________
--- RE-ESTIMATION OPTIONS ---
1. Change initial parameter values
2. Select a different estimator
3. Analyze a different data set
4. Exit ID
Enter option: 4
________________________________________
ADAPT II ID -- PARAMETER ESTIMATION Date: 3/07/1999 Time: 20:37
FORTRAN STOP
Enter (CR) to continue: [cr]
ADAPT II
Release 4
Biomedical Simulations Resource
University of Southern California
Installed at: OUHSC COLLEGE OF PHARMACY
Program Menu:
1. SIM
2. ID
3. SAMPLE
4. Previous executeable image
5. Exit ADAPT
Enter option number: 5
H) Purge (remove) old version of files to save space.
BINGER$ pur