RE: [NMusers] output SE of population PK parameters in Nonmem

Dear All

I think you have to write your own INFN subroutine.
You may write something like this:

The config file SIZES must be on the same place as this code and must be =
the same as the SIZES used by your NONMEM installation

c Begin of own subroutine
      SUBROUTINE INFN (ICALL,THETA,DATREC,INDXS,NEWIND)
      INCLUDE 'SIZES'
      INTEGER PE,PT,PCOV,IERE,IERC,I,MODE
      PARAMETER (PE=LVR)
      PARAMETER (PT=LTH)
      PARAMETER (PCOV=LPAR3)
      
      DIMENSION THETA(*),DATREC(*),INDXS(*)
      DOUBLE PRECISION THETA
   
      COMMON /ROCM6/ THETAF(PT),OMEGAF(PE,PE),SIGMAF(PE,PE)
      COMMON /ROCM7/ SETH(PT),SEOM(PE,PE),SESIG(PE,PE)
      COMMON /ROCM8/ OBJECT
      COMMON /ROCM9/ IERE,IERC
      COMMON /CM12/ COV(PCOV)
      COMMON /CM2/ NETA
      DOUBLE PRECISION OBJECT, OBJECT1 DELTA
      DOUBLE PRECISION THETAF,OMEGAF,SIGMAF
      DOUBLE PRECISION INFTH(PT),INFOM(PE),INFSIG(PE)
      DOUBLE PRECISION SUPTH(PT),SUPOM(PE),SUPSIG(PE)
      DOUBLE PRECISION ETA(PE)
      INTEGER NTH,NETA,NEPS

      CHARACTER*16 FILECOV

1060 FORMAT(80F23.10)
      IF (ICALL.EQ.0) THEN
          OPEN(50,FILE=filecov,status='REPLACE')
        IPROB=1
        ENDIF

      IF (ICALL.EQ.3) THEN

      
        DO 20 I=1,PCOV
c PRINT *,'INFO',COV(I)
          IF (COV(I).EQ.0) THEN
            CLOSE(50)
            GOTO 30
            ENDIF
c PRINT *,'INFO',I,COV(I)

            WRITE (50,1060) COV(I)

            
20 CONTINUE
30 CONTINUE

      ENDIF
      RETURN
      END
C End of own subroutine

In the contol file
Write the following:
$SUBROUTINES ADVAN4 TRANS4 INFN=myown.f

The result will be a vector, which gives you the diagonal half matrix of =
the covariance matrix of estimate. (loaded in R it may look like the =
following lines

1 9.497490e-02
2 1.000000e+10
3 1.000000e+10
4 1.825657e-01
5 1.000000e+10
6 1.332238e+00
....
228 -2.389190e-05
229 1.000000e+10
230 6.468500e-06
231 1.393760e-05

The number of lines in this case 231 lines, shows you that you have a =
21x21 Matrix.

This is in the example the way to fill the results into the matrix
     [,1] [,2] [,3] [,4] [,5] [,6] [,7] [,8] [,9] [,10] [,11] [,12] =
[,13] [,14] [,15] [,16] [,17] [,18] [,19] [,20] [,21]
 [1,] 1 0 0 0 0 0 0 0 0 0 0 0 =
0 0 0 0 0 0 0 0 0
 [2,] 2 3 0 0 0 0 0 0 0 0 0 0 =
0 0 0 0 0 0 0 0 0
 [3,] 4 5 6 0 0 0 0 0 0 0 0 0 =
0 0 0 0 0 0 0 0 0
 [4,] 7 8 9 10 0 0 0 0 0 0 0 0 =
0 0 0 0 0 0 0 0 0
 [5,] 11 12 13 14 15 0 0 0 0 0 0 0 =
0 0 0 0 0 0 0 0 0
 [6,] 16 17 18 19 20 21 0 0 0 0 0 0 =
0 0 0 0 0 0 0 0 0
 [7,] 22 23 24 25 26 27 28 0 0 0 0 0 =
0 0 0 0 0 0 0 0 0
 [8,] 29 30 31 32 33 34 35 36 0 0 0 0 =
0 0 0 0 0 0 0 0 0
 [9,] 37 38 39 40 41 42 43 44 45 0 0 0 =
0 0 0 0 0 0 0 0 0
[10,] 46 47 48 49 50 51 52 53 54 55 0 0 =
0 0 0 0 0 0 0 0 0
[11,] 56 57 58 59 60 61 62 63 64 65 66 0 =
0 0 0 0 0 0 0 0 0
[12,] 67 68 69 70 71 72 73 74 75 76 77 78 =
0 0 0 0 0 0 0 0 0
[13,] 79 80 81 82 83 84 85 86 87 88 89 90 =
91 0 0 0 0 0 0 0 0
[14,] 92 93 94 95 96 97 98 99 100 101 102 103 =
104 105 0 0 0 0 0 0 0
[15,] 106 107 108 109 110 111 112 113 114 115 116 117 =
118 119 120 0 0 0 0 0 0
[16,] 121 122 123 124 125 126 127 128 129 130 131 132 =
133 134 135 136 0 0 0 0 0
[17,] 137 138 139 140 141 142 143 144 145 146 147 148 =
149 150 151 152 153 0 0 0 0
[18,] 154 155 156 157 158 159 160 161 162 163 164 165 =
166 167 168 169 170 171 0 0 0
[19,] 172 173 174 175 176 177 178 179 180 181 182 183 =
184 185 186 187 188 189 190 0 0
[20,] 191 192 193 194 195 196 197 198 199 200 201 202 =
203 204 205 206 207 208 209 210 0
[21,] 211 212 213 214 215 216 217 218 219 220 221 222 =
223 224 225 226 227 228 229 230 231


Some coding in R and you have the result of the covariance matrix of =
estimate in R
Than you can calculate in R with cov2cor the CORRELATION MATRIX OF =
ESTIMATE
Bevor you should delete all rows and columns equal to 1.000000e+10 (INF =
in NONMEM) and as result you should have a covariance matrix of =
estimates in R with your calculated estimates.

I hope this helps.

Mit freundlichen Grüßen / Best regards / Cordialement

Dipl. Ing. Heiner Speth

Sanofi-Aventis Deutschland GmbH
GMPK
Industriepark Hoechst
Bldg. H831, Room 364
D-65926 Frankfurt am Main
t: +49 69 305 2148
f: +49 69 305 942 052
w: www.sanofi-aventis.de

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Main · Handelsregister: Frankfurt am Main, Abt. B Nr. 40661
Vorsitzender des Aufsichtsrats: Hanspeter Spek - Geschäftsführer: =
Dr. Heinz-Werner Meier (Vorsitzender),
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-----Original Message-----
From: owner-nmusers_at_globomaxnm.com [mailto:owner-nmusers_at_globomaxnm.com] =
On Behalf Of Rik Schoemaker
Sent: Wednesday, February 06, 2008 2:31 PM
To: nmusers_at_globomaxnm.com
Subject: RE: [NMusers] output SE of population PK parameters in Nonmem

Dear all,

It's a neat trick and works very well, but can anyone tell me the =
keyword (like for instance SETHET below) for exporting the correlation =
matrix of the estimates and for the non-parametric estimates: 'expected =
value of ETA' and 'Covariance matrix of ETA'....

Thanks in advance,

Rik

-----Original Message-----
From: owner-nmusers_at_globomaxnm.com [mailto:owner-nmusers_at_globomaxnm.com] =
On Behalf Of GIRARD PASCAL
Sent: 01 February 2008 18:08
To: Jin, Bo; nmusers_at_globomaxnm.com
Subject: RE : [NMusers] output SE of population PK parameters in Nonmem

Hi Jin,

See in NONMEM help:
 ___________________________________________________________________
 | |
 | FINALIZATION EXAMPLE ($PRED AND $INFN) |
 |_________________________________________________________________|

 This example contains abbreviated code which can be inserted in a =
$PRED or $INFN block. This code outputs final parameter estimates, =
standard errors, minimum value of the objective function, and condi- =
tional estimates of etas to various user files. The return codes from =
Estimation and Covariance steps (zero for normal termination) are also =
output.

  IF (ICALL.EQ.3) THEN
    DO WHILE(DATA)
    IF (NEWIND.LE.1) WRITE (50,*) ETA
    ENDDO
    WRITE (51,*) OBJECT
    WRITE (52,*) THETA
    WRITE (53,*) SETHET
    WRITE (54,*) OMEGA(BLOCK)
    WRITE (55,*) SEOMEG(BLOCK)
    WRITE (56,*) SIGMA(BLOCK)
    WRITE (57,*) SESIGM(BLOCK)
    WRITE (58,*) IERE,IERC
  ENDIF

Alternatively, you take advantage of the fact that all those estimmates =
are stored in Vectors and matrices of various COMMON:
      COMMON /ROCM6/ THETAF(40),OMEGAF(30,30),SIGMAF(30,30)
      COMMON /ROCM7/ SETH(40),SEOM(30,30),SESIG(30,30)
      COMMON /ROCM8/ OBJECT
      COMMON /ROCM9/ IERE,IERC
      COMMON /CM12/ COV(2850)
and write your own INFN subroutine (see INFN help).

Best regards,
 
Pascal Girard, PhD
EA 3738, CTO
Fac Medecine Lyon-Sud, BP12
69921 OULLINS Cedex, France
pascal.girard_at_adm.univ-lyon1.fr
Tel +33 (0)4 26 23 59 54 / Fax +33 (0)4 26 23 59 76
 
Master Recherche Lyon 1 Santé et Populations, Spécialité PhIT =
http://master-sante-pop.univ-lyon1.fr/

>-----Message d'origine-----
>De : owner-nmusers_at_globomaxnm.com =
[mailto:owner-nmusers_at_globomaxnm.com]
>De la part de Jin, Bo Envoyé : vendredi 1 février 2008 17:48 =
À :
>nmusers_at_globomaxnm.com Objet : [NMusers] output SE of population PK
>parameters in Nonmem
>
>Dear all: I have a question. Is there any way to output the SE or SD
>of a population PK parameter estimate in Nonmem (say typical value of
>Cl) into some files which can be read by SAS or S-Plus etc.? (e.g.
>some excel or TAB files?)
>
>thanks,
>
>- Bo
>
>_____________________________________
>
>BO JIN
>Clinical Pharmacology Statistics
>Merck Research Labs
>Phone: 267-305-7876
>
>
>
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Received on Wed Feb 06 2008 - 11:07:57 EST