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
------------------------------------------------------------------------------
Notice: This e-mail message, together with any attachments, contains
information of Merck & Co., Inc. (One Merck Drive, Whitehouse Station,
New Jersey, USA 08889), and/or its affiliates (which may be known
outside the United States as Merck Frosst, Merck Sharp & Dohme or MSD
and in Japan, as Banyu - direct contact information for affiliates is
available at http://www.merck.com/contact/contacts.html) that may be
confidential, proprietary copyrighted and/or legally privileged. It is
intended solely for the use of the individual or entity named on this
message. If you are not the intended recipient, and have received this
message in error, please notify us immediately by reply e-mail and then
delete it from your system.
output SE of population PK parameters in Nonmem
Hi Bo,
One simple thing you could do would be to insert the following code into
your control stream right before the $ERROR block. This will output the
point estimates and the SE into a ASCII dataset to read into other
applications.
$INFN
IF (ICALL.EQ.3) THEN
OPEN(50,FILE=outparms.txt')
WRITE (50,*) THETA
WRITE (50,*) SETHET
WRITE (50,*) OMEGA(DIAG)
WRITE (50,*) SEOMEG(DIAG)
WRITE (50,*) SIGMA(DIAG)
WRITE (50,*) SESIGM(DIAG)
ENDIF
Best wishes,
Scott Van Wart
Quoted reply history
-----Original Message-----
From: [EMAIL PROTECTED] [mailto:[EMAIL PROTECTED]
On Behalf Of Jin, Bo
Sent: Friday, February 01, 2008 11:48 AM
To: [email protected]
Subject: [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
------------------------------------------------------------------------
------
Notice: This e-mail message, together with any attachments, contains
information of Merck & Co., Inc. (One Merck Drive, Whitehouse Station,
New Jersey, USA 08889), and/or its affiliates (which may be known
outside the United States as Merck Frosst, Merck Sharp & Dohme or MSD
and in Japan, as Banyu - direct contact information for affiliates is
available at http://www.merck.com/contact/contacts.html) that may be
confidential, proprietary copyrighted and/or legally privileged. It is
intended solely for the use of the individual or entity named on this
message. If you are not the intended recipient, and have received this
message in error, please notify us immediately by reply e-mail and then
delete it from your system.
------------------------------------------------------------------------
------
Dear Bo,
If the runs are already completed you could use nmsee to extract the needed
information from the NONMEM output. Using nmsee and grep the extracted
information will be stored in a text file which is readily amenable for use
with read.table in S-plus. I learnt the usage of nmsee by reading Alison's
posting on nmusers:
http://cognigencorp.com/nonmem/nm/97oct171996.html
http://www.mail-archive.com/[email protected]/msg00639.html
Best regards...MNS
Quoted reply history
-----Original Message-----
From: [EMAIL PROTECTED]
[mailto:[EMAIL PROTECTED] Behalf Of Jin, Bo
Sent: Friday, February 01, 2008 11:48 AM
To: [email protected]
Subject: [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
------------------------------------------------------------------------------
Notice: This e-mail message, together with any attachments, contains
information of Merck & Co., Inc. (One Merck Drive, Whitehouse Station,
New Jersey, USA 08889), and/or its affiliates (which may be known
outside the United States as Merck Frosst, Merck Sharp & Dohme or MSD
and in Japan, as Banyu - direct contact information for affiliates is
available at http://www.merck.com/contact/contacts.html) that may be
confidential, proprietary copyrighted and/or legally privileged. It is
intended solely for the use of the individual or entity named on this
message. If you are not the intended recipient, and have received this
message in error, please notify us immediately by reply e-mail and then
delete it from your system.
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
Quoted reply history
-----Original Message-----
From: [EMAIL PROTECTED] [mailto:[EMAIL PROTECTED] On
Behalf Of GIRARD PASCAL
Sent: 01 February 2008 18:08
To: Jin, Bo; [email protected]
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
[EMAIL PROTECTED]
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 : [EMAIL PROTECTED] [mailto:[EMAIL PROTECTED] De
>la part de Jin, Bo
>Envoyé : vendredi 1 février 2008 17:48
>À : [email protected]
>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
>
>
>
>---------------------------------------------------------------------------
>---
>Notice: This e-mail message, together with any attachments, contains
>information of Merck & Co., Inc. (One Merck Drive, Whitehouse Station,
>New Jersey, USA 08889), and/or its affiliates (which may be known
>outside the United States as Merck Frosst, Merck Sharp & Dohme or MSD
>and in Japan, as Banyu - direct contact information for affiliates is
>available at http://www.merck.com/contact/contacts.html) that may be
>confidential, proprietary copyrighted and/or legally privileged. It is
>intended solely for the use of the individual or entity named on this
>message. If you are not the intended recipient, and have received this
>message in error, please notify us immediately by reply e-mail and then
>delete it from your system.
>
>---------------------------------------------------------------------------
>---
Rik, I don't know anything about the non-parametric estimates: 'expected value of ETA' and 'Covariance matrix of ETAI. But, think the correlation matrix is CORRM in COMMON /CM12/ COVM(LPAR3),COVINM(LPAR3),STHTA(LTH),SEN(LVR,LVR), 1 CORRM(LPAR3),NVLS,VLS(LPAR) and you can get at it something like this: C DIMENSTION OF CORRLEATION MATRIX, ONE FOR EACH THETA AND FULL MATRIX FOR EACH OMEGA AND SIGMA C EVEN IF NOT USED WRITE(44,'(A10)') 'R^2 MATRIX' C NUMPAR IS TOTAL SIZE OF THE RANDOM EFFECTS MATRIX, DEFAULT IS 70X70 NUMPAR = LTH + LVR CORR = 0 C P IS THE POSITION IN CORRM, IT IS A 1XNUMPAR ARRAY P = 0 &nbs! p; DO 66 I = 1,NUMPAR DO 65 N = 1,I P = P + 1 C CORRELATION MATRIX IS IN CORRM, LOWER TRIANGULAR ONLY WRITE(44,70) CORRM(P) ABSVAL = ABS(CORRM(P)) C IF (OFF DIAGONAL, I.NE.N) IS > 0.95, FAIL CORRELATION IF((ABSVAL.GT.0.95).AND.(I.NE.N).AND.(ABSVAL.LE.1.00)) THEN CORR = 1 END IF 65 CONTINUE C new line WRITE(44,'(A2)') ' ' 66 CONTINUE Mark Sale MD Next Level Solutions, LLC
www.NextLevelSolns.com
919-846-9185
> -------- Original Message -------- Subject: RE: [NMusers] output SE of population PK parameters in Nonmem From: "Rik Schoemaker" <[EMAIL PROTECTED]> Date: Wed, February 06, 2008 8:30 am To: <
>
> [email protected]
>
> > 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 @globomaxnm.com
>
> [mailto:
>
> owner-nmusers @globomaxnm.com
>
> ] On Behalf Of GIRARD PASCAL Sent: 01 February 2008 18:08 To: Jin, Bo;
>
> nmusers @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 @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 @globomaxnm.com
>
> [mailto:
>
> owner-nmusers @globomaxnm.com
>
> ] De >la part de Jin, Bo >Envoyé : vendredi 1 février 2008 17:48 >À :
>
> nmusers @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 > > > >--------------------------------------------------------------------------- >--- >Notice: This e-mail message, together with any attachments, contains >information of Merck & Co., Inc. (One Merck Drive, Whitehouse Station, >New Jersey, USA 08889), and/or its affiliates (which may be known >outside the United States as Merck Frosst, Merck Sharp & Dohme or MSD >and in Japan, as Banyu - direct contact information for affiliates is >available at
>
> http://www.merck.com/contact/contacts.html
>
> ) that may be >confidential, proprietary copyrighted and/or legally privileged. It is >intended solely for the use of the individual or entity named on this >message. If you are not the intended recipient, and have received this >message in error, please notify us immediately by reply e-mail and then >delete it from your system. > >--------------------------------------------------------------------------- >---
Hi Rik,
$COV PRINT=E
should give you correlation matrix of the
population parameter estimates
As far as I know, there is no way to get SE (and hence covariance matrix) for individual parameter estimates (ETA values).
Leonid
--------------------------------------
Leonid Gibiansky, Ph.D.
President, QuantPharm LLC
web: www.quantpharm.com
e-mail: LGibiansky at quantpharm.com
tel: (301) 767 5566
Rik Schoemaker wrote:
> Dear all,
>
> It's a neat trick and works very well, but can anyone tell me the keyword
> (like for instance SETHET below) for exporting the correlation matrix of the
> estimates and for the non-parametric estimates: 'expected value of ETA' and
> 'Covariance matrix of ETA'....
>
> Thanks in advance,
>
> Rik
>
Quoted reply history
> -----Original Message-----
> From: [EMAIL PROTECTED] [mailto:[EMAIL PROTECTED] On
> Behalf Of GIRARD PASCAL
> Sent: 01 February 2008 18:08
> To: Jin, Bo; [email protected]
> Subject: RE : [NMusers] output SE of population PK parameters in Nonmem
>
> Hi Jin,
>
> See in NONMEM help:
> ___________________________________________________________________
> | |
> | FINALIZATION EXAMPLE ($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
>
> [EMAIL PROTECTED] 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 : [EMAIL PROTECTED] [mailto:[EMAIL PROTECTED] De
> > la part de Jin, Bo
> > Envoyé : vendredi 1 février 2008 17:48
> > À : [email protected]
> > 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
> >
> > ---------------------------------------------------------------------------
> > ---
> > Notice: This e-mail message, together with any attachments, contains
> > information of Merck & Co., Inc. (One Merck Drive, Whitehouse Station,
> > New Jersey, USA 08889), and/or its affiliates (which may be known
> > outside the United States as Merck Frosst, Merck Sharp & Dohme or MSD
> > and in Japan, as Banyu - direct contact information for affiliates is
> > available at http://www.merck.com/contact/contacts.html) that may be
> > confidential, proprietary copyrighted and/or legally privileged. It is
> > intended solely for the use of the individual or entity named on this
> > message. If you are not the intended recipient, and have received this
> > message in error, please notify us immediately by reply e-mail and then
> > delete it from your system.
> >
> > ---------------------------------------------------------------------------
> > ---
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
**************************************************************************************************************************************************************
Sanofi-Aventis Deutschland GmbH · Sitz der Gesellschaft: Frankfurt am Main ·
Handelsregister: Frankfurt am Main, Abt. B Nr. 40661
Vorsitzender des Aufsichtsrats: Hanspeter Spek - Geschäftsführer: Dr.
Heinz-Werner Meier (Vorsitzender),
Dr. Matthias Braun, Hervé Gisserot, Prof. Dr. Dr. Werner Kramer, Dr. Klaus
Menken, Dr. Martin Siewert
**************************************************************************************************************************************************************
Quoted reply history
-----Original Message-----
From: [EMAIL PROTECTED] [mailto:[EMAIL PROTECTED] On Behalf Of Rik Schoemaker
Sent: Wednesday, February 06, 2008 2:31 PM
To: [email protected]
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: [EMAIL PROTECTED] [mailto:[EMAIL PROTECTED] On Behalf Of GIRARD PASCAL
Sent: 01 February 2008 18:08
To: Jin, Bo; [email protected]
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
[EMAIL PROTECTED]
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 : [EMAIL PROTECTED] [mailto:[EMAIL PROTECTED]
>De la part de Jin, Bo Envoyé : vendredi 1 février 2008 17:48 À :
>[email protected] 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
>
>
>
>-----------------------------------------------------------------------
>----
>---
>Notice: This e-mail message, together with any attachments, contains
>information of Merck & Co., Inc. (One Merck Drive, Whitehouse Station,
>New Jersey, USA 08889), and/or its affiliates (which may be known
>outside the United States as Merck Frosst, Merck Sharp & Dohme or MSD
>and in Japan, as Banyu - direct contact information for affiliates is
>available at http://www.merck.com/contact/contacts.html) that may be
>confidential, proprietary copyrighted and/or legally privileged. It is
>intended solely for the use of the individual or entity named on this
>message. If you are not the intended recipient, and have received this
>message in error, please notify us immediately by reply e-mail and then
>delete it from your system.
>
>-----------------------------------------------------------------------
>----
>---
Rik, There is no "keyword" at present for these values. Lets call them
"reserved variables" rather than "keywords".
To make a new reserved variable of this sort, there are three steps.
1) Someone must identify a common in NONMEM that contains the values of
interest. The other responders seem to think that CM12 is the one for
the correlation matrix of the estimate. Whatever, someone must use
verbatim or user-written code to be sure that the commons have the
values under the appropriate circumstances.
2) Let me or ICON know about this, with an example of the code that you
use to display them.
3) NMTRAN could then be revised to make a reserved variable in the same
family as SETHET et. al, and to allow it to be used in WRITE/PRINT
statements in a similar manner.
An easier and faster approach is to use nmsee to mark the values
of interest in the NONMEM output report, and then use grep or findstr to
extract them.
Nmsee can supply the following --
prefixes (appearing in nmsee output with the prefix option):
ti, tu, tl theta initial, upper bound, and lower bound
oi, si omega and sigma initial
tj, oj, sj theta, omega, sigma from init estimates step
gi, gf gradients initial and final
pf scaled transformed parameters final
mm minimum value of objective function
tf, of, sf theta, omega, and sigma final
te, oe, se theta, omega, and sigma std errors
cx, cr, cv covar, correl, and inv covar matrices of est
cy T matrix
xx text lines
I have been planning to change it to mark the following:
xx ETABAR: -0.13E-02 -0.45E-02 -0.25E-01
xx SE: 0.29E-01 0.27E-01 0.21E-01
xx P VAL.: 0.96E+00 0.87E+00 0.24E+00
It is much easier and faster to change nmsee than to change NMTRAN!
Steps 1 and 2 are up to the user community. Step 3 is something that
could be implemented in a future release of NONMEM.
On Wed, 6 Feb 2008 14:30:42 +0100, "Rik Schoemaker"
<[EMAIL PROTECTED]> said:
> 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: [EMAIL PROTECTED] [mailto:owner-
> [EMAIL PROTECTED] On Behalf Of GIRARD PASCAL Sent: 01 February
> 2008 18:08 To: Jin, Bo; [email protected] 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 [EMAIL PROTECTED] 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 : [EMAIL PROTECTED] [mailto:owner-
> >[EMAIL PROTECTED] De la part de Jin, Bo Envoyé : vendredi 1
> >février 2008 17:48 À : [email protected] 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
> >
> >
> >
> >--------------------------------------------------------------------
> >-------
> >---
> >Notice: This e-mail message, together with any attachments, contains
> >information of Merck & Co., Inc. (One Merck Drive, Whitehouse
> >Station, New Jersey, USA 08889), and/or its affiliates (which may be
> >known outside the United States as Merck Frosst, Merck Sharp & Dohme
> >or MSD and in Japan, as Banyu - direct contact information for
> >affiliates is available at
> > http://www.merck.com/contact/contacts.html) that may be confidential,
> >proprietary copyrighted and/or legally privileged. It is intended
> >solely for the use of the individual or entity named on this message.
> >If you are not the intended recipient, and have received this message
> >in error, please notify us immediately by reply e-mail and then
> >delete it from your system.
> >
> >--------------------------------------------------------------------
> >-------
> >---
>
--
Alison Boeckmann
[EMAIL PROTECTED]
Rik, It isn't pretty (but what Fortran is?, wouldn't be Fortran without a GOTO) but this seems to work. The previous wasn't working because I didn't notice that the variables in COMMON /CM12/ are REAL, not the default DOUBLE PRECISION. $INFN " FIRST " INCLUDE 'C:\NMVI\SIZES' " COMMON /CM12/ COVM(LPAR3),COVINM(LPAR3),STHTA(LTH) " 1 ,SEN(LVR,LVR),CORRM(LPAR3) " REAL COVM,COVINM,STHTA,SEN,CORRM " INTEGER I,N,P IF (ICALL.EQ.3) THEN OPEN! (50,FILE='parms') WRITE (50,*) 'THETAS' WRITE (50,*) THETA WRITE (50,*) 'OMEGAS' WRITE (50,*) OMEGA(DIAG) WRITE (50,*) 'MVOF' WRITE (50,*) OBJECT WRITE (50,*) 'SE THETAS' WRITE (50,*) SETHET WRITE (50,*) 'CORR MATRIX EST' " DO 20 I = 1,70 " DO 10 N = 1, I " P = P + 1 " IF(CORRM(P).EQ.0) GOTO 30 " WRITE (50,777) CORRM(P) " 10 CONTINUE " WRITE(50,'(A2)') ' ' " 20 CONTINUE " 30 CONTINUE " 777 FORMAT (' ',F8.6,$) ENDIF Mark Sale MD Next Level Solutions, LLC
www.NextLevelSolns.com
919-846-9185
> -------- Original Message -------- Subject: RE: [NMusers] output SE of population PK parameters in Nonmem From: "Rik Schoemaker" <[EMAIL PROTECTED]> Date: Wed, February 06, 2008 1:23 pm To: <
>
> [email protected]
>
> > Dear Alison, I'm not sure I'm the one to suggest you update NMTRAN! It seems there are enough tools out there to either extract the info from the output file or to use a custom written INFN routine instead (for instance if you want more decimals). It's just that I'd been searching the documentation for a 'reserved variable' and couldn't find it... Thanks! Rik -----Original Message----- From: Alison Boeckmann [mailto:
>
> alisonboeckmann @fastmail.fm
>
> ] Sent: 06 February 2008 18:15 To: Rik Schoemaker;
>
> nmusers @globomaxnm.com
>
> Subject: RE: [NMusers] output SE of population PK parameters in Nonmem Rik, There is no "keyword" at present for these values. Lets call them "reserved variables" rather than "keywords". To make a new reserved variable of this sort, there are three steps. 1) Someone must identify a common in NONMEM that contains the values of interest. The other responders seem to think that CM12 is the one for the correlation matrix of the estimate. Whatever, someone must use verbatim or user-written code to be sure that the commons have the values under the appropriate circumstances. 2) Let me or ICON know about this, with an example of the code that you use to display them. 3) NMTRAN could then be revised to make a reserved variable in the same family as SETHET et. al, and to allow it to be used in WRITE/PRINT statements in a similar manner. An easier and faster approach is to use nmsee to mark the values of interest in the NONMEM output report, and then use grep or findstr to extract them. Nmsee can supply the following -- prefixes (appearing in nmsee output with the prefix option): ti, tu, tl theta initial, upper bound, and lower bound oi, si omega and sigma initial tj, oj, sj theta, omega, sigma from init estimates step gi, gf gradients initial and final pf scaled transformed parameters final mm minimum value of objective function tf, of, sf theta, omega, and sigma final te, oe, se theta, omega, and sigma std errors cx, cr, cv covar, correl, and inv covar matrices of est cy T matrix xx text lines I have been planning to change it to mark the following: xx ETABAR: -0.13E-02 -0.45E-02 -0.25E-01 xx SE: 0.29E-01 0.27E-01 0.21E-01 xx P VAL.: 0.96E+00 0.87E+00 0.24E+00 It is much easier and faster to change nmsee than to change NMTRAN! Steps 1 and 2 are up to the user community. Step 3 is something that could be implemented in a future release of NONMEM. On Wed, 6 Feb 2008 14:30:42 +0100, "Rik Schoemaker" <
>
> rik.schoemaker @exprimo.com
>
> > said: > 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 @globomaxnm.com
>
> [mailto:owner- >
>
> nmusers @globomaxnm.com
>
> ] On Behalf Of GIRARD PASCAL Sent: 01 February > 2008 18:08 To: Jin, Bo;
>
> nmusers @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 @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 @globomaxnm.com
>
> [mailto:owner- > >
>
> nmusers @globomaxnm.com
>
> ] De la part de Jin, Bo Envoyé : vendredi 1 > >février 2008 17:48 À :
>
> nmusers @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 > > > > > > > >-------------------------------------------------------------------- > >------- > >--- > >Notice: This e-mail message, together with any attachments, contains > >information of Merck & Co., Inc. (One Merck Drive, Whitehouse > >Station, New Jersey, USA 08889), and/or its affiliates (which may be > >known outside the United States as Merck Frosst, Merck Sharp & Dohme > >or MSD and in Japan, as Banyu - direct contact information for > >affiliates is available at > >
>
> http://www.merck.com/contact/contacts.html
>
> ) that may be confidential, > >proprietary copyrighted and/or legally privileged. It is intended > >solely for the use of the individual or entity named on this message. > >If you are not the intended recipient, and have received this message > >in error, please notify us immediately by reply e-mail and then > >delete it from your system. > > > >-------------------------------------------------------------------- > >------- > >--- > -- Alison Boeckmann
>
> alisonboeckmann @fastmail.fm
Dear Mark,
Works like a charm! If you have a $PRED instead of a $PK just insert your
lines as the first $PRED statements (without $INFN of course).
Below is some R syntax (adapted from Xpose source code) to read your file
(which should also work if you decide not to output the correlation matrix):
#####################################
## read estimated parameters table ##
#####################################
# obj <- objects()
# remove(obj)
path <-"C:\\DataDir\\"
filename.extra <- paste(path,"FileName.est",sep="")
#Read the file
data.extra <- scan(filename.extra,sep = "\n", what = character())
#The patterns to find the headers in the file
theta.pat <- "^ *THETAS"
omega.pat <- "^ *OMEGAS"
mvof.pat <- "^ *MVOF"
setheta.pat <- "^ *SE THETAS"
corrm.pat <- "^ *CORR MATRIX EST"
#The lines corresponding to the headers
theta.pat.line <- grep(theta.pat, data.extra)
omega.pat.line <- grep(omega.pat, data.extra)
mvof.pat.line <- grep(mvof.pat, data.extra)
setheta.pat.line <- grep(setheta.pat, data.extra)
corrm.pat.line <- grep(corrm.pat, data.extra)
#The number of rows
tot.theta.rows <- omega.pat.line - theta.pat.line - 1
tot.omega.rows <- mvof.pat.line - omega.pat.line - 1
tot.mvof.rows <- setheta.pat.line - mvof.pat.line - 1
if (length(corrm.pat.line)>0) {
tot.setheta.rows <- corrm.pat.line - setheta.pat.line -1
tot.corrm.rows <- length(data.extra) - corrm.pat.line
} else {
tot.setheta.rows <- length(data.extra) - setheta.pat.line}
#Read the different output types
THETA<-
read.table(filename.extra,skip=theta.pat.line,nrows=tot.theta.rows)
ETA<-
read.table(filename.extra,skip=omega.pat.line,nrows=tot.omega.rows)
MVOF <-
read.table(filename.extra,skip=mvof.pat.line,nrows=tot.mvof.rows)
SETHETA<-
read.table(filename.extra,skip=setheta.pat.line,nrows=tot.setheta.rows)
#If you want the entire matrix:
# CORRM<-
read.table(filename.extra,skip=corrm.pat.line,nrows=tot.corrm.rows,fill=T,co
l.names=1:tot.corrm.rows)
#If you only want the correlations for the Thetas:
if (length(corrm.pat.line)>0){
CORRM<-
read.table(filename.extra,skip=corrm.pat.line,nrows=length(THETA),fill=T,col
.names=1:length(THETA))
k<-1
for(i in 1:(length(THETA)-1)) {
k<-k+1
for(j in k:length(THETA)){
CORRM[i,j]<-CORRM[j,i]
}
}
}
CORRMM<-as.matrix.data.frame(CORRM)
If you use S-plus, you need to change the read.table syntax lines to
importData equivalents:
#Read the different output types
THETA<-
importData(filename.extra,type="ASCII",startRow=theta.pat.line,endRow=theta.
pat.line+tot.theta.rows)
ETA<-
importData(filename.extra,type="ASCII",startRow=omega.pat.line,endRow=omega.
pat.line+tot.omega.rows)
MVOF <-
importData(filename.extra,type="ASCII",startRow=mvof.pat.line,endRow=mvof.pa
t.line+tot.mvof.rows)
SETHETA<-
importData(filename.extra,type="ASCII",startRow=setheta.pat.line,endRow=seth
eta.pat.line+tot.setheta.rows)
#If you want the entire matrix:
# CORRM<-
importData(filename.extra,type="ASCII",startRow=corrm.pat.line,endRow=corrm.
pat.line+tot.corrm.rows)
#If you only want the correlations for the Thetas:
if (length(corrm.pat.line)>0){
CORRM<-
importData(filename.extra,type="ASCII",startRow=corrm.pat.line,endRow=corrm.
pat.line+length(THETA),endCol=length(THETA))
k<-1
for(i in 1:(length(THETA)-1)) {
k<-k+1
for(j in k:length(THETA)){
CORRM[i,j]<-CORRM[j,i]
}
}
}
Thanks!
Rik
Quoted reply history
________________________________
From: Mark Sale - Next Level Solutions [mailto:[EMAIL PROTECTED]
Sent: 07 February 2008 01:53
To: Rik Schoemaker
Cc: [email protected]
Subject: RE: [NMusers] output SE of population PK parameters in Nonmem
Rik,
It isn't pretty (but what Fortran is?, wouldn't be Fortran without a GOTO)
but this seems to work. The previous wasn't working because I didn't notice
that the variables in COMMON /CM12/ are REAL, not the default DOUBLE
PRECISION.
$INFN
" FIRST
" INCLUDE 'C:\NMVI\SIZES'
" COMMON /CM12/ COVM(LPAR3),COVINM(LPAR3),STHTA(LTH)
" 1 ,SEN(LVR,LVR),CORRM(LPAR3)
" REAL COVM,COVINM,STHTA,SEN,CORRM
" INTEGER I,N,P
IF (ICALL.EQ.3) THEN
OPEN(50,FILE='parms')
WRITE (50,*) 'THETAS'
WRITE (50,*) THETA
WRITE (50,*) 'OMEGAS'
WRITE (50,*) OMEGA(DIAG)
WRITE (50,*) 'MVOF'
WRITE (50,*) OBJECT
WRITE (50,*) 'SE THETAS'
WRITE (50,*) SETHET
WRITE (50,*) 'CORR MATRIX EST'
" DO 20 I = 1,70
" DO 10 N = 1, I
" P = P + 1
" IF(CORRM(P).EQ.0) GOTO 30
" WRITE (50,777) CORRM(P)
" 10 CONTINUE
" WRITE(50,'(A2)') ' '
" 20 CONTINUE
" 30 CONTINUE
" 777 FORMAT (' ',F8.6,$)
ENDIF
Mark Sale MD
Next Level Solutions, LLC
www.NextLevelSolns.com
919-846-9185
-------- Original Message --------
Subject: RE: [NMusers] output SE of population PK parameters in
Nonmem
From: "Rik Schoemaker" <[EMAIL PROTECTED]>
Date: Wed, February 06, 2008 1:23 pm
To: <[email protected]>
Dear Alison,
I'm not sure I'm the one to suggest you update NMTRAN! It seems
there are
enough tools out there to either extract the info from the output
file or to
use a custom written INFN routine instead (for instance if you want
more
decimals). It's just that I'd been searching the documentation for a
'reserved variable' and couldn't find it...
Thanks!
Rik
-----Original Message-----
From: Alison Boeckmann [mailto:[EMAIL PROTECTED]
http://email.secureserver.net/pcompose.php#Compose ]
Sent: 06 February 2008 18:15
To: Rik Schoemaker; [email protected]
http://email.secureserver.net/pcompose.php#Compose
Subject: RE: [NMusers] output SE of population PK parameters in
Nonmem
Rik, There is no "keyword" at present for these values. Lets call
them
"reserved variables" rather than "keywords".
To make a new reserved variable of this sort, there are three steps.
1) Someone must identify a common in NONMEM that contains the values
of
interest. The other responders seem to think that CM12 is the one
for
the correlation matrix of the estimate. Whatever, someone must use
verbatim or user-written code to be sure that the commons have the
values under the appropriate circumstances.
2) Let me or ICON know about this, with an example of the code that
you
use to display them.
3) NMTRAN could then be revised to make a reserved variable in the
same
family as SETHET et. al, and to allow it to be used in WRITE/PRINT
statements in a similar manner.
An easier and faster approach is to use nmsee to mark the values
of interest in the NONMEM output report, and then use grep or
findstr to
extract them.
Nmsee can supply the following --
prefixes (appearing in nmsee output with the prefix option):
ti, tu, tl theta initial, upper bound, and lower bound
oi, si omega and sigma initial
tj, oj, sj theta, omega, sigma from init estimates step
gi, gf gradients initial and final
pf scaled transformed parameters final
mm minimum value of objective function
tf, of, sf theta, omega, and sigma final
te, oe, se theta, omega, and sigma std errors
cx, cr, cv covar, correl, and inv covar matrices of est
cy T matrix
xx text lines
I have been planning to change it to mark the following:
xx ETABAR: -0.13E-02 -0.45E-02 -0.25E-01
xx SE: 0.29E-01 0.27E-01 0.21E-01
xx P VAL.: 0.96E+00 0.87E+00 0.24E+00
It is much easier and faster to change nmsee than to change NMTRAN!
Steps 1 and 2 are up to the user community. Step 3 is something that
could be implemented in a future release of NONMEM.
On Wed, 6 Feb 2008 14:30:42 +0100, "Rik Schoemaker"
<[EMAIL PROTECTED]
http://email.secureserver.net/pcompose.php#Compose > said:
> 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: [EMAIL PROTECTED]
http://email.secureserver.net/pcompose.php#Compose
[mailto:owner-
> [email protected]
http://email.secureserver.net/pcompose.php#Compose ] On Behalf Of GIRARD
PASCAL Sent: 01 February
> 2008 18:08 To: Jin, Bo; [email protected]
http://email.secureserver.net/pcompose.php#Compose 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 [EMAIL PROTECTED]
http://email.secureserver.net/pcompose.php#Compose 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 : [EMAIL PROTECTED]
http://email.secureserver.net/pcompose.php#Compose
[mailto:owner-
> >[email protected]
http://email.secureserver.net/pcompose.php#Compose ] De la part de Jin, Bo
Envoyé : vendredi 1
> >février 2008 17:48 À : [email protected]
http://email.secureserver.net/pcompose.php#Compose 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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--
Alison Boeckmann
[EMAIL PROTECTED]
http://email.secureserver.net/pcompose.php#Compose