Hello everybody,
I am trying to run a control stream for my data using NONMEM 6. I get the
output file with the objective function and other estimates.
The problem is that I do not get the fit file that can be opened in excel. I
guess I am missing out something in the control stream, but just cannot
figure it out. Any suggestions would be appreciated
The last part in the control stream is posted below
$ESTIMATION METHOD=1 MAXEVAL=9999 PRINT=5 POSTHOC
$COVARIANCE
$TABLE ID TIME AMT MDV DV EVID CMT
NOPRINT ONEHEADER FILE=drug3.sdtab
thanks a lot
Navin
No Fit file
according to your code, your run should have created a file named
"drug3.sdtab". this file contains a table with these columns "ID TIME
AMT MDV DV EVID CMT" and DV PRED RES WRES. You can import this file
into Excel. You will have to manually create the graphs unless you have
a macro that can do it.
Quoted reply history
________________________________
From: [EMAIL PROTECTED] [mailto:[EMAIL PROTECTED]
On Behalf Of navin goyal
Sent: Tuesday, May 22, 2007 2:20 PM
To: nmusers
Subject: [NMusers] No Fit file
Hello everybody,
I am trying to run a control stream for my data using NONMEM 6. I get
the output file with the objective function and other estimates.
The problem is that I do not get the fit file that can be opened in
excel. I guess I am missing out something in the control stream, but
just cannot figure it out. Any suggestions would be appreciated
The last part in the control stream is posted below
$ESTIMATION METHOD=1 MAXEVAL=9999 PRINT=5 POSTHOC
$COVARIANCE
$TABLE ID TIME AMT MDV DV EVID CMT
NOPRINT ONEHEADER FILE=drug3.sdtab
thanks a lot
Navin
_______________________________________________________________________________________________________________________________________
Navin,
If you're not getting the table file you expect, if may be because
NMtran (5 at least) seems to have a small bug that it will sometimes
ignore the last line of a control file if there isn't a carriage
return/line feed at the end. Try just hitting Enter after the $TABLE
record and saving.
WRT plots, two options are Xpose from the Upsala group (R/Splus,
http://xpose.sourceforge.net) or an excel macro from Next Level
Solutions (www.nextlevelsolns.com)
Mark Sale MD
Next Level Solutions, LLC
www.NextLevelSolns.com
Quoted reply history
> -------- Original Message --------
> Subject: RE: [NMusers] No Fit file
> From: "Bachman, William (MYD)" <[EMAIL PROTECTED]>
> Date: Tue, May 22, 2007 2:48 pm
> To: "navin goyal" <[EMAIL PROTECTED]>, "nmusers"
> <[email protected]>
>
> according to your code, your run should have created a file named
> "drug3.sdtab". this file contains a table with these columns "ID TIME
> AMT MDV DV EVID CMT" and DV PRED RES WRES. You can import this file
> into Excel. You will have to manually create the graphs unless you have
> a macro that can do it.
>
> ________________________________
>
> From: [EMAIL PROTECTED] [mailto:[EMAIL PROTECTED]
> On Behalf Of navin goyal
> Sent: Tuesday, May 22, 2007 2:20 PM
> To: nmusers
> Subject: [NMusers] No Fit file
>
>
> Hello everybody,
> I am trying to run a control stream for my data using NONMEM 6. I get
> the output file with the objective function and other estimates.
> The problem is that I do not get the fit file that can be opened in
> excel. I guess I am missing out something in the control stream, but
> just cannot figure it out. Any suggestions would be appreciated
> The last part in the control stream is posted below
>
>
> $ESTIMATION METHOD=1 MAXEVAL=9999 PRINT=5 POSTHOC
> $COVARIANCE
>
> $TABLE ID TIME AMT MDV DV EVID CMT
> NOPRINT ONEHEADER FILE=drug3.sdtab
>
> thanks a lot
>
> Navin
>
>
>
>
>
>
> _______________________________________________________________________________________________________________________________________
>
>
>
>
>
This is not a bug in NM-TRAN. But I can see how it happens in
MS-DOS. Both wordpad and notepad (unlike ms-dos edit and unix vi) will
write a file whose last line does not terminate with cr/lf. Such a line
is invisible to the Fortran I/O libraries that are part of g77
(in the MS-DOS environment) and FORTRAN 77 5.0 (in the Solaris
environment).
I tested this in both MS-DOS and Solaris with a little fortran program
that branches to statement 10 when an end of file condition occurs.
program read
character*10 text
read (5,55,end=10) text
print *,text
55 format (A10)
stop
10 print *,'nothing read'
end
I created a file named infile containing only "1234567890" with no cr/lf
using notepad. I copied it to Solaris using ftp. In both environments,
when the program is run with infile as input, it produces
the output "nothing read". E.g., in Solaris,
% f77 read.for
read.for:
MAIN read:
% a.out<infile
nothing read
I don't know how to overcome this problem. Changing the format from A10
to (say)
A1 or * does not help. It seems to me it is a bug (or maybe a design
feature?) in the Fortran I/O library.
On Tue, 22 May 2007 12:56:18 -0700, "Mark Sale - Next Level Solutions"
<[EMAIL PROTECTED]> said:
> Navin, If you're not getting the table file you expect, if may be
> because NMtran (5 at least) seems to have a small bug that it will
> sometimes ignore the last line of a control file if there isn't a
> carriage return/line feed at the end. Try just hitting Enter after
> the $TABLE record and saving. WRT plots, two options are Xpose from
> the Upsala group (R/Splus, http://xpose.sourceforge.net) or an excel
> macro from Next Level Solutions (www.nextlevelsolns.com)
>
>
>
> Mark Sale MD Next Level Solutions, LLC www.NextLevelSolns.com
>
>
> > -------- Original Message -------- Subject: RE: [NMusers] No Fit
> > file From: "Bachman, William (MYD)" <[EMAIL PROTECTED]> Date: Tue,
> > May 22, 2007 2:48 pm To: "navin goyal" <[EMAIL PROTECTED]>,
> > "nmusers" <[email protected]>
> >
> > according to your code, your run should have created a file named
> > "drug3.sdtab". this file contains a table with these columns "ID
> > TIME AMT MDV DV EVID CMT" and DV PRED RES WRES. You can import
> > this file into Excel. You will have to manually create the graphs
> > unless you have a macro that can do it.
> >
> > ________________________________
> >
> > From: [EMAIL PROTECTED] [mailto:owner-
> > [EMAIL PROTECTED] On Behalf Of navin goyal Sent: Tuesday, May
> > 22, 2007 2:20 PM To: nmusers Subject: [NMusers] No Fit file
> >
> >
> > Hello everybody, I am trying to run a control stream for my data
> > using NONMEM 6. I get the output file with the objective function
> > and other estimates. The problem is that I do not get the fit
> > file that can be opened in excel. I guess I am missing out
> > something in the control stream, but just cannot figure it out.
> > Any suggestions would be appreciated The last part in the control
> > stream is posted below
> >
> >
> > $ESTIMATION METHOD=1 MAXEVAL=9999 PRINT=5 POSTHOC $COVARIANCE
> >
> > $TABLE ID TIME AMT MDV DV EVID CMT NOPRINT ONEHEADER
> > FILE=drug3.sdtab
> >
> > thanks a lot
> >
> > Navin
> >
> >
> >
> >
> >
> >
> > ___________________________________________________________________-
> > ____________________________________________________________________
> >
> >
> >
> >
> >
We never had these problems with punch cards...
Quoted reply history
-----Original Message-----
From: [EMAIL PROTECTED] [mailto:[EMAIL PROTECTED] On
Behalf Of Mark Sale - Next Level Solutions
Sent: Tuesday, May 22, 2007 7:04 PM
Cc: nmusers
Subject: RE: [NMusers] No Fit file
Thanks for clarifying this Alison, I think I did know this is a fortran
I/O issue, not really a NMTRAN issue. Clearly we should all go back to
MS-DOS edit ;-) (only us really old people even remember MS-DOS).
Mark Sale MD
Next Level Solutions, LLC
www.NextLevelSolns.com
> -------- Original Message --------
> Subject: RE: [NMusers] No Fit file
> From: "Alison Boeckmann" <[EMAIL PROTECTED]>
> Date: Tue, May 22, 2007 5:41 pm
> To: "Mark Sale - Next Level Solutions" <[EMAIL PROTECTED]>
> Cc: "nmusers" <[email protected]>
>
> This is not a bug in NM-TRAN. But I can see how it happens in
> MS-DOS. Both wordpad and notepad (unlike ms-dos edit and unix vi) will
> write a file whose last line does not terminate with cr/lf. Such a line
> is invisible to the Fortran I/O libraries that are part of g77
> (in the MS-DOS environment) and FORTRAN 77 5.0 (in the Solaris
> environment).
>
> I tested this in both MS-DOS and Solaris with a little fortran program
> that branches to statement 10 when an end of file condition occurs.
>
>
> program read
> character*10 text
> read (5,55,end=10) text
> print *,text
> 55 format (A10)
> stop
> 10 print *,'nothing read'
> end
>
> I created a file named infile containing only "1234567890" with no cr/lf
> using notepad. I copied it to Solaris using ftp. In both environments,
> when the program is run with infile as input, it produces
> the output "nothing read". E.g., in Solaris,
>
> % f77 read.for
> read.for:
> MAIN read:
> % a.out<infile
> nothing read
>
> I don't know how to overcome this problem. Changing the format from A10
> to (say)
> A1 or * does not help. It seems to me it is a bug (or maybe a design
> feature?) in the Fortran I/O library.
>
>
> On Tue, 22 May 2007 12:56:18 -0700, "Mark Sale - Next Level Solutions"
> <[EMAIL PROTECTED]> said:
> > Navin, If you're not getting the table file you expect, if may be
> > because NMtran (5 at least) seems to have a small bug that it will
> > sometimes ignore the last line of a control file if there isn't a
> > carriage return/line feed at the end. Try just hitting Enter after
> > the $TABLE record and saving. WRT plots, two options are Xpose from
> > the Upsala group (R/Splus, http://xpose.sourceforge.net) or an excel
> > macro from Next Level Solutions (www.nextlevelsolns.com)
> >
> >
> >
> > Mark Sale MD Next Level Solutions, LLC www.NextLevelSolns.com
> >
> >
> > > -------- Original Message -------- Subject: RE: [NMusers] No Fit
> > > file From: "Bachman, William (MYD)" <[EMAIL PROTECTED]> Date: Tue,
> > > May 22, 2007 2:48 pm To: "navin goyal" <[EMAIL PROTECTED]>,
> > > "nmusers" <[email protected]>
> > >
> > > according to your code, your run should have created a file named
> > > "drug3.sdtab". this file contains a table with these columns "ID
> > > TIME AMT MDV DV EVID CMT" and DV PRED RES WRES. You can import
> > > this file into Excel. You will have to manually create the graphs
> > > unless you have a macro that can do it.
> > >
> > > ________________________________
> > >
> > > From: [EMAIL PROTECTED] [mailto:owner-
> > > [EMAIL PROTECTED] On Behalf Of navin goyal Sent: Tuesday, May
> > > 22, 2007 2:20 PM To: nmusers Subject: [NMusers] No Fit file
> > >
> > >
> > > Hello everybody, I am trying to run a control stream for my data
> > > using NONMEM 6. I get the output file with the objective function
> > > and other estimates. The problem is that I do not get the fit
> > > file that can be opened in excel. I guess I am missing out
> > > something in the control stream, but just cannot figure it out.
> > > Any suggestions would be appreciated The last part in the control
> > > stream is posted below
> > >
> > >
> > > $ESTIMATION METHOD=1 MAXEVAL=9999 PRINT=5 POSTHOC $COVARIANCE
> > >
> > > $TABLE ID TIME AMT MDV DV EVID CMT NOPRINT ONEHEADER
> > > FILE=drug3.sdtab
> > >
> > > thanks a lot
> > >
> > > Navin
> > >
> > >
> > >
> > >
> > >
> > >
> > > ___________________________________________________________________-
> > > ____________________________________________________________________
> > >
> > >
> > >
> > >
> > >
Hi Alison,
A simple workaround would be to add a platform-dependent newline to the
control stream in the batchfile before calling NMTRAN.
Jeroen
Quoted reply history
-----Original Message-----
From: [EMAIL PROTECTED] [mailto:[EMAIL PROTECTED]
On Behalf Of Alison Boeckmann
Sent: Tuesday, 22 May, 2007 23:42
To: Mark Sale - Next Level Solutions
Cc: nmusers
Subject: RE: [NMusers] No Fit file
This is not a bug in NM-TRAN. But I can see how it happens in MS-DOS.
Both wordpad and notepad (unlike ms-dos edit and unix vi) will write a
file whose last line does not terminate with cr/lf. Such a line is
invisible to the Fortran I/O libraries that are part of g77 (in the
MS-DOS environment) and FORTRAN 77 5.0 (in the Solaris environment).
I tested this in both MS-DOS and Solaris with a little fortran program
that branches to statement 10 when an end of file condition occurs.
program read
character*10 text
read (5,55,end=10) text
print *,text
55 format (A10)
stop
10 print *,'nothing read'
end
I created a file named infile containing only "1234567890" with no cr/lf
using notepad. I copied it to Solaris using ftp. In both environments,
when the program is run with infile as input, it produces the output
"nothing read". E.g., in Solaris,
% f77 read.for
read.for:
MAIN read:
% a.out<infile
nothing read
I don't know how to overcome this problem. Changing the format from A10
to (say)
A1 or * does not help. It seems to me it is a bug (or maybe a design
feature?) in the Fortran I/O library.
On Tue, 22 May 2007 12:56:18 -0700, "Mark Sale - Next Level Solutions"
<[EMAIL PROTECTED]> said:
> Navin, If you're not getting the table file you expect, if may be
> because NMtran (5 at least) seems to have a small bug that it will
> sometimes ignore the last line of a control file if there isn't a
> carriage return/line feed at the end. Try just hitting Enter after
> the $TABLE record and saving. WRT plots, two options are Xpose from
> the Upsala group (R/Splus, http://xpose.sourceforge.net) or an excel
> macro from Next Level Solutions (www.nextlevelsolns.com)
>
>
>
> Mark Sale MD Next Level Solutions, LLC www.NextLevelSolns.com
>
>
> > -------- Original Message -------- Subject: RE: [NMusers] No Fit
> > file From: "Bachman, William (MYD)" <[EMAIL PROTECTED]> Date: Tue,
> > May 22, 2007 2:48 pm To: "navin goyal" <[EMAIL PROTECTED]>,
> > "nmusers" <[email protected]>
> >
> > according to your code, your run should have created a file named
> > "drug3.sdtab". this file contains a table with these columns "ID
> > TIME AMT MDV DV EVID CMT" and DV PRED RES WRES. You can import
> > this file into Excel. You will have to manually create the graphs
> > unless you have a macro that can do it.
> >
> > ________________________________
> >
> > From: [EMAIL PROTECTED] [mailto:owner-
> > [EMAIL PROTECTED] On Behalf Of navin goyal Sent: Tuesday, May
> > 22, 2007 2:20 PM To: nmusers Subject: [NMusers] No Fit file
> >
> >
> > Hello everybody, I am trying to run a control stream for my data
> > using NONMEM 6. I get the output file with the objective function
> > and other estimates. The problem is that I do not get the fit file
> > that can be opened in excel. I guess I am missing out something in
> > the control stream, but just cannot figure it out.
> > Any suggestions would be appreciated The last part in the control
> > stream is posted below
> >
> >
> > $ESTIMATION METHOD=1 MAXEVAL=9999 PRINT=5 POSTHOC $COVARIANCE
> >
> > $TABLE ID TIME AMT MDV DV EVID CMT NOPRINT ONEHEADER
> > FILE=drug3.sdtab
> >
> > thanks a lot
> >
> > Navin
> >
> >
> >
> >
> >
> >
> > ___________________________________________________________________-
> > ____________________________________________________________________
> >
> >
> >
> >
> >
I think most of us know that the last line of control stream or data file is ignored on WinNT, Win2000 and WinXP in some cases.
My workaround is to add comment line at the end as Jeroen wrote.
Masaki Hiraoka
Elassaiss - Schaap, J. (Jeroen) wrote:
> Hi Alison,
>
> A simple workaround would be to add a platform-dependent newline to the
> control stream in the batchfile before calling NMTRAN.
>
> Jeroen
A number of interesting emails have been sent on this issue.
The most interesting appears to have been sent only to me, so I will
copy it to all of you.
Erik is correct. The characters are read before the EOF condition
occurs.
I have tested this in the two platforms that I used for the original
test.
I believe I can fix NMTRAN, at the points where it reads the control
stream and data file, in a manner similar to what Eric suggests.
Until the fix can be distributed, which may be some time if it is
non-trivial,
please use one of the workarounds that have been suggested, or just be
careful that the last line of the control stream
and data file ends with a cr-lf.
Thank you all!!
On Wed, 23 May 2007 14:01:11 +0200, "Olofsen, E. (ANST)"
<[EMAIL PROTECTED]> said:
> Dear Alison,
>
> I think the text is being read, even though an end-of-file (eof)
> condition occurs, but it is not printed. With
>
> program read
> character*10 text
> read (5,55,iostat=ios) text
> print *,text
> print *,ios
> 55 format (A10)
> stop
> end
>
> it is possible to use text and check later for an eof condition.
>
> Could this be a solution?
>
> Best regards,
>
> Erik
>
>
Quoted reply history
> On Tue, 2007-05-22 at 14:41 -0700, Alison Boeckmann wrote:
> > This is not a bug in NM-TRAN. But I can see how it happens in
> > MS-DOS. Both wordpad and notepad (unlike ms-dos edit and unix vi) will
> > write a file whose last line does not terminate with cr/lf. Such a line
> > is invisible to the Fortran I/O libraries that are part of g77
> > (in the MS-DOS environment) and FORTRAN 77 5.0 (in the Solaris
> > environment).
> >
> > I tested this in both MS-DOS and Solaris with a little fortran program
> > that branches to statement 10 when an end of file condition occurs.
> >
> >
> > program read
> > character*10 text
> > read (5,55,end=10) text
> > print *,text
> > 55 format (A10)
> > stop
> > 10 print *,'nothing read'
> > end
> >
> > I created a file named infile containing only "1234567890" with no cr/lf
> > using notepad. I copied it to Solaris using ftp. In both environments,
> > when the program is run with infile as input, it produces
> > the output "nothing read". E.g., in Solaris,
> >
> > % f77 read.for
> > read.for:
> > MAIN read:
> > % a.out<infile
> > nothing read
> >
> > I don't know how to overcome this problem. Changing the format from A10
> > to (say)
> > A1 or * does not help. It seems to me it is a bug (or maybe a design
> > feature?) in the Fortran I/O library.
> >
> >
> > On Tue, 22 May 2007 12:56:18 -0700, "Mark Sale - Next Level Solutions"
> > <[EMAIL PROTECTED]> said:
> > > Navin, If you're not getting the table file you expect, if may be
> > > because NMtran (5 at least) seems to have a small bug that it will
> > > sometimes ignore the last line of a control file if there isn't a
> > > carriage return/line feed at the end. Try just hitting Enter after
> > > the $TABLE record and saving. WRT plots, two options are Xpose from
> > > the Upsala group (R/Splus, http://xpose.sourceforge.net) or an excel
> > > macro from Next Level Solutions (www.nextlevelsolns.com)
> > >
> > >
> > >
> > > Mark Sale MD Next Level Solutions, LLC www.NextLevelSolns.com
> > >
> > >
> > > > -------- Original Message -------- Subject: RE: [NMusers] No Fit
> > > > file From: "Bachman, William (MYD)" <[EMAIL PROTECTED]> Date: Tue,
> > > > May 22, 2007 2:48 pm To: "navin goyal" <[EMAIL PROTECTED]>,
> > > > "nmusers" <[email protected]>
> > > >
> > > > according to your code, your run should have created a file named
> > > > "drug3.sdtab". this file contains a table with these columns "ID
> > > > TIME AMT MDV DV EVID CMT" and DV PRED RES WRES. You can import
> > > > this file into Excel. You will have to manually create the graphs
> > > > unless you have a macro that can do it.
> > > >
> > > > ________________________________
> > > >
> > > > From: [EMAIL PROTECTED] [mailto:owner-
> > > > [EMAIL PROTECTED] On Behalf Of navin goyal Sent: Tuesday, May
> > > > 22, 2007 2:20 PM To: nmusers Subject: [NMusers] No Fit file
> > > >
> > > >
> > > > Hello everybody, I am trying to run a control stream for my data
> > > > using NONMEM 6. I get the output file with the objective function
> > > > and other estimates. The problem is that I do not get the fit
> > > > file that can be opened in excel. I guess I am missing out
> > > > something in the control stream, but just cannot figure it out.
> > > > Any suggestions would be appreciated The last part in the control
> > > > stream is posted below
> > > >
> > > >
> > > > $ESTIMATION METHOD=1 MAXEVAL=9999 PRINT=5 POSTHOC $COVARIANCE
> > > >
> > > > $TABLE ID TIME AMT MDV DV EVID CMT NOPRINT ONEHEADER
> > > > FILE=drug3.sdtab
> > > >
> > > > thanks a lot
> > > >
> > > > Navin
> > > >
> > > >
> > > >
> > > >
> > > >
> > > >
> > > > ___________________________________________________________________-
> > > > ____________________________________________________________________
> > > >
> > > >
> > > >
> > > >
> > > >