Dear NMusers,
I wish to run a $EST NM.ctl with 500 $PROBLEMs. Is there an automated way to
extract the 500 sets of thetas, omegas, sigmas, and minimization statuses from
the single output that NONMEM provides? Two related questions are: a) What is
the machinery that runs behind WFN for extracting output after nmbs and b)
Xpose31() extracts only a single set (I think it is the first set); will
downloading the newer version of Xpose solve this problem?
Kindly advice...Mahesh
Automated way to extract NM output
Mahesh,
The 'machinery' behind WFN is awk (actually the GNU gawk).
Did you try running your 500 problem run using WFN? WFN should extract the
output and summarise it in the *.smy file in the run output directory.
If WFN doesn't work please send me your control stream and data so I can see
what is happening.
Nick
> "Samtani, Mahesh [PRDUS]" wrote:
>
> Dear NMusers,
> I wish to run a $EST NM.ctl with 500 $PROBLEMs. Is there an automated way to
> extract the 500 sets of thetas, omegas, sigmas, and minimization statuses
> from the single output that NONMEM provides? Two related questions are: a)
> What is the machinery that runs behind WFN for extracting output after nmbs
> and b) Xpose31() extracts only a single set (I think it is the first set);
> will downloading the newer version of Xpose solve this problem?
>
> Kindly advice
Mahesh
>
--
Nick Holford, Dept Pharmacology & Clinical Pharmacology
University of Auckland, 85 Park Rd, Private Bag 92019, Auckland, New Zealand
[EMAIL PROTECTED] tel:+64(9)373-7599x86730 fax:+64(9)373-7090
www.health.auckland.ac.nz/pharmacology/staff/nholford
Dear all,
A comment on Xpose - no, support for multiple $PROBLEM statements is not
present in the current version (4.0PR6U1) - and this is not something
planned for Census, either, come to that. By a show of hands, is this
something people would like to see implemented?
Best regards
Justin Wilkins
Novartis Pharma AG
PH346, MODELING & SIMULATION
CHBS, WSJ-027.1.084
Novartis Pharma AG
Lichtstrasse 35
CH-4056 Basel
Switzerland
Phone: +41 61 324 6549
Fax: +41 61 324 3039
Mobile: +41 76 561 0949
Email : [EMAIL PROTECTED]
Nick Holford <[EMAIL PROTECTED]>
Sent by: [EMAIL PROTECTED]
22.10.2007 08:17
To
[email protected]
cc
Subject
Re: [NMusers] Automated way to extract NM output
Mahesh,
The 'machinery' behind WFN is awk (actually the GNU gawk).
Did you try running your 500 problem run using WFN? WFN should extract the
output and summarise it in the *.smy file in the run output directory.
If WFN doesn't work please send me your control stream and data so I can
see what is happening.
Nick
> "Samtani, Mahesh [PRDUS]" wrote:
>
> Dear NMusers,
> I wish to run a $EST NM.ctl with 500 $PROBLEMs. Is there an automated
way to extract the 500 sets of thetas, omegas, sigmas, and minimization
statuses from the single output that NONMEM provides? Two related
questions are: a) What is the machinery that runs behind WFN for
extracting output after nmbs and b) Xpose31() extracts only a single set
(I think it is the first set); will downloading the newer version of Xpose
solve this problem?
>
> Kindly advice?Mahesh
>
--
Nick Holford, Dept Pharmacology & Clinical Pharmacology
University of Auckland, 85 Park Rd, Private Bag 92019, Auckland, New
Zealand
[EMAIL PROTECTED] tel:+64(9)373-7599x86730 fax:+64(9)373-7090
www.health.auckland.ac.nz/pharmacology/staff/nholford
Dear All,
PsN does this quite well. Running the PsN command "execute" on you model
will produce a file called "raw_results.csv" which is an abbreviated
form of the NONMEM output. It is comma separated table with one row for
each $PROBLEM (and each subproblem). The row contains the final
parameter estimates, among other things.
Regards,
Pontus.
mån 2007-10-22 klockan 09:32 +0200 skrev [EMAIL PROTECTED]:
>
> Dear all,
>
> A comment on Xpose - no, support for multiple $PROBLEM statements is
> not present in the current version (4.0PR6U1) - and this is not
> something planned for Census, either, come to that. By a show of
> hands, is this something people would like to see implemented?
>
> Best regards
> Justin Wilkins
> Novartis Pharma AG
> PH346, MODELING & SIMULATION
> CHBS, WSJ-027.1.084
> Novartis Pharma AG
> Lichtstrasse 35
> CH-4056 Basel
> Switzerland
> Phone: +41 61 324 6549
> Fax: +41 61 324 3039
> Mobile: +41 76 561 0949
> Email : [EMAIL PROTECTED]
>
>
>
>
> Nick Holford
> <[EMAIL PROTECTED]>
> Sent by:
> [EMAIL PROTECTED]
>
> 22.10.2007 08:17
>
>
> To
> [email protected]
> cc
>
> Subject
> Re: [NMusers]
> Automated way to
> extract NM output
>
>
>
>
>
>
>
>
> Mahesh,
>
> The 'machinery' behind WFN is awk (actually the GNU gawk).
>
> Did you try running your 500 problem run using WFN? WFN should extract
> the output and summarise it in the *.smy file in the run output
> directory.
>
> If WFN doesn't work please send me your control stream and data so I
> can see what is happening.
>
> Nick
>
> > "Samtani, Mahesh [PRDUS]" wrote:
> >
> > Dear NMusers,
> > I wish to run a $EST NM.ctl with 500 $PROBLEMs. Is there an
> automated way to extract the 500 sets of thetas, omegas, sigmas, and
> minimization statuses from the single output that NONMEM provides? Two
> related questions are: a) What is the machinery that runs behind WFN
> for extracting output after nmbs and b) Xpose31() extracts only a
> single set (I think it is the first set); will downloading the newer
> version of Xpose solve this problem?
> >
> > Kindly advice…Mahesh
> >
>
> --
> Nick Holford, Dept Pharmacology & Clinical Pharmacology
> University of Auckland, 85 Park Rd, Private Bag 92019, Auckland, New
> Zealand
> [EMAIL PROTECTED] tel:+64(9)373-7599x86730 fax:+64(9)373-7090
> www.health.auckland.ac.nz/pharmacology/staff/nholford
>
I wrote a fortran program (nmsee5.for) intended for exactly this
purpose.
Copy all files from ftp://ftp.globomaxnm.com/Public/nonmem/nmsee
There is a readme file that gives suggetions for compiling and using the
program.
Nmsee5 works with NONMEM V and VI.
On Sun, 21 Oct 2007 23:43:27 -0400, "Samtani, Mahesh [PRDUS]"
<[EMAIL PROTECTED]> said:
> Dear NMusers,
> I wish to run a $EST NM.ctl with 500 $PROBLEMs. Is there an automated way
> to extract the 500 sets of thetas, omegas, sigmas, and minimization
> statuses from the single output that NONMEM provides? Two related
> questions are: a) What is the machinery that runs behind WFN for
> extracting output after nmbs and b) Xpose31() extracts only a single set
> (I think it is the first set); will downloading the newer version of
> Xpose solve this problem?
>
> Kindly advice...Mahesh
>
>
>
>
>
>
>
>
--
Alison Boeckmann
[EMAIL PROTECTED]
This is the kind of programming task SAS is very good at.
I don't know the record structure but I imagine it could be read into SAS
datasets for summary or re-writing as one file per set.
The SAS input statement is very powerful handling all kinds of fixed and
free formats, not to mention multiple records (which awk is not so good at).
I am off contract right now and I could give you some pointers if you like.
I do not have SAS at home right now though so I couldn't write & test a
program for you.
There is also the SAS list for SAS specific questions.
Regards,
Dave Garbutt
Basel, CH
> I wrote a fortran program (nmsee5.for) intended for exactly this
> purpose.
> Copy all files from ftp://ftp.globomaxnm.com/Public/nonmem/nmsee
> There is a readme file that gives suggetions for compiling and using the
> program.
> Nmsee5 works with NONMEM V and VI.
>
> On Sun, 21 Oct 2007 23:43:27 -0400, "Samtani, Mahesh [PRDUS]"
> <[EMAIL PROTECTED]> said:
>> Dear NMusers,
>> I wish to run a $EST NM.ctl with 500 $PROBLEMs. Is there an automated way
>> to extract the 500 sets of thetas, omegas, sigmas, and minimization
>> statuses from the single output that NONMEM provides? Two related
>> questions are: a) What is the machinery that runs behind WFN for
>> extracting output after nmbs and b) Xpose31() extracts only a single set
>> (I think it is the first set); will downloading the newer version of
>> Xpose solve this problem?
>>
>> Kindly advice...Mahesh
>>
>>
>>
>>
>>
>>
>>
>>