Hello everybody,
I am trying to simulate PKPD data for 5000 patients, with each patient
having around 100 time points.
How could I create a data file for this simulation??
Any help is appreciated.
Thanks
Navin
create simulation file for 5000 patients ?
thanks for the reply.
Could excel help me if I had less patients say around 100-200.
I mean.. could i generate an excel file then ??
How could I do it ??
Thanks again.
Navin
Quoted reply history
On 2/27/07, Dennis Fisher <[EMAIL PROTECTED]> wrote:
> use R or Splus
> Excel would be a disaster - it is capped at ~ 64000 lines.
>
> Dennis Fisher MD
>
> P < (The "P Less Than" Company)
>
> Phone: 1-866-PLessThan (1-866-753-7784)
>
> Fax: 1-415-564-2220
>
> www.PLessThan.com
>
> On Feb 27, 2007, at 1:39 PM, navin goyal wrote:
>
> Hello everybody,
> I am trying to simulate PKPD data for 5000 patients, with each patient
> having around 100 time points.
> How could I create a data file for this simulation??
> Any help is appreciated.
> Thanks
>
> Navin
Do the math: 64,000 / 100 = 640 subjects
By the way, Excel 2007 has a much larger number of rows (I forget the new
number).
_____
Quoted reply history
From: [EMAIL PROTECTED] [mailto:[EMAIL PROTECTED] On
Behalf Of navin goyal
Sent: Tuesday, February 27, 2007 10:28 PM
To: Dennis Fisher; [email protected]
Subject: Re: [NMusers] create simulation file for 5000 patients ?
thanks for the reply.
Could excel help me if I had less patients say around 100-200.
I mean.. could i generate an excel file then ??
How could I do it ??
Thanks again.
Navin
On 2/27/07, Dennis Fisher <[EMAIL PROTECTED]> wrote:
use R or Splus
Excel would be a disaster - it is capped at ~ 64000 lines.
Dennis Fisher MD
P < (The "P Less Than" Company)
Phone: 1-866-PLessThan (1-866-753-7784)
Fax: 1-415-564-2220
www.PLessThan.com
On Feb 27, 2007, at 1:39 PM, navin goyal wrote:
Hello everybody,
I am trying to simulate PKPD data for 5000 patients, with each patient
having around 100 time points.
How could I create a data file for this simulation??
Any help is appreciated.
Thanks
Navin
Dennis,
I'll show you how to do it in Excel someday. But the answer is to use
the SUBPROBLEMS option in the SIMULATION record
SUBPROBLEMS=n
Requests that the entire NONMEM problem is to be repeated n times
in succession (including all NONMEM steps: simulation, estima-
tion, covariance, table, scatterplot). Each subproblem includes
the Simulation Step, but the random sources are simply continued
from subproblem to subproblem. If n=0 or n=1, there is only one
subproblem; this is the default. May also be coded SUBPROBS,
NSUBPROBLEMS, NSUBPROBS.
Mark Sale MD
Next Level Solutions, LLC
www.NextLevelSolns.com
>
>
> > -------- Original Message --------
> > Subject: Re: [NMusers] create simulation file for 5000 patients ?
> > From: "navin goyal" <[EMAIL PROTECTED]>
> > Date: Tue, February 27, 2007 10:28 pm
> > To: "Dennis Fisher" <[EMAIL PROTECTED]>, [email protected]
> >
> > thanks for the reply.
> >
> > Could excel help me if I had less patients say around 100-200.
> > I mean.. could i generate an excel file then ??
> > How could I do it ??
> >
> > Thanks again.
> > Navin
> >
> >
> >
> > On 2/27/07, Dennis Fisher <[EMAIL PROTECTED]> wrote: use R or Splus
> > Excel would be a disaster - it is capped at ~ 64000 lines.
> >
> > Dennis Fisher MD P < (The "P Less Than" Company) Phone: 1-866-PLessThan
> > (1-866-753-7784) Fax: 1-415-564-2220 www.PLessThan.com
> > On Feb 27, 2007, at 1:39 PM, navin goyal wrote:
> > Hello everybody,
> > I am trying to simulate PKPD data for 5000 patients, with each patient
> > having around 100 time points.
> > How could I create a data file for this simulation??
> > Any help is appreciated.
> > Thanks
> >
> > Navin
> >
> >
> >
Navin,
There are several approaches but perhaps the simplest would be to create a
NONMEM data file for one patient with the time points you want to use for the
simulation. Then use NONMEM to simulate with 5000 sub-problems. This will
create a table file with 5000 simulated patients. Each patient will have their
own separate table in the table file e.g.
$SIMULATION (123456) ONLYSIM NSUB=5000
$TABLE ID TIME DV NOAPPEND ONEHEADER NOPRINT FILE=sim.tab
However, if you also want to simulate the consequences of having different
covariates in each patient then you will need to include simulation code for
the covariate values so that each sub-problem uses different covariates. The
difficulty of simulating covariates varies from easy to very hard depending on
the number and type of covariates. An easy example would be to simulate age and
weight e.g.
$INPUT ID TIME WT AGE etc
$THETA 70 ; popwt
$THETA 60 ; popage
$OMEGA BLOCK(2)
0.09 ; bsvwt
-0.01 0.09 ; bsvage
$PK
IF (ICALL.EQ.4) THEN
WT=THETA(1)*EXP(ETA(1))
AGE=THETA(2)*EXP(ETA(2))
ENDIF
Finally you will have to put some thought into what you want to do with the
simulated concentration predictions and how you will process them.
Nick
navin goyal wrote:
>
> Hello everybody,
> I am trying to simulate PKPD data for 5000 patients, with each patient having
> around 100 time points.
> How could I create a data file for this simulation??
> Any help is appreciated.
> Thanks
>
> Navin
--
Nick Holford, Dept Pharmacology & Clinical Pharmacology
University of Auckland, 85 Park Rd, Private Bag 92019, Auckland, New Zealand
email:[EMAIL PROTECTED] tel:+64(9)373-7599x86730 fax:373-7556
http://www.health.auckland.ac.nz/pharmacology/staff/nholford/
mark
i know how to do it in excel. but, excel is the saturn next to my porsche (R).
dennis
Dennis Fisher MD
P < (The "P Less Than" Company)
Phone: 1-866-PLessThan (1-866-753-7784)
Fax: 1-415-564-2220
www.PLessThan.com
Quoted reply history
On Feb 28, 2007, at 6:42 AM, Mark Sale - Next Level Solutions wrote:
> Dennis,
>
> I'll show you how to do it in Excel someday. But the answer is to use
>
> the SUBPROBLEMS option in the SIMULATION record
>
> SUBPROBLEMS=n
> Requests that the entire NONMEM problem is to be repeated n times
> in succession (including all NONMEM steps: simulation, estima-
> tion, covariance, table, scatterplot). Each subproblem includes
> the Simulation Step, but the random sources are simply continued
> from subproblem to subproblem. If n=0 or n=1, there is only one
> subproblem; this is the default. May also be coded SUBPROBS,
> NSUBPROBLEMS, NSUBPROBS.
>
> Mark Sale MD
> Next Level Solutions, LLC
> www.NextLevelSolns.com
>
> > > -------- Original Message --------
> > > Subject: Re: [NMusers] create simulation file for 5000 patients ?
> > > From: "navin goyal" <[EMAIL PROTECTED]>
> > > Date: Tue, February 27, 2007 10:28 pm
> > > To: "Dennis Fisher" <[EMAIL PROTECTED]>, [email protected]
> > >
> > > thanks for the reply.
> > >
> > > Could excel help me if I had less patients say around 100-200.
> > > I mean.. could i generate an excel file then ??
> > > How could I do it ??
> > >
> > > Thanks again.
> > > Navin
> > >
> > > On 2/27/07, Dennis Fisher <[EMAIL PROTECTED]> wrote: use R or Splus
> > >
> > > Excel would be a disaster - it is capped at ~ 64000 lines.
> > >
> > > Dennis Fisher MD P < (The "P Less Than" Company) Phone: 1-866- PLessThan (1-866-753-7784) Fax: 1-415-564-2220 www.PLessThan.com
> > >
> > > On Feb 27, 2007, at 1:39 PM, navin goyal wrote:
> > > Hello everybody,
> > >
> > > I am trying to simulate PKPD data for 5000 patients, with each patient having around 100 time points.
> > >
> > > How could I create a data file for this simulation??
> > > Any help is appreciated.
> > > Thanks
> > >
> > > Navin
Navin,
This can be done in SPlus, use command:
data$subject<-rep(1:5000, each=100)
you can create 5000 subjects each have 100 time points
Mei
Quoted reply history
On Tue Feb 27 16:39:02 EST 2007, navin goyal <[EMAIL PROTECTED]> wrote:
> Hello everybody,
>
> I am trying to simulate PKPD data for 5000 patients, with each patient
>
> having around 100 time points.
> How could I create a data file for this simulation??
> Any help is appreciated.
> Thanks
>
> Navin
--
TANG,MEI
Hi Navin,
I have a couple of things to add. As Dr. Holford suggested, use NSUB option
in $SIMULATION to simulate 5000 patients with single subject data. You could
also add a REPI option in your control stream which might help you later to
sort simulations.( http://www.cognigencorp.com/nonmem/nm/99may202003.html).
Here is a simple set up example of a PKPD model data file for one patient i
would create for simulation.
ID TIME AMT DV EVID TYPE
1 0 10 0 1 1
1 0 0 0 0 2
1 1 0 0 0 1
1 1 0 0 0 2
1 2 0 0 0 1
1 2 0 0 0 2
Now, even if you want to build a large database, its possible with Microsoft
Access (other than SAS and SPLUS) as it is capable of handling much larger
data than Excel 2003 (As far as I know). After creating a database you can
export it as .csv file and use it as a input for your NONMEM control stream.
However, I believe Microsoft Access would be helpful when you have large data
to process after simulations.
Hope it helps.
Best Regards
Nitin Mehrotra
Postdoc Research Fellow
Dept Pharmaceutical Sciences
UTHSC, Memphis, TN-USA
navin goyal <[EMAIL PROTECTED]> wrote: Hello everybody,
I am trying to simulate PKPD data for 5000 patients, with each patient having
around 100 time points.
How could I create a data file for this simulation??
Any help is appreciated.
Thanks
Navin
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