Re: [NMusers] An error when running a plasma/urine model in SS. Would you please help?

2024-07-15 Thread Leonid Gibiansky 

If SS with void at t1 after dose is needed, it can be obtained by 2 doses:

TIME=-tau,AMT=0,SS=0, CMT=-4
TIME=-tau,AMT=dose, SS=1, CMT=1
TIME=-tau+t1, AMT=0,SS=0, CMT=4
TIME=0,   AMT=dose, SS=0, CMT=1

I have not tested it, so it is better to check...

Thank you
Leonid



On 7/15/2024 3:01 PM, Abdelrahman Saqr wrote:

Thank you  all for your help.
Yes, that is what I believed in. The urine compartment is the problem. I 
tried the empirical steady state method (ADDL = -ve integer)  with the 
plasma data only and then with the urine. The plasma achieves SS after a 
few number of doses; however, the urine compartment does not even with a 
very large number of doses. And I think this is as Saeheum has mentioned 
due to the emptying process.

I did use the EVID to empty out the urine compartment (EVID = -v integer).
I am not sure if there is a way in NONMEM to select compartments to be 
tested for the SS. (i.e. the central compartment is tested for SS but 
the output compartment is ignored)


C 	ID 	TIME 	TAD 	AMT 	AMT_MOLAR 	AMT_MPA 	AMT_MPA_MOL 	RATE 	DV 
DV_MOLAR 	DV_AMT_MOL 	LN_DV_AMT_MOL 	Uvol 	CMT 	EVID 	MDV 	L2 	ADDL 	II 
SS 	DVID 	DATE
0 	1 	19:30:00 	-24 	500 	0 	369.5 	1.153606 	-1 	0 	0 	0 	0 	0 	1 	1 	1 
	0 	0 	0 	1 	0 	4/4/2018
0 	1 	19:30:00 	-12 	500 	1.153403 	369.5 	1.153606 	0 	0 	0 	0 	0 	0 	1 
	1 	1 	0 	0 	0 	0 	0 	4/4/2018









0 	1 	8:08:00 	0 	0 	0 	0 	0 	0 	2007 	6.266001 	6.266001 	6.266001 	0 
2 	0 	0 	1 	0 	0 	0 	1 	4/5/2018
0 	1 	8:08:00 	0 	500 	1.153403 	369.5 	1.153606 	0 	0 	0 	0 	0 	0 	1 	1 
	1 	0 	0 	0 	0 	0 	4/5/2018









0 	1 	8:08:00 	0 	0 	0 	0 	0 	0 	0 	0 	0 	0 	0 	4 	2 	1 	11 	0 	0 	0 	3 
4/5/2018
0 	1 	8:36:00 	0.5 	0 	0 	0 	0 	0 	17010 	53.10646 	53.10646 	53.10646 
0 	2 	0 	0 	2 	0 	0 	0 	1 	4/5/2018
0 	1 	9:08:00 	1 	0 	0 	0 	0 	0 	21791 	68.03309 	68.03309 	68.03309 	0 
2 	0 	0 	3 	0 	0 	0 	1 	4/5/2018
0 	1 	10:06:00 	2 	0 	0 	0 	0 	0 	6373 	19.89697 	19.89697 	19.89697 	0 
2 	0 	0 	7 	0 	0 	0 	1 	4/5/2018
0 	1 	11:08:00 	3 	0 	0 	0 	0 	0 	4461 	13.92757 	13.92757 	13.92757 	0 
2 	0 	0 	8 	0 	0 	0 	1 	4/5/2018
0 	1 	12:07:00 	4 	0 	0 	0 	0 	0 	3867 	12.07306 	12.07306 	12.07306 	0 
2 	0 	0 	9 	0 	0 	0 	1 	4/5/2018
0 	1 	13:07:00 	5 	0 	0 	0 	0 	0 	7404 	23.11583 	23.11583 	23.11583 	0 
2 	0 	0 	10 	0 	0 	0 	1 	4/5/2018
0 	1 	14:10:00 	6 	0 	0 	0 	0 	0 	5256 	16.40962 	16.40962 	16.40962 	0 
2 	0 	0 	11 	0 	0 	0 	1 	4/5/2018
0 	1 	14:10:00 	6 	0 	0 	0 	0 	0 	3396 	10.60256 	4665.126 	8.44787 	440 
	-4 	0 	0 	600 	0 	0 	0 	3 	4/5/2018
0 	1 	14:10:00 	6 	0 	0 	0 	0 	0 	0 	0 	0 	0 	0 	4 	2 	1 	6 	0 	0 	0 	3 
4/5/2018
0 	1 	15:10:00 	7 	0 	0 	0 	0 	0 	3318 	10.35904 	10.35904 	10.35904 	0 
2 	0 	0 	12 	0 	0 	0 	1 	4/5/2018
0 	1 	16:10:00 	8 	0 	0 	0 	0 	0 	4235 	13.22198 	13.22198 	13.22198 	0 
2 	0 	0 	13 	0 	0 	0 	1 	4/5/2018
0 	1 	17:08:00 	9 	0 	0 	0 	0 	0 	6954 	21.7109 	21.7109 	21.7109 	0 	2 
0 	0 	14 	0 	0 	0 	1 	4/5/2018
0 	1 	18:08:00 	10 	0 	0 	0 	0 	0 	7505 	23.43116 	23.43116 	23.43116 	0 
	2 	0 	0 	4 	0 	0 	0 	1 	4/5/2018
0 	1 	19:08:00 	11 	0 	0 	0 	0 	0 	2390 	7.461755 	7.461755 	7.461755 	0 
	2 	0 	0 	5 	0 	0 	0 	1 	4/5/2018
0 	1 	20:08:00 	12 	0 	0 	0 	0 	0 	20163 	62.95036 	11834.67 	9.378788 
188 	-4 	0 	0 	1200 	0 	0 	0 	3 	4/5/2018
0 	1 	20:10:00 	12 	0 	0 	0 	0 	0 	1316 	4.108648 	4.108648 	4.108648 	0 
	2 	0 	0 	6 	0 	0 	0 	1 	4/5/2018



On Thu, Jul 11, 2024 at 8:28 AM Saeheum Song > wrote:


There is no steady state in urine. Urine is always accumulating and
empty out. You can set ss to the central compartment. After setting
ss to the central compartment, you need to empty and reset urine
compartment using evid.


On Thu, Jul 11, 2024, 2:10 AM Leonid Gibiansky
mailto:lgibian...@quantpharm.com>> wrote:

Could you show the code and the data sample?
It is possible that urine compartment does not have SS, as it
does not
have elimination. It needs to be emptied  time to time, and it
could be
difficult to code SS of this system. To check, you may look on
the urine
compartment concentrations with additional doses: do they
converge to SS
to increase with time?
Leonid

On 7/9/2024 2:41 PM

Re: [NMusers] An error when running a plasma/urine model in SS. Would you please help?

2024-07-11 Thread Saeheum Song 
There is no steady state in urine. Urine is always accumulating and empty
out. You can set ss to the central compartment. After setting ss to the
central compartment, you need to empty and reset urine compartment using
evid.


On Thu, Jul 11, 2024, 2:10 AM Leonid Gibiansky 
wrote:

> Could you show the code and the data sample?
> It is possible that urine compartment does not have SS, as it does not
> have elimination. It needs to be emptied  time to time, and it could be
> difficult to code SS of this system. To check, you may look on the urine
> compartment concentrations with additional doses: do they converge to SS
> to increase with time?
> Leonid
>
> On 7/9/2024 2:41 PM, Abdelrahman Saqr wrote:
> > Dear Colleagues,
> >
> > I am encountering the following error when I run a model that includes
> > plasma and urine data and SS data column =1.
> > When I remove the urine data (modelling only the plasma data), the model
> > runs without any error.
> >
> > When I drop the SS column (run a single dose or even with additional
> > doses), the model runs without any error.
> >
> > When I have both the urine data and SS assigned as 1 or 3, I face the
> > following error :
> >
> > MONITORING OF SEARCH:
> >
> > 0THE INPUT MATRIX IS SINGULAR. SOME OF THE DIAGONAL ELEMENTS OF THE UPPER
> >TRIANGULAR MATRIX U OF THE LU FACTORIZATION ARE CLOSE TO ZERO.
> > 0THE INPUT MATRIX IS SINGULAR. SOME OF THE DIAGONAL ELEMENTS OF THE UPPER
> >TRIANGULAR MATRIX U OF THE LU FACTORIZATION ARE CLOSE TO ZERO.
> >
> > 0PRED EXIT CODE = 1
> > 0INDIVIDUAL NO.   1   ID= 3.002000E+03   (WITHIN-INDIVIDUAL)
> > DATA REC NO.   1
> >   THETA=
> >8.60E+00   1.39E+01   1.78E+02   1.33E-01   1.00E+00
> >   OCCURS DURING SEARCH FOR ETA AT INITIAL VALUE, ETA=0
> >   NUMERICAL DIFFICULTIES WITH INITIAL ESTIMATE OF STEADY-STATE SOLUTION.
> >   DA MATRIX IS NOT INVERTIBLE AT A ZERO STATE VECTOR.
> >   TRY SETTING INITIAL ESTIMATE USING SS=3.
> >
> > I appreciate your help with interpreting and fixing this error.
> > Thanks,
> >
> > --
> > *Abdelrahman Saqr *
> > MS. Experimental and Clinical Pharmacology | University of Minnesota
> > PhD Candidate | Department ofExperimental and Clinical Pharmacology
> > College of Pharmacy | University of Minnesota
> > www.linkedin.com/in/abdelrahman-saqr
> > 
> >
>
>

Re: [NMusers] An error when running a plasma/urine model in SS. Would you please help?

2024-07-10 Thread Leonid Gibiansky 

Could you show the code and the data sample?
It is possible that urine compartment does not have SS, as it does not 
have elimination. It needs to be emptied  time to time, and it could be 
difficult to code SS of this system. To check, you may look on the urine 
compartment concentrations with additional doses: do they converge to SS 
to increase with time?

Leonid

On 7/9/2024 2:41 PM, Abdelrahman Saqr wrote:

Dear Colleagues,

I am encountering the following error when I run a model that includes 
plasma and urine data and SS data column =1.
When I remove the urine data (modelling only the plasma data), the model 
runs without any error.


When I drop the SS column (run a single dose or even with additional 
doses), the model runs without any error.


When I have both the urine data and SS assigned as 1 or 3, I face the 
following error :


MONITORING OF SEARCH:

0THE INPUT MATRIX IS SINGULAR. SOME OF THE DIAGONAL ELEMENTS OF THE UPPER
           TRIANGULAR MATRIX U OF THE LU FACTORIZATION ARE CLOSE TO ZERO.
0THE INPUT MATRIX IS SINGULAR. SOME OF THE DIAGONAL ELEMENTS OF THE UPPER
           TRIANGULAR MATRIX U OF THE LU FACTORIZATION ARE CLOSE TO ZERO.

0PRED EXIT CODE = 1
0INDIVIDUAL NO.       1   ID= 3.002000E+03   (WITHIN-INDIVIDUAL) 
DATA REC NO.   1

  THETA=
   8.60E+00   1.39E+01   1.78E+02   1.33E-01   1.00E+00
  OCCURS DURING SEARCH FOR ETA AT INITIAL VALUE, ETA=0
  NUMERICAL DIFFICULTIES WITH INITIAL ESTIMATE OF STEADY-STATE SOLUTION.
  DA MATRIX IS NOT INVERTIBLE AT A ZERO STATE VECTOR.
  TRY SETTING INITIAL ESTIMATE USING SS=3.

I appreciate your help with interpreting and fixing this error.
Thanks,

--
*Abdelrahman Saqr *
MS. Experimental and Clinical Pharmacology | University of Minnesota
PhD Candidate | Department ofExperimental and Clinical Pharmacology
College of Pharmacy | University of Minnesota
www.linkedin.com/in/abdelrahman-saqr

[NMusers] An error when running a plasma/urine model in SS. Would you please help?

2024-07-09 Thread Abdelrahman Saqr 
Dear Colleagues,

I am encountering the following error when I run a model that includes
plasma and urine data and SS data column =1.
When I remove the urine data (modelling only the plasma data), the model
runs without any error.

When I drop the SS column (run a single dose or even with additional
doses), the model runs without any error.

When I have both the urine data and SS assigned as 1 or 3, I face the
following error :

MONITORING OF SEARCH:

0THE INPUT MATRIX IS SINGULAR. SOME OF THE DIAGONAL ELEMENTS OF THE UPPER
  TRIANGULAR MATRIX U OF THE LU FACTORIZATION ARE CLOSE TO ZERO.
0THE INPUT MATRIX IS SINGULAR. SOME OF THE DIAGONAL ELEMENTS OF THE UPPER
  TRIANGULAR MATRIX U OF THE LU FACTORIZATION ARE CLOSE TO ZERO.

0PRED EXIT CODE = 1
0INDIVIDUAL NO.   1   ID= 3.002000E+03   (WITHIN-INDIVIDUAL)
DATA REC NO.   1
 THETA=
  8.60E+00   1.39E+01   1.78E+02   1.33E-01   1.00E+00
 OCCURS DURING SEARCH FOR ETA AT INITIAL VALUE, ETA=0
 NUMERICAL DIFFICULTIES WITH INITIAL ESTIMATE OF STEADY-STATE SOLUTION.

 DA MATRIX IS NOT INVERTIBLE AT A ZERO STATE VECTOR.

 TRY SETTING INITIAL ESTIMATE USING SS=3.

I appreciate your help with interpreting and fixing this error.
Thanks,

-- 
*Abdelrahman Saqr *
MS. Experimental and Clinical Pharmacology | University of Minnesota
PhD Candidate | Department of Experimental and Clinical Pharmacology
College of Pharmacy | University of Minnesota
www.linkedin.com/in/abdelrahman-saqr