Dear NMUsers,
I am performing scm with PsN. My data have more than 50 covariates, this
should be processed by $SIZES PD=100 at the beginning of the NONMEM file.
However, it seems that scm command modifies this file by putting the block
$PROBLEM at the first line.
Here is the beginning of my code :
$SIZES LVR=150 PD=-100
SPROBLEM empty model
$DATA ID TIME AMT EVID DV CAT1 CAT2 ...
Here is the code transformed in the LST file
$SIZES LVR=150 PD=-100 $PROBLEM empty model
$DATA ID TIME AMT EVID DV CAT1 CAT2 ...
And at the end I have the following error
NM-TRAN MESSAGES
AN ERROR WAS FOUND IN THE CONTROL STATEMENTS.
AN ERROR WAS FOUND ON LINE 1 AT THE APPROXIMATE POSITION NOTED:
$SIZES LVR=150 PD=-100 $PROBLEM empty mod
X
THE CHARACTERS IN ERROR ARE: $
20 UNKNOWN OPTION.
Note that this is an issue for estimating the base model only. During the
forward path scm automatically drops the unnecessary covariates keeping only
the ones added at previous steps and the tested one. First estimate the base
model and use the option -base_ofv seems to work however I will have the same
issue if more than 50 covariates are added during the forward path.
Thank you in advance for any help or any suggestions.
Best Regards,
Emeric Sibieude
Student trainee in Master's degree
Biopharma | R&D | Global Development | Translational Medicine
Merck
Lausanne , Switzerland
[email protected]
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Block SIZE with SCM
Dear Emeric,
The code has negative PD, maybe PsN has problems interpreting this?
I am not sure how PD=-100 would be interpreted by NONMEM, but try PD=100,
instead.
I think this is what you intended to do?
As a side note, PsN (mainly to handle old nonmem versions) has functionality
for dropping (=DROP) covariates on $INPUT, if they are not tested in the
current model during SCM - but only among the ones listed in the configuration
as covariates.
Even if you test 50 covariates, it is not often more than ten different will be
included during forward inclusion, so possibly you can do with the default
PD=50?
Best wishes
Jakob
Quoted reply history
> On 5 Dec 2019, at 08:39, Emeric Sibieude <[email protected]>
> wrote:
>
> Dear NMUsers,
>
> I am performing scm with PsN. My data have more than 50 covariates, this
> should be processed by $SIZES PD=100 at the beginning of the NONMEM file.
>
> However, it seems that scm command modifies this file by putting the block
> $PROBLEM at the first line.
>
>
>
> Here is the beginning of my code :
>
> $SIZES LVR=150 PD=-100
>
> SPROBLEM empty model
>
> $DATA ID TIME AMT EVID DV CAT1 CAT2 ...
>
>
>
> Here is the code transformed in the LST file
>
> $SIZES LVR=150 PD=-100 $PROBLEM empty model
>
> $DATA ID TIME AMT EVID DV CAT1 CAT2 ...
>
>
>
> And at the end I have the following error
>
> NM-TRAN MESSAGES
>
> AN ERROR WAS FOUND IN THE CONTROL STATEMENTS.
>
> AN ERROR WAS FOUND ON LINE 1 AT THE APPROXIMATE POSITION NOTED:
> $SIZES LVR=150 PD=-100 $PROBLEM empty mod
> X
> THE CHARACTERS IN ERROR ARE: $
> 20 UNKNOWN OPTION.
>
>
>
> Note that this is an issue for estimating the base model only. During the
> forward path scm automatically drops the unnecessary covariates keeping only
> the ones added at previous steps and the tested one. First estimate the base
> model and use the option -base_ofv seems to work however I will have the same
> issue if more than 50 covariates are added during the forward path.
>
> Thank you in advance for any help or any suggestions.
>
> Best Regards,
>
> Emeric Sibieude
>
> Student trainee in Master's degree
>
> Biopharma | R&D | Global Development | Translational Medicine
>
> Merck
>
> Lausanne , Switzerland
>
> [email protected] <mailto:[email protected]>
>
>
>
>
>
> This message and any attachment are confidential and may be privileged or
> otherwise protected from disclosure. If you are not the intended recipient,
> you must not copy this message or attachment or disclose the contents to any
> other person. If you have received this transmission in error, please notify
> the sender immediately and delete the message and any attachment from your
> system. Merck KGaA, Darmstadt, Germany and any of its subsidiaries do not
> accept liability for any omissions or errors in this message which may arise
> as a result of E-Mail-transmission or for damages resulting from any
> unauthorized changes of the content of this message and any attachment
> thereto. Merck KGaA, Darmstadt, Germany and any of its subsidiaries do not
> guarantee that this message is free of viruses and does not accept liability
> for any damages caused by any virus transmitted therewith.
>
> Click http://www.merckgroup.com/disclaimer
> http://www.merckgroup.com/disclaimer to access the German, French, Spanish
> and Portuguese versions of this disclaimer.
Dear Jakob,
Thank you for your answer. According to PsN documentation PD = -100 means at
least 100 covariates. I tried with the exact number of covariates (PD = 105)
and I have the same issue.
Yes indeed, I can do it with the default value of PD = 50 because less than 50
are added but I was wondering if there exists a way if more than 50 covariates
are added during the forward path.
Best Regards,
Emeric Sibieude
Student trainee in Master's degree
Biopharma | R&D | Global Development | Translational Medicine
Merck
Lausanne , Switzerland
[email protected]<mailto:[email protected]>
Quoted reply history
From: Jakob Ribbing <[email protected]>
Sent: jeudi 5 décembre 2019 09:11
To: Emeric Sibieude <[email protected]>; [email protected]
Subject: Re: [NMusers] Block SIZE with SCM
Dear Emeric,
The code has negative PD, maybe PsN has problems interpreting this?
I am not sure how PD=-100 would be interpreted by NONMEM, but try PD=100,
instead.
I think this is what you intended to do?
As a side note, PsN (mainly to handle old nonmem versions) has functionality
for dropping (=DROP) covariates on $INPUT, if they are not tested in the
current model during SCM - but only among the ones listed in the configuration
as covariates.
Even if you test 50 covariates, it is not often more than ten different will be
included during forward inclusion, so possibly you can do with the default
PD=50?
Best wishes
Jakob
On 5 Dec 2019, at 08:39, Emeric Sibieude
<[email protected]<mailto:[email protected]>> wrote:
Dear NMUsers,
I am performing scm with PsN. My data have more than 50 covariates, this
should be processed by $SIZES PD=100 at the beginning of the NONMEM file.
However, it seems that scm command modifies this file by putting the block
$PROBLEM at the first line.
Here is the beginning of my code :
$SIZES LVR=150 PD=-100
SPROBLEM empty model
$DATA ID TIME AMT EVID DV CAT1 CAT2 ...
Here is the code transformed in the LST file
$SIZES LVR=150 PD=-100 $PROBLEM empty model
$DATA ID TIME AMT EVID DV CAT1 CAT2 ...
And at the end I have the following error
NM-TRAN MESSAGES
AN ERROR WAS FOUND IN THE CONTROL STATEMENTS.
AN ERROR WAS FOUND ON LINE 1 AT THE APPROXIMATE POSITION NOTED:
$SIZES LVR=150 PD=-100 $PROBLEM empty mod
X
THE CHARACTERS IN ERROR ARE: $
20 UNKNOWN OPTION.
Note that this is an issue for estimating the base model only. During the
forward path scm automatically drops the unnecessary covariates keeping only
the ones added at previous steps and the tested one. First estimate the base
model and use the option -base_ofv seems to work however I will have the same
issue if more than 50 covariates are added during the forward path.
Thank you in advance for any help or any suggestions.
Best Regards,
Emeric Sibieude
Student trainee in Master's degree
Biopharma | R&D | Global Development | Translational Medicine
Merck
Lausanne , Switzerland
[email protected]<mailto:[email protected]>
This message and any attachment are confidential and may be privileged or
otherwise protected from disclosure. If you are not the intended recipient, you
must not copy this message or attachment or disclose the contents to any other
person. If you have received this transmission in error, please notify the
sender immediately and delete the message and any attachment from your system.
Merck KGaA, Darmstadt, Germany and any of its subsidiaries do not accept
liability for any omissions or errors in this message which may arise as a
result of E-Mail-transmission or for damages resulting from any unauthorized
changes of the content of this message and any attachment thereto. Merck KGaA,
Darmstadt, Germany and any of its subsidiaries do not guarantee that this
message is free of viruses and does not accept liability for any damages caused
by any virus transmitted therewith.
Click http://www.merckgroup.com/disclaimer to access the German, French,
Spanish and Portuguese versions of this disclaimer.
This message and any attachment are confidential and may be privileged or
otherwise protected from disclosure. If you are not the intended recipient, you
must not copy this message or attachment or disclose the contents to any other
person. If you have received this transmission in error, please notify the
sender immediately and delete the message and any attachment from your system.
Merck KGaA, Darmstadt, Germany and any of its subsidiaries do not accept
liability for any omissions or errors in this message which may arise as a
result of E-Mail-transmission or for damages resulting from any unauthorized
changes of the content of this message and any attachment thereto. Merck KGaA,
Darmstadt, Germany and any of its subsidiaries do not guarantee that this
message is free of viruses and does not accept liability for any damages caused
by any virus transmitted therewith.
Click http://www.merckgroup.com/disclaimer to access the German, French,
Spanish and Portuguese versions of this disclaimer.
Dear Emeric,
With the PsN version I have used previously, I can confirm it has worked fine
to set items in $SIZES and run scm from that model.
I have for example used this:
;; Initial comments to describe the model
$SIZES PD=121 MAXIDS=18000
$PROBLEM Description of model
$INPUT ...
Maybe there was some strange character in your control stream that made the
line break disappear?
For example, looking down into your previous e-mail I now notice that the
dollar($) sign in front of PROBLEM seems strange (my bold, just below):
“Here is the beginning of my code :
$SIZES LVR=150 PD=-100
SPROBLEM empty model
$DATA..."
What you put into your original e-mail looks like an S (did not notice that
before).
Whatever character that is, it seems to be accepted by NONMEM as a dollar sign,
but not by PsN (and neither by the different means I have to view your e-mail).
If you change that to a proper dollar sign, I think the original setup with
PD=-100 will run in scm, as intended?
Best wishes
Jakob
Quoted reply history
> On 9 Dec 2019, at 09:04, Emeric Sibieude <[email protected]>
> wrote:
>
> Dear Jakob,
>
> Thank you for your answer. According to PsN documentation PD = -100 means at
> least 100 covariates. I tried with the exact number of covariates (PD = 105)
> and I have the same issue.
>
> Yes indeed, I can do it with the default value of PD = 50 because less than
> 50 are added but I was wondering if there exists a way if more than 50
> covariates are added during the forward path.
>
> Best Regards,
>
> Emeric Sibieude
>
> Student trainee in Master's degree
>
> Biopharma | R&D | Global Development | Translational Medicine
>
> Merck
>
> Lausanne , Switzerland
>
> [email protected] <mailto:[email protected]>
>
> From: Jakob Ribbing <[email protected]
> <mailto:[email protected]>>
> Sent: jeudi 5 décembre 2019 09:11
> To: Emeric Sibieude <[email protected]
> <mailto:[email protected]>>; [email protected]
> <mailto:[email protected]>
> Subject: Re: [NMusers] Block SIZE with SCM
>
> Dear Emeric,
>
> The code has negative PD, maybe PsN has problems interpreting this?
> I am not sure how PD=-100 would be interpreted by NONMEM, but try PD=100,
> instead.
> I think this is what you intended to do?
>
> As a side note, PsN (mainly to handle old nonmem versions) has functionality
> for dropping (=DROP) covariates on $INPUT, if they are not tested in the
> current model during SCM - but only among the ones listed in the
> configuration as covariates.
> Even if you test 50 covariates, it is not often more than ten different will
> be included during forward inclusion, so possibly you can do with the default
> PD=50?
>
> Best wishes
>
> Jakob
>
>
> On 5 Dec 2019, at 08:39, Emeric Sibieude <[email protected]
> <mailto:[email protected]>> wrote:
>
> Dear NMUsers,
>
> I am performing scm with PsN. My data have more than 50 covariates, this
> should be processed by $SIZES PD=100 at the beginning of the NONMEM file.
>
> However, it seems that scm command modifies this file by putting the block
> $PROBLEM at the first line.
>
>
>
> Here is the beginning of my code :
>
> $SIZES LVR=150 PD=-100
>
> SPROBLEM empty model
>
> $DATA ID TIME AMT EVID DV CAT1 CAT2 ...
>
>
>
> Here is the code transformed in the LST file
>
> $SIZES LVR=150 PD=-100 $PROBLEM empty model
>
> $DATA ID TIME AMT EVID DV CAT1 CAT2 ...
>
>
>
> And at the end I have the following error
>
> NM-TRAN MESSAGES
>
> AN ERROR WAS FOUND IN THE CONTROL STATEMENTS.
>
> AN ERROR WAS FOUND ON LINE 1 AT THE APPROXIMATE POSITION NOTED:
> $SIZES LVR=150 PD=-100 $PROBLEM empty mod
> X
> THE CHARACTERS IN ERROR ARE: $
> 20 UNKNOWN OPTION.
>
>
>
> Note that this is an issue for estimating the base model only. During the
> forward path scm automatically drops the unnecessary covariates keeping only
> the ones added at previous steps and the tested one. First estimate the base
> model and use the option -base_ofv seems to work however I will have the same
> issue if more than 50 covariates are added during the forward path.
>
> Thank you in advance for any help or any suggestions.
>
> Best Regards,
>
> Emeric Sibieude
>
> Student trainee in Master's degree
>
> Biopharma | R&D | Global Development | Translational Medicine
>
> Merck
>
> Lausanne , Switzerland
>
> [email protected] <mailto:[email protected]>
>
>
>
>
>
> This message and any attachment are confidential and may be privileged or
> otherwise protected from disclosure. If you are not the intended recipient,
> you must not copy this message or attachment or disclose the contents to any
> other person. If you have received this transmission in error, please notify
> the sender immediately and delete the message and any attachment from your
> system. Merck KGaA, Darmstadt, Germany and any of its subsidiaries do not
> accept liability for any omissions or errors in this message which may arise
> as a result of E-Mail-transmission or for damages resulting from any
> unauthorized changes of the content of this message and any attachment
> thereto. Merck KGaA, Darmstadt, Germany and any of its subsidiaries do not
> guarantee that this message is free of viruses and does not accept liability
> for any damages caused by any virus transmitted therewith.
>
> Click http://www.merckgroup.com/disclaimer
> http://www.merckgroup.com/disclaimer to access the German, French, Spanish
> and Portuguese versions of this disclaimer.
>
>
> This message and any attachment are confidential and may be privileged or
> otherwise protected from disclosure. If you are not the intended recipient,
> you must not copy this message or attachment or disclose the contents to any
> other person. If you have received this transmission in error, please notify
> the sender immediately and delete the message and any attachment from your
> system. Merck KGaA, Darmstadt, Germany and any of its subsidiaries do not
> accept liability for any omissions or errors in this message which may arise
> as a result of E-Mail-transmission or for damages resulting from any
> unauthorized changes of the content of this message and any attachment
> thereto. Merck KGaA, Darmstadt, Germany and any of its subsidiaries do not
> guarantee that this message is free of viruses and does not accept liability
> for any damages caused by any virus transmitted therewith.
>
> Click http://www.merckgroup.com/disclaimer
> http://www.merckgroup.com/disclaimer to access the German, French, Spanish
> and Portuguese versions of this disclaimer.
Dear Emeric,
I cannot reproduce this issue in PsN. It looks like a bug, but it might be
triggered by special circumstances or have already been fixed in a later
version.
To know for sure I would need a reproducible example. Best would be if you
could file an issue with a reproducible example directly in the PsN github
issue tracker: https://github.com/UUPharmacometrics/PsN/issues
The option would be to send it to me directly.
Best regards,
Rikard Nordgren
Quoted reply history
On 2019-12-09 09:04, Emeric Sibieude wrote:
Dear Jakob,
Thank you for your answer. According to PsN documentation PD = -100 means at
least 100 covariates. I tried with the exact number of covariates (PD = 105)
and I have the same issue.
Yes indeed, I can do it with the default value of PD = 50 because less than 50
are added but I was wondering if there exists a way if more than 50 covariates
are added during the forward path.
Best Regards,
Emeric Sibieude
Student trainee in Master's degree
Biopharma | R&D | Global Development | Translational Medicine
Merck
Lausanne , Switzerland
[email protected]<mailto:[email protected]>
From: Jakob Ribbing
<[email protected]><mailto:[email protected]>
Sent: jeudi 5 décembre 2019 09:11
To: Emeric Sibieude
<[email protected]><mailto:[email protected]>;
[email protected]<mailto:[email protected]>
Subject: Re: [NMusers] Block SIZE with SCM
Dear Emeric,
The code has negative PD, maybe PsN has problems interpreting this?
I am not sure how PD=-100 would be interpreted by NONMEM, but try PD=100,
instead.
I think this is what you intended to do?
As a side note, PsN (mainly to handle old nonmem versions) has functionality
for dropping (=DROP) covariates on $INPUT, if they are not tested in the
current model during SCM - but only among the ones listed in the configuration
as covariates.
Even if you test 50 covariates, it is not often more than ten different will be
included during forward inclusion, so possibly you can do with the default
PD=50?
Best wishes
Jakob
On 5 Dec 2019, at 08:39, Emeric Sibieude
<[email protected]<mailto:[email protected]>> wrote:
Dear NMUsers,
I am performing scm with PsN. My data have more than 50 covariates, this
should be processed by $SIZES PD=100 at the beginning of the NONMEM file.
However, it seems that scm command modifies this file by putting the block
$PROBLEM at the first line.
Here is the beginning of my code :
$SIZES LVR=150 PD=-100
SPROBLEM empty model
$DATA ID TIME AMT EVID DV CAT1 CAT2 ...
Here is the code transformed in the LST file
$SIZES LVR=150 PD=-100 $PROBLEM empty model
$DATA ID TIME AMT EVID DV CAT1 CAT2 ...
And at the end I have the following error
NM-TRAN MESSAGES
AN ERROR WAS FOUND IN THE CONTROL STATEMENTS.
AN ERROR WAS FOUND ON LINE 1 AT THE APPROXIMATE POSITION NOTED:
$SIZES LVR=150 PD=-100 $PROBLEM empty mod
X
THE CHARACTERS IN ERROR ARE: $
20 UNKNOWN OPTION.
Note that this is an issue for estimating the base model only. During the
forward path scm automatically drops the unnecessary covariates keeping only
the ones added at previous steps and the tested one. First estimate the base
model and use the option -base_ofv seems to work however I will have the same
issue if more than 50 covariates are added during the forward path.
Thank you in advance for any help or any suggestions.
Best Regards,
Emeric Sibieude
Student trainee in Master's degree
Biopharma | R&D | Global Development | Translational Medicine
Merck
Lausanne , Switzerland
[email protected]<mailto:[email protected]>
This message and any attachment are confidential and may be privileged or
otherwise protected from disclosure. If you are not the intended recipient, you
must not copy this message or attachment or disclose the contents to any other
person. If you have received this transmission in error, please notify the
sender immediately and delete the message and any attachment from your system.
Merck KGaA, Darmstadt, Germany and any of its subsidiaries do not accept
liability for any omissions or errors in this message which may arise as a
result of E-Mail-transmission or for damages resulting from any unauthorized
changes of the content of this message and any attachment thereto. Merck KGaA,
Darmstadt, Germany and any of its subsidiaries do not guarantee that this
message is free of viruses and does not accept liability for any damages caused
by any virus transmitted therewith.
Click http://www.merckgroup.com/disclaimer to access the German, French,
Spanish and Portuguese versions of this disclaimer.
This message and any attachment are confidential and may be privileged or
otherwise protected from disclosure. If you are not the intended recipient, you
must not copy this message or attachment or disclose the contents to any other
person. If you have received this transmission in error, please notify the
sender immediately and delete the message and any attachment from your system.
Merck KGaA, Darmstadt, Germany and any of its subsidiaries do not accept
liability for any omissions or errors in this message which may arise as a
result of E-Mail-transmission or for damages resulting from any unauthorized
changes of the content of this message and any attachment thereto. Merck KGaA,
Darmstadt, Germany and any of its subsidiaries do not guarantee that this
message is free of viruses and does not accept liability for any damages caused
by any virus transmitted therewith.
Click http://www.merckgroup.com/disclaimer to access the German, French,
Spanish and Portuguese versions of this disclaimer.
--
Rikard Nordgren
Systems developer
Dept of Pharmaceutical Biosciences
Faculty of Pharmacy
Uppsala University
Box 591
75124 Uppsala
Phone: +46 18 4714308
http://www.farmbio.uu.se/research/researchgroups/pharmacometrics/
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