Re: Block SIZE with SCM
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]>
>
>
>
>
>
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> for any damages caused by any virus transmitted therewith.
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