NONMEM Users Network Archive

Hosted by Cognigen

Re: [NMusers] Covariate modelling question

From: Kajsa Harling <>
Date: Thu, 26 Feb 2015 12:49:03 +0100
Hi Fiona,

retries=1 means a first attempt and then max 1 retry. To make the scm deterministic you can either set retries=0 (only run the first attempt) or set the -seed option to the same value in both scm runs, which will make the tweaking of initial estimates identical. The version_and_option file also contains the value of -seed that will reproduce the results, so you only have to rerun the second scm if you set the seed according to the first scm and leave the retries option as is.

I cannot answer how to set the various options using the wizard, that is a Pirana question.

Best regards,

On 02/26/2015 12:14 PM, Fiona Vanobberghen wrote:
Hi Kajsa

Many thanks for this quick and helpful feedback. I have looked at the txt files you suggested, and they both have retries=1. Does that mean it has one attempt (and no real "retries"), or rather that it has a first attempt and max 1 retry? If the latter then it seems that this might be the reason, based on your explanation below. And if so then is there a way of setting the retries using the wizard (ie retries=0) so that I can double check that in that case I get the results I'm expecting?

Many thanks

On 26/02/2015 10:55, Kajsa Harling wrote:
I have looked at the output now, and am writing the answer to the mailing list in case more people are interested.

In the two different scm runs you get slightly different ofv values, and the small differences lead to different models being selected in the two runs. So why are the ofv:s different? One possible reason is that you used the retries option in PsN (automatic perturbation of initial estimates when a run is not successful) which will give different initial estimates depending on the random seed. You can check the settings of all PsN options, including the ones set by default, in the version_and_option_info.txt file in the top level of the scm run directory.

Best regards,

On 02/26/2015 11:28 AM, Kajsa Harling wrote:
Dear Fiona,

This sounds like a PsN question, but it is impossible to answer without the example output. The mailing list does not accept long messages or attachments, so I suggest you send the original email with all output directly to me ( so that I can have a look.

Best regards,

On 02/26/2015 11:00 AM, Fiona Vanobberghen wrote:
I posted this message a few days ago but it doesn't seem to have been sent to the list - so I'm resending without the example output.
Best wishes

Dear all

I am attempting to do some covariate modelling, using the scm wizard in Pirana. I have seen some results which I wasn't expecting and would be grateful if anyone could shed any light on it for me.

Initially, I used a forward inclusion p value of 0.1 and a backward elimination p value of 0.05. This resulted in quite a complex (implausible) model (we do have a reasonably large dataset), and I decided to be more stringent, using p<0.05 for inclusion (and the same p>0.05 for elimination at the last step). As a shortcut, I could see from the output from the first attempt (with p<0.1) what I expected the final model to look like if I were to run it again with p<0.05, ie where the process would truncate. Just to double check (and verify that nothing would be eliminated at the last step), I re-ran the scm wizard with the more stringent p<0.05. And the results are not what I expected... Below I have pasted the output for the first few forward steps from each attempt. The results are essentially the same up until the third step, although we see some small differences in the OFV creeping in from the second step. However, at the fourth step, the results are completely different. This isn't what I was expecting, based on my understanding of the model selection process. Is this a known behaviour? Has anyone experienced this problem and/or know why these differences might occur? I'd be grateful for any advice.

Many thanks in advance for your help.

Best wishes

Received on Thu Feb 26 2015 - 06:49:03 EST

The NONMEM Users Network is maintained by ICON plc. Requests to subscribe to the network should be sent to: Once subscribed, you may contribute to the discussion by emailing: