Re: Error in Power-model for covariate selection
Hi Sumeet,
It is great that you have considered already that covarite values do not
include zero or negative values, as that would not work with the power model.
Did you have any missing values, and how were they coded?
I would recommend to code these (in your data file) using the default -99 in
your datafile.
You can check the PsN file “covariate_statistics.txt” for your scm run: For BMI
in particular, were there missing values detected by PsN and is the minimum
value >0 or is it -99?
Best regards
Jakob
Quoted reply history
> On 20 Nov 2019, at 05:42, Singla, Sumeet K <[email protected]> wrote:
>
> Hello Everyone,
>
> I am using PsN enabled SCM option in Pirana to analyze selection of
> covariates in the PK 2- Comp model. As long as I am using just linear and
> exponential covariate model, everything runs fine. However, as soon as I add
> power-model in the mix, “some” power models involving continuous covariates
> on parameters fail to run and it gives me the following error:
> “HESSIAN OF POSTERIOR DENSITY IS NON-POSITIVE-DEFINITE DURING SEARCH”
> I understand that individual PK parameter search might be moving into 0 or
> negative territory. I am trying to fix it but didn’t have much success. I
> have set lower bounds, removed lower bounds, changed order of model in valid
> states option in scm configuration file, dataset doesn’t contain any 0 or
> negative value, but nothing is working. FYI: I don’t need to test
> hockey-stick relation as literature and data doesn’t support it, power model
> can only be used on continuous covariates and I have turned on parallel
> states option.
> This is how part of my scm results, followed by scm configuration file,
> followed by base model for PK 2-Comp looks like:
>
> MODEL TEST BASE OFV NEW OFV TEST OFV (DROP)
> GOAL dDF SIGNIFICANT PVAL
> CLAGE-2 PVAL 2618.02603 2616.67228 1.35375 >
> 3.84150 1 0.244620
> CLAGE-5 PVAL 2618.02603 2616.36273 1.66330 >
> 3.84150 1 0.197160
> CLAGE-4 PVAL 2618.02603 2616.65232 1.37371 >
> 3.84150 1 0.241180
> CLBMI-2 PVAL 2618.02603 2612.96657 5.05946 >
> 3.84150 1 YES! 0.024492
> CLBMI-5 PVAL 2618.02603 FAILED FAILED >
> 3.84150 1 999
>
> SCM FILE:
> “
> search_direction=both
> p_forward=0.05
> p_backward=0.01
> continuous_covariates=BMI,AGE
> categorical_covariates=USER,SEX
> parallel_states=1
> retries=2
> threads=6
> tweak_inits=1
> ;;1-NotIncluded, 2-LINEAR, 3-Hockey Stick Relation, 4-Exponential, 5-Power
> [test_relations]
> CL=AGE,SEX,BMI,USER
> V1=AGE,SEX,BMI,USER
> V2=AGE,SEX,BMI,USER
> Q=AGE,SEX,BMI,USER
> [valid_states]
> continuous = 1,2,5,4
> categorical = 1,2
> “
> NONMEM Control Stream:
>
> $SUBROUTINE ADVAN3 TRANS4
>
> $PK
>
> TVV1 = THETA(1) ;Central Volume of distribution
> in L
> V1 = TVV1*EXP(ETA(1))
> TVCL = THETA(2)
> CL = TVCL*EXP(ETA(2)) ; Clearance L/h
> TVQ = THETA(3)
> Q = TVQ*EXP(ETA(3)) ;Intercompartment Clearance
> TVV2 = THETA(4)
> V2 = TVV2*EXP(ETA(4)) ;Peripheral volume in L
> S1=V1
>
> $ERROR
> IPRED=F
> Y= F + F*ERR(1); Proportional Error
>
> $THETA
> (0, 16); [V1] based on PK 2 Comp
> (0, 255); [CL] based on PK 2 Comp
> (0, 33.5); [Q] based on PK 2 Comp
> (0, 29.7); [V2] based on PK 2 Comp
>
> $OMEGA
> (0, 0.08); [P] omega(1,1)
> (0, 0.159); [P] omega(2,2)
> (0, 0.140); [P] omega(3,3)
> (0, 0.19); [P] omega(4,4)
>
> $SIGMA
> (0, 0.06) ;sigma1
>
> $EST METHOD=1 PRINT=5 MAXEVAL=9999 SIG=3 NOABORT
>
>
> Regards,
>
> Sumeet K. Singla
> Ph.D. Candidate
> Division of Pharmaceutics and Translational Therapeutics
> College of Pharmacy | University of Iowa
> Iowa City, Iowa
> [email protected] <mailto:[email protected]>
> 518.577.5881