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Phoenix Template v1.5 for the EMA’s ABEL

EMA ABEL reference-scaling

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#1 Helmut Schütz

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Posted 11 August 2017 - 03:12 PM

Dear all,

 

Michael and I updated the Template.

 

New:

  • Works in Phoenix 6.4 and 7.0.
     
  • Added 4-period 4-sequence designs:
    • TRTR | RTRT | TRRT | RTTR
    • TRTR | RTRT | TTRR | RRTT
      Both are not recommended (confounded effects) and included only for completeness.
  • Added the 3-period 2-sequence (partial) replicate design:
    • TRR | RTR (aka “extra reference design”)
      Not recommended since lacking period effects have to be assumed. Since T is not admini­stered in the third period, the treat­ment comparison will be biased in the presence of true period effects. This design should be avoided and included only for completeness.
  • Plots of standardized residual vs. subject and model predictions.
     
  • Comparison of within-subject variabilities of T and R (full replicate designs only).
     
  • Instructions included in the documents folder.

Changed:

  • The name of both formulations can be specified (previously only the one of the reference).

The run-time is slightly better than in previous versions but needs patience. Since Phoenix swaps inter­mediate results1 to the system drive, it will take a while to complete. On my machine (with a fast solid-state drive) execution of the EMA’s reference data set I takes 2:15 minutes.2 If you have a hard drive, it may take substantially longer.

 

The template was developed in PHX 6.4.0.768 and tested in PHX 7.0.0.2535. The template was cross-validated with 26 data sets (all designs, up to 360 subjects) against SAS 9.4 (Methods A, B, C), R 3.4.1 (A,  B), STATISTICA (A), and partly (Q&A data sets I and II; Methods A, B) against STaTa 14, SPSS 22, and JMP 10. As usual, use at your own risk.

 

When you execute the workflow Final Conclusions, the outlier analysis (boxplot, etc.) is not automatically performed. Navigate to Analysis > ABEL > Outlier Analysis and execute.

 

Reports of defects and experiences with Windows installed on a hard drive are welcome.

 

 1 After execution 4.7 MB (!) in 300 (‼) files. 6 copies each of linmix.exe (292.0 kB) and Dforrt.dll (405.5 kB).

2 In R for comparison: 40 milliseconds…

 PS: Balaam’s design (TR|RT|TT|RR) works but was not seriously tested. Should be avoided due to its terrible power characteristics!

Attached Files


  • bwendt@certara.com likes this

 Best regards,
Helmut

http://forum.bebac.at/


#2 Simon Davis

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Posted 15 August 2017 - 08:44 PM

Helmut - can you remind me of the best place to get the source reference datasets;  I normally use your site;

 

http://bebac.at/down... Design EMA.xls

 

because I can't seem to find them on the EMA site but maybe I ma missing something obvious?

 

 thanks, Simon.



#3 Helmut Schütz

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Posted 15 August 2017 - 09:09 PM

Hi Simon,

 

the data sets are given in the EMA’s Q&A document; there’s a copy in the template’s document folder.

If you are interested not only in them but others check out: https://github.com/H...er/inst/extdata


 Best regards,
Helmut

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#4 j.walczak@polfarmex.pl

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Posted 14 December 2017 - 02:58 PM

Hi,

I need help to execute the template v1.5 - which worksheet should be selected as Worksheet 1 in "Join RR" step? 

Thx nad best regards, Jarek



#5 Helmut Schütz

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Posted 14 December 2017 - 03:24 PM

Hi Jarek,

 

I need help to execute the template v1.5 - which worksheet should be selected as Worksheet 1 in "Join RR" step? 

 

Hhm, once you imported your data and gave the necessary information in Data > 1, 2, 3 you should only execute the last workflow 'Final Conclusions'. Then all mappings should be correctly executed.

 

In the template there is no 'Join RR' object – only Analysis > ABEL > Calculation Steps > Join RR Observations.

If you mean this one:

WS1: Analysis.Calculation Steps.Reference Variability (linear model).Diagnostics

Sort: Diagnostic, Value

WS2: Analysis.Design Conclusions.Data

Sort: DesignConcl, Warning_less_12_TR

 


 Best regards,
Helmut

http://forum.bebac.at/


#6 j.walczak@polfarmex.pl

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Posted 15 December 2017 - 07:51 AM

Hi Helmut,

thank you very much. It was very helpful and I have executed the workflow succesfully.

Regards, Jarek







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