PharmPK Discussion - Creating subsets of xpdb objects in XPOSE

• On 11 Jun 2014 at 09:46:54, Paul Hutson (prhutson.aaa.pharmacy.wisc.edu) sent the message
  

  
  My skills in R are fundamental, and I am having trouble with creating subsets of xpdb.
  
  I have modeled PK and PD data in NONMEM in a indirect model in which my drug concentration is
  estimated with IPRED in compartment (CMT) 2 and the Effect is in CMT=3. After using xpose.data(1) to
  import the xpose tables from the NM output, I would like to create separate xpdb2 and xpdb3 objects
  that contain only the data from compartments CMT=2 and CMT=3, respectively.
  
  I tried this code, and received the error message below it.
  
  > > xpdb2 <- xpdb1[xpdb1.-at-.Data$CMT == 3,] #(same error when = is used instead of ==)
  > >
  Error in xpdb1[xpdb1.-at-.Data$CMT == 3, ] :
    object of type 'S4' is not subsettable
  
  Based upon the ?Data help query, I also tried.
  
  > > xpdb2 <- Data(xpdb1, subset="CMT = 3")
  > >
  However, the resulting output to xpdb2 yielded only one record, which was not the first in the NM
  .FIT output.
  
  > > xpdb2
  > >
    ID TAD TIME IPRED IRES IWRES CWRES
  5 1 5.75 5.75 7.0878 -67.266 -0.056183 -0.14804
    NPDE DV PRED RES WRES ETA1
  5 -0.21043 7.03 6.7886 0.24137 -0.0086168 0.90341
    ETA2 ETA3 ETA4 ETA5 ETA6 SEX DOSE CMT
  5 -0.11998 0.36275 -2.2421 0.29002 -0.01153 0 30 3
    ANALYTE CYCLE NDOSE NAGE NWT
  5 3 0 0.3 1.44 1.2229
  
  How would you recommend separating data from the two CMT values into separate xpdb objects?
  
  (I noted the by= option in basic.gof, but I would like to have the four panel gof separate for each
  compartment.)
  Many thanks.
  Paul
  
  --
  Paul R. Hutson, Pharm.D.
  Professor
  Senior Associate Dean for Academic Affairs
  UW School of Pharmacy
  
  

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• On 11 Jun 2014 at 10:23:48, Kees Duineveld (kees.duineveld.-a-.gmail.com) sent the message
  

  
  Hi Paul,
  
  Without access to that object, I would suggest:
  xpdb2 <- xpdb1.aaa.Data[xpdb1.-a-.Data$CMT == 3,]
  
  or
  
  xpdb2 <- Data(xpdb1, subset="CMT == 3")
  
  Regards,
  Kees
  
  

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• On 11 Jun 2014 at 11:38:58, Paul Hutson (prhutson.aaa.pharmacy.wisc.edu) sent the message
  

  
  Dear Kees:
  Both of your suggestions work well.  Thank you very much for your
  assistance.  I see that I was close, but not close enough.
  Paul
  
  

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• On 11 Jun 2014 at 14:46:11, Paul Hutson (prhutson.aaa.pharmacy.wisc.edu) sent the message
  

  
  Kees' suggestion creates the xpdb2 object, but when I try to perform
  basic.gof() on the resulting spdb2 object, I get the following:
  
  "Error in xvardef(v, object) :
     trying to get slot "Prefs" from an object (class "data.frame") that
  is not an S4 object"
  Only the data remain, without the S4 Slots.
  Are there suggestions on how the S4 structure can be maintained when the
  subset is created?
  Paul
  
  

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• On 11 Jun 2014 at 15:12:29, Sam Liao (sliao.-at-.pharmaxresearch.com) sent the message
  

  
  Dear Paul,
  
  you can use subset='' directly in basic.gof()
  
  Best regards,
  Sam Liao, Ph.D.
  Pharmax Research, Inc.
  
  

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• On 11 Jun 2014 at 15:31:31, Paul Hutson (prhutson.aaa.pharmacy.wisc.edu) sent the message
  

  
  Dear Sam:
  Yes, that works beautifully, and I see that I missed subset in
  xpose.panel.default as an option.
  Embarrassing...
  Thanks very much for your help.
  Paul
  
  

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