Re: [NMusers] Generating TAD with ADDL dosing format

[Bill Denney]

Hi Camila,

It sounds like you've got two questions here-- one related to NONMEM and 
one related to the other program you're using to create your VPC.  The 
NONMEM question appears to be "How do I get TAD in my data without 
changing my dataset?"  The second question appears to be "How to I 
stratify my VPC based on that new TAD variable instead of TIME?"


For the second question, what program are you using for VPC?

For the first question, others may have a more elegant answer, but I 
think that you're right:  ADDL makes many dose-related events 
difficult.  The simplest answer is to revise your dataset adding a TAD 
column.  If you can't do that, then something like this will work 
assuming that you only have one dosing record per subject.  (Note that 
the code below was typed directly into email, so it may have typos.)


; Set TAD to -1 before any dose record for the subject

IF (NEWIND.EQ.2) THEN
  DOSETIME = -1
  ADDLREC = 0
  IIREC = 0
ENDIF
; Capture the (most recent) dosing information for this subject
IF (EVID.EQ.1 .OR. EVID.EQ.4) THEN
  DOSETIME = TIME
  ADDLREC = ADDL
  IIREC = II
ENDIF
; Calculate TAD from the single dose record for a subject in the data 
set assuming
; that there is only one dose record per subject or that the dose 
records occur
; such that the most recent dose record is the only one important for 
calculating
; TAD for a subject.  This assumption would not hold if there is a dose 
record
; with ADDL that has a dose record for a time in the middle of those 
ADDL doses.

IF (DOSETIME.LT.0) THEN
  ; This subject has not received a dose yet, set TAD to -1
  TAD = -1
ELSEIF ((TIME-DOSETIME) .LE. ((ADDLREC+1)*IIREC)) THEN
  ; This subject is in the middle of the ADDL records for this dose,
  ; calculate time since most recent dose.
  TAD = (TIME-DOSETIME) - INT((TIME-DOSETIME)/IIREC)*IIREC
ELSE
  ; This subject is are after the last ADDL dose, calculate time since 
the final

  ; dose (observed so far).
  TAD = (TIME-DOSETIME) - ((ADDLREC+1)*IIREC)
ENDIF

Thanks,

Bill


On 12/20/2016 6:45 AM, de Almeida, Camila wrote:


Hello,

I was wondering if I could get some guidance from this great group. My 
issue is primarily with some diagnostic analysis, but this is taking 
me back to an old NONMEM problem.


My aim is to run a VPC on a model I implemented, and if possible 
change the idv to TAD instead of TIME. The reason for that is the VPC 
graph based on TIME looks dreadful as the data is sparse and from 
different studies of different lengths.


I’m having issues generating the TAD output column from my NONMEM run. 
I naively assumed I could easily do that, but looking at the NONMEM 
archives it seems this gets tricky when your dosing events are written 
using ADDL. Has anyone ever managed to find a solution for this? And 
if not, is there an alternative way to run the VCP on TAD, do we 
really need to get this column from NONMEM’s output?


Thanks all,

*Camila de Almeida, PhD*

PKPD Scientist,

*Modelling & Simulation, IMED Oncology DMPK*

**

*AstraZeneca UK Limited*

*R, Innovative Medicines*

**

P Please consider the environment before printing this e-mail



AstraZeneca UK Limited is a company incorporated in England and Wales 
with registered number:03674842 and its registered office at 1 Francis 
Crick Avenue, Cambridge Biomedical Campus, Cambridge, CB2 0AA.


This e-mail and its attachments are intended for the above named 
recipient only and may contain confidential and privileged 
information. If they have come to you in error, you must not copy or 
show them to anyone; instead, please reply to this e-mail, 
highlighting the error to the sender and then immediately delete the 
message. For information about how AstraZeneca UK Limited and its 
affiliates may process information, personal data and monitor 
communications, please see our privacy notice at www.astrazeneca.com 






Human Predictions Logo *William S. 
Denney, PhD*

Chief Scientist, Human Predictions LLC
+1-617-899-8123
wden...@humanpredictions.com

RE: [NMusers] Generating TAD with ADDL dosing format

[Andrzej Bienczak]

Hi, 

 

I'm not sure what data you're analysing and what your dosage schedules and
sampling are but if ADDL is the same for each patient you could create a new
variable (TVPC) and simply deduct that additional dosing history from your
cumulative time from when you restarted the system (EVID=3 or 4). You code
it simply as:

 

TVPC=TIME- sum of all ADDLs

 

So if you have 3 additional doses, each at a 24h interval it would look
like:

 

TVPC=TIME-72

 

Then you can plot your VPC with TVPC as idv.

 

Regards, 

Andrzej

 

Andrzej Bienczak 

MSc, MPharm, DiplPharm

Pharmacometrics Group

Division of Clinical Pharmacology

Department of Medicine

University of Cape Town

 

K45 Old Main Building

Groote Schuur Hospital

Observatory, Cape Town

7925 South Africa

phone: +27 21 650 4861

mobile: +27 839 842 675

email: andrzej.bienc...@gmail.com <mailto:andrzej.bienc...@gmail.com> 

 

 

 

 

From: owner-nmus...@globomaxnm.com [mailto:owner-nmus...@globomaxnm.com] On
Behalf Of de Almeida, Camila
Sent: 20 December 2016 01:46 PM
To: nmusers@globomaxnm.com
Subject: [NMusers] Generating TAD with ADDL dosing format

 

Hello,

 

I was wondering if I could get some guidance from this great group. My issue
is primarily with some diagnostic analysis, but this is taking me back to an
old NONMEM problem.

 

My aim is to run a VPC on a model I implemented, and if possible change the
idv to TAD instead of TIME. The reason for that is the VPC graph based on
TIME looks dreadful as the data is sparse and from different studies of
different lengths.

 

I'm having issues generating the TAD output column from my NONMEM run. I
naively assumed I could easily do that, but looking at the NONMEM archives
it seems this gets tricky when your dosing events are written using ADDL.
Has anyone ever managed to find a solution for this? And if not, is there an
alternative way to run the VCP on TAD, do we really need to get this column
from NONMEM's output?

 

Thanks all,

 

Camila de Almeida, PhD

PKPD Scientist,

Modelling & Simulation, IMED Oncology DMPK




AstraZeneca UK Limited

R, Innovative Medicines

 

P Please consider the environment before printing this e-mail

 

 

 

 

 

 

 

 

  _  

AstraZeneca UK Limited is a company incorporated in England and Wales with
registered number:03674842 and its registered office at 1 Francis Crick
Avenue, Cambridge Biomedical Campus, Cambridge, CB2 0AA.

This e-mail and its attachments are intended for the above named recipient
only and may contain confidential and privileged information. If they have
come to you in error, you must not copy or show them to anyone; instead,
please reply to this e-mail, highlighting the error to the sender and then
immediately delete the message. For information about how AstraZeneca UK
Limited and its affiliates may process information, personal data and
monitor communications, please see our privacy notice at www.astrazeneca.com
<https://www.astrazeneca.com> 

Re: [NMusers] Generating TAD with ADDL dosing format

[Alejandro Pérez Pitarch]

Hi Camila,

I had this same issue some time ago and, given that in my dataset all
Interdose Intervals (II) were constant for all the patients, I used the
following R function to get a TAD column (IDV in my dataset):

InsertIDV<-function(runn,ii){ # runn is the
run number: for run03 runn="03"; ii is the inter-dose interval
  sdtab<-get(paste("sdtab",runn,sep=""))
  last<-floor(sdtab$TIME/ii)*ii# defines
time at which last dose was administrated
  sdtab$IDV<-sdtab$TIME-last
  assign(paste("sdtab",runn,sep=""),sdtab,envir = .GlobalEnv)
}

I hope this script is useful for your problem.

Regards,


Alejandro Pérez Pitarch
Pharmacy Department
University Clinical Hospital of Valencia







2016-12-20 12:45 GMT+01:00 de Almeida, Camila <
camila.dealme...@astrazeneca.com>:

> Hello,
>
>
>
> I was wondering if I could get some guidance from this great group. My
> issue is primarily with some diagnostic analysis, but this is taking me
> back to an old NONMEM problem.
>
>
>
> My aim is to run a VPC on a model I implemented, and if possible change
> the idv to TAD instead of TIME. The reason for that is the VPC graph based
> on TIME looks dreadful as the data is sparse and from different studies of
> different lengths.
>
>
>
> I’m having issues generating the TAD output column from my NONMEM run. I
> naively assumed I could easily do that, but looking at the NONMEM archives
> it seems this gets tricky when your dosing events are written using ADDL.
> Has anyone ever managed to find a solution for this? And if not, is there
> an alternative way to run the VCP on TAD, do we really need to get this
> column from NONMEM’s output?
>
>
>
> Thanks all,
>
>
>
> *Camila de Almeida, PhD*
>
> PKPD Scientist,
>
> *Modelling & Simulation, IMED Oncology DMPK*
>
>
> **
>
> *AstraZeneca UK Limited*
>
> *R, Innovative Medicines*
>
>
>
> P Please consider the environment before printing this e-mail
>
>
>
>
>
>
>
>
>
>
>
>
>
>
>
>
> --
>
> AstraZeneca UK Limited is a company incorporated in England and Wales with
> registered number:03674842 and its registered office at 1 Francis Crick
> Avenue, Cambridge Biomedical Campus, Cambridge, CB2 0AA.
>
> This e-mail and its attachments are intended for the above named recipient
> only and may contain confidential and privileged information. If they have
> come to you in error, you must not copy or show them to anyone; instead,
> please reply to this e-mail, highlighting the error to the sender and then
> immediately delete the message. For information about how AstraZeneca UK
> Limited and its affiliates may process information, personal data and
> monitor communications, please see our privacy notice at
> www.astrazeneca.com
>

[NMusers] Generating TAD with ADDL dosing format

[de Almeida, Camila]

Hello,

I was wondering if I could get some guidance from this great group. My issue is 
primarily with some diagnostic analysis, but this is taking me back to an old 
NONMEM problem.

My aim is to run a VPC on a model I implemented, and if possible change the idv 
to TAD instead of TIME. The reason for that is the VPC graph based on TIME 
looks dreadful as the data is sparse and from different studies of different 
lengths.

I'm having issues generating the TAD output column from my NONMEM run. I 
naively assumed I could easily do that, but looking at the NONMEM archives it 
seems this gets tricky when your dosing events are written using ADDL. Has 
anyone ever managed to find a solution for this? And if not, is there an 
alternative way to run the VCP on TAD, do we really need to get this column 
from NONMEM's output?

Thanks all,

Camila de Almeida, PhD
PKPD Scientist,
Modelling & Simulation, IMED Oncology DMPK

AstraZeneca UK Limited
R, Innovative Medicines

P Please consider the environment before printing this e-mail










AstraZeneca UK Limited is a company incorporated in England and Wales with 
registered number:03674842 and its registered office at 1 Francis Crick Avenue, 
Cambridge Biomedical Campus, Cambridge, CB2 0AA.

This e-mail and its attachments are intended for the above named recipient only 
and may contain confidential and privileged information. If they have come to 
you in error, you must not copy or show them to anyone; instead, please reply 
to this e-mail, highlighting the error to the sender and then immediately 
delete the message. For information about how AstraZeneca UK Limited and its 
affiliates may process information, personal data and monitor communications, 
please see our privacy notice at 
www.astrazeneca.com