NONMEM 7.4.1
Colleagues
I am trying to use the ACCEPT option in $DATA in order to select a subset of
records (to evaluate the impact of the # of samples/subject on confidence
intervals).
I used the following code:
ACCEPT=(TIME=0, TIME=1, TIME=2, TIME=4, TIME=6, TIME=24)
NMTRAN then creates a dataset but — to my surprise — TIME=6 is not in the
dataset (all the others are).
I am copying the first few rows of the input dataset so that you can see what
is being provided to NMTRAN:
ID,AGE,MONTHS,SEX,WT,AMT,RATE,TIME,EVID,MDV,REPLICATE,IPRED,CWRES,DV,PRED,RES,WRES
1101,12,144,1,30.054,210.38,841.51,0,1,1,1,0,0,0,0,0,0
1101,12,144,1,30.054,0,0,1,0,0,1,187.42,0,179.28,199.26,-19.979,0
1101,12,144,1,30.054,0,0,2,0,0,1,180.92,0,187.92,194.09,-6.1659,0
1101,12,144,1,30.054,0,0,4,0,0,1,169.84,0,177.66,184.37,-6.712,0
1101,12,144,1,30.054,0,0,6,0,0,1,160.61,0,153.43,175.39,-21.96,0
The underlined / boldfaced value (6) in the final row is the problem.
I assume that NMTRAN is reading that value as something other than 6.0 (e.g.,
6.000001) and thereby omitting it.
I have reviewed NMHELP to see if there is some other way to accomplish this.
Ideally, there would be something like:
TIME.GT.5.9.AND.TIME.LT.6.1
but that does not appear to be supported.
The alternative is to modify the dataset to include many possible MDV/EVID
columns. However, it would be more elegant to do this in the control stream.
Or, if there is some way to find out the exact value that NMTRAN sees, I could
specify that value.
Any help would be appreciated.
Dennis
Dennis Fisher MD
P < (The "P Less Than" Company)
Phone / Fax: 1-866-PLessThan (1-866-753-7784)
www.PLessThan.com http://www.plessthan.com/
Use of ACCEPT in $DATA
from the manual:
"When the IGNORE option is used to filter records from the input file, the .EQ., =, .NE., and /= symbols perform literal string comparisons. To provide a numerical equality comparison, use .EQN. for numerical equals, and .NEN. for numerical not equals."
May be there is a space there or something, try .EQN.
Leonid
Quoted reply history
On 8/24/2017 6:16 PM, Dennis Fisher wrote:
> NONMEM 7.4.1
>
> Colleagues
>
> I am trying to use the ACCEPT option in $DATA in order to select a subset of records (to evaluate the impact of the # of samples/subject on confidence intervals).
>
> I used the following code:
> ACCEPT=(TIME=0, TIME=1, TIME=2, TIME=4, TIME=6, TIME=24)
>
> NMTRAN then creates a dataset but — to my surprise — TIME=6 is not in the dataset (all the others are).
>
> I am copying the first few rows of the input dataset so that you can see what is being provided to NMTRAN:
>
> ID,AGE,MONTHS,SEX,WT,AMT,RATE,_TIME_,EVID,MDV,REPLICATE,IPRED,CWRES,DV,PRED,RES,WRES
> 1101,12,144,1,30.054,210.38,841.51,0,1,1,1,0,0,0,0,0,0
> 1101,12,144,1,30.054,0,0,1,0,0,1,187.42,0,179.28,199.26,-19.979,0
> 1101,12,144,1,30.054,0,0,2,0,0,1,180.92,0,187.92,194.09,-6.1659,0
> 1101,12,144,1,30.054,0,0,4,0,0,1,169.84,0,177.66,184.37,-6.712,0
> 1101,12,144,1,30.054,0,0,_6_,0,0,1,160.61,0,153.43,175.39,-21.96,0
>
> The underlined / boldfaced value (6) in the final row is the problem.
>
> I assume that NMTRAN is reading that value as something other than 6.0 (e.g., 6.000001) and thereby omitting it.
>
> I have reviewed NMHELP to see if there is some other way to accomplish this. Ideally, there would be something like:
>
> TIME.GT.5.9.AND.TIME.LT.6.1
> but that does not appear to be supported.
>
> The alternative is to modify the dataset to include many possible MDV/EVID columns. However, it would be more elegant to do this in the control stream. Or, if there is some way to find out the exact value that NMTRAN sees, I could specify that value.
>
> Any help would be appreciated.
>
> Dennis
>
> Dennis Fisher MD
> P < (The "P Less Than" Company)
> Phone / Fax: 1-866-PLessThan (1-866-753-7784)
> www.PLessThan.com http://www.plessthan.com/
Hi Dennis,
I don’t have an elegant solution for you (and I’ve been pining for the use
of combined Boolean operations like “TIME.GT.5.9.AND.TIME.LT.6.1” for a
long time).
An inelegant solution could be to run the model once with a write statement
to see if you can identify the value like 6.0000001 and use it. That would
probably be fragile to different processor/compiler/math library
combinations, so I’d probably end up making the additional indicator column
for certainty.
Thanks,
Bill
*From:* [email protected] [mailto:[email protected]] *On
Behalf Of *Dennis Fisher
*Sent:* Thursday, August 24, 2017 6:16 PM
*To:* [email protected]
*Subject:* [NMusers] Use of ACCEPT in $DATA
NONMEM 7.4.1
Colleagues
I am trying to use the ACCEPT option in $DATA in order to select a subset
of records (to evaluate the impact of the # of samples/subject on
confidence intervals).
I used the following code:
ACCEPT=(TIME=0, TIME=1, TIME=2, TIME=4, TIME=6, TIME=24)
NMTRAN then creates a dataset but — to my surprise — TIME=6 is not in the
dataset (all the others are).
I am copying the first few rows of the input dataset so that you can see
what is being provided to NMTRAN:
ID,AGE,MONTHS,SEX,WT,AMT,RATE,*TIME*
,EVID,MDV,REPLICATE,IPRED,CWRES,DV,PRED,RES,WRES
1101,12,144,1,30.054,210.38,841.51,0,1,1,1,0,0,0,0,0,0
1101,12,144,1,30.054,0,0,1,0,0,1,187.42,0,179.28,199.26,-19.979,0
1101,12,144,1,30.054,0,0,2,0,0,1,180.92,0,187.92,194.09,-6.1659,0
1101,12,144,1,30.054,0,0,4,0,0,1,169.84,0,177.66,184.37,-6.712,0
1101,12,144,1,30.054,0,0,*6*,0,0,1,160.61,0,153.43,175.39,-21.96,0
The underlined / boldfaced value (6) in the final row is the problem.
I assume that NMTRAN is reading that value as something other than 6.0
(e.g., 6.000001) and thereby omitting it.
I have reviewed NMHELP to see if there is some other way to accomplish
this. Ideally, there would be something like:
TIME.GT.5.9.AND.TIME.LT.6.1
but that does not appear to be supported.
The alternative is to modify the dataset to include many possible MDV/EVID
columns. However, it would be more elegant to do this in the control
stream.
Or, if there is some way to find out the exact value that NMTRAN sees, I
could specify that value.
Any help would be appreciated.
Dennis
Dennis Fisher MD
P < (The "P Less Than" Company)
Phone / Fax: 1-866-PLessThan (1-866-753-7784)
www.PLessThan.com http://www.plessthan.com/
Similar to Bill, I also have an inelegant, but workable, solution, which is
to brute force the ignore times by templating them in R.
For example, you can use a simple glue template to churn out ignore
statements. For simplicity this could then be then just copied into control
streams.
library(whisker)
all_times <- c(0, 1, 2, 4, 6, 8, 10, 12, 14, 16, 20, 24)keep_times <-
c(0, 1, 2, 4, 6, 24)drop_times <- all_times[!(all_times %in%
keep_times)]glue::glue(
"IGNORE=(TIME.EQN.{time})", time = drop_times
)#> IGNORE=(TIME.EQN.8)#> IGNORE=(TIME.EQN.10)#>
IGNORE=(TIME.EQN.12)#> IGNORE=(TIME.EQN.14)#> IGNORE=(TIME.EQN.16)#>
IGNORE=(TIME.EQN.20)
# make multiple time scenarios and generate the ignores for all of
them in one goscenarios = list(
c(0, 1, 2, 4, 6, 24),
c(0, 2, 4, 8, 24))
lapply(scenarios, function(.s) {
all_times <- c(0, 1, 2, 4, 6, 8, 10, 12, 14, 16, 20, 24)
keep_times <- .s
drop_times <- all_times[!(all_times %in% keep_times)]
glue::glue(
"IGNORE=(TIME.EQN.{time})", time = drop_times
)})#> [[1]]#> IGNORE=(TIME.EQN.8)#> IGNORE=(TIME.EQN.10)#>
IGNORE=(TIME.EQN.12)#> IGNORE=(TIME.EQN.14)#> IGNORE=(TIME.EQN.16)#>
IGNORE=(TIME.EQN.20)#> #> [[2]]#> IGNORE=(TIME.EQN.1)#>
IGNORE=(TIME.EQN.6)#> IGNORE=(TIME.EQN.10)#> IGNORE=(TIME.EQN.12)#>
IGNORE=(TIME.EQN.14)#> IGNORE=(TIME.EQN.16)#> IGNORE=(TIME.EQN.20)
If you want something more automated and powerful, at the expense of more R
code, you can use the whisker library to actually use full templates. I've
done some bayesian prior sensitivity analysis generating 1000's of control
streams to great success that way. If this is of interest, speak up and I
can provide a more complete example.
Cheers,
Devin
Quoted reply history
On Thu, Aug 24, 2017 at 6:48 PM Bill Denney <[email protected]>
wrote:
> Hi Dennis,
>
>
>
> I don’t have an elegant solution for you (and I’ve been pining for the use
> of combined Boolean operations like “TIME.GT.5.9.AND.TIME.LT.6.1” for a
> long time).
>
>
>
> An inelegant solution could be to run the model once with a write
> statement to see if you can identify the value like 6.0000001 and use it.
> That would probably be fragile to different processor/compiler/math library
> combinations, so I’d probably end up making the additional indicator column
> for certainty.
>
>
> Thanks,
>
>
>
> Bill
>
>
>
> *From:* [email protected] [mailto:[email protected]]
> *On Behalf Of *Dennis Fisher
> *Sent:* Thursday, August 24, 2017 6:16 PM
> *To:* [email protected]
> *Subject:* [NMusers] Use of ACCEPT in $DATA
>
>
>
> NONMEM 7.4.1
>
>
>
> Colleagues
>
>
>
> I am trying to use the ACCEPT option in $DATA in order to select a subset
> of records (to evaluate the impact of the # of samples/subject on
> confidence intervals).
>
>
>
> I used the following code:
>
> ACCEPT=(TIME=0, TIME=1, TIME=2, TIME=4, TIME=6, TIME=24)
>
>
>
> NMTRAN then creates a dataset but — to my surprise — TIME=6 is not in the
> dataset (all the others are).
>
>
>
> I am copying the first few rows of the input dataset so that you can see
> what is being provided to NMTRAN:
>
>
>
> ID,AGE,MONTHS,SEX,WT,AMT,RATE,*TIME*
> ,EVID,MDV,REPLICATE,IPRED,CWRES,DV,PRED,RES,WRES
> 1101,12,144,1,30.054,210.38,841.51,0,1,1,1,0,0,0,0,0,0
> 1101,12,144,1,30.054,0,0,1,0,0,1,187.42,0,179.28,199.26,-19.979,0
> 1101,12,144,1,30.054,0,0,2,0,0,1,180.92,0,187.92,194.09,-6.1659,0
> 1101,12,144,1,30.054,0,0,4,0,0,1,169.84,0,177.66,184.37,-6.712,0
> 1101,12,144,1,30.054,0,0,*6*,0,0,1,160.61,0,153.43,175.39,-21.96,0
>
>
>
> The underlined / boldfaced value (6) in the final row is the problem.
>
>
>
> I assume that NMTRAN is reading that value as something other than 6.0
> (e.g., 6.000001) and thereby omitting it.
>
>
>
> I have reviewed NMHELP to see if there is some other way to accomplish
> this. Ideally, there would be something like:
>
> TIME.GT.5.9.AND.TIME.LT.6.1
>
> but that does not appear to be supported.
>
>
>
> The alternative is to modify the dataset to include many possible MDV/EVID
> columns. However, it would be more elegant to do this in the control
> stream.
>
> Or, if there is some way to find out the exact value that NMTRAN sees, I
> could specify that value.
>
>
>
> Any help would be appreciated.
>
>
>
> Dennis
>
>
>
> Dennis Fisher MD
> P < (The "P Less Than" Company)
> Phone / Fax: 1-866-PLessThan (1-866-753-7784 <(866)%20753-7784>)
> www.PLessThan.com http://www.plessthan.com/
>
>
>
>
>
>
>
Hi Dennis,
Unfortunately, my reply will not provide a solution to your problem. It is more
about drawing attention to the fact that checking conditions numerically is not
exactly the same as checking conditions on a piece of a paper, because of
rounding. I’m sure that the users of the List are well aware of this fact, just
a reminder…
A simple example, I did this in Matlab, you can repeat it in R or other
programming language. I won’t waste your time by describing how I came to this
example. Compare the output of two expressions:
>> a1=0.06;
>> a2=0.05 + 0.01;
You would expect the equality between the two values, a1 and a2, right? True,
on paper. Here is the output of these two values with 20 decimals.
>> fprintf('%22.20f\n',a1)
0.05999999999999999800
>> fprintf('%22.20f\n',a2)
0.06000000000000000500
And, of course, the output of the logical expression (a1 ==a2) is FALSE.
Regards,
Sergei Leonov
ICON Innovation Center
Quoted reply history
From: [email protected] [mailto:[email protected]] On
Behalf Of Bill Denney
Sent: Thursday, August 24, 2017 6:45 PM
To: Dennis Fisher; [email protected]
Subject: RE: [NMusers] Use of ACCEPT in $DATA
Hi Dennis,
I don’t have an elegant solution for you (and I’ve been pining for the use of
combined Boolean operations like “TIME.GT.5.9.AND.TIME.LT.6.1” for a long time).
An inelegant solution could be to run the model once with a write statement to
see if you can identify the value like 6.0000001 and use it. That would
probably be fragile to different processor/compiler/math library combinations,
so I’d probably end up making the additional indicator column for certainty.
Thanks,
Bill
From: [email protected]<mailto:[email protected]>
[mailto:[email protected]<mailto:[email protected]>] On
Behalf Of Dennis Fisher
Sent: Thursday, August 24, 2017 6:16 PM
To: [email protected]<mailto:[email protected]>
Subject: [NMusers] Use of ACCEPT in $DATA
NONMEM 7.4.1
Colleagues
I am trying to use the ACCEPT option in $DATA in order to select a subset of
records (to evaluate the impact of the # of samples/subject on confidence
intervals).
I used the following code:
ACCEPT=(TIME=0, TIME=1, TIME=2, TIME=4, TIME=6, TIME=24)
NMTRAN then creates a dataset but — to my surprise — TIME=6 is not in the
dataset (all the others are).
I am copying the first few rows of the input dataset so that you can see what
is being provided to NMTRAN:
ID,AGE,MONTHS,SEX,WT,AMT,RATE,TIME,EVID,MDV,REPLICATE,IPRED,CWRES,DV,PRED,RES,WRES
1101,12,144,1,30.054,210.38,841.51,0,1,1,1,0,0,0,0,0,0
1101,12,144,1,30.054,0,0,1,0,0,1,187.42,0,179.28,199.26,-19.979,0
1101,12,144,1,30.054,0,0,2,0,0,1,180.92,0,187.92,194.09,-6.1659,0
1101,12,144,1,30.054,0,0,4,0,0,1,169.84,0,177.66,184.37,-6.712,0
1101,12,144,1,30.054,0,0,6,0,0,1,160.61,0,153.43,175.39,-21.96,0
The underlined / boldfaced value (6) in the final row is the problem.
I assume that NMTRAN is reading that value as something other than 6.0 (e.g.,
6.000001) and thereby omitting it.
I have reviewed NMHELP to see if there is some other way to accomplish this.
Ideally, there would be something like:
TIME.GT.5.9.AND.TIME.LT.6.1
but that does not appear to be supported.
The alternative is to modify the dataset to include many possible MDV/EVID
columns. However, it would be more elegant to do this in the control stream.
Or, if there is some way to find out the exact value that NMTRAN sees, I could
specify that value.
Any help would be appreciated.
Dennis
Dennis Fisher MD
P < (The "P Less Than" Company)
Phone / Fax: 1-866-PLessThan (1-866-753-7784)
http://www.plessthan.com/
Sergei
I would accept that if the problem related to decimals. Your code does not
apply to integers (please provide an example if that is the case) - so it would
only apply if NMTRAN does something weird to integers.
Dennis
Dennis Fisher MD
P < (The "P Less Than" Company)
Phone / Fax: 1-866-PLessThan (1-866-753-7784)
www.PLessThan.com http://www.plessthan.com/
Quoted reply history
> On Aug 24, 2017, at 4:25 PM, Leonov, Sergei <[email protected]> wrote:
>
> Hi Dennis,
>
> Unfortunately, my reply will not provide a solution to your problem. It is
> more about drawing attention to the fact that checking conditions numerically
> is not exactly the same as checking conditions on a piece of a paper, because
> of rounding. I’m sure that the users of the List are well aware of this fact,
> just a reminder…
>
> A simple example, I did this in Matlab, you can repeat it in R or other
> programming language. I won’t waste your time by describing how I came to
> this example. Compare the output of two expressions:
> >> a1=0.06;
> >> a2=0.05 + 0.01;
>
> You would expect the equality between the two values, a1 and a2, right? True,
> on paper. Here is the output of these two values with 20 decimals.
> >> fprintf('%22.20f\n',a1)
> 0.05999999999999999800
> >> fprintf('%22.20f\n',a2)
> 0.06000000000000000500
> And, of course, the output of the logical expression (a1 ==a2) is FALSE.
>
> Regards,
> Sergei Leonov
> ICON Innovation Center
>
> From: [email protected] [mailto:[email protected]] On
> Behalf Of Bill Denney
> Sent: Thursday, August 24, 2017 6:45 PM
> To: Dennis Fisher; [email protected]
> Subject: RE: [NMusers] Use of ACCEPT in $DATA
>
> Hi Dennis,
>
> I don’t have an elegant solution for you (and I’ve been pining for the use of
> combined Boolean operations like “TIME.GT.5.9.AND.TIME.LT.6.1” for a long
> time).
>
> An inelegant solution could be to run the model once with a write statement
> to see if you can identify the value like 6.0000001 and use it. That would
> probably be fragile to different processor/compiler/math library
> combinations, so I’d probably end up making the additional indicator column
> for certainty.
>
> Thanks,
>
> Bill
>
> From: [email protected] <mailto:[email protected]>
> [mailto:[email protected] <mailto:[email protected]>]
> On Behalf Of Dennis Fisher
> Sent: Thursday, August 24, 2017 6:16 PM
> To: [email protected] <mailto:[email protected]>
> Subject: [NMusers] Use of ACCEPT in $DATA
>
> NONMEM 7.4.1
>
> Colleagues
>
> I am trying to use the ACCEPT option in $DATA in order to select a subset of
> records (to evaluate the impact of the # of samples/subject on confidence
> intervals).
>
> I used the following code:
> ACCEPT=(TIME=0, TIME=1, TIME=2, TIME=4, TIME=6, TIME=24)
>
> NMTRAN then creates a dataset but — to my surprise — TIME=6 is not in the
> dataset (all the others are).
>
> I am copying the first few rows of the input dataset so that you can see what
> is being provided to NMTRAN:
>
> ID,AGE,MONTHS,SEX,WT,AMT,RATE,TIME,EVID,MDV,REPLICATE,IPRED,CWRES,DV,PRED,RES,WRES
> 1101,12,144,1,30.054,210.38,841.51,0,1,1,1,0,0,0,0,0,0
> 1101,12,144,1,30.054,0,0,1,0,0,1,187.42,0,179.28,199.26,-19.979,0
> 1101,12,144,1,30.054,0,0,2,0,0,1,180.92,0,187.92,194.09,-6.1659,0
> 1101,12,144,1,30.054,0,0,4,0,0,1,169.84,0,177.66,184.37,-6.712,0
> 1101,12,144,1,30.054,0,0,6,0,0,1,160.61,0,153.43,175.39,-21.96,0
>
> The underlined / boldfaced value (6) in the final row is the problem.
>
> I assume that NMTRAN is reading that value as something other than 6.0 (e.g.,
> 6.000001) and thereby omitting it.
>
> I have reviewed NMHELP to see if there is some other way to accomplish this.
> Ideally, there would be something like:
> TIME.GT.5.9.AND.TIME.LT.6.1
> but that does not appear to be supported.
>
> The alternative is to modify the dataset to include many possible MDV/EVID
> columns. However, it would be more elegant to do this in the control stream.
> Or, if there is some way to find out the exact value that NMTRAN sees, I
> could specify that value.
>
> Any help would be appreciated.
>
> Dennis
>
> Dennis Fisher MD
> P < (The "P Less Than" Company)
> Phone / Fax: 1-866-PLessThan (1-866-753-7784)
> www.PLessThan.com http://www.plessthan.com/
>
>
>
>
>
>
>