Re: Table formatting in NONMEM7- can I skip the "Table No." header row?
Hi,
I second what Nick said.
When I run either NONMEM 6 or NONMEM 7 with ONEHEADER and FILE with
multiple tables (e.g. $SIM with NSUB>1) in the output then I get a TABLE
NO. record followed by the header record with every table.
What I did was to generate one simulation table with header, and multiple
simulation table (subprobs>1) without header. Then the header of the
first data file is transferred to the second data file in R. It would be
nice if NONMEM can provide option with just one header per table with
subprobs>1.
Best regards,
Shelley
========================================
Xiao Hu (Shelley), Ph.D.
Senior Scientist,
Clinical Pharmacology and Pharmacometrics
Biogen Idec, Inc.
14 Cambridge Center
Cambridge, MA 02142
Nick Holford <[email protected]>
Sent by: [email protected]
18-May-2011 05:22 AM
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nmusers <[email protected]>
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Subject
Re: [NMusers] Table formatting in NONMEM7- can I skip the "Table No."
header row?
Hi,
The ONEHEADER option was introduced some time ago (NONMEM V?) to get rid
of the repeat of the TABLE and header record after every 900 records
within the same table (I think this was a 'feature' in the days of actual
printing files on paper). It would be nice if this was the default
because I cannot image anybody who wants those extra records in the file
today.
When I run either NONMEM 6 or NONMEM 7 with ONEHEADER and FILE with
multiple tables (e.g. $SIM with NSUB>1) in the output then I get a TABLE
NO. record followed by the header record with every table.
I can't discern any difference between NONMEM 6 and NONMEM 7 in their
table behaviour despite the change in the HELP description.
If you use R or SAS to skip the first TABLE and header records you still
need to figure out how to process the subsequent TABLE and header records
if you your table file has multiple tables as it often does when it is
created by simulation.
It would be nice if NONMEM had the option to just print the TABLE and/or
header info just once per table file.
Nick
Quoted reply history
On 18/05/2011 10:06 a.m., Kristensen, Kim wrote:
Andreas,
NONMEM7 seems to have improved regarding $TABLES and the use of the
ONEHEADER statement in $TABLE (see the help below), thus, you should
able to use the content of the previous 4 mails.
However, for those still using NOMMEM6 a work around would be to use
the NOHEADER statement in $TABLE and then import the table file in to
R- and using the colnames command to insert the column name from $TABLE
in " " this should give you a table file without a new column name row
in row 901,1801.. etc. when using ONEHEADER (See example below).
NONMEM7 help $TABLE
NOHEADER
Used only with the FILE option. No header lines are included in
the table file.
ONEHEADER
Used only with the FILE option. Only the first line of the table
is a header line.
NONMEM6 help $TABLE
NOHEADER
Used only with the FILE option. No header lines are included in
the table file.
ONEHEADER
Used only with the FILE option. Only the first 900-record seg-
ment of the table is preceded by header lines.
Ex. NONMEM6
$TABLE ID TIME DOSE NOPRINT NOHEADER FILE=sdtab1
R- command
DATA<- read.delim("sdtab1", header=F,
sep="", as.is=T) # Read the NM6
table into R-
colnames(DATA) <- c("ID","TIME","DOSE",
"DV,"PRED","RES","WRES") # Insert Column Names
write.table(DATA, "sdtab1.csv", col.names=T, row.names=F,
quote=F, sep=",",eol='\n') # Create a new .csv
table file
NB. The last 4 columns are automatically added if NOAPPAND is not used
in $TABLE
NOAPPEND
Requests that items DV, PRED, RES, WRES not appear automatically.
Regards,
Kim Kristensen
Senior Pharmacokinetisist,
M.Sc.(pharm), PhD
_____________________________________________________________________
AstraZeneca
Clinical Pharmacology & DMPK
AstraZeneca R&D Lund,
SE-221 87, Lund, Sweden,
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-----Original Message-----
From: [email protected] [mailto:[email protected]]
On Behalf Of AVG (Andreas Velsing Groth)
Sent: 17. maj 2011 15:09
To: 'Sebastien Bihorel'; nmusers
Subject: [NMusers] Table formatting in NONMEM7- can I skip the "Table
No." header row?
Dear fellow Nmus,
Does anyone know whether I can make an output table with $TABLE skipping
the "Table No. 1" row and going straight to the row with the actual
column headers? The purpose is to ease import of the output table to
other applications, particularly SAS.
I think that should be possible, but maybe some dirty tricks are
required?
I consider this somewhat related to Sebastiens Q below.
Thanks in advance,
Andreas
Andreas Velsing Groth
Modelling Scientist
Quantitative Clinical Pharmacology
Novo Nordisk A/S
Denmark
-----Original Message-----
From: [email protected] [mailto:[email protected]]
On Behalf Of Sebastien Bihorel
Sent: 2. december 2010 15:58
To: nmusers
Subject: [NMusers] Table formatting in NONMEM7
Dear NMusers,
I was wondering if there is a way to change the default format of output
tables in NONMEM7. I know that the FORMAT option allows the user to
override the default format at each $TABLE statement, but adding this
option in every control stream can become a very burdensome task. I'd
like to change the default format globally... maybe by changing an
installation setting file?
I have tried to look in the manual and on the web but did not find
anything relevant (wrong keywords???)
I would appreciate any feedback for the group.
Thank you
Sebastien
--
Nick Holford, Professor Clinical Pharmacology
Dept Pharmacology & Clinical Pharmacology
University of Auckland,85 Park Rd,Private Bag 92019,Auckland,New Zealand
tel:+64(9)923-6730 fax:+64(9)373-7090 mobile:+64(21)46 23 53
email: [email protected]
http://www.fmhs.auckland.ac.nz/sms/pharmacology/holford