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RE: FW: Output File Format for NONMEM 7

From: Malaz A AbuTarif <mabutarif>
Date: Wed, 17 Dec 2008 18:07:43 +0200

Thank you for the information.

Could you please let us know if there will be a period of beta testing of
the software?

Thanks,

 

Malaz A AbuTarif

Principal Scientist, Schering Plough Research Institute

Adjunct Associate Professor, Long Island University

 

 

 

From: owner-nmusers
Behalf Of Bauer, Robert
Sent: Tuesday, December 16, 2008 10:53 PM
To: nmusers
Subject: [NMusers] FW: Output File Format for NONMEM 7

 

From: Bauer, Robert
Sent: Tuesday, December 16, 2008 2:25 PM
To: nmusers
Cc: Bauer, Robert
Subject: Output File Format for NONMEM 7

Dear NONMEM Users:

ICON Development Solutions (IDS) is in the process of upgrading NONMEM to
incorporate new analysis methods, as well as additional output files. The
format of the standard results file is also being slightly modified, with
improvements to allow third party software to more easily identify portions
of the result file. While NONMEM 7 will not be released until June 2009, we
at IDS would like to disclose the structure of the result and output files,
so that you may modify your software accordingly, in anticipation of NONMEM
7's release.

 

The user has now the ability to request a series of classical or new
estimation methods within the same problem if he so chooses. Each of the
new methods produces slightly different banner text and termination status
text in the standard results file. For example, an iterative two stage
analysis may be requested, followed by an MCMC Bayesian method, followed by
an FOCEI method. The theta, sigma, and omega results of the iterative two
stage method will be passed on as initial values for the MCMC Bayesian
method, to facilitate the MCMC Bayesian analysis, which in turn can supply
initial values for the FOCEI method. Each of these intermittent analyses
will provide output to the results file, and will be identified by unique
text for that method. To allow a program to consistently find the
appropriate positions in the file without having to search for specific
words in the text, the results file is being augmented with special tag
labels that remain constant, regardless of the method used.

 

The tags always begin with #, followed by four letters to indicate the tag
type, followed by a colon (:). The following tags are presently defined:

 

#METH:

This tag specifies that following it, on the same line, will be found a text
that describes the method, for example First Order Conditional Estimation
Method with Interaction.

 

#TERM:

This tag indicates that beginning on the next lines, text describes the
termination status of the analysis.

 

#TERE:

This tag indicates the end of the lines describing the termination status of
the analysis. Thus, a software program may transfer all lines between
#TERM: and #TERE: to a summary file.

 

#OBJT:

Indicates that following it, on the same line, is the text describing the
objective function, such as Minimal Value Of Objective Function.

 

#OBJV:

Indicates that following it, on the same line, is the objective function
value. However, a more efficient way of extracting numerical results from
the analysis is from the new raw output files (see below).

 

#OBJS:

Indicates that following it, on the same line, is the objective function
standard deviation (MCMC Bayesian analysis only). However, a more efficient
way of extracting numerical results from the analysis is from the new raw
output files (see below).

 

 

In addition to the standard results file, a raw output file will be produced
that provide numerical results in a columnar format. The raw output file
name is provided by the user using a new FILE= parameter added to the $EST
command. A raw output file has the following format:

 

A header line that begins with the word Table, such as:

 

TABLE NO. 4: MCMC Bayesian Analysis: Goal Function=AVERAGE VALUE OF
LIKELIHOOD FUNCTION

 

This header line provides the analysis text (same as given on the #METH:
line in the results file), followed by the goal function text (same as given
on the #OBJT: line in the results file).

 

The next line contains the column headers to the table, such as (this is
actually all on one line in the file):

 

ITERATION THETA1 THETA2 THETA3 THETA4
SIGMA(1,1) OMEGA(1,1) OMEGA(2,1) OMEGA(2,2) OMEGA(3,1) OMEGA(3,2)
OMEGA(3,3)

OMEGA(4,1) OMEGA(4,2) OMEGA(4,3) OMEGA(4,4) OBJ

 

This is followed by a series of lines containing the intermittent results
from each printed iteration (six significant digits), based on the PRINT=
parameter setting:

 

          10 1.73786E+00 1.57046E+00 7.02200E-01 2.35533E+00
6.18150E-02 1.82955E-01 -3.18352E-03 1.46727E-01 -4.38860E-02
2.58155E-02 1.45753E-01

 -4.58791E-02 6.28773E-03 5.06262E-02 1.50017E-01
-2301.19773603667

 

Each of the values, up to the next to last one, occupies 13 characters,
including the delimiter (in this example the delimiter is a space). The
last value is the objective function, which occupies 30 characters, to allow
for the largest range of objective function values, and the greatest
expression of precision.

 

The iteration number, which is the first value in every line, is typically
positive, but also may be negative under the following conditions:

 

1) The burn-in iterations of the MCMC Bayesian analysis are given
negative values, starting at -NBURN, the number of burn-in iterations
requested by the user. These are followed by positive iterations of the
stationary phase.

2) The stochastic iterations of the SAEM analysis are given negative
values. These are followed by positive iterations of the accumulation
phase.

3) Iteration -100000000 (negative one billion) indicates that this line
contains the final result (thetas, omegas, and sigmas) of the particular
analysis

4) Iteration -100000001 indicates that this line contains the standard
errors of the final population parameters.

5) Iteration -100000002 indicates that this line contains the Eigen
values of the correlation matrix of the variances of the final parameters.

6) Iteration -100000003 indicates that this line contains the condition
number , lowest, highest, Eigen values of the correlation matrix of the
variances of the final parameters.

7) Additional special iteration number lines may be added in future
versions of NONMEM.

 

It is hoped that with this file structure, third party software may be
easily programmed to search for the line with the appropriate iteration tag
number, read in the values on that line in a systematic manner into the
appropriate locations, and use the values for post-analysis processing, such
as graphing and additional statistical analysis.

 

These raw output files are provided automatically, independent of the
additional formatted output files that may be requested by the user using
the $TABLE command.

 

Example results and raw output files will be e-mailed to those who request
it by contacting Bob Bauer at Robert.Bauer
format of the output files that would be of general use are welcome.

 

 

Robert J. Bauer, Ph.D.
Vice President, Pharmacometrics
ICON Development Solutions

Tel: (215) 616-6428
Mob: (925) 286-0769
Email: Robert.Bauer
Web: www.icondevsolutions.com

 

 

 

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Received on Wed Dec 17 2008 - 11:07:43 EST

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