Date: 16 Oct 99 18:15:18 MDT
From: "Johnny J.Zhu" <firstname.lastname@example.org>
Subject: Modification of the File, nmfe5.bat?
I wonder if anybody in this discussion group has done or will do a job of modifying the batch file, nmfe5.bat, to somehow simplify the PPK analyses. Basically, I hope the change in the current file can makes the following happen. Following a simple command such as "nmfe5 n", a series of runs execute with control1 to controln read in and report1 to reportn output (n can be any number). The differences among the n control files may be different error models , different covariate(s) or different PK models for the same set of data or different data sets for the same PK and error models. I guess this involves some loop statements and may also need to change those del statements to copy statements if we need keep those f* files. However, It's a pity that I am not familiar with the dos commands. As you understand, with such modified nmfe5.bat, we can save n-1 times in typing the "nmfe5 infile outfile" for n runs.
I am looking forward to hearing from some of you soon.
Thanks for your attention.
Johnny J. Zhu
Date: Sun, 17 Oct 1999 20:31:33 +1300
From: Nick Holford <email@example.com>
Subject: Re: Modification of the File, nmfe5.bat?
The DOS batch command language is really not very hard. The most general way to call a series of NONMEM runs using nmfe5 is to put the following in a file called run.bat:
call nmfe5 1.ctl 1.lst
call nmfe5 2.ctl 2.lst
call nmfe5 3.ctl 3.lst
call nmfe5 4.ctl 4.lst
or you can use the primitive looping in DOS with the following single line in run.bat:
for %%f in (1 2 3 4) do call nmfe %%f.ctl %%f.lst
Note that you must use the "call" syntax when executing a DOS batch file from within a batch file if you want to return to the calling batch file.
This will not keep all those f* files but what the f* do you want to keep them for anyway?
An alternative to the laborious nmfe5.bat is to use Wings for NONMEM (wfn99). This is a set of DOS batch files and awk scripts I have developed which you can download from the web:
wfn99 has a command called nmgo that replaces nmfe5 and has a simpler argument list. It assumes that the filename for the output file(s) is the same as the filename for the control stream but differs in the file extension. Iff you have an NM-TRAN control stream in a file called run.ctl then you can call "nmgo run" and the output listing will be run.lst. All the output files are saved in a separate sub-directory (with the name "run" plus an optional extension) so if you want to save all those f* files for each run you can do so. nmgo also extracts the interesting parts of the NONMEM output listing and presents them in a simple table (obj func value, parameter estimates (and SEs)).
Nick Holford, Dept Pharmacology & Clinical Pharmacology
University of Auckland, Private Bag 92019, Auckland, New Zealand
email:firstname.lastname@example.org tel:+64(9)373-7599x6730 fax:373-7556