Wings for NONMEM Download

Wings for NONMEM Download

Download Instructions

The download file is named wfnNnn.exe. The "N" is the major version and the "nn" is the minor version number. It is an executable zip archive file. The default directory to extract the files into is c:\nmvi\wfn6. You may choose a different home directory instead of c:\nmvi\wfn6 when you execute wfnNnn.exe. Please read Installation instructions carefully. The instructions include information on uninstalling wfn.

Upgrading

If you are upgrading from an earlier version you may re-install by overwriting your previous installation. Simply run wfnNnn.exe and unzip the files into the %wfnhome% directory that you are already using. Note that this will not change %wfnhome%\bin\wfn.bat (or %wfnhome%\bin\wfnauto.bat ) which you may have modified during your original installation. You do not need to uninstall wfn.
Sometimes an upgrade will involve a change to wfn.bat (known as wfnauto.bat prior to version 400) and this will be indicated in the version notes. If you are upgrading and if your currently installed version is older than the last version (600) that required a change to wfn.bat then you must create (or re-create) wfn.bat . In this case you should make a new wfn.bat by modifying %wfnhome%\bin\wfn.txt as necessary (see Installation ) and saving it as %wfnhome%\bin\wfn.bat.

Please email to receive notification of future updates to WFN.

Version Notes

20 August 2008 Version 614/412

NMQ4WFN version 6.3.2 is compatible with NONMEM VI 2.0 (Bug Alert #1) and NMQual 6.3.2

27 November 2007 Version 614/412

Bug fix for NMVI feature $INCLUDE. The include file must have a full path or use a ..\ prefix if the file is in the same directory as the original control stream.

Note that if the include file itself refers to another file then this file must have a full path or use a ..\ prefix if the file is in the same directory as the original control stream. This is because NM-TRAN processes the control stream and include file in the run sub-directory.

Bug fix so that EPS correlation is reported when L2 data item is used.

Minor bug fix for nmgosim. Example control streams supplied for nmgosim in the wfn\run directory.

11 September 2007 Version 613/411

NMQ4WFN version 6.2.1 is compatible with NMQual 6.2.1

22 July 2007 Version 613/411

Bug fix for nmctl when used with 'i' option which failed to find SIGMA output

Compiler bug/feature workaround has been added. The bug/feature did not add .exe extension to the NONMEM executable file when there was a period character in the runname.

Documentation for nmbs revised to make it clear that IGNORE=@ cannot be used in control streams being run with nmbs.

16 July 2007 Version 612/410

wfntestver describes a utility for testing the performance of different installation versions of NONMEM.

NMQ4WFN version 6.2.0 is now compatible with NMQual 6.2.0

22 March 2007 Version 612/410

Bug fix for nmctl with more than 24 OMEGA parameters.

nmobj5.awk was missing from WFN611. It is now included for compatibility with NONMEM V.

11 February 2007 Version 611/409

Documentation added for use of NMQual 6 with WFN in wfnnmqual.htm

Documentation added for use of Xpose with WFN in wfnxpose.htm (thanks to Malin Rhodin for help with this)

Bug fix for nmbs when dropped data items contained the character 'C'.

[wfn.bat may need to be reinstalled - see Upgrading]. There are some changes to wfn.bat (WFN601 and WFN409) needed to support use of NMQual . If you want to use these features then you will need to recreate your wfn.bat based on the new wfn.txt file in %wfnhome%\bin.

30 November 2006 Version 600

This version is designed to work with NONMEM VI. A few minor changes have been made to cope with modifications to the NONMEM VI output listing.

Note that this version has been modified for use with NONMEM VI and will not work with NONMEM V.

The default installation directory for WFN is c:\nmvi\wfn6.

The code used by wfn.bat to convert long paths to 8 character format has been disabled. This code caused problems on some versions of Windows. It was there primarily to avoid some warnings when keeping NONMEM up to date with mknm.bat. mknm.bat is no longer included in this version because NMQual does a better job at creating a qualified NONMEM installation (although it does not currently support selective compilation when only some source files have changed which mknm.bat could do).

7 April 2006 Version 409

It is a common problem when running bootstraps that some runs fail with a variety of termination messages. The nmbssxs command can be used to count and summarize the success and failure of runs following the use of nmbs. Run nmbssxs in a directory containing one or more *.bs folders created by nmbs to obtain a summary of the results. A similar command nmrtsxs provides the same kind of information after using the nmrt command.

Improvements to documentation and commands for installing multiple NONMEM compilation versions.

nmone enhanced to find ID column and format numeric output as 'general'.

nmfe5 workalike command added. This is called similarly to the standard NONMEM nmfe5.bat but uses WFN to run NONMEM. If it placed in a directory on the system path e.g. C:\Windows then it can be used by programs such as NextLevelSolutions bootstrap.

Bug fix for converting long file name paths to 8 char paths.

Support for nmqual added. NMQual should be used by all NONMEM users to ensure their source code is up to date.

Note that there are two things to consider when you use NMQual:
1. NMQual patches the source code to get a consistent patch level and compiles a new installation of NONMEM
You can run the NMqual installation without using the special NMqual front end that checks the integrity of the installation every time you run it. Just use WFN and set NMHOME to the NMQual target directory e.g. C:\nmvqdf.

The df and ivf compilers create .obj files and you can use the NMQual generated output with WFN nmgo in the usual way.

The g77 compiler produces .o files so you need to change your NMQual config*.xml file as follows so that .obj files are produced:

Change from:

to
<instruction id='compile'>cmd /c "g77 -c -O *.for && ren *.o *.obj"</instruction>
Change from:

<instruction id='library'>ar -r nonmem.lib *.o</instruction>
to

<instruction id='library'>ar -r nonmem.lib *.obj</instruction>

Change from:

<instruction id='nmtran'>g77 *.o -o nmtran.exe</instruction>

to
<instruction id='nmtran'>g77 *.obj -o nmtran.exe</instruction>

Change from:

Note: Change means you must change the original line. It is not sufficient just to add new lines.

You may also want to remove this line because it doesn't do anything useful as far as I can tell and will stop NMQUAL working if this variable is not defined in your environment.

2. NMQual runs NONMEM and checks that the object code has not been changed since the installation.
I have tested NMQual with WFN and updated WFN to be able to work with it. It requires you to use WFN version 409 or later and make a change to an updated (see below) wfn.bat to allow it to run the NMQual version of NONMEM. I have tested NMQual with df, g77 and ivf compilers.

In wfn.bat you need to specify the name of your nmqual target in wfn.bat. I suggest after 'set F77VER' you should insert 'set NMQUALVER' with the name of your nmqual target e.g.
set F77VER=df
set NMQUALVER=nmvqdf
The nmqual target is the name of the target directory created after you run nmqual. If the target is c:\nmvqdf then the NMQual version needed by wfn.bat is nmvqdf. Note that the target directory is NOT the directory used to install the nmqual files. It is created by NMqual when you run the nmqual.p perl script.

Support for Intel Visual Fortran (ivf) revised. Tested with Intel Visual Fortran Version 9.1

Support for GNU Gfortran added

[wfn.bat may need to be reinstalled - see Upgrading]. There are some changes to wfn.bat needed to support use of NMQual and the Intel and Gfortran compilers. If you want to use these features then you will need to recreate your wfn.bat based on the new wfn.txt file in %wfnhome%\bin.

23 November 2004 Version 408

Further work done on the documentation for the cts system.

Bug fix for cts.bat which was not working with the mksas option.

cts temporary files cleaned up.

nmbs keeps a log file if NM-TRAN finds an error which helps debugging.

nmbs bug when $INPUT line became greater than 80 char long has been fixed.

Bug with %nmctl% if not 4 chars long has been fixed (affected name of $TABLE file output)

Bug fixed in nm2wfn.bat used to convert standard NONMEM compilation versions to WFN named compilation versions.

ncabs now works and is more fully documented. A new command, ncasim, works like nmgosim but instead of doing a NONMEM analysis on the simulated data the analysis step uses nca.awk to do a non-compartmental analysis (AUC, cmax, tmax). nca.awk can be modified to perform any kind of analysis on the simulated data sets created by a NM-TRAN simulation control stream. The nature of the analysis will depend on how the user modifies nca.awk.

16 June 2004 Version 407

nmeigen displays the condition number and the extreme eigenvalues. This requires that $COV has the PRINT=E option and that the covariance step completes. A condition number over 1000 is a sign of overparameterization.

The cts procedures ctssplit.awk and mkctl.awk made more flexible.

Long file names in the NMHOME path will cause problems for WFN. A revised wfn.txt is provided that will automatically convert long file names used for WFNHOME, NMHOME and F77HOME variables into the 8 character short format. This will not work with Windows 98/ME but should work with Windows XP, Windows200*. If you want to take advantage of this feature you will need to replace your existing wfn.bat by saving wfn.txt as wfn.bat (see Upgrading). You will need to transfer all changes you have made to your original wfn.bat to the new version.

17 May 2004 Version 406

$THETA, $OMEGA, $SIGMA not recognized if $ was not first char of record. ntcs.awk has been fixed.

DIMTOK increased in LSIZES for s7t, 57t compilation versions

nmcg now refreshes the data descriptor file (*.dsc) if nmcg has been run previously

nmctl has an optional second argument ("i") which will use INTER.txt instead of the run listing file as the source to update parameter values.

Further work done on the documentation for the cts system.

25 November 2003 Version 405

nmgosim command provides a work around for NONMEM unreliable simulation and estimation steps in single problem.

Improved installation tools (wfninst

and wfnsetup) and documentation for named NONMEM compilation versions.

New version of gawk (3.1.2)

Users may specify the NMIGNORE character to match the value specified in the IGNORE option of the $DATA NM-TRAN record. This value is used by nmbs and nmrt commands. The value is set in wfn.bat. The default value is #.

wfn.txt bug fixed to support ms compiler

Missing web files for index page added.

wfnlink.awk changed to support French version of output from DOS echo command

Extended control stream recognizes parameter names embedded in logical expressions e.g. IF (CL.LE.0) becomes IF (THETA(1).LE.0)

Parameter names followed immediately by "(" or "{" or "[" or ";" are now recognized e.g. all of the following will find "POPE0" as the parameter name.

$THETA (0,150 ) ;POPE0(1)
$THETA (0,150 ) ;POPE0{1}
$THETA (0,150 ) ;POPE0[1]
$THETA (0,150 ) ;POPE0;1

"F" is ignored if it used as a parameter name.

Bug fix in ntcs.awk to prevent name conflict problem if data item and parameter names are the same.

Case sensitivity of file names preserved if more than one TABLE file is requested.

Bug fix for nmfesf.bat for Win9x versions.

nmllp changed to recognize wider variety of parameter name syntax.

10 June 2003 Version 404

wc modified for the free Open Watcom F77/32 compiler (http://www.openwatcom.org). This may cause older (obsolete) Watcom versions not to work.

Bug fix for nmmbt and nmobj to handle multiple problems in the same run and remove spurious nmmbt output in SE columns. Note that SE output is only included after setting the nmmbtse environment variable e.g. set nmmbtse=y before running nmmbt.

More than one nmbs and nmrt can be started in the same directory at the same time as long as the runnames are different.

8 May 2003 Version 403

%wfnhome%\run directory and files now restored to WFN distribution file.

2 May 2003 Version 402

Log likelihood profiles can be created with the assistance of nmllp.

nmbs now allows comma separated values in $INPUT list of data items.

Bug fix for column headings in *.smy files. Heading was being omitted if last item in control stream comment was numeric.

Standard errors no longer included in nmmbt output in order to make tables clearer. Standard errors can be included by setting the nmmbtse environment variable e.g. set nmmbtse=y before running nmmbt.

nmobj modified to let negative objective function values be sorted so that lowest OBJ appears first.

Minor changes to remove case sensitivity of options in $DATA record and to allow more flexibility in formatting of $THETA records.

Various attempts to improve the web based documentation.

11 Jan 2003 Version 401

wfn.txt changed so that wfn.bat will set nmobj correctly if it is not specified on the command line used to start wfn.bat.

Bug in nmlink.awk fixed affecting users with NONMEM default locations for compiled files.

23 Dec 2002 Version 400

[wfn.bat should be installed - see Upgrading].
The name of these files (wfn.txt and wfn.bat) has changed from WFN Version 3xx to Version 4xx. If you upgrade to Version 4xxx your wfnauto.bat should still work. However, to take advantage of the new multiple compiler and NONMEM compilation version support it is recommended that you make a new wfn.bat from wfn.txt and use wfn.bat instead of wfnauto.bat. Don't forget to change any shortcuts you may have created to start WFN. You will need to change wfnauto.bat to wfn.bat.

wfn command line arguments are now position independent e.g. wfn df std or wfn std df or wfn df or wfn std. If compiler or version argument is missing then previous option is used. Default options are set in wfn.bat.

Source and binary directory structure revised.

GeoCities web site no longer supported.

nmac no longer fills up all disk space if there is a syntax error in the NM-TRAN autocovariate code.

Bug in nmobj.awk fixed which prevented output from multiple problems in the same control stream appearing in the *.smy file

wfn.bat unsets nmnice if OS is Win9x.

Support for Intel Fortran 7.0 compiler added (compiler code is ivf).

The nmraw option shows the raw OMEGA and SIGMA values in the *.smr file as well as the *.smy file and the nmbs *.txt file. Non-zero off-diagonal elements of OMEGA are reported unchanged when the nmraw option is used. The default when nmraw is not set it to report the correlation of the corresponding diagonal elements of OMEGA.

14 July 2002 Version 304

nmosort.awk was omitted from Version 303 (sorry). Now included so that nmobj and related commands will work.
Support for NM-TRAN library included (just in case you want to spend time figuring out if it has any use...).

Objective function formatting changed so that all digits reported by NONMEM are retained when the value is large.

Bug with identical objective function values fixed when using nmobj.

nmctl now recognizes BLOCK size when there are blank characters after "BLOCK" and before "(".
nmbs and nmrt allow more flexibility in control stream record format ($DATA can now follow $INPUT, EVID no longer confused with ID)

26 June 2002 Version 303

Formatting of nmobj output improved (esp. OBJ now sorted in numerical not alphabetic order).
If you use the ln() transform both sides method you may wish to untransform the DV, PRED and IPRED (Y) values in the NONMEM table file. This can be done using nmuntbs e.g. if the run name is lntheopd:

nmuntbs lntheopd

Note that the RES and WRES values are not untransformed. The original table file will be renamed with the extension ".ln".
Users of WinXP/2K/NT can run NONMEM with low priority by setting the DOS environment variable nmnice e.g.
set nmnice=y
If you want to use this as the default then add set nmnice=y to your wfnauto.bat. . All WFN commands that invoke NONMEM e.g. nmgo, nmbs, nmac, nmrt, will run at low priority. Note that ctrl-C is disabled when low priority jobs are running . You must use ctrl-Break to stop NONMEM execution.
The default presentation of OMEGA estimates as their square root and standard error estimates as a % can be changed by setting the DOS environment variable nmraw e.g.
set nmraw=y
When nmraw is set the OMEGA and standard error estimates will be presented in the original scale as they are displayed in the NONMEM output listiing.
Workaround to allow g77 compiler to send NONMEM intermediate output to the console screen (see g77inst.htm ). Requires modifying nm\BEGIN.for.
Format of $INPUT specifying ID (nmbs and nmrt) and for permuted covariate (nmrt) data item made more flexible. They no longer are required to be on the same line as $INPUT.
Timing information for NONMEM runs made less dependent on regional language options.
If covariance step runs successfully the number of sig digits in the estimated parameters will be pre-pended with "+" e.g. sig=+3.3
22 Mar 2002 Version 302
User specified forward and backward delta OBJ criteria added to wfnac (see wfnac.htm for details).
Bug in nmac example file theoe0m5.ctl fixed.
WFN version information included in WFN log file.
Default value for NMLOG supplied by nmargs.bat
23 Jan 2002 Version 301
NMLOG option added to allow user selected WFN log file extension (see wfninst.htm for details).
nmrt bug fixed so that it now uses permuted values of randomized covariate rather than randomization with replacement.
Distributed version of gawk is now gawk31 (was 3.04). Check installed version with '%nmawk% --version' at DOS prompt.
Bug fix for nmctl for argument list in generated PRIOR.for and number of prior df for OMEGA.
Bug fix in several files e.g. nmbs, to use %nmout%, %nmctl%, %nmtbl% instead of .lst, .ctl, .fit.
Bug fix for nmbs, nmctl (did not use NMCTL and NMOUT).
Bug fix for nmmbt to handle irregular OMEGA block format in NONMEM output listing.
Bug fix for nmsmyhdr.awk to recognize parameter names when no space between parameter value and ";".
Bug fix for nmctl with BCV option (FIX added to prior OMEGA; value predicted from BCV now squared).
Extended control stream format for $OMEGA BLOCK() SAME parameters made more flexible (see wfncs.htm )
23 July 2001 Version 300
Support for multiple NONMEM versions and use of GNU make for NONMEM installation and maintenance.
Project created on SourceForge to improve user support.
The wfn Project can be used to discuss WFN features, report bugs, download files.
Feature/bug fix in nmsmyhdr.awk to append headings for standard error so that these appear in *.smy and nmmbt output.
Bug fix in wfnauto.txt (set NMAWK=gawk (not gawk31)). This change must be made in wnfauto.bat if this was created with Version 223 wfnauto.txt .
Bug fix in nmobj.awk for multiple problem output in *.smy.
The g77 support and randomization test files were unfortunately omitted from the Version 222 and 223 releases. They are now included.

20 June 2001 Version 223
Changes made to wfnauto.txt to simplify installation. Please see wfninst.htm for details.
[wfnauto.bat must be re-installed to use g77 - see Upgrading].
8 May 2001 Version 222 Support for randomization of treatment assignment in data files (see rtmethod.htm for background). The command nmrt is similar to nmbs (see wfnrt.htm ).
Support for GNU g77 compiler added (see g77inst.htm ). [wfnauto.bat must be re-installed to use g77 - see Upgrading]
Bug fix for ntcs so that it recognizes OMEGA names on the LHS of an expression.
Bug fix for nmbs so that it works with comma separated data files.
The Minimization field in *.smy file records has been truncated so that ETABAR information is no longer included.
27 Feb 2001 Version 221

Work around for nmbs so that it works with Windows 2000. There seems to be a bug affecting piping standard output to gawk. Installation instruction now updated to include Windows 2000.
16 Jan 2001 Version 220

Bug fix for nmctl Bayesian option to allow for BLOCK on OMEGA. Naming conventions for random effects parameter names modified to distinguish random effects from their variance parameters e.g. CVE0 changed to ETAE0. This only affects the documentation of examples. It does not affect the way that WFN works on existing control streams.
3 Jan 2001 Version 219

Behaviour of nmctl changed when creating Bayesian prior control stream. The new control stream is named runname.ctp instead of overwriting the original runname.ctl file. Bugs affecting nmpe removed.
1 Dec 2000 Version 218

More bugs affecting nmac and nmcg removed.
15 Nov 2000 Version 217

Bugs introduced in Version 209 affecting nmac removed.
14 Nov 2000 Version 216

Enhanced Crossgraphs support (see wfncg.htm ). Model building table generated from *.smy files ( nmmbt).
7 Nov 2000 Version 215

Crossgraph dsn files no longer overwrite existing files in run directory.
22 Oct 2000 Version 214

User registration added to download page. Crossgraphs dsn files copied to run directory (see wfncg.htm ).
12 Oct 2000 Version 213

Minor bug fix for ntcs translation of control stream.
1 Sept 2000 Version 212

Missing nmpesmy.awk file included, nmobj now handles multiple problems in single NONMEM output listing.
16 Aug 2000 Version 211

Bug fixes for nmobj and nmpe.
7 Aug 2000 Version 210

Bug fixes for nmover. Addition of new procedures for computing prediction error ( nmpe).
29 Jun 2000 Version 209

Bug fix for nmobj and nmlst introduced in Version 208. Note that smy file format has changed so that all parameter values are stored in a single record. This new format is especially helpful when using NONMEM for simulation with multiple sub-problems. The old smy format is still available at the start of the smr file. The int.txt and RIDO tbl file are no longer created in results directory because these files had little use.
26 Jun 2000 Version 208

nmobj.awk and nmsmyhdr.awk have had a variety of minor bugs fixed. These will help fix some of the problems of extracting parameter values from NONMEM output listings especially with BLOCKs and multiple simulation sub-problems and when using nmbs.
8 Jun 2000 Version 207

nmctl now works with more flexible formatting of $THETA, $OMEGA, $SIGMA records.
Note that nmctl still assumes that you have only parameter per line but no longer requires $THETA, $OMEGA, $SIGMA before each parameter.
6 Jun 2000 Version 206

nmctl bug fix for BLOCK SAME
Improvements to wfnsetup and wfnpatch batch files for installing NONMEM.
Bug fix for nmmsf so that it uses standard control stream.
nmbs made more efficient so that it only creates NONMEM executable once per call to nmbs.
24 May 2000 Version 205

Minor formatting fix in nmobj. Minor change in wfnauto.bat making interpretation of arguments more robust.
CrossGraphs design files provided for graphs of individual fits, predictions vs DV and residual plots.
11 May 2000 Version 204

Improvements to nmctl for making Bayesian prior control streams
25 Apr 2000 Version 203

Improvements to wfnsetup and wfnpatch batch files for installing NONMEM.
12 Apr 2000 Version 202

Fix for odd NONMEM output list formatting affecting results summary.
nmlst table output formatted better for reading into Excel.
20 Mar 2000 Version 201

Download file name includes version.
14 Mar 2000

Bug that erased any options after MSFO and FILE options in control stream has been fixed.
Single record run summary used by nmbs now includes warning and error information produced by NONMEM after minimization is complete (min) and a message about the covariance step results.
5 Mar 2000

Information on upgrading and re-installation of wfnauto.bat added to this page.
3 Mar 2000

Bugs in Autocovariate program fixed. Now works with gawk.
nmobj and nmlst now work even if user has changed dircmd environment variable.
nmctl has option that will create control stream suitable for use with PRIOR and Bayesian estimation.
Run summary table format changed to show standard errors expressed a % of parameter estimate.
ETASD:se and ERRSD:se changed to OMEGA:se% and SIGMA:se%
These items are no longer computed using sqrt(OMEGA:se) and sqrt(SIGMA:se)
15 Jan 2000

Support for user defined extensions for NONMEM output listing and table files.
[wfnauto.bat must be re-installed - see Upgrading]
Location of nmbs output and nmbs sub-directory name changed.
14 Jan 2000

Bug fix for nmbs when wfnhome is different from nmhome.
Verbatim code in control streams is now completely ignored.
6 Jan 2000

Watcom support for user defined subroutines (e.g. prior.for) fixed.

Send comments and suggestions to Nick Holford .