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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 for wfn7 to
extract the files into is C:\nmNnn\wfn7. You may choose a
different home directory instead of C:\nmNnn\wfn7 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 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 major version (700) 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
19 Jun 2022 Version 751
Release
for WFN751 supporting NM7.5.1. Version compatible with NONMEM 7.4, NONMEM 7.3
and NONMEM Version 7.2.
NM
version information enhanced with NMVERMIN.
A change to NMVERMIN from “0” to “1” in
wfn.bat is advised to complete the installation of this version.
NONMEM table output format width can be specified e.g.
set nmwidth=13
to automatically include FORMAT=s1PE13.7 in the $TABLE record
Support for 7zip added to fix but unzipping large NONMEM tables files.
Remote Job Management (RJM) support now uses funcX and Globus for running
WFN on the NeSI cluster. nmwaitonly option no longer required to restart jobs.
23 Mar 2021 Version 750
Release for
WFN750 supporting NM7.5.0. Version compatible with NONMEM 7.4, NONMEM 7.3 and
NONMEM Version 7.2.
NM
version information enhanced with NMVERMIN.
A change may be required to wfn.bat to
complete the installation of this version.
For NONMEM 7.5:
set NMVER=7
set NMVERMIN=5
set NMVERNUM=0
For NONMEM 7.2,7.3,7.4 recommended change
set NMVERNUM to NONMEM number e. 3 for NONMEM 7.4.3
24 Feb 2021 Version 744b
Bug fix:
line 148 of _nmbs.bat has full path to nca.awk
Call to
nmgog writes a log file with job number.
22 Jan 2021 Version 744
VPC files
include examples for continuous variables and for time to event. Further
examples of VPCs are provided based on warfarin PKPD and amikacin PK. Additional
options are provided for VPC layout and themes (colours, symbol size, line
width). These options require using the updated versions of nmvpc.bat,
nmvpc2awk.awk, vpc.R and nmvpc_functions.R. Existing versions of nmvpc.bat
will continue to function with the updated files. In order to take advantage of
these new features existing nmvpc.bat file details will need to be used
and customized based on the new code in the updated nmvpc.bat. See
details in http://wfn.sourceforge.net/wfnvpc.htm.
nmfewfn74.bat updated for NM7.4.4. nmctl allows more flexible user format
for ctl file. Various changes to support working with NeSI cluster (e.g.
support for NM4.4, cleanup worker directories, nmwaitonly improved, default
memory reduced from 3G to 500M).
A change may be required to wfn.bat to
complete the installation of this version.
See notes
below for version 742 with addition of the NMVERMIN variable which should be
set to 4.
19 Aug 2017 Version 743
bin\vpc
files included in distribution.
A change may be required to wfn.bat to
complete the installation of this version.
See notes
below for version 742.
4 May 2017 Version 742
A change is required to wfn.bat to complete the
installation of this version.
Version
compatible with NONMEM 7.4, NONMEM 7.3 and NONMEM Version 7.2.
The
NMVERMIN environment variable must be set in wfn.bat (after the NMVER variable) to reflect the minor version
number e.g.
For NONMEM 7.4:
set
NMVER=7
set NMVERMIN=4
For NONMEM 7.3:
set
NMVER=7
set NMVERMIN=3
For NONMEM 7.2:
set
NMVER=7
set NMVERMIN=2
nmbs now recognizes when NONMEM output listing file is
not created and gives a more helpful error message.
Bug fix
for VPC to display observation scatterplots.
29 August 2015 Version 741
Updated nmobj, nmmbt, nmretbl to allow
result folder name to be different from result folder NONMEM output listing
file name.
nmgrid web changed to describe nmwaitonly.
27 August 2015 Version 740
Bug fix
to show standard errors for ETA estimates.
13 July 2015 Version 739
Bug fix
to show standard errors when there are no ETA or EPS estimates.
Bug fix
for nmbsi which hung because lock
file was not deleted.
Bug fix
for nmbs when used with fixed width
data file format.
26 April 2015 Version 738
Bug fix
for summary output displayed at end of run and stored in .smr file when results
do not include standard errors.
Bug fix
for nmobj when results folder does
not contain .smy file.
15 March 2015 Version 737
The
results folder .smy file includes ETA P values and ETA and EPS shrinkage. The
.smr file displays EPS correlations.
nmstopg will cancel all jobs started by rjm_batch_submit
using the *localdirs.txt files to identify submitted jobs.
Bug fixed
when paths contain blanks (nmcmd)
26 October 2014 Version 736
Grid runs
no longer return data file to run directory.
Bug fix
for run results directory when using nmgog
(renamed to remove *cmd1.*).
Bug fix
in mlxmbt to use output list file
when results created using mlxgo
4 October 2014 Version 735
Corrections
to documentation describing WFN output from a NONMEM run.
Bug fix
in VPC.R to remove observations less than LLOQ
20 September 2014 Version 734
Support
for rjm_tools for grid execution.
Bug fix
for nmbs.bat to stop hanging when cmds not set or cmds=1.
18 March 2014 Version 733
Support
for Monolix 4.3.0 instead of Monolix 4.2.2.
Bug fix
so that the usual results folder files are included when using nmgog
and mlxgog are used instead of
just .smy and .log files. The data file used for the model is also included in
the results folder after these kind of grid runs.
Bug fix
for bootstrap summary files so that header line is created even if bootstrap
has not been run with 1st replication.
06 March 2014 Version 732
Support
for remote job management tools to allow running jobs on the NeSI PAN cluster.
See NESI grid installation instructions.
Bug fix
to allow Monolix standard errors to appear in .smy
Bug fix
to allow nmgosimg execution of NONMEM
to simulate data and wait until finished before starting Monolix estimation.
8 December 2013 Version 731
A change is required to wfn.bat to complete
the installation of this version.
Version compatible
with NONMEM 7.3.0 and NONMEM Version 7.2.
The
NMVERMIN environment variable should be set in wfn.bat after the NMVER variable to reflect the minor version
number e.g.
For NONMEM 7.3:
set
NMVER=7
set NMVERMIN=3
For NONMEM 7.2:
set
NMVER=7
set NMVERMIN=2
If the
environment variable nmraw is set (e.g. set nmraw=n) then if a nmbs.cov file is
created during a nmbs or nmbsgosim run it will be saved in
nmbsall.cov in the results directory. The nmbs.cov file is only created if the
covariance step is successful. The nmbsall.cov file records if the covariance
step failed and collects nmbs.cov if it was successful.
If the
–prdefault option is not used then a common directory is created for recompiled
modules which is shared by all models (this mimics the default behavior of
standard NONMEM). A user specified directory for recompiled modules may be
defined by setting the nmpdir environment variable e.g. set nmpdir=temp.dir.
The
–mapall option has been added to the MPI pnm files. This allows Windows network
drives to be used as the data source drive when using the MPI parallel method.
Because
of internal errors within NONMEM it may not be possible to simulate with more
than 1 subproblem. When using nmgosim
to perform a parametric bootstrap the default is to request NONMEM to simulate
the required number of replications using a data file representing one
replication. Setting the NSUBPROBLEM environment variable to 1 will set the
$SIMULATION option NSUB to the value of NSUBPROBLEM instead of the number or
replications. The user should supply a data file containing the required number
of replications.
The runname.ext file created by NM7.2 and
later is no longer deleted at the end of a run.
Visual predictive
checks may be created using nmvpc.bat
and any version of NONMEM or WFN. The R statistical programming system must be
installed in order to create VPCs. See the VPC
instructions.
Parallelised
thread execution has been simplified. The separate mpi parafiles provided with
WFN720 are no longer needed. The environment variable cpus should be set to the
desired number of parallel execution nodes e.g. to use 4 nodes when running
nmgo:
set cpus=4
nmgo theopd
Note that the number of cpus assumes they are available on the same host.
Parallelised
command execution has been added. This is more efficient than parallelized
thread execution with WFN commands that have multiple calls to NONMEM e.g.
nmbs, nmgosim. nmrt. The environment variable cmds should be set to the desired
number of parallel commands e.g. to use 4 commands when running nmbs:
set cmds=4
nmbs theopd 1 100
The number of bootstrap runs will be divided among each of the parallel
commands. Parallelised thread and parallelised command execution maybe
combined. There should be at least as many nodes as cmds*cpus for this to be
time efficient e.g. on a cluster with at least 400 nodes this following
commands will execute 100 bootstrap runs in parallel with each run performing
one bootstrap with 4 parallelised thread nodes. Depending on the cluster
overhead this can complete the bootstrap runs in not much more time than it
takes to perform one run.
set cmds=100
set cpus=4
nmbs theopd 1 100
Support
for $THETAI and $THETAR records allowing reference to THETA parameters by name.
Support
for Monolix command line execution with non-parametric and parametric
bootstrap. See Using Monolix for instructions.
01 June 2011 Version 720
This version is for use only with NONMEM
7.2. It does not work with NONMEM 7.1.
NONMEM
7.2 has a number of optional arguments to the nmfe72.bat command e.g.
nmfe72 infile outfile [-background]
[-PARAFILE=file.pnm] [-licfile=filename] [-prsame] [-prdefault] [-prcompile]
[-trskip] [-rundir=dirname][-runpdir=dirname] [-nmexec=filename] [-xmloff]
The wfn7 commands
for executing NONMEM remain simple with just one argument (the runname) e.g.
nmgo runname
Optional
arguments for NONMEM 7.2 should be specified in an environment variable called
ARGS7 e.g.
set ARGS7=-prdefault
The
–prdefault value will restore the usual behavior of previous versions of NONMEM
and skip the dynamic resizing process (which may add a substantial overhead to
total runtimes). It is suggested that this command be added at the start of the
wfn.bat file (see wfn.txt). The ARGS7 variable can be
changed at any time before running wfn7 commands that execute NONMEM (e.g. nmgo, nmbs, nmgosim).
Both file
(fpi) and message passing interfaces (mpi) have been tested with wfn7. The
parafiles (wfn_fpi2.pnm, wfn_mpi2.pnm, wfn_fpi8.pnm, wfn_mpi8.pnm) in the %wfnhome%\run folder may be used as
templates.
Set the
ARGS7 variable to the parafile name before running NONMEM e.g. if you have a
two core computer with MPICH2 installed enter these commands:
set ARGS7=”-parafile=wfn_mp2.pnm”
nmgo theopd
Note that
the quotation marks around the parafile argument are required. The parafile
must be put in the same folder as the run control stream file used by WFN. Do
not use the –nmexec option because WFN uses that to create a NONMEM executable
using the runname. See Installation for examples of testing fpi and mpi
methods.
Other Changes
Formatting
of nmobj command no longer attempts
to show results when run folder does not contain a .smy file.
nmbs command now allows runnames with %NMCTL% extension e.g. nmbs theopd.ctl 1 1000 or nmbs theopd 1 1000 are equivalent
Bug in nminstall.bat for installing updates has
been fixed. The installation destination directory is created if it does not
already exist.
20 June 2010 Version 703
This version is for NONMEM 7.1. It does not
work with NONMEM 7.2.
The wfn7 nmbs command now reports the results
from all estimation methods used for a given problem instead of just the first
estimation method.
The nminstall command has been changed to
support the NONMEM version update process. The revised nminstall.txt should be used to create an updated nminstall.bat file in the wfn7
directory.
A bug in
adding EPS estimates to the *.smr file when there is more than 1 sub-problem
has been fixed. A bug when a comment followed $OMEGA in forming the header line
for the *.smr file has been fixed.
A bug has
been fixed (again) for reporting the estimation method. Version 702 reported
FOCE when it should have been FOCEI. A bug in the nmretbl command introduced in version 701 has been fixed.
14 February 2010 Version 702/616
Users of
Monolix can create a model building table from Monolix projects with the mlxmbt command. The format of the output
is the same as that used with the nmmbt command. Note: When Monolix is asked to compute the
log likelihood it adds a constant term equal to Obs*ln(2*pi) that is not added
by NONMEM. The Monolix derived “Obj” value reported by the mlxmbt command can be converted to the equivalent value computed by
NONMEM by subtracting Obs*ln(2*pi) from the Monolix value. Unfortunately
Monolix does not save the number of observations (Obs) so this cannot currently
be done automatically by mlxmbt.
WFN
Version 702 and 616 have an improved model building summary table format. The
nmmbt.txt file sequence of column headings is more likely to be presented in a
useful format when multiple runs are combined.
The WFN
extended control stream format supports the use of $OMEGA parameter names when
MU referencing is used. When the MU index is the same as the corresponding ETA
used for that MU then MU referencing can be coded without counting ETA values
e.g.
$THETA 10 ; POP_CL
$OMEGA 0.5 ; PPV_CL [this corresponds to eta(1)]
$PK
MU_1=LOG(POP_CL)
CL=EXP(MU_1+ETA(1))
Can be
written:
$PK
MU_PPV_CL=LOG(POP_CL)
CL=EXP(MU_PPV_CL+PPV_CL)
Note: the
use of parameter names for MU referencing is optional. If you use the $OMEGA
parameter name then WFN will replace it with a suitable numeric value for
NM-TRAN to process otherwise the code will not be changed by WFN.
A bug has
been fixed for reporting the estimation method. Version 701 reported FOCE when
it should have been FOCEI.
20 September 2009 Version 701/615
WFN Version
701 has had several changes to enable it to work with the first release of
NONMEM 7. It supports simple switching between different sized versions of
NONMEM. The first release of NONMEM 7 offers a regular size (‘reg’) and a big
size (‘big’). WFN supports switching to custom sized NONMEM installations.
Support
is provided for NONMEM installations created with Intel Visual Fortran (‘ivf’),
gfortran (‘gf’) and g95 (‘g95’) compilers. Limited benchmarking indicates that
the ivf compiler is faster than gf. The g95 compiler is much slower than ivf.
The results from all 3 compilers appear to be identical.
WFN
Version 615 formats NONMEM VI output in the same way as NONMEM 7 i.e.
estimation method and time information are included in the runname.smy and nmmbt.txt
files.
A bug
affecting the use of the INCLUDE abbreviated code record has been fixed in
Versions 701 and 615.
1 June 2009 Version 700/614
Version 700 is designed to work with
NONMEM 7. Changes have been made to cope with modifications to the NONMEM 7 output
listing.
Note that this version has been
modified for use with NONMEM 7 and will not work with NONMEM VI or NONMEM V.
The default installation directory for
WFN is C:\nm7\wfn7
The default output for standard errors
of OMEGA and SIGMA is to report the relative standard error as OMEGA:se% and
SIGMA:se%. This is obtained by dividing the standard error by NONMEM’s estimate
of the variance of OMEGA or SIGMA. An alternative output with an approximation
to the relative standard error of the sqrt(variance) of OMEGA and SIGMA can be
obtained by setting the environment variable nmraw to include the characters “SD” e.g.
set nmraw=SD
http://www.mail-archive.com/nmusers@globomaxnm.com/msg00845.html
http://www.mail-archive.com/nmusers@globomaxnm.com/msg00847.html
Version 614 includes some minor bug
fixes for use with NONMEM VI.
11 September 2007 Version 613/411
Bug fix for nmctl when used with 'i' option which failed to find SIGMA output
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:
<instruction id='compile'>g77 -c
-O *.for</instruction>
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:
<suffix
id='object'>o</suffix>
to
<suffix
id='object'>obj</suffix>
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.
<!--test class='environment'
variable='CPU'/-->
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
.
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