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Last Updated: 4 May 2017
WFN Command Files are intended for direct command line
use. WFN Support Files are used by the command files and are not typically
useful by themselves.
Some environment variables may be set by the user
either at the command line or in wfn.bat
to reflect user preferences.
NMNICE If set to y then NONMEM will run at low
priority. This has negligible impact on actual run-times but allows more system
responsiveness to user actions.
NMRAW If set to y then WFN will report the variance of OMEGA and SIGMA
estimates. 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
F77TRACE The standard NONMEM group installation creates an nmfe7.bat
file with the compiler options set in the environment variable op. It includes a run time /traceback option that slows down execution by about 10% and
has little value for users. The WFN Fortran compiler options do not include
this option by default. It can be activated by setting the environment variable
F77TRACE=y in wfn.bat.
MLXGO.BAT This is the equivalent of nmgo.bat for use with Monolix.
The control file argument must have the extension .mlxtran.
The extension is not required on the command line when mlxgo.bat is used.
mlxgo MLX_warfpk
MLXBS.BAT This is the equivalent of nmbs.bat for use with Monolix.
The control file argument must have the extension .mlxtran.
The extension is not required on the command line when mlxbs.bat is used.
mlxbs MLX_warfpk 100
MLXMBT.BAT This is the equivalent of nmmbt.bat for use with Monolix. Note that the likelihood calculated by Monolix is not directly comparable with the objective function
value calculated by NONMEM. 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.
MPI.BAT Used to test the function of the Message Passage
Interface method of parallelization. It uses the theopd.ctl
control stream only. The user can specify the number of CPUs (equivalent to
cores) to use for parallelization. Eg. mpi 2 will use 2
CPUs.
NMAC.BAT Automatic search for
covariate model. Requires an autocovariate control
stream that includes all the covariate models that are to be
tested. A stepwise forward inclusion search is performed with inclusion of a
covariate if it improves the objective function by at least 3.84. The full
model is then pruned by removing covariates one at a time with replacement and
only covariates which produce at least a 10.83 change in objective function are
accepted for the final model.
e.g. The following
command uses the theoe0.ctl autocovariate control
stream and systematically explores the five covariates shown. If more than 9
covariates are specified then they must be written as a single string joined by
# characters e.g. AGE#WT#SEX#RACE#DIAG
nmac theoe0 AGE WT SEX RACE DIAG
NMBS.BAT
Performs a bootstrap of a NONMEM run. eg.
nmbs theopd 100 will invoke nmgo with 100 bootstrap
sampled data sets taken from theopd.dat. The output is saved in runname.bs.%NMDIR%\runname.bs.smy
e.g. theopd.bs.nm7\theopd.bs.smy. Assumes that the value of the IGNORE option
for $DATA is #. If another value is used then you must set nmignore
to the desired IGNORE character. Note that you cannot use IGNORE=@ with nmbs. Several
executions of nmbs
can be run in parallel starting from the same directory but ONLY if the runname is different. E.g. you might copy theopd.ctl theopd2.ctl and then run nmbs
theopd 1 500 and nmbs
theopd2 501 1000 at the same time.
nmbs theopd 200; run from 1 to 200 bootstraps
nmbs theopd 1 200 ; run from 1 to 200 bootstrap data sets
nmbs theopd 5 5 ; just run the 5th bootstrap data set
nmbs theopd 501 1000 ; run from 501 to 1000 bootstrap data sets
NMBSI.BAT Similar to nmbs.bat but uses NONMEM $SIM BOOTSTRAP=-1 option to generate
bootstrap data sets.
nmbsi theopd 200; run from 1 to 200 bootstraps using NONMEM to
generate bootstrap data sets
NMBSSXS.BAT 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 a runname.bs
directory created by nmbs to obtain a summary
of the results.
NMCG.BAT
Creates CrossGraphs files from
NONMEM table output.
NMCTL.BAT Takes
final parameter estimates from runname.lst file and
puts them in the original control stream. e.g. nmctl theopd. The original control stream will be named theopd.org.
If used with the
BCV option e.g. nmctl runname BCV
the control stream will be formatted for use with the user defined PRIOR
subroutine which applies a Bayesian prior to the parameters. BCV may be the
letter "b" or a number between 0 and 1 to indicate the fractional
coefficient of variation to use as the default value for defining the prior
uncertainty on THETA. The number form is used if the run did not include a
covariance step or the covariance step failed and the estimated standard errors
on THETA are not defined.
The second argument
to nmctl can be the letter "i" to specify that parameter values should be read
from INTER.txt e.g. nmctl runname i
This is helpful if
a run terminates unexpectedly and the NONMEM output listing is not created
properly. Using nmctl
will retrieve the parameter estimates obtained so far from
INTER.txt. INTER.txt is only created if the MSFO option is specified and BLKDAT
is changed to rename the intermediate output file from the default value of
INTER to INTER.txt i.e.
1/'nul','con','PRDERR','INTER.txt','nul'/
NMEIGEN.BAT 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 e.g. the condition number for the theopd example is 36.8 which suggests the model is not overparameterized.
nmeigen theopd_eigen
theopd_eigen cond=36.8159 6.03E-02 2.22E+00
NMFE5.BAT 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. The user should edit nmfe5.bat to makes sure it starts by
calling wfn.bat using the same
arguments that are used with the normal WFN shortcut method of starting WFN.
nmfe5 theopd.ctl theopd.lst
NMINT.BAT Displays intermediate THETA values during NONMEM run (wc) e.g. nmint runnname.
Use of this command requires that the $ESTIMATION
record includes the MSFO=runname.msf option. This is
because an intermediate output file is only produced if the MSFO option is in
effect.
NMGO.BAT
Invokes NONMEM run with runname
control stream argument e.g. nmgo theopd
NMGOSIM.BAT Combines simulation and estimation which may be used for performing a
parametric bootstrap. It uses a simulation control stream (simctl)
to generate a specified number (nrep) of simulated
data sets. Each data set is then used by an estimation control stream (estctl). The parameter estimates from all nrep runs are saved in a single file (estctl.smy) in the estctl
run directory e.g. nmgosim simctl estctl 1000
This command will
simulate and estimate 1000 data sets. Note that the simulation control stream
must create a table file with data items that match the data items input by the
estimation control stream. The nmgosim procedure will
replace the $DATA file in the estimation control stream with each simulated
data set so that it can be used for estimation. It is recommended (but not
necessary) that the $TABLE NOAPPEND option be used in the simulation control
stream to prevent creation of the PRED, RES and WRES data items that are usually
not used by the estimation control stream.
set fixarg= -v PK=1 –v PD=0
rem Replace raw simulated .csv with transformed data
set gotsampascsv=n
rem Keep data after simulation
set ctsthisgotdata=n
call nmgosim pkpdsimctl
pkestctl 1000
set fixarg= -v PK=1 –v PD=1
rem Use transformed data .csv
set gotsampascsv=y
rem Use previously simulated data
set ctsthisgotdata=y
call nmgosim pkpdsimctl
pkpdestctl 1000
A Monolix
control file (with the .mlxtran) extension may be
used for estimation. Simulation must be performed with a NM-TRAN control file.
The following example uses NONMEM with the NM_warfpk_sim.ctl
file to simulate 1000
data sets which is then followed by estimation using Monolix
with the MLX_warfpk_pbs.mltran control file.
call nmgosim NM_warfpk_sim.ctl
MLX_warfpk_pbs.mlxtran 1000
NMLLP.BAT
Creates and executes a series of runs with a specified
parameter fixed to each of a set of user specified values. Can be used to create
a log likelihood profile. Usage is nmllp runname pname val1 val2 ... e.g. nmllp theopd
pope0 -100 0 100.1 150 200. Because of compiler
restrictions on file names the resulting runnames
will have any decimal points in parameter values replaced by "p". In
the previous example the parameter value of 100.1 will have a runname of theopd_pope0100p1.
NMMBT.BAT Creates model building
table. This is a combination of nmobj and *.smy file results. Merges parameter estimates from all runs
into a single table. Accounts for different names for parameters. Tab delimited
format makes it suitable for reading into Excel. Standard errors can be
included by setting the nmmbtse environment
variable e.g. set nmmbtse=y
before running nmmbt. nmmbt
has replaced the nmlst command.
NMMSF.BAT Converts full control stream to use MSFI file e.g. nmmsf theopd
NCABS.BAT Works like nmbs.bat but performs a non-compartmental analysis
instead of calling NONMEM with the bootstrap data sets. The control stream used
with ncabs is used to only identify a dataset
containing id, time, concentration and mdv values.
This dataset is used to create non-parametric bootstrap datasets. The nca.awk script should be edited to specify a variety
of parameters to control the nca computation. Look at
%wfnhome%\bin\nca.awk for
details. The nca results are put in a directory with
the .nca extension. Statistics computed are cmax, tmax, auc
to infinity, %extrapolated auc, auc
0 to last time and time to reach target concentration. 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.
NCASIM.BAT Works like nmgosim.bat but performs a non-compartmental analysis
instead of calling NONMEM with the simulated data sets. The control stream used
with ncasim is typically used to create a
parametric bootstrap dataset containing id, time, concentration
and mdv values. Usage is ncasim runname start end
where runname is a simulation control stream and start and end specify the beginning and
end replication numbers to be used for simulation of datasets. 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.
NMONE.BAT Creates a tab delimited file with one record per subject e.g. from a
NONMEM table file. Assumes the ID data item is in the first field of each
record and headings are on the second record. The first argument is the runname. e.g. nmone theopd. An output file
named runname.txt will be created in the run directory. The tab
delimited format is suitable for reading into Excel.
NMOBJ.BAT
Displays sorted list of run summary objective function
lines
NMRT.BAT
Like nmbs this command invokes multiple NONMEM
runs. It randomizes a covariate so that the null model of no effect will be
true. This can be used to find the probability of the difference in objective
function between two models one of which uses the covariate in the model. The
syntax is nmrt covname
runname nboot e.g.
nmrt sex theopd 1000, where covname is
the covariate data item name in the $INPUT record, runname
is the name of the NM-TRAN control stream, nboot is
the number of replications to be performed. See rtmethod
for an example applied to NONMEM and Kelly P. Overview of Computer Intensive
Statistical Inference Procedures. http://garnet.acns.fsu.edu/~pkelly/resampling.html
for an overview of the randomization test.
NMRTSXS.BAT It is a common problem when running
bootstraps that some runs fail with a variety of termination messages. The nmrtsxs command can be used to count and
summarize the success and failure of runs following the use of nmbs. Run nmrtsxs
covname runname in
a directory containing a runname.rt_covname directory
created by nmrt to obtain a summary of the
results.
NMRUNMV.BAT Renames runname
control stream, results directory and associated
files e.g. nmrunmv theopd theopdnew
NMTBL.BAT Creates run summary from NONMEM output listing e.g. nmtbl theopd
NTCS.BAT Can do a reverse translation to convert standard control streams to
extended control streams by using the -r option. E.g. ntcs -r theopd will convert theopd.ctl. The original control stream will be
named theopd.std.
Can also be used to translate exended
into standard control streams. e.g. ntcs theopd will convert theopd.ctl. The original
control stream will be named theopd.ext.
NMCG.BAT Can be used to
make it easier to use CrossGraphs to view NONMEM
table file output. See wfncg.htm for details.
UNWFN.BAT Used to uninstall WFN. Must be executed from the %wfnhome% directory.
WFN.BAT Initializes DOS environment variables for specific compiler and NONMEM
installation.
ITEM2AWK.BAT Utility to create an awk
script for reading and reformatting text files e.g. .csv format
NMVPC.BAT Used to create visual predictive checks. See wfnvpc.htm for details.
_NMBSI.BAT Invoked by nmcmd.bat to execute NONMEM bootstrap using nmbsi.bat.
_NMGO.BAT Invoked by nmcmd.bat to execute NONMEM or Monolix
model execution.
_NMGOSIM.BAT Invoked by nmcmd.bat to execute NONMEM or Monolix
parametric bootstrap.
ITEM2AWK.AWK Invoked by item2awk.bat
NCA.AWK Invoked by ncabs.bat
NMAC.AWK Invoked by nmac.bat
NMACF.AWK Invoked by nmac.bat
NMARGS.BAT Checks validity of command line arguments.
NMBS.AWK Invokedby nmbs.bat
NMBSINIT.AWK Invokedby nmbs.bat
NMCMD.BAT Controls parallel execution of all modelling
commands.
NMCOV.AWK Invoked by nmgo.bat
NMCTL.AWK Invoked by nmctl.bat
NMDET.AWK Computes determinant from standard errors
NMDSC.BAT
Creates a CrossGraphs
descriptor file from a NONMEM table file. The descriptor file is used by CrossGraphs to display
individual plots of predicted and observed values.
NMDSC.AWK Invoked by nmdsc.bat
NMEXEC.BAT
Invokes NONMEM executable (wc)
NMFEWC.BAT
Invokes NM-TRAN and compile, link steps for NONMEM
executable (wc)
NMFEWFN.BAT
Invokes NM-TRAN, compile, link and execution of NONMEM
7.2 (ivf,ivf11,gf,g95)
NMFESF.BAT
Invokes NM-TRAN, compile, link and execution of NONMEM
7.1 or earlier (ivf,ivf11,gf,g95,g77)
NMFENMQUAL.BAT Invokes NM-TRAN, compile, link and execution of NONMEM with nmqual
(ivf, ivf11, df,
g77)
NMINT.AWK Invoked by nmint.bat
NMFIXCTL.AWK Invoked by nmgo.bat
NMG42.BAT Processes autocovariate
control stream and creates covariate specific control stream.
NMG42.AWK Invoked by nmg42.bat
NMHDR.AWK Invoked by nmtbl.bat
NMLINK.AWK Invoked by nmfewc.bat
NMLST.AWK Invoked by nmtbl.bat
NMEXTLST.AWK Invoked by nmobj.bat and nmlst.bat
NMMSF.AWK Invoked by nmmsf.bat
NMOBJ.AWK Invoked by nmtbl.bat
NMOTBL.AWK Invoked by nmtbl.bat
NMOVER.BAT Finishes up after
NONMEM run.
NMTBL.AWK Invoked by nmtbl.bat
NMVPC2R.AWK Invoked by nmvpc.bat
NTCS.AWK Invoked by nmgo.bat to translate
extended control stream to standard control stream.
NMTIME.AWK Invoked by nmfewc.bat and nmfesf.bat
and nmover.bat to compute run times
NMLINKDF.FOR Source for Digital Visual Fortran to
create nmlinkdf.exe. This allows more flexible location of object files.
NMVPC_FUNCTIONS.R Used by nmvpc.bat
VPC.R Used by nmvpc.bat
NMCR.TXT Used to provide a carriage return for DOS date
and time commands
GAWK.EXE The fundamental tool used by WFN to process
files
ZIP.EXE and UNZIP.EXE File archive utilities.
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