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Updated: 15 July 2007
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.
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\runname.txt e.g. theopd.bs\theopd.txt.
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. Should be edited to call wfn.bat using the same arguments used to setup a WFN shortcut.
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 Work around for NONMEM unreliable simulation and estimation steps in single problem. 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.txt) 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. If the $TABLE ONEHEADER option is used in the simulation control stream it is replaced by NOHEADER. 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.
NMLST.BAT Displays list of all run summaries from *.smr files.
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.
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
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
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)
NMFESF.BAT Invokes NM-TRAN, compile, link and execution of NONMEM (ms, df)
NMFENMQUAL.BAT Invokes NM-TRAN, compile, link and execution of NONMEM with nmqual (g77, df)
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
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.
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.
Home| Installation| Control Streams| Autocovariate| Bootstrap| Randomization Test | Files | References